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ML Foundations Development 49

It seems to me that the addition of electrons and protons as you move across a period would cause an atom to become larger. However, I'm told it gets smaller. Why is this?

Why do atoms generally become smaller as one moves left to right across a period?

My understanding is that NaCl is an ionic compound, in which Cl becomes (effectively) Cl$^-$ and Na becomes Na$^+$. So I understand why I would get a "sea" of particles that would stick together. But why does the above mean that it will have a face centered cubic structure with the ions held in place so rigidly?

How does NaCl maintain its crystalline structure?

A reaction proceeds towards the direction of lesser Gibbs Free energy (at constant T and P). So, we could say that Gibbs free energy at equilibrium is _minimum_. On the other hand, we have $$\Delta G=\Delta G^o + RT\ln Q$$, where $Q$ is the reaction quotient. At equilibrium, $Q=K_{eq}$, and we already know that $\Delta G^o=-RT\ln K_{eq}$. Substituting, we get $\Delta G=0$ at equilibrium. But, we know that $G$ minimized itself--thus there _was_ a change in $G$ and $\Delta G < 0$. What am I missing here?

Gibbs free energy-minimum or zero?

When [N,N-dimethylaniline][1] is reacted with H$_2$SO$_4$ and HNO$_3$ it gives mainly the *meta* product, even though NMe$_2$ is an *ortho* / *para* directing group. Why is this? [1]: http://en.wikipedia.org/wiki/Dimethylaniline

Why does nitration yield a meta product in this reaction?

Recrystallization is a nice way of purifying a reaction, but choosing a suitable solvent if you can't rely on the literature seems like a lot of trial-and-error. Are there any general rules on which kind of solvents could be used for recrystallization? Which criteria should one use when trying to recrystallize a compound for which no literature on useable conditions exists?

Are there any general rules for choosing solvents for recrystallization?

I often hear that water gets purified by beeing in a silver vessel, which sounds plausible because of becrtericidal feature of silver. What doesn't sound plausible, though, is the way it's explained: that silver realeses ions into the water. Since silver is noble metal, why would any "reaction" at all occur with something as neutral as water? Is the above explanation nonsense? Does the "disinfection" of water happen only on contact with the metal?

In environmental chemistry, most of the organophosphorous compounds we worry about are actually organophosphate compounds. Is there something about the C-P bond that makes it less stable (and thus less persistent in the environment) than a C-O-P bond?

Stability of organophosphorous vs organophosphates?

Organic compounds are typically defined as “molecules containing carbon”. [Wikipedia states][1] that there for some historical (read: non-logical) reasons, > *a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon, and cyanides, as well as the allotropes of carbon such as diamond and graphite, are considered inorganic.* I thus wonder: **is [activated charcoal](http://en.wikipedia.org/wiki/Activated_carbon) (also known as activated carbon) typically classified as an organic or inorganic material?** If I follow the list of exceptions given by Wikipedia, it should be organic (it's not an allotrope of carbon, in particular), but I get the feeling that most people in the field of porous materials would classify it as inorganic. So, I'm looking for an authoritative reference on this question. [1]: http://en.wikipedia.org/wiki/Organic_compound

Is activated carbon classified as organic or inorganic?

What software is available out there to calculate the equilibrium in a set of reactions in aqueous solution? In particular, I'm interested in software general enough to simulate things like titration curves involving acido-basicity, complex formation, precipitation… A web search turns up plenty of academic papers giving algorithms to find the equilibrium of such systems, but I'd like to find software that actually performs it. In particular, it would be really helpful if there existed such software that included a decent database of reaction constants for some well-known reactions (pKa for common acide-base couples, complexation and precipitation constants, etc.).

What software can simulate aqueous reactions?

How can one choose which group has more shifting tendency in 1,2 carbocation rearrangement? The obvious order is via the stability of the carbocation of the group. But, phenylic groups have high shifting tendency--and a phenylic carbocation is unstable. Is there a way of predicting these? I was thinking that it will be related to the delocalization in the triangular intermediate formed.

What software can simulate aqueous solution equilibria?

The reagent [APTES](http://www.sigmaaldrich.com/catalog/product/aldrich/440140?lang=en&region=US) is a fairly common "ink" for microcontact printing, a technique that forms covalent bonds between the silanols found on the surface of the glass and the silane in the the APTES. It's also been demonstrated that the mono-layer then polymerizes somewhat, forming bonds between neighboring silanols. What is the mechanism by which the printing and polymerization occur and what is the reason for using APTES instead of a more reactive trichlorosilane?

What is the mechanism of APTES mono-layer formation on glass substrates?

I've heard quite a few times that the chromate and permanganate have a $d^3s$ configuration. Also, their colors arise due to a rapid switching of electrons between the oxygen and metal atoms. I don't really understand the 'rapid switching' part--it's obvious why it can give color, but I fail to see why there is a need for such a switching-what's so special about Cr and Mn? (I also do not know what the switching exactly is) An explanation of $d^3s$ would be appreciated, though not necessary.

The <a href="http://en.wikipedia.org/wiki/Vitamin_B12_total_synthesis"> total synthesis </a> of B-12 by Burns Woodward and Eschenmoser, is over 30 years old. At its time, it was considered a landmark in the field. > With current developments (e.g. olefin metathesis, palladium catalysis, etc.) is it possible to optimize this synthesis? By "optimize" I mean reduce the number of steps in the synthesis.

Can recent developments improve the total synthesis of B-12?

It is known that impurities in a desired isolated product lower the melting point of the mixture, even if the impurities melting point is much higher than the desired product. Why is that?

Why do any impurities lower the melting point of an isolated substance?

In a crystal structure I've determined, a triazole ring on my ligand appears to be stacking with a tyrosine (top in picture): <a href="https://i.stack.imgur.com/Irazz.jpg"><img src="https://i.stack.imgur.com/Irazz.jpg" height="300" alt="stacking interactions in a protein"></a> However, there is also an amide, courtesy a glutamine, near it (bottom). Is it likely this terminal amide is engaging in &pi;-&pi; interactions with the triazole or just weaker dispersion forces? How would I quantify how significant the interaction is?

Do terminal amides participate in $\pi$ stacking?

What conditions promote a nucleophile to undergo the Michael reaction over the nucleophilic attack at the alpha carbon of the carbonyl group in an alpha-beta-unsaturated ketone? I'm looking for an answer that considers organic and inorganic nucleophiles (like organocuprates/organolithium compounds).

Michael reaction or nucleophilic attack at the alpha carbon of an alpha-beta-unsaturated ketone?

It's a very general statement, but it's not always true. For example, impurities of gold in silver will increase the melting point. --- Your majority component B and the impurity (let's call it A) form a binary system. In most cases, such binary mixtures exhibit a solid–liquid phase diagram as follows: ![enter image description here][1] (image taken from [these lecture notes](http://research.pbsci.ucsc.edu/chemistry/li/teaching/chem268/Interpretation%20of%20Phase%20Diagram.pdf)). This binary phase diagram has pure A on the left, pure B on the right. A and B form, somewhere, a eutectic. It is the point here at concentration *e* and temperature *y*. Because the existence of a eutectic point is guaranteed for any A/B binary system, and because the eutectic corresponds to a lower temperature, your liquidus curve decreases with increasing impurity concentration, and the impurity thus lowers the melting point. However, not all binary mixtures form a eutectic. In the words of [Wikipedia][2]: > Not all binary alloys have a eutectic point; for example, in the silver-gold system the melt temperature (liquidus) and freeze temperature (solidus) both increase monotonically as the mix changes from pure silver to pure gold. The corresponding phase diagram is as follows: [![enter image description here][3]](http://www.crct.polymtl.ca/fact/phase_diagram.php?file=Ag-Au.jpg&dir=SGTE) [1]: https://i.stack.imgur.com/5Og92.png [2]: http://en.wikipedia.org/wiki/Eutectic_system [3]: https://i.stack.imgur.com/fidq0.jpg

> How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic Triazole and amide is a rather straightforward process. This process is referred to as the supramolecular approach. I'll point you to a paper that analyzes the [benzene dimer][1]. This method is strictly a computational one so a bit of knowledge in computational chemistry is necessary. **The Supramolecular Approach** ------------------------------- **The What** The supramolecular approach boils down to this. $E_{int} = E_{dimer} - (E_{mon1} + E_{mon2})$ Here we have some interaction energy ($E_{int}$) determined from the difference of a dimer energy ($E_{dimer}$) and the sum of the two monomers ($E_{monomer}$). If both monomers were equivalent (say, you were interested in the interaction energy of the benzene dimer where each monomer was a benzene ring), you could simplify the summation to two times the energy of one monomer ($2E_{mon}$). In your particular case, you have two different monomers. The whole idea is if I have two interacting molecules, I can determine the energy of each molecule individually (as if they were separated at infinite distance) as well as their complex. So as you bring these molecules closer and closer together, the energy starts to go down (the interaction energy). **The How** NOTE: Your geometry is from a crystal structure. Do NOT modify this geometry. You will want to keep everything exactly as is. This means you don't want to optimize your system. You do not want to eyeball monomer placement. Take everything from your known structure and be careful not to change it otherwise it can ruin this process. EDIT: We are modifying the structure by truncating and capping but intermolecular parameters must stay the same for whatever it is you are trying to model. 1. Define your monomers. You will need to determine what part of your 'dimer' system is important for describing this weak interaction. I recommend keeping the aromatic ring and truncating the ring with something similar to what is being truncated. You could cap your monomer with a hydrogen or a methyl group for example. 2. Define your dimer. Your dimer is simply a combination of your two defined monomers. 3. Determine the method you want to implement. [Post-Hartree Fock methods][2] are essential for this. Note that if you use the widely-implemented MP2 method, your answer may be way off (can over-estimate pi-pi interactions by as much as 200%!). The CCSD(T) method is recommended. 4. Determine the energies of your monomers and dimer. You will want to run a single-point energy calculation on your monomers and your dimer. 5. Determine the interaction energy. Plug your energies into the equation given above and determine the interaction energy. Convert to whatever units you wish to use (I prefer kJ/mol but most people use kcal/mol so you may want to use that). I hope this helps. Looks like an interesting project to say the least. [1]: http://pubs.acs.org/doi/abs/10.1021/ja025896h [2]: http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock

> How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic Triazole and amide is a rather straightforward process. This process is referred to as the supramolecular approach. I'll point you to a paper that analyzes the [benzene dimer][1]. This method is strictly a computational one so a bit of knowledge in computational chemistry is necessary. **The Supramolecular Approach** ------------------------------- **The What** The supramolecular approach boils down to this. $E_{int} = E_{dimer} - (E_{mon1} + E_{mon2})$ Here we have some interaction energy ($E_{int}$) determined from the difference of a dimer energy ($E_{dimer}$) and the sum of the two monomers ($E_{monomer}$). If both monomers were equivalent (say, you were interested in the interaction energy of the benzene dimer where each monomer was a benzene ring), you could simplify the summation to two times the energy of one monomer ($2E_{mon}$). In your particular case, you have two different monomers. The whole idea is if I have two interacting molecules, I can determine the energy of each molecule individually (as if they were separated at infinite distance) as well as their complex. So as you bring these molecules closer and closer together, the energy starts to go down (the interaction energy). **The How** NOTE: Your geometry is from a crystal structure. Do NOT modify this geometry. You will want to keep everything exactly as is. This means you don't want to optimize your system. You do not want to eyeball monomer placement. Take everything from your known structure and be careful not to change it otherwise it can ruin this process. EDIT: We are modifying the structure by truncating and capping but intermolecular parameters must stay the same for whatever it is you are trying to model. 1. Define your monomers. You will need to determine what part of your 'dimer' system is important for describing this weak interaction. I recommend keeping the aromatic ring and truncating the ring with something similar to what is being truncated. You could cap your monomer with a hydrogen or a methyl group for example. 2. Define your dimer. Your dimer is simply a combination of your two defined monomers. 3. Determine the method you want to implement. [Post-Hartree Fock methods][2] are essential for this. Note that if you use the widely-implemented MP2 method, your answer may be way off (can over-estimate pi-pi interactions by as much as 200%!). The CCSD(T) method is recommended. 4. Define your basis set. For aromatic systems your best bet would be to use Dunning-Hunzaga's correlation consistent family of basis sets. I recommend using aug-cc-pVTZ for good results. 5. Determine the energies of your monomers and dimer. You will want to run a single-point energy calculation on your monomers and your dimer. 6. Determine the interaction energy. Plug your energies into the equation given above and determine the interaction energy. Convert to whatever units you wish to use (I prefer kJ/mol but most people use kcal/mol so you may want to use that). I hope this helps. Looks like an interesting project to say the least. [1]: http://pubs.acs.org/doi/abs/10.1021/ja025896h [2]: http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock

> How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic Triazole and amide is a rather straightforward process. This process is referred to as the supramolecular approach. I'll point you to a paper that analyzes the [benzene dimer][1]. This method is strictly a computational one so a bit of knowledge in computational chemistry is necessary. **The Supramolecular Approach** ------------------------------- **The What** The supramolecular approach boils down to this. $E_{int} = E_{dimer} - (E_{mon1} + E_{mon2})$ Here we have some interaction energy ($E_{int}$) determined from the difference of a dimer energy ($E_{dimer}$) and the sum of the two monomers ($E_{monomer}$). If both monomers were equivalent (say, you were interested in the interaction energy of the benzene dimer where each monomer was a benzene ring), you could simplify the summation to two times the energy of one monomer ($2E_{mon}$). In your particular case, you have two different monomers. The whole idea is if I have two interacting molecules, I can determine the energy of each molecule individually (as if they were separated at infinite distance) as well as their complex. So as you bring these molecules closer and closer together, the energy starts to go down (the interaction energy). **The How** NOTE: Your geometry is from a crystal structure. Do NOT modify this geometry. You will want to keep everything exactly as is. This means you don't want to optimize your system. You do not want to eyeball monomer placement. Take everything from your known structure and be careful not to change it otherwise it can ruin this process. We are modifying the structure by truncating and capping but intermolecular parameters must stay the same for whatever it is you are trying to model. 1. Define your monomers. You will need to determine what part of your 'dimer' system is important for describing this weak interaction. I recommend keeping the aromatic ring and truncating the ring with something similar to what is being truncated. You could cap your monomer with a hydrogen or a methyl group for example. 2. Define your dimer. Your dimer is simply a combination of your two defined monomers. 3. Determine the method you want to implement. [Post-Hartree-Fock methods][2] are essential for this. Note that if you use the widely-implemented MP2 method, your answer may be way off (can over-estimate pi-pi interactions by as much as 200%!). The CCSD(T) method is recommended. 4. Define your basis set. For aromatic systems your best bet would be to use Dunning-Hunzaga's correlation consistent family of basis sets. I recommend using aug-cc-pVTZ for good results. Whatever you decide, be sure your basis set includes polarization and diffuse functions. The suggested basis set does this (augmented means diffuse on all atoms whereas pVTZ means 'polarized-valence triple zeta'). 5. Determine the energies of your monomers and dimer. You will want to run a single-point energy calculation on your monomers and your dimer. 6. Determine the interaction energy. Plug your energies into the equation given above and determine the interaction energy. Convert to whatever units you wish to use (I prefer kJ/mol but most people use kcal/mol so you may want to use that). I hope this helps. Looks like an interesting project to say the least. **A quick note about the 'valence' basis-set:** Typically core electrons do not participate in any sort of interesting chemistry (they are so much lower in energy than the valence electrons that they do not play a role in things like chemical bonding). When you perform these energy computations, you will be invoking the frozen-core approximation (default on many quantum software packages but be sure to check the documentation first). The pVTZ basis set expands the basis functions out to triple-zeta quality for valence electrons only. The core electrons are given *s*-type functions and that is it. If you ever find yourself in a situation where the core electrons are important to your system of interest, you would want to use the pCVXZ basis sets (where X = D,T,Q, etc.) which stands for polarized core-valence X zeta. Here the core electrons are given the full set of X-zeta quality basis functions. However this means you've just made your computation much more expensive. The frozen-core approximation is typically used. [1]: http://pubs.acs.org/doi/abs/10.1021/ja025896h [2]: http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock

> How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic Triazole and amide is a rather straightforward process. This process is referred to as the supramolecular approach. I'll point you to a paper that analyzes the [benzene dimer][1]. This method is strictly a computational one so a bit of knowledge in computational chemistry is necessary. **The Supramolecular Approach** ------------------------------- **The What** The supramolecular approach boils down to this. $E_{int} = E_{dimer} - (E_{mon1} + E_{mon2})$ Here we have some interaction energy ($E_{int}$) determined from the difference of a dimer energy ($E_{dimer}$) and the sum of the two monomers ($E_{monomer}$). If both monomers were equivalent (say, you were interested in the interaction energy of the benzene dimer where each monomer was a benzene ring), you could simplify the summation to two times the energy of one monomer ($2E_{mon}$). In your particular case, you have two different monomers. The whole idea is if I have two interacting molecules, I can determine the energy of each molecule individually (as if they were separated at infinite distance) as well as their complex. So as you bring these molecules closer and closer together, the energy starts to go down (the interaction energy). **The How** NOTE: Your geometry is from a crystal structure. Do NOT modify this geometry. You will want to keep everything exactly as is. This means you don't want to optimize your system. You do not want to eyeball monomer placement. Take everything from your known structure and be careful not to change it otherwise it can ruin this process. We are modifying the structure by truncating and capping but intermolecular parameters must stay the same for whatever it is you are trying to model. You will want to optimize your cap meaning, run an optimization on your capped-monomer but freeze everything but the thing you are using to cap. 1. Define your monomers. You will need to determine what part of your 'dimer' system is important for describing this weak interaction. I recommend keeping the aromatic ring and truncating the ring with something similar to what is being truncated. You could cap your monomer with a hydrogen or a methyl group for example. If the piece you've cut out is highly polarizable, cap with something with a similar propety. If your truncated piece is neutral in charge, cap with something that is neutral. You get the idea. 2. Define your dimer. Your dimer is simply a combination of your two defined monomers. 3. Determine the method you want to implement. [Post-Hartree-Fock methods][2] are essential for this. Note that if you use the widely-implemented MP2 method, your answer may be way off (can over-estimate pi-pi interactions by as much as 200%!). The CCSD(T) method is recommended. 4. Define your basis set. For aromatic systems your best bet would be to use Dunning-Hunzaga's correlation consistent family of basis sets. I recommend using aug-cc-pVTZ for good results. Whatever you decide, be sure your basis set includes polarization and diffuse functions. The suggested basis set does this (augmented means diffuse on all atoms whereas pVTZ means 'polarized-valence triple zeta'). 5. Determine the energies of your monomers and dimer. You will want to run a single-point energy calculation on your monomers and your dimer. Optimize your monomers first but freeze all atoms except those you added to cap your monomer. 6. Determine the interaction energy. Plug your energies into the equation given above and determine the interaction energy. Convert to whatever units you wish to use (I prefer kJ/mol but most people use kcal/mol so you may want to use that). I hope this helps. Looks like an interesting project to say the least. **A quick note about the 'valence' basis set:** Typically core electrons do not participate in any sort of interesting chemistry (they are so much lower in energy than the valence electrons that they do not play a role in things like chemical bonding). When you perform these energy computations, you will be invoking the frozen-core approximation (default on many quantum software packages but be sure to check the documentation first). The pVTZ basis set expands the basis functions out to triple-zeta quality for valence electrons only. The core electrons are given *s*-type functions and that is it. If you ever find yourself in a situation where the core electrons are important to your system of interest, you would want to use the pCVXZ basis sets (where X = D,T,Q, etc.) which stands for polarized core-valence X zeta. Here the core electrons are given the full set of X-zeta quality basis functions. However this means you've just made your computation much more expensive. The frozen-core approximation is typically used. [1]: http://pubs.acs.org/doi/abs/10.1021/ja025896h [2]: http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock

"Color" is what we see when electrons transition from a high-energy orbital to a less energetic one, if the energy associated with that transition happens to produce a photon within the visible spectrum. It might be helpful to stop thinking of electrons as being on either the metal or the oxygen, and to consider that in these cases electrons occupy molecular orbitals, which can encompass more than one atom. In this case, it seems likely that one of the orbitals in question might have higher electron density around the metal, while the other could have higher electron density around oxygen. Why are Cr and Mn special? I would interpret it as coincidence that the oxides of these metals are prone to electronic transitions that generate photons which register as vibrant colors to our eyes.

One synthesis of [**quinolones**](http://en.wikipedia.org/wiki/Quinolone) begins with the formation of an **ethyl ethoxymethylenemalonate**, as seen in this _Organic Syntheses_ [paper](http://orgsyn.org/OrgSyn/orgsyn/orgsyn_form.asp?formgroup=basenpe_form_group&dbname=orgsyn&formmode=edit&unique_id=undefined&commit_type=undefined&indexvalue=44&form_change=false&time=67470.8). I've been asked if the **malonate** derivative would be formed if **methylmalonate** was treated with **trimethyl orthoformate** with a catalytic amount of $\mathrm{H^+}$, _without_ heating. The nature of the solvent isn't mentioned, but I guess the reaction is carried out in a non-aqueous medium with an [ion-exchange resin](http://www.amberlyst.com/sac.htm), since I think **trimethyl orthoformate** acts as a water trap. My hunch is that there shouldn't be a significant quantity of product formed. We're dealing with an **activated methylene**, why not simply use a base and then carry on with our addition? I can't imagine how, under normal circumstances, the elimination product **ethyl ethoxymethylenemalonate** will be formed. How can this reaction happen in a mechanistically reasonable way?

[This question](http://chemistry.stackexchange.com/questions/2/how-does-nacl-maintain-its-crystalline-structure) on NaCl crystalization actually got me wondering: are there any ionic amorphous solids? Like ionic crystals are crystalline materials of electrostatically-attracted ions, can ions form an amorphous phase? I can see no reason why not, but I cannot think of any example either…

Are there any ionic amorphous solids?

One synthesis of [**quinolones**](http://en.wikipedia.org/wiki/Quinolone) begins with the formation of an **ethyl ethoxymethylenemalonate**, as seen in this _Organic Syntheses_ [paper](http://www.orgsyn.org/orgsyn/orgsyn/prepContent.asp?prep=cv3p0395). ![enter image description here][1] I've been asked if the **malonate** derivative would be formed if **methylmalonate** was treated with **trimethyl orthoformate** with a catalytic amount of $\mathrm{H^+}$, _without_ heating. The nature of the solvent isn't mentioned, but I guess the reaction is carried out in a non-aqueous medium with an [ion-exchange resin](http://www.amberlyst.com/sac.htm), since I think **trimethyl orthoformate** acts as a water trap. My hunch is that there shouldn't be a significant quantity of product formed. We're dealing with an **activated methylene**, why not simply use a base and then carry on with our addition? I can't imagine how, under normal circumstances, the elimination product **ethyl ethoxymethylenemalonate** will be formed. How can this reaction happen in a mechanistically reasonable way? [1]: https://i.stack.imgur.com/2taiJ.png

> How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic Triazole and amide is a rather straightforward process. This process is referred to as the supramolecular approach. I'll point you to a paper that analyzes the [benzene dimer][1]. This method is strictly a computational one so a bit of knowledge in computational chemistry is necessary. **The Supramolecular Approach** ------------------------------- **The What** The supramolecular approach boils down to this. $E_{int} = E_{dimer} - (E_{mon1} + E_{mon2})$ Here we have some interaction energy ($E_{int}$) determined from the difference of a dimer energy ($E_{dimer}$) and the sum of the two monomers ($E_{monomer}$). If both monomers were equivalent (say, you were interested in the interaction energy of the benzene dimer where each monomer was a benzene ring), you could simplify the summation to two times the energy of one monomer ($2E_{mon}$). In your particular case, you have two different monomers. The whole idea is if I have two interacting molecules, I can determine the energy of each molecule individually (as if they were separated at infinite distance) as well as their complex. So as you bring these molecules closer and closer together, the energy starts to go down (the interaction energy). **The How** NOTE: Your geometry is from a crystal structure. Do NOT modify this geometry. You will want to keep everything exactly as is. This means you don't want to optimize your system. You do not want to eyeball monomer placement. Take everything from your known structure and be careful not to change it otherwise it can ruin this process. We are modifying the structure by truncating and capping but intermolecular parameters must stay the same for whatever it is you are trying to model. You will want to optimize your cap meaning, run an optimization on your capped-monomer but freeze everything but the thing you are using to cap. 1. Define your monomers. You will need to determine what part of your 'dimer' system is important for describing this weak interaction. I recommend keeping the aromatic ring and truncating the ring with something similar to what is being truncated. You could cap your monomer with a hydrogen or a methyl group for example. If the piece you've cut out is highly polarizable, cap with something with a similar property. If your truncated piece is neutral in charge, cap with something that is neutral. You get the idea. 2. Define your dimer. Your dimer is simply a combination of your two defined monomers. 3. Determine the method you want to implement. [Post-Hartree-Fock methods][2] are essential for this. Note that if you use the widely-implemented MP2 method, your answer may be way off (can over-estimate pi-pi interactions by as much as 200%!). The CCSD(T) method is recommended. 4. Define your basis set. For aromatic systems your best bet would be to use Dunning-Hunzaga's correlation consistent family of basis sets. I recommend using aug-cc-pVTZ for good results. Whatever you decide, be sure your basis set includes polarization and diffuse functions. The suggested basis set does this (augmented means diffuse on all atoms whereas pVTZ means 'polarized-valence triple zeta'). 5. Determine the energies of your monomers and dimer. You will want to run a single-point energy calculation on your monomers and your dimer. Optimize your monomers first but freeze all atoms except those you added to cap your monomer. 6. Determine the interaction energy. Plug your energies into the equation given above and determine the interaction energy. Convert to whatever units you wish to use (I prefer kJ/mol but most people use kcal/mol so you may want to use that). I hope this helps. Looks like an interesting project to say the least. **A quick note about the 'valence' basis set:** Typically core electrons do not participate in any sort of interesting chemistry (they are so much lower in energy than the valence electrons that they do not play a role in things like chemical bonding). When you perform these energy computations, you will be invoking the frozen-core approximation (default on many quantum software packages but be sure to check the documentation first). The pVTZ basis set expands the basis functions out to triple-zeta quality for valence electrons only. The core electrons are given *s*-type functions and that is it. If you ever find yourself in a situation where the core electrons are important to your system of interest, you would want to use the pCVXZ basis sets (where X = D,T,Q, etc.) which stands for polarized core-valence X zeta. Here the core electrons are given the full set of X-zeta quality basis functions. However this means you've just made your computation much more expensive. The frozen-core approximation is typically used. [1]: http://pubs.acs.org/doi/abs/10.1021/ja025896h [2]: http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock

An **$\alpha,\beta$-unsaturated ketone** is electrodeficient at the $\beta$ position. This can be seen if you draw the resonance structures of such a molecule. The $\beta$ carbon is thus a good site for nucleophilic attack. But, as you know, carbonyls are also prone to nucleophilic attack. To discriminate between the two, you need to look at how the reaction is _controlled_, either _thermodynamically_ or _kinetically_. In a kinetically controlled reaction, the product that is formed fastest predominates. In a thermodynamically controlled reaction, the predominant product is the energetically favored one. A Michael addition is a 1-4 addition, where a nucleophile attacks the $\beta$ carbon, and produces the thermodynamically favored product. On the other hand, a 1-2 reaction (on the carbonyl) gives the kinetic product, and is obtained at low temperatures. Why is the 1-4 product thermodynamically more stable? Because the resulting product benefits from keto-enol tautomerism, which results in lowering the energy of the system. Usually, the more resonance forms a compound has, the more its electrons are delocalized, the more stable it is. Draw the resonance forms of the 1-4 and 1-2 products, and see. ---------- You asked for specific affinities of different organometallics in 1-4/1-2 additions. My knowledge is that organocuprates ($\mathrm{R-CuLi}$) will perform Michael additions, and that organolithians seem to prefer 1-2 addition. Also, according to [this source](http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch18/ch18-4-2.html), Grignard reagents do not seem to have a preference.

An **$\alpha,\beta$-unsaturated ketone** is electrodeficient at the $\beta$ position. This can be seen if you draw the resonance structures of such a molecule. The $\beta$ carbon is thus a good site for nucleophilic attack. But, as you know, carbonyls are also prone to nucleophilic attack. To discriminate between the two, you need to look at how the reaction is _controlled_, either _thermodynamically_ or _kinetically_. In a kinetically controlled reaction, the product that is formed fastest predominates. In a thermodynamically controlled reaction, the predominant product is the energetically favored one. A Michael addition is a 1-4 addition, where a nucleophile attacks the $\beta$ carbon, and produces the thermodynamically favored product. On the other hand, a 1-2 reaction (on the carbonyl) gives the kinetic product, and is obtained at low temperatures. Why is the 1-4 product thermodynamically more stable? Because the resulting product benefits from keto-enol tautomerism, which results in lowering the energy of the system. Usually, the more resonance forms a compound has, the more its electrons are delocalized, the more stable it is. Draw the resonance forms of the 1-4 and 1-2 products, and see. ---------- You asked for specific affinities of different organometallics in 1-4/1-2 additions. My knowledge is that organocuprates ($\mathrm{R-CuLi}$) will perform Michael additions, and that organolithians seem to prefer 1-2 addition. Also, according to [this source](http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch18/ch18-4-2.html), Grignard reagents do not seem to have a preference. My take on this is that the cuprate is less reactive, and therefore can form the thermodynamic product, whereas the lithium reagent is so destabilized that it reacts right away.

Many of us have experienced the failure of nitrile gloves when exposed to chloroform. What's going on at a mechanistic level when this occurs? I would guess that the chloroform dissolves some of the polymer into its constituent monomers, but I've never heard anything more definite than that. Is it a similar mechanism to what happens when chloroform is left overnight in an HDPE bottle?

What software is available out there to calculate the equilibrium in a set of reactions in aqueous solution? In particular, I'm interested in software general enough to simulate things like titration curves involving acido-basicity, complex formation, precipitation… A web search turns up plenty of academic papers giving algorithms to find the equilibrium of such systems, but I'd like to find software that actually performs it. In particular, it would be really helpful if there existed such software that included a decent database of reaction constants for some well-known reactions (pKa for common acide-base couples, complexation and precipitation constants, etc.). --- *Edit:* Apparently I was unclear: I'm not looking for molecular simulation codes, but for software that can calculate chemical equilibrium in solution from initial concentrations and a database of equilibrium constants for each possible reaction. The kind of thing teachers can use to predict titration curve and demonstrate the effect of various initial concentrations to students.

What software can calculate aqueous solution equilibria?

It's a very general statement, but it's not always true. I'll explain why it's often true, and give a counter-example at the end. --- Your majority component B and the impurity (let's call it A) form a binary system. In most cases, such binary mixtures exhibit a solid–liquid phase diagram as follows: ![enter image description here][1] (image taken from [these lecture notes](http://research.pbsci.ucsc.edu/chemistry/li/teaching/chem268/Interpretation%20of%20Phase%20Diagram.pdf)). This binary phase diagram has pure A on the left, pure B on the right. A and B form, somewhere, a eutectic. It is the point here at concentration *e* and temperature *y*. Because the existence of a eutectic point is guaranteed for any A/B binary system, and because the eutectic corresponds to a lower temperature, your liquidus curve decreases with increasing impurity concentration, and the impurity thus lowers the melting point. However, not all binary mixtures form a eutectic. In the words of [Wikipedia][2]: > Not all binary alloys have a eutectic point; for example, in the silver-gold system the melt temperature (liquidus) and freeze temperature (solidus) both increase monotonically as the mix changes from pure silver to pure gold. The corresponding phase diagram is as follows: [![enter image description here][3]](http://www.crct.polymtl.ca/fact/phase_diagram.php?file=Ag-Au.jpg&dir=SGTE) [1]: https://i.stack.imgur.com/5Og92.png [2]: http://en.wikipedia.org/wiki/Eutectic_system [3]: https://i.stack.imgur.com/fidq0.jpg

Crystals have inspired a great many chemists because they are fascinating *for a good reason*. Not only are they aesthetically pleasing, but they serve as an excellent subject to tour a variety of theoretical subjects important for understanding high-level chemistry. Crystalline materials are made up of periodic structures. We're only going to primarily focus on binary compounds where there is **not** a high degree of covalency. There are several ways to think about this problem, but let's start with the melting of a crystal. We say that at some definite temperature a highly ordered crystal will melt into a liquid. Those of us familiar with the language of equilibrium thermodynamics might recognize that the change in free energy for this phase change can be written, at constant temperature, as, $$ G_{liquid} - G_{crystal} = H_{liquid} - H_{crystal} - T ( S_{liquid} - S_{crystal} ) $$ $$ \Delta G = \Delta H - T \Delta S $$ If we suppose that this process is spontaneous then we would say that the change in Gibbs' free energy is negative, i.e. $\Delta G < 0$. This is true if and only if, $$\Delta H < T \Delta S$$ Traditionally we interpret this as saying that there is a thermally-driven increase in entropy when we melt a highly ordered crystal into a liquid which more than offsets the energy cost associated with the enthalpies of the interactions holding that crystal together. A chemist tends to learn early on that the reverse is not necessarily true: at some definite temperature a perfect crystal **rarely** forms from the liquid. This inability to just heat up any substance and always produce a perfect crystal by cooling illustrates how crystal formation is a case of [kinetic- rather than thermodynamic- control][1]. So the process by which you form your crystal could possibly result in a different crystal structure. Sometimes crystal structures change just by altering the temperature of the chamber you're measuring the crystal structure in! Now neither of these cases apply to sodium chloride to the best of my knowledge. The formation of an ionic crystal such as sodium chloride is a delicate balance between electrostatic attraction and Pauli repulsion. Electrostatic attraction says that between two different charges, $q_+$ and $q_-$, there is a [Coulomb force][2] given by, $$F= \frac{k q_+ q_-}{r^2}$$ where $r$ is the distance between the two charges. If one plays with the numbers then it's easy to see that at short distances the force is strongest, but there is a limit to how close they may come together. Eventually a repulsive force due to a quantum mechanical principle called the [Pauli Exclusion Principle][3] overpowers the attraction. An equilibrium results in which the atoms sit a certain distance from one another so that, if you will humor me, the "forces" between them balance out. This is why we traditionally represent crystal packing using marbles with a unique radii. The radii of the hard marble represents where the Pauli repulsion overpowers the attraction. You might say, "Sure, we have these kinetic, electrostatic and quantum mechanical factors to consider, but how do these help with the final crystal structure?" Hold your horses, we're getting there. A famous mathematician and scientist thought about the most efficient ways to pack spheres of the same size together. By most efficient I mean this in terms of what FedEx considers efficient, fitting things together into the smallest possible volume. This is also what electrostatics want. [Kepler][4] suggested that the best way to pack spheres with this in mind can be maximized in two ways: [fcc][5] and [hcp][6]. This conjecture, however, rests on all the spheres being uniform. We can't assume this is the same for the atoms in table salt because the cation, sodium, is said to be smaller than the chloride anion. A tool that is useful as a *guide* for helping predict the structure is based off of the relative size of the cation, $r_C$, to the anion, $r_A$. This radius ratio, $r_C / r_A$, is mostly only useful for simple binary species. These $r_C$ and $r_A$ are tabulated as ionic radii in many chemistry books; they are contrived by various rules proposed by researchers, such as [Linus Pauling][7], applied to the experimentally determined interionic distances. In this system we find it useful to discuss how many neighbors an anion or a cation has of the opposite charge. The coordination number (CN) tells us how many neighbors a type of atom has around it. A certain $r_C / r_A$ gives us a feel for the probable CN. From one source I was able to calculate the ratio for NaCl as $r_{Na^+} / r_{Cl^-} = 0.564$. Most textbooks will say that if your ratio is 0.414-0.732, then you have CN=6. I'll show you how to calculate the minimum value for CN=6. The easiest way to obtain the maximum is to obtain the minimum for CN=8. Briefly, if we put a small cation on a XY plane and surround it in the manner shown below then we could also place two circles in the Z-axis above and below the central cation for CN=6. (I won't show those two in the Z-axis for clarity.) We would say that a given CN is stable only if the spheres are all touching each other. We would say that for the ratios drawn that a CN=8 is not stable because our cation's sphere would be too small and wouldn't touch all eight of its neighbors. A higher density is always preferred, so CN=4 is not preferred when CN=6 is stable. ![for CN=6][8] Clearly, $\angle DAC = 45 ^{\circ}$. Moreover, we can say that $\overline{DC} = r_A$ and $\overline{AC} = r_A + r_C$. Trigonometry will tells us that $$\sin 45 ^{\circ} = \frac{\overline{DC}}{\overline{AC}}$$ Substituting in those values just determined, $$\frac{\sqrt{2}}{2} = \frac{r_A}{\overline{r_A + r_C}}$$ Solving for $r_C/r_A$ gives, $$r_C/r_A=\frac{2}{\sqrt{2}} -1 = 0.414$$ which is the lower bound desired. So we can say that the CN=6 for the cation. Similarly you can figure out that CN=6 for the anion. This is why we say it has a 6:6 coordination pattern, which is indicative of a sodium chloride type structure. Cesium chloride, on the other hand, is 8:8 and indicative of its structure type. We tend to say that these patterns are consistent with a certain crystal structure because all the pieces fit together consistently. This geometric concept is based purely on sphere packing and is not without its limitations. A more quantitative way to figure out which geometry is preferred is to calculate the elecrostatic energies for the different geometries. A Russian by the name of Kapustinskii derived a [formula][9] to do this, $$E_{lattice} (kJ/mol) = \frac{\alpha}{r_C + r_A} $$ From here you need to put it in terms of the radius ratio with a constant $r_A$, (I should note that this is evil algebra: $ \frac{ a/b}{d/b + 1}= \frac{a}{b+d} $ where $a=\alpha$, $b=r_A$, $d=r_C$.) $$E_{lattice} = \frac{\alpha/r_A}{\frac{r_C}{r_A} + 1} $$ Basically $\alpha$ is different for a change in the crystal structure type and from there you compare which has the preferred energy. You can reproduce the geometric trends using this more quantitative model. There are problems with this approach too, such as the neglected dipole and quadrupole and covalency. Yes, even in NaCl there is some covalent character. I think we say that NaCl 67 % ionic character. These become important when two different crystal structures are close in energy or when more exact calculations are required. [1]: http://en.wikipedia.org/wiki/Thermodynamic_versus_kinetic_reaction_control [2]: http://en.wikipedia.org/wiki/Coulomb%27s_law [3]: http://en.wikipedia.org/wiki/Pauli_exclusion_principle [4]: http://en.wikipedia.org/wiki/Kepler_conjecture [5]: http://en.wikipedia.org/wiki/Face-centered_cubic [6]: http://en.wikipedia.org/wiki/Hexagonal_close_packing [7]: http://en.wikipedia.org/wiki/Linus_Pauling [8]: https://i.stack.imgur.com/H6TV6.png [9]: http://en.wikipedia.org/wiki/Kapustinskii_equation

In the hydrogenation of unsaturated compounds with hydrogen gas and a catalyst, the choice of palladium on carbon is able to hydrogenate alkenes and alkynes, but is unable to hydrogenate aromatic compounds. Using rhodium or Raney nickel, however, allows one to hydrogenate aromatics. How does the choice of catalyst affect what kind of unsaturated compounds can be hydrogenated?

How does the choice of metal (oxide) catalyst affect the range of unsaturated compounds that can be hydrogenated?

The most notable characteristic of polytetrafluoroethylene (PTFE, DuPont's Teflon) is that *nothing* sticks to it. This complete inertness is attributed to the fluorine atoms completely shielding the carbon backbone of the polymer. If nothing indeed sticks to Teflon, how might one coat an object (say, a frying pan) with PTFE?

How is Teflon adhered to frying pans?

Solvent extraction in a separation funnel is a very common method in preparative organic chemistry. But sometimes you don't get a nice phase separation between the organic and the water phase. What are the possible causes that can prevent the formation of two distinct phases, and how can you force a phase separation when you encounter such situations?

What can I do if I don't get a phase separation between my organic and water phases?

How can one choose which group has more shifting tendency in 1,2 carbocation rearrangement? The obvious order is via the stability of the carbocation of the group. But, phenylic groups have high shifting tendency--and a phenylic carbocation is unstable. Is there a way of predicting these? I was thinking that it will be related to the delocalization in the triangular intermediate formed. Update: I'm talking about comparing "migratory aptitude" of the $R$ groups in a system similar to $>C(+)-C(R_1R_2R_3)$

I've heard quite a few times that the chromate and permanganate have a $d^3s$ configuration. Also, their colors arise due to a rapid switching of electrons between the oxygen and metal atoms. I don't really understand the 'rapid switching' part--it's obvious why it can give color, but I fail to see why there is a need for such a switching-what's so special about $\mathrm{Cr}$ and $\mathrm{Mn}$? (I also do not know what the switching exactly is) An explanation of $d^3s$ would be appreciated, though not necessary.

My understanding is that $\mathrm{NaCl}$ is an ionic compound, in which $\mathrm{Cl}$ becomes (effectively) $\mathrm{Cl^-}$ and $\mathrm{Na}$ becomes $\mathrm{Na^+}$. So I understand why I would get a "sea" of particles that would stick together. But why does the above mean that it will have a face centered cubic structure with the ions held in place so rigidly?

I'm currently taking VCE (Victorian Certificate of Education) Chemistry classes, and we're currently studying the interpretation of spectra produced by Hydrogen NMR (Nuclear Magnetic Resonance) spectroscopy. I won't provide too much background information, for I believe a fair level of knowledge in the subject is required on the matter; I'll also not abstain from the jargon. When studying the spectra of High Resolution 'H NMR, the peaks representing the different Hydrogen environments are split into multiplets based on the protons surrounding these environments. There has been a considerable amount of confusion in my classes over the actual principles / rules of thumb on how to calculate the multiplets for a particular environment of a known chemical (i.e.; known structue), based off the 'n + 1' rule. (i.e.; an environment with n neighbours will be split into n+1 multiplets). We are absolute on the principles that; - Peaks of a particular Hydrogen environment are not split by neighbouring protons in equivalent environments. - OH does not, and is not split by, it's neighbouring environments. However, immense confusion arised over whether the following principle was correct. - Peaks of a particular Hydrogen environment will only be split by the protons in neighbouring environments once for each type of neighbouring environment. e.g. The middle "CH2" environment in "CH3-CH2-CH3" will only have 4 peaks; Although it has 6 neighbouring protons, they are two lots of the same environment (CH3). As a class, we found numerous examples from different text books and sources that provide examples of 'H NMR spectra which did not clarify the matter; Some considered all neighbouring protons as neighbours, others discriminated on the repeated neighbouring environments. For example, the CH2 in CH3-CH2-CH3 was sometimes split into 4 peaks or 7 peaks, depending on the source. Many Chemistry teachers contradicted each other on the matter. There was repeated self corrections made by the teachers, such that now nobody really knows whether this principle is correct or not. So, is there anybody that has the correct information on the matter? Is there a reasonable explanation behind this strange lack of correlation, or is there a common misconception about multiplet splitting? Ultimately; How many multiplets should the CH2 in CH3-CH2-CH3 have? Thanks! (Note that if there is a complicated explanation that I am currently only at Year 12 VCE level, so links to resources I can pursue would be extremely helpful! It's been established that VCAA (an authority for the education system in Australia) ensures that the chemicals featured in the exams for NMR analysis will not be of a structure so as to allow the ambiguity above.)

I am curious about the timescales of protonation and deprotonation of solvent systems. As a followup, how is this effected when the proton source is separated by an organic phase?

Our work is faced with the issue of determining the charge of compounds that are dissolved in chloroform. One could realistically determine the charge of the relevant moieties knowing the pKa of those groups. However, how would you determine or calculate the pH of an organic solvent? An alternative way of asking this question is how would one calculate the concentration of hydronium ions or free protons in a nonaqueous solution.

After some more search, I have found two pieces of software who do titration simulation, but are (as far as I can tell) only available in French: - [Xem](http://www.linux-france.org/prj/xem/) and (I can't believe what I'm about to do)… [Google translation](http://translate.google.com/translate?sl=fr&tl=en&js=n&prev=_t&hl=en&ie=UTF-8&layout=2&eotf=1&u=http%3A%2F%2Fwww.linux-france.org%2Fprj%2Fxem%2F&act=url) of the same page - [Dozzzaqueux](http://jeanmarie.biansan.free.fr/dozzzaqueux.html) and [translation](http://translate.google.com/translate?sl=fr&tl=en&js=n&prev=_t&hl=en&ie=UTF-8&layout=2&eotf=1&u=http%3A%2F%2Fjeanmarie.biansan.free.fr%2Fdozzzaqueux.html&act=url)

It has to be so common a question that the answer is actually given in various places on Dupont's own website (Dupont are the makers of Teflon): > [**“If nothing sticks to Teflon®, then how does Teflon® stick to a pan?"**][1]<br/> Nonstick coatings are applied in layers, just like paint. The first layer is the primer—and it's the special chemistry in the primer that makes it adhere to the metal surface of a pan. And from [this other webpage][2] of theirs: ![enter image description here][3] The primer (or primers, if you include the “mid coat” in the picture above) adheres to the roughened surface, often obtained by sandblasting, very strongly: it's chemisorption, and the primer chemical nature is chosen as to obtain strong bonding to both the metal surface. Then, the PTFE chain extremities create bonds with the primer. And thus, it stays put. [1]: http://www2.dupont.com/Teflon/en_US/products/qanda_cookware_care.html#careq1 [2]: http://www2.dupont.com/Teflon/en_US/products/cookware_how_it_works.html [3]: https://i.stack.imgur.com/I7aAt.gif

All arenes, when treated with hot. conc. acidic $\rm KMnO_4$, are oxidised to benzoic/pthallic/etc acids. I've tried to examine how this happens, using the mechanism of oxidation of double bonds via cyclic intermediate as a reference, but I can't manage to cook up a satisfactory one. In an older book, I have read that there is no (known) mechanism for many organic oxidation reactions. I'm inclined to think that this may have changed. So, is there a mechanism for this? If so, what is it? If not, what are the hurdles in finding this mechanism? (eg why don't other proposed mechanisms, if they exist, work?)

I often hear that water gets purified by being in a silver vessel, which sounds plausible because of bactericidal feature of silver. What doesn't sound plausible, though, is the way it's explained: that silver releases ions into the water. Since silver is a noble metal, why would any "reaction" at all occur with something as neutral as water? Is the above explanation nonsense? Does the "disinfection" of water happen only on contact with the metal?

Recrystallization is a nice way of purifying a product, but choosing a suitable solvent if you can't rely on the literature seems like a lot of trial-and-error. Are there any general rules on which kind of solvents could be used for recrystallization? Which criteria should one use when trying to recrystallize a compound for which no literature on useable conditions exists?

In environmental chemistry, most of the organophosphorous compounds we worry about are actually organophosphate compounds. Is there something about the $\mathrm{C-P}$ bond that makes it less stable (and thus less persistent in the environment) than a $\mathrm{C-O-P}$ bond?

When [**N,N-dimethylaniline**][1] is reacted with $\mathrm{H_2SO_4}$ and $\mathrm{HNO_3}$ it gives mainly the *meta* product, even though $\mathrm{NMe_2}$ is an *ortho* / *para* directing group. Why is this? [1]: http://en.wikipedia.org/wiki/Dimethylaniline

I am curious about the timescales of protonation and deprotonation of solvent systems. As a followup, how is this affected when the proton source is separated by an organic phase? [](http://makemelonger.com)

I'm currently taking VCE (Victorian Certificate of Education) Chemistry classes, and we're currently studying the interpretation of spectra produced by Hydrogen NMR (Nuclear Magnetic Resonance) spectroscopy. When studying the spectra of High Resolution ¹H NMR, the peaks representing the different Hydrogen environments are split into multiplets based on the protons surrounding these environments. There has been a considerable amount of confusion in my classes over the actual principles / rules of thumb on how to calculate the multiplets for a particular environment of a known chemical (i.e.; known structue), based off the 'n + 1' rule. (i.e.; an environment with n neighbours will be split into n+1 multiplets). We are absolute on the principles that; - Peaks of a particular Hydrogen environment are not split by neighbouring protons in equivalent environments. - OH does not, and is not split by, it's neighbouring environments. However, immense confusion arised over whether the following principle was correct. - Peaks of a particular Hydrogen environment will only be split by the protons in neighbouring environments once for each type of neighbouring environment. e.g. The middle "CH2" environment in "CH3-CH2-CH3" will only have 4 peaks; Although it has 6 neighbouring protons, they are two lots of the same environment (CH3). As a class, we found numerous examples from different text books and sources that provide examples of 'H NMR spectra which did not clarify the matter; Some considered all neighbouring protons as neighbours, others discriminated on the repeated neighbouring environments. For example, the CH2 in CH3-CH2-CH3 was sometimes split into 4 peaks or 7 peaks, depending on the source. Many Chemistry teachers contradicted each other on the matter. There was repeated self corrections made by the teachers, such that now nobody really knows whether this principle is correct or not. So, is there anybody that has the correct information on the matter? Is there a reasonable explanation behind this strange lack of correlation, or is there a common misconception about multiplet splitting? Ultimately; How many multiplets should the CH2 in CH3-CH2-CH3 have? (Note that if there is a complicated explanation that I am currently only at Year 12 VCE level, so links to resources I can pursue would be extremely helpful! It's been established that VCAA (an authority for the education system in Australia) ensures that the chemicals featured in the exams for NMR analysis will not be of a structure so as to allow the ambiguity above.)

Splitting of multiplets in 1H NMR spectra?

I am curious about the timescales of protonation and deprotonation of solvent systems. As a followup, how is this affected when the proton source is separated by an organic phase? For instance, it is known that the pH inside a liposome can be maintained from the outside. What are the timescales of protonation when the protons need to be transported across various micelles thickness. [](http://makemelonger.com)

EDIT: It is clear now that NickT was looking for an experimental solution. My post deals with a computational solution. We can delete my response if need be until a more relevant question arises. > How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic Triazole and amide is a rather straightforward process. This process is referred to as the supramolecular approach. I'll point you to a paper that analyzes the [benzene dimer][1]. This method is strictly a computational one so a bit of knowledge in computational chemistry is necessary. **The Supramolecular Approach** ------------------------------- **The What** The supramolecular approach boils down to this. $E_{int} = E_{dimer} - (E_{mon1} + E_{mon2})$ Here we have some interaction energy ($E_{int}$) determined from the difference of a dimer energy ($E_{dimer}$) and the sum of the two monomers ($E_{monomer}$). If both monomers were equivalent (say, you were interested in the interaction energy of the benzene dimer where each monomer was a benzene ring), you could simplify the summation to two times the energy of one monomer ($2E_{mon}$). In your particular case, you have two different monomers. The whole idea is if I have two interacting molecules, I can determine the energy of each molecule individually (as if they were separated at infinite distance) as well as their complex. So as you bring these molecules closer and closer together, the energy starts to go down (the interaction energy). **The How** NOTE: Your geometry is from a crystal structure. Do NOT modify this geometry. You will want to keep everything exactly as is. This means you don't want to optimize your system. You do not want to eyeball monomer placement. Take everything from your known structure and be careful not to change it otherwise it can ruin this process. We are modifying the structure by truncating and capping but intermolecular parameters must stay the same for whatever it is you are trying to model. You will want to optimize your cap meaning, run an optimization on your capped-monomer but freeze everything but the thing you are using to cap. 1. Define your monomers. You will need to determine what part of your 'dimer' system is important for describing this weak interaction. I recommend keeping the aromatic ring and truncating the ring with something similar to what is being truncated. You could cap your monomer with a hydrogen or a methyl group for example. If the piece you've cut out is highly polarizable, cap with something with a similar property. If your truncated piece is neutral in charge, cap with something that is neutral. You get the idea. 2. Define your dimer. Your dimer is simply a combination of your two defined monomers. 3. Determine the method you want to implement. [Post-Hartree-Fock methods][2] are essential for this. Note that if you use the widely-implemented MP2 method, your answer may be way off (can over-estimate pi-pi interactions by as much as 200%!). The CCSD(T) method is recommended. 4. Define your basis set. For aromatic systems your best bet would be to use Dunning-Hunzaga's correlation consistent family of basis sets. I recommend using aug-cc-pVTZ for good results. Whatever you decide, be sure your basis set includes polarization and diffuse functions. The suggested basis set does this (augmented means diffuse on all atoms whereas pVTZ means 'polarized-valence triple zeta'). 5. Determine the energies of your monomers and dimer. You will want to run a single-point energy calculation on your monomers and your dimer. Optimize your monomers first but freeze all atoms except those you added to cap your monomer. 6. Determine the interaction energy. Plug your energies into the equation given above and determine the interaction energy. Convert to whatever units you wish to use (I prefer kJ/mol but most people use kcal/mol so you may want to use that). I hope this helps. Looks like an interesting project to say the least. **A quick note about the 'valence' basis set:** Typically core electrons do not participate in any sort of interesting chemistry (they are so much lower in energy than the valence electrons that they do not play a role in things like chemical bonding). When you perform these energy computations, you will be invoking the frozen-core approximation (default on many quantum software packages but be sure to check the documentation first). The pVTZ basis set expands the basis functions out to triple-zeta quality for valence electrons only. The core electrons are given *s*-type functions and that is it. If you ever find yourself in a situation where the core electrons are important to your system of interest, you would want to use the pCVXZ basis sets (where X = D,T,Q, etc.) which stands for polarized core-valence X zeta. Here the core electrons are given the full set of X-zeta quality basis functions. However this means you've just made your computation much more expensive. The frozen-core approximation is typically used. [1]: http://pubs.acs.org/doi/abs/10.1021/ja025896h [2]: http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock

Some information on **Side chain oxidation in alkylbenzenes** is available here: http://www.chemguide.co.uk/organicprops/arenes/other.html > An alkylbenzene is simply a benzene ring with an alkyl group attached > to it. Methylbenzene is the simplest alkylbenzene. > > **Alkyl groups are usually fairly resistant to oxidation. However, when they are attached to a benzene ring, they are easily oxidised by > an alkaline solution of potassium manganate(VII) (potassium > permanganate).** > > Methylbenzene is heated under reflux with a solution of potassium > manganate(VII) made alkaline with sodium carbonate. The purple colour > of the potassium manganate(VII) is eventually replaced by a dark brown > precipitate of manganese(IV) oxide. > > The mixture is finally acidified with dilute sulphuric acid. > > Overall, the methylbenzene is oxidised to benzoic acid. > > ![AlkylBenzene][1] > > Interestingly, any alkyl group is oxidised back to a -COOH group on > the ring under these conditions. So, for example, propylbenzene is > also oxidised to benzoic acid. > > ![Benzoic acid][2] A Chemistry student at UBC did his doctorate on the mechanism: https://circle.ubc.ca/handle/2429/32304 and for the pdf see: [https://circle.ubc.ca/bitstream/handle/2429/32304/UBC_1973_A1%20S65.pdf?sequence=1][3] > It was found that the most vigorous oxidant was permanganyl ion > (MnO₃⁺), with some contributing oxidation by both permanganic acid > (HMnO₄) and permanganate ion (MnO₄⁻) in the case of easily oxidized > compounds such as alcohols, aldehydes, or enols. The mechanism of the > acidic permanganate oxidation of alkanes (ethane to n-tridecane) was > found to proceed via rate-determining homolytic carbon-hydrogen bond > scission as depicted below. [See Thesis for Diagrams] The -mechanism > of arene oxidation was shown to proceed via rate-determining > electrophilic attack by permanganyl ion on the aromatic ring to yield > ring degradation products. Phenols are believed to be intermediates in > this process as depicted below. [See Thesis for Diagrams] The > mechanisms of the oxidation of alcohols, ketones, aldehydes, and > formic acid were determined and shown to be consistent with mechanisms > previously established under other conditions. [1]: https://i.stack.imgur.com/KGsmw.gif [2]: https://i.stack.imgur.com/2OzZ5.gif [3]: https://circle.ubc.ca/bitstream/handle/2429/32304/UBC_1973_A1%20S65.pdf?sequence=1

I have a solution of Copper Acetate and I would like to play around with the ligands to get different colors. Background: The Copper Acetate was made through mixing Vinegar (5% acetic acid), NaCl, and Copper(s). The deep blue colored Copper Acetate spontaneously formed during a month in my dark storage room. Question(s): What easily obtained household chemicals may be mixed with samples of the Copper Acetate to change the ligands attached to the Copper and thereby alter the color? Will heating or cooling the solution change the color and/or ligands?

How May Copper Acetate Ligands Be Manipulated To Change Colors?

One frequent argument against the safety of the synthetic sweetener aspartame is that it can be hydrolyzed, with one of the hydrolysis products being methanol, which is known to be toxic. Of course, usually not much aspartame is added in food anyway to yield a sufficient amount of methanol or its oxidation product formaldehyde, but this does beg the question: why wasn't, say, the ethyl ester chosen to be developed as an artificial sweetener? Is there a structure-activity relationship between the alcohol used to esterify the dipeptide and the sweetness of the product?

During the development of aspartame, why was the methyl ester chosen?

The nucleobases in DNA and RNA are generally present in the keto-form, and not in the enol-form. As an interesting historical note, James Watson and Francis Crick did initially believe them to adopt the enol-form, which isn't compatible with the correct model of the DNA they later proposed. But there are some reports indicating that in certain RNA structures guanosine and uridine form essentially a Watson-Crick basepair where one of the two bases is present in the enol-form, instead of the usual G-U wobble base pair. Is there anything known on how large the energy difference between the keto- and the enol-form of those bases actually is?

How large is the energy difference between keto- and enol-form of guanine and uracil?

**Setting the scene for your question** In Environmental Chemistry there are several pathways a chemical might travel through including: - being subjected to the biochemistry of an animal - photodegradation - chemical degradation (perhaps it slowly reacts with water, etc.) - uptake as a metabolite in plants - degradation by soil microorganisms and this is ignoring aquatic and air pathways. Say, within a mouse or a fly, a possible pathway for degradation for some insecticide is cleavage of the P-O bond. How they have determined this in the past is noteworthy; a synthetic chemist would [isotope label][1] an atom in the molecule, say $^{33}$[P][2]-labeled or $^{14}$[C][3]-labeled, and he purified it before finally determining its [specific activity][4]. Then a biochemist would dose a mouse with a solution of the compound dissolved in an appropriate solvent, such as olive oil. Urine and feces were collected after administration. An aliquot of the collected urine, for example, would have its radioactivity measured using [scintillation counting][5]. The organo-soluble species would be extracted from the rest of the urine and the distribution of radioactivity could then be determined between the aqueous and organic layers. Then one could investigate what were present by [TLC][6] if you're old school -- they would actually run, via cochromatography, all the possible metabolite products they could independently think of and synthesize to identify a TLC spot! (That is a lot of work.) These days we can cheat with [HPLC-MS][7]. So, you might ask, "are results from this generalizable?" I have to tell you that they generalize in a very rough way. Enzymes are responsible for all the nifty biochemistry and they tend to be rather selective towards a given substrate and, in many cases, [chirality][8] even matters! What they are picky about is a tough problem that is tailored to each individual enzyme. One can make all kinds of generalizations about the chemical nature of the bonds and some possible predictions from it, but those won't necessarily hold up in an animal model with a different molecule. So nitty-gritty mechanisms might not be what we want to look at. Instead we'll step back and take a broader view of this landscape. We need to look at bigger items in terms of physical properties, namely: 1) Persistence: what is its half-life in soil, etc. This is a matter of degradation, whereas the next is all about movement of an intact molecule. A simple chemical way to test this is how they resist hydrolysis. 2) Mobility: over time, does the compound tend to sit or spread itself around? For example, factors that influence this are: - [sorption][9]: how much does our chemical bind to our soil? - water solubility: how easy it is to move in water for our chemical? - vaporizability: how likely is the material to evaporate away from its source? A famous organophosphate is [malathion][10]. The [partition coefficient][11], according to the wiki page, is 2.36. This implies its solubility is greater in organics than water, but some of it will most certainly dissolve in water. I think, based on its size, it is reasonable to assume it has a negligible vapor pressure too. These factors suggest it will have a low mobility: it will tend to stick to organics, won't appreciably evaporate away and will take quite a lot of water to wash it away. Contrast this with a famous organochlorine, [DDT][12], which has an even higher partition coefficient (on the order of 10, so even more sticky and less soluble in water) and an even higher mass (so probably a lower vapor pressure) and thus an even lower mobility. Indeed, organophosphates largely replaced organochlorines as pesticides, in part, because they persist for shorter periods of times in the environment. Many of these organophosphates were tested by us and their history is relevant. World Wars I and II ushered in a new era of chemical warfare agents and pesticides, notably of the classes of organochlorines, organophosphates and carbamates. Some organophosphates hardly persist at all, such as tetraethyl pyrophosphate, but they are pretty toxic to mammals. Many other organophosphates were screened for low toxicity towards mammals and increased persistence. We actually sought longer-lasting half-lives for these compounds! It turns out that we see alkyl phosphates with shorter lives than the longer-lived aryl species. We tend to see certain trends within the different organophosphates, such as the water solubility being greater for the less complex and more polar compounds. An ethyl- is less soluble than a methyl- derivative and an aryl-substituted species get partition coefficients approaching those of the organochlorines. "All this is fine and interesting, but it doesn't have much to do with my direct question," you might say. And most of the above just sets the scene for my answer to your question. Your specific query, I believe, requires us to go back to a nitty-gritty detail which is really only relevant in the case of your comparison between a phosphate (P-O-C) and an organophosphorus compound (P-C). **My answer to your question** In the biochemistry of most life, phosphates are pretty ubiquitous. As a result, many enzymes have evolved to manipulate them in many different forms; one class of these enzymes is called [phosphatases][13] and they assist dephosphorylation reactions. They certainly cannot manipulate just any ol' phosphate (hence why more complex phosphates have longer residues). We could say organophosphates are more "natural" than your typical organophosphorus compound. There is, therefore, a greater chance of having a tool -- an enzyme -- that can pick your more "natural" looking compound apart than your harder to find P-C bond. As you've indicated, these phosphates are actually pretty stable. It's why DNA is built using them! But when you compare the bond lengths between P-C and P-O and O-C, there's a decent chance of finding that a P-C bond length is longer than a P-O or O-C. This leads me to believe that there are many cases in which P-O and O-C are actually stronger than P-C! This, I think, is why we have to step-back and look at the bigger picture: the exact physical properties vary considerably from one compound to another and to paint a landscape that says the issue is complicated. Perhaps, instead of it being a mere thermodynamic issue dealing with a comparison of the general bonding energies, it has more to do with the kinetic advantage of having enzymes equipped to slice the P-O-C rather than P-C. Of course, your mileage may vary depending on your specific examples. [1]: http://en.wikipedia.org/wiki/Isotopic_labeling [2]: http://en.wikipedia.org/wiki/Isotopes_of_phosphorus [3]: http://en.wikipedia.org/wiki/Isotopes_of_carbon [4]: http://en.wikipedia.org/wiki/Specific_activity [5]: http://en.wikipedia.org/wiki/Liquid_scintillation_counting [6]: http://en.wikipedia.org/wiki/Thin_layer_chromatography [7]: http://en.wikipedia.org/wiki/Liquid_chromatography%E2%80%93mass_spectrometry [8]: http://en.wikipedia.org/wiki/Chirality_%28chemistry%29 [9]: http://en.wikipedia.org/wiki/Sorption [10]: http://en.wikipedia.org/wiki/Malathion [11]: http://en.wikipedia.org/wiki/Partition_coefficient [12]: http://en.wikipedia.org/wiki/DDT [13]: http://en.wikipedia.org/wiki/Phosphatase

I am working on metal and its ion. The problem is, i would like to know whether the metal has been converted to its ionic form or not. The hypothesis for the analysis is: Metals are good conductors and ions possess redox potential. Therefore, by measuring the conductance and red-ox potential is it possible to differentiate whether i have metal or metal ion. The question is 1. Based on the hypothesis, can i expect a positive result? 2. Apart from this, is there any other technique where i can qualitatively / quantitatively measure metal and its ion?

How to differentiate Metal from its ion?

**Setting the scene for your question** In Environmental Chemistry there are several pathways a chemical might travel through including: - being subjected to the biochemistry of an animal - photodegradation - chemical degradation (perhaps it slowly reacts with water, etc.) - uptake as a metabolite in plants - degradation by soil microorganisms and this is ignoring aquatic and air pathways. Say, within a mouse or a fly, a possible pathway for degradation for some insecticide is cleavage of the P-O bond. How they have determined this in the past is noteworthy; a synthetic chemist would [isotope label][1] an atom in the molecule, say $^{33}$[P][2]-labeled or $^{14}$[C][3]-labeled, and he purified it before finally determining its [specific activity][4]. Then a biochemist would dose a mouse with a solution of the compound dissolved in an appropriate solvent, such as olive oil. Urine and feces were collected after administration. An aliquot of the collected urine, for example, would have its radioactivity measured using [scintillation counting][5]. The organo-soluble species would be extracted from the rest of the urine and the distribution of radioactivity could then be determined between the aqueous and organic layers. Then one could investigate what were present by [TLC][6] if you're old school -- they would actually run, via cochromatography, all the possible metabolite products they could independently think of and synthesize to identify a TLC spot! (That is a lot of work.) These days we can cheat with [HPLC-MS][7]. So, you might ask, "are results from this generalizable?" I have to tell you that they generalize in a very rough way. Enzymes are responsible for all the nifty biochemistry and they tend to be rather selective towards a given substrate and, in many cases, [chirality][8] even matters! What they are picky about is a tough problem that is tailored to each individual enzyme. One can make all kinds of generalizations about the chemical nature of the bonds and some possible predictions from it, but those won't necessarily hold up in an animal model with a different molecule. So nitty-gritty mechanisms might not be what we want to look at. Instead we'll step back and take a broader view of this landscape. We need to look at bigger items in terms of physical properties, namely: 1) Persistence: what is its half-life in soil, etc. This is a matter of degradation, whereas the next is all about movement of an intact molecule. A simple chemical way to test this is how they resist hydrolysis. 2) Mobility: over time, does the compound tend to sit or spread itself around? For example, factors that influence this are: - [sorption][9]: how much does our chemical bind to our soil? - water solubility: how easy it is to move in water for our chemical? - vaporizability: how likely is the material to evaporate away from its source? A famous organophosphate is [malathion][10]. The [partition coefficient][11], according to the wiki page, is 2.36. This implies its solubility is greater in organics than water, but some of it will most certainly dissolve in water. I think, based on its size, it is reasonable to assume it has a negligible vapor pressure too. These factors suggest it will have a low mobility: it will tend to stick to organics, won't appreciably evaporate away and will take quite a lot of water to wash it away. Contrast this with a famous organochlorine, [DDT][12], which has an even higher partition coefficient (on the order of 10, so even more sticky and less soluble in water) and an even higher mass (so probably a lower vapor pressure) and thus an even lower mobility. Indeed, organophosphates largely replaced organochlorines as pesticides, in part, because they persist for shorter periods of times in the environment. Many of these organophosphates were tested by us and their history is relevant. World Wars I and II ushered in a new era of chemical warfare agents and pesticides, notably of the classes of organochlorines, organophosphates and carbamates. Some organophosphates hardly persist at all, such as tetraethyl pyrophosphate, but they are pretty toxic to mammals. Many other organophosphates were screened for low toxicity towards mammals and increased persistence. We actually sought longer-lasting half-lives for these compounds! It turns out that we see alkyl phosphates with shorter lives than the longer-lived aryl species. We tend to see certain trends within the different organophosphates, such as the water solubility being greater for the less complex and more polar compounds. An ethyl- is less soluble than a methyl- derivative and an aryl-substituted species get partition coefficients approaching those of the organochlorines. "All this is fine and interesting, but it doesn't have much to do with my direct question," you might say. And most of the above just sets the scene for my answer to your question. Your specific query, I believe, requires us to go back to a nitty-gritty detail which is really only relevant in the case of your comparison between a phosphate (P-O-C) and an organophosphorus compound (P-C). **My answer to your question** In the biochemistry of most life, phosphates are pretty ubiquitous. As a result, many enzymes have evolved to manipulate them in many different forms; one class of these enzymes is called [phosphatases][13] and they assist dephosphorylation reactions. They certainly cannot manipulate just any ol' phosphate (hence why more complex phosphates have longer residues). We could say organophosphates are more "natural" than your typical organophosphorus compound. There is, therefore, a greater chance of having a tool -- an enzyme -- that can pick your more "natural" looking compound apart than your harder to find P-C bond. As you've indicated, these phosphates are actually pretty stable. It's why DNA is built using them! But when you compare the bond lengths between P-C and P-O and O-C, there's a decent chance of finding that a P-C bond length is longer than a P-O or O-C. This leads me to believe that there are many cases in which P-O and O-C are actually stronger than P-C! The same could easily be said in the other way too! This, I think, is why we have to step-back and look at the bigger picture: the exact physical properties vary considerably from one compound to another and to paint a landscape that says the issue is complicated. Perhaps, instead of it being a mere thermodynamic issue dealing with a comparison of the general bonding energies, it has more to do with the kinetic advantage of having enzymes equipped to slice the P-O-C rather than P-C. Of course, your mileage may vary depending on your specific examples. [1]: http://en.wikipedia.org/wiki/Isotopic_labeling [2]: http://en.wikipedia.org/wiki/Isotopes_of_phosphorus [3]: http://en.wikipedia.org/wiki/Isotopes_of_carbon [4]: http://en.wikipedia.org/wiki/Specific_activity [5]: http://en.wikipedia.org/wiki/Liquid_scintillation_counting [6]: http://en.wikipedia.org/wiki/Thin_layer_chromatography [7]: http://en.wikipedia.org/wiki/Liquid_chromatography%E2%80%93mass_spectrometry [8]: http://en.wikipedia.org/wiki/Chirality_%28chemistry%29 [9]: http://en.wikipedia.org/wiki/Sorption [10]: http://en.wikipedia.org/wiki/Malathion [11]: http://en.wikipedia.org/wiki/Partition_coefficient [12]: http://en.wikipedia.org/wiki/DDT [13]: http://en.wikipedia.org/wiki/Phosphatase

**Setting the scene for your question** In Environmental Chemistry there are several pathways a chemical might travel through including: - being subjected to the biochemistry of an animal - photodegradation - chemical degradation (perhaps it slowly reacts with water, etc.) - uptake as a metabolite in plants - degradation by soil microorganisms and this is ignoring aquatic and air pathways. Say, within a mouse or a fly, a possible pathway for degradation for some insecticide is cleavage of the P-O bond. How they have determined this in the past is noteworthy; a synthetic chemist would [isotope label][1] an atom in the molecule, say $^{33}$[P][2]-labeled or $^{14}$[C][3]-labeled, and he purified it before finally determining its [specific activity][4]. Then a biochemist would dose a mouse with a solution of the compound dissolved in an appropriate solvent, such as olive oil. Urine and feces were collected after administration. An aliquot of the collected urine, for example, would have its radioactivity measured using [scintillation counting][5]. The organo-soluble species would be extracted from the rest of the urine and the distribution of radioactivity could then be determined between the aqueous and organic layers. Then one could investigate what were present by [TLC][6] if you're old school -- they would actually run, via cochromatography, all the possible metabolite products they could independently think of and synthesize to identify a TLC spot! (That is a lot of work.) These days we can cheat with [HPLC-MS][7]. So, you might ask, "are results from this generalizable?" I have to tell you that they generalize in a very rough way. Enzymes are responsible for all the nifty biochemistry and they tend to be rather selective towards a given substrate and, in many cases, [chirality][8] even matters! What they are picky about is a tough problem that is tailored to each individual enzyme. One can make all kinds of generalizations about the chemical nature of the bonds and some possible predictions from it, but those won't necessarily hold up in an animal model with a different molecule. So nitty-gritty mechanisms might not be what we want to look at. Instead we'll step back and take a broader view of this landscape. We need to look at bigger items in terms of physical properties, namely: 1) Persistence: what is its half-life in soil, etc. This is a matter of degradation, whereas the next is all about movement of an intact molecule. A simple chemical way to test this is how they resist hydrolysis. 2) Mobility: over time, does the compound tend to sit or spread itself around? For example, factors that influence this are: - [sorption][9]: how much does our chemical bind to our soil? - water solubility: how easy it is to move in water for our chemical? - vaporizability: how likely is the material to evaporate away from its source? A famous organophosphate is [malathion][10]. The [partition coefficient][11], according to the wiki page, is 2.36. This implies its solubility is greater in organics than water, but some of it will most certainly dissolve in water. I think, based on its size, it is reasonable to assume it has a negligible vapor pressure too. These factors suggest it will have a low mobility: it will tend to stick to organics, won't appreciably evaporate away and will take quite a lot of water to wash it away. Contrast this with a famous organochlorine, [DDT][12], which has an even higher partition coefficient (on the order of 10, so even more sticky and less soluble in water) and an even higher mass (so probably a lower vapor pressure) and thus an even lower mobility. Indeed, organophosphates largely replaced organochlorines as pesticides, in part, because they persist for shorter periods of times in the environment. Many of these organophosphates were tested by us and their history is relevant. World Wars I and II ushered in a new era of chemical warfare agents and pesticides, notably of the classes of organochlorines, organophosphates and carbamates. Some organophosphates hardly persist at all, such as tetraethyl pyrophosphate, but they are pretty toxic to mammals. Many other organophosphates were screened for low toxicity towards mammals and increased persistence. We actually sought longer-lasting half-lives for these compounds! It turns out that we see alkyl phosphates with shorter lives than the longer-lived aryl species. We tend to see certain trends within the different organophosphates, such as the water solubility being greater for the less complex and more polar compounds. An ethyl- is less soluble than a methyl- derivative and an aryl-substituted species get partition coefficients approaching those of the organochlorines. "All this is fine and interesting, but it doesn't have much to do with my direct question," you might say. And most of the above just sets the scene for my answer to your question. Your specific query, I believe, requires us to go back to a nitty-gritty detail which is really only relevant in the case of your comparison between a phosphate (P-O-C) and an organophosphorus compound (P-C). **My answer to your question** In the biochemistry of most life, phosphates are pretty ubiquitous. As a result, many enzymes have evolved to manipulate them in many different forms; one class of these enzymes is called [phosphatases][13] and they assist dephosphorylation reactions. They certainly cannot manipulate just any ol' phosphate (hence why more complex phosphates have longer residues). We could say organophosphates are more "natural" than your typical organophosphorus compound. There is, therefore, a greater chance of having a tool -- an enzyme -- that can pick your more "natural" looking compound apart than your harder to find P-C bond. As you've indicated, these phosphates are actually pretty stable. It's why DNA is built using them! But when you compare the bond lengths between P-C and P-O and O-C, there's a decent chance of finding that a P-C bond length is longer than a P-O or O-C. This leads me to believe that there are many cases in which P-O and O-C are actually stronger than P-C! The same could easily be said in the other way too! This, I think, is why we have to step-back and look at the bigger picture: the exact physical properties vary considerably from one compound to another and paint a landscape that says the issue is complicated. Perhaps, instead of it being a mere thermodynamic issue dealing with a comparison of the general bonding energies, it has more to do with the kinetic advantage of having enzymes equipped to slice the P-O-C rather than P-C. Of course, your mileage may vary depending on your specific examples. [1]: http://en.wikipedia.org/wiki/Isotopic_labeling [2]: http://en.wikipedia.org/wiki/Isotopes_of_phosphorus [3]: http://en.wikipedia.org/wiki/Isotopes_of_carbon [4]: http://en.wikipedia.org/wiki/Specific_activity [5]: http://en.wikipedia.org/wiki/Liquid_scintillation_counting [6]: http://en.wikipedia.org/wiki/Thin_layer_chromatography [7]: http://en.wikipedia.org/wiki/Liquid_chromatography%E2%80%93mass_spectrometry [8]: http://en.wikipedia.org/wiki/Chirality_%28chemistry%29 [9]: http://en.wikipedia.org/wiki/Sorption [10]: http://en.wikipedia.org/wiki/Malathion [11]: http://en.wikipedia.org/wiki/Partition_coefficient [12]: http://en.wikipedia.org/wiki/DDT [13]: http://en.wikipedia.org/wiki/Phosphatase

Whilst we are taught to represent benzene as below (A) due to its delocalised electrons, however when two benzene rings share carbons (e.g. naphtalene) it seems to be more commonly represented in textbooks as two conjugated rings (B). Whilst I realise that the result is the same, what is the advantage gained by drawing them like this rather than (C)? Is it simply a matter of clarity? A: ![Benzene Ring][1] B: ![Naphtalene Kekule's Form][2] C: ![Naphtalene][3] Whilst draing those in Marvin I wondered if it was as the delocalisation between the shared carbons isn't shown? I.e. it looks like the electrons are delocalised across both rings separately rather than as one big ring? [1]: https://i.stack.imgur.com/qV6kP.png [2]: https://i.stack.imgur.com/p698c.png [3]: https://i.stack.imgur.com/nqf2e.png

Why are arenes with conjoined benzene rings drawn as they are?

Whilst we are taught to represent benzene as below (A) due to its delocalised electrons, however when two benzene rings share carbons (e.g. naphtalene) it seems to be more commonly represented in textbooks as two conjugated rings (B). Whilst I realise that the result is the same, what is the advantage gained by drawing them like this rather than (C)? Is it simply a matter of clarity? A: ![Benzene Ring][1] B: ![Naphtalene Kekule's Form][2] C: ![Naphtalene][3] Whilst draing those in Marvin I wondered if it was as the delocalisation between the shared carbons isn't shown? I.e. it looks like the electrons are delocalised across both rings separately rather than as one big ring? [1]: https://i.stack.imgur.com/c1fY8.png [2]: https://i.stack.imgur.com/ePDgv.png [3]: https://i.stack.imgur.com/AKN2w.png

> The obvious order is via the stability of the carbocation of the > group. I think You meant the migrating groups stability? This is not what textbooks say. Reactions are ruled by the delta G of the activated complex. This may be close to educts, or to products, or some halfway state or a real intermediate minimum is on the reaction path. So, in some cases the model of a separate carbenium ion (in a ionic pair maybe) is useful, sometimes You need to think of a three-center bond state.

> The obvious order is via the stability of the carbocation of the > group. I think You meant the migrating groups stability? This is not what textbooks say. Reactions are ruled by the delta G of the activated complex. This may be close to educts, or to products, or some halfway state or a real intermediate minimum is on the reaction path. So, in some cases the model of a separate carbenium ion (in a ionic pair maybe) is useful, sometimes You need to think of a three-center bond state.

(Too long for a comment.) With drawing it as in diagram B, although we lose the information that the electrons are in reality delocalized, it makes for easier electron accounting when we start "pushing electrons" (that is to say, in illustrating the mechanism of a reaction). The thing is that representing electron delocalization in Lewis structures requires crutches like resonance structures or that circle/circle arc business. At least you can say that there's an electron pair in a single bond. How many electrons are there in the circle? If you don't deal much in the illustration of reaction mechanisms, I suppose the first and third drawings are okay. My point is that those circles don't really play nice with arrows.

I am working on metal and its ion. The problem is, I would like to know whether the metal has been converted to its ionic form or not. The hypothesis for the analysis is: Metals are good conductors and ions possess redox potential. Therefore, by measuring the conductance and red-ox potential is it possible to differentiate whether I have metal or metal ion. The question is 1. Based on the hypothesis, can I expect a positive result? 2. Apart from this, is there any other technique where I can qualitatively / quantitatively measure metal and its ion?

I'm currently taking VCE (Victorian Certificate of Education) Chemistry classes, and we're currently studying the interpretation of spectra produced by Hydrogen NMR (Nuclear Magnetic Resonance) spectroscopy. When studying the spectra of High Resolution ¹H NMR, the peaks representing the different Hydrogen environments are split into multiplets based on the protons surrounding these environments. There has been a considerable amount of confusion in my classes over the actual principles / rules of thumb on how to calculate the multiplets for a particular environment of a known chemical (i.e.; known structue), based off the 'n + 1' rule. (i.e.; an environment with n neighbours will be split into n+1 multiplets). We are absolute on the principles that; - Peaks of a particular Hydrogen environment are not split by neighbouring protons in equivalent environments. - OH does not, and is not split by, it's neighbouring environments. However, immense confusion arised over whether the following principle was correct. - Peaks of a particular Hydrogen environment will only be split by the protons in neighbouring environments once for each type of neighbouring environment. e.g. The middle "CH₂" environment in "CH₃–CH₂–CH₃" will only have 4 peaks; Although it has 6 neighbouring protons, they are two lots of the same environment (CH₃). As a class, we found numerous examples from different text books and sources that provide examples of ¹H NMR spectra which did not clarify the matter; Some considered all neighbouring protons as neighbours, others discriminated on the repeated neighbouring environments. For example, the CH₂ in CH₃–CH₂–CH₃ was sometimes split into 4 peaks or 7 peaks, depending on the source. Many Chemistry teachers contradicted each other on the matter. There was repeated self corrections made by the teachers, such that now nobody really knows whether this principle is correct or not. So, is there anybody that has the correct information on the matter? Is there a reasonable explanation behind this strange lack of correlation, or is there a common misconception about multiplet splitting? Ultimately; How many multiplets should the CH₂ in CH₃–CH₂–CH₃ have? (Note that if there is a complicated explanation that I am currently only at Year 12 VCE level, so links to resources I can pursue would be extremely helpful! It's been established that VCAA (an authority for the education system in Australia) ensures that the chemicals featured in the exams for NMR analysis will not be of a structure so as to allow the ambiguity above.)

Splitting of multiplets in ¹H NMR spectra?

Many of us have experienced the failure of nitrile gloves when exposed to chloroform. What's going on at a mechanistic level when this occurs? I would guess that the chloroform dissolves some of the polymer into its constituent monomers, but I've never heard anything more definite than that. Is it a similar mechanism to what happens when chloroform is left too long in a plastic bottle?

How to differentiate a metal from its ion?

> The obvious order is via the stability of the carbocation of the > group. I think you meant the migrating groups stability? This is not what textbooks say. Reactions are ruled by the delta G of the activated complex. This may be close to educts, or to products, or some halfway state or a real intermediate minimum is on the reaction path. So, in some cases the model of a separate carbenium ion (in a ionic pair maybe) is useful, sometimes You need to think of a three-center bond state.

It is known that although only the *(S)*-enantiomer of the infamous sedative thalidomide possesses teratogenic properties, it is not very useful to administer the pure *(R)*-enantiomer since it is racemized within the body. Are there other known examples of drugs that are stereoconverted *in vivo*? How does the body perform the conversion?

What are known examples of drugs that racemize/stereoconvert in vivo, and how are they converted?

*Although I can't think of any drug examples other than thalidomide, here's information on thalidomide's mechanism:* The chiral carbon of thalidomide can tautomerize in basic conditions into an enol, which is achiral. A reversal back to the ketone results in a mix of *(R)* and *(S)* enantiomers. ![Chemical diagram for s-thalidomide][1] In the body, this tautomerization is generally catalyzed by basic amino acids. Specifically, albumin is the main catalyst in humans. While this is beyond the scope of your question, the reason that only *(S)*-thalidomide causes birth defects is that it can insert itself into DNA and suppresses certain genes necessary for embryonic development. <hr> 1. [Reddy - *Chirality in Drug Design and Development*][3] 2. http://www.ncbi.nlm.nih.gov/pubmed/9860497 [1]: https://i.stack.imgur.com/w1k3n.png [2]: http://www.ncbi.nlm.nih.gov/pubmed/9860497 [3]: http://books.google.com/books?id=HibwXSgofi0C&pg=PA330&lpg=PA330&dq=albumin+thalidomide+racemization&source=bl&ots=8aLGIAbZa9&sig=uaQhWP7tAzUScQiQ0AuRom-v09k&hl=en&sa=X&ei=mHubT43TOeGD6AGG1oXuDg&ved=0CB8Q6AEwAA#v=onepage&q&f=false

I'm looking at the melting temperature of metallic elements, and notice that the metals with high melting temperature are all grouped in some lower-left corner of the $d$ block. If I take for example the periodic table with physical state indicated at 2,165 K: ![enter image description here][1] I see that (apart from boron and carbon) the only elements still solid at that temperature form a rather well-defined block aroung tungsten (which melts at 3,695 K). So what makes this group of metals melt at such high temperature? [1]: https://i.stack.imgur.com/LTl0N.png