Where does computational chemistry overlap with organic chemistry?

Question

I was wondering what research exists that combines computational chemistry and organic chemistry.

For the past three years, I've been using Amber and Gaussian (in hopes) to identify and understand trends in intramolecular interactions. This really just serves as an example of my past research which incorporated both physical chemistry and computational chemistry.

I would like to know what kind of research could be done that combines both organic chemistry with computational chemistry.

I've Googled computational research in organic chemistry, but haven't found much information. What are some examples of projects that have been done in organic chemistry that rely heavily on the computational side of things?

Answer 1

The first thing that comes to mind: read the backlist of Henry Rzepa's and (especially) Steven Bachrach's blogs. Depending exactly on what resources you have available, there are lots of things they do on the computational side of organic chemistry that you could at first imitate and then use as a springboard to innovate.

In particular, I've found Bachrach's posts on reaction dynamics to be especially fascinating. This is the phenomenon where the topography of the potential energy surface near a transition state is such that the reactions don't always follow the minimum-energy path due, effectively, to the inertia of the nuclei as they cross the TS.

I also have a personal interest in Bader's Quantum Theory of Atoms in Molecules, which uses the topology of the electron density to divide molecules up into atoms, where each atomic volume is enclosed by a 'zero-flux surface' in the electron density. (There's some ongoing controversy over the theory, but it makes good sense to me, for whatever that's worth.) Bader's book is a good place to start; or, you can search the journal literature for Richard Bader and a whole bunch of examples will surely turn up. I engaged with Dr. Rzepa last year in the comment thread of a post of his about electrides that touched on QTAIM, the electron localization function (ELF), non-covalent interactions (NCI), etc.

Finally, I've been very curious lately about 'charge-shift bonding', a relatively newly described class of bond where the nuclear framework tries to cram so many electrons into a small space that in the end Pauli repulsion drives them apart, causing what might otherwise appear to be a covalent bond to instead take the form of a resonance between two ionic structures. (The electronic structure of $\ce{F_2},$ for example, is better described as a balanced resonance between $\ce{F- \!- F+}$ and $\ce{F+ \!- F-}$ overlaid atop a very weak covalent interaction, than as a purely covalent $\ce{F\!-F}$ species.) Search the literature for Sason Shaik's work for more information and examples.

Other things that I've come across that have seemed interesting include carbenes, cyclic alkynes, unusual Diels-Alder reactions, and fullerene systems.

I would also subscribe to, e.g., Computational Chemistry Highlights, CCL, and Jan Jensen's Computational Chemistry Daily -- the posts and/or questions that come across there might give you some inspiration.

Answer 2

I have complemented most of my organic chemistry ("wet chemistry") work with computational chemistry, and it's, in fact, quite common to do so today. I would say it pretty much depends on your interests. There are probably other members in the group of your professor. Maybe they face some problem where computational chemistry can assist in. One example is the possibility to simulate NMR, IR, UV-VIS or (V)CD spectra. Another is the calculation of ground states, intermediates and transition states of catalytic cycles in case the group is doing catalysis. Actually, I would say there definitely should be the possibility to apply computational chemistry in any chemistry group, the remaining question being how good the support will be and if your professor will appreciate what you are doing. There are many good books about (organic) computational chemistry out there. I particularly liked

• Computational organic chemistry by Steven M. Bachrach
• A Chemist’s Guide to Density functional theory by the authors Wolfram Koch, Max C. Holthausen
• Exploring Chemistry with Electronic Structure Methods by James B. Foresman
• Essentials of Computational Chemistry by Christopher J. Cramer
• Introduction to Computational Chemistry by Frank Jensen

more or less in that order. But there are lots of other good books of course. Another book for you, being interested in both physical and organic chemistry, is

• Modern Physical Organic Chemistry by Eric V. Anslyn, Dennis A. Dougherty

which by the way has a nice treatment of some organic computational chemistry topics as well.

Answer 3

One thing that would be interesting to tie together is the relationship between chiral resolution and resolving agent structure. Looking at the Dutch resolution on a molecular level would be cool. Relating Fogassy parameters with what happens at the molecular level is another aspect of the same area of work.