Hybrid quantum mechanics / molecular mechanics (QM/MM) method is developed and implemented into a molecular dynamics program, GENESIS (GENeralized Ensemble SImulation System). A general interface is implemented, which generates an input file from a template, invokes a quantum chemistry program through a shell script, and retrieves the QM energy and gradients from log files (Figure 1). Furthermore, the QM/MM potential is coupled with anharmonic vibrational calculations, namely, the vibrational self-consistent field (VSCF) and vibrational quasi-degenerate perturbation theory (VQDPT). The method is applied to phosphate ion in solution and a pentagonal hydrogen bond (HB) network in bacteriorhodopsin (Figure 2). We demonstrate that the calculated infrared spectrum reproduces the experiment with high accuracy. Given the high sensitivity of vibrational spectra with respect to structural changes in proteins (protonation, HB reorientation, etc.), the method developed in this work together with experiment is a powerful tool to elucidate the reaction mechanism and biological functions of proteins.

QM/MM in GENESIS: Applications to anharmonic vibrational analysis of biomolecules

256th National Meeting (2018)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.