Organic Quasi-Liquid Schiff Bases from Biomolecules: Synthesis, Structure and Quantum Mechanical Studies

Phenylacetaldehyde, a naturally occurring plant-derived, occurs in vegetables and flowers during storage. We synthesized Schiff bases using phenylacetaldehyde and three natural biomoleculesadenine, cytosine, and l-leucine. We characterized them using various spectroscopic methods like FTIR, FT-NMR, UV-VIS, etc., followed by multiple theoretical tools. Detailed vibrational and electronic spectral explanations are reported using experimental and theoretically simulated spectra. The density functional theory analysis of molecules was optimized ground-state calculations using DFT/B3LYP method with 6-311G+ (2d, p) as a basis set, and this optimized structure undergoes electronic spectra were generated using energy calculations by TD-DFT/CAM-B3LYP method, 6-311G+ (2d, p) as a basis set with water as a solvent. Schiff base from cytosine was found to show excellent light-harvesting properties (86.51%). Analysis of wave function-based properties like electrostatic potential, ALIE, noncovalent interactions, etc., provide information about the reactivity and stability features. PASS and subsequent docking studies indicate that the first Schiff base shows DNA Lyase inhibition, and the other two show anti-eczematic properties.


Introduction
Tea is a non-alcoholic beverage as the most popular globally [1] made from the tea plant [2]. The aroma of tea is generally called flavonoids, classified by their functional groups are flavones, flavonols, flavones, isoflavones, anthocyanins, and catechins [1]. The aromatic odors phenylacetic acid and phenylacetaldehyde are also found to be present in fruits [3]. Phenylacetaldehyde is a volatile compound isolated from thyme honey from different geographical origins [4]. Formation of phenylacetaldehyde from polyphenols by the kinetic mechanism determined intermediates based on the interaction between Maillard reaction [5,6], from 1-phenylethan-1,2-diol by the selective acid dehydration process using versatile and straightforward acid catalyst [7]. The bioactivity of phenylacetaldehyde is the norartocarpetin which inhibits PhIP formation [8] and the excellent enzyme activity of mushroom tyrosinase in 30 ml of methanol had been heated at 70 o C on the water bath for 4-hrs in the presence of few drops of glacial acetic acid. The compound was recrystallized from methanol and then dried over a vacuum desiccator. (m.p: semisolid at room temperature). Scheme 1. The synthesis scheme of phenylacetaldehyde with various amino acids to form Schiff bases.

Spectroscopic characterization.
The electronic spectra were recorded using a Perkin-Elmer/Lambda-65 with a solution of 1*10 -5 M concentration in double distilled water as the solvent, and vibrational spectra were recorded using a Perkin-Elmer/Spectrum RX-1 using KBr. The NMR spectra were taken in JEOL_NMR 600 MHz for proton and 125 MHz for carbon-13 spectrum using DMSO-d6 as the solvent.

Electronic spectra of the compound and light-harvesting efficiency (LHE) for Schiff bases.
The compound's UV-visible absorption is recorded in the water at the concentration of 1*10 -5 M under ambient conditions. The electronic transition of Schiff bases was studied by TD-DFT utilizing CAM-B3LYP/6-311+G(2d,p) in a water implicit solvent atmosphere IEFPCM solvation model. The UV-Vis spectrum is given in Figure 2, and the orbitals involved in the transition are given in Figure 3. Light-harvesting efficiency (LHE) for Schiff bases show in Table 2. Schiff bases Compound-1 absorbs at 260.05 nm (expt) and 274.52 nm (simulated) with absorbance 0.40, and oscillator strength is 0.60. Compound-2 absorbs at 200.00 nm and 277.61 nm (simulated) ) with absorbance 0.45, oscillator strength is 0.65, and Compound-3 absorbs at 253.53 nm (expt), and 256.55 nm (simulated), with absorbance 0.87, and oscillator strength as 0.87. The compounds' experimental absorbance is 0.40, 0.45, and 0.87, which means the molecules can have good absorbance of light. Hence these compounds can be used as photosensitizers in organic DSSC's.  Theoretically, its efficiency can be calculated as light-harvesting efficiency [41][42][43][44][45][46][47][48], expressed as a function of the oscillator strength related as LHE=1-10-f [49][50][51]. The values are 0.60, 0.65, and 0.86 for the transition, which means that the Schiff bases compounds can absorb 60.20, 64.51, and 86.51 percent of the incident light energy for electronic excitation that particular wavelength. From this result, Compound-3 has higher light-harvesting efficiency [52,53].

Vibrational assignments for Schiff bases.
The harmonic-vibrational frequencies were calculated for the Schiff bases using the RB3LYP/6-311+ (2d,p) basis set. In our study, we used the scaling factor of 0.9613. Table S2 shows the fundamental frequencies for Schiff bases, and Figure 4 shows vibrational spectra for Schiff bases. Compound-1 belongs to the C1 point group of symmetry. It has 29 atoms; hence 81 normal modes of fundamental vibrations are possible, and the total dipole moment is 3.89 debye. All the 81 fundamental vibrations are active in FT-IR spectra. The frequencies for, the N-H stretching in purin-shows at 3305.49, and 3509.34 cm -1 (expt and simulated) respectively, the C-H stretching in azomethin-shows at 3123.43, and 3134.07 cm -1 (expt and simulated) respectively, the C-H symmetry and asymmetry stretching occurs between 2982.53 and 2797.90, and 2877.98 and 2877.98 cm -1 (expt and simulated) respectively, the C=C in purinshows at 1723.96, and 1550.65 cm -1 (expt and simulated) respectively, the N=C in azomethinshows at 1672.07, and 1625.66, the N=C in purin-shows at 1604.07, and 1499.17 cm -1 are expt and simulated respectively, the C-C in purin-shows at 1449.06, and 1489.73 cm -1 (expt and simulated) respectively, the C-H bending in azomethin-shows at 1417.86, and 1462.04 cm -1 (expt and simulated) respectively, the N-H bending in purin-shows at 1367.17, and 1328.73 cm -1 (expt and simulated) respectively, the N-C in purin-shows at 1286.50, and 1208.64 cm -1 (expt and simulated) respectively, and the C-H bending in purin-shows at 939.38, and 919.262 cm -1 (expt and simulated) respectively. Compound-2 belongs to the C1 point group of symmetry. It has 27 atoms; hence 75 normal modes of fundamental vibrations are possible, and the total dipole moment is 4.84 debye. All the 75 fundamental vibrations are active in FT-IR spectra. The frequencies for the N-H stretching in pyridine-shows at 3414.98 and 3457.46 cm -1 (expt and simulated) respectively, the C-H symmetry and asymmetry stretching occurs between 3339.12 and 3206.76, and 3102.71 and 3016.45 cm -1 (expt and simulated), respectively, the C-H stretching in azomethine-shows at 3078.93, and 2971.36 cm -1 (expt and simulated), respectively, the N=C in azomethine-shows at 1719.18, and 1585.90 cm -1 (expt and simulated), respectively, the C=O in pyridine-shows at 1655.13, and 1555.75 cm -1 (expt and simulated), respectively, N=C in pyridine-shows at 1504.68, and 1441.09 cm -1 (expt and simulated), respectively, the C-H bending occurs between 1451.19 and 1285.43, and 1418.36 and 1357.37 cm -1 (expt and simulated), respectively, the N-C in pyridine-shows at 1238.89, and 1190.95 cm -1 (expt and simulated), respectively, and the C-H bending in pyridine-shows at 950.46, and 926.37 cm -1 (expt and simulated), respectively. Compound-3 belongs to the C1 point group of symmetry. It has 33 atoms; hence 93 normal modes of fundamental vibrations are possible, and the total dipole moment is 3.13 debye. All the 93 fundamental vibrations are active in FT-IR spectra. The frequencies for the O-H stretching in 2-methylbutanoic acid shows at 3424.80, and 3462.00 cm -1 (expt and simulated), respectively, the C-H stretching in azomethine-shows at 3062.48, and 2956.31 cm -1 (expt and simulated), respectively, the C-H symmetry and asymmetry stretching occurs between 2955.11 and 2528.98, and 3048.28 and 2801.10 cm -1 (expt and simulated), respectively, the C=O in 2-methylbutanoic acid shows at 1726.19, and 1579.35 cm -1 (expt and simulated), respectively, the N=C in azomethine-shows at 1615.76, and 1564.86 cm -1 (expt and simulated), respectively, the C=C in phenyl-shows at 1587.39, and 1549.98 cm -1 (expt and simulated), respectively, the C-H bending occurs between 1513.86 and 1469.67, and 1461.79 and 1403.58 cm -1 (expt and simulated), respectively, the C-H bending in azomethine-shows at 1413.97, and 1352.80 cm -1 (expt and simulated) respectively, and O-H bending in 2-methylbutanoic acid shows at 699.29, and 652.002 cm -1 (expt and simulated), respectively. Figure 5 presents the proton-NMR, while Figure 6 shows the Carbon-13 NMR spectra for Schiff bases.    The study of light-matter interactions is significant, especially for organic molecules. This property is also called frequency conversion and explains the chirality property for Schiff bases. The simulation is carried out at the same theoretical level as the optimization and is compared with a standard non-linear optically active substance, p-nitro acetanilide [54]. The non-linear optics property parameters for Schiff bases are shown in Table 3. The charge separation property of the whole molecule is also called dipole moments (μ) for Compound-1, 2, and 3 are 1.43, 1.74, and 1.12 D. The tendency of matter in another word polarizability of Schiff bases having the hyperpolarizability (β) for Compound-1, 2, and 3 are 3.09*10 -30 , 1.29*10 -30 , and 1.80*10 -30 esu, mean polarizability (α0) for Compound-1, 2, and 3 are 2.50*10 -23 , 2.27*10 -23 , and 2.28*10 -23 esu, and degree of polarization is also called anisotropy of the polarizability (Δα) for Compound-1, 2, and 3 are 6.28*10 -23 , 5.93*10 -23 , and 5.75*10 -23 esu. The sum of molecular refractions (MR) for Compound-1, 2, and 3 are 63.17, 57.36, and 57.61 esu.

Average localized ionization energy (ALIE) for Schiff bases.
The average localized ionization energy (ALIE) study predicts the local ionization energy required for the electronic excitations [62][63][64][65][66][67][68]. This wavefunction-based property is determined using the multiwave function software with the optimized geometry. Figure 7 represents the ALIE profile of the three compounds under study. Schiff bases Compound-1, 2, and 3 have regions from blue to red as the scale values between 0.000 and 2.000, and the molecule within -10.31 to 11.20, -12.73 8.49 -8.33 to 12.49 Bohr 3, respectively. Schiff bases molecules color blueish-green indicates moving electrons or delocalization of electrons in Compound-1 at the sites are purine-, and phenyl-rings, and purine-ring to azomethine-chain, for Compound-2 at the sites are pyridine-ring to azomethine-chain and propylene-to azomethine-chain, and Compound-3 at the sites are carbonyl-, and hydroxyl-oxygens in 4-methylpentanoic acid groups, respectively. Schiff bases Compound-1, 2, and 3 are blue indicates the sigma bond and the stable bond between atoms in the molecule, which the sites are from protons to carbons in the whole molecule, and lone pair of electrons in all the nitrogen atoms. Schiff bases Compound-1, 2, and 3 are red, indicating multiple bonds occur in the molecule. Fortunately, this molecule has not any numerous bonds.
The average localized ionization energy (ALIE) explained the stability and reactivity of molecules. The red color indicates core electrons, blue indicates bonded electrons, and these are localized, but greenish-yellow indicates delocalized electrons of molecules. These delocalized electrons explain the stability of molecules by the number of resonance structures and reactivity by electronic sites; if bonded electrons move automatically, electronic rich and poor sites can form, and these sites undergo electrophilic and nucleophilic reactions.

Molecular electrostatic potentials (MESP) from electronic charges and nuclear charges for Schiff bases.
Electrostatic potential can indicate the molecules' 3D charge distribution, identifying its possible electrophilic and nucleophilic centers [69-77]. The potential can be due to the presence of electrons and the fact of nuclear charge. The electrostatic potentials study for derivatives of flavonoid wavefunction was generated using DFT-B3LYP, 6-311G+ (2d,p) as a basis set. Figure 8 shows the molecular electrostatic potentials (MESP) for Schiff bases by electronic charges. Schiff bases Compound-1, 2, and 3 show from the color blue to red, scale values from -0.10 to 0.100, and range from -10.02 to 14.31, from -12.66 to 10.63, and from -8.29 to 12.43 Bohr 3, respectively. Schiff bases, Compound-1 having the on all the nitrogen atoms in purine-ring, and imine nitrogen, these are electron-rich sites, so electrophiles can quickly attack these sites. The red color on all the carbons has a sigma bond with hydrogen atoms in the whole molecule; these are electron-poor sites, so nucleophiles can quickly attack these sites, Compound-2 has the blue color on all the ketonic-oxygen and nitrogen atoms in the pyridine-ring, and imine nitrogen, these are electron-rich sites, so electrophiles can easily attack these sites. The red color on all the carbons has a sigma bond with hydrogen atoms in the whole molecule; these are electron-poor sites, so nucleophiles can easily attack these sites, and Compound-3 has the blue color on carbonyl-, hydroxyl-oxygens in the 4-methylpentanoic acid group, and imine nitrogen, these are electron-rich sites, so electrophiles can quickly attack these sites. The red color on all the carbons having a sigma bond with hydrogen atoms in the whole molecule represents electron-poor sites, where nucleophiles can easily attack. Figure 9 shows the molecular electrostatic potentials (MESP) for Schiff bases by nuclear charges. Schiff bases Compound-1, 2, and 3 show from the color blue to red, values from 0.00 to 50.00, and within from -11.85 to 11.95, from -12.73 to 10.73, and from -10.53 to 8.33 Bohr 3, respectively. Schiff bases compounds 1-3 having a nuclear charge between 47.00 and 50.00, has negative electrostatic potentials that show high electron density, leading to prominent attractions of protons with nuclei due to the core and lone pair of electrons in heavy atoms are carbons, nitrogens, and oxygen in the molecule and nuclear charges between 17.00 and 23.00 having positive electrostatic potentials show large repulsions of protons with nuclei due to no neutrons, core, and lone pair of electrons in all the hydrogens in the whole molecule.

Molecular docking studies of Schiff bases.
A molecular docking study can explain the interactions between Schiff bases and protein to provide a medicinal effect. The compound's related Schiff bases can show biological activity, so the reported three new compounds may also show medicinal properties [83,84]. This was confirmed by using the prediction of the biological activity using the PASS online tool [35] and is given in Table 4. The first two compounds are found to show anti-eczematic activity, and the third compound is antiarthritic activity. The proteins responsible for these activities are downloaded from the protein data bank [38], cleaned, and subjected to molecular docking with Autodock Vina. The downloaded proteins are (PDB ID: 1B5T) for H+transporting two-sector ATPase inhibitor, (PDB ID: 2P9W) for anti-eczematic activity, and (PDB ID: 1FQ7) for acrocylindropepsin inhibitor. The binding affinity for Schiff bases shows in Table 5, and binding affinities for Compound-1, 2, and 3 are -7.60, -7.80, and -6.30 kcal/mol at zero roots mean square deviation (rmsd) at the lower and upper base, respectively. Figures 11 and 12 show the skeletal and 2D structure of interactions between Schiff bases molecules and proteins.    Table S9 shows the favorable, unfavorable, and unsatisfied bonds for Schiff bases molecules and proteins by distance (Å), category, type, from chemistry to chemistry. The favorable non-bonds for Compound-1 having two conventional hydrogen bonds, one pi-anion, one pi-donor hydrogen bond, one pi-sigma, two pi-pi stacked bonds, two pi-pi T-shaped bonds, and four pi-alkyl bonds, for Compound-2 having four conventional hydrogen bonds, one pianion bond, and two pi-alkyl bonds, for Compound-3 having three traditional hydrogen bonds, one pi-alkyl bond. The unfavorable non-bond for Compound-3 has one bond. The unsatisfied bonds for hydrogen atoms act as donors, and nitrogen atoms act as acceptors in Compound-1 and 2.

Conclusions
The simulated and scaled vibration spectra match with the experimentally observed spectra of the Schiff bases compounds. The frontier molecular orbital property was analyzed Schiff bases compounds, Compound-3 having a more significant energy gap (∆E) than other Schiff bases, and Compound-2 having a smaller energy gap (∆E) than other Schiff bases. FMO gives some information via chemical descriptors for Schiff bases compounds. From the lightharvesting efficiency (LHE) study, Compound-3 has a high percentage of light-harvesting efficiency properties. From the NLO study, Compound-2 has a more excellent dipole moment than other Schiff bases compounds, urea, and p-nitro acetanilide. Compound-1 has higher mean-polarizability and molar refractivity than other Schiff bases compounds, urea, and p-nitro acetanilide. NBO studies revealed the intensity of various intramolecular interactions for Schiff bases compounds. Nature of localized electrons for Schiff bases compounds discussed in ALIE study. The electrostatic potentials by electronic and nuclear charges for Schiff bases compounds are explained in the MESP study. The weak, strong hydrogen bonds and steric bond attractions are defined for Schiff-based compounds in the NCI study. The structure relative activity confirmed from PASS and Compound-2 has a higher binding affinity among Schiff bases molecules.