Introduction Theoretical computer calculations to determine the structures and energies of molecules have been used for many years in the Bowers Group to help explain our experimental observations. Initially these types of calculations were restricted to relatively small systems and consisted of ab initio and semiempirical molecular orbital calculations on carbon clusters and transition metal complexes. In recent years, with the advent of ionization techniques such as MALDI and ESI, our group has begun to investigate larger chemical systems experimentally. To keep up with these changes on the experimental side, we've adopted molecular mechanics (MM) calculations as a theoretical method. MM calculates structures and energies based on a force field determined by classicalmechanical motions of the atoms in the molecule. The National Institutes of Health's Center for Molecular Modeling has a helpful online guide to MM which explains the principles behind the method. MM calculations are much faster than ab initio and semiempirical molecular orbital calculations and can be applied to much larger systems. This makes it possible to perform dynamics calculations that track changes to molecular geometry over time and temperature variations (see Structure Sampling). Our group uses the AMBER set of molecular mechanics/dynamics programs to investigate many systems including synthetic polymers, biopolymers and materials. Several example structures calculated by MM are shown below. We also collaborate with Prof. JoanEmma Shea's theoretical/biophysical research group on modeling projects.

