Computational Chemistry focuses on applying the methods of Physical Chemistry to various problems inside a computer, rather than in a more traditional laboratory setting.  Sometimes computational chemistry is used to examine problems which are experimentally either very difficult or even impossible to investigate (for example, looking at the properties of very unstable or short-lived chemical species).  It is also possible to use it to test theory against experiment by calculating results for which experimental data is known (as is done in spectroscopy).  It may be cheaper or otherwise more efficient to run a series of calculational experiments as a sort of screening process, and then only test the most promising compounds or reactions in the lab (as many pharmaceutical companies are doing in screening molecules with potential pharmacological activity).   All of these activities are often referred to Molecular Modeling, for additional information and examples, see the Websites of the Consortium for Molecular Modeling or the Lycoming Department of Chemistry's 3-D Molecules page.

    We have done molecular modeling using the HyperChem and CAChe programs.  With these programs one is able to draw molecules on the computer screen using a mouse.  The program then makes an initial structure based on expected bond distances and angles for the atoms in the molecule (for example, bonds around four-coordinate carbon atoms are assigned the tetrahedral angle of 109.45 degrees).  Subsequently, more sophisticated refinement of the structure can be done.  The mechanics method applies various algorithms to minimize the total energy of all the bond distances and angles involved. More sophisticated quantum mechanical calculations can also be done.

    These results can be used to determine a host of useful molecular properties, such as the molecular orbitals, enthalpies of formation, or molecular spectra.  For example, the three-dimensional structure of a molecule can be accurately calculated without first determining its structure by X-ray crystallography or Nuclear Magnetic Resonance (NMR).  It is also possible to look at conformers and assess their relative stabilities.  We have used this process to examine the conformational behavior of cyclic organic carbamates synthesized by Dr. Chriss E. McDonald and coworkers.  We were able to calculate the lowest energy conformations of these molecules in an effort to understand their unusual NMR spectra.  While the results were not what was expected initially, they are consistent with the observed NMR spectra.  We have also calculated three-dimensional molecular coordinates for the Department of Chemistry's 3-D Molecules page.

Figure: the most stable conformer of a molecule, as calculated by CAChe.

Last updated October 3, 2003.
The URL for this page is http://www.lycoming.edu/chem/research/chmres2.htm