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Chiral recognition studies
Medicinal and bioorganic studies
Non-covalent interactions
NMR Theoretical Calculations
Molecular Properties of Heterocyclic Compounds
Heterocyclic compounds with the SO2 moiety
Tables of "Synthesis and Properties of Acetylenic Derivatives of Pyrazoles"
Chemistry & Origami
Conferences & papers: J. Elguero
Home Research Non-covalent interactions
Phys. Chem. Chem. Phys. 24, 25822-25833 (2022)
I. Alkorta, A. Legon
DOI: 10.1039/D2CP03999K (OpenAccess)
Reduced nucleophilicity: an intrinsic property of the Lewis base atom interacting with H in hydrogen-bonds with Lewis acids HX (X = F, Cl, Br, I, CN, CCH, CP)
Equilibrium hydrogen-bond dissociation energies De for the process B⋯HX = B + HX are calculated at the CCSD(T)(F12c)/cc-pVDZ-F12 level for ∼190 complexes B⋯HX. As established earlier, De values for such complexes can be described by the equation De = cNBEA, in which NB and EHX are the nucleophilicity and electrophilicity of the Lewis base B and the Lewis acid HX, respectively, and the constant c = 1 kJ mol−1. Graphs of De as the ordinate and EHX as the abscissa are presented for 26 series of hydrogen-bonded complexes B⋯HX. The Lewis base is fixed and HX is HF, HCl, HBr, HI, HCN, HCCH and HCP in each series. Each plot yields a good straight line, the slope of which is the nucleophilicity NB of B. The Lewis bases are chosen for their simplicity and all have at least one non-bonding electron pair carried by the atom directly involved in the B⋯HX hydrogen bond. The direction of the minimum value σmin of the molecular electrostatic surface potential on the 0.001 e bohr−3 iso-surface in the chosen bases B usually coincides with the axis of a non-bonding electron pair. The gradient of a graph of De/σmin plotted against EHX defines a reduced nucleophilicity ИB = NB/σmin in the sense that ИB appears to be a property only of the atom of B that is directly involved in the B⋯HX hydrogen bond, independent of the remainder of B. For example, the values of the reduced nucleophilicity for the series of isocyanide complexes CH3NC⋯HX, HNC⋯HX and FNC⋯HX are 0.0343(16), 0.0337(18) and 0.0332(18), respectively, while those for the corresponding series of cyanide complexes are 0.0337(23), 0.0329(24) and 0.0333(23).
Int. J. Quantum. Chem. 122, e26986 (2022)
R. Lopez-Sánchez, J. M. Oliva-Enrich, I. Alkorta, J. Elguero
DOI: 10.1002/qua.26986 (OpenAccess)
Anion complexes of diborane derivatives inserted to benzene
The complexes formed between three molecules where the diboryl units (HBH2BH) replace the C2H2 moiety in benzene (B6H12, C2B4H10, and C4B2H8) and 10 anions (H−, F−, Cl−, Br−, OH−, CCH−, CH3−, CN−, N3−, and CNO−) have been studied using MP2 computational methods with the complete basis set (CBS) extrapolation scheme. The stability of the complexes for a given anion increases with the number of diborane units in the molecules, and these energy values are correlated with the presence of different anions and number of diborane units. The electron density of the complexes has been characterized and analyzed using the quantum theory of atoms in molecules (QTAIM) and electron density shift (EDS) models.
ChemPhysChem, 23, 202200204 (2022)
M. Ferrer, I. Alkorta, J. Elguero, J.M. Oliva-Enrich
DOI: 10.1002/cphc.202200204 (OpenAccess)
Use of 5,10-Disubstituted Dibenzoazaborines and Dibenzophosphaborines as Cyclic Supports of Frustrated Lewis Pairs for the Capture of CO2
The reactivity of 5,10-disubstituted dibenzoazaborines and dibenzophosphaborines towards carbon dioxide is studied at the DFT level. The profile of this reaction comprises of three stationary points: the pre-reactive complex and adduct minima and the TS linking both minima. An equation is developed relating the properties (acidity, basicity and boron hybridization) of the isolated dibenzophosphaborine derivatives with the CO2 adduct energy.
J.C. López, I. Alkorta, A. Macario, S. Blanco
DOI: 10.1039/D2CP01611G
Characterizing the n→π* interaction of pyridine with small ketones: a rotational study of pyridine⋯acetone and pyridine⋯2-butanone
Complexes formed by pyridine and small ketones such as acetone and 2-butanone have been generated in a supersonic jet and characterized by broadband Fourier transform microwave spectroscopy combined with high-level theoretical computations. The spectra of the complexes show a quadrupole coupling hyperfine structure due to the presence of a nitrogen atom and the splittings owing to the low barriers of the internal rotation of the methyl groups bonded to the carbonyl group. The corresponding barriers have been determined from the analysis of the spectra. We show in both complexes that pyridine closes a cycle with a ketone carbonyl group through an N⋯C=O n→π* tetrel interaction and a C–H⋯O contact. The n→π* tetrel bond involves the pyridine N atom lone pair and the ketone carbonyl group with a geometry approaching the Bürgi–Dunitz trajectory for the nucleophilic attack to a carbonyl group.
Phys. Chem. Chem. Phys., 24, 14365-14374 (2022)
I. Alkorta, J. M. C. Plane, J. Elguero, J. Z. Dávalos, A. Ulises Acuña, A. Saiz-Lopez
Theoretical study of the NO3 radical reaction with CH2ClBr, CH2ICl, CH2BrI, CHCl2Br, and CHClBr2
The potential reaction of the nitrate radical (NO3), the main nighttime atmospheric oxidant, with five alkyl halides, halons (CH2ClBr, CH2ICl, CH2BrI, CHCl2Br, and CHClBr2) has been studied theoretically. The most favorable reaction corresponds to a hydrogen atom transfer. The stationary points on the potential energy surfaces of these reactions have been characterized. The reactions can be classified into two groups based on the number of hydrogen atoms in the halon molecules (1 or 2). The reactions with halons with only one hydrogen atom show more exothermic profiles than those with two hydrogen atoms. In addition, the kinetics of the reaction of NO3 + CH2BrI was studied in much higher detail using a multi-well Master Equation solver as a representative example of the nitrate radical reactivity against these halocarbons. These results indicate that the chemical lifetime of the alkyl halides would not be substantially affected by nitrate radical reactions, even in the case of NO3-polluted atmospheric conditions.
DOI: 10.1039/D2CP01565J (OpenAccess)
Nucleophilicity of the boron atom in compounds R–B, (R = F, Cl, Br, I, CN, NC, CH3, SiH3, CF3, H): a new look at the inductive effects of the group R
Nucleophilicities NR–B of molecules R–B (R = F, Cl, Br, I, CN, NC, CH3, SiH3, CF3, H) are determined from the equilibrium dissociation energies De of 70 hydrogen-bonded complexes R–B⋯HX (X = F, Cl, Br, I, HCN. HCCH, HCP). The change in NR–B relative to NH–B of H–B allows a quantitative measure of the inductive effect IR of each group R because only the group R affects the electron density associated with the axial non-bonding electron pair carried by the boron in R–B. An alternative definition of IR, suggested by the strong correlation of the NR–B values with the minimum value σmin of the molecular electrostatic surface potential on the 0.001 e Bohr−3 iso-surface along the R–B axis leads to ex..cellent agreement between the two definitions.
J. Chem. Phys. 156, 194303 (2022)
M. M. Montero-Campillo, O. Mó, I. Alkorta, J. Elguero, M. Yáñez
DOI: 10.1063/5.0089716 (OpenAccess)
Disrupting bonding in azoles through beryllium bonds: Unexpected coordination patterns and acidity enhancement
Although triazoles and tetrazole are amphoteric and may behave as weak acids, the latter property can be hugely enhanced by beryllium bonds. To explain this phenomenon, the structure and bonding characteristics of the complexes between triazoles and tetrazoles with one and two molecules of BeF2 have been investigated through the use of high-level G4 ab initio calculations. The formation of the complexes between the N basic sites of the azoles and the Be center of the BeF2 molecule and the (BeF2)2 dimer leads to a significant bonding perturbation of both interacting subunits. The main consequence of these electron density rearrangements is the above-mentioned increase in the intrinsic acidity of the azole subunit, evolving from a typical nitrogen base to a very strong nitrogenous acid. This effect is particularly dramatic when the interaction involves the (BeF2)2 dimer, that is, a Lewis acid much stronger than the monomer. Although the azoles investigated have neighboring N-basic sites, their interaction with the (BeF2)2 dimer yields a monodentate complex. However, the deprotonated species becomes extra-stabilized because a second N–Be bond is formed, leading to a new N-N-Be(F2)-Be- five-membered ring, with the result that the azole-(BeF2)2 complexes investigated become stronger nitrogenous acids than oxyacids such as perchloric acid.
ChemPhysChem, 23, e202200088 (2022)
C. Martín-Fernández, I. Alkorta, M. M. Montero-Campillo, J. Elguero
DOI: 10.1002/cphc.202200088
Stand up for Electrostatics: The Disiloxane Case
Molecular Electrostatic Potential is used to explain why Lewis basicity in disiloxane increases when the Si−O−Si angle is reduced. Arguments based on atomic charges seem to contradict the observed trends and could (wrongly) make one think that electrostatic considerations fail to provide a proper understanding of this system. However, the present study shows that this is not the case and highlights once again the importance of electrostatics and polarization in the description of noncovalent interactions.
Phys. Chem. Chem. Phys. 24, 6856-6865 (2022)
I. Alkorta. A. Legon
DOI: 10.1039/d2cp00779g (OpenAccess)
A reduced electrophilicity for simple Lewis acids A involved in non-covalent interactions with Lewis bases
Dissociation energies De for B⋯A = B + A can be written De = c′NBEA, where NB and EA are the nucleophilicities and electrophilicities of the Lewis base B and the Lewis acid A, respectively. A reduced electrophilicity is defined ΞA = EA/σmax, where σmax is the maximum electrostatic surface potential on iso-surface of A, the atom directly involved in the non-covalent interaction. This definition is tested for halogen-bonded complexes B⋯YX, with Lewis bases B = N2, CO, C2H2, C2H4, H2S, HCN H2O or NH3. De plotted against NB for several series B⋯YX yields straight lines of gradient EA. When De/σmax is the ordinate, the straight lines conflate to a single line, gradient ΞIX = EIX/σmax. Hydrogen-bonded complexes B⋯HX (X = F, Cl, Br, I), coinage-metal complexes B⋯MX (M = Cu, Ag, Au; X = F, Cl, Br, I), and alkali-metal bonded complexes B⋯MX (M = Li, Na: X = F, H, CH3) behave similarly. ΞA is an intrinsic property of the atom immediately involved in the non-covalent bond.
Molecules 27, 17 (2022)
A. Macario, S. Blanco, I. Alkorta, J. C. López
DOI: 10.3390/molecules27010017 (OpenAccess)
Perfluorination of Aromatic Compounds Reinforce Their van der Waals Interactions with Rare Gases: The Rotational Spectrum of Pentafluoropyridine-Ne
The rotational spectrum of the pentafluoropyridine-Ne complex, generated in a supersonic jet, has been investigated using chirped-pulse microwave Fourier transform spectroscopy in the 2–8 GHz range. The spectra of the 20Ne and 22Ne species have been observed, and the rotational constants have been used to determine the structure of the complex. This structure, and those of the previously experimentally studied complexes benzene-Ne and pyridine-Ne, are an excellent benchmark for the theoretical calculations on these adducts. These complexes and hexafluorobenzene-Ne have been investigated at the CCSD/6-311++G(2d,p) level. The calculations reproduce the experimental structures well and show how the van der Waals complexes are stronger for the perfluorinated compound.
ChemistrySelect, 6, 13897-13905 (2021)
M. M. Muriel-Olaya, I. Alkorta, J. Elguero
DOI: 10.1002/slct.202103919
Anion Complexation Strongly Influences the Reactivity of Octafluorocyclooctatetraene
Six stationary points (three minima and three TS) in the thermal energy profile of octafluorocyclooctatetraene (F8-COT) have been explored. The TSs corresponding to the inversion process of F8-COT and its transformation in perfluoro bicyclo[2.2.2]octa-2,5,7-triene (F8-BOT) and subsequent to perfluoro tetracyclo[4.2.0.02.02,8,05,7]octene (F8-TCO) have been characterized. The results have been compared to the energy profile in the parent compound (cyclooctatetraene or COT). In addition, the effect of the formation of anion-π complexes in the reaction profile has been explored. The results have been rationalized using the electrostatic potential of the isolated stationary points and thermodynamic cycles involving the complex formation in the minima and TS and the barriers in the isolated molecules. Moreover, the electron density has been analyzed with the AIM methodology.
Can. J. Chem. 99, 950-955 (2021)
I. Alkorta, J. Elguero, J. E. Del Bene
DOI: 10.1139/cjc-2021-0072
1,2-Dihydro-1,3,2-diazaborinine tautomer as an electron-pair donor in hydrogen-bonded complexes
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate 1,2-dihydro-1,3,2-diazaborinine:HX complexes for HX = H+, HF, HCl, H2O, HCN, NH3, HCP, and HCCH. Most complexes are stabilized by linear, traditional hydrogen bonds except for those with H2O and NH3, which have bridging structures and nonlinear hydrogen bonds. H-atom transfer from N to B can occur in complexes with HF and HCl, with formation of a traditional F–H···N bond and a proton-shared Cl···H···N bond. The binding energies of the uncharged complexes range from 25 to 88 kJ mol−1. Spin-spin coupling constants have been used to characterize these hydrogen-bonded complexes.
Eur. J. Inorg. Chem. 4393–4401 (2021)
M. M. Montero-Campillo, I. Alkorta, O. Mó, J. Elguero, M. Yáñez
DOI: 10.1002/ejic.202100737
Clustering of Electron Deficient B- and Be-Containing Analogues: In the Fight for Tetracoordination, Beryllium Takes the Lead
The stability of clusters involving Be- and B-containing analogues is dictated by the number of Be−Be and Be−B interactions with a clear preference for maximizing facing Be subunits. The most striking consequence is that in mixed trimers and tetramers the global minima always have Be-derivatives at the center.
Chem. Eur. J. 27, 13870-13878 (2021)
J.C. López, A. Macario, A. Maris, I. Alkorta, S. Blanco
DOI: 10.1002/chem.202102163 OpenAccess
How Aromatic Fluorination Exchanges the Interaction Role of Pyridine with Carbonyl Compounds: The Formaldehyde Adduct
The rotational spectrum of the weakly bound complex pentafluoropyridine⋅⋅⋅formaldehyde has been investigated using Fourier transform microwave spectroscopy. From the analysis of the rotational parameters of the parent species and of the 13C and 15N isotopologues, the structural arrangement of the adduct has been unambiguously established. The full ring fluorination of pyridine has a dramatic effect on its binding properties: It alters the electron density distribution at the π-cloud of pyridine creating a π-hole and changing its electron donor-acceptor capabilities. In the complex, formaldehyde lies above the aromatic ring with one of the oxygen lone pairs, as conventionally envisaged, pointing toward its centre. This lone pair⋅⋅⋅π-hole interaction, reinforced by a weak C−H⋅⋅⋅N interaction, indicates an exchange of the electron-acceptor roles of both molecules when compared to the pyridine⋅⋅⋅formaldehyde adduct. Tunnelling doublets due to the internal rotation of formaldehyde have also been observed and analysed leading to a discussion on the competition between lone pair⋅⋅⋅π-hole and π⋅⋅⋅π stacking interactions.
J. Phys. Chem. A 125, 32, 6976–6984 (2021)
M. Ferrer, I. Alkorta, J. Elguero, J. M. Oliva-Enrich
DOI: 10.1021/acs.jpca.1c04787 (OpenAccess)
Sequestration of Carbon Dioxide with Frustrated Lewis Pairs Based on N-Heterocycles with Silane/Germane Groups
Frustrated Lewis pairs (FLPs) based on nitrogen heterocycles (pyridine, pyrazole, and imidazole) with a silane or germane group in the α-position of a nitrogen atom have been considered as potential molecules to sequestrate carbon dioxide. Three stationary points have been characterized in the reaction profile: a pre-reactive complex, an adduct minimum, and the transition state connecting them. The effect of external (solvent) or internal (hydroxyl group) electric fields in the reaction profile has been considered. In both cases, it is possible to improve the kinetics and thermodynamics of the complexation of CO2 by the FLP and favor the formation of adducts.
ChemPlusChem 86, 1097–1105 (2021)
P. Sánchez-Andrada, A. Vidal-Vidal, T. Prieto, J. Elguero, I. Alkorta, M. Marín-Luna
DOI: 10.1002/cplu.202100235 (OpenAccess)
Alkylammonium Cation Affinities of Nitrogenated Organobases: The Roles of Hydrogen Bonding and Proton Transfer
Alkylammonium cation affinities of 64 nitrogen-containing organobases, as well as the respective proton transfer processes from the alkylammonium cations to the base, have been computed in the gas phase by using DFT methods. The guanidine bases show the highest proton transfer values (191.9–233 kJ mol−1) whereas the cis-2,2'-biimidazole presents the largest affinity towards the alkylammonium cations (>200 kJ mol−1) values. The resulting data have been compared with the experimentally reported proton affinities of the studied nitrogen-containing organobases revealing that the propensity of an organobase for the proton transfer process increases linearly with its proton affinity. This work can provide a tool for designing senors for bioactive compounds containing amino groups that are protonated at physiological pH.
Mol. Phys. 119, e1933637 (2021)
J. E. Del Bene, I. Alkorta, J. Elguero
DOI: 10.1080/00268976.2021.1933637 OpenAccess
Microsolvation of the Be-F bond in complexes of BeF2, BeF3–1, and BeF4–2 with nH2O, for n = 1–6
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of complexes of BeF2, BeF3–1, and BeF4–2 with n H2O molecules, with n = 1–6. For each series of complexes with BeF2, BeF3–1, and BeF4–2, the binding energies increase as the number of water molecules increases, but the binding energies per intermolecular bond for complexes formed between BeF2 and BeF4–2 and nH2O decrease as the number of water molecules increases. The binding energies per bond of the BeF3–1 complexes show little dependence on the number of H2O molecules present. Intermolecular O-H … F hydrogen bonds (HB) stabilise all complexes of H2O with the beryllium bases except for BeF2:1H2O and BeF2:2H2O. Complexes of BeF2 are also stabilised by O … Be beryllium bonds (BeB) and O-H … O hydrogen bonds. EOM-CCSD calculations have also been performed to determine the spin–spin coupling constants. The one-bond coupling constants 1J(Be-F) increase as the Be-F distance decreases, and exhibit an excellent second-order correlation with that distance. 2hJ(O-F) coupling constants across O-H … F hydrogen bonds also exhibit a second-order dependence on distance. Coupling constants 1beJ(O-Be) and 2hJ(O-O) are found in complexes with BeF2 and exhibit a linear dependence on the Be-O and O-O distances, respectively.
Chem. Phys. Lett. 778, 138809 (2021)
G.S. Denisov, H. H. Limbach, I. Alkorta, J. Elguero
DOI: 10.1016/j.cplett.2021.138809 (OpenAccess)
Stationary states of systems with intermolecular interactions dominated by electrostatics: Structure of trimethylammonium and tetramethylammonium chlorides and bromides in the gas phase, monomers and dimers
This work reports the theoretical study carried out with the M06-2x functional and the aug-cc-pVTZ basis set of four ammonium and two phosphonium salts, Me3NH+Cl–, Me3NH+Br–, Me4N+Cl–, Me4N+Br–, Me4P+Cl– and Me4P+Br–. The structure of the monomeric and dimeric complexes (between 1 and 5 conformations each) has been analyzed in what concern geometries, energies and NH+ stretching frequencies. The ammonium geometries were successfully compared with the X-ray structures found in the CSD.
J. Phys. Chem. A 125, 4741–4749 (2021)
I. Iribarren, G. Sánchez-Sanz, I. Alkorta, J. Elguero, C. Trujillo
Evaluation of Electron Density Shifts in Noncovalent Interactions
In the present paper, we report the quantitative evaluation of the electron density shift (EDS) maps within different complexes. Values associated with the total EDS maps exhibited good correlation with different quantities such as interaction energies, Eint, intermolecular distances, bond critical points, and LMOEDA energy decomposition terms. Besides, EDS maps at different cutoffs were also evaluated and related with the interaction energies values. Finally, EDS maps and their corresponding values are found to correlate with Eint within systems with cooperative effects. To our knowledge, this is the first time that the EDS has been quanitatively evaluated.
Molecules 26, 3401 (2021)
T.I-Ting, M. M. Montero-Campillo, I. Alkorta, J. Elguero, M. Yáñez
Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives
Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol−1 are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.
Perturbing the O–H···O Hydrogen Bond in 1‐Oxo‐3‐hydroxy‐2‐propene
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH2, and BeF2. Two equilibrium structures, one with the acid interacting with the C=O group and the other with the interaction occurring at the O–H group, exist on all surfaces. These structures are separated by transition structures that present the barriers to the interconversion of the two equilibrium structures. The structures with the acid interacting at the C=O group have the greater binding energies. Since the barriers to convert the structures with interaction occurring at the O–H group are small, only the isomers with interaction occurring at the C=O group could be experimentally observed, even at low temperatures. Charge-transfer energies were computed for equilibrium structures, and EOM-CCSD spin–spin coupling constants 2hJ(O–O), 1hJ(H–O), and 1J(O–H) were computed for equilibrium and transition structures. These coupling constants exhibit a second-order dependence on the corresponding distances, with very high correlation coefficients.
ChemPlusChem, 86, 778-784 (2021)
I. Alkorta, A.C. Legon
The Electrophilicities of XCF3 and XCl (X=H, Cl, Br, I) and the Propensity of These Molecules To Form Hydrogen and Halogen Bonds with Lewis Bases: An Ab Initio Study
Equilibrium dissociation energies, De, of four series of halogen‐ and hydrogen‐bonded complexes B⋅⋅⋅XCF3 (X=H, Cl, Br and I) are calculated ab initio at the CCSD(T)(F12c)/cc‐pVDZ‐F12 level. The Lewis bases B involved are N2, CO, PH3, C2H2, C2H4, H2S, HCN, H2O and NH3. Plots of De versus NB, where the NB are the nucleophilicities assigned to the Lewis bases previously, are good straight lines through the origin, as are those for the corresponding set of complexes B⋅⋅⋅XCl. The gradients of the De versus NB plots define the electrophilicities EXCF3 and EXCl of the various Lewis acids. The determined values are: EXCF3=2.58(22), 1.40(9), 2.15(2) and 3.04(9) for X=H, Cl, Br and I, respectively, and EXCl=4.48(22), 2.31(9), 4.37(27) and 6.06(37) for the same order of X. Thus, it is found that, for a given X, the ratio EXCl/ EXCF3 is 2 within the assessed errors, and therefore appears to be independent of the atom X and of the type of non‐covalent interaction (hydrogen bond or different varieties of halogen bond) in which it is involved. Consideration of the molecular electrostatic surface potentials shows that De and the maximum positive electrostatic potential σmax (the most electrophilic region of XCF3 and XCl, which lies on the symmetry axes of these molecules, near to the atom X) are strongly correlated.
DOI: 10.1080/00268976.2021.1905191 (OpenAccess)
IR and NMR properties of N-base:PH2F:BeX2 ternary and corresponding binary complexes stabilised by pnicogen and beryllium bonds
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to determine selected stretching frequencies and chemical shieldings for ternary complexes N-base:PH2F:BeX2 and the corresponding binary complexes, with NH3, H2C=NH, and HCN as the nitrogen bases and H, F, and Cl as the substituents X. Be-F and P-F stretching frequencies depend on the Be-F and P-F distances, respectively, while P and F chemical shieldings depend on the N-P and P-F distances, respectively. The graph of the P chemical shieldings versus the P-F distance bears a remarkable resemblance to the graph of the P-F stretching frequencies versus that same distance. EOM-CCSD spin–spin coupling constants have also been evaluated for binary and ternary complexes. 1pJ(N-P) is negative at the longer N-P distances found in ternary complexes with HCN in which the N···P bond is a traditional pnicogen bond with some phosphorous-shared character, gains phosphorus-shared character as the N-P distance continues to decrease, and then becomes a phosphorous-transferred bond with ion-pair character at the shorter distances in the complexes with NH3 and H2C=NH. 1J(P-F) values are large and negative in complexes with HCN, but increase and become positive in complexes with H2C=NH and NH3 as the P-F distance increases.
Crystals 391, 11 (2021)
DOI: 10.3390/cryst11040391 OpenAccess
Carboranes as Lewis Acids: Tetrel Bonding in CB11H11 Carbonium Ylide
High-level quantum-chemical computations (G4MP2) are carried out in the study of complexes featuring tetrel bonding between the carbon atom in the carbenoid CB11H11—obtained by hydride removal in the C-H bond of the known closo-monocarbadodecaborate anion CB11H12(−) and acting as Lewis acid (LA)—and Lewis bases (LB) of different type; the electron donor groups in the tetrel bond feature carbon, nitrogen, oxygen, fluorine, silicon, phosphorus, sulfur, and chlorine atomic centres in neutral molecules as well as anions H(−), OH(−), and F(−). The empty radial 2pr vacant orbital on the carbon centre in CB11H11, which corresponds to the LUMO, acts as a Lewis acid or electron attractor, as shown by the molecular electrostatic potential (MEP) and electron localization function (ELF). The thermochemistry and topological analysis of the complexes {CB11H11:LB} are comprehensively analysed and classified according to shared or closed-shell interactions. ELF analysis shows that the tetrel C⋯X bond ranges from very polarised bonds, as in H11B11C:F(-) to very weak interactions as in H11B11C⋯FH and H11B11C⋯O=C=O.
E. Vos, I. Corral, M. M. Montero-Campillo, O. Mó, J. Elguero, I. Alkorta, M. Yáñez
Spontaneous bond dissociation cascades induced by Ben clusters (n = 2,4)
High-level single and multireference ab initio calculations show that the Be4 cluster behaves as a very efficient Lewis acid when interacting with conventional Lewis bases such as ammonia, water or hydrogen fluoride, to the point that the corresponding acid–base interaction triggers a sequential dissociation of all the bonds of the Lewis base. Notably, this behavior is already found for the simplest beryllium cluster, the Be2 dimer. However, whereas for Be2 the first dissociation process involves a low activation barrier which is above the reactants, for Be4 all the bond dissociation processes involve barriers below the entrance channel leading to a cascade of successive exothermic processes, which end up spontaneously in a global minimum in which the bonding patterns of both the base and the Lewis acid are completely destroyed. Indeed, the global minimum, in all cases, is stabilized by three-center Be–H–Be bonds and covalent interactions between the Be atoms and the basic center of the base, which replace the initial metallic bond stabilizing the Be4 cluster. As a consequence, in the global minimum the basic atoms (N, O and F) behave as hyper-coordinated centers. Also importantly, the Be4 cluster and its complexes present RHF–UHF instabilities (not reported before for Be4), which require the use of multireference methods to correctly describe them.
Inorganics 9, 13 (2021)
I. Alkorta, N.R. Walker, A.C. Legon
DOI: 10.3390/inorganics9020013 OpenAccess
Non-Covalent Interactions of the Lewis Acids Cu–X, Ag–X, and Au–X (X = F and Cl) with Nine Simple Lewis Bases B: A Systematic Investigation of Coinage–Metal Bonds by Ab Initio Calculations
The equilibrium geometry and two measures (the equilibrium dissociation energy in the complete basis set limit, De(CBS) and the intermolecular stretching force constant kσ) of the strength of the non-covalent interaction of each of six Lewis acids M–X (M = Cu, Ag, Au) with each of nine simple Lewis bases B (B = N2, CO, HCCH, CH2CH2, H2S, PH3, HCN, H2O, and NH3) have been calculated at the CCSD(T)/aug-cc-pVTZ level of theory in a systematic investigation of the coinage–metal bond. Unlike the corresponding series of hydrogen-bonded B⋯HX and halogen-bonded B⋯XY complexes (and other series involving non-covalent interactions), De is not directly proportional to kσ. Nevertheless, as for the other series, it has been possible to express De in terms of the equation De = cNB.EMX, where NB and EMX are the nucleophilicities of the Lewis bases B and the electrophilicities of the Lewis acids M–X, respectively. The order of the EMX is determined to be EAuF > EAuCl > ECuF > ECuCl > EAgF≈EAgCl. A reduced electrophilicity defined as (EMX/σmax) is introduced, where σmax is the maximum positive value of the molecular electrostatic surface potential on the 0.001 e/bohr3 iso-surface. This quantity is, in good approximation, independent of whether F or Cl is attached to M.
ChemPhysChem 21, 2701–2708 (2020)
E. Vos, M. M. Montero-Campillo, I. Corral, M. Yáñez, I. Alkorta, J. Elguero
From Very Strong to Inexistent Be-Be Bonds in the Interactions of Be2 with π-Systems
Isolated Be2 is a typical example of a weakly bound system, but interaction with other systems may give rise to surprising bonding features. The interactions between Be2 and a set of selected neutral CnHn (n=2–8) π‐systems have been analyzed through the use of G4 and G4MP2 ab initio methods, along with multireference CASPT2//CASPT2 calculations. Our results systematically show that the CnHn−Be2−CnHn clusters formed are always very stable. However, the nature of this interaction is completely different when the π‐system involved is a closed shell species (n=2, 4, 6, 8), or a radical (n=3, 5, 7). In the first case, the interaction does not occur with the π‐system as a whole, but with specific C centers yielding rather polar but strong C−Be bonds. Nonetheless, although the Be−Be distances in these complexes are similar to the ones in compounds with ultra‐strong Be−Be bonds, a close examination of their electron density distribution reveals that no Be−Be bonds exist. The situation is totally different when the interaction involves two π‐radicals, CnHn−Be2−CnHn (n=3, 5, 7). In these cases, a strong Be−Be bond is formed. Indeed, even though Be is electron deficient, the Be2 moiety behaves as an efficient electron donor towards the two π‐radicals, so that the different CnHn−Be2−CnHn (n=3, 5, 7) clusters are the result of the interaction between Be22+ and two L− anions. The characteristics of these two scenarios do not change when dealing with bicyclic π‐compounds, such as naphthalene and pentalene, because the interaction with the Be2 moiety is localized on one of the unsaturated cycles, the other being almost a spectator.
I. Alkorta, J. Elguero, J. M. Oliva-Enrich, M. Yáñez, O. Mó, M. M. Montero-Campillo
DOI: 10.3390/molecules25245876 OpenAccess
The Importance of Strain (Preorganization) in Beryllium Bonds
In order to explore the angular strain role on the ability of Be to form strong beryllium bonds, a theoretical study of the complexes of four beryllium derivatives of orthocloso-carboranes with eight molecules (CO, N2, NCH, CNH, OH2, SH2, NH3, and PH3) acting as Lewis bases has been carried out at the G4 computational level. The results for these complexes, which contain besides Be other electron-deficient elements, such as B, have been compared with the analogous ones formed by three beryllium salts (BeCl2, CO3Be and SO4Be) with the same set of Lewis bases. The results show the presence of large and positive values of the electrostatic potential associated to the beryllium atoms in the isolated four beryllium derivatives of ortho-carboranes, evidencing an intrinsically strong acidic nature. In addition, the LUMO orbital in these systems is also associated to the beryllium atom. These features led to short intermolecular distances and large dissociation energies in the complexes of the beryllium derivatives of ortho-carboranes with the Lewis bases. Notably, as a consequence of the special framework provided by the ortho-carboranes, some of these dissociation energies are larger than the corresponding beryllium bonds in the already strongly bound SO4Be complexes, in particular for N2 and CO bases. The localized molecular orbital energy decomposition analysis (LMOEDA) shows that among the attractive terms associated with the dissociation energy, the electrostatic term is the most important one, except for the complexes with the two previously mentioned weakest bases (N2 and CO), where the polarization term dominates. Hence, these results contribute to further confirm the importance of bending on the beryllium environment leading to strong interactions through the formation of beryllium bonds.
ChemPhysChem 21, 2557-2563 (2020)
G. Sánchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero
Rivalry between Regium and Hydrogen Bonds Established within Diatomic Coinage Molecules and Lewis Acids/Bases
A theoretical study of the complexes formed by Ag2 and Cu2 with different molecules, XH (FH, ClH, OH2, SH2, HCN, HNC, HCCH, NH3 and PH3) that can act as hydrogen‐bond donors (Lewis acids) or regium‐bond acceptors (Lewis bases) was carried out at the CCSD(T)/CBS computational level. The heteronuclear diatomic coinage molecules (AuAg, AuCu, and AgCu) have also been considered. With the exception of some of the hydrogen‐bonded complexes with FH, the regium‐bonded binary complexes are more stable. The AuAg and AuCu molecules show large dipole moments that weaken the regium bond (RB) with Au and favour those through the Ag and Cu atoms, respectively.
DOI: 10.1016/j.cplett.2020.137916
Probing the structures, binding energies, and spin-spin coupling constants of halogen-bonded Azine:ClF complexes
Ab initio MP2/aug'-cc-pVTZ calculations were performed to determine the structures, binding energies, and charge-transfer energies of azine:ClF complexes. Binding energies and charge-transfer energies exhibit excellent correlations with the N-Cl distance, decreasing as the number of N atoms increases. EOM-CCSD spin-spin coupling constants 1xJ(N-Cl) do not correlate well with the N-Cl distance, although patterns emerge for each subgroup of complexes that have the same number of nitrogen atoms in the ring. The average value of the coupling constants for each subgroup exhibits an excellent correlation with the average distance, and illustrates the changing nature of the halogen bond.
CrystEngComm, 22, 6979-6982 (2020)
C. Ramírez de Arellano, R. Adam, R. Ballesteros-Garrido, B. Abarca, R. Ballesteros, I. AlKorta, J. Elguero, E. Escrivà
DOI: 10.1039/D0CE01272F
A C(pi-hole)⋯Cl–Zn tetrel interaction driving a metal–organic supramolecular assembly
A brominated pyrimidinyl triazolopyridine ligand (bptpy) forms a C(π-hole)⋯Cl–Zn tetrel interaction that plays a determining role in the formation of supramolecular layers through chain assembly in 18 membered metallacycle [(ZnCl2)2(μ-bptpy)2] crystals. Supramolecular chains are formed through C–H⋯X interactions. The observed interactions are supported by DFT calculations using model dimers.
Int. J. Mol. Sci. 21, 8036 (2020)
I. Alkorta, J. Elguero, C. Trujillo, G. Sánchez-Sanz
DOI: 10.3390/ijms21218036 (OpenAccess)
Interaction between Trinuclear Regium Complexes of Pyrazolate and Anions, a Computational Study
The geometry, energy and electron density properties of the 1:1, 1:2 and 1:3 complexes between cyclic (Py-M)3 (M = Au, Ag and Cu) and halide ions (F−, Cl− and Br−) were studied using Møller Plesset (MP2) computational methods. Three different configurations were explored. In two of them, the anions interact with the metal atoms in planar and apical dispositions, while in the last configuration, the anions interact with the CH(4) group of the pyrazole. The energetic results for the 1:2 and 1:3 complexes are a combination of the specific strength of the interaction plus a repulsive component due to the charge:charge coulombic term. However, stable minima structures with dissociation barriers for the anions indicate that those complexes are stable and (Py-M)3 can hold up to three anions simultaneously. A search in the CSD confirmed the presence of (Pyrazole-Cu)3 systems with two anions interacting in apical disposition.
Angew. Chem. Int. Ed., 59, 17482–17487 (2020). Angew. Chem., 132, 17635-17640 (2020)
A. Bauzá, I. Alkorta, J. Elguero, T. J. Mooibroek, A. Frontera
Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements
The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron‐rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp–ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI‐MP2/aug‐cc‐pVTZ level of theory, atoms‐in‐molecules, and natural bond orbital analyses and by examining solid‐state structures in the Cambridge Structure Database.
I. Alkorta, J. G. Hill, A. C. Legon
DOI: 10.1039/d0cp02697b
An ab initio investigation of alkali–metal noncovalent bonds B···LiR and B···NaR (R = F, H or CH3) formed with simple Lewis bases B: the relative inductive effects of F, H and CH3
The alkali–metal bonds formed by simple molecules LiR and NaR (R = F, H or CH3) with each of the six Lewis bases B = OC, HCN, H2O, H3N, H2S and H3P were investigated by ab initio calculations at the CCSD(T)/AVTZ and CCSD(T)/awCVTZ levels of theory with the aim of characterising this type of non-covalent interaction. In some complexes, two minima were discovered, especially for those involving the NaR. The higher-energy minimum (referred to as Type I) for a given B was found to have geometry that is isomorphous with that of the corresponding hydrogen-bonded analogue B⋯HF. The lower-energy minimum (when two were present) showed evidence of a significant secondary interaction of R with the main electrophilic region of B (Type II complexes). Energies DCBSe for dissociation of the complexes into separate components were found to be directly proportional to the intermolecular stretching force constant kσ The value of DCBSe could be partitioned into a nucleophilicity of B and an electrophilicity of LiR or NaR, with the order ELiH ≳ ELiF = ELiCH3 for the LiR and ENaF > ENaH ≈ ENaCH3 for the NaR. For a given B, the order of the electrophilicities is ELiR > ENaR, which presumably reflects the fact that Li+ is smaller than Na+ and can approach the Lewis base more closely. A SAPT analysis revealed that the complexes B⋯LiR and B⋯NaR have larger electrostatic contributions to De than do the hydrogen- and halogen-bonded counterparts B⋯HCl and B⋯ClF.
Struct. Chem. 31, 1909-1918 (2020)
J.E. Del Bene, I. Alkorta, J. Elguero
DOI: 10.1039/d0cp02009e (OpenAccess)
Hydrogen bonds and halogen bonds in complexes of carbones L→C←L as electron donors to HF and ClF, for L = CO, N2, HNC, PH3, and SH2
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of the carbone complexes in which the carbone L→C←L acts as an electron pair donor to one and two HF or ClF molecules, for L = CO, N2, HNC, PH3, and SH2. The binding energies increase with respect to the ligand in the order CO < NN < CNH ≪ PH3 < SH2, and increase with respect to the acid in the order HF < 2 HF < ClF < 2 ClF. The complexes with the ligands CO, N2 and PH3 have C2v symmetry while those with CNH and SH2 have Cs symmetry, except for H2S→C←SH2:2HF which has C2 symmetry and a unique structure among all of the carbone complexes. F–H and Cl–F stretching frequencies in the complexes decrease as the F–H and Cl–F distances, respectively, increase. EOM-CCSD spin–spin coupling constants 2hJ(F–C) increase with decreasing F–C distance. Although the F–H⋯C hydrogen bonds gain some proton-shared character in the most tightly bound complexes, the hydrogen bonds remain traditional hydrogen bonds. 1xJ(Cl–C) values indicate that the Cl⋯C halogen bonds have chlorine shared character even at the longest distances. 1xJ(Cl–C) then increases as the Cl–C distance decreases, and reaches a maximum for chlorine-shared halogen bonds. As the Cl–C distance further decreases, the halogen bond becomes a chlorine-transferred halogen bond.
J. Phys. Chem. A, 124, 5871−5878 (2020)
I. Alkorta, J. Elguero, J. E. Del Bene, O. Mó, M. M. Montero-Campillo, M. Yáñez
DOI: 10.1021/acs.jpca.0c03689
Mutual Influence of Pnicogen Bonds and Beryllium Bonds: Energies and Structures in the Spotlight
Pnicogen bonds, which are weak noncovalent interactions (NCIs), can be significantly modified by the presence of beryllium bonds, one of the strongest NCIs known. We demonstrate the importance of this influence by studying ternary complexes in which both NCIs are present, that is, the ternary complexes formed by a nitrogen base (NH3, NHCH2, and NCH), a phosphine (fluorophosphane, PH2F) and a beryllium derivative (BeH2, BeF2, BeCl2, BeCO3, and BeSO4). Energies, structures, and nature of the chemical bonding in these complexes are studied by means of ab initio computational methods. The pnicogen bond between the nitrogen base and the phosphine and the beryllium bond between the fluorine atom of fluorophosphane and the beryllium derivative show large cooperativity effects both on energies and geometries, with dissociation energies up to 296 kJ mol–1 and cooperativity up to 104 kJ mol–1 in the most strongly bound complex, CH2HN:PH2F:BeSO4. In the complexes between the strongest nitrogen bases and the strongest beryllium donors, phosphorus-shared and phosphorus-transfer bonds are found.
D. Quiñonero, I. Alkorta, J. Elguero
Metastable Dianions and Dications
A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX32− and LX42− (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M3X2+ (M=Li and Na, X=F and Cl), YH32+ and ZH42+ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono‐ions. The dissociation profile of the molecules in two mono‐ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.
New J. Chem., 44, 11870-11878 (2020)
M. Ferrer, M. M. Montero-Campillo, O. Mó, M. Yáñez, I. Alkorta, J. Elguero
DOI: 10.1039/d0nj01803a
Bonding between electron-deficient atoms: strong Lewis-acid character preserved in X–Y–X (X = B, Al; Y = Be, Mg) bridges
The structure, stability and bonding of beryllium bis(diazaborolyl) derivatives and their Mg and Al-containing analogues have been investigated through the use of G4-high level ab initio methods. This survey allowed us to conclude that not only the Be/B compounds, recently reported in the literature, but also their analogues in which Be is replaced by Mg and B is replaced by Al should exhibit similar bonding characteristics and stability and therefore should be, in principle, also experimentally accessible. In general, in all these derivatives B and Al, in spite of being intrinsically electron-deficient systems, behave as nucleophiles towards Be and Mg. One of the consequences of having two electron-deficient atoms involved in a bond is that the net charge associated to both of them is usually positive, in contrast with typical Be or Mg containing compounds, such as BeF2 or MgF2. However, this apparent dissimilarity is not so, because of the role of the second neighbors. Indeed, in the systems investigated, even though the Be–B, Be–Al, Mg–B or Mg–Al bonds are not too polar as compared with Be–F or Mg–F, the cluster can be viewed as the interaction between a positively charged Be(Mg) atom with two negatively charged ligands. Consistently, the homolytic dissociation enthalpies of the Be–ligand bonds, though smaller than that of the Be–F one, are still significantly large. Also importantly, the Lewis acid character of Be is still preserved, as all the Be compounds investigated lead to rather strong beryllium bonds when interacting with one or two typical Lewis bases, such as methylamine. The same behavior is observed for the corresponding Mg-containing analogues.
Struct. Chem. 31, 1273–1279 (2020)
I. Alkorta, J. Elguero. J.M. Oliva-Enrich
Complexes between bicyclic boron derivatives and dihydrogen: the importance of strain
The 1:1 complexes of neutral derivatives of borabicyclo[2.2.2] and borabicyclo[3.3.3] with dihydrogen have been studied by means of MP2 computational methods. In all cases, an interaction between the boron atom and the sigma bond of dihydrogen is observed. The chemical environment of the boron atom plays an important role in the observed intermolecular distance and binding energies. Very short intermolecular distances (B-H distances shorter than 1.5 Å) are obtained for several cases and binding energies up to − 97 kJ mol−1. The importance of strain has been confirmed with analogous non-cyclic systems that have been distorted to increase the non-planarity of the boron atom.
Unusual Complexes of P(CH)3 with FH, ClH, and ClF
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of complexes formed by phosphatetrahedrane, P(CH)3, and HF, HCl, and ClF. Four types of complexes exist on the potential energy surfaces. Isomers A form at the P atom near the end of a P-C bond, B at a C-C bond, C at the centroid of the C-C-C ring along the C3 symmetry axis, and D at the P atom along the C3 symmetry axis. Complexes A and B are stabilized by hydrogen bonds when FH and ClH are the acids, and by halogen bonds when ClF is the acid. In isomers C, the dipole moments of the two monomers are favorably aligned but in D the alignment is unfavorable. For each of the monomers, the binding energies of the complexes decrease in the order A > B > C > D. The most stabilizing Symmetry Adapted Perturbation Theory (SAPT) binding energy component for the A and B isomers is the electrostatic interaction, while the dispersion interaction is the most stabilizing term for C and D. The barriers to converting one isomer to another are significantly higher for the A isomers compared to B. Equation of motion coupled cluster singles and doubles (EOM-CCSD) intermolecular coupling constants J(X-C) are small for both B and C isomers. J(X-P) values are larger and positive in the A isomers, negative in the B isomers, and have their largest positive values in the D isomers. Intramolecular coupling constants 1J(P-C) experience little change upon complex formation, except in the halogen-bonded complex FCl:P(CH3) A.
I. Alkorta, A. F. Silva, P. L. A. Popelier
An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study of the Halogen Bond with Explicit Analysis of Electron Correlation
Energy profiles of seven halogen-bonded complexes were analysed with the topological energy partitioning called Interacting Quantum Atoms (IQA) at MP4(SDQ)/6–31+G(2d,2p) level of theory. Explicit interatomic electron correlation energies are included in the analysis. Four complexes combine X2 (X = Cl or F) with HCN or NH3, while the remaining three combine ClF with HCN, NH3 or N2. Each complex was systematically deformed by translating the constituent molecules along its central axis linking X and N, and reoptimising its remaining geometry. The Relative Energy Gradient (REG) method (Theor. Chem. Acc. 2017, 136, 86) then computes which IQA energies most correlate with the total energy during the process of complex formation and further compression beyond the respective equilibrium geometries. It turns out that the covalent energy (i.e., exchange) of the halogen bond, X…N, itself drives the complex formation. When the complexes are compressed from their equilibrium to shorter X…N distance then the intra-atomic energy of N is in charge. When the REG analysis is restricted to electron correlation then the interatomic correlation energy between X and N again drives the complex formation, and the complex compression is best described by the destabilisation of the through-space correlation energy between N and the "outer" halogen.
L.M. Azofra, J. Elguero, I. Alkorta
DOI: 10.1039/d0cp01321h
Stabilisation of dianion dimers trapped inside cyanostar macrocycles
Interanionic H-bonds (IAHBs) are unfavourable interactions in the gas phase becoming favoured when anions are in solution. Dianion dimers are also susceptible to being trapped inside the cavities of cyanostar (CS) macrocycles, and thus, the formation of 2 : 2 anion : cyanostar aggregates is mainly supported by three kinds of interactions: IAHBs between the dianions, π–π stacking between the confronted cyanostars, and the presence of an intricate network of multiple C(sp2)H⋯O H-bonds between cyanostar ligands and the anionic moieties. An analysis of the interaction energies supported by NBO reveals a slight cooperative effect of the CSs on the IAHB stabilisation.
M. O. Miranda, D. J. R. Duarte, I. Alkorta
Anion-Anion Complexes Established between Aspartate Dimers
Stable dimers aspartate‐aspartate have been studied in aqueous and gas phase through theoretical simulations. The polarizable continuum model (PCM) has been applied to simulate the effect of the hydration on monomers and complexes. The quantum theory of atoms in molecules (QTAIM) and the interacting quantum atoms (IQA) scheme has been used to inquire into if, in the aqueous phase, individual hydrogen bonds have attractive electrostatic components. In all cases a spontaneous formation of the complexes in the aqueous phase are observed, while in the gas phase a considerable energy barrier must be overcome (between 100.8 to 263.2 kJ mol−1). The intermolecular distance at which this barrier is indicates when the hydrogen‐bond interactions begin to take importance between the dimers and the corresponding molecular recognition among them. The IQA analysis shows that in aqueous phase, the hydrogen bonds N−H⋅⋅⋅O are mainly electrostatic in nature with a certain covalent character which increases linearly with the decrease of internuclear distances H⋅⋅⋅O. The H⋅⋅⋅H interactions observed are stabilizing and they are mainly quantum in nature.
Materials 13, 2163 (2020)
I. Alkorta, J. Elguero, J.M. Oliva-Enrich
DOI: 10.3390/ma13092163, OpenAccess
Hydrogen vs. Halogen Bonds in 1-Halo-Closo-Carboranes
A theoretical study of the hydrogen bond (HB) and halogen bond (XB) complexes between 1-halo-closo-carboranes and hydrogen cyanide (NCH) as HB and XB probe has been carried out at the MP2 computational level. The energy results show that the HB complexes are more stable than the XBs for the same system, with the exception of the isoenergetic iodine derivatives. The analysis of the electron density with the quantum theory of atoms in molecules (QTAIM) shows the presence of a unique intermolecular bond critical point with the typical features of weak noncovalent interactions (small values of the electron density and positive Laplacian and total energy density). The natural energy decomposition analysis (NEDA) of the complexes shows that the HB and XB complexes are dominated by the charge-transfer and polarization terms, respectively. The work has been complemented with a search in the CSD database of analogous complexes and the comparison of the results, with those of the 1-halobenzene:NCH complexes showing smaller binding energies and larger intermolecular distances as compared to the 1-halo-closo-carboranes:NCH complexes.
ChemPhysChem 21, 741-748 (2020)
Complexes H2CO:PXH2 and HCO2H:PXH2 for X=NC, F, Cl, CN, OH, CCH, CH3, and H: Pnicogen Bonds and Hydrogen Bonds
Ab initio MP2/aug'‐cc‐pVTZ calculations have been carried out to investigate H2CO : PXH2 pnicogen‐bonded complexes and HCO2H : PXH2 complexes that are stabilized by pnicogen bonds and hydrogen bonds, with X=NC, F, Cl, CN, OH, CCH, CH3, and H. The binding energies of these complexes exhibit a second‐order dependence on the O−P distance. DFT‐SAPT binding energies correlate linearly with MP2 binding energies. The HCO2H : PXH2 complexes are stabilized by both a pnicogen bond and a hydrogen bond, resulting in greater binding energies for the HCO2H : PXH2 complexes compared to H2CO : PXH2. Neither the O−P distance across the pnicogen bond nor the O−P distance across the hydrogen bond correlates with the binding energies of these complexes. The nonlinearity of the hydrogen bonds suggests that they are relatively weak bonds, except for complexes in which the substituent X is either CH3 or H. The pnicogen bond is the more important stabilizing interaction in the HCO2H : PXH2 complexes except when the substituent X is a more electropositive group. EOM‐CCSD spin‐spin coupling constants 1pJ(O−P) across pnicogen bonds in H2CO:PXH2 and HCO2H : PXH2 complexes increase as the O−P distance decreases, and exhibit a second order dependence on that distance. There is no correlation between 2hJ(O−P) and the O−P distance across the hydrogen bond in the HCO2H : PXH2 complexes. 2hJ(O−P) coupling constants for complexes with X=CH3 and H have much greater absolute values than anticipated from their O−P distances.
J. Phys. Chem. A 124, 2207-2214 (2020)
L. M. Azofra, J. Elguero, I. Alkorta
DOI: 10.1021/acs.jpca.9b10681
A Conceptual DFT Study of Phosphonate Dimers: Dianions Supported by H-Bonds
A conceptual DFT study of the dissociation of anionic and neutral phosphonate dimers has been carried out. In addition, the dianion complexes have been studied in the presence of two solvents, water and tetrahydrofuran. The dissociation of the dianion complexes in the gas phase and in solution present a maximum along the reaction coordinate that is not present in the neutral–neutral and anion–neutral complexes. The principal chemical descriptors (chemical potential, reaction electronic flux, hardness, and global electrophilicity index) do not show changes in their trends along the dissociation profiles even when there is an energy maximum in the case of the anion–anion complexes.
Crystals 10, 180 (2020)
I. Alkorta, J. Elguero, A. Frontera
DOI: 10.3390/cryst10030180, Download from the journal web page (OpenAccess)
Not Only Hydrogen Bonds: Other Noncovalent Interactions
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name "Spodium bonds" is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
J. Phys. Chem. A 124, 1515−1521 (2020)
O. Mó, M. M. Montero-Campillo, M. Yáñez, I. Alkorta, J. Elguero
Are Anions of Cyclobutane Beryllium Derivatives Stabilized through Four-Center One-Electron Bonds?
High-level G4 ab initio calculations allowed us to show that C4H4(BeX)4 (X = H, Cl) derivatives behave as rather efficient electron capturers due to their ability to trap the extra electron through the formation of a four-membered beryllium ring. This finding is in agreement with previous work showing the ability of highly electron-deficient atoms, such as beryllium, to lead to multicenter one-electron bonds. In our particular case, the formation of the four-center bond is characterized, in very good harmony, by different topological methods such as quantum theory of atoms in molecules (QTAIM), the electron localization function (ELF), and the noncovalent interactions (NCI) approach and is accompanied by large electron affinity values, around 300 kJ·mol–1, in the gas phase. Preliminary results may anticipate that the ability of groups of beryllium atoms to trap electrons decays on going to bigger systems.
J. M. Oliva-Enrich, I. Alkorta, J. Elguero
DOI: 10.3390/molecules25051042, Download from the journal web page (OpenAccess)
Complexes Between Adamantane Analogues B4X6 -X = {CH2, NH, O ; SiH2, PH, S} - and Dihydrogen, B4X6:nH2 (n = 1–4)
In this work, we study the interactions between adamantane-like structures B4X6 with X = {CH2, NH, O ; SiH2, PH, S} and dihydrogen molecules above the Boron atom, with ab initio methods based on perturbation theory (MP2/aug-cc-pVDZ). Molecular electrostatic potentials (MESP) for optimized B4X6 systems, optimized geometries, and binding energies are reported for all B4X6:nH2 (n = 1–4) complexes. All B4X6:nH2 (n = 1–4) complexes show attractive patterns, with B4O6:nH2 systems showing remarkable behavior with larger binding energies and smaller B···H2 distances as compared to the other structures with different X.
I. Alkorta, C. Trujillo, G. Sánchez-Sanz, J. Elguero
Regium Bonds between Silver(I) Pyrazolates Dinuclear Complexes and Lewis Bases (N2, OH2, NCH, SH2, NH3, PH3, CO and CNH)
A theoretical study and Cambridge Structural Database (CSD) search of dinuclear Ag(I) pyrazolates interactions with Lewis bases were carried out and the effect of the substituents and ligands on the structure and on the aromaticity were analyzed. A relationship between the intramolecular Ag–Ag distance and stability was found in the unsubstituted system, which indicates a destabilization at longer distances compensated by ligands upon complexation. It was also observed that the asymmetrical interaction with phosphines as ligands increases the Ag–Ag distance. This increase is dramatically higher when two simultaneous PH3 ligands are taken into account. The calculated 109Ag chemical shielding shows variation up to 1200 ppm due to the complexation. Calculations showed that six-membered rings possessed non-aromatic character while pyrazole rings do not change their aromatic character significantly upon complexation.
G. Sánchez‐Sanz I. Alkorta, J. Elguero, C. Trujillo
Sequestration of CO2 by Phosphatrane Molecules
The stationary points for the reaction between the CO2 and nine different phosphatranes molecules have been characterized by means of MP2 computational methods. Two minima structures have been located: a pnicogen bonded complex where one of the oxygen atoms of CO2 acts as electron donor and an adduct that presents a covalent P−C linkage. The corresponding transition state structure linking the two minima has also been characterized. In gas phase, the pnicogen bonded complex is more stable than the corresponding adduct except in one case. In contrast, the inclusion of the solvent effect (toluene and THF), reverts the stability, being in all cases the different adducts more stable than the pnicogen bonded complexes. The electronic properties of the systems have been analysed with the Quantum Theory of Atoms in Molecules (QTAIM) and Electron Density Shift (EDS) methods.
I. Alkorta, J. Elguero, M. Yáñez, O. Mó, M. M. Montero-Campillo
Relativistic Effects on NMR Parameters of Halogen-Bonded Complexes
Relativistic effects are found to be important for the estimation of NMR parameters in halogen-bonded complexes, mainly when they involve the heavier elements, iodine and astatine. A detailed study of 60 binary complexes formed between dihalogen molecules (XY with X, Y = F, Cl, Br, I and At) and four Lewis bases (NH3, H2O, PH3 and SH2) was carried out at the MP2/aug-cc-pVTZ/aug-cc-pVTZ-PP computational level to show the extent of these effects. The NMR parameters (shielding and nuclear quadrupolar coupling constants) were computed using the relativistic Hamiltonian ZORA and compared to the values obtained with a non-relativistic Hamiltonian. The results show a mixture of the importance of the relativistic corrections as both the size of the halogen atom and the proximity of this atom to the basic site of the Lewis base increase.
J. Phys. Chem. A 123, 10086−10094 (2019)
What Types of Noncovalent Bonds Stabilize Dimers (XCP)2, for X = CN, Cl, F, and H?
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out in search of equilibrium dimers on (XCP)2 potential energy surfaces, for X = CN, Cl, F, and H. Five equilibrium dimers with D∞h, C∞v, Cs, C2h, and C2 symmetries exist on the (ClCP)2 potential energy surface, four on the (FCP)2 and (HCP)2 surfaces, and three on the (NCCP)2 surface. These dimers are stabilized by traditional halogen, pnicogen, and tetrel bonds, and one of them by a hydrogen bond. The binding energies of the dimers (XCP)2 vary from 3.0 to 22.0 kJ·mol–1, with the strongest and weakest bonds found for complexes on the (NCCP)2 surface. The binding energies of the linear D∞h and C∞v dimers on each surface differ by no more than 1.0 kJ·mol–1, except for (NCCP)2, which has D∞h and C∞v complexes with binding energies of 3.0 and 11.0 kJ·mol–1, respectively. The highly symmetric complexes with D∞h and C∞v symmetry are found on all surfaces and are the most weakly bound complexes on each surface. The structures of these dimers, the nature and strengths of charge-transfer interactions, the molecular graphs, and the molecular electrostatic potentials are useful for determining the type of intermolecular bond that stabilizes the dimers. EOM-CCSD spin–spin coupling constants 1pJ(P–P) for complexes with P···P pnicogen bonds and D∞h symmetry are the largest coupling constants, ranging from 119 to 170 Hz. These increase with decreasing distance and follow a second-order trendline. The nature of the spin–spin coupling constants of these complexes is consistent with the type of noncovalent bond that stabilizes the dimers.
Phys.Chem.Chem. Phys. 21, 23645-23650 (2019)
C. Trujillo, I. Rozas, J. Elguero, I. Alkorta, G. Sánchez-Sanz
DOI: 10.1039/c9cp03694f
Modulating intramolecular chalcogen bonds in aromatic (thio)(seleno)phene-based derivatives
Intramolecular interactions have been proven to be the key to conformational control in drug-design. While chalcogen interactions have been shown to be present in certain ligands of the GK–GKRP target protein, in the present study, intramolecular chalcogen interactions through selenium are found to be even more promising since they form stronger interactions. Also, the flexibility/rigidity of the carbon backbone of the corresponding ligands is crucial in the conformational stability
Chem. Eur. J. 25, 11688 – 11695 (2019)
O. Mó, M. M. Montero-Campillo, I. Alkorta, J. Elguero, M. Yáñez
DOI: 10.1002/chem.201901641
Ternary Complexes Stabilized by Chalcogen and Alkaline-Earth Bonds: Crucial Role of Cooperativity and Secondary Noncovalent Interactions
High‐level G4 calculations show that the strength of chalcogen interactions is enhanced dramatically if chalcogen compounds simultaneously form alkaline‐earth bonds. This phenomenon is studied by exploring binary YX2⋅⋅⋅N‐Base complexes and two types of ternary MCl2⋅⋅⋅YX2⋅⋅⋅N‐Base, YX2⋅⋅⋅N‐Base⋅⋅⋅MCl2 complexes, in which YX2 is a chalcogen compound (Y=S, Se; X=F, Cl), the N‐Bases are sp, sp2, and sp3 bases (NCH, HN=CH2, NH3), and MCl2 are alkaline‐earth BeCl2 or MgCl2 derivatives. Starting from the chalcogen‐bonded complexes YX2⋅⋅⋅NH3 and YX2⋅⋅⋅HN=CH2, the binding site of a new incoming alkaline‐earth bond is found, surprisingly, to depend on the nature of the halogen atom attached to the chalcogen. For the YF2 binary complexes the association site is the F atom of the YF2 subunit, whereas for YCl2 it is the N atom of the nitrogen base. Regarding YX2⋅⋅⋅NCH complexes, N is the most favorable site for an alkaline‐earth interaction in ternary complexes, regardless of which YX2 derivative is used. The explanation relies on the interplay of all the noncovalent interactions involved: the strong cooperativity between chalcogen and alkaline‐earth bonds, and the appearance of secondary noncovalent interactions in the form of hydrogen bonds.
N...C and S...S Interactions in Complexes, Molecules, and Transition Structures N(CH)SX:SCO, for X = F, Cl, NC, CCH, H, and CN
Ab initio Møller–Plesset perturbation theory (MP2)/aug'-cc-pVTZ calculations have been carried out in search of complexes, molecules, and transition structures on HN(CH)SX:SCO potential energy surfaces for X = F, Cl, NC, CCH, H, and CN. Equilibrium complexes on these surfaces have C1 symmetry, but these have binding energies that are no more than 0.5 kJ·mol–1 greater than the corresponding Cs complexes which are vibrationally averaged equilibrium complexes. The binding energies of these span a narrow range and are independent of the N–C distance across the tetrel bond, but they exhibit a second-order dependence on the S–S distance across the chalcogen bond. Charge-transfer interactions stabilize all of these complexes. Only the potential energy surfaces HN(CH)SF:SCO and HN(CH)SCl:SCO have bound molecules that have short covalent N–C bonds and significantly shorter S…S chalcogen bonds compared to the complexes. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin-spin coupling constants 1tJ(N–C) for the HN(CH)SX:SCO complexes are small and exhibit no dependence on the N–C distance, while 1cJ(S–S) exhibit a second-order dependence on the S–S distance, increasing as the S–S distance decreases. Coupling constants 1tJ(N–C) and 1cJ(S–S) as a function of the N–C and S–S distances, respectively, in HN(CH)SF:SCO and HN(CH)SCl:SCO increase in the transition structures and then decrease in the molecules. These changes reflect the changing nature of the N…C and S…S bonds in these two systems.
J. E. Del Bene, I. Alkorta, J Elguero
Potential Energy Surfaces of HN(CH)SX:CO2 for X = F, Cl, NC, CN, CCH, and H: N···C Tetrel Bonds and O···S Chalcogen Bonds
MP2/aug′-cc-pVTZ calculations have been performed in search of complexes, molecules, and transition structures on the HN(CH)SX:CO2 potential energy surfaces, for X = F, Cl, NC, CN, CCH, and H. Complexes stabilized by traditional N···C tetrel bonds and O···S chalcogen bonds exist on all surfaces and are bound relative to the isolated monomers. Molecules stabilized by an N–C covalent bond and an O···S chalcogen bond are found when X = F, Cl, and NC, but only the HN(CH)SF:CO2 molecule is bound. The binding energies of these complexes correlate with the O–S distance but not with the N–C distance. Binding energies of complexes rotated by 90° about the N···C tetrel bond and by 90° about the O···S chalcogen bond provide estimates of these bond energies. Charge-transfer energies across tetrel and chalcogen bonds correlate with the N–C and O–S distances, respectively. As a function of the N–C distance, equation-of-motion coupled cluster singles and doubles spin–spin coupling constants 1tJ(N–C) for complexes and transition structures and 1J(N–C) for molecules describe the evolution of the N···C tetrel bonds in the complexes and transition structures to N–C covalent bonds in the molecules. The O···S chalcogen bond gains some covalency in the transition structures and again in the molecules but does not become a covalent bond.
I. Alkorta, M. M. Montero-Campillo, O. Mó, J. Elguero, M. Yáñez
Weak Interactions Get Strong: Synergy between Tetrel and AlkalineEarth Bonds
Weak and strong noncovalent interactions such as tetrel bonds and alkaline-earth bonds, respectively, cooperate and get reinforced when acting together in ternary complexes of general formula RN··· SiH3F···MY, where MY is a Be or Mg derivative and RN is a N-containing Lewis base with different hybridization patterns. Cooperativity has been studied in the optimized MP2/aug′-cc-pVTZ ternary complexes by looking at changes on geometries, binding energies, 29Si NMR chemical shifts, and topological features according to the atoms in molecules theoretical framework. Our study shows that cooperativity in terms of energy is in general significant: more than 40 kJ/mol, and up to 83.6 kJ/mol in the most favorable case. The weakest the isolated interaction, the strongest the reinforcement in the ternary complex; in this sense, the tetrel bond is shortened enormously, between 0.3 and 0.6 Å. This dramatic reinforcement of the tetrel bond is also nicely reflected in the positive variations of the 29Si chemical shifts in all the ternary complexes. At the same time the ternary complexes are characterized by the presence of totally planar silyl group, due to the pentacoordination of the Si atom. Both the hybridization of the N base and the geometry imposed by the alkaline-earth ligands have a strong influence on the binding energies, as they modify the donor ability of N and the Lewis acid character of the alkaline-earth metal.
Phys.Chem.Chem.Phys. 21, 16914-16922 (2019)
DOI: 10.1039/c9cp03463c
Systematic behaviour of electron redistribution on formation of halogen-bonded complexes B...XY, as determined via XY halogen nuclear quadrupole coupling constants
Equilibrium nuclear quadrupole coupling constants associated with the di-halogen molecule XY in each of 60 complexes B⋯XY (where B is one of the Lewis bases N2, CO, HCN, H2O, H2S, HCCH, C2H4, PH3, NH3 or (CH3)3N and XY is one of the di-halogens Cl2, BrCl, Br2, ICl, IBr or I2) have been calculated ab initio. The Townes–Dailey model for interpreting the changes in the coupling constants when XY enters the complex was used to describe the electron redistribution in the di-halogen molecule in terms of the fraction δi of an electron transferred from the Lewis base B to atom X and the fraction δp of an electron transferred simultaneously from atom X to atom Y. Systematic relationships between the δi values for the six series are established. It is shown that, in reasonable approximation, δi decays exponentially as the first ionisation energy IB of the Lewis base B increases, that is δi = A exp(−bIB). It is concluded from the results for the series B⋯BrCl, B⋯Br2, B⋯ICl, B⋯IBr and B⋯I2 that the coefficients A and b in regression fits to the corresponding logarithmic version ln(δi) = ln(A) − b(IB) of the equation are not strongly dependent on either the halogen atom X directly involved in the halogen bond in B⋯XY or, for a given X, on the nature of Y. The behaviour of PH3 as a Lewis base appears to be anomalous. Values of δi and δp calculated by the quantum theory of atoms-in-molecules and natural bond orbital methodologies are very close to those from application of the Townes–Dailey approach described.
Chem. Phys. Lett. 730, 466-471 (2019)
DOI: 10.1016/j.cplett.2019.05.044
Exploring N…C tetrel and O…S chalcogen bonds in HN(CH)SX:OCS systems, for X = F, NC, Cl, CN, CCH, and H
Ab initio MP2/aug'-cc-pVTZ calculations were carried out to investigate HN(CH)SX:OCS potential energy surfaces. Bound equilibrium complexes stabilized by N…C tetrel bonds and O…S chalcogen bonds have been found on all HN(CH)SX:OCS surfaces, but HN(CH)SF:OCS is the only bound molecule. Charge-transfer interactions are consistent with the nature of the intermolecular bonds in these complexes. Spin-spin coupling constants 1tJ(N-C) for HN(CH)SF:OCS are consistent with the changing nature of the N…C bond as the complex passes through the transition state to become a molecule. 1cJ(O-S) describes an intermolecular chalcogen bond in the complex, transition structure, and molecule.
Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au2:HX Complexes
A theoretical study of the regium and hydrogen bonds (RB and HB, respectively) in Au2:HX complexes has been carried out by means of CCSD(T) calculations. The theoretical study shows as overall outcome that in all cases the complexes exhibiting RB are more stable that those with HB. The binding energies for RB complexes range between −24 and −180 kJ ⋅ mol−1, whereas those of the HB complexes are between −6 and −19 kJ ⋅ mol−1. DFT‐SAPT also indicated that HB complexes are governed by electrostatics, but RB complexes present larger contribution of the induction term to the total attractive forces. 197Au chemical shifts have been calculated using the relativistic ZORA Hamiltonian.
Mol. Phys., 117, 1142-1150 (2019)
I. Alkorta, M. M. Montero-Campillo, J. Elguero, M. Yáñez, O. Mó
Complexes between H2 and neutral oxyacid beryllium derivatives. The role of angular strain
The complexes between 14 different Be-salts of oxyacids from groups 13 to 16 with one and two molecules of H2 have been investigated by means of the MP2/aug-cc-pVTZ ab initio molecular orbital theory method, which was found to be reliable for the treatment of these weakly bound species. The main conclusion is that these Be-salts yield rather stable complexes with dihydrogen, with binding energies one order of magnitude larger than other typical H2 complexes reported in the literature. This strong binding is shown to be due to an enhancement of the electron-deficient nature of Be when attached to an oxyacid moiety, which depends more on the type of coordination of the central atom of the oxyacid moiety. The formation of these complexes is followed by a significant lengthening of the H2internuclear distance and a concomitant red-shift of the H–H stretching frequency, which becomes a good indicator of the strength of the interaction. The charge shifting from the bonding region of the H2molecule to the interboundary Be···H2 region is the physical phenomenon behind the stability of these complexes. Accordingly, the most important contributor to this stability is the inductive term, followed by the electrostatic interactions. The ability of Be to bind H2 is enhanced by the angular arrangement of the O–Be–O electron-acceptor group.
Mol. Phys. 117, 1117–1127 (2019)
Pnicogen bonds in complexes with CO and CS: differentiating properties
Ab initio MP2/aug'-cc-pVTZ calculations have been performed on pnicogen-bonded complexes with CO and CS as electron-pair donors to PH2X, for X = F, NC, OH, CN, CCH, and H. CO:PH2X and OC:PH2X complexes are stabilised by traditional pnicogen bonds. CS is an electron-pair donor through its in-plane π system to four PH2X molecules. It forms C··· P phosphorus-shared bonds with some ion-pair character with PH2F, PH2(OH-Z), and PH2(OH-E), and traditional pnicogen bonds with all PH2X except PH2F. C-O and C-S stretching frequencies are blue-shifted for C···P pnicogen bonds, and red-shifted for O···P and S···P bonds. EOM-CCSD spin-spin coupling constants 1pJ(P-C) for OC:PH2X and 1pJ(P-O) for CO:PH2X are characteristic of complexes stabilised by traditional pnicogen bonds. Coupling constants 1pJ(P-C) as a function of the P-C distance for SC:PH2X illustrate the evolution of the C···P pnicogen bond. They increase as the P-C distance decreases in complexes with traditional bonds, reach a maximum for SC:PH2OH transition structures as the P-C distance further decreases and the bonds gain phosphorus-shared character, and then change sign and continue to decrease as the P-C distance further decreases and the phosphorus-shared pnicogen bonds gain ion-pair character. They approach the values of 1J(P-C) for the cation (H2PCS)+.
Can a Cl−H···F Hydrogen Bond Replace a Cl···F Halogen Bond? H2XP:ClY:ZH versus H2XP:ClY:HZ for Y, Z = F, Cl
Ab initio MP2/aug'-cc-pVTZ (where MP2 is Møller–Plesset perturbation theory) calculations have been carried out on four series of complexes, H2XP:ClF:HCl, H2XP:ClF:HF, H2XP:ClCl:HF, and H2XP:ClCl:HCl, to answer the question raised in the title of this paper. When X is F or Cl, binary complexes containing a P(V) molecule hydrogen bonded to an acid are found on all potential surfaces except H2ClP:ClF:HF, where an ion–pair complex exists. Ion–pair complexes also result from the optimization of H2XP:ClF:HF for X = NC, CN, and H. Changing the central molecule from ClF to ClCl has a dramatic effect on the nature of the optimized complexes when the substituents are NC, CN, and H. On the potential surfaces H2XP:ClCl:FH for X = NC and CN, open ternary complexes stabilized by a pnicogen bond and a hydrogen bond are found. Optimization of H3P:ClCl:FH leads to an ion pair. For H2(NC)P:ClCl:HCl and H2(CN)P:ClCl:HCl, cyclic ternary complexes stabilized by pnicogen, halogen, and hydrogen bonds result from optimization. Optimization of H3P:ClCl:HCl leads to a reaction in which H2ClP and a second HCl molecule are formed, and the resulting cyclic ternary complex is stabilized by two hydrogen bonds and a pnicogen bond. Thus, the type of complex resulting from the optimization of the starting ternary complex H2XP:ClY:HZ depends on the nature of the central molecule ClF or ClCl, the terminal molecule HCl or HF, and the substituent X. It is not possible to simply turn around the terminal HZ molecule in complexes H2XP:ClF:ZH for Z = F and Cl to give H2XP:ClF:HZ, thereby replacing a halogen bond by a hydrogen bond. Complexes H2XP:ClCl:HZ for X = NC and CN are stable complexes, but the corresponding halogen-bonded complexes H2XP:ClCl:ZH are not.
Theor. Chem. Acc. 138, 62 (2019)
M. M. Montero‑Campillo, O. Brea, O. Mó, I. Alkorta, J. Elguero, M. Yáñez
Gas‑phase reactivity tuned through the interaction with alkaline‑earth derivatives
The cooperativity between MX2:XH alkaline-earth bonds and XH:NH3 hydrogen bonds (M = Mg, Ca; X = F, Cl) was investigated at the G4 level of theory. The cooperativity between these two non-covalent linkages is extremely large, to the point that the increase in their bond dissociation enthalpies may be as large as 240%. More importantly, the weaker the interaction, the larger the increase, so in some cases the linkage that stabilizes the most is the alkaline-earth bond, whereas in others is the hydrogen bond. In all cases, the formation of the MX2:XH:NH3ternary complex is followed by a spontaneous proton transfer, very much as previously found for the Be-containing analogues. Similarly, MX2:FCl:NH3 complexes evolve from a chlorine-shared ternary complex (MX2F···Cl···NH3) or from an ion pair (MX2F−···NH3Cl+) if M = Ca. Although F is the only halogen without σ-hole, MgCl2 derivatives induce the appearance of a σ-hole on it, though less deep than those induced by BeCl2. We have also studied whether Mg and Ca bond-containing complexes MR2:FY (R = H, F, Cl; Y = NH2, OH, F, Cl) may react to form radicals, as it has been found for the Be-containing analogues. These interactions provoke a drastic decrease in the F–Y bond dissociation enthalpy, very much as the one reported for the corresponding Be-analogues, to the point that in some cases the formation of the corresponding MR2F• + Y· radicals becomes exothermic. Hence, the general conclusion of this study is that Mg or Ca derivatives give place to similar or even larger perturbations on the electron density than those induced by Be, a result not easily predictable.
I. Alkorta, A. C. Legon
DOI: 10.3390/inorganics7030035 (OpenAccess)
Non-Covalent Interactions Involving Alkaline-Earth Atoms and Lewis Bases B: An ab Initio Investigation of Beryllium and Magnesium Bonds, B···MR2 (M = Be or Mg, and R = H, F or CH3)
Geometries, equilibrium dissociation energies (De), intermolecular stretching, and quadratic force constants (kσ) determined by ab initio calculations conducted at the CCSD(T)/aug-cc-pVTZ level of theory, with De obtained by using the complete basis set (CBS) extrapolation [CCSD(T)/CBS energy], are presented for the B···BeR2 and B···MgR2 complexes, where B is one of the following Lewis bases: CO, H2S, PH3, HCN, H2O or NH3, and R is H, F or CH3. The BeR2 and MgR2 precursor molecules were shown to be linear and non-dipolar. The non-covalent intermolecular bond in the B···BeR2 complexes is shown to result from the interaction of the electrophilic band around the Be atom of BeR2 (as indicated by the molecular electrostatic potential surface) with non-bonding electron pairs of the base, B, and may be described as a beryllium bond by analogy with complexes such as B···CO2, which contain a tetrel bond. The conclusions for the B···MgR2 series are similar and a magnesium bond can be correspondingly invoked. The geometries established for B···BeR2 and B···MgR2 can be rationalized by a simple rule previously enunciated for tetrel-bonded complexes of the type B···CO2. It is also shown that the dissociation energy, De, is directly proportional to the force constant, kσ, in each B···MR2 series, but with a constant of proportionality different from that established for many hydrogen-bonded B···HX complexes and halogen-bonded B···XY complexes. The values of the electrophilicity, EA, determined from the De for B···BeR2 complexes for the individual Lewis acids, A, reveal the order A = BeF2 > BeH2 > Be(CH3)2—a result that is consistent with the −I and +I effects of F and CH3 relative to H. The conclusions for the MgR2 series are similar but, for a given R, they have smaller electrophilicities than those of the BeR2 series. A definition of alkaline-earth non-covalent bonds is presented.
Chem. Phys. Lett. 721, 86-90 (2019)
Probing C⋯S chalcogen bonds in complexes SC:SHX, for X = NO2, NC, F, Cl, CN, CCH, and NH2
MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of complexes SC:SHX, for X = NO2, NC, F, Cl, CN, CCH, and NH2. Complexes with traditional chalcogen bonds exist on all surfaces except for X = F and Cl, while complexes with sulfur-shared chalcogen bonds exist when X = F, NO2, NC, and Cl. The transition structures which present the barriers to converting one equilibrium structure to another on surfaces with double minima have been obtained. Charge-transfer energies, AIM parameters, NMR chemical shieldings, and EOM-CCSD spin-spin coupling constants across chalcogen bonds characterize these complexes.
Phys. Chem. Chem. Phys., 21, 5796-5802 (2019)
I. Iribarren, M. M. Montero-Campillo, I. Alkorta, J. Elguero, D. Quiñonero
DOI: 10.1039/c8cp07542e (Open Access)
Cations brought together by hydrogen bonds: the protonated pyridine–boronic acid dimer explained
According to the Cambridge Structural Database, protonated pyridine–boronic acid dimers exist in the solid phase, apparently defying repulsive coulombic forces. In order to understand why these cation–cation systems are stable, we carried out M06-2X/6-311++G(3df,2pd) electronic structure calculations and used a set of computational tools (energy partitioning, topology of the electron density and electric field maps). The behavior of the charged dimers was compared with the corresponding neutral systems, and the effect of counterions (Br− and BF4−) and the solvent (PCM model) on the binding energies has been considered. In the gas-phase, the charged dimers present positive binding energies but are local minima, with a barrier (16–19 kJ mol−1) preventing dissociation. Once the environment is included via solvent effects or counterions, the binding energies become negative; remarkably, the strength of the interaction is very similar in both neutral and charged systems when a polar solvent is considered. Essentially, all methods used evidence that the intermolecular region where the HBs take place is very similar for both neutral and charged dimers. The energy partitioning explains that repulsion and electrostatic terms are compensated by the desolvation and exchange terms in polar solvents, thus giving stability to the charged dimer.
E. Gougoula, C. Medcraft, I. Alkorta, N. R. Walker, A. C. Legon
A chalcogen-bonded complex H3N· · ·S=C=S formed by ammonia and carbon disulfide characterised by chirped-pulse, broadband microwave spectroscopy
Ground-state rotational spectra were observed for ten symmetric-top isotopologues H3N⋯S=C=S, H3N⋯34S=C=S, H3N⋯S=C=34S, H3N⋯S=13C=S, H315N⋯S=C=S, H315N⋯34S=C=S, H315N⋯S=C=34S, H315N⋯S=13C=S, H315N⋯33S=C=S, and H315N⋯S=C=33S, the first five in their natural abundance in a mixture of ammonia and carbon disulphide in argon and the second group with enriched 15NH3. The four asymmetric-rotor isotopomers H2DN⋯S=C=S, H2DN⋯34S=C=S, H2DN⋯S=C=34S, and HD2N⋯S=C=S were investigated by using a sample composed of ND3mixed with CS2. Rotational constants, centrifugal distortion constants, and 33S nuclear quadrupole coupling constants were determined from spectral analyses and were interpreted with the aid of models of the complex to determine its symmetry, geometry, one measure of the strength of the intermolecular binding, and information about the subunit dynamics. The complex has C3v symmetry, with nuclei in the order H3N⋯S=C=S, thereby establishing that the non-covalent interaction is a chalcogen bond involving the non-bonding electron pair of ammonia as the nucleophile and the axial region near one of the S atoms as the electrophile.The small intermolecular stretching force constant kσ = 3.95(5) N m−1 indicates a weak interaction and suggests the assumption of unperturbed component geometries on complex formation. A simple model used to account for the contribution of the subunit angular oscillations to the zero-point motion leads to the intermolecular bond length r(N⋯S) = 3.338(10) Å.
Adv. Inorg. Chem. 73, 73-121 (2019)
M. M. Montero-Campillo, O. Mó, M. Yáñez, I. Alkorta, J. Elguero
DOI: 10.1016/bs.adioch.2018.10.003
The beryllium bond
This chapter describes the strong and weak interactions of beryllium to form covalent bonds and beryllium bonds. We start from the challenging description of bonding in the beryllium dimer, trimer and larger clusters, followed by a brief review of other beryllium-beryllium bonds and organoberyllium compounds. Thereafter, the beryllium bond is defined and characterized in binary complexes, and it's very strong effects on the acid/base properties of the attached molecules reported. The last sections discuss the effect of the beryllium bond on reactivity and cooperative effects of compounds containing several beryllium bonds.
J. Heter. Chem. 56, 359-370 (2019)
I. Alkorta, J. Elguero
DOI: 10.1002/jhet.3331
Interaction of N‐Heterocyclic Carbenes and Simple Carbenes with Small Molecules (One to Three Atoms) Excluding Metals: Formation of Covalent C–X Bonds
This review reports the reactivity of carbenes (>C:), both N‐heterocyclic and simpler ones, with 29 small molecules to form C–X bonds and some weak interactions. The structures thus obtained belong to many functional groups proving the characteristic reactivity of N‐heterocyclic carbenes. Particular attention has been paid to X‐ray structures that are useful for theoretical calculations.
M. M. Montero-Campillo, O. Brea, O. Mó, I. Alkorta, J. Elguero, M. Yáñez
DOI: 10.1039/c8cp06908e
Modulating the intrinsic reactivity of molecules through non-covalent interactions
Non-covalent interactions unavoidably involve a certain disturbance of the electronic density of the interacting systems. Such perturbations are particularly strong when dealing with electron deficient systems such as boron, beryllium, magnesium (pre-p elements) or calcium (a pre-d element) derivatives. Indeed, these compounds have been shown to modify the intrinsic reactivity of the systems interacting with them. In the first part of this paper, we present an overview on (i) how electron deficient systems, acting as Lewis acids, modulate the intrinsic acidity of Lewis bases, explaining for instance why a typical base, such as aniline, can be converted by association with borane into an acid as strong as phosphoric acid; (ii) how other weak non-covalent interactions, such as halogen bonds, permit one to modulate the intrinsic basicity of typical oxyacids changing them into strong Brønsted bases; (iii) how cooperativity between different non-covalent interactions may lead to the spontaneous formation of ion-pairs in the gas phase; (iv) how non-covalent interactions generate σ-holes in systems where this feature is not present; and (v) how these interactions can induce exergonic and spontaneous formation of neutral radicals. In the second part of the paper, we show, by using G4 high-level ab initio calculations, that the acidity enhancement phenomenon is a general mechanism whenever a given base interacts with non-protic and protic acids. In the non-protic acid case, the underlying mechanism behind the enhancement is similar to the one reported for electron-deficient compounds, whereas the protic acid case appears in complexes stabilized through conventional hydrogen bonds. We also show that the former could be classified as an a priori mechanism, whereas the latter would be an a posteriori mechanism. This same a posteriori mechanism is behind the significant basicity enhancement of water and ammonia when interacting with conventional N-bases. Finally, we present a detailed analysis of the role that deformation can play in the intensity and nature of these enhancements.
Molecules 24, 308 (2019)
C. Trujillo, I. Alkorta, J. Elguero, G. Sánchez-Sanz
DOI: 10.3390/molecules24020308
Cooperative Effects in Weak Interactions: Enhancement of Tetrel Bonds by Intramolecular Hydrogen Bond
A series of silyl and germanium complexes containing halogen atoms (fluorine and chlorine atoms) and exhibiting tetrel bonds with Lewis bases were analyzed by means of Møller-Plesset computational theory. Binding energies of germanium derivatives were more negative than silicon ones. Amongst the different Lewis bases utilized, ammonia produced the strongest tetrel bonded complexes in both Ge and Si cases, and substitution of the F atom by Cl led to stronger complexes with an ethylene backbone. However, with phenyl backbones, the fluorosilyl complexes were shown to be less stable than the chlorosilyl ones, but the opposite occurred for halogermanium complexes. In all the cases studied, the presence of a hydroxyl group enhanced the tetrel bond. That effect becomes more remarkable when an intramolecular hydrogen bond between the halogen and the hydrogen atom of the hydroxyl group takes places.
I. Alkorta, I. Mata, E. Molins, E. Espinosa
Energetic, Topological and Electric Field Analyses of Cation-Cation Nucleic Acid Interactions in Watson-Crick Disposition
A theoretical study of the effect of the diprotonation on the nucleic acid bases (A : U, A : T and G : C) in Watson‐Crick conformation has been carried out by means of DFT computational methods in vacuum. In addition, the corresponding neutral and monoprotonated binary complexes have been considered. Most of the diprotonated species studied are stable, even though the binding energy is positive due to the overall repulsive electrostatic term. Local electrostatic attractive forces in the regions of hydrogen bonds (HBs) are responsible for equilibrium geometries, as shown by the electric field lines connecting the electrophilic and nucleophilic sites involved in the HB interactions. Secondary electrostatic effects also affect the assembling of the nucleic acid complexes in either neutral or cationic form. In particular, the electric field lines flowing from electrophilic sites in one base to nucleophilic sites in the other reinforce the linking between them. Hence, when the nucleophilic site concerns the free lone pair of the heteroatom involved in the HB interaction as acceptor, the HB distance shortens. However, if the free lone pair of the HB acceptor interacts with an electrophilic site in the same molecule, the HB distance elongates, weakening the HB interaction. The topological analysis of the electron density distribution in HB regions indicates that neutral, monoprotonated and diprotonated complexes show no differences in the nature of their HB's.
RSC Adv. 9, 853-862 (2019)
E. Vessally, I. Alkorta, S. Ahmadi, R. Mohammadi, A. Hosseinian
DOI: 10.1039/C8RA06031B
A DFT study on nanocones, nanotubes (4,0), nanosheets and fullerene C60 as anodes in Mg-ion batteries
In this article, we studied the interactions between Mg atom and Mg2+ ion and four nanostructures, including a nanocone, nanotube (4,0), nanosheet, and C60 nanocage, to obtain the cell voltages (V) for Mg-ion batteries (MIBs). Total energy, geometry optimization, frontier molecular orbital (FMO) and density of states (DOS) analyses have been performed using the ωB97XD level of theory and the 6-31G(d) basis set. The DFT calculations clarified that the changes in energy adsorption between Mg2+ ion and the nanostructures, Ead, are in the order tube > cone > sheet > cage. However, Vcell for the nanocone is the highest. The changes in Vcell of the MIBs are in the order cone > tube > sheet > cage. This study theoretically considers the possibilities of Mg as an anode in batteries due to its high Vcell values.
Comp. Theor. Chem. 1149, 17-23 (2019)
N. Salehi, L. Edjlali, E. Vessally, I. Alkorta, M. Es'haghi
DOI: 10.1016/j.comptc.2018.12.014
Lin@Tetracyanoethylene (n = 1–4) systems: Lithium salt vs lithium electride
Electrides are interesting and promising materials with cavity-trapped electrons which can be used as source of electron donor in different systems. Hereby, we have explored the possible formation of electride materials based on tetracyanoethylene (TCNE) backbone at MP2 computational level. This is achieved by systematic addition of up to four Li atoms to TCNE backbone. Our results predict high thermodynamic stability in the Lin@TCNE (n = 1–4) systems. Moreover, based on the evaluation of four criteria, non-nuclear attractor (NNA), electron localization function (ELF), electron density laplacian, and non-linear optical (NLO), TCNE-Li1 and TCNE-Li2 and TCNE-Li4 species are conventional donor-acceptor systems (lithium salt). In contrast, the TCNE-Li3 species can be introduced as lithium electride with cavity-trapped electrons. Therefore, Li:TCNE ratio is very significant factor to provide species with electride feature through the addition of Li atoms to TCNE backbone.
Reaction of ClF and Cl2 with PH2X: The oxidation of P(III) to P(V)
Ab initio MP2/aug′-cc-pVTZ calculations have been performed to examine the oxidation of P(III) to P(V) in reactions involving FCl and Cl2 as the oxidizing agents of PH2X molecules, for X = F, Cl, H, NC, and CN. Stable P(III) binary complexes and P(V) molecules, and the transition states which connect these minima exist on all (PH2X + ClF) and (PH2X + Cl2) potential surfaces. Profiles of binding energies, 31P chemical shieldings, and EOM-CCSD spin-spin coupling constants J(P-Cl) on these surfaces exhibit similar patterns, with minimum values for transition structures.
Inorganics 6, 110 (2018)
I. Alkorta, C. Trujillo, G. Sanchez-Sanz, J. Elguero
DOI: 10.3390/inorganics6040110 (Open Access PDF)
Solvent and Substituent Effects on the Phosphine + CO2 Reaction
A theoretical study of the substituent and solvent effects on the reaction of phosphines with CO2 has been carried out by means of Møller-Plesset (MP2) computational level calculations and continuum polarizable method (PCM) solvent models. Three stationary points along the reaction coordinate have been characterized, a pre-transition state (TS) assembly in which a pnicogen bond or tetrel bond is established between the phosphine and the CO2 molecule, followed by a transition state, and leading finally to the adduct in which the P–C bond has been formed. The solvent effects on the stability and geometry of the stationary points are different. Thus, the pnicogen bonded complexes are destabilized as the dielectric constant of the solvent increases while the opposite happens within the adducts with the P–C bond and the TSs trend. A combination of the substituents and solvents can be used to control the most stable minimum.
ChemPhysChem, 19, 2486-2491 (2018)
M. M. Montero-Campillo, I. Alkorta, J. Elguero
Enhancement of Thermodynamic Gas‐Phase Acidity and Basicity of Water by Means of Secondary Interactions
A series of A⋅water, B⋅water complexes (A=acid, B=base) are studied at the G4 level of theory to show that water acidity or basicity can be modulated by non‐covalent interactions. Protic and non‐protic acids interacting with water form hydrogen bonds or other kinds of non‐covalent interactions, respectively, that may dramatically change the acidity of water up to almost 360 kJ ⋅ mol−1 in terms of enthalpy. Similarly, hydrogen bonds responsible for the interaction between typical small nitrogen‐containing Lewis bases and water can enhance the proton affinity of water by almost 300 kJ ⋅ mol−1. Our results reveal that these large enhancements are linearly related with the binding energy of the charged complexes, and are determined by the Lewis acid−base properties of the molecule involved in the interaction, allowing a quite precise modulation of the corresponding acid−base properties of water.
J. Phys. Chem. Lett., 9, 5906–5914 (2018)
I. Uriarte, A. Insausti, E. J. Cocinero, A. Jabri, I. Kleiner, H. Mouhib, I. Alkorta
DOI: 10.1021/acs.jpclett.8b02339
Competing Dispersive Interactions: From Small Energy Differences to Large Structural Effects in Methyl Jasmonate and Zingerone
Modern structural studies of biologically relevant molecules require an exhaustive interplay between experiment and theory. In this work, we present two examples where a poor choice of the theoretical method led to a misinterpretation of experimental results. We do that by performing a rotational spectroscopy study on two large and flexible biomolecules: methyl jasmonate and zingerone. The results show the enormous potential of rotational spectroscopy as a benchmark to evaluate the performance of theoretical methods.
Dalton Trans., 47, 12516-12520 (2018)
I. Alkorta, M. M. Montero-Campillo, J. Elguero, M. Yañez, O. Mo
DOI: 10.1039/c8dt01679h
Complexes between neutral oxyacid beryllium salts and dihydrogen: a possible way for hydrogen storage?
Accurate ab initio calculations reveal that oxyacid beryllium salts yield rather stable complexes with dihydrogen. The binding energies range between −40 and −60 kJ mol−1 for 1 : 1 complexes, remarkably larger than others previously reported for neutral H2 complexes. The second H2 molecule in 1 : 2 complexes is again strongly bound (between −18 and −20 kJ mol−1). The incoming H2 molecules in 1 : n complexes (n = 3–6) are more weakly bound, confirming the preference of Be for tetracoordinated arrangements.
J. E. Del Bene, I. Alkorta, M.M. Montero-Campillo, J. Elguero
Using protonation to change a Cl...N halogen bond in N-Base:ClOH complexes to a Cl...O halogen bond
Ab initio MP2/aug′-cc-pVTZ calculations demonstrate that protonation of N-Base:ClOH complexes at O leads to complexes (N-Base-Cl)+:OH2, as a traditional N...Cl halogen bond is replaced by a chlorine-transferred Cl...O bond. For a fixed base, the binding energies of the latter complexes are more than an order of magnitude greater than the former. As a function of the Cl-N distance, EOM-CCSD Cl-N coupling constants show the evolution of the traditional halogen bond in the N-Base:ClOH complexes, to a chlorine-shared halogen bond in N2:ClOH2+, to a covalent bond in (N-Base-Cl)+:OH2. 1J(Cl-N) values for these complexes resemble 1J(Cl-N) for the ions (N-Base-Cl)+.
DOI: 10.3390/molecules23092250 (Open Access)
An Ab Initio Investigation of the Geometries and Binding Strengths of Tetrel-, Pnictogen-, and Chalcogen-Bonded Complexes of CO2, N2O, and CS2 with Simple Lewis Bases: Some Generalizations
Geometries, equilibrium dissociation energies (De), and intermolecular stretching, quadratic force constants (kσ) are presented for the complexes B⋯CO2, B⋯N2O, and B⋯CS2, where B is one of the following Lewis bases: CO, HCCH, H2S, HCN, H2O, PH3, and NH3. The geometries and force constants were calculated at the CCSD(T)/aug-cc-pVTZ level of theory, while generation of De employed the CCSD(T)/CBS complete basis-set extrapolation. The non-covalent, intermolecular bond in the B⋯CO2 complexes involves the interaction of the electrophilic region around the C atom of CO2 (as revealed by the molecular electrostatic surface potential (MESP) of CO2) with non-bonding or π-bonding electron pairs of B. The conclusions for the B⋯N2O series are similar, but with small geometrical distortions that can be rationalized in terms of secondary interactions. The B⋯CS2 series exhibits a different type of geometry that can be interpreted in terms of the interaction of the electrophilic region near one of the S atoms and centered on the C∞ axis of CS2 (as revealed by the MESP) with the n-pairs or π-pairs of B. The tetrel, pnictogen, and chalcogen bonds so established in B⋯CO2, B⋯N2O, and B⋯CS2, respectively, are rationalized in terms of some simple, electrostatically based rules previously enunciated for hydrogen- and halogen-bonded complexes, B⋯HX and B⋯XY. It is also shown that the dissociation energy De is directly proportional to the force constant kσ, with a constant of proportionality identical within experimental error to that found previously for many B⋯HX and B⋯XY complexes.
Complexes of O=C=S with Nitrogen Bases: Chalcogen Bonds, Tetrel Bonds, and Other Secondary Interactions
Ab initio MP2/aug'‐cc‐pVTZ calculations have been carried out to investigate chalcogen‐bond formation through the σ‐hole at S and tetrel‐bond formation through the π‐hole at C in complexes of OCS with a series of nitrogen bases. The binding energies of chalcogen‐ and tetrel‐bonded complexes with the sp‐hybridized bases correlate exponentially with the N−S and N−C distances, respectively. The presence of secondary interactions between an N−H or C−H group of an sp2‐hybridized base and OCS in chalcogen‐bonded complexes decreases the correlation between binding energies and the N−S distance. These secondary interactions are stronger in the tetrel‐bonded complexes with the sp2 bases, particularly in the isomers of OCS:imidazole and OCS : N2H2, where they may be described as distorted N−H⋅⋅⋅O or N−H⋅⋅⋅S hydrogen bonds. Charge‐transfer interactions are consistent with the nature of the primary and secondary interactions in these complexes. The in‐plane OCS bending frequencies are blue‐shift in the chalcogen‐bonded complexes, and red‐shifted in the tetrel‐bonded complexes. EOM‐CCSD spin‐spin coupling constants 1cJ(N4−S) across chalcogen bonds have absolute values less than 9.0 Hz, while the two‐bond coupling constants 2cJ(N4−C) do not exceed 4.0 Hz. These are greater in absolute value that the one‐bond coupling constants 1tJ(N4−C) across tetrel bonds that are less than 0.5 Hz at much shorter N−C distances.
New J. Chem. 42, 13889-13898 (2018)
DOI: 10.1039/C8NJ01879K
A theoretical study of perovskites related to CH3NH3PbX3 (X = F, Cl, Br, I)
The bond dissociation energies of MAPI (CH3NH3PbI3) and related perovskites (with F, Cl, Br instead of I and with bases other than methylamine) have been calculated using a simplified model consisting of a corner of the perovskite (PbX3−) and the methyl ammonium (CH3NH3+) and other protonated bases. The values obtained show that besides the size (related to the tolerance factor), the energy of the interaction should be considered. Using relativistic corrections (ADF), the 1H, 13C, 15N and 207Pb absolute shieldings were calculated and transformed into chemical shifts by empirical equations established here. The 13C and 15N light nuclei were well reproduced by the "corner" model but the 207Pb chemical shifts need a large correction factor owing to the fact that lead in the perovskites is surrounded by six iodine atoms instead of the "corner's" three atoms.
Mol. Phys. 116, 2396-2405 (2018)
M.C. Caputo, I. Alkorta, P. F. Provasi, S. P. A. Sauer
Analysis of the interactions in FCCF:(H2O) and FCCF:(H2O)2 complexes through the study of their indirect spin–spin coupling constants
A theoretical study of FCCF:(H2O)n complexes, with n = 1 and 2, has been carried out by means of ab initio computational methods. Three kinds of interactions are observed in the complexes: H···π and H···F hydrogen bonds and O···FC tetrel bonds. The indirect spin–spin coupling constants have been calculated at the CCSD/aug-cc-pVTZ-J computational level. Special attention has been paid to the dependence of the different intramolecular coupling constants in FCCF on the distance between the coupled nuclei and the presence or absence of water molecules. The exceptional sensitivity shown by these coupling constants to the presence of water molecules is quite notorious and can provide information on the bonding structure of the molecule.
Phys.Chem.Chem.Phys., 20, 19552-19559 (2018)
Binding indirect greenhouse gases OCS and CS2 by nitrogen heterocyclic carbenes (NHCs)
Carbon disulfide (CS2) and carbonyl sulfide (OCS) are indirect greenhouse gases that can be effectively trapped by classical, abnormal and remote nitrogen heterocyclic carbenes (NHCs), according to high level ab initiocalculations. The process is described through a reaction profile involving two minima, a non-covalent complex and a covalently bound product, connected by a single transition state. Both CS2 and OCS react towards NHCs in a similar way, forming a new C–C bond and leading to very stable products with feasible barriers in many cases, although they vary significantly depending on the NHC structure. The barriers are larger than those reported for CO2, oscillating from barrierless processes up to a maximum of 57.9 kJ mol−1, whereas the products are more stabilized than those incorporating CO2. The lowest barriers for the CS2 + NHC reactions correspond to the largest C–C distances in the products, unlike the CO2 case. Remarkably, the most favored reactions, which are those involving a remote NHC, do not exhibit the highest interaction energies at the TS, but low distortion energy values of the OCS/CS2 moieties. The decomposition of the interaction energy allowed to confirmed that in fact the remote carbene is the less favored one in terms of the electrostatic and exchange terms. Substitution in CO2 of O by a more polarizable atom such as S have a great influence on the balance between the steric plus orbital interaction and the kinetic energy terms, thus making the products between NHCs and OCS/CS2 more stable. Both OCS and CS2 become better charge acceptors than CO2 on going from the starting complexes to the products.
M.M. Montero-Campillo, O. Mó, M .Yáñez, I. Alkorta, J. Elguero
Be‐ and Mg‐Based Electron and Anion Sponges
By using G4(MP2) high‐level ab initio methods, we show that Be and Mg derivatives of cyclopropane exhibit very large electron and anion affinities, reflecting the electron‐deficient nature of the −BeX and −MgX (X=CH3, F, Cl, CN) substituents. In particular, these compounds present electron affinities among the largest reported for neutral closed‐shell systems. Their anion affinities are also among the largest reported for single neutral molecules, indeed higher than the 1,8‐diBeX‐naphthalene (X=F, Cl, CN) derivatives, recently shown to behave as anion sponges. Quite unexpectedly, our results indicate that the intrinsic anion affinity of the Mg‐containing compounds is higher than that of the Be‐containing analogs
DOI: 10.1039/c8nj00470f
Strengths of non-covalent interactions in hydrogen-bonded complexes B···HX and halogen-bonded complexes B···XY (X, Y = F, Cl): an ab initio investigation
The intermolecular quadratic stretching force constants kcalc.σ of a series of hydrogen-bonded and halogen-bonded complexes B⋯HX and B⋯XY, where B is N2, CO, HCCH, C2H4, H2S. PH3, H2O or NH3 and X and Y are F or Cl, have been calculated ab initio at the CCSD(T)/aug-cc-pVTZ level of theory. The values obtained are compared with those kexp.σ values available from experimental centrifugal distortion constants by the use of a model based on the assumption of rigid, unperturbed component molecules at their equilibrium separation. Although the expressions resulting from the model involve equilibrium spectroscopic constants of B, HX (or XY), and B⋯HX (or XY), only zero-point quantities are normally available and are therefore used. A graph of kexp.σversus kcalc.σ for all complexes investigated can be fitted by linear regression as a straight line through the origin and with gradient 0.94(3), with a small scatter of points relative to the line. The scatter is attributed mainly to the use of zero-point spectroscopic constants in place of equilibrium values. Values of the equilibrium dissociation energy De(CBS) calculated at the CCSD(T)/CBS level (where CBS indicates complete basis set extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets) for all complexes are found to be directly proportional to kcalc.σ to a good degree of approximation, with a constant of proportionality obtained from the fit of the hydrogen-bonded complexes identical to that for halogen-bonded complexes within two standard deviations.
P. Sanz, M. M. Montero-Campillo, O. Mó, M. Yáñez, I. Alkorta, J. Elguero
Intramolecular magnesium bonds in malonaldehyde-like systems: a critical view of the resonance-assisted phenomena
Through the use of high-level G4-theory calculations, we have investigated the structure, stability, and bonding of a set of Mg derivatives formed by replacing the –OH group of malonaldehyde or only the hydrogen atom of this group by a –MgH group. To give insight into the resonance-assisted phenomenon, which might be involved in the stabilization of these compounds, we also included the corresponding saturated analogs in our survey. The effect of the rigidity of the molecular framework was considered by analyzing the Mg derivatives of (Z)-4-(hydroxymethylene)cyclobut-2-enone, obtained through the same substitutions mentioned above. The effect of replacing the carbonyl group by an imino group was also contemplated. In all cases, the global minimum is a cyclic conformer stabilized through the formation of rather strong intramolecular magnesium bonds. The strength of these interactions is directly related with the intrinsic basicity of the carbonyl group (or the imino group) and the intrinsic acidity of the –MgH group, rather than with a resonance-assisted phenomenon. As a matter of fact, for all the investigated systems, the conclusion is that resonance in the cyclic conformer is directly correlated with the strength of the intramolecular magnesium bond, and not vice versa. Interestingly, the strength and characteristics of these interactions for these Mg-containing derivatives are very similar to those of the corresponding Be-containing analogs.
Croat. Chem. Acta 91, 121–124 (2018)
M. H. Abraham, J. Elguero, I. Alkorta
DOI: 10.5562/cca3258 (OpenAccess)
The Hydrogen-bond Basicity of Carbenes
We have evaluated theoretically in the gas-phase (MP2/aug-cc-pVTZ) the hydrogen-bond basicity of simple carbenes and vinylidenes and compared them to the corresponding nitrogen and oxygen derivatives using HF as Lewis acid. These values fit conveniently with B values only if sp3 and sp2 atoms are treated separately, which is a consequence of the gas-phase (calculated) vs. solution (measured) effects.
I. Alkorta, M. M. Montero-Campillo, J. Elguero, M. Yáñez, Otilia Mó
Trapping One Electron between Three Beryllium Atoms: Very Strong One-Electron Three-Center Bonds
The ability of a set of beryllium‐substituted cyclohexane derivatives to trap electrons was determined by evaluating their electron affinities at the G4(MP2) level of theory. The nature of bonding and the effect of the different substituents attached to beryllium were studied by different computational methods (quantum theory of atoms in molecules, electron localization function, natural bond orbital, and analysis of the spin density), revealing the existence of a one‐electron/Be3 cyclic bonding in trisubstituted species. This peculiar bond is the key for the high electron affinity values found in the tri‐BeX derivatives (X=F, Cl, CN), such as the triberyllium cyano derivatives of cyclohexane, reaching values of 294 kJ mol−1, only marginally smaller than the values reported for tetracyanoethylene (305 kJ mol−1) and for some fullerenes (306 kJ mol−1).
C. Martin-Fernandez, M.M. Montero-Campillo, I. Alkorta, J. Elguero
Weak interactions and cooperativity effects on disiloxane: a look at the building block of silicones
The behaviour of disiloxane 1 towards a set of Lewis acids (LA) and Lewis bases (LB) forming complexes through its oxygen and silicon atoms, respectively, was studied at the MP2/aug′-cc-pVTZ level of theory, exploring a wide variety of non-covalent interactions. Disiloxane is a moderate electron acceptor and a good electron donor, exhibiting in the latter case binding energies up to almost −100 kJ/mol with BeCl2. Cooperativity effects were also analysed by looking at ternary 1:LA:LB complexes. Shorter intermolecular distances than in the corresponding binary complexes and a negative contribution of the three-body term to the binding energy indicate that the non-covalent interactions allowed by disiloxane through its acid and basic centres cooperate between them to reinforce both donor–acceptor pairs. These effects are particularly strong in complexes involving beryllium and triel bonds, but are also relevant for complexes containing hydrogen bonds.
J. E. Del Bene, J. Elguero, I. Alkorta
Complexes of CO2 with the Azoles: Tetrel Bonds, Hydrogen Bonds and Other Secondary Interactions
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to investigate the complexes of CO2 with the azoles pyrrole, pyrazole, imidazole, 1,2,3- and 1,2,4-triazole, tetrazole and pentazole. Three types of complexes have been found on the CO2:azole potential surfaces. These include ten complexes stabilized by tetrel bonds that have the azole molecule in the symmetry plane of the complex; seven tetrel-bonded complexes in which the CO2 molecule is perpendicular to the symmetry plane; and four hydrogen-bonded complexes. Eight of the planar complexes are stabilized by Nx···C tetrel bonds and by a secondary interaction involving an adjacent Ny-H bond and an O atom of CO2. The seven perpendicular CO2:azole complexes form between CO2 and two adjacent N atoms of the ring, both of which are electron-pair donors. In three of the four hydrogen-bonded complexes, the proton-donor Nz-H bond of the ring is bonded to two C-H bonds, thereby precluding the planar and perpendicular complexes. The fourth hydrogen-bonded complex forms with the strongest acid pentazole. Binding energies, charge-transfer energies and changes in CO2 stretching and bending frequencies upon complex formation provide consistent descriptions of these complexes. Coupling constants across tetrel bonds are negligibly small, but 2hJ(Ny-C) across Nz-H···C hydrogen bonds are larger and increase as the number of N atoms in the ring increases.
Chem. Select 3, 3855-3859 (2018)
P. Sabater, F. Zapata, A. Caballero, I. Alkorta, C. Ramirez de Arellano J. Elguero, P. Molina
Synthesis, Structure and Anion Sensing Properties of a Dicationic Bis(imidazolium)‐Based Cyclophane
The preparation and sensing properties of a tetracyclic cyclophane receptor containing two imidazolium rings as anion binding sites and two fluorene rings as fluorescent signaling units, are reported. The receptor behaves as a selective fluorescent chemosensor molecule for inorganic phosphates. 1H‐NMR spectroscopical data clearly indicate the simultaneous occurrence of charge‐assisted aromatic and aliphatic C−H noncovalent interactions. PCM/DFT calculations have been carried out to predict the structures of the complexes formed with one and two molecules of PF6−, H2PO4− and HP2O73−
J. Phys. Chem. A, 122, 3313–3319 (2018)
Fostering the Basic Instinct of Boron in Boron–Beryllium Interactions
A set of complexes L2HB···BeX2 (L = CNH, CO, CS, N2, NH3, NCCH3, PH3, PF3, PMe3, OH2; X = H, F) containing a boron–beryllium bond is described at the M06-2X/6-311+G(3df,2pd)//M062-2X/6-31+G(d) level of theory. In this quite unusual bond, boron acts as a Lewis base and beryllium as a Lewis acid, reaching binding energies up to −283.3 kJ/mol ((H2O)2HB···BeF2). The stabilization of these complexes is possible thanks to the σ-donor role of the L ligands in the L2HB···BeX2 structures and the powerful acceptor nature of beryllium. According to the topology of the density, these B–Be interactions present positive laplacian values and negative energy densities, covering different degrees of electron sharing. ELF calculations allowed measuring the population in the interboundary B–Be region, which varies between 0.20 and 2.05 electrons upon switching from the weakest ((CS)2HB···BeH2) to the strongest complex ((H2O)2HB···BeF2). These B–Be interactions can be considered as beryllium bonds in most cases.
Hydrogen and Halogen Bonding in Cyclic FH(4-n):FCln Complexes, for n = 0–4
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the six unique cyclic quaternary complexes FH:FH:FH:FH, FH:FH:FH:FCl, FH:FH:FCl:FCl, FH:FCl:FH:FCl, FH:FCl:FCl:FCl, and FCl:FCl:FCl:FCl stabilized by F–H···F hydrogen bonds and F–Cl···F halogen bonds. The binding energies of these complexes decrease as the number of FH molecules decreases, and therefore as the number of hydrogen bonds decreases, indicating that hydrogen bonds are primarily responsible for stabilities. Nonadditivities of binding energies are synergistic for complexes with 4, 3, and 2 FH molecules, but antagonistic for those with 1 and 0 FH molecules. In addition to depending on changes in F–F, F–H, and F–Cl distances, complex binding energies are also influenced by two sets of angular parameters. These include the external F–F–F angles which must sum to 360° in these cyclic structures, and the internal H–F–F angles for hydrogen bonds and F–Cl–F angles for halogen bonds, which measure the deviation from linearity of these bonds. Transition structures present the barriers to converting an equilibrium structure to an equivalent equilibrium structure on the potential surfaces. These barriers increase as the number of FH molecules decreases. EOM-CCSD spin–spin coupling constants 2hJ(F–F) across hydrogen bonds in complexes tend to increase with decreasing F–F distance. They increase dramatically in transition structures, but show no dependence on the F–F distance. The one-bond coupling constants 1hJ(F–H) are relatively small and negative in complexes, increase dramatically, and are positive in transition structures. 1J(F–H) values are greatest for the covalent F–H bond. Coupling constants 1xJ(F–Cl) across halogen bonds are relatively small and positive in complexes, and increase dramatically in transition structures. The largest values of 1J(F–Cl) are found for covalent bonds.
Chem. Phys. Lett. 694, 48–52 (2018)
I. Alkorta, M. M. Montero-Campillo, J. Elguero
Remote modulation of singlet–triplet gaps in carbenes
The modulation of the singlet-triplet (S/T) gap of phenyl-carbene derivatives by hydrogen bond formation has been studied using the G4(MP2) computational method. The complexation of the aromatic ring substituents (–NH2, –OH, –PH2, –SH) in meta- and para-positions with water and the protonation or deprotonation of such groups have a remarkable influence on the S/T gaps, reaching S/T gap variations from 25.7 to 93.7 kJ mol−1. This variation is linearly related to the binding energy difference of the S/T configurations. Importantly, the triplet and singlet electronic configurations are systematically favored in the protonated and deprotonated forms, respectively, in all cases.
I. Alkorta, C. Martín-Fernández, M. M. Montero-Campillo, J. Elguero
Hydrogen-Bonding Acceptor Character of Be3, the Beryllium Three-Membered Ring
The ability of Be3 as a hydrogen bond acceptor has been explored by studying the potential complexes between this molecule and a set of hydrogen bond donors (HF, HCl, HNC, HCN, H2O, and HCCH). The electronic structure calculations for these complexes were carried out at the MP2 and CCSD(T) computational levels together with an extensive NBO, ELF, AIM, and electrostatic potential characterization of the isolated Be3 system. In all the complexes, the Be–Be σ bond acts as electron donor, with binding energies between 19 and 6 kJ mol–1. A comparison with the analogous cyclopropane:HX complexes shows similar binding energies and contributions of the DFT-SAPT energetic terms. A blue-shift of the harmonic frequencies of Be3 is observed upon complexation.
Chem. Eur. J. 24, 1971 – 1977 (2018)
C. Martín-Fernández, M. M. Montero-Campillo, I. Alkorta, M. Yáñez, O. Mó, J. Elguero
Large Proton-Affinity Enhancements Triggered by Noncovalent Interactions
The proton affinity (PA) of the hydroxyl group of a series of compounds YHxOH (x=0–3; Y=Li, Na, Be, Mg, B, Al, Si, P, S, Cl, H) always increases on interaction with Lewis bases (LB=NH3, H2CNH, HCN) according to electronic structure calculations at the G4 level of theory. The LB:YHxOH complexes experience enhancements of PA from 24.8 to 304.8 kJ mol−1 for the OH group with respect to the free compounds. This enhancement is related to the ability of these YHxOH compounds, acting as Lewis acids, to form noncovalent interactions of different kinds. Interestingly, weakly interacting systems can give rise to PA enhancements equal to or even larger than those of strongly interacting systems, as observed in the halogen-bonded complex H2CNH⋅⋅⋅ClOH, whereby the free compound (PA=642.4 kJ mol−1) is transformed into a base (PA=947.2 kJ mol−1) that is stronger than pyridine.
M. Merced Montero-Campillo, Pablo Sanz, Otilia Mó, Manuel Yáñez, Ibon Alkorta, José Elguero
DOI: 10.1039/C7CP07891A
Alkaline-earth (Be, Mg and Ca) bonds at the origin of huge acidity enhancements
The interaction between alkaline-earth derivatives with the general formula X2M (X = H, F and Cl; M = Be, Mg and Ca) and a set of Lewis bases, including first and second-row hydrides, namely YHn (Y = O, N, F, S, P and Cl) hydrides, as well as other typical cyclic organic bases, such as aniline, 1H-1,2,3-triazole, 1H-tetrazole and phenylphosphine, was investigated using the G4 ab initio composite method. Contrary to what was expected, it was found that the interactions involving Mg and Ca derivatives were not necessarily weaker than those between beryllium bonds. The origin is two-fold: larger deformation of the interacting systems when Be-derivatives are involved and appearance of secondary non-covalent interactions in the formation of some of the Mg- and Ca-containing complexes. Hence, the dissociation of the latter complexes may require higher enthalpies than that of the Be complexes. These deformations are triggered by a significant redistribution of electron density of the two interacting moieties, which also result in dramatic changes in the reactivity of the interacting compounds and in particular in the intrinsic basicity of the Lewis bases investigated, to the point that conventional bases, such as ammonia or aniline, upon complexation with MCl2 (M = Be, Mg and Ca), become stronger Brønsted acids than phosphoric acid, whereas other bases, such as 1H-tetrazole, become stronger acids than perchloric acid.
J. Mol. Mod. 24, 16 (2018)
O. Brea, O. Mó, M. Yáñez, M. Merced Montero-Campillo, I. Alkorta, J. Elguero
Are beryllium-containing biphenyl derivatives efficient anion sponges?
The structures and stabilities of 2,2′-diBeX-1,1′-biphenyl (X = H, F, Cl, CN) derivatives and their affinities for F−, Cl−, and CN− were theoretically investigated using a B3LYP/6–311 + G(3df,2p)//B3LYP/6–31 + G(d,p) model. The results obtained show that the 2,2′-diBeX-1,1′-biphenyl derivatives (X = H, F, Cl, CN) exhibit very high F−, Cl−, and CN− affinities, albeit lower than those reported before for their 1,8-diBeX-naphthalene analogs, in spite of the fact that the biphenyl derivatives are more flexible than their naphthalene counterparts. Nevertheless, some of the biphenyl derivatives investigated are predicted to have anion affinities larger than those measured for SbF5, which is considered one of the strongest anion capturers. Therefore, although weaker than their naphthalene analogs, the 2,2′-diBeX-1,1′-biphenyl derivatives can still be considered powerful anion sponges. This study supports the idea that compounds containing –BeX groups in chelating positions behave as anion sponges due to the electron-deficient nature and consequently high intrinsic Lewis acidity of these groups.
ChemPhysChem, 18, 3498–3503 (2017)
G. J. Buralli, D. J. R. Duarte, N. M. Peruchena, I. Alkorta
Simultaneous Occurrence of Quadruple Lewis Acid–Base Interactions between Selenium Atoms in Selenocarbonyl Dimers
High-level quantum chemical calculations are performed to investigate C=Se⋅⋅⋅Se=C interactions. Bounded structures are found with binding energies between −4 and −7 kJ mol−1. An energy decomposition analysis shows that dispersion is the more attractive term, and in all cases save one, the electrostatic interaction is attractive despite each selenium atom having a positive σ-hole at the extension of the C=Se bond. The topological analysis of the molecular electrostatic potential and L(r)=−∇2ρ(r) function, and natural bond orbital analysis reveal that these particular Se⋅⋅⋅Se contacts can be considered to be quadruple Lewis acid–base interactions.
S. M. Chalanchi, I. Alkorta, J. Elguero, D. Quiñonero
Hydrogen Bond versus Halogen Bond in Cation–Cation Complexes: Effect of the Solvent
Competition between hydrogen- (HB) and halogen-bonded (XB) 4-ammoniumpyridine and halogenammonium (NHnF3−nX+; n=0–3; X=F, Cl, Br, and I) cation–cation complexes are explored by means of DFT calculations. HB and XB minima structures are found for all systems in the gas phase. As the number of fluorine atoms increases, the HB complexes are more favored than those of XB. Proton transfer is generally observed in complexes with two, three, or four halogen atoms. The XB complexes evolve from traditional halogen bonds, to halogen-shared complexes, and to ionic complexes as the number of fluorine atoms increases. The dissociation transition states and their corresponding barriers are also characterized; the barriers increase as the number of fluorine atoms increases. The results if solvent effects are considered indicate that, even in an apolar solvent, such as n-hexane, most of the complexes have favorable binding energies. Atoms-in-molecules theory is used to analyze the complexes, and results in good correlations between electron density and total electron energy density (Η) values with the intermolecular bond length. According to the Η values obtained, the covalency of these interactions starts to manifest at distances around 72–74 % the sum of the van der Waals radii of the interacting atoms.
Enhancing Intramolecular Chalcogen Interactions in 1-Hydroxy-8-YH-naphthalene Derivatives
Forty-two peri-substituted naphthalene derivatives presenting chalcogen weak interactions were studied. They correspond to O···Y interactions, Y being O, S, and Se. While the O atom bears H or CH3 substituents (OH and OCH3 groups), the Y atom is substituted by H, F, and CN to explore the effect of these electron-donating and electron-withdrawing substituents on the chalcogen bond strength. The effect of F and CH3 substituents on positions ortho/para (2,4,5,7 of the naphthalene ring) was also studied. Optimizations were performed at the MP2/aug-cc-pVDZ, and binding energies were performed at the MP2/aug-cc-pVDZ followed by an MP2/CBS estimation. The main properties studied were geometries, energies (Eb, Eiso, and Edef), the molecular electrostatic potential, electron density shifts, natural bond order E(2) energies, and the relationship between these properties.
Halogen Bonding Involving CO and CS with Carbon as the Electron Donor
MP2/aug'-cc-pVTZ calculations have been carried out to investigate the halogen-bonded complexes formed when CO and CS act as electron-pair donors through C to ClF, ClNC, ClCl, ClOH, ClCN, ClCCH, and ClNH2. CO forms only complexes stabilized by traditional halogen bonds, and all ClY molecules form traditional halogen-bonded complexes with SC, except ClF which forms only an ion-pair complex. Ion-pair complexes are also found on the SC:ClNC and SC:ClCl surfaces. SC:ClY complexes stabilized by traditional halogen bonds have greater binding energies than the corresponding OC:ClY complexes. The largest binding energies are found for the ion-pair SC–Cl+:−Y complexes. The transition structures which connect the complex and the ion pair on SC:ClNC and SC:ClCl potential surfaces provide the barriers for inter-converting these structures. Charge-transfer from the lone pair on C to the σ-hole on Cl is the primary charge-transfer interaction stabilizing OC:ClY and SC:ClY complexes with traditional halogen bonds. A secondary charge-transfer occurs from the lone pairs on Cl to the in-plane and out-of-plane π antibonding orbitals of ClY. This secondary interaction assumes increased importance in the SC:ClNH2 complex, and is a factor leading to its unusual structure. C–O and C–S stretching frequencies and 13C chemical shieldings increase upon complex formation with ClY molecules. These two spectroscopic properties clearly differentiate between SC:ClY complexes and SC–Cl+:−Y ion pairs. Spin–spin coupling constants 1xJ(C–Cl) for OC:ClY complexes increase with decreasing distance. As a function of the C–Cl distance, 1xJ(C–Cl) and 1J(C–Cl) provide a fingerprint of the evolution of the halogen bond from a traditional halogen bond in the complexes, to a chlorine-shared halogen bond in the transition structures, to a covalent bond in the ion pairs.
DOI: 10.1021/acs.jpca.7b08393 (open access)
Carbon–Carbon Bonding between Nitrogen Heterocyclic Carbenes and CO2
Ab initio MP2/aug′-cc-pVTZ calculations were performed to identify equilibrium complexes and molecules and the transition structures that interconvert them, on the potential energy surfaces of a series of seven binary systems that have nitrogen heterocyclic carbenes (NHCs) as the electron-pair donors to CO2. Seven of the NHCs form complexes stabilized by C···C tetrel bonds, and six of these seven are also stabilized by a secondary interaction between an O of CO2 and the adjacent N–H group of the carbene. Six of the seven NHCs also form stable molecules with C–C covalent bonds, and with one exception, these molecules have binding energies that are significantly greater than the binding energies of the complexes. Charge-transfer stabilizes all of the NHC:CO2 complexes and occurs from the C lone pair of the carbene to the CO2 molecule. The six complexes that have secondary stabilizing interactions are also stabilized by back-donation of charge from the O to the adjacent N–H group of the carbene. Transition structures present barriers to the interconversion of complexes and molecules. With one exception, the barrier for converting a molecule to a complex is much greater than the barrier for the reverse reaction. Atoms in Molecules bonding parameters, shifts of IR C–O stretching and O–C–O bending frequencies, changes in NMR 13C chemical shieldings, and changes in C–C and C–O coupling constants as 1tJ(C–C) and J(C–O) for complexes and transition structures become 1J(C–C) and 2J(C–O) for molecules, are all consistent with the changing nature of the C···C tetrel bond in the complex through the transition state to a covalent C–C bond in the molecule.
Nucleophilicities of Lewis Bases B and Electrophilicities of Lewis Acids A Determined from the Dissociation Energies of Complexes B···A Involving Hydrogen Bonds, Tetrel Bonds, Pnictogen Bonds, Chalcogen Bonds and Halogen Bonds
It is shown that the dissociation energy De for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N2, CO, HC≡CH, CH2=CH2, C3H6, PH3, H2S, HCN, H2O, H2CO and NH3) and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H2O, F2, Cl2, Br2, ClF, BrCl, H3SiF, H3GeF, F2CO, CO2, N2O, NO2F, PH2F, AsH2F, SO2, SeO2, SF2, and SeF2) can be represented to good approximation by means of the equation De=c′NBEA , in which NB is a numerical nucleophilicity assigned to B, EA is a numerical electrophilicity assigned to A, and c′ is a constant, conveniently chosen to have the value 1.00 kJ mol−1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1) the hydrogen bond; (2) the halogen bond; (3) the tetrel bond; (4) the pnictogen bond; and (5) the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of NB and EA so determined define properties of the individual molecules. The values of NB and EA can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy
DOI: 10.1021/acs.jpca.7b08505 (OpenAccess)
Azines as Electron-Pair Donors to CO2 for N···C Tetrel Bonds
Ab initio MP2/aug′-cc-pVTZ calculations were performed to investigate tetrel-bonded complexes formed between CO2 and the aromatic bases pyridine, the diazines, triazines, tetrazines, and pentazine. Of the 23 unique equilibrium azine:CO2 complexes, 14 have planar structures in which a single nitrogen atom is an electron-pair donor to the carbon of the CO2 molecule, and 9 have perpendicular structures in which two adjacent nitrogen atoms donate electrons to CO2, with bond formation occurring along an N–N bond. The binding energies of these complexes vary from 13 to 20 kJ mol–1 and decrease as the number of nitrogen atoms in the ring increases. For a given base, planar structures have larger binding energies than perpendicular structures. The binding energies of the planar complexes also tend to increase as the distance across the tetrel bond decreases. Charge transfer in the planar pyridine:CO2 complex occurs from the N lone pair to a virtual nonbonding orbital of the CO2 carbon atom. In the remaining planar complexes, charge transfer occurs from an N lone pair to the remote in-plane π*C–O orbital. In perpendicular complexes, charge transfer occurs from an N–N bond to the adjacent π*O–C–O orbital of CO2. Decreases in the bending frequency of the CO2 molecule and in the 13C chemical shielding of the C atom of CO2 upon complex formation are larger in planar structures compared to perpendicular structures. EOM-CCSD spin–spin coupling constants 1tJ(N–C) for complexes with planar structures are very small but still correlate with the N–C distance across the tetrel bond.
Faraday Discuss. 203, 29-45 (2017)
DOI: 10.1039/C7FD00048K
Using one halogen bond to change the nature of a second bond in ternary complexes with P⋯Cl and F⋯Cl halogen bonds
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the effect of the presence of one halogen bond on the nature of the other in ternary complexes H2XP:ClF:ClH and H2XP:ClF:ClF, for X = F, Cl, H, NC, and CN. The P⋯Cl bonds remain chlorine-shared halogen bonds in the ternary complexes H2XP:ClF:ClH, although the degree of chlorine sharing increases relative to the corresponding binary complexes. The F⋯Cl bonds in the ternary complexes remain traditional halogen bonds. The binding energies of the complexes H2XP:ClF:ClH increase relative to the corresponding binary complexes, and nonadditivities of binding energies are synergistic. In contrast, the presence of two halogen bonds in the ternary complexes H2XP:ClF:ClF has a dramatic effect on the nature of these bonds in the four most strongly bound complexes. In these, chlorine transfer occurs across the P⋯Cl halogen bond to produce complexes represented as (H2XP–Cl)+:−(F:ClF). In the ion-pair, the cation is also halogen bonded to the anion by a Cl⋯F− halogen bond, while the anion is stabilized by an −F⋯Cl halogen bond. The central ClF molecule no longer exists as a molecule. The binding energies of the ternary H2XP:ClF:ClF complexes are significantly greater than the binding energies of the H2XP:ClF:ClH complexes, and nonadditivities exhibit large synergistic effects. The Wiberg bond indexes for the complexes H2XP:ClF, H2XP:ClF:ClH, and H2XP:ClF:ClF, and the cations (H2XP–Cl)+ reflect the changes in the P–Cl and Cl–F bonds. Similarly, EOM-CCSD spin–spin coupling constants are also consistent with the changes in these same bonds. In particular, 1xJ(P–Cl) in H2XP:ClF complexes becomes 1J(P–Cl) in the ternary complexes with chlorine-transferred halogen bonds. A plot of these coupling constants shows a change in the curvature of the trendline as chlorine-shared halogen bonds in H2XP:ClF:ClH become chlorine-transferred halogen bonds in H2XP:ClF:ClF. 1xJ(F–Cl) coupling constants also reflect changes in the nature of F⋯Cl halogen bonds.
J. Phys. Org. Chem. 30, e3690 (2017)
DOI: 10.1002/poc.3690
Is it possible to use the 31P chemical shifts of phosphines to measure hydrogen bond acidities (HBA)? A comparative study with the use of the 15N chemical shifts of amines for measuring HBA
The geometries, energies, and nuclear magnetic resonance (NMR) chemical shifts of 3 bases (trimethylphosphine, trimethylamine, and trimethylphosphine oxide), their 3 protonated cations, and 15 hydrogen-bonded complexes (corresponding to the HF, HNC, HCN, HCCH, H2O, and CH3OH Brønsted acids) have been calculated at the B3LYP/6-311++G(d,p) level. The determination of hydrogen bond acidities by NMR is classically performed using the 31P chemical shifts Me3PO. This method is more reliable than the use of the 15N NMR chemical shifts of Me3N. This work shows that the 31P NMR chemical shifts of Me3P cannot be used. The raison of the difference between Me3P on one hand and Me3PO and Me3N on the other will be discussed.
C. Martín-Fernández, M. M. Montero-Campillo, I. Alkorta, J. Elguero
Modulating the Proton Affinity of Silanol and Siloxane Derivatives by Tetrel Bonds
The proton affinity (PA) on the oxygen atom in silanol and siloxane derivatives is enhanced by the formation of tetrel bonds with small Lewis bases [B···R3SiOH, B···R3SiOSiR3, B···R3SiOSiR3···B; B = H2O, CO, NH3, HCN, H2S; R = H, Me], as shown by MP2/jul-cc-pVTZ calculations. The complexed systems become more basic than ether and other carbon-related compounds, and even more basic than pyridine in some specific cases, reaching values up to 959.4 kJ/mol (H3N···H3SiOSiH3···NH3 complex). Changes on PAs are directly related to very large binding energies for the protonated species. Topological methods and the natural bond orbital scheme are used to rationalize the observed trends. The PA enhancement should be taken into account when dealing with silanols and siloxanes in different environments.
Borylene as an electron-pair donor for P…B pnicogen bonds
Ab initio MP2/aug'-cc-pVTZ calculations have been performed on the complexes (CO)2(HB):PXH2 and (N2)2(HB):PXH2, for X = F, Cl, NC, OH, CN, CCH, CH3, and H, in order to investigate the properties of these complexes which are stabilized by P…B pnicogen bonds, with B the electron-pair donor. The binding energies of these complexes exhibit an exponential dependence on the P-B distance, but they do not correlate with the MEP minima for (CO)2(HB) and (N2)2(HB), nor with the MEP maxima for PXH2. For fixed X, the binding energy of (N2)2(HB):PXH2 is greater than that of (CO)2(HB):PXH2. Charge-transfer stabilizes both series of complexes, and occurs from the B electron pair to the antibonding P-A σ orbital, with A the atom of X directly bonded to P. These charge-transfer energies also exhibit an exponential dependence on the P-B distance. In the complexes (CO)2(HB):PXH2, there is a second charge-transfer interaction from the lone pair on P to the antibonding π orbitals of the two C-O groups. Electron density analyses indicate that the P…B bonds in these complexes are stabilized by relatively weak interactions with little covalent character. The chemical shieldings of 11B are essentially unaffected by complex formation. In contrast, the shieldings of 31P increase from 10 to 50 ppm in the four most strongly bound complexes, but decrease by −4 to −12 ppm in the remaining complexes. For each series of complexes, EOM-CCSD spin-spin coupling constants 1pJ(P-B) increase quadratically with decreasing P-B distance. For fixed X, 1pJ(P-B) is greater for (CO)2(HB):PXH2 compared to (N2)2(HB):PXH2.
M. M. Montero-Campillo, I. Corral, O. Mó, M. Yáñez, I. Alkorta, J. Elguero
Beryllium-based fluorenes as efficient anion sponges
The F−, Cl−, CN−, NO2−, NO3−, and SO42− anion affinities of 4,5-bis(BeX)-fluorene (X = H, F, Cl, CN, NC, and OCH3) derivatives have been calculated at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level of theory. The reliability of this approach was assessed using, for some suitable cases, the accurate G4MP2 ab initio composite method as a reference. The values obtained indicate that these derivatives exhibit anion affinities which are among the largest ones reported for single neutral molecules, and therefore these compounds behave as anion sponges, very much as their 1,8-diBeX-naphthalene analogues. This finding seems to confirm that both molecular frameworks, when adequately substituted at positions 1,8 in the case of naphthalene and 4,5 in the case of fluorene, may behave either as proton sponges, when the substituents are good electron donors, such as alkylamino groups, or as anion sponges, when the substituents are BeX groups, which are excellent electron acceptors. The behavior of these compounds in aqueous solution was also investigated. The interaction with water decreases the anion affinities, but still they are very large. More importantly the trends observed do not differ significantly from those found in the gas phase, in particular when monoanions are considered.
Modulation of in:out and out:out conformations in [X.X′.X′′] phosphatranes by Lewis acids
A theoretical study of [X.X′.X′′]phosphatrane:Lewis acid complexes has been carried out in order to analyze how the in:out and out:out conformations can be modulated by the interaction with Lewis acids (LA). It has been found that in:out structures are more stable in larger systems i.e. in [4.4.3]:LA and [4.4.4]:LA than in [3.3.3]:LA and [4.3.3]:LA. The results obtained for the relative energies in conjunction with electron density properties showed that upon complexation, in:out conformers become more stable with the increasing acidity of the corresponding Lewis acid. In fact, the binding energies found for in:out complexes are larger than those obtained for out:out complexes. The complexes with the largest relative energy favoring the in:out structure correspond to those with charged Lewis acids, followed by the complexes with ClF. In all cases, the complexes are cooperative, reaching a maximum value of 168.5 kJ mol−1 for the [4.3.3]:F+ complex.
Halogen bonding with carbene bases
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of complexes formed from five singlet carbene bases acting as electron-pair donors to four ClX acids. Complexes with ClCCH and ClCN are stabilized by traditional halogen bonds. With one exception, complexes with ClNC and ClF are stabilized by (carbene-Cl)+⋯–NC and (carbene-Cl)+⋯–F ion-pair halogen bonds subsequent to chlorine transfer. These complexes have been characterized in terms of their structures, binding energies, charge-transfer energies, bonding properties, and spin-spin coupling constants.
J. Phys. Chem. A 2017, 121, 5665−5674
M. M. Quesada-Moreno, A. J. Cruz-Cabeza, J.R. Avilés-Moreno, P. Cabildo, R. M. Claramunt, I. Alkorta, J. Elguero, F. J. Zuñiga, J. J. López-González
The Curious Case of 2‑Propyl‑1H‑benzimidazole in the Solid State: An Experimental and Theoretical Study
2-Propyl-1H-benzimidazole (2PrBzIm) is a small molecule, commercially available, which displays a curious behavior in the solid state. 2PrBzIm, although devoid of chirality by fast rotation about a single bond of the propyl group in solution, crystallizes as a conglomerate showing chiroptical properties. An exhaustive analysis of its crystal structure and a wide range of experiments monitored by vibrational circular dichroism spectroscopy eliminated all possibilities of an artifact. What remains is a new example of the unexplained phenomenon of persistent supramolecular chirality.
Chem. Eur. J. 23, 10604–10609 (2017)
Trapping CO2 by Adduct Formation with Nitrogen Heterocyclic Carbenes (NHCs): A Theoretical Study
Carbon dioxide can form compounds with nitrogen heterocyclic carbenes (NHCs) based on azoles through noncovalent interactions or by covalent bonding. A narrow dependence on the carbene structure has been observed for the preference for one or the other type of bonding, as revealed by a series of physicochemical descriptors. In our survey, a set of NHCs based on the azole family (three classical, three abnormal, and one remote) was shown to bind CO2 at the accurate G4MP2 computational level. In most cases, exothermic reaction profiles towards the covalently bound form were found, which reached stabilization enthalpies of up to −77 kJ mol−1 for the remote carbene case. Both noncovalent and covalent minima and the corresponding transition state that connects them have been identified as stationary points along the reaction coordinate.
Nature, Scientific Reports 7, 6115 (2017)
OpenAcess
Activation of Dinitrogen as A Dipolarophile in 1,3-Dipolar Cycloadditions: A Theoretical Study Using Nitrile Imines as "Octet" 1,3-Dipoles
Theoretical calculations at the G4MP2 level of theory demonstrate that it is possible to activate dinitrogen to make it react in dipolar cycloadditions using neutral beryllium derivatives and other neutral metallic compounds. For the particular case of beryllium, the barrier decreases more than 40 kJ·mol–1 with respect to the non-catalysed reaction. The activation achieved is lower than using diazonium salts (models of protonated N2), but still in a range that can be experimentally attainable.
J. Mol. Struct. 1148, 150-161 (2017)
I. Alkorta, J. Elguero, E. Elguero
DOI: 10.1016/j.molstruc.2017.06.101
Nitroxide stable radicals interacting as Lewis bases in hydrogen bonds: A search in the Cambridge structural data base for intermolecular contacts
1125 X-ray structures of nitroxide free radicals presenting intermolecular hydrogen bonds have been reported in the Cambridge Structural Database. We will report in this paper a qualitative and quantitative analysis of these bonds. The observation in some plots of an excluded region was statistically analyzed using convex hull and kernel smooting methodologies. A theoretical study at the MP2 level with different basis has been carried out indicating that the nitronyl nitroxide radicals (five electrons) lie just in between nitroso compounds (four electrons) and amine N-oxides (six electrons) as far as hydrogen-bond basicity is concerned.
Carbenes as Electron-Pair Donors for P⋅⋅⋅C Pnicogen Bonds
Ab initio MP2/aug′-cc-pVTZ calculations were performed on the P⋅⋅⋅C pnicogen-bonded complexes of the singlet carbene molecules C(NH2)2, C(OH)2, and cyclic C(OCH)2 [OHC] with H2XP molecules, with X=F, Cl, NC, OH, CH3, CN, CCH, and H. The H2XP:C(NH2)2 and H2XP:C(OH)2complexes have Cs symmetry and two different structures: one in which the symmetry plane of the complex and the local symmetry plane of the carbene are non-coplanar, and the other in which they are coplanar. The non-coplanar H2XP:C(NH2)2 and H2XP:C(OH)2 complexes arise only when X is one of the more electronegative substituents. Coplanar H2XP:C(NH2)2 complexes form when X is one of the more electropositive substituents, whereas coplanar H2XP:C(OH)2 complexes exist for all X. H2XP:C(NH2)2 and H2XP:C(OH)2 are stabilized by covalent P−C bonds or P⋅⋅⋅C pnicogen bonds, but co-planar H2(CH3)P:C(OH)2 and H3P:C(OH)2 are stabilized by O−H⋅⋅⋅P hydrogen bonds. The H2XP:OHC complexes have non-coplanar structures that are also stabilized by P−C covalent bonds or pnicogen bonds. The H2(CH3)P:OHC and H3P:OHC complexes in which the symmetry plane of the complex and the local symmetry plane of the carbene are perpendicular are stabilized by P⋅⋅⋅π bonds with P acting as the electron-pair donor to the OHC π system. The H2XP:C(NH2)2, H2XP:C(OH)2, and H2XP:OHC complexes are described in terms of their binding energies, charge-transfer energies, electron density properties, and equation-of-motion coupled cluster singles and doubles spin–spin coupling constants.
Janet E. Del Bene, Ibon Alkorta, Jose Elguero
Carbenes as Electron-Pair Donors to CO2 for C···C Tetrel Bonds and C−C Covalent Bonds
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to identify stable complexes and molecules and the transition structures that interconvert them on the potential surfaces of ten singlet carbene bases acting as electron-pair donors to CO2. The carbene bases include cyclic C(NHCH)2 or NHC, C(NH2)2, an oxygen heterocyclic carbene C(OCH)2 or OHC, C(OH)2, C(CH3)2, cyclic C3H2, CCCH2, CCl2, CCH2, and CF2. Carbene:CO2 complexes stabilized by C···C tetrel bonds have been found on all potential surfaces, whereas carbene–CO2 molecules stabilized by C–C covalent bonds have been found on eight surfaces. Three of these molecules have open structures with C2v symmetry, whereas the remaining have cyclic three membered C–O–C rings with Cs symmetry. The transition structures which connect the complex and the molecule are bound on three of the potential surfaces. Whether the transition structure is bound or unbound relative to the carbene and CO2 depends on the relationship among C–C distances at the three stationary points on the surface. Charge-transfer interactions stabilize carbene:CO2complexes. The primary charge transfer in complexes arises from electron donation from the carbene lone-pair to the CO2 molecule. There is also back-donation of charge from CO2 to the carbene in three complexes. Systematic changes in bonding properties occur as complexes go through transition structures and become molecules. EOM-CCSD inter- and intramolecular C–C and C–O spin–spin coupling constants have been computed and compared for complexes and molecules. A search of the CSD database found the (NH2)2C–CO2 structure and 17 NHC–CO2derivatives. Computed bond distances and angles have been compared with experimental data.
Hydrogen-bonded complexes with carbenes as electron-pair donors
Ab initio MP2/aug′-cc-pVTZ calculations have been performed to investigate X-H⋯C hydrogen-bonded complexes involving eleven different carbene molecules as electron-pair donors and the acids FH, CNH, and NCH. Binding energies and charge-transfer energies increase as the X-C distances decrease, and exhibit an exponential dependence on these distances. EOM-CCSD spin-spin coupling constants 2hJ(X-C) increase quadratically in absolute value as the corresponding X-C distance decreases. 1J(F-H) and 1J(N-H) decrease as the F-H and N-H distances, respectively, increase, but 1J(C-H) shows little dependence on distance. All of these carbene complexes are stabilized by traditional hydrogen bonds.
Theor Chem Acc 136, 41 (2017)
M. Marín-Luna, I. Alkorta, J. Elguero
A theoretical study of the HnF4−nSi:N‑base (n = 1–4) tetrel‑bonded complexes
Tetrel-bonded complexes of HnF4−nSi with a N-base for n = 0–4 were explored by MP2 calculations. Configurations with H–Si···N and F–Si···N linear or nearly linear alignment in complexes were considered. Nine sp3 hybridized nitrogen bases NH3, NH2Cl, NH2F, NHCl2, NCl3, NFCl2, NHF2, NF2Cl, NF3 and nine sp ones NCNH2, NCCH3, NCOH, NP, NCCl, NCH, NCF, NCCN, N2 have been studied. It is shown that binding energies of the complexes depend strongly on the nature of the base involved in the complex. Complexes with NH3 bases present the highest binding energies. In the stronger complexes, the silicon molecules suffer important geometrical distortions. NBO and AIM methodologies have been applied in order to describe properly the intermolecular Si···N contact. F atoms in equatorial position at silicon acid provoke a deviation from linearity of the Si···N electron density bond path trajectory.
J. Phys. Chem. A, 2017, 121, 1362–1370
J. E. Del Bene, I. Alkorta, J. Elguero, G. Sanchez-Sanz
Lone-Pair Hole on P: P···N Pnicogen Bonds Assisted by Halogen Bonds
Ab initio MP2/aug'-cc-pVTZ calculations have been performed on the binary complexes XY:PH3for XY = ClCl, FCl, and FBr; and PH3:N-base for N-base = NCH, NH3, NCF, NCCN, and N2; and the corresponding ternary complexes XY:PH3:N-base, to investigate P···N pnicogen bond formation through the lone-pair hole at P in the binary complexes and P···N pnicogen-bond formation assisted by P···Y halogen bond formation through the σ-hole at Y. Although the binary complexes PH3:N-base that form through the lone-pair hole have very small binding energies, they are not equilibrium structures on their potential surfaces. The presence of the P···Y halogen bond makes PH3 a better electron-pair acceptor through its lone-pair hole, leading to stable ternary complexes XY:PH3:N-base. The halogen bonds in ClCl:PH3 and ClCl:PH3:NCCN are traditional halogen bonds, but in the remaining binary and ternary complexes, they are chlorine- or bromine-shared halogen bonds. For a given nitrogen base, the P···N pnicogen bond in the ternary complex FCl:PH3:N-base appears to be stronger than that bond in FBr:PH3:N-base, which is stronger than the P···N bond in the corresponding ClCl:PH3:N-base complex. EOM-CCSD spin–spin coupling constants for the binary and ternary complexes with ClCl and FCl are also consistent with the changing nature of the halogen bonds in these complexes. At long P–Cl distances, the coupling constant 1xJ(P–Cl) increases with decreasing distance but then decreases as the P–Cl distance continues to decrease, and the halogen bonds become chlorine-shared bonds. At the shorter distances, 1xJ(P–Cl) approaches the value of 1J(P–Cl) for the cation +(Cl–PH3). The coupling constants 1pJ(P–N) are small and, with one exception, are greater in ClCl:PH3:N-base complexes compared to that in FCl:PH3:N-base, despite the shorter P–N distances in the latter.
Molecules 2017, 22, 227
G.Sánchez–Sanz, Ibon Alkorta, José Elguero
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Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds
A theoretical study of the peri interactions, both intramolecular hydrogen (HB) and chalcogen bonds (YB), in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se) being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO) analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y-H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.
M.M. Quesada-Moreno, J.R. Avilés-Moreno, J.J. López-González, K. Jacob, L. Vendier, M. Etienne, I. Alkorta, J. Elguero, R. M. Claramunt
DOI: 10.1039/C6CP04940K
Supramolecular organization of perfluorinated 1H-indazoles in the solid state using X-ray crystallography, SSNMR and sensitive (VCD) and non sensitive (MIR, FIR and Raman) to chirality vibrational spectroscopies
1H-Indazole derivatives exhibit a remarkable property since some of them form chiral supramolecular structures starting from achiral monomers. The present work deals with the study of three perfluorinated 1H-indazoles that resolve spontaneously as conglomerates. These conglomerates can contain either a pure enantiomer (one helix) or a mixture of both enantiomers (both helices) with an enantiomeric excess (e.e.) of one of them. The difficulty of the structural analysis of these types of compounds is thus clear. We outline a complete strategy to determine the structures and configurations (M or P helices) of the enantiomers (helices) forming the conglomerates of these perfluorinated 1H-indazoles based on X-ray crystallography, solid state NMR spectroscopy and different solid state vibrational spectroscopies that are either sensitive (VCD) or not (FarIR, IR and Raman) to chirality, together with quantum chemical calculations (DFT).
Chem. Eur. J. 22, 18322–18325, 2016.
O. Brea, I. Corral, O. Mó, M. Yáñez, I. Alkorta, J. Elguero.
Beryllium-Based Anion Sponges: Close Relatives of Proton Sponges
Through the use of high-level ab initio and density functional calculations it is shown that 1,8-diBeX-naphthalene (X=H, F, Cl, CN, CF3, C(CF3)3) derivatives behave as anion sponges, very much as 1,8-bis(dimethylamino)naphthalene derivatives behave as proton sponges. The electron-deficient nature of the BeX substituents, which favors strong charge transfer from the anion towards the former, results in anion affinities that are among the largest ones reported for single neutral molecules.
PCCP, 2016, 18, 32593 - 32601
DOI: 10.1039/c6cp06474d
Unusual acid–base properties of the P4 molecule in hydrogen-, halogen-, and pnicogen-bonded complexes
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate hydrogen bonding, halogen bonding, and pnicogen bonding involving tetrahedral P4 and the FH, ClH, and FCl molecules. P4 has three unique interaction sites: at a vertex (designated the P1 atom); at an edge (the P2–P3 bond); and at the P2–P3–P4 face. The uniqueness of molecular P4 is its ability to act as an electron donor and an electron acceptor at the same site, except for the P2–P3 bond, which is only an electron donor. FCl and FH form five different complexes with P4, but ClH forms only three. The type of complex formed and its binding energy depend on both the interaction site of molecular P4 and the interacting molecule. For all complexes with FH, ClH, and FCl, the binding energies at a given site with the P4 molecule acting as the base are greater than the binding energies when P4 is the acid. Thus, P4 is a better electron donor than an electron acceptor. Charge-transfer interactions and EOM-CCSD spin–spin coupling constants across hydrogen, halogen, and pnicogen bonds are reported for all of the P4 complexes. Relative to 1J(Pi–Pj) in molecular P4, 1J(P1–P2) coupling constants decrease in absolute value and 1J(P2–P3) coupling constants increase in pnicogen-bonded complexes and the complex with FCl that has a P⋯F halogen bond. Absolute values of 1J(P1–P2) increase and those of 1J(P2–P3) decrease in hydrogen-bonded complexes and complexes with P⋯Cl halogen bonds. 1J(P1–P2) and 1J(P2–P3) exhibit a single linear correlation with the corresponding Pi–Pj distances.
New J. Chem., 2016,40, 9060-9072
D. Quiñonero, A. Bauzá, G. Sánchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero
DOI: 10.1039/C6NJ01334A
Weak interactions within nitryl halide heterodimers
A theoretical study of nitryl halide heterodimers has been carried out using SCS-RI-MP2 and CCSD(T) at the complete basis set (CBS) calculations. For this purpose, 66 heterodimers have been characterized as minima and arranged in six groups depending on the interactions involved and their geometrical arrangements. The CCSD(T)/CBS interaction energies vary between −0.6 and −11.1 kJ mol−1. The heavier the halogen atoms, the larger the interaction energies. Natural bond orbital (NBO) and "atoms-in-molecules" (AIM) theories were then used to analyze the complexes, confirming the presence of halogen, chalcogen, and π-hole interaction bonds. The largest charge-transfer energy contributions were found for halogen bonded complexes (up to 29.1 kJ mol−1). Furthermore, the physical nature of the interactions was studied using symmetry-adapted perturbation theory (SAPT) calculations, and it was concluded that dispersion was the major source of attraction, although electrostatics is important in halogen bonded complexes.
Phys. Chem. Chem. Phys., 2016,18, 27939-27950
Cation–cation and anion–anion complexes stabilized by halogen bonds
Stable minima showing halogen bonds between charged molecules with the same sign have been explored by means of theoretical calculations. The dissociation transition states and their corresponding barriers have also been characterized. In all cases, the results indicate that the complexes are thermodynamically unstable but kinetically stable with respect to the isolated monomers in gas phase. A corrected binding energy profile by removing the charge–charge repulsion of the monomers shows a profile similar to the one observed for the dissociation of analogous neutral systems. The nature of the interaction in the minima and TSs has been analyzed using the symmetry adapted perturbation theory (SAPT) method. The results indicate the presence of local favorable electrostatic interactions in the minima that vanish in the TSs. Natural bond orbital (NBO) and "atoms-in-molecules" (AIM) theories were used to analyze the complexes, obtaining good correlations between Laplacian and electron density values with both bond distances and charge-transfer energy contributions E(2). The largest E(2) orbital interaction energies for cation–cation and anion–anion complexes are 561.2 and 197.9 kJ mol−1, respectively.
Boron as an Electron-Pair Donor for B···Cl Halogen Bonds
MP2/aug'-cc-pVTZ calculations have been carried out to investigate boron as an electron-pair donor in halogen-bonded complexes (CO)2(HB):ClX and (N2)2(HB):ClX, for X = F, Cl, OH, NC, CN, CCH, CH3, and H. Equilibrium halogen-bonded complexes with boron the electron-pair donor have been found on all of the potential surfaces except for (CO)2(HB):ClCH3 and (N2)2(HB):ClF. The majority of these complexes are stabilized by traditional halogen bonds, except for (CO)2(HB):ClF, (CO)2(HB):ClCl, (N2)2(HB):ClCl, and (N2)2(HB):ClOH which are stabilized by chlorine-shared halogen bonds. These complexes have increased binding energies and shorter B-Cl distances. Charge transfer stabilizes all complexes, and occurs from the B lone pair to the σ* Cl-A orbital of ClX, with A the atom of X directly bonded to Cl. A second reduced charge transfer interaction occurs in (CO)2(HB):ClX complexes from the Cl lone pair to the π* C≡O orbitals. EOM-CCSD spin-spin coupling constants 1xJ(B-Cl) across the halogen bonds are also indicative of the changing nature of this bond. 1xJ(B-Cl) values for both series of complexes are positive at long distances, increase as the distance decreases, and then decrease as the halogen bonds change from traditional to chlorine-shared bonds, and begin to approach the values for the covalent bonds in the corresponding ions [(CO)2(HB)-Cl]+ and [(N2)2(HB)-Cl]+. Changes in 11B chemical shieldings upon complexation correlate with changes in the charges on B.
J. Org. Chem., 81, 7448–7458 (2016)
P. Sabater, F. Zapata, A. Caballero, N. de la Visitación, I. Alkorta, J. Elguero, P. Molina
DOI: 10.1021/acs.joc.6b01146
Comparative Study of Charge-Assisted Hydrogen- and Halogen-Bonding Capabilities in Solution of Two-Armed Imidazolium Receptors toward Oxoanions
Two-armed imidazolium-based anion receptors have been prepared. The central 2,7-disubstituted naphthalene ring features two photoactive anthracene end-capped side arms with central 2-bromoimidazolium or hydrogen-bonding imidazolium receptors. Combined emission and 1H and 31P NMR studies carried out in the presence of a wide variety of anions reveal that only HP2O73–, H2PO4–, SO42–, and F– anions promoted noticeable changes. The halogen receptor 62+·2PF6– acts as a selective fluorescent molecular sensor for H2PO4– anions, since only this anion promotes the appearance of the anthracene excimer emission band, whereas it remains unchanged in the presence of the other tested anions. In addition this halogen receptor behaves as a chemodosimeter toward HP2O73– anion, through its transformation into the corresponding bis-imidazolone after debromination by the action of the basic anion. The association constant values of the halogen-bonding complexes in a competitive solvent CD3CN/MeOD (8/2) mixture with H2PO4– and SO42– anions are higher than those found for the hydrogen-bonding counterpart. In contrast, in the less competitive CH3CN solvent higher binding affinity for anions corresponds to the hydrogen-bonding receptor 72+·2PF6–. In addition, the receptor 62+·2PF6– represents a useful alternative as an imaging agent in living cells in a wide range of emission wavelengths.
B4H4 and B4(CH3)4 as Unique Electron Donors in Hydrogen-Bonded and Halogen-Bonded Complexes
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out on B4H4 and B4(CH3)4 to investigate the base properties of these molecules with Td symmetry. Each face of the tetrahedral structure of B4H4 and B4(CH3)4 is stabilized by a two-electron, three-center B–B–B bond. The face uses these two electrons to act uniquely as an electron-pair donor for the formation of stable hydrogen-bonded and halogen-bonded complexes with C3v symmetry. The hydrogen-bonded complexes are B4H4:HY and B4(CH3)4:HY, with HY = HNC, HF, HCl, HCN, and HCCH; the halogen-bonded complexes are B4H4:ClY and B4(CH3)4:ClY, with ClY = ClF, ClCl, ClNC, ClCN, ClCCH, and ClH. The absolute values of the binding energies of the hydrogen-bonded complexes B4(CH3)4:HY and of the halogen-bonded complexes B4(CH3)4:ClY are significantly greater than the binding energies of the corresponding complexes with B4H4. The binding energies of each series correlate with the distance from the hydrogen-bonded H atom or halogen-bonded Cl atom to the centroid of the interacting face. Charge transfer stabilizes all complexes and occurs from the B2–B3–B4 orbital of the face to the antibonding H–X orbital of HY in hydrogen-bonded complexes and to the antibonding Cl–X orbital of ClY in halogen-bonded complexes, with X being the atom of Y that is directly bonded to either H or Cl. For fixed HY, EOM-CCSD spin–spin coupling constants J(X–B1) are greater than J(X–Bn) for complexes B4H4:HY, even though the X–B1 distances are longer. B1 and Bn are the atoms at the apex and in the interacting face, respectively. Similarly, for complexes B4H4:ClY, J(Cl–B1) is greater than J(Cl–Bn). In the halogen-bonded complexes, both coupling constants correlate with the corresponding distances.
Angew. Chem. Int. Ed. 55, 8736–8739 (2016).
O. Brea, I. Alkorta, O. Mó, M. Yáñez, J. Elguero, I. Corral
Exergonic and Spontaneous Production of Radicals through Beryllium Bonds
High-level ab initio calculations show that the formation of radicals, by the homolytic bond fission of Y−R (Y=F, OH, NH2; R=CH3, NH2, OH, F, SiH3, PH2, SH, Cl, NO) bonds is dramatically favored by the association of the molecule with BeX2 (X=H and Cl) derivatives. This finding is a consequence of two concomitant effects, the significant activation of the Y−R bond after the formation of the beryllium bond, and the huge stabilization of the F. (OH., NH2.) radical upon BeX2 attachment. In those cases where R is an electronegative group, the formation of the radicals is not only exergonic, but spontaneous.
Comp. Theor. Chem. 1090, 171–179 (2016)
G. Sanchez-Sanz, C. Trujillo, I. Alkorta
Structure, binding energy and chiral discrimination in oxathiirane homodimers
Oxathiirane (XHCSO) homodimers bonded by hydrogen bonds (HB) and chalcogen bonds (YB) were studied at the Møller-Plesset (MP2) computational level. Binding energies obtained at the Coupled-Cluster level up to the Complete Basis Set limit [CCSD(T)/CBS] indicate that HB complexes present stronger binding modes than the YB complexes. In terms of chiral discrimination energy, R,S complexes are favored over R,Rcomplexes with the exceptions of SiCl3 and SiF3 derivatives. Natural Bond Orbital (NBO) results are in agreement with the interaction energies in the case of the HB complexes, but could not discriminate between R,R and R,S in the YB complexes. The lack of correlation between molecular electrostatic values on the 0.001 a.u. and binding energies, in addition to the discrepancies between Atoms in Molecules (AIM) and NBO results may suggest that the electrostatics is not the dominant term in the interaction energy. This was corroborated by the Localized Molecular Orbital Energy Decomposition Analysis (LMOEDA) calculations which showed that the exchange and dispersion terms are the most important attractive components for all the complexes studied, contributing up to 50.6% and 42.5% to the total attractive forces respectively.
Chem. Eur. J. 22, 9226–9234 (2016)
Charged versus Neutral Hydrogen-Bonded Complexes: Is There a Difference in the Nature of the Hydrogen Bonds?
A theoretical study on some carboxylic acid dimers formed by positively or negatively charged molecules has been carried out by using DFT methods. The resulting dimers possess either a charge of +2 or −2. In addition, the corresponding neutral complexes have also been considered. The electron density distribution described by the atoms in molecules and the natural bond orbital methods, as well as the electric field maps of the systems, have been analyzed and compared without finding significant differences between the neutral and ionic complexes. The interaction energy along the dissociation path of the charged dimers shows both a local minimum and a local maximum, defining a stability region between them. When this energetic profile is recalculated by removing the repulsion between the charged groups, it resembles to those of the neutral molecules. Hence, the characteristics of the charged dimers are similar to those of the neutral ones: the addition of a repulsion term for the charged groups permits to retrieve the energetic profiles dependence with the distance in the charged system. The interacting quantum atom (IQA) method has been used to calculate the interaction energy terms, including the classic Coulombic term between the whole molecules and the corresponding of the carboxylic acid groups. The IQA results show repulsive electrostatic interactions when the whole molecules are considered in the ionic complexes, but attractive ones between the carboxylic groups in both neutral and ionic complexes.
Chem. Phys. Lett. 655-656, 115–119 (2016)
Anionic complexes of F- and Cl- with substituted methanes: Hydrogen, halogen, and tetrel bonds
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the anionic complexes X–:CX(FnH3-n), for X = F, Cl, and n = 0 - 3. These complexes are stabilized by tetrel, hydrogen, and halogen bonds. Hydrogen-bonded complexes are the most stable complexes and halogen-bonded complexes are the least stable, with one exception. Charge-transfer across intermolecular bonds stabilizes all complexes, and occurs from the anion lone-pair to a σ∗ orbital of the substituted methane. EOM-CCSD spin-spin coupling constants 1tJ(X-C) across intermolecular tetrel bonds, 2hJ(C-X) across hydrogen bonds, and 1xJ(Cl-Cl) and 2xJ(C-Cl) across halogen bonds correlate with intermolecular distances.
Using (FH)2 and (FH)3 to Bridge the σ-Hole and the Lone Pair at P in Complexes with H2XP, for X=CH3, OH, H, CCH, F, Cl, NC, and CN
Ab initio MP2/aug′-cc-pVTZ calculations are used to investigate the binary complexes H2XP:HF, the ternary complexes H2XP:(FH)2, and the quaternary complexes H2XP:(FH)3, for X=CH3, OH, H, CCH, F, Cl, NC, and CN. Hydrogen-bonded (HB) binary complexes are formed between all H2XP molecules and FH, but only H2FP, H2ClP, and H2(NC)P form pnicogen-bonded (ZB) complexes with FH. Ternary complexes with (FH)2 are stabilized by F−H⋅⋅⋅P and F−H⋅⋅⋅F hydrogen bonds and F⋅⋅⋅P pnicogen bonds, except for H2(CH3)P:(FH)2 and H3P:(FH)2, which do not have pnicogen bonds. All quaternary complexes H2XP:(FH)3 are stabilized by both F−H⋅⋅⋅P and F−H⋅⋅⋅F hydrogen bonds and P⋅⋅⋅F pnicogen bonds. Thus, (FH)2 with two exceptions, and (FH)3 can bridge the σ-hole and the lone pair at P in these complexes. The binding energies of H2XP:(FH)3complexes are significantly greater than the binding energies of H2XP:(FH)2 complexes, and nonadditivities are synergistic in both series. Charge transfer occurs across all intermolecular bonds from the lone-pair donor atom to an antibonding σ* orbital of the acceptor molecule, and stabilizes these complexes. Charge-transfer energies across the pnicogen bond correlate with the intermolecular P−F distance, while charge-transfer energies across F−H⋅⋅⋅P and F−H⋅⋅⋅F hydrogen bonds correlate with the distance between the lone-pair donor atom and the hydrogen-bonded H atom. In binary and quaternary complexes, charge transfer energies also correlate with the distance between the electron-donor atom and the hydrogen-bonded F atom. EOM-CCSD spin-spin coupling constants 2hJ(F–P) across F−H⋅⋅⋅P hydrogen bonds, and 1pJ(P–F) across pnicogen bonds in binary, ternary, and quaternary complexes exhibit strong correlations with the corresponding intermolecular distances. Hydrogen bonds are better transmitters of F–P coupling data than pnicogen bonds, despite the longer F⋅⋅⋅P distances in F−H⋅⋅⋅P hydrogen bonds compared to P⋅⋅⋅F pnicogen bonds. There is a correlation between the two bond coupling constants 2hJ(F–F) in the quaternary complexes and the corresponding intermolecular distances, but not in the ternary complexes, a reflection of the distorted geometries of the bridging dimers in ternary complexes.
L. Gonzá'lez, F. Zapata, A. Caballero, P. Molina, C. Ram†írez de Arellano, I. Alkorta, J. Elguero
Host–Guest Chemistry: Oxoanion Recognition Based on Combined Charge-Assisted C¢H or Halogen-Bonding Interactions and Anion···Anion Interactions Mediated by Hydrogen Bonds
Several bis-triazolium-based receptors have been synthesized and their anion-recognition capabilities have been studied. The central chiral 1,1′-bi-2-naphthol (BINOL) core features either two aryl or ferrocenyl end-capped side arms with central halogen- or hydrogen-bonding triazolium receptors. NMR spectroscopic data indicate the simultaneous occurrence of several charge-assisted aliphatic and heteroaromatic C−H noncovalent interactions and combinations of C−H hydrogen and halogen bonding. The receptors are able to selectively interact with HP2O73−, H2PO4−, and SO42− anions, and the value of the association constant follows the sequence: HP2O73−>SO42−>H2PO4−. The ferrocenyl end-capped 72+⋅2 BF4− receptor allows recognition and differentiation of H2PO4− and HP2O73− anions by using different channels: H2PO4− is selectively detected through absorption and emission methods and HP2O73− by using electrochemical techniques. Significant structural results are the observation of an anion⋅⋅⋅anion interaction in the solid state (2:2 complex, 62+⋅[H2P2O7]2−), and a short C−I⋅⋅⋅O contact is observed in the structure of the complex [82+][SO4]0.5[BF4].
Theor Chem Acc 135, 140_1-13 (2016)
G. Sánchez‑Sanz, C. Trujillo, I. Alkorta, J. Elguero
Competition between intramolecular hydrogen and pnictogen bonds in protonated systems
A theoretical study of the competition between hydrogen (HB) and pnictogen bonds (ZB) in three different families of compounds, (Z)-1,2-disubstituted ethenes (Eth), 1,2-disubstituted benzenes (Phe) and 1,8-disubstituted naphthalenes (Naph), with a charged group, ZH3 + and a neutral one, Z′H2 (Z, Z′ = N, P, As) as interacting moieties, has been carried out. In those structures with a NH3 +motif, intramolecular hydrogen bond structures are minima while pnictogen interactions are transition states. The opposite is true for PH3 + and AsH3 + moieties. An analysis of isodesmic energies (Eiso), interaction energies (E b) and deformation energies (E def) shows that in Eth derivatives, the most stable compound corresponds to P+–N ZB while in the Phe and Naph ones, the N+–N HB interaction presents the largest negative isodesmic energy. Also, Eth and Phe derivatives show negative E iso values for all the compounds under study; however, in some cases of Naphderivatives positive isodesmic energies have been found. The Atoms in Molecules (AIM) analysis of the electron density, natural bond orbital (NBO) second-order orbital energies and electron density shift maps (EDS) have been used to better understand these intramolecular interactions.
Struct. Chem. 27, 753–762 (2016)
M. Marin-Luna, I. Alkorta, J. Elguero
A computational study on [(PH2X)2]+ homodimers involving intermolecular two-center three-electron bonds
A computational study at CCSD(T) theoretical level has been carried out on radical cation [(PH2X)2]·+ homodimers. Four stable minima configurations have been found for seven substituted phosphine derivatives, X = H, CH3, CCH, NC, OH, F and Cl. The most stable minimum presents an intermolecular two-center three-electron P···P bond except for X = CCH. The other three minima correspond to an alternative P···P pnicogen bonded complex, to a P···X contact and the last one to the complex resulting from a proton transfer, PH3X+:PHX·. The complexes obtained have been compared with those of the corresponding neutral ones, (PH2X)2, and the analogous protonated ones, PH3X+:PH2X, recently described in the literature. The spin and charge densities of the complexes have been examined. The electronic characteristics of the complexes have been analyzed with the NBO and AIM methods. The results obtained for the spin density, charge and NBO are coherent for all the complexes.
Tetrahedron 72, 1978-1983 (2016)
DOI: 10.1016/j.tet.2016.02.062
Interaction of beryllium derivatives with N-methylated DNA bases: 9-methylguanine and 1-methylcytosine
The effect of beryllium bonds (BeB) on the tautomerism of 9-methyl-guanine and 1-methylcytosine has been theoretically studied at MP2/aug-cc-pVDZ computational level. It is predicted that BeB will be able to strongly modify the tautomeric behaviour of these nucleobases and, by extension, of DNA and RNA bases. Thus, while the oxo-amino is the most stable tautomer for 9-methyl-guanine and 1-methylcytosine when isolated, they present a relative energy above 33 and 17 kJ mol−1, respectively, with respect to the most stable tautomer when they form complexes with BeR2 systems (amino-hydroxy and imino-oxo, respectively). In both cases, the most stable complexes are associated to N⋯Be interactions with binding energies up to 180 kJ mol−1.
Modulating intramolecular P⋯N pnictogen interactions
A computational study of the intramolecular pnictogen bond in 8-phosphinonaphthalen-1-amine derivatives (1-NX2, 8-PX2 with X = H, F, Cl, Br, CH3, CN and NC), proton sponge analogues, has been carried out to determine their structural and geometric parameters, interaction energies and electronic properties such as the electron density of the intramolecular interaction. Our results show that substitution of H atoms in the PH2 group by electron withdrawing groups on the Lewis acid moiety strengthens the P⋯N pnictogen bond, evidenced by the increasing electron density values at the bond critical point and by shorter distances. However, substitutions on the Lewis base moiety (NX2) show weaker P⋯N interactions than when the substitution is done on the Lewis acid counterpart (PX2). Nevertheless, in all cases, pnictogen bonds are enhanced upon substitution with respect to the parent 1-NH2, 8-PH2 system. Second-order orbital interaction energies, electron density maps, electron delocalization functions and charge transfer corroborate the evolution of the P⋯N strength upon substitution.
Phys. Chem. Chem. Phys., 2016,18, 7300-7309
D. J. R. Duarte, G. L. Sosa, N. M. Peruchena, I. Alkorta
Halogen bonding. The role of the polarizability of the electron-pair donor
The nature of F–Br⋯X–R interactions (with X = F, Cl, Br, I and R = –H, –F) has been investigated through theoretical calculation of molecular potential electrostatic (MEP), molecular polarizability, atoms in molecules (AIM) analysis and energetic decomposition analysis (EDA). A detailed analysis of the MEPs reveals that considering only the static electrostatic interactions is not sufficient to explain the nature of these interactions. The molecular polarizabilities of X–R molecules suggest that the deformation capacity of the electronic cloud of the lone pairs of the X atom plays an important role in the stability of these complexes. The topological analysis of the L(r) = −¼∇2ρ(r) function and the detailed analysis of the atomic quadrupole moments reveal that the Br⋯X interactions are electrostatic in nature. The electron acceptor Br atom causes a polarization of the electronic cloud (electronic induction) on the valence shell of the X atom. Finally, the electrostatic forces and charge transfer play an important role not only in the stabilization of the complex, but also in the determination of the molecular geometry of equilibrium. The dispersive and polarization forces do not influence the equilibrium molecular geometry.
M. Marín-Luna, I. Alkorta, J. Elguero, O. Mó, M. Yáñez
Fullerene and corannulene derivatives acting as insulators of Cl− and BeH2
The capacity of corannulene and its benzo-derivatives CxH10 (x = 20–60) as prototypes of non-planar π-aromatic systems which mimic the end of carbon nanotubes to act as insulators between BeH2 and Cl− chemical entities has been explored by means of M06-2x/cc-pVDZ and M06-2x/6-311+G(d) calculations. For the sake of completeness, the set investigated includes also fullerene, C60. All these aromatic derivatives lead to stable binary complexes either with BeH2 or halogen (Cl−) anions. For BeH2, however, only the complexes in which the interaction involves the convex face of the aromatic system are stable. No significant changes are observed when the binding energies (BEs) of the BeH2 complexes are compared to those involving planar aromatic compounds, but the ones involving Cl− with the concave face of the aromatic moiety can be very large, because its curvature favors many contacts of the anion with the carbon atoms of the π-aromatic system. The formation of these binary complexes changes to a large extent the electrostatic potential on the free face of the aromatic system leading to a mutual reinforcement of both interactions, the beryllium bond and the interaction with Cl−, when the ternary complexes are formed. As a result, the BEs for the triads are larger than the sum of the BEs of the corresponding binary complexes and the distances between the aromatic subunit and BeH2 or Cl− become shorter in the triads than in the binary complexes. A MBIE analysis also indicates that the enhanced stability of ternary complexes arises mainly from the reinforcement of the beryllium bonds as well as from the three-body terms. An exploration of all the minima for BeH2:C60H10:Cl− shows that BeH2 binds preferentially to the peripheral aromatic rings than those in the more curved region.
J. Phys. Chem. A 2016, 120, 648−656
M. Marin-LunaI. Alkorta, J. Elguero
Cooperativity in Tetrel Bonds
A theoretical study of the cooperativity in linear chains of (H3SiCN)n and (H3SiNC)n complexes connected by tetrel bonds has been carried out by means of MP2 and CCSD(T) computational methods. In all cases, a favorable cooperativity is observed, especially in some of the largest linear chains of (H3SiNC)n, where the effect is so large that the SiH3 group is almost equidistant to the two surrounding CN groups and it becomes planar. In addition, the combination of tetrel bonds with other weak interactions (halogen, chalcogen, pnicogen, triel, beryllium, lithium, and hydrogen bond) has been explored using ternary complexes, (H3SiCN)2:XY and (H3SiNC)2:XY. In all cases, positive cooperativity is obtained, especially in the (H3SiNC)2:ClF and (H3SiNC)2:SHF ternary complexes, where, respectively, halogen and chalcogen shared complexes are formed.
Crystals, 6, 19 (2016); DOI:10.3390/cryst6020019
I. Alkorta, J.E. Del Bene, J. Elguero
Download from the journal web page, DOI: 10.3390/cryst6020019
H2XP:OH2 Complexes: Hydrogen vs. Pnicogen Bonds
A search of the Cambridge Structural Database (CSD) was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug'-cc-pVTZ calculations carried out on complexes H2XP:OH2, for X = NC, F, Cl, CN, OH, CCH, H, and CH3. Only hydrogen-bonded complexes are found on the H2(CH3)P:HOH and H3P:HOH potential surfaces, while only pnicogen-bonded complexes exist on H2(NC)P:OH2, H2FP:OH2, H2(CN)P:OH2, and H2(OH)P:OH2 surfaces. Both hydrogen-bonded and pnicogen-bonded complexes are found on the H2ClP:OH2 and H2(CCH)P:OH2 surfaces, with the pnicogen-bonded complexes more stable than the corresponding hydrogen-bonded complexes. The more electronegative substituents prefer to form pnicogen-bonded complexes, while the more electropositive substituents form hydrogen-bonded complexes. The H2XP:OH2 complexes are characterized in terms of their structures, binding energies, charge-transfer energies, and spin-spin coupling constants 2hJ(O-P), 1hJ(H-P), and1J(O-H) across hydrogen bonds, and 1pJ(P-O) across pnicogen bonds.
Comput. Theor. Chem. 1076, 101-108 (2016)
The effect of cytosine methylation on its halogen-bonding properties
This study shows the influence of a 5-methyl substituent on the interaction between 1-methylcytosine, 1,5-dimethylcytosine, 1-methyluracil and 1-methylthymine and dichloride (Cl2) and fluorine chloride (ClF). The methyl derivatives were selected because of the important role played by a methyl group at position 5 of the pyrimidine ring on the biological properties of nucleobases. Besides binding energies obtained at the MP2/aug-cc-pVDZ level, a variety of theoretical methods were used to analyze the structures of the different minima obtained. A total of 116 complexes have been studied.
Mol. Phys., 114, 102-117 (2016)
Properties of cationic pnicogen-bonded complexes F4-nHnP+:N-base with H–P···N linear and n = 1–4
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the pnicogen-bonded complexes F4-nHnP+:N-base, for n = 1–4, each with a linear or nearly linear Hax–P···N alignment. The sp3-hybridised nitrogen bases include NH3, NClH2, NFH2, NCl2H, NCl3, NFCl2, NF2H, NF2Cl, and NF3, and the sp bases are NCNH2, NCCH3, NP, NCOH, NCCl, NCH, NCF, NCCN, and N2. Binding energies increase as the P–N distance decreases, with an exponential curve showing this relationship when complexes with sp3 and sp hybridised bases are treated separately. However, the correlations are not as good as they are for the complexes F4-nHnP+:N-base for n = 0–3 with F–P···N linear. Different patterns are observed for the change in the binding energies of complexes with a particular base as the number of F atoms in the acid changes. Thus, the particular acid–base pair is a factor in determining the binding energies of these complexes.
Three different charge-transfer interactions stabilise these complexes, namely Nlp→σ*P–Hax, Nlp→σ*P–Feq, and Nlp→σ*P–Heq. Unlike the corresponding complexes with F–P···N linear, Nlp→σ*P–Hax is not always the dominant charge-transfer interaction, since Nlp→σ*P–Feq is greater in some complexes. Nlp→σ*P–Heq makes the smallest contribution to the total charge-transfer energy. The total charge-transfer energies of all complexes increase exponentially as the P–N distance decreases in a manner very similar to that observed for the series of complexes with F–P···N linear.
Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin–spin coupling constants 1pJ(P–N) across the pnicogen bond vary with the P–N distance, but different patterns are observed which depend on the nature of the acid, and for some acids, on the hybridisation of the nitrogen base. 1pJ(P–N) values for complexes of F3HP+ initially increase as the P–N distance decreases, reach a maximum, and then decrease with decreasing P–N distance as the P···N bond acquires increased covalent character. 1pJ(P–N) for complexes with H–P···N linear and those with F–P···N linear exhibit similar distance dependencies depending on the number of F atoms in equatorial positions and the hybridisation of the base. Complexation may increase, decrease, or leave the P–Hax distance unchanged, but1J(P–Hax) always decreases relative to the corresponding isolated ion. Decreasing 1J(P–Hax) can be related to decreasing intermolecular P–N distance.
J. Phys. Chem. A, 119, 11701–11710 (2015)
Exploring the (H2C═PH2)+:N-Base Potential Surfaces: Complexes Stabilized by Pnicogen, Hydrogen, and Tetrel Bonds
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to determine the structures, binding energies, and bonding properties of complexes involving the cation (H2C═PH2)+ and a set of sp-hybridized nitrogen bases including NCCH3, NP, NCCl, NCH, NCF, NCCN, and N2. On each (H2C═PH2)+:N-base surface, four types of unique equilibrium structures exist: a complex with a P···N pnicogen bond formed through the π system of (H2C═PH2)+ (ZB-π); a complex with a P···N pnicogen bond formed through the σ system of (H2C═PH2)+ (ZB-σ); a hydrogen-bonded complex with a P—H···N hydrogen bond (HB); and a tetrel-bonded complex with a C···N bond (TB). Binding energies of complexes stabilized by the same type of intermolecular interaction decrease in the order NCCH3 > NP > NCCl > NCH > NCF > NCCN > N2. For a given base, binding energies decrease in the order ZB-π > HB > ZB-σ > TB, except for a reversal of HB and ZB-σ with the weakest base N2. Binding energies of ZB-π, HB, and ZB-σ complexes increase exponentially as the corresponding P—N distance decreases, but the correlation is not as good between the binding energies of TB complexes and the intermolecular C—N distance. Charge-transfer energies stabilize all complexes and also exhibit an exponential dependence on the corresponding intermolecular distances. EOM-CCSD spin–spin coupling constants 1pJ(P—N) for ZB-π and ZB-σ complexes, and 2hJ(P—N) for HB complexes increase quadratically as the corresponding P—N distance decreases. Values of 1tJ(C—N) for TB are small and show little dependence on the C—N distance. 1J(P—H) values for the hydrogen-bonded P—H bond in HB complexes correlate with the corresponding P—H distance, whereas values of 1J(P—H) for the non-hydrogen-bonded P—H correlate with the P—N distance.
Can HN=NH, FN=NH, or HN=CHOH bridge the σ-hole and the lone pair at P in binary complexes with H2XP, for X = F, Cl, NC, OH, CN, CCH, CH3, and H?
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the properties of complexes formed between H2XP, for X = F, Cl, NC, OH, CN, CCH, CH3, and H, and the possible bridging molecules HN═NH, FN═NH, and HN═CHOH. H2XP:HNNH and H2XP:FNNH complexes are stabilized by P⋯N pnicogen bonds, except for H2(CH3)P:FNNH and H3P:FNNH which are stabilized by N–H⋯P hydrogen bonds. H2XP:HNCHOH complexes are stabilized by P⋯N pnicogen bonds and nonlinear O–H⋯P hydrogen bonds. For a fixed H2XP molecule, binding energies decrease in the order HNCHOH > HNNH > FNNH, except for the binding energies of H2(CH3)P and H3P with HNNH and FNNH. Binding energies of complexes with HNCHOH and HNNH increase as the P–N1 distance decreases, but binding energies of complexes with FNNH show little dependence on this distance. The large binding energies of H2XP:HNCHOH complexes arise from a cooperative effect involving electron-pair acceptance by P to form a pnicogen bond, and electron-pair donation by P to form a hydrogen bond. The dominant charge-transfer interaction in these complexes involves electron-pair donation by N across the pnicogen bond, except for complexes in which X is one of the more electropositive substituents, CCH, CH3, and H. For these, lone-pair donation by P across the hydrogen bond dominates. AIM and NBO data for these complexes are consistent with their bonding characteristics, showing molecular graphs with bond critical points and charge-transfer interactions associated with hydrogen and pnicogen bonds. EOM-CCSD spin–spin coupling constants 1pJ(P–N) across the pnicogen bond for each series of complexes correlate with the P–N distance. In contrast, 2hJ(O–P) values for complexes H2XP:HNCHOH do not correlate with the O–P distance, a consequence of the nonlinearity of these hydrogen bonds.
Exploring the PX3:NCH and PX3:NH3 potential surfaces, with X = F, Cl, and Br
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to explore the PX3:NCH and PX3:NH3 potential surfaces, with X = F, Cl and Br. Four unique minima exist on the PX3:NCH surfaces, and three on the PX3:NH3 surfaces. Complexes stabilized by pnicogen bonds, hydrogen bonds, halogen bonds, and electrostatic interactions have been found at these minima. The global minimum on each surface is a complex with a P···N pnicogen bond. Binding energies at corresponding minima are ordered with respect to the PX3 molecules as PF3 < PCl3 < PBr3. Charge-transfer stabilizes all complexes with intermolecular bonds.
Chem. Eur. J. 21, 12676–12682 (2015).
O. Brea, O. Mó, M. Yáñez, I. Alkorta, J. Elguero
Creating σ-Holes through the Formation of Beryllium Bonds
Through the use of ab initio theoretical models based on MP2/aug-cc-pVDZ-optimized geometries and CCSD(T)/aug-cc-pVTZ and CCSD(T)/aug-c-pVDZ total energies, it has been shown that the significant electron density rearrangements that follow the formation of a beryllium bond may lead to the appearance of a σ-hole in systems that previously do not exhibit this feature, such as CH3OF, NO2F, NO3F, and other fluorine-containing systems. The creation of the σ-hole is another manifestation of the bond activation–reinforcement (BAR) rule. The appearance of a σ-hole on the F atoms of CH3OF is due to the enhancement of the electronegativity of the O atom that participates in the beryllium bond. This atom recovers part of the charge transferred to Be by polarizing the valence density of the F into the bonding region. An analysis of the electron density shows that indeed this bond becomes reinforced, but the F atom becomes more electron deficient with the appearance of the σ-hole. Importantly, similar effects are also observed even when the atom participating in the beryllium bond is not directly attached to the F atom, as in NO2F, NO3F, or NCF. Hence, whereas the isolated CH3OF, NO2F, and NO3F are unable to yield F⋅⋅⋅Base halogen bonds, their complexes with BeX2 derivatives are able to yield such bonds. Significant cooperative effects between the new halogen bond and the beryllium bond reinforce the strength of both noncovalent interactions.
C. Trujillo, G. Sanchez-Sanz, I. Alkorta, J. Elguero
DOI: 10.1039/C5NJ00600G
Halogen, chalcogen and pnictogen interactions in (XNO2)2 homodimers (X = F, Cl, Br, I)
A theoretical study of the XNO2 homodimers (X = F, Cl, Br and I) has been carried out by means of the Møller–Plesset (MP2) methodology. Twenty-two different minimum structures have been found, involving pnictogen, chalcogen and halogen bonds. MP2 interaction energies range between −0.4 to −17.5 kJ mol−1. Atoms in molecules (AIM) and natural bond orbital (NBO) approaches have been used to analyse the nature of the interaction within both monomers, obtaining good correlations between Laplacian values and bond distances. NBO E(2) orbital interaction energies are found to be up to 39.0 kJ mol−1. Charge transfer between monomers is in agreement with those in AIM and NBO findings, showing the highest charge transferred in those asymmetric dimers which involve pure halogen bonds. Symmetry adapted perturbation theory (SAPT-DFT) results show that the interactions are driven by the dispersion term, followed by the electrostatic one. The induction term presents the lowest contribution with the exception of complexes 1 and 5 of the iodine derivative in which E(2)i shows the maximum contribution to the total forces.
Simultaneous Aromatic–Beryllium Bonds and Aromatic–Anion Interactions: Naphthalene and Pyrene as Models of Fullerenes, Carbon Single-Walled Nanotubes, and Graphene
The possibility of forming stable BeR2:ArH:Y− (R=H, F, Cl; ArH=naphthalene, pyrene; Y=Cl, Br) ternary complexes in which the beryllium compounds and anions are located on the opposite sides of an extended aromatic system is explored by means of MP2/aug-cc-pVDZ ab initio calculations. Comparison of the electron-density distribution of these ternary complexes with the corresponding BeR2:ArH and ArH:Y−binary complexes reveals the existence of significant cooperativity between the two noncovalent interactions in the triads. The energetic effects of this cooperativity are quantified by evaluation of the three-body interaction energy Δ3E in the framework of the many-body interaction-energy (MBIE) approach. Although an essential component of the interaction energies is electrostatic and is well reflected in the changes in the molecular electrostatic potential of the aromatic system on complexation, strong polarization effects, in particular for the BeR2:ArH interactions, also play a significant role. The charge transfers associated with these polarization effects are responsible for significant distortion of both the BeR2 and the aromatic moieties. The former are systematically bent in all the complexes, and the latter are curved to a degree that depends on the nature of the R substituents of the BeR2 subunit.
J. Organomet. Chem. 794, 206-215 (2015)
DOI: 10.1016/j.jorganchem.2015.07.013
Theoretical study of the geometrical, energetic and NMR properties of atranes
Theoretical calculations of 87 atranes, 113 considering the different endo/exoconformations, with combinations of B, C, N, Al, Si, P and Ge atoms at the bridgehead positions have been performed at the B3LYP/6-311++G(d,p) level. Using the optimized minimum energy geometries we have calculated their chemical shifts (GIAO approximation) and their indirect spin–spin coupling constants J as well as the reduced coupling constants K. Besides, a topological analysis was carried out with the Atoms in Molecules Theory (AIM). When available, experimental data will be reported and compared with calculations.
Tetrahedron 71 (2015) 5260-5266
The influence of intermolecular halogen bonds on the tautomerism of nucleobases. I. Guanine
In this paper, we report a computational study of the influence of halogen bonds (XB) on the tautomerism of 9-methylguanine, a model of guanosine and GTP. Molecular Electrostatic Potentials (MEP), interaction energies, Atoms in Molecules (AIM) and Natural Bond Orbitals (NBO) were used to characterize the complexes between three tautomers of 9-methylguanine (one oxo and two hydroxy) and five dihalogens molecules (Br2, BrCl, BrF, Cl2 and ClF). The results concerning the halogen bonds were compared with the effect of hydrogen bonds using hydrogen fluoride as a hydrogen bond donor. The binding energies of the complexes have been analyzed using a Free-Wilson model to obtain the individual interactions. An important conclusion of this study is that halogen bonds are able to strongly modify the order of stability of the three most stable tautomers that, in turn, could induce mutations according to the 'rare tautomer hypothesis'.
Chem. Eur. J. 21, 9797-9808 (2015)
F. Zapata, L. Gonzalez, A. Caballero, I. Alkorta, J. Elguero, P. Molina
Dual Role of the 1,2,3-Triazolium Ring as a Hydrogen-Bond Donor and Anion–π Receptor in Anion-Recognition Processes
Several bis(triazolium)-based receptors have been synthesized as chemosensors for anion recognition. The central naphthalene core features two aryltriazolium side-arms. NMR experiments revealed differences between the binding modes of the two triazolium rings: one triazolium ring acts as a hydrogen-bond donor, the other as an anion–π receptor. Receptors 92+⋅2BF4− (C6H5), 112+⋅2BF4− (4-NO2 C6H4), and 132+⋅2BF4− (ferrocenyl) bind HP2O73− anions in a mixed-binding mode that features a combination of hydrogen-bonding and anion–π interactions and results in strong binding. On the other hand, receptor 102+⋅2 BF4− (4-CH3O C6H4) only displays combined Csp2 H/anion–π interactions between the two arms of the receptors and the bound anion rather than triazolium (CH)+⋅⋅⋅anion hydrogen bonding. All receptors undergo a downfield shift of the triazolium protons, as well as the inner naphthalene protons, in the presence of H2PO4− anions. That suggests that only hydrogen-bonding interactions exist between the binding site and the bound anion, and involve a combination of cationic (triazolium) and neutral (naphthalene) C H donor interactions. Theoretical calculations relate the electronic structure of the substituent on the aromatic group with the interaction energies and provide a minimum-energy conformation for all the complexes that explains their measured properties.
Properties of Cationic Pnicogen-Bonded Complexes F4–nHnP+:N-Base with F–P···N Linear and n = 0–3
Ab initio MP2/aug′-cc-pVTZ calculations were performed to investigate the pnicogen-bonded complexes F4–nHnP+:N-base, for n = 0–3, each with a linear or nearly linear F–P···N alignment. The nitrogen bases include the sp3 bases NH3, NClH2, NFH2, NCl2H, NCl3, NFCl2, NF2H, NF2Cl, and NF3 and the sp bases NCNH2, NCCH3, NP, NCOH, NCCl, NCH, NCF, NCCN, and N2. The binding energies vary between −20 and −180 kJ·mol–1, while the P–N distances vary from 1.89 to 3.01 Å. In each series of complexes, binding energies decrease exponentially as the P–N distance increases, provided that complexes with sp3 and sp hybridized bases are treated separately. Different patterns are observed for the change in the binding energies of complexes with a particular base as the number of F atoms in the acid changes. Thus, the particular acid–base pair is a factor in determining the binding energies of these complexes. Three different charge-transfer interactions stabilize these complexes. These arise from the nitrogen lone pair to the σ*P–Fax, σ*P–Feq, and σ*P–Heq orbitals. The dominant single charge-transfer energy in all complexes is Nlp → σ*P–Fax. However, since there are three Nlp → σ*P–Feq charge-transfer interactions in complexes with F4P+ and two in complexes with F3HP+, the sum of the Nlp → σ*P–Feq charge-transfer energies is greater than the Nlp → σ*P–Fax charge-transfer energies in the former complexes, and similar to the Nlp → σ*P–Fax energies in the latter. The total charge-transfer energies of all complexes decrease exponentially as the P–N distance increases. Coupling constants 1pJ(P–N) across the pnicogen bond vary with the P–N distance, but different patterns are observed for complexes with F4P+ and complexes of the sp3 bases with F3HP+. These initially increase as the P–N distance decreases, reach a maximum, and then decrease with decreasing P–N distance as the P···N bond acquires increased covalent character. For the remaining complexes, 1pJ(P–N) increases with decreasing P–N distance. Complexation increases the P–Fax distance and 1J(P–Fax) relative to the corresponding isolated ion. 1J(P–Fax) correlates quadratically with the P–N distance.
Molecules, 20, 9961-9976 (2015)
M. Marta-Marin, I. Alkorta, J. Elguero, O. Mo, M. Yañez
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Interplay between Beryllium Bonds and Anion-π Interactions in BeR2:C6X6:Y− Complexes (R = H, F and Cl, X = H and F, and Y = Cl and Br)
A theoretical study of the beryllium bonds in BeR2:C6X6 (R = H, F, Cl and X = H and F) has been carried out by means of MP2/aug′-cc-pVDZ computational methods. In addition, the ternary complexes BeR2:C6X6:Y− (Y = Cl and Br) have been analyzed. Geometric, energetic and electronic aspects of the complexes have been taken into account. All the parameters analyzed provide a clear indication of favorable cooperativity in both interactions observed, beryllium bond and aromatic ring:anion interaction.
Challenges and Advances in Computational Chemistry and Physics 19, 191-263 (2015)
The Pnicogen Bond in Review: Structures, Binding Energies, Bonding Properties, and Spin-Spin Coupling Constants of Complexes Stabilized by Pnicogen Bonds
Extensive ab initio MP2/aug'-cc-pVTZ studies have been carried out in our laboratories to determine the structures, binding energies, bonding properties, and EOM-CCSD spin-spin coupling constants of various series of complexes stabilized by pnicogen bonds. These systematic studies provide insight into the nature of the pnicogen bond, and how changes in this bond are reflected in the properties of these complexes.
Chirality, 27, 339-343 (2015)
I. Alkorta, J. Elguero, P. Cintas
DOI: 10.1002/chir.22438
Adding Only One Priority Rule Allows Extending CIP Rules to Supramolecular Systems
There are frequent situations both in supramolecular chemistry and in crystallography that result in stereogenic centers, whose absolute configuration needs to be specified. With this aim we propose the inclusion of one simple additional rule to the Cahn-Ingold-Prelog (CIP) system of priority rules stating that noncovalent interactions have a fictitious number between 0 and 1.
D. J. R. Duarte, N. M. Peruchena, I. Alkorta
DOI: 10.1021/jp511118s
Double Hole–Lump Interaction between Halogen Atoms
In this paper a theoretical study has been carried out to investigate the nature of the unusual halogen–halogen contacts in the complexes R–X···X–R (with R = −H, −Cl, −F and X = Cl, Br, I). AIM, NBO, and MEP analyses have been used to characterize X···X interactions. Formation of the unusual X···X interactions leads to a significant increase of electron charge density in the bonding region between the two halogen atoms. The geometry and stability of these complexes is mainly due to electrostatic interactions lump(X1) → hole(X2) and lump(X2) → hole(X1) [or equivalently [VS,min(X1) → VS,max(X2) and VS,min(X2) → VS,max(X1)] and the charge transfers LP(X1) → σ*(R–X2) and LP(X2) → σ*(R–X1). In other words, these findings suggest that the electrostatic interactions and the charge transfer play a substantial role in determining the optimal geometry of these complexes, as in conventional halogen bonds, even though the dispersion term is the most important attractive term for all the complexes studied here, save one.
The influence of halogen bonds on tautomerism: the case of 3-mercapto-1,2-azoles (pyrazoles, isoxazoles, isothiazoles)
DFT calculations at the B3LYP/6-311++G(d,p) computational level have been carried out on three tautomeric pairs of 3-mercapto-1,2-azoles (pyrazoles, isoxazoles, and isothiazoles) to study the effect of halogen bonds (XBs) on the position of the equilibrium. As halogen bond donors, we have selected Br2, Cl2, BrCl, ClF and BrF and compare them with HF as a hydrogen bond donor. Several linear relationships were found between binding energies of different halogen bond donors. The main conclusion of this study is that the XB inverts the tautomeric equilibrium while an HB does not.
P···N Pnicogen Bonds in Cationic Complexes of F4P+ and F3HP+ with Nitrogen Bases
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out on cationic pnicogen-bonded complexes F4P+:N-base and F3HP+:N-base, with linear Fax–P···N and Hax-P···N, respectively. The bases include the sp3-hybridized nitrogen bases NH3, NClH2, NFH2, NCl2H, NCl3, NFCl2, NF2H, NF2Cl, and NF3, and the sp bases NCNH2, NCCH3, NP, NCOH, NCCl, NCH, NCF, NCCN, and N2. The binding energies of these complexes span a wide range, from −15 to −180 kJ mol–1, as do the P–N distances, which vary from 1.89 to 3.11 Å. There is a gap in the P–N distances between 2.25 and 2.53 Å in which no complexes are found. Thus, the equilibrium complexes may be classified as inner or outer complexes based on the value of the P–N distance. Inner complexes have P···N bonds with varying degrees of covalent character, whereas outer complexes are stabilized by intermolecular P···N bonds with little or no covalency. Charge-transfer stabilizes these pnicogen-bonded complexes. For complexes F4P+:N-base, the dominant charge-transfer interaction is from the lone pair on N to the σ*P–Faxorbital. In addition, there are three other charge-transfer interactions from the lone pair on N to the σ*P–Feq orbitals, which taken together, are more stabilizing than the interaction involving σ*P–Fax. In contrast, the dominant charge-transfer interaction for complexes F3HP+:N-base is from the lone pair on N to the σ*P–Feq orbitals. Computed EOM-CCSD Fermi-contact terms are excellent approximations to the total spin–spin coupling constants 1pJ(P–N) and 1J(P–Hax), but are poor approximations to 1J(P–Fax). 1pJ(P–N) values increase with decreasing P–N distance, approach a maximum, and then decrease and change sign as the P–N distance further decreases and the pnicogen bond acquires increased covalency. 1J(P–Fax) values for F4P+:N-base complexes increase with decreasing distance. Although the P–Hax distance changes very little in complexes F3HP+:N-base, patterns exist which suggest that changes in 1J(P–Hax) reflect the hybridization of the nitrogen base and whether the complex is an inner or outer complex.
Theor. Chem. Acta, 134, 30 (2015)
I. Alkorta, L. M. Azofra, J. Elguero
Ab initio study in the hydration process of metaphosphoric acid: the importance of the pnictogen interactions
A theoretical study of the hydration of metaphosphoric acid to yield phosphoric acid has been carried out by means of MP2/6-31+G(d,p) and MP2/aug-cc-pVTZ computational levels. Up to three explicit water molecules have been considered as well as the PCM solvation model to account for the effect of the bulk water. The reaction profile has been analyzed using the conceptual DFT methodology. The reactant structure is very dependent on the number of water molecules. The inclusion of more than one water molecule produces important cooperative effects and a shortening of the O···P pnictogen interaction besides the reaction barrier drops about 50 kJ mol−1. Reaction force at ξ 1 indicates the decreasing in the angular stress in the reaction site before reaching the TS as more explicit water molecules are taken into account. The analysis of the reaction electronic flux shows that for the three mechanisms studied, the principal reactive changes occur in the TS zone, while reactants and products remain in a zero-flux regime.
J. Phys. Chem. A, 119, 535–541 (2015)
L. M. Azofra, I. Alkorta, S. Scheiner
DOI: 10.1021/jp511828h
Chalcogen Bonds in Complexes of SOXY (X, Y = F, Cl) with Nitrogen Bases
SOF2, SOFCl, and SOCl2 were each paired with a series of N bases. The potential energy surface of the binary complexes were characterized by MP2 calculations with double and triple-ξ basis sets, extrapolated to complete sets. The most stable configurations contained a S···N chalcogen bond with interaction energies as high as 6.8 kcal/mol. These structures are stabilized by a Nlp → σ*(S–Z) electron transfer (Z = O, F, Cl), complemented by Coulombic attraction of N to the σ-hole opposite the Z atom. N···S–F and N···S–Cl chalcogen bonds are stronger than N···S═O interactions. Formation of each chalcogen bond elongates all of the internal covalent bonds within SOXY, especially the S–Cl bond. Halogen-bonded (N···Cl–S) complexes were also observed, but these are more weakly bound, by less than 3 kcal/mol.
I. Alkorta, J. Elguero, S. J. Grabowski
Pnicogen and hydrogen bonds: complexes between PH3X+ and PH2X systems
The charge-assisted complexes between PH3X+ and PH2X have been analyzed. MP2/aug′-cc-pVTZ calculations were performed and the results were supported by the Quantum Theory of Atoms in Molecules approach and the Natural Bond Orbitals method. It was found that three different configurations could be formed, i.e. those linked through a P P or a P X pnicogen bond and those linked through a P–H P hydrogen bond. The P P configurations are the most stable ones corresponding to the strongest interactions; for all complexes the P P configuration exists, while the P X and P–H P ones are present only for some of them. Different relations between the parameters were found, especially for the P P interactions where there are correlations between the P P distance and the electron density at the P P bond critical point (ρPP) as well as between ρPP and the charge transfer energy.
Comput. Theoret. Chem. 1053, 305-314 (2015).
G. Sanchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero
Theoretical study of cyanophosphines: Pnicogen vs. dipole–dipole interactions
Cyanophosphine derivative dimers, [HXP(CN)]2 with X = H, F and Cl, have been characterized by means of CCSD(T)/aug′-cc-pVTZ//MP2/aug′-cc-pVTZ computational level calculations. Different interactions have been found upon complexation, such as hydrogen bonds, pnicogen bonds and dipole···dipole interactions. The intermolecular distances range between 2.84 and 3.53 Å and the binding energies between −34.7 and −3.6 kJ mol−1. Compounds with dipole···dipole interactions present shorter contact distances and larger (more negative) binding energies than those with pure P···P pnicogen bonds. Electron density shift maps show larger variations in compounds with dipole···dipole interactions than in those with pure pnicogen ones, in line with the energetic results. However, NBO analysis suggests that the complexes with P···P pnicogen bonds, in special those with XP···PX (X = F, Cl) show E(2) orbital interaction energies much larger than the dipole···dipole ones.
J. Phys. Chem. A, 224–233, 119 (2015)
DOI: 10.1021/jp5117504
Substituent Effects on the Properties of Pnicogen-Bonded Complexes H2XP:PYH2, for X, Y = F, Cl, OH, NC, CCH, CH3, CN, and H
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out on the pnicogen-bonded homodimers (PH2X)2 and the binary complexes H2XP:PYH2, for X, Y = F, Cl, OH, NC, CCH, CH3, CN, and H. The binding energies of these complexes are influenced by the nature of the X,Y pair, the intermolecular distance, the relative orientation of the interacting molecules, and the charge-transfer energies from the lone pair of one P to the σ-hole of the other. Binary complexes with X,Y = F, Cl, OH, and NC, as well as the homodimers, have a trans arrangement of the P–A and P–A′ bonds with respect to the P···P bond, with A and A′, the atoms of X and Y, respectively, bonded to the P atoms. The trendlines for the homodimers in plots of the binding energy versus the P–P distance, and the binding energy versus the total charge-transfer energy, exhibit better correlations than the trendlines for the binary complexes. The trendlines for the homodimers mark the boundary of the region in which points for the binary complexes appear. Pnicogen-bond radii for P in PH2X molecules have been determined from the P–P distances in the homodimers. The sum of these radii provides an excellent approximation to the P–P distance in the corresponding binary complex. EOM-CCSD spin–spin coupling constants 1pJ(P–P) have also been computed for all complexes. Coupling constants for the dimers and binary complexes exhibit a similar linear increase as the P–P distance decreases.
I. Mata, E. Molins, I. Alkorta, E. Espinosa
DOI: 10.1021/jp510198g
The Paradox of Hydrogen-Bonded Anion–Anion Aggregates in Oxoanions: A Fundamental Electrostatic Problem Explained in Terms of Electrophilic···Nucleophilic Interactions
A theoretical study of anionic complexes formed by two partly deprotonated oxoacids joined by hydrogen bonds has been carried out at the MP2 computational level. In spite of the ionic repulsion, local energy minima are found both in the gas phase and in aqueous solution. Electrostatic potential and electron density topologies, and the comparison with neutral complexes formed by oxoacids, reveal that the ionization has no significant effect on the properties of the hydrogen bonds. The stability of the complexes in the gas phase is explained by attractive forces localized in a volume situated in the hydrogen bond and defined as the electrostatic attraction region (EAR) and determined by the topological analyses of the electron density and the electrostatic potential, and by the electric field lines. In solution, the strong anionic repulsion is mostly screened by the effect of the surrounding polar solvent, which only leads to a weak destabilizing interaction in the hydrogen bond region and finally favors the overall stability of the complexes. The anion–anion complexes have been compared with the corresponding neutral ones (as salts or protonated forms), showing that EAR remains unchanged along the series.
Phys. Chem. Chem. Phys., 2015, 17, 2259-2267
I. Alkorta, J. Elguero, O. Mo, M. Yañez, J. E. Del Bene
Using Beryllium Bonds to Change Halogen Bonds From Traditional to Chlorine-shared to Ion-pair
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the structures, binding energies, and bonding characteristics of binary complexes HFBe:FCl, R2Be:FCl, and FCl:N-base, and of ternary complexes HFBe:FCl:N-base and R2Be:FCl:N-base for R = H, F, Cl; N-base = NH3, NHCH2, NCH. Dramatic synergistic cooperative effects have been found between the Be···F beryllium bonds and the Cl···N halogen bonds in ternary complexes. The Cl···N traditional halogen bonds and the Be···F beryllium bonds in binary complexes become significantly stronger in ternary complexes, while the F–Cl bond weakens. Charge-transfer from F to the empty p(σ) orbital of Be leads to a bending of the XYBe molecule and a change in the hybridization of Be, which in the limit becomes sp2. As a function of the intrinsic basicity of the nitrogen base and the intrinsic acidity of the Be derivative, the halogen-bond type evolves from traditional to chlorine-shared to ion-pair bonds. The mechanism by which an ion-pair complex is formed is similar to that involved in the dissociative proton attachment process. EOM-CCSD spin–spin coupling constants 1XJ(Cl–N) across the halogen bond in these complexes also provide evidence of the same evolution of the halogen-bond type.
A. Martín-Sómer, M. M. Montero-Campillo, O. Mó, M. Yáñez, I. Alkorta, J. Elguero
DOI: 10.5562/cca2458
Some Interesting Features of Non-Covalent Interactions
Interactions between closed-shell systems exhibit some common features, four of which are particularly strong for beryllium bonds: geometrical distortion, cooperativity, changes in intrinsic reactivity and changes in the magnetic properties of the interacting subunits, which reflect the perturbations of their electron densities through polarization effects. Structural changes lead to interaction energies that can only be adequately accounted for when the effects of the distortion on the intrinsic reactivity of the system, and not only its deformation energy, are taken into consideration. Self-assembling of ditopic systems may lead to n-mers stabilized by strong cooperative effects. Chemical shifts and coupling constants also reflect the perturbations of the electron density and accordingly cooperative effects. These four features are common to any interaction involving two closed-shell systems, one acting as Lewis acid and the other as Lewis base, and the only difference between the nature of the interactions is quantitative.
A theoretical study of the thermodynamic and hydrogen-bond basicity of TEMPO radical and related nitroxides
The use of B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) calculations on TEMPO and four related nitroxide radicals having another oxygen functionality (ketone, hydroxyl and ether) has allowed to determine the relative basicities (thermodynamic and hydrogen-bonded) of the oxygen lone pair relative to the nitroxide radical. The differences are small, especially the B3LYP ones, but in all cases they favor the radical. This is consistent with experimental results in the case of the hydroxyl group but not in the case of the keto group.
J. Phys. Chem. A, 118, 10144–10154 (2014).
DOI: 10.1021/jp509353a
Pnicogen-Bonded Complexes HnF5–nP:N-Base, for n = 0–5
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out on the pnicogen-bonded complexes HnF5–nP:N-base, for n = 0–5 and nitrogen bases NC–, NCLi, NP, NCH, and NCF. The structures of these complexes have either C4v or C2v symmetry with one exception. P–N distances and interaction energies vary dramatically in these complexes, while Fax–P–Feqangles in complexes with PF5 vary from 91° at short P–N distances to 100° at long distances. The value of this angle approaches the Fax–P–Feq angle of 102° computed for the Berry pseudorotation transition structure which interconverts axial and equatorial F atoms of PF5. The computed distances and Fax–P–Feq angles in complexes F5P:N-base are consistent with experimental CSD data. For a fixed acid, interaction energies decrease in the order NC– > NCLi > NP > NCH > NCF. In contrast, for a fixed base, there is no single pattern for the variations in distances and interaction energies as a function of the acid. This suggests that there are multiple factors that influence these properties. The dominant factor appears to be the number of F atoms in equatorial positions, and then a linear Fax–P···N rather than Hax–P···N alignment. The acids may be grouped into pairs (PF5, PHF4) with four equatorial F atoms, then (PH4F, PH2F3) with Fax–P···N linear, and then (PH3F2 and PH5) with Hax–P···N linear. The electron-donating ability of the base is also a factor in determining the structures and interaction energies of these complexes. Charge transfer from the N lone pair to the σ* P–Aax orbital stabilizes HnF5–nP:N-base complexes, with Aax either Fax or Hax. The total charge-transfer energies correlate with the interaction energies of these complexes. Spin–spin coupling constants 1pJ(P–N) for (PF5, PHF4) complexes with nitrogen bases are negative with the strongest bases NC– and NCLi but positive for the remaining bases. Complexes of (PH4F, PH2F3) with these same two strong bases and H4FP:NP have positive 1pJ(P–N) values but negative values for the remaining bases. (PH5, PH3F2) have negative values of 1pJ(P–N) only for complexes with NC–. Values of 1J(P–Fax) and 1J(P–Hax) correlate with the P–Fax and P–Haxdistances, respectively.
Theor. Chem. Acc. 133, 1586 (2014)
Noncovalent interactions in dimers and trimers of SO3 and CO
The SO3:CO heterodimer has been found by ab initio calculations to form a complex in which the C lone pair of CO interacts with the π*(SO) antibond via the π-hole lying directly above the S atom of SO3. The binding energy of this complex is 4.3 kcal/mol, with Coulombic attraction as its main component. There is also a secondary minimum, with half that strength, wherein the CO molecule is rotated so that it is its O atom that interacts with SO3. The most stable SO3:(CO)2 heterotrimer has the two CO molecules approaching the S atom from above and below the SO3 plane with the C atoms of the CO interacting with the S of the SO3. A strong chalcogen bond between SO3 molecules is the dominant feature of the (SO3)2:CO trimer, supplemented by a S···C chalcogen bond in the SO3:CO dimer.
O. Donoso-Tauda, P. Jaque, J. Elguero, I. Alkorta
DOI: 10.1021/jp506663x
Traditional and Ion-Pair Halogen-Bonded Complexes Between Chlorine and Bromine Derivatives and a Nitrogen-Heterocyclic Carbene
A theoretical study of the halogen-bonded complexes (A–X···C) formed between halogenated derivatives (A–X; A = F, Cl, Br, CN, CCH, CF3, CH3, H; and X = Cl, Br) and a nitrogen heterocyclic carbene, 1,3-dimethylimidazole-2-ylidene (MeIC) has been performed using MP2/aug′-cc-pVDZ level of theory. Two types of A–X:MeIC complexes, called here type-I and -II, were found and characterized. The first group is described by long C–X distances and small binding energies (8–54 kJ·mol–1). In general, these complexes show the traditional behavior of systems containing halogen-bonding interactions. The second type is characterized by short C–X distances and large binding energies (148–200 kJ·mol–1), and on the basis of the topological analysis of the electron density, they correspond to ion-pair halogen-bonded complexes. These complexes can be seen as the interaction between two charged fragments: A– and +[X–CIMe] with a high electrostatic contribution in the binding energy. The charge transfer between lone pair A(LP) to the σ* orbital of C–X bond is also identified as a significant stabilizing interaction in type-II complexes.
L.M. Azofra, I. Alkorta, S. Scheiner
Strongly bound noncovalent (SO3)n:H2CO complexes (n = 1, 2)
The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by S O chalcogen bonds, supplemented by weaker CH O and/or O C bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol−1. Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original molecules. The trimers are strongly bound, with total interaction energies of more than 20 kcal mol−1. Most such trimers show positive cooperativity, with shorter S O distances, and three-body interaction energies of nearly 3 kcal mol−1.
J. Org. Chem., 2014, 79, 6959–6969.
F. Zapata, A. Caballero, P. Molina, I. Alkorta, J. Elguero
DOI: 10.1021/jo501061z
Open Bis(triazolium) Structural Motifs as a Benchmark To Study Combined Hydrogen- and Halogen-Bonding Interactions in Oxoanion Recognition Processes
We have designed a series of triazolium-pyrene-based dyads to probe their potential as fluorescent chemosensors for anion recognition through combinations of hydrogen and halogen bonding. Cooperation between the two distinct noncovalent interactions leads to an unusual effect on receptor affinity, as a result of fundamental differences in the interactions of halogen and hydrogen bond donor groups with anions. Absorption, emission spectrophotometries and proton and phosphorus NMR spectroscopies indicate that the two interactions act in concert to achieve the selective binding of the hydrogen pyrophosphate anion, a conclusion supported by computational studies. Hence, as clearly demonstrated with respective halogen- and hydrogen-bonding triazolium receptors, the integration of a halogen atom into the anion receptor at the expense of one hydrogen-bonding receptor greatly influences the anion recognition affinity of the receptor. The association constant values of the halogen-bonding complexes are larger than the hydrogen-bonding counterpart. Thus, halogen bonding has been exploited for the selective fluorescent sensing of hydrogen pyrophosphate anion. Halogen bonding has been demonstrated to increase the strength of hydrogen pyrophosphate binding, as compared to the hydrogen-bonded analogue. Grimme's PBE-D functional, which adequately reproduces the pyrene stacking energies, has been successfully applied to model the affinity for anions, especially hydrogen pyrophosphate, of the new receptors.
G. Sánchez-Sánz, C. Trujillo, I. Alkorta, J. Elguero
DOI: 10.1039/C4CP01072H
Intramolecular pnicogen interactions in phosphorus and arsenic analogues of proton sponges
A computational study of the intramolecular pnicogen bond in 1,8-bis-substituted naphthalene derivatives (ZXH and ZX2 with Z = P, As and X = H, F, Cl, and Br), structurally related to proton sponges, has been carried out. The aim of this paper is the study of their structural parameters, interaction energies and electronic properties such as electron density on the intramolecular interaction. The calculated geometrical parameters associated to the P P interaction are in reasonably good agreement with the crystal structures found in a CSD search, in particular those of the halogen derivatives. Isodesmic reactions where the 1,8-bis-substituted derivatives are compared to monosubstituted derivatives have been calculated, indicating that the 1,8 derivatives are more stable than the monosubstituted ones for those cases with X–Z Z–X and F–Z Z–H alignments. Electron densities and Laplacians at the BCP on the pnicogen interactions suggest that they can be classified as pure closed shell interactions with a partial covalent character. Electron density shift maps are consistent with the results for intermolecular pnicogen interactions. Relationships between interatomic distance and electron density at the bond critical points and between interatomic distance and the orbital charge transfer stabilization energies have been found.
An exploration of the ozone dimer potential energy surface
The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions fromelectrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of thewavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm−1. In addition to the five minima, 11 higher-order stationary points are identified.
DOI: 10.1021/jp503436f
Characterizing Traditional and Chlorine-Shared Halogen Bonds in Complexes of Phosphine Derivatives with ClF and Cl2
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out on the halogen-bonded complexes H2XP:ClF and H2XP:Cl2, with X = F, Cl, OH, NC, CN, CCH, CH3, and H. H2XP:ClF complexes are stabilized by chlorine-shared halogen bonds with short P–Cl and significantly elongated Cl–F distances. H2XP:Cl2 complexes with X = OH and CH3 form only chlorine-shared halogen bonds, while those with X = H, NC, and CN form only traditional halogen bonds. On the H2FP:Cl2, H2(CCH)P:Cl2, and H2ClP:Cl2 potential surfaces small barriers separate two equilibrium structures, one with a traditional halogen bond and the other with a chlorine-shared bond. The binding energies of H2XP:ClF and H2XP:Cl2 complexes are influenced by the electron-donating ability of H2XP and the electron accepting ability of ClF and ClCl, the nature of the halogen bond, other secondary interactions, and charge-transfer interactions. Changes in electron populations on P, F, and Cl upon complex formation do not correlate with changes in the chemical shieldings of these atoms. EOM-CCSD spin–spin coupling constants for complexes with chlorine-shared halogen bonds do not exhibit the usual dependencies on distance. 2XJ(P–F) and 2XJ(P–Cl) for complexes with chlorine-shared halogen bonds do not correlate with P–F and P–Cl distances, respectively. 1XJ(P–Cl) values for H2XP:ClF correlate best with the Cl–F distance, and approach the values of 1J(P–Cl) for the corresponding cations H2XPCl+. Values of 1XJ(P–Cl) for complexes H2XP:ClCl with chlorine-shared halogen bonds correlate with the binding energies of these complexes. 1J(F–Cl) and 1J(Cl–Cl) for complexes with chlorine-shared halogen bonds correlate linearly with the distance between P and the proximal Cl atom. In contrast, 2XJ(P–Cl) and 1XJ(P–Cl) for complexes with traditional halogen bonds exhibit more normal distance dependencies.
F. Blanco, D. G. Lloyd, I. Alkorta, J. Elguero
Neutral Alkaline-Metal and Alkaline-Earth-Metal Derivatives of Imidazole and Benzimidazole
A theoretical study of the minima and connecting transition states of the neutral complexes formed by alkaline-metal and alkaline-earth-metal derivatives of imidazolate and benzimidazolate anions has been carried out using B3LYP/6-31+G(d,p), B3LYP/6-311+G(3df,2p), and G3B3 methods. Two and three nondegenerated minima and two and four TS structures have been identified for imidazole and benzimidazole derivatives, respectively. The most stable minima of the alkaline-metal derivatives of both systems correspond to the metal interacting with the imidazole ring, whereas in the alkaline-earth-metal derivatives, the preferred minima depend on the substituent. A remarkable feature of some minima is the fact that some of the metal–aromatic interactions follow the classical π–cation pattern, even though the global structure corresponds to a neutral salt, constituting a class of noncovalent interaction of great interest in the chemistry of aromatic and heterocyclic complexes. A CSD search has confirmed that the two bonding modes, N−σ and π, are present in the solid phase. The π mode has been analyzed by comparison with other azoles.
DOI: 10.1021/jp502667k
Pnicogen-Bonded Anionic Complexes
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the pnicogen-bonded complexes H2YP:X–, for X,Y = Cl, NC, F, CCH, and CH3. Of the 36 possible complexes, only 21 are unique equilibrium structures. All substituents form (H2XPX)− complexes with symmetric X–P–X bonds. The P–A ion–molecule pnicogen bonds in these and some additional complexes have partial covalent character, while some P–A′ covalent bonds have partial ion–molecule character. A and A′ are the atoms of X and Y, respectively, which are directly bonded to P. Complexes with these types of bonds include the symmetric complexes (H2XPX)−, H2(CH3)P:F–, H2(CCH)P:F–, H2FP:NC–, H2FP:Cl–, H2FP:CN–, and H2(NC)P:Cl–. Charge transfer from A to the P–A′ σ* orbital stabilizes H2YP:X– complexes and leads to a reduction of the negative charge on X. For fixed X, the smallest negative charge occurs in the symmetric complex. Then, for a given X, the order of decreasing negative charge with respect to Y is CH3 > CCH > CN (bonded through C) > F > NC (bonded through N) > Cl, which is also the order of decreasing P–A distance. EOM-CCSD spin–spin coupling constants 1pJ(P–A) differentiate between shorter ion–molecule pnicogen bonds with partial covalent character and longer P···A ion–molecule pnicogen bonds. Similarly, coupling constants 1J(P–A′) differentiate between longer covalent P–A′ bonds with partial ion–molecule character and shorter P–A′ covalent bonds.
Chem. Commun., 50, 4680-4682 (2014)
A. Caballero, F. Zapata, L. González, P. Molina, I. Alkorta, J. Elguero
DOI: 10.1039/C4CC00169A
Discovery of anion–π interactions in the recognition mechanism of inorganic anions by 1,2,3-triazolium rings
A bis(triazolium)-based receptor designed for anion recognition is presented. NMR spectroscopic data indicate that one triazolium ring is acting as a hydrogen bond donor, whereas the second triazolium ring behaves as an anion–π receptor. The simultaneous presence of two noncovalent interactions allows us to achieve a highly selective binding of the hydrogenpyrophosphate anion.
DOI: 10.1021/jp500915c
Influence of Substituent Effects on the Formation of P···Cl Pnicogen Bonds or Halogen Bonds
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out in search of equilibrium structures with P···Cl pnicogen bonds or halogen bonds on the potential energy surfaces H2FP:ClY for Y = F, NC, Cl, CN, CCH, CH3, and H. Three different types of halogen-bonded complexes with traditional, chlorine-shared, and ion-pair bonds have been identified. Two different pnicogen-bonded complexes have also been found on these surfaces. The most electronegative substituents F and NC form only halogen-bonded complexes, while the most electropositive substituents CH3 and H form only pnicogen-bonded complexes. The halogen-bonded complexes involving the less electronegative groups Cl and CN are more stable than the corresponding pnicogen-bonded complexes, while the pnicogen-bonded complexes with CCH are more stable than the corresponding halogen-bonded complex. Traditional halogen-bonded complexes are stabilized by charge transfer from the P lone pair to the Cl–A σ* orbital, where A is the atom of Y directly bonded to Cl. Charge transfer from the Cl lone pair to the P–F σ* orbital stabilizes pnicogen-bonded complexes. As a result, the H2FP unit becomes positively charged in halogen-bonded complexes and negatively charged in pnicogen-bonded complexes. Spin–spin coupling constants 1XJ(P–Cl) for complexes with traditional halogen bonds increase with decreasing P–Cl distance, reach a maximum value for complexes with chlorine-shared halogen bonds, and then decrease and change sign when the bond is an ion-pair bond. 1pJ(P–Cl) coupling constants across pnicogen bonds tend to increase with decreasing P–Cl distance.
σ–σ and σ–π pnicogen bonds in complexes H2XP:PCX, for X = F, Cl, OH, NC, CN, CCH, CH3, and H
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out on complexes H2XPs:PtCX, for X = F, Cl, OH, NC, CN, CCH, CH3, and H, in search of complexes stabilized by P···P pnicogen bonds. These intermolecular bonds arise when a pnicogen atom acts as a Lewis acid for complex formation. Three sets of equilibrium structures have been found on the H2XPs:PtCX potential surfaces. Conformation A complexes have P···P σ–σ pnicogen bonds, which involve the σ systems of both P atoms. Conformations B and C are stabilized by σ–π pnicogen bonds, which involve the σ system of H2XP and the π system of PCX. Binding energies of B and C complexes are similar and are greater than the binding energies of the A conformers. Charge transfer stabilizes A, B, and C conformers. In A complexes, the dominant charge transfer is from the lone pair of PCX to the antibonding σ*P–A orbital of PH2X, with A the atom of X directly bonded to P. For conformations B and C, the dominant charge transfer is from the P=C π orbital to the σ*P–A orbital of H2XP. Although the binding energies of these complexes do not correlate with the intermolecular P–P distances, both the charge-transfer energies and the equation-of-motion coupled cluster singles and doubles one-bond 31P–31P spin–spin coupling constants do correlate with the P–P distances. The largest coupling constants 1pJ(P–P) are found for complexes with conformation A, due to the nature of the σ–σ pnicogen bond and the dominance of the Fermi contact term. For a given X, 1pJ(P–P) values are ordered A > C > B.
Mol. Phys. 112, 592-600 (2014)
O. Mo, M. Yañez, I. Alkorta, J. Elguero
Spontaneous proton transfers induced by beryllium bonds
Through the use of B3LYP/6-311+G(d,p) density functional theory (DFT) calculations, we have shown that when a molecule participates as a proton donor in a complex, it yields much stronger hydrogen bonds (HBs) if it participates simultaneously in beryllium bonds. This is indeed the case of the complexes formed by oxyacids such as acetic, benzoic and phosphinic acids with BeCl2, which yield much stronger HBs with different bases than the isolated oxyacids due to a significant acidity enhancement, triggered by the charge transfer from the oxyacid to BeCl2. More importantly, depending on the intrinsic basicity of the base acting as proton acceptor, a spontaneous proton transfer from the oxyacid to the base may occur, leading to the formation of an ion pair in the gas phase. This is indeed the case in complexes involving ammonia. For slightly weaker bases, such as trimethylphosphine, two local minima are stable: one in which the proton remains attached to the oxyacid and one in which this proton has been transferred to the trimethylphosphine, the latter being always the most stable. When a compound is able to act simultaneously as a proton donor and as a proton acceptor, its participation in a beryllium bond necessarily leads to an enhancement and a dampening of both properties, respectively. Hence, the HB in which they participate as proton donors becomes stronger, whereas the HB in which they act as proton acceptors becomes weaker. The dimers of 1H-tetrazole and the dimers of isatin nicely illustrate this finding.
I. Alkorta, G. Sánchez-Sanz, J. Elguero, J. E. Del Bene
Pnicogen Bonds between X=PH3 (X = O, S, NH, CH2) and Phosphorus and Nitrogen Bases
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the pnicogen bonded complexes formed between the acids O═PH3, S═PH3, HN═PH3, and H2C═PH3 and the bases NH3, NCH, N2, PH3, and PCH. All nitrogen and phosphorus bases form complexes in which the bases are lone pair electron donors. The binding energies of complexes involving the stronger bases NH3, NCH, and PH3 differentiate among the acids, but the binding energies of complexes with the weaker bases do not. These complexes are stabilized by charge transfer from the lone pair orbital of N or P to the σ*P═A orbital of X═PH3, where A is the atom of X directly bonded to P. PCH also forms complexes with the X═PH3 acids as a π electron donor to the σ*P═A orbital. The binding energies and the charge-transfer energies of the π complexes are greater than those of the complexes in which PCH is a lone pair donor. Whether the positive charge on P increases, decreases, or remains the same upon complex formation, the chemical shieldings of 31P decrease in the complexes relative to the corresponding monomers. 1pJ(P–N) and 1pJ(P–P) values correlate best with the corresponding P–N and P–P distances as a function of the nature of the base. 1J(P–A) values do not correlate with P–A distances. Rather, the absolute values of 1J(P–O), 1J(P–S), and 1J(P–N) decrease upon complexation. Decreasing 1J(P–A) values correlate linearly with increasing complex binding energies. In contrast, 1J(P–C) values increase upon complexation and correlate linearly with increasing binding energies.
J. Phys. Chem. A 118, 947−953 (2014)
I. Alkorta, J. Elguero, M. Solimannejad
DOI: 10.1021/jp412144r
Single Electron Pnicogen Bonded Complexes
A theoretical study of the complexes formed by monosubstituted phosphines (XH2P) and the methyl radical (CH3) has been carried out by means of MP2 and CCSD(T) computational methods. Two minima configurations have been obtained for each XH2P:CH3 complex. The first one shows small P–C distances and, in general, large interaction energies. It is the most stable one except in the case of the H3P:CH3 complex. The second minimum where the P–C distance is large and resembles a typical weak pnicogen bond interaction shows interaction energies between −9.8 and −3.7 kJ mol–1. A charge transfer from the unpaired electron of the methyl radical to the P–X σ* orbital is responsible for the interaction in the second minima complexes. The transition state (TS) structures that connect the two minima for each XH2P:CH3 complex have been localized and characterized.
Phys. Chem. Chem. 16, 4305-4312 (2014)
I. Alkorta, J. Elguero, M. Yáñez, O. Mó
Cooperativity in beryllium bonds
A theoretical study of the beryllium bonded clusters of the (iminomethyl)beryllium hydride and (iminomethyl)beryllium fluoride [HC(BeX)═NH, X = H, F] molecules has been carried out at the B3LYP/6-311++G(3df,2p) level of theory. Linear and cyclic clusters have been characterized up to the decamer. The geometric, energetic, electronic and NMR properties of the clusters clearly indicate positive cooperativity. The evolution of the molecular properties, as the size of the cluster increases, is similar to those reported in polymers held together by hydrogen bonds.
Phys. Chem. Chem. Phys. 2017, 19, 23052-23059
M. Yañez, O. Mo, I. Alkorta, J. Elguero
Spontaneous ion-pair formation in the gas phase induced by Beryllium bonds
The changes in the structure and bonding of the hydrogen bonded complexes between hydrogen halides and ammonia, phosphine and water, when the hydrogen halides form beryllium bonds with BeCl2 have been investigated by CCSD(T)/aug-cc-pVTZ ab initio calculations. Although the experimental evidence showed that a spontaneous proton transfer (PT) from hydrogen halides toward ammonia does not occur, and only is observed for HI when interacting with trimethylamine, we have found that a spontaneous PT does occur when the halide forms beryllium bonds with BeCl2. The complexes so formed are the result of the interaction of Cl2BeX− with NH4+, PH4+, H3O+, respectively.
Properties of Complexes H2C═(X)P:PXH2, for X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2: P···P Pnicogen Bonding at σ-Holes and π-Holes
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out on complexes H2C═(X)P:PXH2, for X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2. Three sets of complexes have been found on the potential surfaces. Conformation A complexes have A–P···P–A approaching linearity, with A the atom of X directly bonded to P. Conformation B complexes have A–P···P linear, but the P···P═C orientation of H2C═PX may differ significantly from linearity. Conformation C complexes are unique, since the pnicogen bond involves π-electron donation and acceptance by H2C═PX. The order of binding energies of the three conformations of H2C═(X)P:PXH2 is C > A > B, with two exceptions. Although the binding energies of conformation C complexes tend to be greater than the corresponding conformation A complexes, intermolecular distances in conformation C tend to be longer than those in conformation A. Charge transfer stabilizes H2C═(X)P:PXH2 complexes. The preferred direction of charge transfer is from H2C═PX to PXH2. In conformations A and B, charge transfer occurs from a P lone pair on one molecule to an antibonding σ* orbital on the other. However, in conformation C, charge transfer occurs from the π orbital of H2C═PX to the σ*P–A orbital of PXH2, and from the lone pair on P of PXH2 through the π-hole to the π*P═C orbital of H2C═PX. Changes in charges on P upon complexation do not correlate with changes in 31P chemical shieldings. Computed EOM-CCSD spin–spin coupling constants correlate with P–P distances. At each distance, the ordering of 1pJ(P–P) is A > B > C. Binding energies and spin–spin coupling constants of conformation A complexes of (PH2X)2, H2C═(X)P:PXH2, and (H2C═PX)2 with A–P···P–A approaching linearity have been compared. For complexes with the more electronegative substituents, binding energies are ordered (PH2X)2 > H2C═(X)P:PXH2 > (H2C═PX)2, while the order is reversed for complexes formed from the more electropositive substituents. A plot of ΔE(PH2X)2/ΔE(H2C═PX)2 versus ΔE[H2C═(X)P:PXH2]/ΔE(H2C═PX)2 indicates that there is a systematic relationship among the stabilities of these complexes. Complexes (PH2X)2 tend to have larger spin–spin coupling constants and shorter P–P distances than H2C═(X)P:PXH2, which in turn have larger coupling constants and shorter P–P distances than (H2C═PX)2, although there is some overlap. Complexes having similar P–P distances have similar values of1pJ(P–P).
J. Chem. Theory Comput. 9, 5201–5210 (2013)
A. Bauza, I. Alkorta, A. Frontera, J. Elguero
DOI: 10.1021/ct400818v
On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors
In this article, we report a comprehensive theoretical study of halogen, chalcogen, and pnicogen bonding interactions using a large set of pure and hybrid functionals and some ab initio methods. We have observed that the pure and some hybrid functionals largely overestimate the interaction energies when the donor atom is anionic (Cl– or Br–), especially in the halogen bonding complexes. To evaluate the reliability of the different DFT (BP86, BP86-D3, BLYP, BLYP-D3, B3LYP, B97-D, B97-D3, PBE0, HSE06, APFD, and M06-2X) and ab initio (MP2, RI-MP2, and HF) methods, we have compared the binding energies and equilibrium distances to those obtained using the CCSD(T)/aug-cc-pVTZ level of theory, as reference. The addition of the latest available correction for dispersion (D3) to pure functionals is not recommended for the calculation of halogen, chalcogen, and pnicogen complexes with anions, since it further contributes to the overestimation of the binding energies. In addition, in chalcogen bonding interactions, we have studied how the hybridization of the chalcogen atom influences the interaction energies.
DOI: 10.1021/jp407097e
Pnicogen Bonded Complexes of PO2X (X = F, Cl) with Nitrogen Bases
n ab initio MP2/aug′-cc-pVTZ study has been carried out on complexes formed between PO2X (X = F and Cl) as the Lewis acids and a series of nitrogen bases ZN, including NH3, H2C═NH, NH2F, NP, NCH, NCF, NF3, and N2. Binding energies of these complexes vary from −10 to −150 kJ/mol, and P—N distances from 1.88 to 2.72 Å. Complexes ZN:PO2F have stronger P...N bonds and shorter P—N distances than the corresponding complexes ZN:PO2Cl. Charge transfer from the N lone pair through the π-hole to the P—X and P—O σ* orbitals leads to stabilization of these complexes, although charge-transfer energies can be evaluated only for complexes with binding energies less than −71 kJ/mol. Complexation of PO2X with the strongest bases leads to P···N bonds with a significant degree of covalency, and P—N distances that approach the P—N distances in the molecules PO2NC and PO2NH2. In these complexes, the PO2X molecules distort from planarity. Changes in 31P absolute chemical shieldings upon complexation do not correlate with changes in charges on P, although they do correlate with the binding energies of the complexes. EOM-CCSD spin–spin coupling constants 1pJ(P—N) are dominated by the Fermi-contact term, which is an excellent approximation to total J. 1pJ(P—N) values are small at long distances, increase as the distance decreases, but then decrease at short P—N distances. At the shortest distances, values of1pJ(P—N) approach 1J(P—N) for the molecules PO2NC and PO2NH2.
J. Phys. Chem. B. 117, 11608–11616 (2013)
F. Blanco, B. Kelly, G. Sánchez-Sanz, C. Trujillo, I. Alkorta , J. Elguero , I. Rozas
DOI: 10.1021/jp407339v
Non-Covalent Interactions: Complexes of Guanidinium with DNA and RNA Nucleobases
Considering that guanidine-based derivatives are good DNA minor groove binders, we have theoretically studied, using the Polarizable Continuum model mimicking water solvation, the complexes formed by the biologically relevant guanidinium cation and the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine, and uracil). The interactions established within these complexes both by hydrogen bonds and by cation−π interactions have been analyzed by means of the Atoms in Molecules and Natural Bond Orbital approaches. Moreover, maps of electron density difference have been produced to understand the cation−π complexes. Finally, the NICS and three-dimensional NICS maps of the cation−π complexes have been studied to understand the effect of the guanidinium cation on the aromaticity of the nucleobases.
Comp. Rend. Chim. 16, 937-944 (2013)
D. Sanz, R. M. Claramunt, F. Mathey, I. Alkorta, G. Sánchez-Sanz, J. Elguero
DOI: 10.1016/j.crci.2013.05.016
Intermolecular spin–spin coupling constants between 31P atoms
This paper reports the study by NMR spectroscopy and ab initio methods of the structure of 3,4-dimethyl-1-cyanophosphole and its dimer. The dimer presents a P...P interaction of the pnictogen type due to the presence ofs-holes. NMR of the monomer was recorded in CDCl3 solution while NMR of the dimer corresponds to the solid state (CPMAS) experiments. The 2pJPP spin–spin coupling constan thas not been measured, but calculated at the B3LYP level. AIM, NBO and ELF methodologies have been used to describe the electronic structure of the dimer
J. Mol. Model. 19, 4139–4145 (2013)
O. Mó, M. Yañez, I. Alkorta, J. Elguero
Enhancing and modulating the intrinsic acidity of imidazole and pyrazole through beryllium bonds
The structure and electronic properties of the complexes formed by the interaction of imidazole and pyrazole with different BeXH(BeX2) (X = H, Me, F, Cl) derivatives have been investigated via B3LYP/6−311+G(3df,2p)//B3LYP/6−31+G(d,p) calculations. The formation of these azole:BeXH(BeX2) complexes is accompanied by a dramatic enhancement of the intrinsic acidity of the azole, as the deprotonated azole is much more stable after the aforementioned interaction. Most importantly, the increase in acidity is so large that the azole:BeXH or azole:BeX2 complexes behave as NH acids, which are stronger than typical oxyacids such as phosphoric acid and oxalic acid. Interestingly, the increase in acidity can be tuned through appropriate selection of the substituents attached to the Be atom, permitting us to modulate the electron-accepting ability of the BeXH or BeX2 molecule.
Characterizing Complexes with Pnicogen Bonds Involving sp2 Hybridized Phosphorus Atoms: (H2C═PX)2 with X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2
Ab initio MP2/aug′-cc-pVTZ searches of the potential surfaces of (H2C═PX)2 complexes, with X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2, have been carried out to identify and characterize the properties of complexes with P···P pnicogen bonds. All (H2C═PX)2 form equilibrium conformation A dimers with C2h symmetry in which A–P···P–A approaches a linear alignment, with A the atom of X directly bonded to P. Conformation A dimers containing the more electronegative substituents are stabilized by a P···P pnicogen bond, have shorter P–P distances, and have binding energies which correlate with the P–P distance. Dimers stabilized by a P···P pnicogen bond and two P···Hb interactions consist of those with the more electropositive substituents, have shorter P–Hb distances, and have binding energies which are too high for their P–P distances. Conformation A complexes with P···Hbinteractions in addition to the P···P bond are more stable than the corresponding (PH2X)2complexes, while with only one exception, complexes stabilized by only a P···P bond are less stable than the corresponding (PH2X)2 complexes. In the region of the potential surfaces with C–P···P–C approaching linearity (conformation B), the only planar equilibrium complex is (H2C═POH)2, which is stabilized primarily by two O–H···P hydrogen bonds. The remaining (H2C═PX)2 complexes are not stabilized by pnicogen bonds, but by π interactions between the two H2C═PX monomers which are in parallel planes. When A–P···P–C approaches linearity, two types of equilibrium structures with P···P bonds exist. Of the conformation C dimers, (H2C═POH)2 is planar and the most stable, with a P···P pnicogen bond and an O–H···P hydrogen bond. (H2C═PH)2 and (H2C═PCH3)2 are also planar, and stabilized by a P···P pnicogen bond and a P···Hb interaction. The absence of a P···Hb interaction results in nonplanar C′ conformations with structures in which the monomers essentially retain their symmetry plane, but the plane of one molecule is rotated about the P···P bond relative to the other. C and C′ dimers are less stable than the corresponding A dimers, except for (H2C═PCH3)2. 31P chemical shielding patterns are consistent with the changing nature of the interactions which stabilize (H2C═PX)2 complexes. EOM-CCSD 31P–31P spin–spin coupling constants increase quadratically as the P–P distance decreases.
G. Sanchez-Sanz, C. Trujillo, M. Solimannejad, I. Alkorta, J. Elguero
Orthogonal interactions between nitryl derivatives and electron donors: pnictogen bonds
Pnictogen complexes between nitryl derivatives (NO2X, X = CN, F, Cl, Br, NO2, OH, CCH, and C2H3) and molecules acting as Lewis bases (H2O, H3N, CO, HCN, HNC and HCCH) have been obtained at the MP2/aug-cc-pVTZ computational level. A total of 53 minima have been located. Their energy, geometry, DFT-SAPT energy terms, electronic properties (NBO, AIM, ELF, and NCI) and NMR shieldings have been calculated and analyzed. Finally, a search in the CSD database has been carried out, showing a large number of similar interactions in crystallographic structures.
M. Solimannejad, M. Malekani, I. Alkorta
DOI: 10.1021/jp405211p
Substituent Effects on the Cooperativity of Halogen Bonding
DFT calculations (B97-1) with the 6-31+G(d,p)-LanL2DZdp basis set were used to analyze the intermolecular interactions in 4-Z-Py···XCN···XCN triads (Z = H, F, OH, OCH3, CH3, NH2, NO2, and CN; Py = pyridine; and X = Cl and Br) that are connected by halogen-bond interactions. To understand the properties of the systems better, the corresponding dyads are also studied. Particular attention is given to parameters such as cooperative energy. All complexes show cooperative energy ranging from −1.39 to −3.46 kJ mol–1 and −2.61 to −5.84 kJ mol–1 for X = Cl and Br, respectively. We show that the effect of the substituents on the title interactions strongly depends on the nature of the substituents (Z). Thus, the electron-donor and electron-acceptor substituents increase and decrease the stability of complexes, respectively. The electronic properties of the complexes have been analyzed using molecular electrostatic potential (MEP) and minimum average local ionization energy, and the parameters were derived from the atoms in molecules (AIM) and natural bond orbital (NBO) methodologies.
Z. Phys. Chem. 227, 821–839 (2013)
J. E. Del Bene, I. Alkorta, G. Sanchez-Sanz, J. Elguero
DOI: 10.1524/zpch.2013.0367
Ab Initio Study of Cooperative Effects in Complexes X:HBO:Z, with X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO: Structures, Binding Energies, and Spin-Spin Coupling Constants across Intermolecular Bonds
A systematic ab initio investigation has been carried out to determine the structures, binding energies, and spin-spin coupling constants of ternary complexes X:HBO:Z for X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO. All complexes X:HBO:Z are linear with C∞v symmetry, except for HCl:HBO:Z and ClF:HBO:Z which have Cs symmetry, thereby reflecting the structures of the corresponding X:HBO and HBO:Z complexes. Cooperative effects on energies are synergistic in all ternary complexes. The enhanced binding energies of complexes X:HBO:Z correlate with the binding energies of the X:HBO and HBO:Z complexes. Coupling constants 1J(B-H) and 2hJ(B-A) across B-H···A hydrogen bonds correlate with the B-A distance, and exhibit synergistic effects due to the presence of Z. 1hJ(H-A) indicates that these bonds have little proton-shared character. Coupling constants across D-H···O hydrogen bonds, H-Li···O lithium bonds, and F-Cl···O halogen bonds are also sensitive to the synergistic effects arising from the presence of X. D-H···O hydrogen bonds in ternary complexes are traditional (normal) hydrogen bonds.
J. Mol. Struct. 108, 138-151 (2013)
C. Trujillo, G. Sánchez-Sanz, I. Alkorta, J. Elguero, O. Mó, M. Yáñez
Resonance assisted hydrogen bonds in open-chain and cyclic structures of malonaldehyde enol: A theoretical study
In 1989 Gilli, Bellucci, Ferretti and Bertolasi introduced the notion of Resonance Assisted Hydrogen Bonding (RAHB) one of the most fruitful concepts in structural chemistry. After reviewing our previous contributions to this topic, the present work analyzes theoretically this concept especially in non-cyclic structures. Geometries, electron densities and Laplacian at the bond critical points, cooperativity through many body interaction energies, deformation energies as well as NMR properties (chemical shifts and 2hJOO coupling constants) are used for the discussion.
Pnicogen-Bonded Cyclic Trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of cyclic trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2. Except for [PH2(CH3)]3, these complexes have C3h symmetry and binding energies between −17 and −63 kJ mol–1. Many-body interaction energy analyses indicate that the two-body terms are dominant, accounting for 97–103% of the total binding energy. Except for the trimer [PH2(OH)]3, the three-body terms are stabilizing. Charge transfer from the lone pair on one P atom to an antibonding σ* orbital of the P atom adjacent to the lone pair plays a very significant role in stabilization. The charge-transfer energies correlate linearly with the trimer binding energies. NBO, AIM, and ELF analyses have been used to characterize bonds, lone pairs, and the degree of covalency of the P···P pnicogen bonds. The NMR properties of chemical shielding and 31P–31P coupling constants have also been evaluated. Although the 31P chemical shieldings in the five most strongly bound trimers increase relative to the corresponding isolated monomers, there is no correlation between the chemical shieldings and the charges on the P atoms. EOM-CCSD 31P–31P spin–spin coupling constants computed for four (PH2X)3 trimers fit nicely onto a plot of 1pJ(P–P) versus the P–P distance for (PH2X)2dimers. A coupling constant versus distance plot for the four trimers has a second-order trendline which has been used to predict the values of 1pJ(P–P) for the remaining trimers.
G. Sanchez-Sanz, I. Alkorta, C. Trujillo, J. Elguero
Intramolecular Pnicogen Interactions in PHF(CH2)nPHF (n=2–6) Systems
A computational study of the intramolecular pnicogen bond in PHF (CH2)n PHF (n=2–6) systems was carried out. For each compound, two different conformations, (R,R) and (R,S), were considered on the basis of the chirality of the phosphine groups. The characteristics of the closed conformers, in which the pnicogen interaction occurs, were compared with those of the extended conformer. In several cases, the closed conformations are more stable than the extended conformations. The calculated interaction energies of the pnicogen contact, by means of isodesmic reactions, provide values between −3.4 and −26.0 kJ mol−1. Atoms in molecules and electron localization function analysis of the electron density showed that the systems in the closed conformations with short P⋅⋅⋅P distances have a partial covalent character in this interaction. The calculated absolute chemical shieldings of the P atoms showed an exponential relationship with the P⋅⋅⋅P distance. In addition, a search in the Cambridge crystallographic database was carried out to detect those compounds with a potential intramolecular pnicogen bond in the solid phase.
J. Phys. Org. Chem. 26, 378-385 (2013)
I. Rozas, G. Sanchez-Sanz, I. Alkorta, J. Elguero
Solvent effects on guanidinium-anion interactions and the problem of guanidinium Y-aromaticity
We have calculated the complexes formed by guanidine/guanidinium and HCl/Cl−, HNO3/NO3− and H2SO4/HSO4− both in the gas and aqueous Polarizable Continuum Model (PCM) phase to understand the effect that solvation has on their interaction energies. In the gas phase, the cation–anion complexes are much more stable than the rest; however, when PCM-water is considered, this energetic difference is not as large due to the extra stabilization that the ions suffer when in aqueous solution. All the complexes were analyzed in terms of their AIM and NBO properties. In all cases, water solvation seems to "dampen" those properties observed in the gas phase. The values of Nucleus Independent Chemical Shift (NICS)(1) and NICS(2) indicate a huge influence of the proximity of the carbon atom for short distances; thus, the 3D NICS values on the van der Waal isosurfaces have been used to evaluate the possible Y-aromaticity of the guanidinium system. The isosurface in this system is more similar to cyclohexane than to benzene as indication of poor aromaticity.
S. Grabowski, I. Alkorta, J. Elguero
Complexes between Dihydrogen and Amine, Phosphine, and Arsine Derivatives. Hydrogen Bond versus Pnictogen Interaction
A theoretical study of the complexes between dihydrogen, H2, and a series of amine, phosphine, and arsine derivatives (ZH3 and ZH2X, with Z = N, P, or As and X = F, Cl, CN, or CH3) has been carried out using ab initio methods (MP2/aug-cc-pVTZ). Three energetic minima configurations have been characterized for each case with the H2 molecule in the proximity of the pnictogen atom (Z). In configuration A, the σ-electrons of H2 interact with σ-hole region of the pnictogen atom generated by the of X–Z bond. These complexes can be ascribed as pnictogen bonded. In configuration C, the lone electron pair of Z acts as the Lewis base, and H2 plays the role of the Lewis acid. Finally, configuration B presents a variety of noncovalent interactions depending on the binary complex considered. The atoms-in-molecules theory (AIM), natural bond orbitals (NBO) method as well as the density functional theory–symmetry adapted perturbation theory (DFT-SAPT) approach were used in this study to deepen the nature of the interactions considered.
DOI: 10.1021/jp401480y
Phosphorus As a Simultaneous Electron-Pair Acceptor in Intermolecular P···N Pnicogen Bonds and Electron-Pair Donor to Lewis Acids
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to investigate the structures and energies of binary complexes LA:PH2F and LA:PH3 and of ternary complexes LA:H2FP:NFH2 and LA:H3P:NH3 in which the pnicogen-bonded P atom also acts as an electron-pair donor to a Lewis acid (LA), for LA = BH3, NCH, ClH, FH, FCl, and HLi. Hydrogen bonds, halogen bonds, and dative covalent bonds are found at P in some cases, depending on the nature of the Lewis acid. HLi forms a lithium bond with P only in the binary complex HLi:PH3. The binding energies of ternary complexes exhibit a classical synergistic effect, although the computed cooperativity may be overestimated due to neglect of the interaction of the Lewis acid with NH2F or NH3 in some cases. The hydrogen-bonding Lewis acids appear to have little effect on the strength of the P···N bond, while the remaining Lewis acids strengthen the pnicogen bond. 31P absolute chemical shieldings increase in LA:H2FP:NFH2complexes relative to the corresponding LA:PH2F complexes as the positive charge on P decreases, while chemical shieldings decrease in LA:H3P:NH3 relative to the corresponding LA:PH3 complexes as the positive charge increases. Absolute values of 1pJ(P–N) spin–spin coupling constants in complexes LA:H2FP:NFH2 decrease as the P–N distance decreases. It appears that this behavior is associated with the presence of a second intermolecular interaction, whether electron-donation by P or hydrogen bond formation at P–F.
I. Alkorta, G. Sánchez-Sanz, J. Elguero
DOI: 10.1039/C2CE26786A
Linear free energy relationships in halogen bonds
Four models of halogen bonds were used to quantify this bond using the DFT B97D/6-311+G(d) computational level: para-substituted iodobenzenes, para- and meta-substituted bromobenzenes complexed with three simple Lewis bases (NH3, NCH and CNH), 1-bromo-4-substituted-bicyclo[2.2.2]octanes with NH3 and 3- and 4-substituted pyridines complexed with BrCl and BrF. In addition, the combination of the para-substituted bromobenzenes with the 4-substituted pyridines has been studied. A total of 459 complexes have been optimized and are discussed in the present article. The energetic and geometric results have been analyzed based on the properties of the substituents and the isolated molecules involved in the interaction. The Hammett–Taft parameters provide reasonable correlations with the interaction energies. However, excellent correlations are obtained in all the cases when the electrostatic properties of the two molecules involved in the interaction are considered (R2 > 0.99).
Struct. Chem. 24, 491-497 (2013)
M. Solimannejad, M. Gharabaghi, I. Alkorta
DOI:10.1007/s11224-012-0099-7
Ab initio study of water clustering in the presence of a methyl radical
The geometrical structure and binding energy of small clusters of methyl radical and water molecules (up to five water molecules) in gas phase and water media have been investigated at the MP2 level of theory using 6-311++G(2df,2p) basis set. The complexes characterized contain OH···O, CH···O, and OH···C attractive interactions with stabilization energies in the range 6–143 kJ mol−1. The solvent has an enhancing influence on the stabilities of studied clusters. The atoms in molecules theory were also applied to explain the nature of the complexes. The interaction energies have been partitioned with the natural energy decomposition analysis showing that the most important attractive term corresponds to the charge transfer one.
J. Phys. Chem. A, 117, 183−191 (2013)
I. Alkorta, G. Sanchez-Sanz, J. Elguero, J. E. Del Bene
Exploring (NH2F)2, H2FP:NFH2, and (PH2F)2 Potential Surfaces:Hydrogen Bonds or Pnicogen Bonds?
An ab initio MP2/aug'-cc-pVTZ study has been carried out to identify local minima on the (NH2F)2, H2FP:NFH2, and (PH2F)2 potential surfaces, to characterize the types of interactions which stabilize the complexes found at these minima, and to evaluate their binding energies. With one exception, (NH2F)2 complexes are stabilized by N–H···N or N–H···F hydrogen bonds. Only one complex, that with the smallest binding energy, has a pnicogen N···N bond. In contrast, (PH2F)2 complexes are stabilized by P···P or P···F pnicogen bonds or by an antiparallel alignment of the dipole moment vectors of the two monomers, but not by hydrogen bonds. The most stable complex has an F–P···P–F alignment which approaches linearity. Both hydrogen-bonded and pnicogen-bonded complexes exist on the H2FP:NFH2surface, with the most stable being the pnicogen-bonded complex with F–P···N–F approaching a linear arrangement. Charge transfer transitions from a lone pair on a P, N, or F atom in one molecule to an antibonding σ* orbital of the other stabilize these complexes. These transitions are most important for complexes with pnicogen bonds. Although net charge transfer occurs in complexes in which the two monomers are inequivalent, charges on N and P do not correlate with N and P absolute chemical shieldings. Rather, these shieldings also reflect charge distributions and overall bonding patterns. EOM-CCSD two-bond spin–spin coupling constants 2hJ(X–Y) across X–H···Y hydrogen bonds tend to be small, due in part to the nonlinearity of many of the hydrogen bonds. 1pJ values across a particular kind of pnicogen bond are relatively large and vary significantly but do not correlate with corresponding distances.
I. Mata, I. Alkorta, E. Molins, E. Espinosa
DOI:10.1016/j.cplett.2012.10.073
Tracing environment effects that influence the stability of anion–anion complexes: The case of phosphate–phosphate interactions
The effect of the environment on the stability of the (H3PO4), (H2PO4-) and (HPO42-)2 hydrogen bonded dimers has been explored by the topological analyses of the theoretical electron density and the electrostatic potential. The environment has little effect on the hydrogen-bonding interaction, while it induces a significant one on the Coulombic component of the dimer. The interaction energy is represented in terms of hydrogen-bond and non-hydrogen-bond contributions, being only the latter affected by the charge or the environment. While the non-hydrogen bond contribution dominates the interaction energy in the gas phase, it becomes balanced in a polarizable environment.
J. Phys. Org. Chem., 25, 1286-1292 (2012)
L. M. Azofra, I. Alkorta, J. Elguero
A theoretical study of hemiacetal formation from the reaction of methanol with derivatives of CX3CHO (X = H, F, Cl, Br and I)
A theoretical study of the hemiacetal formation reaction between methanol and CX3CHO (X = H, F, Cl, Br, and I) has been carried out using density functional theory and Becke, three-parameter, Lee–Yang–Parr/6-311++G(d,p) computational methods. The stationary points of the reaction between the isolated molecules and the reaction catalyzed by an additional methanol molecule have been characterized. Because the final products present a stereogenic center, the potential autocatalysis of the reaction has been examined and also the possibility of spontaneous generation of chirality when the hemiacetal molecules are involved in the transition state structure. High barriers are found in the reaction between the isolated molecules that are reduced by the assistance of an additional molecule (methanol or hemiacetal product). The reactions catalyzed by the hemiacetal products show higher barriers than the one catalyzed by methanol.
Comput. Theor. Chem. 998, 98-105 (2012)
P. F. Provasi, M. C. Caputo, S. P.A. Sauer, I. Alkorta, J. Elguero
DOI:10.1016/j.comptc.2012.07.002
Analysis of the interactions between difluoroacetylene and one or two hydrogen fluoride molecules based on calculated spin–spin coupling constants
A theoretical study of FCCF:(HF)n complexes, with n = 1 and 2, has been carried out by means of ab initio computational methods. Two types of complexes are formed: those with FH⋯π interactions and those with FH⋯FC hydrogen bonds. The indirect spin–spin coupling constants have been calculated at the CCSD/aug-cc-pVTZ-J computational level. Special attention has been paid to the dependence of the different intramolecular coupling constants in FCCF on the distance between the coupled nuclei and the presence or absence of the hydrogen fluoride molecule. The sensitivity shown by these coupling constants to the presence of hydrogen fluoride is quite notorious.
J. Phys. Chem. A, 116, 3056-3060 (2012)
J. E. Del Bene, I. Alkorta, G. Sánchez-Sanz, J. Elguero
DOI: 10.1021/jp300763d
Structures, Binding Energies, and Spin-Spin Coupling Constants of Geometric Isomers of Pnicogen Homodimers (PHFX)2, X = F, Cl, CN, CH3, NC
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to determine the structures and binding energies of homodimers (PHFX)2 for X = F, Cl, CN, CH3, and NC. Geometric isomers of these complexes with Ci symmetry exist, which are differentiated in terms of the nature of the atoms (F–P···P–F, H–P···P–H, or A–P···P–A, with A being the atom of X directly bonded to P), which approach a nearly linear alignment. Of these, isomers having F–P···P–F linear are the most stable. Binding energies, intermolecular distances, and EOM-CCSD spin–spin coupling constants are sensitive to both the nature of X and the atoms that assume the linear alignment.
Electrostatics at the Origin of the Stability of Phosphate-Phosphate Complexes Locked by Hydrogen Bonds
Ab initio calculations reveal that hydrogen bonds can lock phosphates into stable gas-phase complexes, showing that hydrogen bonding can overcome anion–anion repulsion. These complexes present a large energetic barrier of dissociation (see picture). The stability of the complexes can be explained in terms of the electrostatic interaction in the hydrogen-bond region.
I. Alkorta, G. Sánchez-Sanz, J. Elguero, J.E. Del Bene
FCl:PCX Complexes: Old and New Types of Halogen Bonds
MP2/aug′-cc-pVTZ calculations have been performed to investigate the halogen-bonded complexes FCl:PCX, for X = NC, CN, F, H, CCH, CCF, CH3, Li, and Na. Although stable complexes with a F–Cl···P halogen bond exist that form through the lone pair at P (configuration I), except for FCl:PCCN, the more stable complexes are those in which FCl interacts with the C≡P triple bond through a perturbed π system (configuration II). In complexes I, the nature of the halogen bond changes from traditional to chlorine-shared and the interaction energies increase, as the electron-donating ability of X increases. The anionic complex FCl:PC– has a chlorine-transferred halogen bond. SAPT analyses indicate that configuration I complexes with traditional halogen bonds are stabilized primarily by the dispersion interaction. The electrostatic interaction is the most important for configuration I complexes with chlorine-shared halogen bonds and for configuration II complexes except for FCl:PCNa for which the induction term is most important. The F–Cl stretching frequency is red-shifted upon complexation. EOM-CCSD/(qzp,qz2p) spin–spin coupling constants have been obtained for all FCl:PCX complexes with configuration I. 1J(F–Cl) decreases upon complexation. 2XJ(F–P) values are quadratically dependent upon the F–P distance and are very sensitive to halogen-bond type. 1XJ(Cl–P) tends to increase as the Cl–P distance decreases but then decreases dramatically in the chlorine-transferred complex FCl:PC– as the Cl–P interaction approaches that of a covalent Cl–P bond. Values of 1J(F–Cl) for configuration II are reduced relative to configuration I, reflecting the longer F–Cl distances in II compared to those of the neutral complexes of I. Although the F–P and Cl–P distances in configuration II complexes are shorter than these distances in the corresponding configuration I complexes,2XJ(F–P) and 1XJ(Cl–P) values are significantly reduced, indicating that coupling through the perturbed C–P π bond is less efficient. The nature of F–P coupling for configuration II is also significantly different, as evidenced by the relative importance of PSO, FC, and SD components.
ChemPhysChem, 13, 496-503 (2012)
Intermolecular Weak Interactions in HTeXH Dimers (X=O, S, Se, Te): Hydrogen Bonds, Chalcogen-Chalcogen Contacts and Chiral Discrimination
A theoretical study of the HTeXH (X=O, S, Se and Te) monomers and homodimers was carried out by means of second-order Møller-Plesset perturbation theory (MP2) computational methods. In the case of monomers, the isomerization energy from HTeXH to H2Te=X and H2X=Te (X=O, S, Se, and Te) and the rotational transition-state barriers were obtained. Due to the chiral nature of these compounds, homo and heterochiral dimers were found. The electron density of the complexes was characterized with the atoms-in-molecules (AIM) methodology, finding a large variety of interactions. The charge transfer within the dimers was analyzed by means of natural bond orbitals (NBO). The density functional theory-symmetry adapted perturbation theory (DFT-SAPT) method was used to compute the components of the interaction energies. Hydrogen bonds and chalcogen–chalcogen interactions were characterized and their influence analyzed concerning the stability and chiral discrimination of the dimers.
Struct.Chem. 23, 873-877 (2012)
I. Alkorta, G. Sanchez-Sanz, C. Trujillo, L. M. Azofra, J. Elguero
A theoretical reappraisal of the cyclol hypothesis
Theoretical calculations at the B3LYP/6-31G(d) level have been carried out on the isomerization of cyclic-tri-glycine into the corresponding tri-cyclol. The results confirmed that the cyclol hypothesis was untenable both from a thermodynamic as well as from a kinetic point of view.
M. Solimannejad, M. Gharabaghi, I. Alkorta, G. Sanchez-Sanz
A theoretical study of 1:1 and 1:2 complexes of acetylene with nitrosyl hydride
Ab initio calculations at MP2 computational level using aug-cc-pVTZ basis set were used to analyze the interactions between 1:1 and 1:2 complexes of acetylene and nitrosyl hydride. The structures obtained have been analyzed with the atoms in molecules and the density functional theory–symmetry adapted perturbation theory methodologies. Four minima were located on the potential energy surface of the 1:1 complex. Twenty-four different structures have been obtained for the 1:2 complexes. Five types of interactions are observed, CH···O, CH···N, NH···π hydrogen bonds and orthogonal interactions between the π clouds of triple bond, or the lone pair of oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of the 1:1 and 1:2 clusters including basis set superposition error and ZPE are in the range 3–8 and 6–17 kJ mol−1 at MP2/aug-cc-pVTZ computational level, respectively. Blue shift of NH bond upon complex formation in the ranges between 18–30 and 20–96 cm−1 is predicted for 1:1 and 1:2 clusters, respectively. The total nonadditive energy in the 1:2 cluster, calculated as the sum of the supermolecular nonadditive MP2 energy and the three-body dispersion energy, presents values between −1.48 and 1.20 kJ mol−1.
Homo- and heterochiral dimers (PHFX)2, X = Cl, CN, CH3, NC: To what extent do they differ?
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to determine if intermolecular P–P distances, Z–P–P angles, binding energies, 31P chemical shieldings, or EOM–CCSD spin–spin coupling constants can differentiate between corresponding C2 (homochiral) and Ci (heterochiral) dimers (PHFX)2, X = Cl, CN, CH3, NC. With one exception, Ci isomers have shorter P–P distances than corresponding C2 isomers. Neither binding energies, Z–P–P angles, chemical shieldings, nor spin–spin coupling constants 1pJ(P–P) exhibit patterns which distinguish between corresponding C2 and Ci isomers. 1pJ(P–P) values correlate linearly with P–P distances, so that experimental values of 1pJ(P–P) could be used to extract intermolecular P–P distances.
M. Solimannejad, V. Ramezani, C. Trujillo, I. Alkorta, G. Sanchez-Sanz, J. Elguero
DOI: 10.1021/jp300540z
Competition and Interplay between sigma-Hole and pi-Hole Interactions: A Computational Study of 1:1 and 1:2 Complexes of Nitryl Halides (O2NX) with Ammonia
Quantum calculations at the MP2 cc-pVTZ, MP2 aug-cc-pVTZ, and CCSD(T) cc-pVTZ levels have been used to examine 1:1 and 1:2 complexes between O2NX (X = Cl, Br, and I) with NH3. The 1:1 complexes can easily be differentiated using the stretching frequency of the N–X bond. Thus, those complexes with σ-hole interaction show a blue shift of the N–X bond stretching whereas a red shift is observed in the complexes along the π-hole. The SAPT-DFT methodology has been used to gain insight on the source of the interaction energy. In the 1:2 complexes, the cooperative and diminutive energetic effects have been analyzed using the many-body interaction energies. The nature of the interactions has been characterized with the atoms in molecules (AIM) and natural bond orbital (NBO) methodologies. Stabilization energies of 1:1 and 1:2 complexes including the variation of the zero point vibrational energy (ΔZPVE) are in the ranges 7–26 and 14–46 kJ mol–1, respectively.
Comput. Theor. Chem. 991, 124-133 (2012)
Electron density shift description of non-bonding intramolecular interactions
A new methodology is described for the study of the electron density shift in intramolecular interactions. The methodology has been tested in an intermolecular complex and compared to the electron density shift obtained as the difference between the complex and the isolated monomers. The molecular fragmentation procedures and its application to hydrogen bonds, chalcogen–chalcogen interactions, nitrogen–boron interactions, dihydrogen interactions and silicon–nitrogen interactions are described. A careful selection of the fragmentation scheme is necessary in order to describe correctly the electron density shift in the intramolecular interactions. For this reason, different orders of fragmentation have been studied and analyzed pointing out the problems and limitations which are inherent to the methodology. It has been found that this methodology is a new tool which provides a good qualitative description of the electron density shift within the interacting region between two or more contacts, in both inter and intramolecular contacts with a reasonable low computational cost.
Phys.Chem.Chem.Phys. 14, 9880-9889 (2012)
G. Sanchez-Sanz , C. Trujillo , I. Alkorta, J. Elguero
Weak interactions between hypohalous acids and dimethylchalcogens
The complexes formed between dimethylchalcogens X(CH3)2 (X = S, Se, and Te) and hypohalous acids YOH (Y = F, Cl, Br, and I) have been studied at the MP2/aug'-cc-pVTZ computational level, five minima structures being located. Two of them correspond to hydrogen bonds (HB), another two to halogen bonds (XB) with the chalcogen acting as an electron donor, the last one showing a C–H⋅⋅⋅O contact. The most stable complexes of IOH and BrOH acids present halogen⋅⋅⋅chalcogen interactions with interaction energies, Ei, up to −49 kJ mol−1. In the case of the ClOH and FOH molecules, the hydrogen bonded complexes are more stable with interaction energies between −27 and −34 kJ mol−1. Linear correlations between the molecular electrostatic potential (MEP) stationary points at the van der Waals surface and the interaction energy have been found. The contribution of the different energy terms to the total interaction energy was analyzed by means of the DFT–SAPT theory finding that the electrostatic attractive term is dominant in the complexes with HB and XB, excepting a few cases in which the dispersion and induction terms become more important than the electrostatic one.
J. Chem. Theor. Comput. 8, 2293-2300 (2012)
O. Mo, M. Yanez, I. Alkorta, J. Elguero
DOI: 10.1021/ct300243b
Modulating the Strength of Hydrogen Bonds through Beryllium Bonds
The mutual influence between beryllium bonds and inter- or intramolecular hydrogen bonds (HBs) has been investigated at the B3LYP/6-311++G(3df,2p) level of theory, using the complexes between imidazole dimer and malonaldehyde with BeH2 and BeF2 as suitable model systems. Imidazole and its dimer form very strong beryllium bonds with both BeH2 and BeF2, accompanied by a significant geometry distortion of the Lewis acid. More importantly, we have found a clear cooperativity between these two noncovalent interactions, since the intermolecular HB between the two imidazole molecules in the dimer–BeX2 complex becomes much stronger than in the isolated dimer, whereas the beryllium bond becomes also stronger in the dimer–BeX2 complex, with respect to that found in the imidazole–BeX2 complex. The effects of beryllium bonds are also dramatic on the strength of intramolecular HBs. Depending on to which center the BeX2 is attached, the intramolecular HB becomes much stronger or much weaker. The first situation is found when the beryllium derivative is attached to the HB donor, whereas the second occurs if it is attached to the HB acceptor. The first effect can be so strong as to produce a spontaneous proton transfer, as it is actually the case of the malonaldehyde–BeF2 complex.
DOI: 10.1021/ct300399y
Influence of Hydrogen Bonds on the P...P Pnicogen Bond
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the influence of F–H···F hydrogen bonds on the P···P pnicogen bond in complexes nFH:(PH2F)2 for n = 1–3. The formation of F–H···F hydrogen bonds leads to a shortening of the P–P distance, a lengthening of the P–F distance involved in the hydrogen bond, a strengthening of the P···P interaction, and changes in atomic populations, NMR 31P chemical shieldings, and 1pJ(P–P) coupling constants. The magnitude of these changes depends on the number of FH molecules and their positions in the complex and are relatively modest except for complexes 2FH:(PH2F)2and 3FH:(PH2F)2 that have all FH molecules hydrogen bonded to the same F-atom. For these two complexes, 1pJ(P–P) decreases as the P–P distance decreases and approaches the value of 1J(P–P) for P2H4. The dramatic changes in these two complexes reflect the changing nature of the hydrogen bonds and the pnicogen bond. Thus, the complex 3FH:(PH2F)2 acquires ion-pair character represented as [3(FH)F–:(H2P–PH2F)+], and the P···P pnicogen bond acquires significant covalent character. These changes are observed to a lesser extent in 2FH:(PH2F)2
Compt. Theor. Chem. 994, 81-90 (2012)
Thermodynamic and hydrogen-bond basicity of phosphine oxides: Effect of the ring strain
A theoretical study of acidity and hydrogen bond acceptor properties of tetrahedric phosphine oxide derivatives have been carried out by means of MP2 computational methods. The results obtained for the mentioned complexes have been compared with the analogous ones of trimethylphosphine oxide. The strain decreases the complexation energy with metallic atoms as well as the thermodynamic and hydrogen bond acceptor (HBA) ability of the tetrahedric derivatives.
Chem. Phys. Lett. 538, 5-9 (2012)
Variations in the structures and binding energies of binary complexes with HBO
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of binary complexes formed by HBO with a series of small molecules A. Three different types of structures have been identified, which depend on the nature of A. In one structure A:HBO, HBO acts as a weak proton donor. In the second HBO:A, HBO is a relatively strong base. The third type of complex A||HBO has HBO and A in an approximately parallel arrangement. The dipole moment of A influences both the type of complex formed and its binding energy.
Interplay of F-H...F Hydrogen Bonds and P...N Pnicogen Bonds
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the influence of F–H···F hydrogen bonds on the P···N pnicogen bond in complexes nFH:(H2FP:NFH2) for n = 1–2, and a selected complex with n = 3. The NBO analysis indicates that the N(lp) → P–Fσ* charge-transfer transition has a much greater stabilizing effect than the P(lp) → N–Fσ* transition. When hydrogen bonding occurs at P–F, charge transfer associated with the pnicogen bond and the hydrogen bond are in the same direction but are in opposite directions when hydrogen bonding occurs at N–F. As a result, the formation of F–H···F hydrogen bonds at P–F leads to shorter P···N distances, increased strength of P···N bonds, and synergistic energetic effects; hydrogen bonding at N–F has opposite effects. 31P and 15N chemical shieldings do not correlate with charges on P and N, respectively, but 31P shieldings correlate quadratically with the P–N distance. 1pJ(P–N) coupling constants do not correlate with the intermolecular P–N distance. However, when hydrogen bonding occurs only at P–F, 1pJ(P–N) decreases in absolute value as the P–N distance decreases, thereby approaching 1J(P–N) for H2P–NH2. However, the P···N bond in 3FH:(H2FP:NFH2) has little covalent character, unlike the P···P bond in the corresponding complex 3FH:(PH2F)2.
G. Sanchez-Sanz, I. Alkorta, J. Elguero
Theoretical study of the HXYH dimers (X, Y = O, S, Se). Hydrogen bonding and chalcogen-chalcogen interactions
A theoretical study of the HXYH (X, Y = O, S and Se) monomers and dimers has been carried out by means of MP2 computational methods. For the monomers, isomerization (H2X=Y//HXYH) and rotational transition state barriers have been calculated. Additionally, the molecular electrostatic potential of the isolated monomers has also been analysed. Due to the chiral nature of these compounds, homo and heterochiral dimers have been explored. The number of minima found for the dimers range between 13 and 22. The electron density of the complexes has been characterized with the Atoms in Molecules (AIM) methodology finding a large variety of interactions. The DFT-SAPT method has been used to analyse the components of the interaction energies. Concerning chalcogen–chalcogen interactions, although the most stable minima are formed through hydrogen bonds (especially if OH groups are present in the molecules) as the size of the atoms involved in the interaction increase, the chalcogen–chalcogen contacts become more important.
J. Phys. Chem. A 115 , 13124-13132 (2011)
Simultaneous Interactions of Anions and Cations with Cyclohexane and Adamantane: Aliphatic Cyclic Hydrocarbons as Charge Insulators
With ab initio MP2 computational methods, a theoretical study has been carried out to characterize the interaction between aliphatic cyclic hydrocarbons, as models of molecular hydrocarbon monolayers, with cations (Li+, Na+, and K+), anions (F–, Cl–, and Br–), and both simultaneously in opposite faces of the hydrocarbons. In addition, the energetic barrier for the cation crossing through the hydrocarbon ring has been calculated. The hydrocarbons chosen for this study are cyclohexane (C6H12) and adamantane (C10H16). The energies obtained for the M+:hydrocarbon:X– complexes indicate positive cooperativity in the cases where the hydrocarbon is cyclohexane while diminutive effects are found in the adamantane complexes. The density functional theory–symmetry adapted perturbation theory analysis of the interaction energies shows that the most important term in the complexes with cations is the induction, while in the complexes with anion and with cations and anions simultaneously the most important term is the repulsion-exchange one. The electron density of the complexes has been analyzed using the atoms in molecules methodology and provides some insight to the electron transfer within the complexes.
J. Phys. Chem. A 115, 12677-12687 (2011)
DOI: 10.1021/jp203576j
Ab Initio Study of Ternary Complexes X:(HCNH)+:Z with X, Z = NCH, CNH, FH, ClH, and FCl: Diminutive Cooperative Effects on Structures, Binding Energies, and Spin-Spin Coupling Constants Across Hydrogen Bonds
Ab initio calculations have been performed on a series of complexes in which (HCNH)+ is the proton donor and CNH, NCH, FH, ClH, and FCl (molecules X and Z) are the proton acceptors in binary complexes X:HCNH+ and HCNH+:Z, and ternary complexes X:HCNH+:Z. These complexes are stabilized by C–H+···A and N–H+···A hydrogen bonds, where A is the electron-pair donor atom of molecules X and Z. Binding energies of the ternary complexes are less than the sum of the binding energies of the corresponding binary complexes. In general, as the binding energy of the binary complex increases, the diminutive cooperative effect increases. The structures of these complexes, data from the AIM analyses, and coupling constants 1J(N–H), 1hJ(H–A), and 2hJ(N–A) for the N–H+···A hydrogen bonds, and 1J(C–H), 1hJ(H–A), and2hJ(C–A) for the C–H+···A hydrogen bonds provide convincing evidence of diminutive cooperative effects in these ternary complexes. In particular, the symmetric N···H+···N hydrogen bond in HCNH+:NCH looses proton-shared character in the ternary complexes X:HCNH+:NCH, while the proton-shared character of the C···H+···C hydrogen bond in HNC:HCNH+ decreases in the ternary complexes HNC:HCNH+:Z and eventually becomes a traditional hydrogen bond as the strength of the HCNH+···Z interaction increases.
Structures, Energies, Bonding, and NMR Properties of Pnicogen Complexes H2XP:NXH2 (X=H, CH3, NH2, OH, F, Cl)
Ab initio calculations have been carried out in a systematic investigation of P···N pnicogen complexes H2XP:NXH2 for X ═ H, CH3, NH2, OH, F, and Cl, as well as selected complexes with different substituents X bonded to P and N. Binding energies for complexes H2XP:NXH2 range from 8 to 27 kJ mol–1 and increase to 39 kJ mol–1 for H2FP:N(CH3)H2. Equilibrium structures have a nearly linear A–P–N arrangement, with A being the atom directly bonded to P. Binding energies correlate with intermolecular N–P distances as well as with bonding parameters obtained from AIM and SAPT analyses. Complexation increases 31P chemical shieldings in complexes with binding energies greater than 19 kJ mol–1. One-bond spin–spin coupling constants 1pJ(N–P) across the pnicogen interaction exhibit a quadratic dependence on the N–P distance for complexes H2XP:NXH2, similar to the dependence of 2hJ(X–Y) on the X–Y distance for complexes with X–H···Y hydrogen bonds. However, when the mixed complexes H2XP:NX′H2 are included, the curvature of the trendline changes and the good correlation between 1pJ(N–P) and the N–P distance is lost.
Tuning the Interaction Energy of Hydrogen Bonds: The Effect of the Substituent
The effect of the substituent R in the hydrogen bonding properties of FH···FR (R = H, Al, Li, Cl and CCH) complexes has been studied by theoretical calculations. The dependency of the interaction energy with the hydrogen bond distance and R is explained in terms of the topologies of the electron density and the electrostatic potential. A simple model of the hydrogen bond interaction energy, which can be assimilated to an interaction potential, is defined in terms of a stabilizing mutual polarization of the monomers and an overall destabilizing contribution associated with the electron density reorganization when the overlap of the closed shells is large enough. This model shows an excellent agreement with the ab initio interaction energies and is common for all the analyzed complexes. The substituent effect is represented in the model by a single parameter that can be calculated from the electron distribution in the acceptor atom region. The perturbation in the hydrogen bonding interaction induced by the change of R presents a close similarity with that produced by an external electric field of the same order of magnitude than those found in crystalline solids, indicating that both perturbations should play a significant and similar role on the properties of hydrogen bonds in condensed matter.
31P-31P spin-spin coupling constants for pnicogen homodimers
Ab initio calculations have been carried out in a systematic investigation of pnicogen homodimers (PH2X)2, for X = F, OH, NC, NH2, CCH, CN, CH3, H, and BH2. Complex binding energies range from 7 to 34 kJ mol−1, which is within the range observed for neutral hydrogen-bonded complexes. One-bond spin–spin coupling constants across the pnicogen interaction 1pJ(P–P) exhibit a quadratic dependence on the P–P distance, similar to the dependence of 2hJ(X–Y) on the X–Y distance for complexes with X–H⋯Y hydrogen bonds. Thus, computed values of 1pJ(P–P) could be used to extract P–P distances from experimentally measured coupling constants.
Cooperativity between the hydrogen bonding and halogen bonding in F3CX...NCH(CNH)...NCH(CNH) complexes (X=Cl, Br)
MP2 calculations with the cc-pVTZ basis set were used to analyse the intermolecular interactions in F3CX ··· NCH(CNH) ··· NCH(CNH) triads (X=Cl, Br), which are connected via hydrogen and halogen bonds. Molecular geometries, binding energies, and infrared spectra of the dyads and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention was given to parameters such as the cooperative energies, cooperative dipole moments, and many-body interaction energies. All studied complexes, with the simultaneous presence of a halogen bond and a hydrogen bond, show cooperativity with energy values ranging between −1.32 and −2.88 kJ mol−1. The electronic properties of the complexes were analysed using the Molecular Electrostatic Potential (MEP), electron density shift maps and the parameters derived from the Atoms in Molecules (AIM) methodology.
I. Alkorta, I. Soteras, J. Elguero, J. E. Del Bene
The boron-boron single bond in diborane(4) as a non-classical electron donor for hydrogen bonding
An ab initio study of an isomer of diborane(4) [B2H4] has been carried out at MP2/aug-cc-pVTZ to investigate the ground-state properties of this unusual molecule, a derivative of which has been described in the recent literature. The geometric, electronic and orbital characteristics of B2H4(4)have been analyzed using AIM, NBO, and ELF methodologies. A region with a high concentration of electron density is located near and along the B–B bond, on the opposite side of this bond relative to the bridging H atoms. This site serves as an electron-donor site to electrophiles, resulting in hydrogen-bonded complexes of B2H4 with proton donors HF, HNC,HCl, HCN, and HCCH, and a van der Waals complex with H2. These complexes have C2vsymmetry and stabilization energies that vary from 2 to 27 kJ mol−1. The SAPT2 energydecomposition analysis shows that the relative importance of the various terms that contribute to the interaction energy depends on the strength of the interaction.
An ab initio study of cooperative effects in ternary complexes X:CNH:Z with X, Z=CNH, FH, ClH, FCl, and HLi: structures, binding energies, and spin-spin coupling constants across intermolecular bonds
A systematic ab initio investigation has been carried out to determine the structures, binding energies, and spin–spin coupling constants of ternary complexes X:CNH:Z and corresponding binary complexes X:CNH and CNH:Z, for X, Z = CNH, FH, ClH, FCl, and HLi. The enhanced binding energies of ternary complexes X:CNH:Z for fixed X as a function of Z decrease in the same order as the binding energies of the binary complexes CNH:Z. In contrast, the enhanced binding energies of the ternary complexes for fixed Z as a function of X do not decrease in the same order as the binding energies of the binary complexes X:CNH, a consequence of the increased stabilities of ternary complexes FCl:CNH:Z due to very strong chlorine-sharedhalogen bonds. For complexes in which the X⋅⋅⋅CNH interaction is a D–H⋅⋅⋅C hydrogen bond for D–H the proton–donor group (N–H, F–H, or Cl–H), spin–spin coupling constants 1J(D–H) and 2hJ(D–C) in ternary complexes X:CNH:Z decrease in absolute value as the binding energies of binary complexes CNH:Z and the enhanced binding energies of the ternary complexes for fixed X as a function of Z also decrease. However, 2XJ(F–C) increases as the enhanced binding energies of the ternary complexes FCl:CNH:Z decrease, a consequence of the nature of the chlorine-shared halogen bond. The one-bond coupling constants 1J(N–H) for the CNH⋅⋅⋅Z interaction in ternary complexes vary significantly, depending on the nature of the X⋅⋅⋅CNH interaction. The largest values of 1J(N–H) are found for ternary complexes with FCl as X. Two-bond coupling constants 2hJ(N–A) for A the proton-acceptor atom of Z, and 2dJ(N–H) decrease in absolute value in the order of decreasing enhancement energies of ternary complexes X:CNH:Z for fixed Z as a function of X.
Pure Appl. Chem., 83, 1637-1641 (2011)
E. Arunan, G. R. Desiraju, R. A. Klein, J. Sadlej, S. Scheiner, I. Alkorta, D. C. Clary, R. H. Crabtree, J. J. Dannenberg, P. Hobza, H. G. Kjaergaard, A. C. Legon, B. Mennucci, D. J. Nesbitt
DOI: 10.1351/PAC-REC-10-01-02
Definition of the hydrogen bond
A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This definition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
DOI: 10.1351/PAC-REP-10-01-01
Defining the hydrogen bond: An account (IUPAC Technical Report)
The term "hydrogen bond" has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.
F. Blanco, B. Kelly, I. Alkorta, I. Rozas, J. Elguero
Cation-pi interactions: Complexes of guanidinium and simple aromatic systems
We have theoretically studied, in gas phase and using PCM-water solvation, the complexes established by the biologically relevant guanidinium cation and simple aromatic systems (benzene, naphthalene and pyridine). In gas phase only hydrogen bonded complexes were obtained, whereas using PCM-water different cation–π complexes for the three aromatic systems were found. The interactions established within these complexes have been analyzed by means of the atoms in molecules and natural bond orbital approaches. Finally, experimental evidence of the cation–π interactions created by guanidinium was found in the crystal structure of N-(5-methylpyridin-2-yl)guanidinium chloride, which was also theoretically analyzed.
I. Alkorta, C. Trujillo, J. Elguero, M. Solimannejad
A theoretical study of the hydrogen bonding properties of H2BNH2: Some considerations on the basis set superposition error issue.
The HB complexes formed by H2B═NH2 with five small molecules that can act as hydrogen bond acceptors and donors have been theoretically studied. Three different kinds of complexes have been found to be minima: conventional hydrogen bonds, dihydrogen bonds and those with the π system of H2B═NH2. The geometric, electronic and spectroscopic properties of these complexes have been characterized at the MP2/aug-cc-pVDZ computational level. Special attention has been taken on the Basis Set Superposition Error (BSSE) issue using the full counterpoise (CP) method. The interaction energies have been calculated at MP2/aug-cc-pVXZ (X = D, T, Q, and 5) levels with and without BSSE counterpoise correction. These values have been used to extrapolate to the Complete Basis Set (CBS) energy. The results indicate that for the MP2/aug-cc-pVDZ calculations, the smallest errors in the interaction energy are obtained by correcting the interaction energy with the corresponding half of the BSSE correction. For the remaining cases, the CP corrected interaction energies are closer to the CBS ones than to those without correction.
Int. J. Quant. Chem. 111, 3057-3069 (2011)
M. Solimannejad, S. Massahi, I. Alkorta
DOI: 10.1002/qua.22652
Glyoxal oligomers: A computational study
Ab initio calculations at MP2/6-311++G(2d,2p) computational level was used to analyze interactions between glyoxal (OCHCHO) dimers and trimers in the gas phase. The structures obtained have been analyzed with the atoms in molecules and natural bond orbital methodologies. Eight minima were located on the potential energy surface of the dimers. Eighteen different structures have been obtained for the trimers. CH···O type of interactions is clustering OCHCHO molecules in studied oligomers. Stabilization energies of dimers and trimers including basis set superposition error and ZPE corrections are in the range 4–8 kJ mol−1 and 12–19 kJ mol−1, respectively. Blue shift of CH bond upon complex formation in the ranges between 30–45 and 30–55 cm−1 was predicted for dimers and trimers, respectively.
Chem. Phys. Lett. 508. 6-9 (2011)
Do nitrogen bases form chlorine-shared and ion-pair halogen bonds?
Ab initio calculations have been carried out to investigate the structures, binding energies, and spin–spin coupling constants of complexes with FCl as the Lewis acid and a series of sp, sp2, and sp3 hybridized nitrogen bases. These properties indicate that neutral complexes are stabilized by traditional F–Cl…N halogen bonds, although the chlorine-shared character of the bond is greater with sp2 and sp3 bases. Thus, these complexes are dramatically different from neutral complexes FCl:CNX with sp hybridized carbon bases, which exhibit traditional, chlorine-shared, and ion-pair halogen bonds.
I. Matta, I. Alkorta, E. Espinosa, E. Molins
DOI:10.1016/j.cplett.2011.03.05
Relationships between interaction energy, intermolecular distance and electron density properties in hydrogen bonded complexes under external electric fields
The hydrogen bond interaction energy ðEHBÞ of F H F R (R = H, Li, Al, Cl, CCH) complexes under external electric fields is investigated in terms of the bonding distance and of several properties at the bond critical point. All these properties can be used for the estimation of EHB, being the positive curvature along the hydrogen bond path the most suited for the application to experimental electron densities.
Theor. Chem. Acc. 128, 563-567 (2011)
An ab initio study of the proton transfer and tautomerization processes in hydroxycarbene
We have investigated the hydrogen-bonded complexes formed by hydroxycarbene in trans configuration at MP2 and CCSD computational levels. In addition, these complexes have been used as starting point in the potential tautomerization of hydroxycarbene to produce formaldehyde. The presence of molecules that can be involved in the tautomerization significantly reduces its barrier. The electron density of the different structures obtained has been analyzed with the Atoms in Molecules methodology.
J. Phys. Chem. A 115, 201-210 (2011)
I. Alkorta, J. Elguero, M. Solimannejad, S. J. Grabowski
Dihydrogen Bonding vs Metal-sigma Interaction in Complexes between H2 and Metal Hydride
The complexes formed by hydrogen with metal hydrides (LiH, NaH, BeH2, MgH2, BH3, AlH3, Li2H2, Na2H2, Be2H4, and Mg2H4) have been theoretically studied at the MP2/aug-cc-pVTZ, MP2/aug-cc-pVQZ and CCSD(T)/aug-cc-pVTZ//CCSD/aug-cc-pVTZ levels of theory. The hydrogen molecule can act as a Lewis acid or base. In the first case, a dihydrogen bonded complex is obtained and in the second an interaction between the σ-bond of the hydrogen molecule and an empty orbital of the metal atoms is found. Quantum theory of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Additionally, the cooperativity effects are analyzed for selected complexes with two H2 molecules where both kinds of interactions exist simultaneously.
Phys. Chem. Chem. Phys. 13, 674-683 (2011)
F. Blanco, I. Alkorta, I. Rozas, M. Solimannejad, J. Elguero
A theoretical study of the interactions of NF3 with neutral ambidentate electron donor and acceptor molecules
A theoretical study of the complexes (dimers and trimers) formed between nitrogen trifluoride(NF3) and the ambidentate electron donor/acceptor systems HF, FCl, HCN, and HNC has been carried out using DFT [M05-2x/6-311++G(d,p)] and ab initio methods [(MP2/6-311++G(d,p) and MP2/aug-cc-pVTZ)]. Due to its structure, the NF3 molecule can interact with both electron acceptors and electron donors through its N and F atoms. Thus, five minimum energy structures have been located for the dimers and four minima structures have been studied for the trimer complexes. New σ-hole bonding complexes have been located.
DOI: 10.1021/jp110295n
Do Traditional, Chlorine-shared, and Ion-pair Halogen Bonds Exist? An ab Initio Investigation of FCl:CNX Complexes
Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to determine the structures, binding energies, and bonding of complexes FCl:CNX, with X = CN, NC, NO2, F, CF3, Cl, Br, H, CCF, CCH, CH3, SiH3, Li, and Na. Equation-of-motion coupled cluster calculations have also been carried out to determine the coupling constants 1J(F−Cl), 1XJ(Cl−C), and 2XJ(F−C) across these halogen bonds. As the strength of the base is systematically increased, the nature of the halogen bond changes from traditional, to chlorine-shared, to ion-pair. The type of halogen bond present in a complex can be readily determined from its structure, binding energy, AIM bonding analyses, and spin−spin coupling constants. Coupling constants across halogen bonds are compared with corresponding coupling constants across traditional, proton-shared, and ion-pair hydrogen bonds.
J. Mag. Reson. 206, 274279 (2010)
R. M. Claramunt, M. Perez-Torralba, D. Santa Maria, D. Sanz, B. Elena, I. Alkorta, J. Elguero
DOI: 10.1016/j.jmr.2010.07.015
15N-15N spin-spin coupling constants through intermolecular hydrogen bonds in the solid state
A 2hJNN intermolecular spin–spin coupling constant (SSCC) of 10.2 ± 0.4 Hz has been measured for the powdered tetrachlorogallate salt of pyridinium solvated by pyridine (pyridine–H+⋯pyridine cation 3). Density Functional Theory (DFT) calculations at the B3LYP/6-311++G(d, p) level reproduced this value and two others reported in the literature for 2hJ intermolecular SSCCs, which were measured for complexes in solution.
J. Phys. Org. Chem. 23, 1155-1172 (2010)
F. Blanco, I. Alkorta, I. Rozas, J. Elguero
Chiral recognition in self-complexes of diketopiperazine derivatives
The chiral discrimination in the self-association of 2,5-diketopiperazines derivatives has been studied using density functional theory (DFT) methods. Hence, clusters from dimers to tetramers have been considered. We have found a variety of linear and cyclic structures depending on the geometry of the monomers. In general, the heterochiral dimers (RR:SS or SS:RR) are more stable than the homochiral ones (RR:RR or SS:SS) with slight energetic differences. Nevertheless, most of the larger clusters (trimers and tetramers) show changes in stability, the homochiral cyclic structures being favored due to the better geometry of the hydrogen bond and/or the higher number of interactions. Some interesting correlations between the hydrogen bond geometrical descriptors and theoretical parameters obtained from the Natural Bond Orbital analysis (NBO), Natural energy decomposition analysis (NEDA), and the Atoms in Molecules theory (AIM) have been found. The chiral discrimination in the recognition process of these self-complexes has been evaluated. In addition, evidence of cooperative effects has been observed.
Cooperative and Diminutive Unusual Weak Bonding In F3CX...HMgH...Y and F3CX...Y...HMgH Trimers (X = Cl, Br; Y = HCN, and HNC)
MP2 calculations with cc-pVTZ basis set were used to analyze intermolecular interactions in F3CX···HMgH···Y and F3CX···Y···HMgH triads (X = Cl, Br; Y = HCN, and HNC) which are connecting with three kinds of unusual weak interactions, namely halogen−hydride, dihydrogen, and σ-hole. To understand the properties of the systems better, the corresponding dyads are also studied. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads were investigated at the MP2 cc-pVTZ computational level. Particular attention is given to parameters such as cooperative energies, cooperative dipole moments, and many-body interaction energies. Those complexes with simultaneous presence of a σ-hole bond and a dihydrogen bond show cooperativity energy ranging between −1.02 and −2.31 kJ mol−1, whereas those with a halogen−hydride bond and a dihydrogen bond are diminutive, with this energetic effect between 0.1 and 0.63 kJ mol−1. The electronic properties of the complexes have been analyzed using the molecular electrostatic potential (MEP), the electron density shift maps, and the parameters derived from the atoms in molecules (AIM) methodology.
An ab initio investigation of the properties of H2:HX hydrogen-bonded complexes
Eight complexes H2:HX formed with the σ-bond of the H2 molecule as the proton acceptor and proton donors HCCH, HCCLi, HCCF, HCN, HNC, H2O, HF, and HCl have been optimized at MP2/aug-cc-pVTZ. Analyses of the electron densities indicate that these are weakly-bound hydrogen-bonded complexes, in contrast to H2:HH which is a van der Waals complex. H–H bond stretching frequencies of the H2 molecule, 1H chemical shieldings, and indirect spin–spin coupling constants have been computed in order to identify the most promising spectroscopic tool for characterizing these complexes. The H2 stretching vibration is the property which is most sensitive to complex formation.
DOI:10.1021/jp1003159
Ab Initio Study of Nonadditivity Effects: Spin-Spin Coupling Constants for Tetrafluoroethene in Ternary pi Complexes
C2F4 coupling constants have been evaluated at EOM-CCSD/(qzp,qz2p) in binary complexes with electron donors X (X = HLi, Cl−, CN−) and with the electron acceptor FH, and in ternary complexes FH:C2F4:X in which X and FH are located on opposite faces of the C2F4 π cloud. The electron donors X and the electron acceptor FH have opposite effects on 1J(C−C), 1J(C−F), 2J(C−F), and 3J(F−F) in binary complexes. Effects of X and FH on a particular coupling constant in a ternary complex are additive if the change in the coupling constant in this complex relative to C2F4 is within 1 Hz of the sum of the changes in the corresponding binary complexes. This is the case for 1J(C−F). Both positive and negative nonadditivities are computed for the remaining coupling constants. Although the values of most coupling constants lie between the values for FH:C2F4 and C2F4:X, that is not the case for 2J(C−F), and the effect of FH is enhanced by the presence of X. Moreover, values of 3J(F−F) trans and cis for FH:C2F4:X when X is Cl− or CN− bonded through C are within 1 Hz of the values for the corresponding binary complex C2F4:X. Significant differences can be found between the relative contributions of the PSO, FC, and SD terms to total J and to the nonadditivities of J in ternary complexes FH:C2F4:X.
DOI::10.1139/V09-177
Do corresponding coupling constants in hydrogen-bonded homo- and hetero-chiral dimers differ?
Ab initio equation-of-motion coupled cluster singles and doubles (EOM–CCSD) calculations have been carried out to evaluate spin–spin coupling constants in six pairs of homo- and hetero-chiral dimers: (HOOH)2, (H2NNH2)2, (FOOH)2, (FHNNH2)2, (HOOOH)2, and (FOOOH)2. Corresponding spin–spin coupling constants in these isomeric pairs of C2 and Ci symmetry may differ, but these differences are small and may not be detectable experimentally. For the complexes with O1–H···O and O1–H···F hydrogen bonds, 1J(O1–H) has a larger absolute value in the C2 isomer. For the same set of complexes, 1J(O1–O2) has a larger absolute value in theCi isomer. No distinguishable patterns could be discerned in the remaining spin–spin coupling constants in the C2 and Ci isomers of these complexes, nor in complexes with N–H···N hydrogen bonds.
M. Solimannejad, F. Shahbazi, I. Alkorta
A Computational Study of the Potential Energy Surface of Peroxyformic Acid Dimers
MP2 and M05-2x calculations with aug-cc-pVDZ basis sets were used to analyze intermolecular interactions in peroxyformic acid dimers. A total of 18 and 16 minima were located on the potential energy surface of HOOCHO dimer complexes at M05-2x and MP2 computational levels, respectively. The BSSE corrected interaction energies are in a range between 9 and 34 kJ mol−1 at the MP2/aug-cc-pVDZ computational level. The atoms-in-molecules (AIM) theory was also applied to explain the nature of the complexes. The interaction energies have been partitioned with the natural energy decomposition analysis (NEDA) showing that the most important attractive term corresponds to the charge transfer.
DOI: 10.1021/jp105220w
Ab Initio Study of Ternary Complexes A...NCH...C with A,C ) HCN, HF, HCl, ClF, and LiH: Energetics and Spin-Spin Coupling Constants across Intermolecular Bonds
A systematic ab initio study has been carried out to investigate the structures, binding energies, and spin−spin coupling constants of binary complexes A···NCH and NCH···C and ternary complexes A···NCH···C for A,C = HCN, HF, HCl, FCl, and HLi. These complexes are stabilized by some combination of hydrogen bonds, dihydrogen bonds, halogen bonds, and lithium bonds. The binding energies of the ternary complexes are enhanced relative to those of the corresponding binary complexes, suggesting that A···NCH is a stronger proton-donor acid and NCH···C is a stronger base relative to the isolated monomer HCN. The ternary complexes with the largest enhancement energies are FH···NCH···HLi, HLi···NCH···NCH, and HLi···NCH···HLi, each containing molecules with large dipole moments, and each with a linear head-to-tail arrangement of dipole moment vectors. The equation-of-motion coupled-cluster single and doubles method (EOM-CCSD) has been employed to evaluate spin−spin coupling constants across intermolecular bonds for binary complexes A···NCH and NCH···C and for ternary complexes A···NCH···C. These data are used to investigate how the presence of C influences coupling constants associated with the A···NCH interaction, and how the presence of A influences coupling constants for the NCH···C interaction. Changes in coupling constants in the ternary complexes relative to the binary may be related to the binding energies of corresponding binary complexes and the enhanced binding energies of the ternary complexes. Two-bond coupling constants across X−H···Y hydrogen bonds [2hJ(X−Y)] are related to changes in intermolecular distances.
I. Alkorta, F. Blanco, J. Elguero
Dihydrogen Bond Cooperativity in Aza-borane Derivatives
A theoretical study of the dihydrogen-bonded clusters of three aza-borane derivatives, H−N····B−H, has been carried out using DFT, M05-2X, computational methods. Clusters consisting of up to 10 monomers have been considered. The energetic results show an increment of the average interaction energy per monomer as the size of the cluster increases. Similarly, a shortening of the intermolecular distances up to 0.1 Å is observed. Among the electrostatic properties, an increment of the dipole moment and the absolute values of the molecular electrostatic potential at the interacting point of the cluster are observed. Finally, the orbital interaction responsible for the dihydrogen bond follows the same pattern observed for the bond distances. Thus, it can be concluded that these systems show behavior, with respect to cooperativity, similar to those observed in standard hydrogen bonds.
Theochem, 955, 140-144 (2010)
M. Solimannejada, M. Malekania, I. Alkorta
DOI: 10.1016/j.theochem.2010.06.004
Theoretical study of the halogen-hydride complexes between XeH2 and carbon halogenated derivatives
The halogen-bonded complexes formed between XeH2 with different halogen donor molecules have been studied at the MP2/6-311++G(2d,2p)/def2-TZVPP, MP2/DGDZVP, and B3LYP/DGDZVP computational levels. The complexes formed present stabilities between −4.8 and −24.6 kJ/mol at MP2/6-311++G(2d,2p)/def2-TZVPP level. Red shifts of C–X along with blue shifts of Xe–H vibrational stretching frequencies were predicted. Linear correlations have been found between the total charge transfer due to the complex formation and other parameters as dipole moment enhancement (R2 = 0.98), and electron density at bond critical points (R2 = 0.97).
K. K. Zborowski, I. Alkorta, J. Elguero
A theoretical study of the sulfenate-sulfoxide rearrangement. Effect of the hydrogen bond complexation
A DFT study of the thermal and radical sulfenate–sulfoxide rearrangement of derivatives of 3-propenyl sulfoxide has been carried out. The effect of the substitution and hydrogen bond complexation has been analyzed. The results show that without external factors the radical breakdown path is the one preferred by the alkyl and aromatic derivatives while the unsubstituted system proceeds preferentially through a two-step series of [1,3]- and [2,3]-sigmatropic shifts. The inclusion of a hydrogen bond donor interacting with the oxygen atom increases the stability of all the species except the radical and the final products. Thus, in the dimethyl derivative the radical and two-step processes present similar limiting steps. The analysis of the electron density of the systems provides some relationships between the properties at the bond critical point and the interatomic distances for the S···C and H···O cases.
Theor. Chem. Acc. 126, 1-14 (2010)
I. Alkorta, F. Blanco, P. M. Deya, J. Elguero, C. Estarellas, A. Frontera, D. Quinonero
Cooperativity in multiple unusual weak bonds
This review covers two aspects concerning cooperativity in multiple weak bonds: a summary of literature results and a theoretical study of a complete series of model complexes. All the 15 combination of five weak bonds were explored: hydrogen bonds, hydric bonds, dihydrogen bonds, halogen bonds and ion–π interactions. Since in several cases there were no examples reported, a systematic exploration has been carried out on simple models at the MP2/aug-cc-pVTZ level. The results thus obtained have been analyzed using the atoms in molecules methodology.
Inor. Chim. Acta 363, 1332-1342 (2010)
M. A. Garcia, P. Cabildo, R. M. Claramunt, E. Pinilla, M. R. Torres, I. Alkorta, J. Elguero
DOI:10.1016/j.ica.2009.12.059
The interplay of hydrogen bonds and halogen bonds in the structure of NH-pyrazoles bearing C-aryl and C-halogen substituents
The behavior in solution and in the solid state of 3(5)-phenyl-1H-pyrazole (7), 3(5)-phenyl-4-chloro-1H-pyrazole (6), 3(5)-phenyl-4-bromo-1H-pyrazole (1), and 3(5)-p-chlorophenyl-4-bromo-1H-pyrazole (8) is discussed in relation to their 3-phenyl (a)/5-phenyl (b) annular tautomerism. Two new X-ray structures are reported: a new polymorph of 1 and the structure of 6. The new polymorph is a 3-phenyl-1H-pyrazole 1a′ trimer while the new structure is a 5-phenyl-1H-pyrazole 6b trimer. The combined use of NMR at low temperature and DFT calculations allows to discuss the tautomerism of the first three pyrazoles and to predict that the fourth one should be a tetramer formed by both tautomers, 8a and 8b.
Chem. Eur. J. 16, 2442-2452 (2010).
Universal Features of the Electron Density Distribution in Hydrogen-Bonding Regions: A Comprehensive Study Involving H...X (X=H, C, N, O, F, S, Cl, pi) Interactions
Topological analyses of the theoretically calculated electron densities for a large set of 163 hydrogen-bonded complexes show that H⋅⋅⋅X interactions can be classified in families according to X (X=atom or π orbital). Each family is characterised by a set of intrinsic dependencies between the topological and energetic properties of the electron density at the hydrogen-bond critical point, as well as between each of them and the bonding distance. Comparing different atom-acceptor families, these dependencies are classified as a function of the van der Waals radius rX or the electronegativity χX, which can be explained in terms of the molecular orbitals involved in the interaction. According to this ordering, the increase of χX leads to a larger range of H⋅⋅⋅X distances for which the interaction is of pure closed-shell type. Same dependencies observed for H⋅⋅⋅O interactions experimentally characterised by means of high-resolution X-ray diffraction data show a good agreement with those obtained from theoretical calculations, in spite of a larger dispersion of values around the expected fitting functions in the experimental case. Theoretical dependencies can thus be applied to the analysis of the experimental electron density for detecting either unconventional hydrogen bonds or problems in the modelling of the experimental electron density.
Central Eur. J. Chem. 7, 683-689 (2009)
A theoretical study of the neutral and the double-charged cation of cyclo[8]pyrrole and its interaction with inorganic anions.
A theoretical study of the complexation of cyclo[8]pyrrole dication, 2, and the corresponding system in neutral form, 3, with six anionic molecules has been carried out up to the B3LYP/6–311++G(2d,2p) computational level. The effect of the water solvation has been taken into account by means of the PCM method. The gas phase results correspond to the very large interaction energies expected for the interaction of molecules of opposite charge. In all the complexes, the analysis of the electron density by means of the Atoms In Molecules (AIM) methodology shows the presence of eight intermolecular interactions between the individual molecules. The results, using the water solvent model, indicate that the 2:SO4 2−complex is more stable than the 2:NO3 −, in agreement with experimental results.
Bioorg. Med. Chem. 17, 8027-8031 (2009)
J. Elguero, I. Alkorta, R. M. Claramunt, C. Lopez, D. Sanz, D. Santa Maria
DOI: 10.1016/j.bmc.2009.10.006
Theoretical calculations of a model of NOS indazole inhibitors: Interaction of aromatic compounds with Zn-porphyrins
We report a theoretical approach, at the M05-2x/6-311+G(d) level, to explain the affinity of indazoles for nitric oxide synthases using a simplified model of porphyrin. The theoretical Erel = Ei stacking–Ei apical values correlate with the experimental inhibition percents allowing to predict that 3,7-dinitro-1H-indazole should be a good NOS inhibitor.
Mag. Reson. Chem. 47, 917-924 (2009)
C. Lopez, R. M. Claramunt, E. Pinilla, M. R. Torres, I. Alkorta, J. Elguero
DOI: 10.1002/mrc.2483
Molecular complexes between pi-excedent heterocycles (indoles and carbazole) and pi-deficient polynitrobenzenes
Five charge-transfer complexes 1–5 derived from indoles (including a carbazole) and halogenopolynitrobenzenes (ClDNB, FDNB, ClTNB) as well as their individual components have been studied in the solid state by 13C CPMAS NMR. The stacking effects on the 13C chemical shifts have been rationalized by means of M05-2X functional and GIAO/B3LYP/6-311 ++G(d,p) calculations. The results, although only semiquantitative, are very promising for studying such structures.
Chem. Phys. 362, 1-7 (2009)
M. Solimannejad, S. Massahi, I. Alkortai, I. Alkorta
DOI: 10.1016/j.chemphys.2009.04.006
A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions
Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH⋯N and NH⋯O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4–8 kJ mol−1 and 12–19 kJ mol−1, respectively. Blue shift of NH bond upon complex formation in the ranges between 30–80 and 14,114 cm−1 is predicted for dimers and trimers, respectively.
I. Alkorta, F. Blanco, J. Elguero, J.A. Dobado, s. Melchor Ferrer, I. Vidal
Carbon...Carbon Weak Interactions
A theoretical study of the complexes formed by systems with electron-deficient and electron-excessive carbon atoms was carried out using DFT and ab initio methods up to the CCSD(T)/aug-cc-pVTZ computational level. Stable complexes with interaction energies between −6.0 and −22.8 kJ mol−1 were obtained that correspond to weak C···C interactions. The atoms in molecules analysis of the complexes confirmed the presence of these interactions. Natural energy decomposition analysis and electron localization function analysis were performed to gain further insight into the nature of the interaction. Polarization is the most important stabilizing term in these complexes.
J. Chem. Theory Comput. 5, 1186-1194 (2009)
I. Alkorta, F. Blanco, J. Elguero, C. Estarellas, A. Frontera, D. Quinonero, P. M. Deya
DOI: 10.1021/ct800444e
Simultaneous Interaction of Tetrafluoroethene with Anions and Hydrogen-Bond Donors: A Cooperativity Study
A computational study of the complexes formed by tetrafluoroethylene, C2F4, with anions has been carried out by means of density functional theory (DFT) and second-order Möller−Plesset (MP2) computational methods, up to MP2/aug-cc-pVTZ level. In addition, the possibility of cooperativity in the interaction of anions and hydrogen-bond donors (FH, ClH, and H2O) when interacting with different faces of the C2F4 molecule has been explored. Electron density of the complexes has been analyzed by means of atoms in molecules (AIM) methodology, while natural bond orbital (NBO) methodology has been used to characterize the orbital interaction. In addition, natural energy decomposition analysis (NEDA) has been applied to analyze the source of the interaction. The energetic results indicate that C2F4 is a weaker anion receptor than C6F6, but in combination with the anions, it became a stronger hydrogen acceptor than C2H4. Cooperativity effects are observed in YH·C2F4·X− clusters. In C2F4·X− complexes the dominant attractive terms are the electrostatic and polarization ones, while in YH·C2F4·X− complexes the charge transfer increases significantly, becoming the most important term for most of the FH and ClH complexes studied here.
M. Solimannejad, I. Alkorta, J. Elguero
Stabilities and properties of ozone-nitrosyl hydride (O3-HNO) complexes: A computational study
MP2 and M05-2x calculations with two basis sets, 6-311++G(2d, 2p) and aug-cc-pVTZ, were used to analyze the interaction between nitrosyl hydride (HNO) and ozone. Four minima were located on the potential energy surface of HNO⋯O3complexes at these computational levels. The BSSE corrected interaction energies are in a range between 9 and 14 kJ mol−1at the MP2/aug-cc-pVTZ computational level. The atoms in molecules (AIM) theory was also applied to explain the nature of the complexes. The interaction energies have been partitioned with the Natural Energy Decomposition Analysis (NEDA) showing that the most important attractive term corresponds to the charge transfer one.
F. Blanco, I. Alkorta, M. Solimannejad, J. Elguero
Theoretical Study of the 1:1 Complexes between Carbon Monoxide and Hypohalous Acids
A theoretical study of the complexes formed between carbon monoxide, CO, and the hypohalous acids (HOX, X = F, Cl, Br, and I) has been carried out using DFT [M05-2x/6-311++G(2d,2p)] and ab initio methods [(MP2/6-311++G(2d,2p) and MP2/aug-cc-pVTZ)]. Six minima were found, which correspond to two hydrogen-bonded complexes, two halogen-bonded complexes, and two van der Waals complexes. The hydrogen-bonded complexes with the carbon atom of the CO molecule are the most stable for hypohalous acids with X = F, Cl, and Br, whereas for X = I, the halogen-bonded complex with the same atom of carbon monoxide is the most stable. A blue shift in the stretching frequency of the OH bond in the hydrogen-bonded complexes with the carbon atom of CO was observed. In addition, a blue shift was observed in the bond of the hypohalous acid not involved in the interaction.
C. Estarellas, A. Frontera, D. Quinonero, I. Alkorta, P. M. Deya, J. Elguero
Energetic vs Synergetic Stability: A Theoretical Study
The aim of this manuscript is to define a new concept, namely synergetic stability, which can be useful in systems where the interplay of noncovalent interactions is important. Usually, the stability of a noncovalent complex is related to the complexation energy, which is directly proportional to the strength of the noncovalent interactions that are involved in the complex. In ternary complexes characterized by the presence of two different noncovalent interactions, three situations regarding the variation of the strength of the interactions (in comparison to the binary complexes) can be present. The coexistence of the interactions causes, first a strengthening of both interactions, second, a weakening of both, and, third, a strengthening of one interaction at expenses of the weakening of the other. This study deals with ternary complexes where ion−π and either hydrogen bonding, dihydrogen bonding, or halogen bonding interactions coexist.
Collect. Czech. Chem. Commun., 74, 299-312 (2009)
D. H. O'Donovan, I. Rozas, F. Blanco, I. Alkorta, J. Elguero
DOI:10.1135/cccc2008169
Chiral recognition in bicyclic guanidines
A theoretical study of chiral recognition in bicyclic guanidines has been carried out by means of B3LYP/6-31+G(d,p) DFT calculations. A series of complexes between protonated 4,8-dimethyl-1,5,7-triazabicyclodecene (DTBD) and 2,5-disubtituted chiral cyclopentanones have been evaluated for chiral recognition, both in the gas phase and in benzene solution as per the polarizable continuum model (PCM) and analyzed by AIM and NBO methodologies. An inversion in the sense of chiral recognition has been observed between gas phase and solvated results for cyclopentanone complexes. Among the different correlations found (i.e. between electron density, hydrogen bond distance, second-order perturbation energy), a linear correlation has been established between thechiral recognition energy and different molecular parameters.
Struct. Chem. 20, 63-71 (2009)
A computational study of the cooperativity in clusters of interhalogen derivatives
The clusters, up to four monomers, of the interhalogen derivatives (FCl, FBr, and ClBr) have been studied by means of ab initio and DFT methods, up to MP2/aug-cc-pVTZ computational methods. Two dispositions, linear and cyclic, of the clusters have been studied. Cooperative effects in the geometry, energy, and electron density have been observed in the linear and cyclic dispositions of these clusters. The Natural Energy Decomposition Analysis shows that the main source of the interaction corresponds to the polarization term.
Mag. Res. Chem. 47, 249-256 (2009)
DOI:10.1002/mrc.2382
A theoretical structural analysis of the factors that affect 1JNH, 1hJNH and 2hJNN in N-H...N hydrogen-bonded complexes
Calculations of 1JNH, 1hJNH and 2hJNN spin–spin coupling constants of 27 complexes presenting N–H·N hydrogen bonds have allowed to analyze these through hydrogen-bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, − 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states 'proton-in-the-middle' is considerable.
I.Mata, E. Molins, I. Alkorta, E. Espinosa
Effect of an external electric field on the dissociation energy and the electron density properties: The case of the hydrogen bonded dimer HF...HF
The effect of a homogeneous external electric field parallel to the hydrogen bond in theFH⋯FH dimer has been studied by theoretical methods. The quantum theory of atoms in molecules methodology has been used for analyzing the electron distribution of the dimer, calculated with different hydrogen bond distances and external field magnitudes. It is shown that an electric field in the opposite direction to the dipole moment of the system strengthens the interaction due to a larger mutual polarization between both molecules and increases the covalent character of the hydrogen bond, while an external field in the opposite direction has the inverse effect. The properties of the complex at its equilibrium geometry with applied field have been calculated, showing that dependencies between hydrogen bond distance, dissociation energy, and properties derived from the topological analysis of the electron distribution are analogous to those observed in families ofXDH⋯AY complexes. The application of an external field appears as a useful tool for studying the effect of the atomic environment on the hydrogen bond interaction. In the case of FH⋯FH, both the kinetic energy density and the curvature of the electron density along the hydrogen bond at the bond critical point present a surprisingly good linear dependence on the dissociation energy. The interaction energy can be modeled by the sum of two exponential terms that depend on both the hydrogen bond distance and the applied electric field. Moreover, as indicated by the resulting interaction energy observed upon application of different external fields, the equilibrium distance varies linearly with the external field, and the dependence of the dissociation energy on either the hydrogen bond distance or the external electric field is demonstrated to be exponential.
Top Heterocycl Chem 19, 155-202 (2009)
DOI:10.1007/7081_2008_1
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How Aromaticity Affects the Chemical and Physicochemical Properties of Heterocycles: A Computational Approach
Our publications dealing with problems related to aromatic heterocycles are discussed with the appropriate references from the literature. The three main topics are theoretical calculations, tautomerism, and NMR spectroscopy but other aspects are also discussed, such as crystal structures, proton transfer, hydrogen bonds, IR, etc.
I. Rozas, I. Alkorta, J. Elguero
Hydrogen bonds and ionic interactions in Guanidine/Guanidinium complexes: a computational case study
It is frequently said that hydrogen bonds (HBs) are enhanced by ionic interactions and in this article we intend to determine the degree at which this reinforcement happens. Considering our interest in the Guanidine(neutral)/Guanidinium(cation) system and its particular nature, all the possible 1:1 complexes with the Chloride(anion)/Hydrochloric acid(neutral) system have been studied at different levels of computation (B3LYP with 6-31+G* and TZVP basis sets; MP2 with 6-31+G*, 6-311++G** and aug-cc-pVDZ basis sets; CBS-QB3 and G3MP2). The nature of these interactions established in all the systems and, when possible, at all the levels of computation used in this study, has been analyzed using Atoms in Molecules and Natural Bond Orbital methodologies. By examining the interaction energy, the electron density at the bond critical bonds, the atomic energy, the charge transfer, the orbital energy, and the deformation energy we can conclude that HBs are stronger when the ionic interaction is stronger. Thus, both interactions do not work in an independent manner but one reinforces the other to different degrees depending on the nature of the charges present. Several correlations with the interaction energy have been found and a partition of the contributions of both the HB and ionic forces to the total interactions is proposed.
J. Phys. Chem. A, 112, 10856-10863 (2008)
I. Alkorta, F. Blanco, M. Solimannejad, J. Elguero
DOI: 10.1021/jp806101t
Competition of Hydrogen Bonds and Halogen Bonds in Complexes of Hypohalous Acids with Nitrogenated Bases
A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH3, N2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH···N hydrogen bond and the other one with a X···N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.
Theor. Chem. Acc. 121, 181-186 (2008).
F. Blanco, M. Solimannejad, I. Alkorta, J. Elguero
Inverse hydrogen bonds between XeH2 and hydride and fluoride derivatives of Li, Be, Na and Mg
A theoretical study of the inverse hydrogen bonds complexes formed by the XeH2 molecule and hydride and fluoride derivatives of Li, Be, Na and Mg has been carried out by means of DFT (B3LYP/DGDZVP) and ab initio [MP2/DGDZVP and MP2/LJ18/6-311++G(2d,2p)] calculations. The complexes obtained present interaction energies up to −81 kJ/mol. The analysis of the electron density shows electron transfer from the XeH2 to the electron acceptor molecules. The calculated absolute chemical shieldings show the high sensitivity of the xenon atom upon complexation.
Dihydrogen bond cooperativity in (HCCBeH)n clusters
A theoretical study has been carried out on the clusters formed by the association of ethynylhydroberyllium (HC ≡ CBeH) monomers. The monomer presents a linear disposition with a dipole moment of 0.94 D. Clusters from two to six monomers have been calculated for three different configurations (linear, cyclic with dihydrogen bonds, and cyclic with hydrogen bonds to the π-cloud), the third one being the most stable. The electronic properties of the clusters have been analyzed by means of the atoms in molecules and natural bond orbitals methodologies. Cooperative effects, similar to the ones described for standard hydrogen bonded clusters, are observed in those configurations where dihydrogen bonds are the main interacting force.
Spin-Spin Coupling across Intermolecular F-Cl...N Halogen Bonds
Ab initio EOM-CCSD calculations have been performed to determine one- and two-bond spin−spin coupling constants 1J(F−Cl), 1XJ(Cl−N), and 2XJ(F−N) across F−Cl···N halogen bonds in complexes with F−Cl as the Lewis acid and N2, FCN, HCN, (CH3)CN, LiCN, Z-HNNH, H2CNH, NH2F, NH3, cyclic-NH(CH2)2, and NH2(CH3) as Lewis bases. The structures of these complexes were optimized at MP2 with the aug′-cc-pVTZ basis set. The absolute value of 2XJ(F−N) increases in these complexes as the F−N distance decreases, a behavior similar to that of2hJ(F−N) for complexes stabilized by F−H···N hydrogen bonds. 1XJ(Cl−N) also tends to increase in absolute value with decreasing F−N distance. 1J(F−Cl) is always positive, decreases upon complex formation as the F−Cl distance increases, and appears to be sensitive to the hybridization of the nitrogen base. The relatively large differences in the values of these coupling constants in the various complexes and their variation along the chlorine-transfer coordinate for F−Cl···NH3 suggest that they should be amenable to experimental investigation.
J. Phys. Chem. A 112, 6753-6759 (2008).
I. Alkorta, F.Blanco, J.Elguero
pi-Systems as Simultaneous Hydride and Hydrogen Bond Acceptors
A theoretical study of the hydride bond complexes with tetrafluoro- and tetracyanoethylene, C2F4 and C2(CN)4, has been carried out by means of density functional theory (DFT) and ab initio methods, up to the MP2/aug-cc-pVTZ computational level. In addition, the ternary complexes formed by an additional standard hydrogen bond donor, such as hydrogen fluoride, have been explored. The results show that the hydride bond complexes are stable and an electron transfer took place from the hydride to the C2F4 and C2(CN)4 molecules. While these molecules are not able to form stable complexes between the π-electrons and hydrogen bond donors, the presence of the hydrides in the opposite face of the π-system of C2F4 stabilizes the ternary complexes showing cooperativity effects.
D. Quinonero, A. Frontera, P. M. Deya, I. Alkorta, J. Elguero
Interaction of positively and negatively charged aromatic hydrocarbons with benzene and triphenylene: Towards a model of pure organic insulators
A theoretical study of the complexes formed by two aromatic charged hydrocarbons, cyclopropenyl cation and phenalenyl anion, with benzene and triphenylene has been carried out. The binary complexes between the charged molecules and the neutral ones have been characterized as well as the ternary systems with the neutral systems acting as insulators of the charged ones. In the ternary complex a cooperative effect is observed both in the energy and in the geometry. In general, the interaction with ions reduces the aromaticity of the insulators.
J. Phys. Chem. A, 112, 6338-6343 (2008).
Ab Initio EOM-CCSD Spin-Spin Coupling Constants for Hydrogen-Bonded Formamide Complexes: Bridging Complexes with NH3, (NH3)2, H2O, (H2O)2, FH, and (FH)2
EOM-CCSD spin−spin coupling constants across hydrogen bonds have been computed for complexes in which NH3, H2O, and FH molecules and their hydrogen-bonded dimers form bridging complexes in the amide region of formamide. The formamide one-bond N−H coupling constant [1J(N−H)] across N−H···X hydrogen bonds increases in absolute value upon complexation. The signs of the one-bond coupling constants 1hJ(H−X) indicate that these complexes are stabilized by traditional hydrogen bonds. The two-bond coupling constants for hydrogen bonds with N−H as the donor [2hJ(N−X)] and the carbonyl oxygen as the acceptor [2hJ(X−O)] increase in absolute value in the formamide/dimer relative to the corresponding formamide/monomer complex as the hydrogen bonds acquire increased proton-shared character. The largest changes in coupling constants are found for complexes of formamide with FH and (FH)2, suggesting that bridging FH monomers and dimers in particular could be useful NMR spectroscopic probes of amide hydrogen bonding.
Magn. Reson. Chem.; 46, 457-463 (2008).
Spin-spin coupling across intramolecular N...H+...N hydrogen bonds in models for proton sponges: an ab initio investigation
Ab initio calculations have been performed to obtain structures and coupling constants 1J(N H), 1hJ(H N), and 2hJ(N N) for models of proton sponges with symmetric and asymmetric N H+ N intramolecular hydrogen bonds (IMHBs). For a given model, the asymmetric structure has a lower energy, a longer N N distance, and a hydrogen bond which has a greater deviation from linearity. The computed values of 2hJ(N N) for the models are significantly less than predicted values based on the distance dependence of 2hJ(N N) for complexes with intermolecular N H+ N hydrogen bonds. However, the reduced values of 2hJ(N N) cannot be attributed solely to the distortion of the hydrogen bond in the models, but also reflect differences in s electron populations at the nitrogens in both the ground state and the excited states which couple to it through the Fermi-contact (FC) operator. Values of 2hJ(N N) for IMHBs can be related quadratically to the N N distances in the models, and demonstrate that there is no discrepancy between computed values of2hJ(N N) at the short N N distances found in these systems and experimental data for proton sponges.
How To Determine Whether Intramolecular H...H Interactions Can Be Classified as Dihydrogen Bonds
Different types of intramolecular H···H interactions have been analyzed using the MP2/6-311++G(d,p) level of approximation. These are C−H··· H−B, C−H···H−Al, C−H···H−C, C−H···H−O, O−H···H−Al and O−H···H−B contacts. Quantum theory of atoms in molecules and natural bond orbitals methods were applied to better understand the nature of these interactions. It was found that some of the species analyzed possess the characteristics of typical hydrogen bonds, such as the O−H···O ones. The electron charge transfer from the Lewis base to the antibonding X−H (for example O−H) orbital of the Lewis acid is one such characteristic. The NBO method may be considered decisive to classify any system as dihydrogen bonded.
A computational study of dimers and trimers of hypohalous acids
Ab initio calculations [MP2/6-311++G(2d,2p] were used to analyze the interactions between hypohalous acids (HOX) dimers and trimers, for X equal to F, Cl, and Br. Two minima for X = F and three minima for X = Cl and Br were located on the potential energy surface of the dimers. Eight different structures have been obtained for the trimers, six of them cyclic and two open structures. The six cyclic minima for X = F present similar interaction energies, while for X = Cl and Br, those with three O–H···O interactions are the most stable ones.
J. Phys. Chem. A 112, 1817 -1822 (2008).
Molecular Complexes of Pentazolo[1,2-a]pentazole, N8
A theoretical study of the complexes formed by pentazolo[1,2-a]pentazole, N8, with neutral electron donors, hydrogen-bond donors, and anions has been carried out at the B3LYP and MP2 computational levels. In addition, the clusters formed by two, three, and four molecules of N8 have been studied. The results show that, in general, the interaction of the central N−N bond is preferred over the formation of a HB complex with neutral molecules. A comparison of the energetic results for the N8 complexes obtained in the present article with those for analogous complexes of C6F6 demonstrates that the N8 complexes exhibit a stronger interaction with both neutral and anionic systems. Small cooperative effects are observed in the calculated clusters of N8.
Stabilities and properties of O3-HOCl complexes: A computational study
MP2/6-311++G(2d,2p) and MP2/aug-cc-pVTZ calculations are used to analyze the interaction between hypochlorous acid (HOCl) and ozone. Six and five minima are located on the potential energy surface of HOCl⋯O3 complexes at MP2/6-311++G(2d,2p) and MP2/aug-cc-pVTZ computational levels, respectively. The more strongly bound contains OH⋯O along with O⋯Cl bond. The rest of the minima present in addition to the OH⋯O hydrogen bond, O⋯O and O⋯Cl interactions. Binding energies of the complexes corrected with BSSE lies in the range of 6–12 and 9–16 kJ mol−1 at MP2/6-311++G(2d,2p) and MP2/aug-cc-pVTZ levels, respectively. The atom in molecules (AIM) theory was also applied to explain the nature of the complexes.
J. Mol. Struct., 846, 97-107 (2007)
S. Goswami, S. Dey, J. F. Gallagher, A. J. Lough, S. García-Granda, L. Torre-Fernández, I. Alkorta, J. Elguero
Tailor-made naphthyridines: Self-assembling multiple hydrogen-bonded supramolecular architectures from dimer to helix
Stepwise changes of functional oxo and amino groups in 1,8-naphthyridines to modify the supramolecular architecture have been carried out. The first example of a naphthyridine helix has been found and its structure established by X-ray crystallography. The design is based on hydroxy and amido tautomeric naphthyridines which crystallize in dimers or catemers, one of them attaining helicity. The most stable tautomer present in all the compounds discussed in this paper, as well as the formation of hydrogen-bonded dimers or catemers, was established by X-ray crystallography and rationalized with theoretical calculations.
Theochem 819, 136-141 (2007).
A comparative ab initio study of SF6...X- and CF4...X- complexes (X= H,F, Cl, CN, NC, N3 and NCO)
Ab initio calculations at MP2/6-311++G(d, p) and MP2/aug-cc-pVTZ levels are used to analyze the interaction between SF6 and CF4 neutral molecules and anions, X− (X = H, F, Cl, CN, NC, N3, NCO) in gas phase. Minimum with C3v symmetry are located on the potential energy surface of complexes with binding energies in the range of 10–23 kJ/mol. The energetic and geometric characteristics of the complexes obtained in both series have been compared. The Atoms In Molecules methodology has been used to analyze the electron density and to obtain atomic contributions to the total energy and charge of the systems.
J. Phys. Chem. A, 111, 9924 -9930 (2007)
HCP and H3C-CP as Proton Acceptors in Protonated Complexes Containing Two Phosphorus Bases: Structures, Binding Energies, and Spin-Spin Coupling Constants
Ab initio calculations at the MP2/aug'-cc-pVTZ level have been carried out to investigate the structures and binding energies of cationic complexes involving protonated sp, sp2, and sp3phosphorus bases as proton donor ions and the sp-hybridized phosphorus bases H−C≡P and H3C−C≡P as proton acceptors. These proton-bound complexes exhibit a variety of structural motifs, but all are stabilized by interactions that occur through the π cloud of the acceptor base. The binding energies of these complexes range from 6 to 15 kcal/mol. Corresponding complexes with H3C−C≡P as the proton acceptor are more stable than those with H−C≡P as the acceptor, a reflection of the greater basicity of H3C−C≡P. In most complexes with sp2- or sp3-hybridized P−H donor ions, the P−H bond lengthens and the P−H stretching frequency is red-shifted relative to the corresponding monomers. Complex formation also leads to a lengthening of the C≡P bond and a red shift of the C≡P stretching vibration. The two-bond coupling constants 2πhJ(P−P) and 2πhJ(P−C) are significantly smaller than 2hJ(P−P) and 2hJ(P−C) for complexes in which hydrogen bonding occurs through lone pairs of electrons on P or C. This reflects the absence of significant s electron density in the hydrogen-bonding regions of these π complexes.
M. Solimannejad, I. Alkorta
Ab initio study of complexes pairing HRgX and H2 (Rg = Ar, Kr and X = F, Cl, CN)
MP2/aug-cc-pVTZ calculations are used to analyze the interaction between hydrogen molecule and rare gas containing compounds HRgX (Rg = Ar, Kr and X = F, Cl, CN). One T-shape C2v minima are located on the potential energy surface of each complex. Binding energies of the complexes corrected with BSSE are in the range of 1.3–2.9 kJ/mol at the MP2/aug-cc-pVTZ computational level, being the H2⋯HArF the most strongly bound and H2⋯HKrCN the least. Blue shift of H–Rg stretching frequencies within each subunit caused by complexation is predicted in the range of 30–200 cm−1. The atoms in molecules (AIM) theory was applied in order to analyze the physical nature of the stabilization of these complexes.
I. Alkorta, M. Solimannejad, P. Provasi, J. Elguero
DOI: 10.1021/jp073112m
Theoretical study of complexes and fluoride cation transfer between N2F+ and electron donors
A theoretical study of the complexes formed by the N2F cation (fluorodiazonium ion) and a series of small molecules containing nitrogen atoms have been carried out at the MP2 computational level. In addition, fluorine transfer has been studied. The electron density, NMR shielding and indirect coupling constants of the complexes have been evaluated. The covalent or halogen bonding characteristics of the N···F interactions observed in the complexes are defined by the interatomic distance. It has been determined that the limiting value is 1.6 Å.
Topological properties of the electrostatic potential in weak and moderate N...H hydrogen bonds
The topological analyses of the electrostatic potential φ(r) and the electron density distribution ρ(r) have been performed for a set of 20 neutral complexes with weak and moderate N···H bonds. In all cases, a zero flux surface of the electrostatic potential containing a saddle point analogous to the bond critical point of the electron density distribution is observed. These surfaces define an equivalent of the atomic basin of ρ(r) for the electrostatic potential, which exhibits zero net charge and can be regarded as an electrostatically isolated region if its volume is finite. The φ(r) and ρ(r) zero flux surfaces divide the hydrogen-bonding region in three parts, being the central one related to the electrostatic interaction between donor and acceptor. This central region exhibits a relative size of 13−14% of the N···H distance dNH, it belongs to the outermost shell of the nitrogen and is mainly associated with its lone pair. Topological properties of both ρ(r) and φ(r), as well as the electron kinetic (G) and potential (V) energy densities, show similar dependences with dNH at both bond critical points (φ-BCP and ρ-BCP). Phenomenological proportionalities between the ρ(r) curvatures and G and V are also found at the electrostatic potential critical point. The curvatures of the electrostatic potential, which are interpreted in terms of the electrostatic forces in the bonding region, present the same exponential dependency as the electron density distribution, to which they are related by Poisson's equation.
Probing P-H+-P Hydrogen Bonds: Structures, Binding Energies, and Spin-Spin Coupling Constants
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of 22 open and 3 cyclic complexes formed from the sp2 [H2C=PH and HP=PH (cis and trans)] and sp3 [PH2(CH3) and PH3] hybridized phosphorus bases and their corresponding protonated ions. EOM-CCSD calculations have been carried out to obtain 31P−31P and 31P−1H coupling constants across P−H+−P hydrogen bonds. Two equilibrium structures with essentially linear hydrogen bonds have been found along the proton-transfer coordinate, except for complexes with P(CH3)H3+ as the proton donor to the sp2 bases. Although the isomer having the conjugate acid of the stronger base as the proton donor lies lower on the potential energy surface, it has a smaller binding energy relative to the corresponding isolated monomers than the isomer with the conjugate acid of the weaker base as the donor. The hydrogen bond of the latter has increased proton-shared character. All of the complexes are stabilized by traditional hydrogen bonds, as indicated by positive values of the reduced coupling constants 2hKP-P and 1KP-H, and negative values of 1hKH-P. 2hJP-Pcorrelates with the P−P distance, a correlation determined primarily by the nature of the proton donor. For open complexes, 1JP-H always increases relative to the isolated monomer, while1hJH-P is relatively small and negative. 2hJP-P values are quite large in open complexes, but are much smaller in cyclic complexes in which the P−H+−P hydrogen bonds are nonlinear. Thus, experimental measurements of 2hJP-P should be able to differentiate between open and cyclic complexes.
I. Alkorta, D. Quiñonero, C. Garau, A. Frontera, J. Elguero, P. M. Deyà
Dual Cation and Anion Acceptor Molecules. The Case of the (C6H6)(C6F6)Cr(0) Complex
In this manuscript we report high-level ab initio (RI-MP2(full)/6-31++G**) and DFT (B3LYP/ 6-31++G** and MPWB1K/6-31++G**) calculations on complexes between the bis(arene)chromium complex (η6-C6H6)(η6C6F6)Cr(0) (1) and cations/anions. This interesting molecule 1, which is synthetically available, exhibits a dual binding mode to anions and cations, with interaction energies similar to those previously reported for benzene with cations and hexafluorobenzene with anions. In addition, the simultaneous interaction with cations and anions is also studied.
I. Alkorta, J. Elguero, K. Zborowski
Chiral Recognition in Diaziridine Clusters and the Problem of Racemization Waves
Theoretical calculations (B3LYP/6-31+G**) of chiral clusters of diaziridines have been carried out. Five configurations of chiral and nonchiral clusters with up to eight monomers have been considered. The proton transfer within the neutral and protonated clusters has been studied as a possible source of racemization waves. The optical rotatory power (ORP) has been calculated for the neutral and protonated homochiral clusters. The results show that the clusters with alternated chiral molecules are the preferred ones and that the proton transfer proceeds with low energetic barriers in the protonated systems. The ORP results are very dependent on the shape of the clusters and the neutral or protonated state of them.
M. Solimannejad, I. Alkorta, J.Elguero
Weakly Bound Complexes of N2O: An ab Initio Theoretical Analysis Toward the Design of N2O Receptors
Ab initio calculations at MP2/6-311++G(2d,2p) and MP2/6-311++G(3df,3pd) computational levels have been used to analyze the interactions between nitrous oxide and a series of small and large molecules that act simultaneously as hydrogen bond donors and electron donors. The basis set superposition error (BSSE) and zero point energy (ZPE) corrected binding energies of small N2O complexes (H2O, NH3, HOOH, HOO, HONH2, HCO2H, H2CO, HCONH2, H2CNH, HC(NH)NH2, SH2, H2CS, HCSOH, HCSNH2) vary between -0.93 and -2.90 kcal/mol at MP2/6-311++G(3df,3pd) level, and for eight large complexes of N2O they vary between -2.98 and -3.37 kcal/mol at the MP2/6-311++G(2d,2p) level. The most strongly bound among small N2O complexes (HCSNH2-N2O) contains a NHââN bond, along with S f N interactions, and the most unstable (H2S-N2O) contains just S f N interactions. The electron density properties have been analyzed within the atoms in molecules (AIM) methodology. Results of the present study open a window into the nature of the interactions between N2O with other molecular moieties and open the possibility to design N2O abiotic receptors.
Competition between Nonclassical Hydrogen-Bonded Acceptor Sites in Complexes of Neutral AH2 Radicals (A ) B, Al, and Ga): A Theoretical Investigation
An ab initio computational study of the properties of the neutral AH2 radicals (A = B, Al, Ga) as hydrogen-bond (HB) acceptors, with H−X (X = F, Cl, Br, CN, and CCH) as HB donors, is carried out at the UMP2/6-311++G(2d,2p) level. Two different minima have been found for each of the 15 possible dimers. One structure corresponds to a single-electron hydrogen-bonded complex (SEHB), with the A atom acting as an HB acceptor. The second corresponds to a dihydrogen bond complex between one of the hydrogen atoms of AH2 and the H−X molecule. Thus, all the atoms of the neutral AH2 molecule can act as HB acceptors and none as donors. The stability of the SEHB complexes decreases as BH2 > AlH2 > GaH2, while for the dihydrogen-bonded complexes the order is AlH2 > GaH2 > BH2. For the BH2 radical the SEHB complexes are stronger than the dihydrogen bonded ones, while the opposite is found for the AlH2 and GaH2systems. Regarding the HB donors, the order found for the binding energy in the two types of complexes is H2A···HF > H2A···HCl > H2A···HBr > H2A···HCN > H2A···HCCH.
J. Phys. Chem. A; 110, 10279-10286 (2006)
I. Alkorta, K. Zborowski, J. Elguero, M. Solimannejad
Theoretical Study of Dihydrogen Bonds between (XH)2, X = Li, Na, BeH, and MgH, and Weak Hydrogen Bond Donors (HCN, HNC, and HCCH)
The dihydrogen-bonded (DHB) complexes formed by (XH)2, with X = Li, Na, BeH, and MgH, with one, two, and four protonic molecules (HCN, HNC, and HCCH) have been studied. These complexes have been compared to those of the XH monomers with the same hydrogen bond donor molecules. The energetic results have been rationalized based on the electrostatic potential of the isolated hydridic systems. The electron density properties have been analyzed within the AIM methodology, both at the bond critical points and the integrated values at the atomic basins. Exponential relationships between several properties calculated at the bond critical points (ρ, 2ρ, λi, G, and V) and variation of integrated properties (energy, charge, and volume) vs the DHB distance have been obtained.
I. Alkorta, K. Zborowski, J. Elguero
Self-aggregation as a source of chiral discrimination
A theoretical study of the hydrogen peroxide clusters, (HOOH)n, from 2 to 10 monomers, has been carried out using DFT/B3LYP and MP2 ab initio methods. The results show that for n = 2 and 3, the cluster with mixed chirality is preferred while for larger clusters, the homochiral cluster is favoured. The Optical Rotatory Power and Vibrational Circular Dichroism spectra of some of the systems have been calculated and analyzed.
Org. Biomol. Chem. 4, 3096-3101 (2006)
DOI: 10.1039/b607871k
Theoretical models of directional proton molecular transport
The important topic of proton transport through molecular wires is usually associated with the Grotthuss mechanism. In this paper we propose an alternative conductor based on chains of lone pairs. B3LYP/6–31+G** and PW91 DFT calculations on model compounds (1,2,3,4-tetrasubstituted benzenes) show that these compounds could play the role of proton conductors.
K. Zborowski, I. Alkorta, J. Elguero
DOI:10.1021/jp060791c
Effect of Dimerization and Racemization Processes on the Electron Density and the Optical Rotatory Power of Hydrogen Peroxide Derivatives
The variation of the electron density properties and optical rotatory power of the monomers and dimers of seven monosubstituted hydrogen peroxide derivatives, HOOX (X = CCH, CH3, CF3, t-Bu, CN, F, Cl), upon racemization has been studied using DFT (B3LYP/6-31+G**) and MP2 (MP2/6-311+G**) methods. The geometrical results have been rationalized on the basis of natural bond orbital (NBO) analysis. The atomic partition of the electron density properties within the atoms in molecules (AIM) methodology has allowed investigating the energy and charge redistribution in the different structures considered. The calculated optical rotatory power (ORP) of the dimers are, in general, twice of the values obtained for the monomers.
Chem. Phys. 324, 459-464 (2006)
DOI:10.1016/j.chemphys.2005.11.007
Theoretical study of dihydrogen bonds in HnMH...HArF and HnMH...HKrF complexes (n = 1-3; M = Be, Al, Ga, Si, Ge)
An ab initio computational study of the properties of 10 dihydrogen-bonded complexes of HnMH (M = Be, Al, Ga, Si, Ge) with the rare gas derivatives HArF and HKrF has been carried out at the MP2(full)/6-311++G(2d,2p) level of theory. Red shifts of H–Rg and Rg–F along with blue shifts of M–H vibrational stretching frequency were predicted. Variations of the 1H chemical shielding of the HRgF molecules versus the H⋯H distance of the complexes were also studied.
Chem. Phys. Lett., 422, 226-229 (2006)
M. Solimannejad, L. Mohammadi Amlashi, I. Alkorta, J. Elguero
XeH2 as a proton-accepting molecule for dihydrogen bonded systems: A theoretical study
Ab initio and density functional studies of the properties of 11 linear dihydrogen-bonded complexes pairing XeH2 with different proton donor molecules was undertaken at the MP2/6-311++G(2d,2p)/LJ18, MP2/DGDZVP, and B3LYP/DGDZVP computational levels. Red shifts of H–X along with blue shifts of Xe–H vibrational stretching frequencies were predicted. A linear correlation was established between interaction energies versus dipole moment enhancements of neutral complexes (R2 = 0.99). It is shown that there are linear correlations between absolute chemical shielding of 129Xe and 1H versus the charge on these atoms in XeH2 studied complexes (R2 = 0.99 and 0.96, respectively).
J. Phys. Chem. A 110, 2259 - 2268 (2006)
DOI:10.1021/jp056886g
Chiral Recognition in Self-complexes of Tetrahydroimidazo[4,5-d]imidazole Derivatives: From Dimers to Heptamers
The chiral discrimination in the self-association of chiral 1,3a,4,6a-tetrahydroimidazo[4,5-d]imidazoles has been studied using density functional theory methods. Clusters from dimers to heptamers have been considered. The heterochiral dimers (RR:SS orSS:RR) are more stable than the homochiral ones (RR:RR or SS:SS) with energy differences up to 17.5 kJ/mol. Besides, in larger clusters the presence of two adjacent homochiral molecules impose an energetic penalty when compared to alternated chiral systems (RR:SS:RR:SS...). The differences in interaction energy within the dimers of the different derivatives have been analyzed based on the atomic energy partition carried out within the atoms in molecules framework. The mechanism of proton transfer in the homo- and heterochiral dimers shows large transition-state barriers except in those cases in which a third additional molecule is involved in the transfer. The optical rotatory power of several clusters of the parent compound have been calculated and rationalized based on the number of homochiral interactions and the number of monomers of each enantiomer within the complexes.
New. J. Chem., 29, 1450-1453 (2005)
I. Alkorta, C. Cativiela, J. Elguero, A. M. Gil, A. I. Jiménez
DOI: 10.1039/b509368f
A theoretical study of the influence of nitrogen angular constraints on the properties of amides: rotation/inversion barriers and hydrogen bond accepting abilities of N-formylaziridine and -azirine
Theoretical calculations at the MP2/6-311++G** level have been carried out on three compounds: N,N-dimethylformamide (1), N-formylaziridine (2) and N-formylazirine (3). The barriers to rotation and inversion have been calculated, together with the properties of the nitrogen and oxygen atoms of these amides as hydrogen bond acceptors. The results provide a quantitative picture of the influence of ring strain on the properties of amides, with special emphasis on the effects associated with nitrogen pyramidalization.
J. Phys. Chem. B, 109, 18189-18194 (2005)
M. Sanchez, P. F. Provasi, G. A. Aucar, I. Alkorta, J. Elguero
Theoretical Study of HCN and HNC Neutral and Charged Clusters
A theoretical study of linear and cyclic clusters of (HCN)n and (HNC)n (up to n = 10) has been carried out by means of DFT and MP2 ab initio methods. The transition states linking the cyclic clusters show high energetic barriers that prevent the spontaneous transformation of the high-energy clusters, (HNC)n, into the low-energy ones, (HCN)n. The effect of the protonation/deprotonation of the linear clusters has also been explored. The results show that (HNC)n clusters with n values larger than six are thermodynamically more stable as charged systems than as neutral ones. The geometrical results have been analyzed using a Steiner−Limbach plot. The electron density and its Laplacian at the bond critical points correlate with the corresponding bond distances by means of two exponential functions, one for the open shell and another for the closed shell cases.
I. Alkorta, J. Elguero, O. Mó, M. Yáñez, J. E. Del Bene
Are RAHBs "resonance assisted"? A theoretical NMR study
The concept of resonance-assisted hydrogen bonds (RAHBs) is one of the most frequently used concepts in structural chemistry. Computed equation-of-motion coupled cluster singles and doubles (EOM–CCSD) O–O and N–N coupling constants through intramolecular X–H–X hydrogen bonds (2hJX–X) and MP2 1H chemical shifts of the X–H–X protons have been used to investigate RAHBs in model saturated and unsaturated systems. The computed results suggest that the NMR properties of these molecules do not receive significant contributions from resonance, but are a consequence of the σ-skeleton framework.
P. F. Provasi, G. A. Aucar, M. Sanchez, I. Alkorta, J. Elguero, S. P.A. Sauer
Interaction Energies and NMR Indirect Nuclear Spin-Spin Coupling Constants in Linear HCN and HNC Complexes
The cooperativity effects on both the electronic energy and NMR indirect nuclear spin−spin coupling constants J of the linear complexes (HCN)n and (HNC)n (n = 1−6) are discussed. The geometries of the complexes were optimized at the MP2 level by using the cc-pVTZ basis sets. The spin−spin coupling constants were calculated at the level of the second-order polarization propagator approximation with use of the local dense basis set scheme based on the cc-pVTZ-J basis sets. We find strong correlations in the patterns of different properties such as interaction energy, hydrogen bond distances, and spin−spin coupling constants for both series of compounds. The intramolecular spin−spin couplings are with two exceptions dominated by the Fermi contact (FC) mechanism, while the FC term is the only nonvanishing contribution for the intermolecular couplings. The latter do not follow the Dirac vector model and are important only between nearest neighbors.
E. Espinosa, I. Alkorta, I. Mata, E. Molins
Topological Analysis of the Electron Density Distribution in Perturbed Systems. I. The Effect of Charge on the Bond Properties of Hydrogen Fluoride
Within the framework of the molecular orbital (MO) theory, the addition of one electron to the 4σ antibonding orbital of the neutral (F···H) system or the removal of one electron from its π nonbonding orbitals, leading to (F···H)- and to (F···H)+, has permitted the investigation of these charge perturbations on the bond properties of the hydrogen fluoride molecule by using the topological analysis of ρ(r). For (F···H), (F···H)-, and (F···H)+, the topological and energetic properties calculated at the F···H bond critical point (BCP) have been related to the 3σ bonding molecular orbital (BMO) distribution, as this orbital is the main contributor to ρ(r) at the interatomic surface. The analysis has been carried out at several F···H internuclear distances, ranging from 0.8 to 3.0 Å. As far as the BMO distribution results from its interaction with the average Coulomb and exchange potential generated by the charge filling the other MOs, and in particular by the π and 4σ electrons, the comparison between the BCP properties calculated for the charged systems and those corresponding to the neutral one permits the interpretation of the differences in terms of the charge perturbation on BMO. Along with the BCP properties of (F···H), (F···H)-, and (F···H)+, the interaction energy magnitudes of these systems have been also calculated within the same range of internuclear distances, indicating that the applied perturbations do not break the F−H bond but soften it, giving rise to the stable species (F−H)- and (F−H)+. Comparing the three systems at their equilibrium geometries, the most stable configuration, which corresponds to the unperturbed (F···H) system, shows the highest quantity and the most locally concentrated charge density distribution, along with the largest total electron energy density magnitude, at the interatomic surface as a consequence of the BMO contraction toward the fluorine nucleus in (F···H)+ and of the BMO expansion toward both nuclei in (F···H)-. On the other hand, if the comparison is carried out at the equilibrium distance of (F···H) (deq0), this one exhibits both the smallest total energy density magnitude and the largest quantity of bonding charge at the interatomic surface. Hence, being the signature of the most stable configuration, the characteristic magnitudes of the neutral system ρ(deq0), 2ρ(deq0), and H(deq0) appear as boundary conditions at the interatomic surface of its unperturbed and relaxed electron distribution.
O. Picazo, I. Alkorta, J. Elguero
Dimers of 1,8a-dihydro-1,8-naphthyridine derivatives as models of chiral self-recognition
A theoretical study of the dimer formation of chiral 1,8a-dihydro-1,8-naphthyridine derivatives has been carried out by means of DFT calculations. In the cases treated, the heterochiral dimers (RS orSR) are always more stable than the homochiral ones (RR or SS). Two possible proton transfer processes have been studied, the concerted and the non-concerted ones. The non-concerted TS corresponds to a true TS while the concerted one presents two imaginary frequencies. The geometrical characteristics of the hydrogen bonds in all the structures calculated have been correlated using the Steiner–Limbach model.
K. Zborowski, L. M. Proniewicz, I. Alkorta, J. Elguero
Effect of HB complexation on the optical rotatory power of oxiranes
The effect produced by the formation of hydrogen bonded complexes on the optical rotatory power of two oxiranes has been studied theoretically using DFT and MP2 methods. The results obtained have been rationalized based on a model oxirane where the chirality is induced by the HB formed. In addition, the effect of solvent continuum models has been calculated for the complexes.
O. Picazo , I. Alkorta , J. Elguero, Otilia Mó , Manuel Yáñez
DOI: 10.1002/poc.901
Chiral recognition in phosphinic acid dimers
A theoretical study of chiral recognition in the minimum and proton transfer transition state structures of 15 pairs of chiral phosphinic acid dimers was carried out using DFT and MP2 methods, up to the MP2/6–311++G(3df,2p) level. The proton transfer proceeds via a concerted pathway in all cases studied. Even though these complexes show high interaction energies, of the order of 120 kJ mol−1, and short interatomic HB distances, our results show small energy differences between the homochiral (RR or SS) and the heterochiral dimers (RSor SR) both in the equilibrium configuration and in the proton transfer transition state owing to the disposition of the nonoxygen substituents of the phosphorus atom as proved with additional model complexes.
Chem. Phys. Lett. 412, 97-100 (2005)
A theoretical investigation of N–H⋯O═P hydrogen bonds through15N–31P and 1H–31P coupling constants
The Fermi contact terms corresponding to 3hJNP and 2hJHP for complexes involving N–H⋯O–P hydrogen bonds have been calculated at the EOM-CCSD level of theory. The N–H donors in these complexes are urea or two hydrogen isocyanide molecules, and the proton acceptor is . Experimentally measurable3hJNP values are predicted only for linear or nearly linear N–H⋯O═P hydrogen bonds. Computed 2hJHPvalues appear to be too small to detect the presence of these hydrogen bonds.
ChemPhysChem, 6, 1411-1418 (2005)
O. Mo, M. Yanez, J. E. Del Bene, I. Alkorta, J. Elguero
Cooperativity and Proton Transfer in Hydrogen-Bonded Triads
Ab initio MP2/6-311+G(3df,2pd) and MP2/aug-cc-pVTZ calculations have been carried out to investigate the structures and properties of AH⋅XH⋅YH3 (A=F, Cl; X=F, Cl; Y=N, P) hydrogen-bonded complexes. Significant cooperative effects are observed in the XH⋅YH3 dyads in the triads due to the presence of the polar near-neighbor AH. These effects are greater when the polar partner is HF, which is a better proton donor than HCl. Structural changes, red shifts of proton-donor stretching frequencies, nonadditive interaction energies, and electron density redistributions unambiguously demonstrate that the X-H⋅⋅⋅Y hydrogen bond (HB) is stronger in the triads than in the corresponding dyads, while the X-H bond of the proton donor becomes weaker. Even more pronounced cooperative effects are observed in the AH⋅XH dyads due to the presence of the YH3 partner. These effects are weaker in complexes having PH3 rather than NH3as the proton acceptor, since NH3 is a stronger base. Cooperativity also enhances the proton-donating ability of the YH3 moiety, with the result that all complexes except FH⋅FH⋅PH3 are cyclic. Cooperativity, together with the ease of breaking the Cl-H bond in ClH⋅ClH⋅NH3and FH⋅ClH⋅NH3, leads to proton transfer (PT), so that these two complexes are better described as approaching hydrogen-bonded ClHCl−⋅+HNH3 and FHCl−⋅+HNH3 ion pairs.
I. Alkorta, O. Picazo, J. Elguero
Chiral Recognition in Cyclic alpha-Hydroxy Carbonyl Compounds: A Theoretical Study
A theoretical study (DFT and MP2) of the self-association of homochiral (RR or SS) and heterochiral (RS or SR) dimers of three series of cyclic α-hydroxy-carbonyl derivatives has been carried out. The solvation effect on the parent derivative dimers has been explored, showing nonsignificant changes in the configurations preferred but altering in some cases the homo/heterochiral preference of the dimers. The results in the gas phase of the systems with different substituents show a preference for the heterochiral dimers. The energetic results have been analyzed with the NBO and AIM methodologies. Optical rotatory power calculations of the monomers and homochiral dimers show large variations of this parameter depending on the substituents and the complexation.
J. E. Del Bene, J. Elguero, I. Alkorta, O. Mo, M. Yañez
Ab Initio Study of the Influence of Trimer Formation on One- and Two-Bond Spin-Spin Coupling Constants Across an X-H-Y Hydrogen Bond: AH:XH:YH3 Complexes for A, X = 19F, 35Cl and Y = 15N,31P
Ab initio equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) calculations have been carried out to investigate the effect of a third polar near-neighbor on one-bond (1JX-H and 1hJH-Y) and two-bond (2hJX-Y) spin−spin coupling constants in AH:XH:YH3complexes, where A and X are 19F and 35Cl and Y is either 15N or 31P. The changes in both one- and two-bond spin−spin coupling constants upon trimer formation indicate that the presence of a third molecule promotes proton transfer across the X−H−Y hydrogen bond. The proton-shared character of the X−H−Y hydrogen bond increases in the order XH:YH3 < ClH:XH:YH3 < FH:XH:YH3. This order is also the order of decreasing shielding of the hydrogen-bonded proton and decreasing X−Y distance, and is consistent with the greater hydrogen-bonding ability of HF compared to HCl as the third molecule. For all complexes, the reduced X−H and X−Y spin−spin coupling constants (1KX-H and 2hKX-Y) are positive, consistent with previous studies of complexes in which X and Y are second-period elements in hydrogen-bonded dimers. 1hKH-Y is, as expected, negative in these complexes which have traditional hydrogen bonds, except for ClH:FH:NH3 and FH:FH:NH3. In these two complexes, the F−H−N hydrogen bond has sufficient proton-shared character to induce a change of sign in 1hKH-Y. The effects of trimer formation on spin−spin coupling constants are markedly greater in complexes in which NH3 rather than PH3 is the proton acceptor.
Tet. Asym. 16, 755-760 (2005)
DOI: 10.1016/j.tetasy.2005.01.022
Effect of fluoro substituents and central atom nature on chiral derivatives of bisdiphenylborates and isoelectronic structures
A DFT study of the geometrical, electronic, and energetic parameters of homo- and heterochiral complexes of fluoro derivatives of diphenylborate and isoelectronic structures where the central atom has been substituted by carbon and nitrogen has been carried out. The results have allowed correlation of the relative energies (hetero- minus homochiral complex) versus the presence of fluorine in the different positions on the aromatic rings and the presence of different central atoms. Other correlations between geometrical parameters and the relative energy have also been found. Some of the predictions have been confirmed with the calculation of new derivatives.
Org. Biomol. Chem., 3 , 366-371 (2005)
Modelling protein-RNA interactions: an electron density study of the guanidinium and formate complexes with RNA bases
The complexes formed by the double interaction established between RNA bases and guanidinium and formate ions, as a model for the interacting groups of arginine and glutamic or aspartic amino acid side chains, have been theoretically studied. A density functional theory method (B3LYP/6-31 + G**) has been used for this study. The range of interaction energies obtained allowed for a distinction between bidentate and bifurcate hydrogen bond interactions. The analysis of the electron density and the natural bond orbital analysis shows that these complexes are bound by double hydrogen bonds established between the donor and acceptor groups of guanidinium and formate respectively and those of the RNA bases. Comparisons are made with the results obtained in some previous theoretical and experimental studies.
Theochem 680, 191-198 (2004)
Theoretical study of peptide model dimers. Homo versus heterochiral complexes
The study of possible chiral recognition of a series of peptide models (For-Gly-NH2, For-Ala-NH2 and four of their fluoro substituted derivatives) has been carried out by means of DFT calculations. Homo (L,L) and heterochiral (L,D) dimers formed by hydrogen bond (HB) complexation have been considered. Initially, the conformational preferences of the monomers have been calculated and used to generate all the possible homo and heterochiral dimers. The energetic results show that in most cases, the β monomers are the most stable while in the dimers, the γ–γ complexes show the strongest interaction energies. In three of the four chiral cases studied, a heterochiral dimer is the most stable one. In addition, the electron density and nuclear shielding of the complexes have been studied.
New J. Chem., 700-707 (2004)
C.Alvarez-Rua , S. García-Granda , S. Goswami , R. Mukherjee , S. Dey , R. M. Claramunt , M. D. Santa María , I. Rozas , N. Jagerovic , I. Alkorta and J. Elguero
DOI: 10.1039/b315692c
Multiple hydrogen bonds and tautomerism in naphthyridine derivatives
The behaviour of three 2,7-disubstituted 1,8-naphthyridines able to exhibit tautomerism has been studied by NMR in solution and in two cases in the solid state. The three derivatives studied are 2,7-dihydroxy- (1), 2-acetamido-7-amino- (3) and 2,7-diacetamido-1,8-naphthyridine (4). To explore the problem of secondary interactions, a series of complexes, with up to four simultaneous hydrogen bonds, where the monomers are generated using pyridine and 4-pyridone as building blocks, have been theoretically studied. The calculated interaction energies have been correlated with the number of hydrogen bonds and with attractive and repulsive secondary interactions. Further analysis of the electron density and orbital interactions shows that the secondary interactions, both attractive and repulsive, have a purely electrostatic origin. The X-ray structure of compounds 3 and 4 have been determined. In the solid state these compounds exist in the "diamino" tautomers with the N–H proton of the amido groups pointing towards the naphthyridine nitrogen. DFT and GIAO calculations have been essential to disentangle the problem of the structure of these compounds.
J. Phys. Chem. B 108, 3335-3341 (2004)
Modelling Protein-RNA interactions: An electron density study of the formamide and formic acid complexes with RNA Bases
The complexes formed by the double interaction established between the four RNA bases (adenine, cytosine, guanidine, and uracil) and formamide and formic acid as a model for the interacting groups of certain amino acid side chains have been theoretically studied. Density functional theory (B3LYP/6-31+G**) methods have been used for this study. The interaction energies obtained range between 10 and 19 kcal mol-1. The analysis of the electron density and the natural bond orbital analysis show that these complexes are bound by medium strength double hydrogen bonds established between the donor and acceptor groups of formamide and formic acid and those of the RNA bases. Comparisons are made with the results obtained in some experimental studies and the analysis of protein−RNA interactions databases.
Theor. Chem. Acc. 111, 31-35 (2004)
Karplus-type relationships betweeen scalar coupling constants: 3JHH molecular vs. 4hJHH supramolecular coupling constants
The 3 J HH coupling constants in six H–X–Y–H systems (ethane, methylamine, methanol, hydrazine, hydroxylamine and hydrogen peroxide) and 4h J HH coupling constants in four H–...XH...Y–H, namely [H3NHNH3]+ (two arrangements), HOHNH3 and HOHOH2 have been calculated theoretically as a function of the torsion angle φ. For covalent situations, the corresponding Karplus equations have been fitted to calculated 3 J HH=acos2 φ+bcos φ+c. The a, b and c terms have been analyzed as a function of the electronegativities of X and Y. In the case of ammonium/ammonia complexes (proton shared and not), water/ammonia, and water dimer the values are low (maximum 0.5 Hz) but follow closely a Karplus relationship.
Tet. Asym. 15, 1391-1399 (2004)
Chiral discrimination and isomerization processes in monomers, dimers and trimers of sulfoxides and thioperoxides
The chiral discrimination in cyclic dimers and trimers of mono-substituted sulfoxides and thioperoxides has been studied by means of DFT (B3LYP/6-31+G**) and ab initio (MP2/6-311+G**) calculations. In addition, the inter- and intramolecular proton transfer processes that interconvert these two classes of compounds have been considered for the isolated molecules and clusters. The thioperoxide clusters are more stable than the corresponding sulfoxides even though the strongest hydrogen bonds are found in the latter complexes. Correlations have been found between the relative energies of the sulfoxide versus the thioperoxide compounds and the transition state barriers. The geometry of the hydrogen bonds has been analyzed using a Steiner–Limbach relationship.
J. Chem. Phys. 120, 3237-3243 (2004)
J.E. Bene, J. Elguero, I. Alkorta, M. Yañez, O. Mo
19F–19F spin–spin coupling constant surfaces for (HF)2 clusters: The orientation and distance dependence of the sign and magnitude of JF–F
Ab initio calculations using the equation-of-motion coupled cluster method have been carried out to investigate 19F–19F spin–spin coupling constants for a pair of HF molecules. The overall features of the JF–F coupling surface with respect to the F–F distance and the orientation of the pair of HF molecules reflect those of the Fermi-contact (FC) surface, although the FC term may not be a good quantitative estimate of JF–F. The hydrogen-bonded HF dimer exhibits unusual behavior compared to other hydrogen-bonded complexes, since both the FC term and 2hJF–F exhibit variations in sign and magnitude as the F–F distance changes and the linearity of the hydrogen bond is destroyed. The FC term for F–F coupling is relative small and negative for the equilibrium dimer. At the dimer F–F distance, the maximum negative value for the FC term is found for the linear arrangement F–H⋯H–F, while the maximum positive value is found for the linear H–F⋯F–H arrangement, despite the fact that neither of these structures is bound. Changes in the sign and magnitude of the FC term are analyzed using the nuclear magnetic resonance triplet wave function model, which relates the orientation of magnetic nuclei to the phases of the wave functions for excited triplet states that couple to the ground state. The FC term for a particular orientation is a result of competing positive and negative contributions from different triplet states, the sign of each contribution being determined by the alignment of the nuclear magnetic moments in that state. Factors are identified which must play a role in determining which types of wave functions dominate.
Aromatic Systems as Charge Insulators: Their Simultaneous Interaction with Anions and Cations.
A theoretical approach, using ab initio MP2(full)/6-31++G** and MP2(full)/6-311++G** levels, has been used to characterize the interaction of the π-cloud of C6F6 with cations (Y+ = Li+, Na+, and K+). In addition, the situation where C6H6 and C6F6 simultaneously interact with an anion (X- = F-, Cl-, and Br-) and a cation in opposite faces of the aromatic ring has been studied. For comparative purposes, other dispositions, such as those of the isolated cations and the anions and the complexes between neutral XY salts and the aromatic systems, have been considered. Complexes where the π-cloud of the aromatic ring interacts with a cation or, simultaneously, with a cation and an anion have been found to be mimima structures. However, these complexes show high relative energies when compared to other minima of the potential hypersurface. The interaction energy has been decomposed into MEP, polarization and charge−charge interaction terms.
Hydrogen bonding properties of krypton derivatives
The effect of the insertion of a krypton atom in the C–H bond of acetylene and hydrogen cyanide in their electronic properties and as hydrogen bond acceptor and donor has been evaluated by means of ab initio calculations, up to MP2/6-311++G(2d,2p) level. The results indicate that the noble gas atom transfer part of its electrons to the rest of the molecule, increasing its ability as HB acceptor and decreasing the HB donor ones.
ARKIVOC (xiv) 31-36 (2003)
http://www.arkat-usa.org/get-file/18817/
Hydrogen bond acceptor properties of two radicals: nitric oxide molecule and hydrogen atom
Two very significant, although for different reasons, radicals NO. and H. have been examined theoretically as hydrogen bond acceptors (HBA). Two acids have been studied as hydrogen bond donors (HBD), hydrogen fluoride and ammonium. Nitrogen oxide should be a nitrogen base towards both neutral and cationic acids as HBD. Atomic hydrogen, although a much weaker hydrogen-bonded base, should form stable complexes with the ammonium cation. A conclusion of this work is that DFT methods only work acceptably well for relatively strong HBs.
J. Org. Chem. 68, 7485-7489 (2003)
DOI: 10.1021/jo035026y
Large Chiral Recognition in Hydrogen-Bonded Complexes and Proton Transfer in Pyrrolo[2,3-b]pyrrole Dimers
The chiral recognition in the formation of hydrogen-bonded (HB) dimers of 1,6a-dihydropyrrolo[2,3-b]pyrrole derivatives as well as in their proton-transfer processes have been studied by means of ab initio calculations. The heterochiral dimers are in general the most stable ones, but amphiprotic substituents that are able to form attactive interactions with twin groups revert this tendency. Energy differences up to 4.0 kcal/mol have been found favoring the homo- or heterochiral complexes. Two possible proton-transfer processes have been studied, the concerted one and the nonconcerted one. The compresion of the systems in the transition structures produce an increase in the energetic differences when compared to the corresponding minima complexes. A Steiner−Limbach relationship has been found for the geometrical properties of the HB in the minima and transition states calculated here. The electron density and its Laplacian at the bond critical point have been found to correlate with the HB distance.
J. Phys. Chem. B, 107, 5306 -5310, (2003)
Interaction of Protein Backbone with Nucleic Acid Bases
A theoretical study of the hydrogen-bonded (HB) complexes between a protein model and nucleic acid bases (NAB) has been carried out. As protein models, N-formylglycinamide (For-Gly-NH2, 2-formylaminoacetamide), 1, in beta- and gamma-conformations and as NABs, the isolated ones, and the AU, GC dimers in the Watson-Crick (WC) disposition have been considered. Only those dispositions with a double HB between the protein model and the nucleic acid bases have been studied. The aromatic CH groups of the nucleic acids have been included as HB donor. The results indicate that the strongest HBs between the individual NAB and the protein models involve the atoms that participate in the formation of the WC dimers. In the trimeric complexes, no significant preference is obtained for the 1-AU trimers studied while in the 1-GC ones the complex where formylglycinamide interacts simultaneously with the carbonyl group of guanine and the amino of cytosine is favored. The electron density of the complexes has been analyzed using the atoms in molecules methodology, finding exponential relationships between the electron density and its Laplacian vs the bond distance. Finally, the effect in the nuclear chemical shielding due to the complexation has been explored. Exponential relationships have been found for the variation of the chemical shift of the 1H signal for the NH···O and NH···N interactions with the HB distance.
J. Phys. Chem. A , 107, 3222-3227 (2003)
J. E. Del Bene, S. A. Perera, R. J. Bartlett, M. Yañez, O. Mo, J. Elguero, I. Alkorta
DOI: 10.1021/jp021619l
Two-Bond 13C-15N Spin-Spin Coupling Constants (2hJC-N) Across C-H-N Hydrogen Bonds
Ab initio EOM-CCSD calculations have been performed to determine 13C−15N spin−spin coupling constants (2hJC-N) across C−H−N hydrogen bonds in 17 neutral, 3 cationic, and 3 anionic complexes. The contributions of the paramagnetic spin−orbit, diamagnetic spin−orbit, and spin−dipole terms to the total 13C−15N spin−spin coupling constants (2hJC-N) are negligible, so 2hJC-N is determined solely by the Fermi contact term, which is distance-dependent. 2hJC-N for complexes stabilized by C−H···N hydrogen bonds exhibits some dependence on the nature of the hybridization and the nature of the bonding at the C atom of the proton-donor C−H group. Nevertheless, a single curve can be constructed from 2hJC-N and C−N distances for the equilibrium structures of the entire set of complexes that should be useful for estimating C−N distances from experimental measurements of coupling constants across C−H−N hydrogen bonds. Small deviations from linearity of the C−H−N hydrogen bond lead to only small changes in 2hJC-N.
Two-Bond 15N-19F Spin-Spin Coupling Constants (2hJN-F) across N-H+...F Hydrogen Bonds
Two-bond 15N−19F NMR spin−spin coupling constants (2hJN-F) have been computed using equation-of-motion coupled cluster singles and doubles theory (EOM-CCSD) for a variety of cationic complexes stabilized by traditional N−H+···F hydrogen bonds. The proton donors include protonated sp bases derived from HCN, protonated sp2 aromatic rings and imines, and protonated sp3 bases derived from NH3, with FH as the proton acceptor. 2hJN-F is determined solely by the Fermi-contact term, which is distance dependent. The absolute values of N−F coupling constants for cationic complexes are significantly greater than the F−N coupling constants for neutral complexes stabilized by traditional F−H···N hydrogen bonds over a range of N−F distances. This may be attributed to the greater proton-shared character of hydrogen bonds in cationic complexes. Moreover, at a given distance, values of 2hJN-F for complexes with sp and sp2 nitrogens as proton donors are considerably greater than 2hJN-F values for complexes with sp3 nitrogens as donors. When the cationic complexes are grouped according to the hybridization of the nitrogen, good correlations are found between 2hJN-F and the N−F distance. Small perturbations of the N−H+···F hydrogen bond from linearity are associated with only small decreases in 2hJN-F.
Two-Bond 19F−15N Spin−Spin Coupling Constants (2hJF-N) across F−H···N Hydrogen Bonds
Equation-of-motion coupled cluster calculations (EOM-CCSD) have been performed to determine two-bond 19F−15N spin−spin coupling constants (2hJF-N) for thirteen neutral complexes stabilized by F−H···N hydrogen bonds. The proton acceptors include nitrogens that are sp (HCN and its derivatives), sp2 (aromatic azines), and sp3 (NH3 and its derivatives) hybridized. 2hJF-N is determined by the Fermi-contact term, which is strongly dependent on the intermolecular F−N distance but varies only slightly with small perturbations of the hydrogen bond from linearity. 2hJF-N is more sensitive to the hybridization and bonding at the nitrogen in F−H···N hydrogen bonds than is 2hJN-N for complexes stabilized by N−H−N and N−H+−N hydrogen bonds. As a result, 2hJF-N at the same F−N distance for different complexes can vary by 10−15 Hz, and this reduces the quality of the quadratic curve used to relate 2hJF-N to the F−N distance. However, if the complexes are grouped according to the hybridization of the nitrogen, excellent quadratic correlations are found between 2hJF-N and the F−N distance. Moreover, if the same groupings are used, 2hJF-N also correlates with the charge density at the bond critical point of the hydrogen bond.
Int. J. Mol. Sci. 4, 64-92 (2003)
DOI: 10.3390/i4030064
Review on DFT and ab initio Calculations of Scalar Coupling Constants
The present review summarizes the information available on the ab initio calculations of spin-spin nuclear coupling constants through hydrogen bonds or in van der Waals complexes. It also reports the sources of experimental data on nhJXY scalar couplings.
J. Phys. Chem. B, 107, 323-330 (2003)
M. Peters, I. Rozas, I. Alkorta, J. Elguero
DOI: 10.1021/jp026684+
DNA Triplexes: A Study of Their Hydrogen Bonds
Since their discovery, DNA triplexes have received a large amount of interest because of their potential as viable strategy for control of gene expression and their formation with some specific drugs. For that reason, we have studied, by means of ab initio calculations, the structure of the bases of these DNA triplexes in terms of their interaction energies and electron densities for the different hydrogen bonds, which is one of the interactions that determine the structure and dynamics of nucleic acid molecules. A good agreement has been found with experimental results and previous calculations. In general, when a third base is added to a dimer, the strength of the hydrogen bonds of the dimer becomes modified provoking changes in their structures by increasing the distance in the major groove and decreasing the space in the minor groove.
J. Am. Chem. Soc. 124, 1488-1493 (2002)
Ibon Alkorta, and Jose Elguero
Doi: 10.1021/ja011348c
Self-Discrimination of Enantiomers in Hydrogen-Bonded Dimers
The homochiral and heterochiral hydrogen-bonded (HB) dimers of a set of small model molecules (alfa-amino alcohols) have been studied by means of ab initio methods. The gas-phase calculations have been carried out with the hybrid HF/DFT B3LYP method and the 6-311++G** basis set. The electron density of the complexes has been analyzed using the atoms in molecules (AIM) methodology, which allows characterization of the HB interactions and additional intermolecular contacts. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the deltaGsolv. The gas-phase results show that the heterochiral dimers are the most stable ones for each case studied, while in solution for several cases, the relative stability is reversed and the homochiral dimers become more stable. The AIM analysis shows the typical bond critical points characteristic of the HB and additional bond critical points denoting, in this case, destabilization of intermolecular interaction as CF3...F3C and CH3...H3C contacts.
J. E. del Bene, S.A. Perera, R.J. Barlett, J. Elguero, I. Alkorta, C. Lopez-Leonardo, M. Alajarin
DOI: 10.1021/ja011755o
3hJ(15N-31P) Spin-Spin Coupling Constants across N-H···O-P Hydrogen Bonds
Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been performed to evaluate three-bond 15N−31P coupling constants (3hJN-P) across N−H···O−P hydrogen bonds in model cationic and anionic complexes including NH4+:OPH, NH4+:OPH3, NH3:-O2PH2, NFH2:-O2PH2, and NF2H:-O2PH2. Three-bond coupling constants can be appreciable when the phosphorus is P(V), but are negligible with P(III). 3hJN-P values in complexes with cyclic or open structures are less than 1 Hz, a consequence of the nonlinear arrangement of N, H, O, and P atoms. For complexes with these structures, 3hJN-P may not be experimentally measurable. In contrast, complexes in which the N, H, O, and P atoms are collinear or nearly collinear have larger values of 3hJN-P , even though the N−P distances are longer than N−P distances in cyclic and open structures. In linear complexes, 3hJN-P is dominated by the Fermi-contact term, which is distance dependent. Therefore, N−P (and hydrogen-bonding N−O) distances in these complexes can be determined from experimentally measured 15N−31P coupling constants.
J. E. Del Bene, S. A. Perera, R. J. Bartlett, I. Alkorta, J. Elguero, O. Mo, M. Yañez
One-Bond (1dJH-H) and Three-Bond (3dJX-M) Spin-Spin Coupling Constants Across X-H···H-M Dihydrogen Bonds
In our continuing effort to identify NMR spin−spin coupling constants as fingerprints for hydrogen bond type and use these to obtain structural information, EOM-CCSD calculations have been performed to determine one-bond (1dJH-H) and three-bond (3dJX-M) spin−spin coupling constants across X−H···H−M dihydrogen bonds for complexes with 13C−1H, 15N−1H, and 17O−1H proton-donor groups and proton-acceptor metal hydrides 7Li−1H and 23Na−1H. Unlike two-bond spin−spin coupling constants across N−H−N, N−H−O, O−H−O, and Cl−H−N hydrogen bonds that are determined solely by the Fermi-contact term, 1dJH-H receives nonnegligible contributions from the paramagnetic spin−orbit and diamagnetic spin−orbit terms. However, these terms tend to cancel, so that the curve for the distance dependence of1dJH-H is determined by the distance dependence of the Fermi-contact term. The value of1dJH-H is dependent on the nature of the proton donor and proton acceptor, and the relative orientation of the bonded pair. Hence, it would be difficult to extract structural information from experimentally measured coupling constants unless EOM-CCSD calculations were performed on a model complex that closely resembles the experimental complex. 3dJC-Li values for the equilibrium structures of seven linear complexes stabilized by C−H···H−Li bonds are dependent on C−Li distances, and are also sensitive to structural changes which remove any one of these four atoms from the dihydrogen bond. 3dJO-M for the complexes HOH:HLi and HOH:HNa exhibit unusual behavior as a function of the O−M distance, increasing with increasing distance through a change of sign, reaching a maximum, and then subsequently decreasing.
J. Phys. Chem. A, 106 , 9325-9330 (2002)
I. Alkorta, J. Elguero, O. Mo, M. Yanez, J. E. del Bene
Ab Initio Study of the Structural, Energetic, Bonding, and IR Spectroscopic Properties of Complexes with Dihydrogen Bonds
The results of an ab initio study of complexes with X−H···H−M dihydrogen bonds are presented. The proton donors include HCCH and its derivatives HCCF, HCCCl, and HCCCN; HCN and its derivatives HCNLi+ and HCNNa+; CNH, and H2O, and the proton acceptor is LiH. For comparison, selected complexes with NaH as the proton acceptor have also been investigated. The structures, binding energies and harmonic vibrational frequencies of all complexes were obtained at the MP2/aug'-cc-pVTZ level of theory. The most stable complexes with C−H groups as proton donors are the cationic complexes NaNCH+:HLi and LiNCH+:HLi. These complexes exhibit very short H····H distances and are prototypical of dihydrogen-bonded complexes that may dissociate by eliminating H2. The calculated binding energies correlate with the H···H distance, the elongation of the C−H donor bond, the amount of charge transfer into the H····H bonding region, and the charge density at the H···H bond critical point. As in conventional hydrogen-bonded complexes, the elongation of the proton donor C−H group correlates with the strength of the interaction, and with the red shift of the C−H stretching frequency. Although changes in the Li−H bond length do not follow a simple pattern, the Li−H stretching frequency is blue-shifted in the complexes.
I. Alkorta and J. Elguero
Discrimination of hydrogen-bonded complexes with axial chirality
The chiral self-discrimination of twelve molecules showing axial chirality has been studied. They included peroxides, hydrazines, carboxylic acids, amides, and allenes. The homo and heterochiral dimers of the selected compounds, that present two hydrogen bonds, have been studied by means of density functional theory (B3LYP/6-31+G∗∗) andab initio (MP2/6-31+G∗∗ and MP2/6-311++G∗∗) methods. The energetic differences found for the complexes of each compound have been rationalized based on their electron density maps and the natural bond orbital analysis. In some cases, intermolecular oxygen–oxygen interactions have been found and interpreted as additional stabilizing contacts.
E. Espinosa, I. Alkorta, J. Elguero, E. Molins
DOI:10.1063/1.1501133
From weak to strong interactions: A comprehensive analysis of the topological and energetic properties of the electron density distribution involving X-H...F-Y systems
The topological and energetic properties of the electron density distribution ρ(r) of the isolated pairwise H⋯F interaction have been theoretically calculated at several geometries (0.8<d<2.5 Å) and represented against the corresponding internuclear distances. From long to short geometries, the results presented here lead to three characteristic regions, which correspond to three different interaction states. While the extreme regions are associated to pure closed-shell (CS) and shared-shell (SS) interactions, the middle one has been related to the redistribution of ρ(r) between those electronic states. The analysis carried out with this system has permitted to associate the transit region between pure CS and SS interactions to internuclear geometries involved in the building of the H–F bonding molecular orbital. A comparative analysis between the formation of this orbital and the behavior of some characteristic ρ(r) properties has indicated their intrinsic correspondence, leading to the definition of a bond degree parameter [BD = HCP/ρCP; HCP and ρCP being the total electron energy density and the electron density value at the H⋯F (3,−1) critical point]. Along with the isolated pairwiseH⋯F interaction, 79 X–H⋯F–Y (neutral, positively and negatively charged) complexes have been also theoretically considered and analyzed in terms of relevant topological and energetic properties of ρ(r) found at their H⋯F critical points. In particular, the interaction energies of X–H⋯F–Y pure CS interactions have been estimated by using the bond degree parameter. On the other hand, the [F⋯H⋯F]− proton transfer geometry has been related to the local maximum of the electron kinetic energy density (GCP)max.
I. Alkorta, I. Rozas, J. Elguero
DOI: 10.1021/ja025693t
Interaction of Anions with Perfluoro Aromatic Compounds
The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 (MP2/6-31++G** and MP2/6-311++G**) ab initio methods. The minimum structures show the anion interacting with the π-cloud of the aromatic compounds. The interaction energies obtained range between −8 and −19 kcal mol-1. The results obtained at the MP2/6-31++G** and MP2/6-311++G** levels are similar. However, the B3LYP/6-31++G** results provide longer interaction distances and smaller interaction energies than do the MP2 results. The interaction energies have been partitioned using an electrostatic, polarization, and van der Waals scheme. The AIM analysis of the electron density shows a variety of topologies depending on the aromatic system considered.
Theochem, 585, 27-34 (2002)
I. Alkorta, , C. Wentrup, J. Elguero
A theoretical study of the origin of rotational barriers in push-pull ethylenes
Using the B3LYP/6-31G∗ ab initio method, we have studied the rotation about the CC bonds in 15 push–pull ethylenes of the general formula (X,Y)CC(CHO)2 [X, Y=NH2, NHCH3, N(CH3)2, OCH3, SCH3] in the gas phase. Two stationary points (minimum and transition state) were located for all compounds. The geometry, dipole moments, natural bond orbital atomic charges, as well as the rotational barriers were examined. The torsion angle θ depends essentially on the presence or absence of intramolecular hydrogen bonds, and the barrier is a function of the torsion angle.
Phys. Chem. Chem. Phys., 4 , 2123-2129 (2002)
M. Alcami , O. Mo , M. Yanez , I. Alkorta and J. Elguero
Triaziridine and tetrazetidine vs. cyclic water trimer and tetramer: A computational approach to the relationship between molecular and supramolecular conformational analysis
The potential energy surfaces of cyclic water trimer and tetramer, as typical examples of supramolecular systems, have been compared with those of triaziridine and tetrazetidine, which can be considered as their suitable molecular analogues. The survey was performed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level of theory and includes also the monomethyl and monofluoro derivatives of both the trimer and the tetramer. This comparison leads to the conclusion that supramolecular systems, where the molecular components are held together by weak interactions, exhibit the same conformational features as the analogous molecular compounds, where the constituent atoms are held together by strong covalent bonds. More importantly, even though in the former the energy required to induce conformational rearrangements is much smaller than that needed for typical molecular systems, there is a fairly good linear relationship between both magnitudes. We have also found that this quantitative relationship can be perturbed when the through-space interactions, either repulsive or attractive, between the substituents are sufficiently strong.
J. Chem. Soc., Perkin Trans. 2, 894-898 (2002)
I. Alkorta , J. Elguero , S. Goswami and R. Mukherjee
DOI: 10.1039/B200915N
Interaction of adenine with synthetic receptors: a theoretical study
The interaction of adenine with synthetic macrocyclic receptors has been modelled using, as simplified molecular systems, the monoamide derivatives of pyridine and 1,8-naphthyridine. DFT methods (B3LYP/6-31+G**) have been used to characterise the complexes stabilised by multiple hydrogen bonds. The theoretical results indicate that while the synthetic receptors with pyridines can interact simultaneously forming pseudo-Watson–Crick and pseudo-Hoogsten complexes with adenine, in the case of the 1,8-naphthyridines only one of the complexes is possible. The energetic results that favour the pyridine receptors are in agreement with the experimental binding constants.
DOI: 10.1021/jo016069m
Influence of Intermolecular Hydrogen Bonds on the Tautomerism of Pyridine Derivatives
The effect of the dimerization, by hydrogen-bond (HB) complexation, on the tautomerism of 2-hydroxypyridine and a series 2-aminopyridines has been carried using ab initio methods. The results obtained for 2-hydroxypyridine fit satisfactorily with the experimental data and show that the 2-pyridone/2-pyridone homodimer complex is the most stable. For 2-aminopyridines, the effect of the substituent on the amino group has been investigated. For the monomers studied, the most favorable tautomer is the 2H; however, with electronegative substituents, the 1H/1H homodimers are more stable than the corresponding 2H/2H ones. The atom in molecule methodology has been used to characterize the HBs formed. Exponential relationships have been found between the electron density and its laplacian at the HB critical point vs the HB distance.
Int. J. Quantum Chem. 86, 122-129 (2002)
DOI: 10.1002/qua.1613
Theoretical study of the Si-H group as potential hydrogen bond donor
The ability of the Si–H group as hydrogen bond (HB) donor has been studied theoretically. Most of the selected molecules include the Si–H group in a polar environment that could produce an electron deficiency on the hydrogen atom. In addition, analogous derivatives where the silicon atom has been replaced by a carbon atom have been considered. In all cases, ammonia has been used as HB acceptor. The calculations have been carried out at the MP2/6-311++G** computational level. The electron density of the complexes has been characterized within the atoms in molecules (AIM) framework. A search in the Cambridge Structural Database (CSD) has been carried out to verify the existence of this kind of interactions in solid phase. The results of the theoretical study on these HB complexes between ammonia and the silicon derivatives provides long HB distances (2.4 to 3.2 Å) and small interaction energies (−2.4 to −0.2 kcal/mol). In all cases, the HBs of the corresponding carbon analogs show shorter interaction distances corresponding to stronger complexes. The CSD search provides a small number of short interactions between Si and other heavy atoms in agreement with the small stabilizing energy of the Si–HN HB and the lack of SiH bond in polar environment within the database.
J. Am. Chem. Soc., 123, 7898-7906 (2001)
C. Foces-Foces, A. Echevarría, N. Jagerovic, I. Alkorta, J. Elguero, U. Langer, O. Klein, M. Minguet-Bonvehí, H. H. Limbach
DOI: 10.1021/ja002688l
A Solid-State NMR, X-ray Diffraction, and ab Initio Computational Study of Hydrogen-Bond Structure and Dynamics of Pyrazole-4-Carboxylic Acid Chains
Using high-resolution solid-state 15N CMAS NMR, X-ray crystallography, and ab initio calculations, we have studied the structure of solid pyrazole-4-carboxylic acid (1). The crystal structure was determined at 295 and 150 K. Molecules of 1 are located on a two-fold axis, implying proton disorder of the NH and OH groups; no phase transition was observed between these two temperatures. The compound forms quasi-linear ribbons in which the molecules are linked by cyclic hydrogen bonds between pyrazole and carboxylic acid groups with disordered hydrogen-bonded protons. Crystallography is unable to decide whether the disorder is dynamic or static. NMR shows that this disorder is dynamic, that is, consisting of very fast degenerate double proton transfers between two rapidly interconverting O−H···N and O···H−N hydrogen bridges. However, at low temperature, NMR shows a proton disorder−order transition where the protons are preferentially localized on given nitrogen and oxygen atoms. An amorphous phase exhibiting proton order is observed when the compound is precipitated rapidly. In this case, the defects are annealed by moderate heating. Ab initio calculations performed on oligomers of 1 show that the O−H···N hydrogen bridge is about 0.064 Å shorter and less bent (∼171°) than the O···H−N hydrogen bridge (∼150°). For an isolated ribbon, this result leads to structures with localized protons, either to a cycle with about 200 molecules, or to a quasi-linear ribbon involving an undulated structure, or to a combination of both motifs. Only the undulated structure is compatible with the linear ribbon observed by X-ray crystallography, where the fast proton transfer in the high-temperature phase is assisted by the motions of the undulated chain. A disordered structure is assigned to the amorphous phase, which exhibits the combination of the curved and the undulated motifs.
Chem. Phys. Lett. 350 , 325-330 (2001)
P. Prieto, A. de la Hoz, I. Alkorta, I. Rozas, J. Elguero
Strained pi-systems as hydrogen bond acceptors: The case of benzyne
The behaviour of strained pi-systems with regard to their interaction with hydrogen bond (HB) donors was studied. The interaction of a model system, strained acetylene, and ortho-benzyne with hydrogen fluoride in their singlet and triplet electronic configuration was explored at the B3LYP/6-311++G** and MP2/6-311++G** levels. The energetic results indicate that there are two preferred approaches, the first with the hydrogen fluoride pointing towards one of the radical carbon atoms and the second that corresponds to the HB perpendicular the p bond. The Atoms in Molecules analysis of the electron density shows a conflict catastrophic situation for several of the approaches
Intramolecular Hydrogen Bonds in ortho-Substituted Hydroxybenzenes and in 8-Susbtituted 1-Hydroxynaphthalenes: Can a Methyl Group Be an Acceptor of Hydrogen Bonds?
Considering the findings of Fujii et al. showing that the cis isomer of the o-cresol radical cation shows a low-frequency shift of the OH stretching attributed to an intramolecular hydrogen bond with the CH3 group and considering the studies of Knak Jensen et al. concluding that such an O−H···C interaction was not possible, the work presented in this article tries to understand if this is a consequence of the nature of the hydrogen bond acceptor (a CH3group) or of the five-member ring that would be formed as a result of the intramolecular interaction. Thus, we have studied o-cresol, 8-methyl-1-hydroxynaphthalene, 1-hydroxy-1-propene, 1-hydroxy-3-methyl-1,3-butadiene, and their derivatives in which the −CH3 group has been substituted by a −F atom or by an −OH group. Taking into account interaction distances and angles, interaction energies (from isodesmic reactions), and electron density characteristics, we can conclude that, in general, a methyl group cannot behave as a hydrogen bond acceptor. In addition, we found that the formation of intramolecular hydrogen bonds driving to the formation of five-member rings is not favored even in the presence of a good acceptor. Moreover, different methods of evaluating intramolecular interaction energies have been analyzed.
DOI:10.1023/A:1012276824422
A theoretical and experimental study of the interaction of C6F6 with electron donors
The NMR effects produced on the nitrogen absolute shieldings in a series of electron donors when they interact with hexafluorobenzene, C6F6, have been theoretically studied. The complexes have been optimized at the B3LYP/6-311++G** level and the NMR shieldings have been calculated using the GIAO method. The results obtained have allowed devising an experiment (C6F6···NCCH3complex) that is compatible with the theoretical calculations.
I. Alkorta, I. Rozas, O. Mo, M. Yañez, J. Elguero
Hydrogen bond vs. proton transfer between neutral molecules in the gas phase
The possibility of observing a spontaneous proton transfer (PT) between a proton donor AH and a proton acceptor B has been analyzed using, as suitable model systems, the hydrogen bond complexes between HF, HCl, and HBr and a set of bases which covers a large range in the gas-phase basicity scale. This analysis was based on theoretical estimates obtained by means of high-level density functional theory calculations. We propose a model which permits us to predict that, when ΔacidH(AH) + PA(B) + 102 is ≥0 (in kcal mol-1), ΔacidH(AH) being the acidity of AH and PA(B) the proton affinity of B, a spontaneous PT from AH toward B should be observed. In contrast, if the value of this expression is negative, only a hydrogen-bonded cluster between the corresponding neutrals would be stable. We have also reached the conclusion that, to obtain a strong hydrogen bonded complex, a very polarized A−H bond and a sufficiently strong Lewis base, B, are necessary, whereas to observe a spontaneous PT the acidity of A−H and the basicity of B are determining factors, and to a much lesser extent the size of the interacting systems.
E. Espinosa , I. Alkorta , I. Rozas , J. Elguero , E. Molins
About the evaluation of the local kinetic, potential and total energy densities in closed-shell interactions
The local kinetic G(r), potential V(r) and total E(r) energy densities, calculated at the critical points of 37 H⋯F closed-shell interactions by quantum mechanical methods, have been compared to their estimated values obtained by using an approximate evaluation of G(r) and the local form of the virial theorem. The results presented here show very small differences between the corresponding quantities, and therefore support the validity of the estimations. Thus, the equations used in this procedure provide useful information for topological studies of experimental electron densities, permitting the evaluation of those energetic properties from the modelling of the topological properties of the electron density distribution.
Transition metals as hydrogen bond acceptors: a theoretical study
The ability of the (CO)4Co− organometallic complex as a HB acceptor has been studied. For this theoretical study, several standard HB donors such as HF, HCN and HNC have been used. The inclusion of the HN(CH3)3+ cation as HB donor, allows the comparison of theoretical and experimental results. In order to consider the importance of the formal negative charge of (CO)4Co− in the interaction with other systems, the isoelectronic neutral (CO)4Ni organometallic complex has been considered as HB acceptor. The electronic changes, within the Atoms in Molecules (AIM) and Natural Bond Orbitals (NBO) methodologies, have been evaluated. Geometry, protonation energy, interaction energy, and electron density results confirm that the stability as a protonated species of the organometallic complexes (i.e. their gas-phase basicity) studied here gives an indication of their ability to act as a HB acceptor. It can be concluded that the Co organometallic anion seems to be a better HB acceptor than the Ni derivative, due to the formal charge of the former, more than the corresponding electronic distribution.
DOI: 10.1021/jp002808b
Molecular Complexes between Silicon Derivatives and Electron-Rich Groups
Theoretical calculations on a series of SiXY3···ZW complexes, where X and Y are H, F, and Cl, and Z corresponds to an electron donor atom (ZW = NH3, NCH, CNH, OH2, FH), were performed. The calculations were carried out using B3LYP/6-311++G**, MP2/6-311++G** and MP2/6-311++G(2d,2p) computational methods. The electron density was characterized by means of the atoms in molecules (AIM) methodology, and the interaction nature was studied with the NBO method. Finally, the effect of the complexation on the nuclear chemical shieldings was evaluated with the GIAO method. The results display a wide range of interaction distances that vary from 2.1 to 4.1 Å. The complexes with shorter interaction distances (∼2.1 Å) show important distortion effects and large dipole moment enhancements. The NBO analysis indicates that in those complexes an ionic interaction is formed between the Si and Z atoms. Comparison of the chemical shieldings of the complexes and the monomers indicates that these interactions could be detected experimentally using 29Si NMR. In addition, in the case of the complexes with NH3 and OH2, the use of 15N NMR and 17O NMR could be adequate to check the potential formation of the corresponding complexes.
Basicity and proton transfer in proton sponges and related compounds: an ab initio study
Theoretical calculations at the B3LYP/6-31G* level were carried out on a family of 1,8-diR-naphthalenes, which include the proton sponge (1,8-bisdimethylaminonaphthalene, R = NMe2) and other substituents (R = NH2, R = OH, R = CH3, R = F). Their basicity was compared with that of the corresponding monosubstituted benzenes. The dianion of 1,8-dihydroxynaphthalene should be a compound of extraordinary high basicity. The barriers to proton transfer, geometry, and density at the bond critical point of the hydrogen bond have been calculated and compared with experimental data when available.
Acta Cryst. B56, 1018-1028 (2000)
C. Foces-Foces, I. Alkorta, J. Elguero
doi:10.1107/S0108768100008752
Supramolecular structure of 1H-pyrazoles in the solid state: a crystallographic and ab initio study
The secondary structure of 1H-unsubstituted pyrazole derivatives bearing only one hydrogen donor group and one or more acceptor groups has been analyzed in terms of some descriptors representing the substituents at C3 and C5. The substituent at C4 appears to affect mainly the tertiary or quaternary structure of these compounds. The proposed semi-quantitative model, which explains most hydrogen-bonded motifs as a combination of the effects of substituents at C3 and C5, has also been examined as a function of the steric and polarizability effects of these substituents represented by molar refractivity. The model also applies to other five-membered rings (1,2,4-triazoles, 1,2,4-diazaphospholes and 1,2,4-diazaarsoles). Furthermore, ab initio calculations at RHF/6-31G* have been performed to discover the relative stability of three of the four hydrogen-bond patterns displayed by several symmetrical pyrazoles (dimers, trimers, tetramers). The fourth motif, catemers, has only been discussed geometrically.
J. Am. Chem. Soc., 122, 11154-11161 (2000)
The behaviour of ylides containing N, O and C atoms as hydrogen bond acceptors
The hydrogen bond (HB) basicity of a series of ylides containing nitrogen, oxygen, or carbon as heavy atoms, as well as the influence of the formation of the HB complexes on their structure, has been studied. In addition, in this paper we propose the formation of some rather strong HBs (that could be considered low-barrier hydrogen bonds, LBHBs) between ylides and different neutral molecules. The ylides chosen for the study were H3N+−N-H, Me3N+−N-H, H2O+−N-H, Me2O+−N-H, H2O+−O-, Me2O+−O-, and Me3N+−C-H2. As HB donors, classical donors such as HF, HCN, and HCCH were used. The analysis of the protonation energies of the ylides and the optimized geometries, interaction energies, and characteristics of the electron density of the complexes shows that these ylides are very good HB acceptors, forming stable complexes even with weak HB donors. With strong donors, when the proton transfer did not take place, very strong HBs were formed with quite large interaction energies and very short HB distances which could be considered as LBHBs. Moreover, we have found that the sign of the Laplacian of the electron density at the bond critical point ( 2ρBCP) and that of the energy density (HBCP) could characterize the strength of HBs. Thus, weak HBs (EI < 12.0 kcal/mol) show both 2ρBCP and HBCP > 0, and medium HBs (12.0 < EI < 24.0 kcal/mol) show 2ρBCP > 0 and HBCP < 0, while strong HBs (and therefore LBHBs; EI > 24.0 kcal/mol) show both 2ρBCPand HBCP < 0.
J. E. Del Bene, S. A. Perera, R. J. Bartlett, I. Alkorta and J. Elguero
4h J(31 P- 31 P) Coupling Constants through N-H + -N Hydrogen Bonds: A Comparsion of Computed ab Initio and Experimental Data
EOM-CCSD calculations have been performed to evaluate the 31P−31P coupling constant (4hJP-P) across an N−H+−N hydrogen bond in a model system. Computed 4hJP-P values were obtained as a function of distance and are in agreement with an experimentally measured value of the 31P−31P coupling constant across an N−H+−N hydrogen bond.
Angew. Chem. Int. Ed. 39,717-721 (2000)
J. M. Ugalde, I. Alkorta, and J. Elguero
DOI:10.1002/(SICI)1521-3773(20000218)39:4<717::AID-ANIE717>3.0.CO;2-E
Also: Angew. Chem., 112, 733-737 (2000)
Water Clusters: Towards an Understanding Based on First Principles of Their Static and Dynamic Properties
At the molecular – supramolecular border lie water clusters. Such molecular water clusters, Wi, fori=2 to i=10, have been used to discuss some fundamental problems, such as the covalent nature of hydrogen bonds, the properties of bulk water, and their conformations. The picture represents some examples of W8.
Spect. Acta A, 56, 1469-1498 (2000)
J. M. Orza, M. V. Garcia, I. Alkorta and J. Elguero
DOI:N/A
Vibrational spectra of 3,5-dimethylpyrazole and deuterated derivatives
The infrared (IR) and Raman spectra of 3,5-dimethylpyrazole have been recorded in the vapor, liquid (melt and solution) and solid states. Two deuterated derivatives, C5H7N-ND and C5D7N-NH, were also studied in solid state and in solutions. Instrumental resolution was relatively low, 2.0 cm(-1) in the IR and approximate to 2.7 cm(-1) in the Raman spectra, The solids are made of cyclic hydrogen-bonded trimers. These trimers, present also in chloroform and acetone solutions, give rise to characteristic high absorption IR spectra in the 3200-2500 cm(-1) region, related to Fermi resonance involving nu(NH) vibrations. Bands from trimers are not present in water solutions but these solutions show spectral features similar in several ways to thoseof the trimer, attributable to solvent-bonded complexes. Evidence of H-bonding interactions with the other solvents is also visible in the high-frequency region. The two very intense bands in the Raman spectra of the solids appearing at 115 and 82 cm(-1) in the parent compound are also connected with a trimer formation. To interpret the experimental data, ab initio computations of the harmonic vibrational frequencies and IR and Raman intensitieswere carried out using the Gaussian 94 program package after full optimization at the RHF/6-31G* level for the three monomeric compounds as well as for three models of the trimer, with C-3h, C-3 and C-1 symmetry. The combined use of experiments and computations allow a firm assignment of most of the observed bands for all the systems. In general, the agreement between theory and experiment: is very good, with the exception of the IR and Raman intensities of some transitions. Particularly noticeable is the failure of the theoretical calculation in accounting for the high intensity of the Ramanbands of the solid about 115 and 82 cm(-1)
I. Alkorta, L. Barrios, I. Rozas, and J. Elguero
Comparison of models to correlate electron density at the bond critical point and bond distance
Two models proposed in the literature to correlate the electron density at the bond critical point with the bond distance have been compared. The first one, proposed independently by Knop–Boyd and Destro, considers an implicit double logarithmic relationship between these two properties. We propose a second model, which uses a logarithmic relationship. Van der Waals and hydrogen bond interactions as well as traditional covalent bonds have been considered in order to have a broader range of the compared properties. The results indicate that both models provide good results when individual bond types are correlated, although the logarithmic model seems to be slightly better than the double logarithmic one. Finally, a unique equation corresponding to model 2 has been devised to correlate all the H–X or C–X bonds.
J. Fluorine Chem. 101, 233-238 (2000)
I. Alkorta, , I. Rozas, and J. Elguero
DOI:/10.1016/S0022-1139(99)00164-5
Effect of fluorine substitution on hydrogen bond interactions
The effect of fluorine substitution on a series of hydrogen-bonded (HB) systems has been studied with the aid of theoretical ab initio methods. The effect on HB donors has been examined using a series of fluoromethane derivatives as hydrogen bond donors in their interaction with water. The results indicate a 0.1 Å shortening of the HB bond distance for each additional fluorine atom and 1 kcal/mol increase for the interaction energy. The fluorine effects have been considered in several HB acceptors like hexafluorobenzene and a series of small molecules. The π-cloud of hexafluorobenzene forms stable complexes with electron rich atoms, behaviour that is the opposite to what is observed for benzene. For the small molecules acting as HB acceptors, a weakening of the HB is observed. In some cases, the effect is so important that HB properties are reverted as the case of the hexafluorobenzene. Finally, the atomic properties of a series of charge transfer and HB complexes have been compared.
I. Rozas, I. Alkorta and J. Elguero
DOI: 10.1021/jp991358o
Monohydride and Monofluoride Derivatives of B, Al, N and P. Theoretical Study of Their Ability as Hydrogen Bond Acceptors
The characteristics of low-valence derivatives (monohydrides and monofluorides) of boron, aluminum (group 13 of the periodic system), nitrogen, and phosphorus (group 15 of the periodic system) have been investigated. Several aspects of these derivatives have been studied such as the energy gap between their singlet and triplet configuration, their proton affinity in the different parts of the molecule, and their ability as hydrogen bond acceptors. The geometries and energies of all the monomers and complexes have been fully optimized using a hybrid method (B3LYP) and the second-order Møller−Plesset (MP2) levels with the 6-311++G** basis set. In addition, the G2 and MCSCF methodologies were also used. The natural population analysis and the natural bond orbital analysis have been used to evaluate the charge transfer and second-order interaction energies, respectively. Topological properties of the electron density have been characterized using the atoms in molecules methodology. Our results show surprisingly strong hydrogen bonds for the boron derivatives. By use of principal component analysis, it was possible to express the interaction energy as a function of the acidity or basicity and the softness of the molecules involved in the complexes following Pearson's model. As well, it was found, by the natural bond orbital analysis, that the charge is transferred by a nHBA → σ*HBD donor−acceptor interaction, similar to standard hydrogen bonds. Moreover, different correlations have been found between the interaction energies and the second-order interaction energies or the charge-transfer calculated for both of the parameters, from the natural bond orbital analysis. The slopes of those correlations vary with the group of the periodic system to which the accepting atom belongs.
I. Alkorta,I. Rozas and J. Elguero
How strong can be the complexes between methane radical cation and noble gas atoms?
This article studies the interaction the methane radical cation (C2v) with noble gas atoms (He, Ne, Ar, and Kr). A number of stationary points, between 5 and 7, have been located depending on the interacting noble gas atom. MP2, MP4 and CCSD-T computational levels with the 6-311++G(d,p) and 6-311++G(2d,2p) basis sets have been used. The minima show different characteristics depending on the interacting hydrogen atom, similar to hydrogen-bonded or van der Waals complexes. The transition states obtained indicate an easy transfer between the symmetrical and non-symmetrical complexes.
Struct. Chem. 10,159-161 (1999)
A general equation holds for the geometry of hydrogen bonds with O and N acceptors
A unique equation able to correlate two geometrical parameters in hydrogen bonded (HB) systems, the X-H covalent bond distance in the donor and the H...Y distance of the acceptor, has been devised. The mentioned equation is able to fit simultaneously calculated and high quality crystallographic data of different HB donors and several nitrogen and oxygen acceptors.
J. Phys. Chem A. 103, 272-279 (1999)
Theoretical study of strong hydrogen bonds between neutral molecules.The case of amine oxides and phosphine oxides as hydrogen bond acceptors
A theoretical study of the ability of amine oxides and phosphine oxides as hydrogen bond (HB) acceptors has been carried out using ammonium oxide, trimethylamine oxide, and phosphine oxide as model systems. The analysis of the energetic results indicate that only small spatial preferences are observed in the HB interaction. The value of the interaction energies are in several cases within the range of strong HB (>12 kcal/mol), and in complexes between amine oxides and strong acids in the gas phase, a spontaneous proton transfer is obtained. A logarithmic correlation between the electron density at the HB critical points and the HB distance that is able to fit not only calculated data but also experimental ones has been obtained. Finally, a linear relationship has been found between the number of HBs and the 31P NMR shielding in the H3PO···(HF)n series, in good agreement with experimental reports.
J. Phys. Chem. A, 102, 2398 (1998)
Unusual hydrogen bonds: H···pi interactions (addition/correction)
We present theoretical proof that the nature of the interactions existent in the complexes formed between hydrogen fluoride and a series of π-systems (acetylene, ethylene, cyclopropene, cyclobutadiene, and benzene) and three-memebered-ring derivatives (cyclopropane and tetrahedrane) is that of a hydrogen bond between the hydrogen atom and the π-cloud. Geometric and energetic data and mainly the study of the topology of the electronic density within the frame of the theory of atoms in molecules established by Bader have been used for this analysis.
J. Chem. Soc. Perkin II, 2671-2675 (1998)
I. Alkorta, I. Rozas, and J. Elguero
DOI: 10.1039/A804677H
A computational approach to intermolecular proton transfer in the solid state: assistance by proton acceptor molecules
Ab initio (B3LYP/6-311++G**) calculations have been carried out on the proton transfer of 2H-tetrazole and 5-phenyl-2H-tetrazole with and without the assistance of different nitrogen bases (hydrogen cyanide, ammonia and imidazole). In the absence of base, the proton transfer barrier amounts to 210 kJ mol–1 while in the presence of ammonia it is lowered to 119 kJ mol–1. Moreover, the inclusion of a solvent cavity of the Onsager type, which increases the first barrier, decreases the second one to 67 kJ mol–1 (for ε = 5) which is consistent with experimental data for irbesartan (a 5-aryl-2H-tetrazole derivative).
J. Chem. Soc. Perkin II, 2497-2503, (1998)
DOI:10.1039/A804086I
1,2-Proton shifts in pyrazole and related systems: a computational study of [1,5]-sigmatropic migrations of hydrogen and related phenomena
Three different approaches are used to discuss the possible analogy between the [1,5] hydrogen shift in cyclopentadiene and the prototropy in 1H-pyrazole. In the first, a series of NH→HN hydrogen shifts in cyclic conjugated molecules are considered demonstrating that the case of pyrazole is not intrinsically different from the other systems which are unrelated to [1,5] H shifts. The second approach compares pyrazole and cyclopentadiene with their open-ring structures, pentadiene and aminoazadiene, proving that the N–N bond is essential to describe pyrazole while the C(sp3)–C(sp2) bond in cyclopentadiene can be considered as a perturbation. Finally, the third approach is a study of cyclopentadienide and pyrazolide anions as hydrogen-bond acceptors, the first one being a π-acceptor while the second one is a σ-acceptor through the nitrogen lone pair. The conclusion is that N(sp2)–N(sp2) migrations of hydrogen in aromatic azoles are outside the Woodward–Hoffmann domain of application.
I. Rozas, I. Alkorta, and J. Elguero
Bifurcated hydrogen bonds: Three-centered interactions
The nature of bifurcated or three-centered hydrogen bonds (HB) has been investigated. Different families of compounds were chosen: monomers with intramolecular three-centered HB, dimers with a HB donor (HBD) and a molecule with two HB acceptor (HBA) groups, and trimers with one HBD and two HBAs. All the systems were optimized at the B3LYP/6-31G* level, and, in the case of the complexes, the interaction energies were evaluated and corrected with the basis set superposition error (BSSE). The electronic nature of these three-centered HBs was analyzed by means of the atoms in molecules (AIM) approach. The present study indicates the existence of bifurcated bond paths in the AIM analysis with electron densities that can be classified as follows: (i) compounds with symmetric three-centered HBs presenting two symmetric bond critical points with equal values of electron density; (ii) compounds with asymmetric three-centered HBs presenting two bond critical points with different values of electron density; (iii) compounds with a regular HB and a van der Waals interaction showing two bond critical points with different electron density values one of which is very small; (iv) van der Waals complexes with two bond critical points having very small electron densities. Therefore, looking at the geometry, electron density, and energy results, the nature as HB of these three-centered interactions has been confirmed.
I. Alkorta, N. Campillo, I. Rozas, and J. Elguero
DOI: 10.1002/chin.199912026
Ring strain and hydrogen bond acidity
The ability of strained hydrocarbons to act as hydrogen bond donors has been explored with a hybrid HF-DFT ab initio method, B3LYP, and the 6-31G* and 6-311++G** basis sets. The results have been correlated with geometrical parameters (number of three- and four-membered rings, bond angles, and hydrogen bond distances), electronic characteristics of the complexes and isolated monomers (electron density at the bond critical points, atomic charges, and dipolar magnetization), and other properties (gas-phase acidities and atomic volume and energy). The results have been rationalized on the basis of a simple strain model and compared to nonsaturated hydrocarbons with donor C-H groups.
Charge transfer complexes between dihalogen compounds and electron donors
A theoretical study of the charge-transfer complexes formed by dihalogen compounds (F2, Cl2, Br2, FBr, FCl, and ClBr) and electron donors (FH, OH2, NH3, CO, NCH, and C2H2) has been carried out. The geometries, energies, and electronic and spectroscopic properties of these complexes have been compared with the corresponding properties of the hydrogen bonded complexes of FH with the same electron donors. The hybrid HF-DFT, B3LYP, and second-order Møllet−Plesset perturbation, MP2, methods have been used. The properties analyzed include geometry, energy, electron distribution using the atoms in molecules (AIM) methodology, and spectroscopic constants of the complexes and monomers. Similarities in the variations of the geometries, in the trends in the interaction energetic, and in the topological electron density characteristics between the properties of the HB complexes and the dihalogen charge-transfer systems are pointed out. The main differences correspond to the variation trend of the atomic properties and the NMR shielding when going from the monomers to the complexes.
The additive properties of the electron density at the bond critical points in hydrogen-bonded complexes
The study of a large variety of hydrogen-bonded complexes (protic, hydric and protic-hydric) leads to the conclusion that the electron density at the bond critical point (ρBCP) is an additive property when it is expressed relatively (dimensionless). Equation [ρBCP(01)/ρBCP(1)]+[ρBCP(02)/ρBCP(2)]=1 represents the additive property for the protic cases, for the hydric cases the sum being equal to 2. The isolated molecules can be used to estimate ρBCP(O1) and ρBCp(02) provided a scaling factor of 0.98 is used.
Ber. Bunsenges. Phys. Chem., 102, 429-435 (1998)
Radicals as hydrogen bond acceptors
The ability of carbon radicals to act as hydrogen bond acceptors has been evaluated using ab initio theoretical methods. A hybrid Hartree-Fock Density Functional Theory based method (B3LYP), Moller-Plesset at the second perturbation order (MP2), and Quadratic CI methods that include single and double excitation (QCISD), have been used. The complexes formed by four radicals CH3(d), C2H4(t), (CH3)2C(t) and (CH3)3C(d)] with four standard hydrogen bond donors [FH, H2O, HCN and H3N] have been studied and their geometry, inter-action energy, and electronic properties, within the Atoms in Molecules (AIM) methodology framework have been analyzed. The energy and geometry results show that the studied radicals are poor hydrogen bond (HB) acceptors and the strength of the HBs qualitatively correlates with the molecular electrostatic potential (MEP) minimum of the isolated radicals. The atomic partition of different properties using the AIM methodology indicates that HBs complexes involving radicals behave differently to other HBs formed between neutral molecules.
Struct. Chem. 9, 243-247 (1998)
Bond lenght-bond order relationship from Covalent bond to van der Waals interactions
It is possible to treat bond distances of covalent C-H bonds and C⋯H hydrogen bonds simultaneously assuming a logarithmic relationship with the electron density at the bond critical point. Similar relationships have been found for other X-H/X⋯H bonds. The data used for obtaining these equations have been determined theoretically. All the systems have been fully optimized and their electron densities calculated at the B3LYP/6-311 + + G(d,p) level.
Chem. Soc. Rev. 27, 163-170 (1998)
DOI: 10.1039/a827163z
Non-convenional hydrogen bonds
Hydrogen bonds (HBs) are the most important 'weak' interactions encountered in solid, liquid and gas phases. The HB can be defined as an attractive interaction between two molecular moieties in which at least one of them contains a hydrogen atom that plays a fundamental role. Classical HBs correspond to those formed by two heteroatoms, A and B, with a hydrogen atom bonded to one of them and located approximately in between (A–H···B). Recently, knowledge of the number of functional groups which act as hydrogen bond donors or acceptors has increased considerably and most of these new groups are discussed.
Theor. Chem. Acc., 99, 116-123 (1998)
DOI:10.1007/s002140050313
Isocyanides as hydrogen bond acceptors
A theoretical study of the capability of hydrogen isocyanide (HNC) as a hydrogen bond acceptor has been carried out. The geometry, interaction energy and electronic properties of the corresponding complexes with HF, HCl, HBr, H2O, NH3, HCCH, HCN and HNC itself indicate that it is able to form strong hydrogen bonds. A search in the Cambridge Structural Database has shown the presence of isocyanides involved in hydrogen bonds in solid phase. Finally, the comparison of the properties of HNC with its isomer, hydrogen cyanide, shows strong similarities between both compounds.
M. Ramos, I. Alkorta, J. Elguero, N.S. Golubev, G.S. Denisov, H. Benedict and H.H. Limbach
Theoretical study of the influence of electric fields on hydrogen-bonded acid-base complexes
Matrix effects on the optimized geometries and the electronic properties of acid−base complexes XHB, with HX = HF, HCl, HBr, HCN and B = NH3, have been modeled using ab initio methods (6-31G** and 6-311++G** basis sets) in two different ways. Model A corresponds to the Onsager SCRF model, and model B corresponds to a homogeneous electric field F = 2qe0/re2 = 2.88 × 105q V/cm of varying strength generated by two distant charges +qe0 and −qe0 of opposite sign placed at distances of re = 100 Å. In both models, the minima and reaction coordinate of proton transfer has been calculated. As the electric interactions are increased, both models predict an increase of the dipole moments associated with a proton shift from X to B, i.e., a conversion of the molecular to the zwitterionic complexes. Both models predicts double minima for some electric fields; in model B electric fields are found where the neutral complex is not stable, evolving to the ion pair complex. These fields can be used to characterize the acidity of the donor toward the base without the necessity of assuming a proton-transfer equilibrium. In both models a similar field-induced correlation between the two hydrogen bond distances r1 ≡ X···H and r2 ≡ H···B is observed for all configurations. This correlation indicates in the molecular complexes a hydrogen bond compression when the proton is shifted toward the base and in the zwitterionic complexes a widening. The minimum of the X···B distance r1 + r2 occurs when the proton-transfer coordinate r1 − r2 = r01 − r02, wherer01 and r02 represent the distances