Várnai, C and Bernstein, N and Mones, L and Csányi, G (2013) Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution. J Phys Chem B, 117. pp. 12202-12211.Full text not available from this repository.
We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.
|Divisions:||Div C > Applied Mechanics|
|Depositing User:||Unnamed user with email firstname.lastname@example.org|
|Date Deposited:||16 Jul 2015 13:10|
|Last Modified:||30 Nov 2015 08:23|