Combined quantum mechanical and molecular mechanical methods to study chemical events in complex biological environments

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

Motivated by the long-term goal of understanding vectorial biological processes such as proton transport (PT) in biomolecular ion pumps, a number of developments were made to establish combined quantum mechanical/molecular mechanical (QM/MM) methods suitable for studying chemical reactions involving significant charge separation in the condensed phase. These developments were summarized and dis...

Development and Application of Combined Quantum Mechanical and Molecular Mechanical Methods

ion reaction is a hydroxo intermediate and a radical. Therefore, the obtained TS geometry is reasonable. In this view, the H atom at the active site should be closer to O atom than to the C atom. Inspection of the spin density of the RS and TS shows that there Figure 3-8. Visualization of spin densities in TS

Photodynamics in complex environments: ab initio multiple spawning quantum mechanical/molecular mechanical dynamics.

Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochemistry. Because most practical pho...

Quantum Mechanical and Molecular Mechanical Study of Solvent Effects

A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations

A combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of the MNDO and AM1 type are used, while the molecular mechanics part is treated with the CHARMM force field. Specific prescriptions are given for the interactions between the QM and MM portion...