Mixed quantum–classical simulation of vibrational frequency modulations of a diatomic molecule in a rare gas fluid

Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent

Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.

Adiabatic transfer of population in a dense fluid: The role of dephasing statistics

We report the results of simulation studies of the statistics of vibrational dephasing of a YCl (Y=H, D, T, and I) diatom in dense fluid Ar at two temperatures, including the effect of strong field driving on the energy level modulation statistics. The distribution of energy level modulations is found to be non-Gaussian with a high energy tail. Aspects of stimulated Raman adiabatic passage (STIRAP) between the vibrational levels of HCl in dense fluid Ar have been investigated. For HCl with nearly degenerate v=0-->v=1 and v=1-->v=2 transitions, the combined effect of modulation and power broadening reduces the STIRAP efficiency for population transfer from v=0 to v=2 of the order of 30%. However, if the transitions used have very different frequencies, as in the original model studied by Demirplak and Rice [J. Chem. Phys. 116, 8028 (2002)], the STIRAP efficiency for population transfer remains high, of the order of 80%, even with non-Gaussian modulation of energy levels.