CHARMM: the biomolecular simulation program

BR Brooks, CL Brooks III… - Journal of …, 2009 - Wiley Online Library
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

The sudden vector projection model for reactivity: Mode specificity and bond selectivity made simple

H Guo, B Jiang - Accounts of Chemical Research, 2014 - ACS Publications
Conspectus Mode specificity is defined by the differences in reactivity due to excitations in
various reactant modes, while bond selectivity refers to selective bond breaking in a …

A computational methodology for accurate predictions of rate constants in solution: Application to the assessment of primary antioxidant activity

A Galano, JR Alvarez‐Idaboy - Journal of computational …, 2013 - Wiley Online Library
The accurate prediction of rate constants for chemical reactions in solution, using
computational methods, is a challenging task. In this work, a computational protocol …

Variational transition state theory with multidimensional tunneling

A Fernandez-Ramos, BA Ellingson… - Reviews in …, 2007 - Wiley Online Library
This review describes the application of variational transition state theory (VTST) to the
calculation of chemical reaction rates. In 1985, two of us, together with Alan D. Isaacson …

Searching configurations in uncertainty space: Active learning of high-dimensional neural network reactive potentials

Q Lin, L Zhang, Y Zhang, B Jiang - Journal of Chemical Theory …, 2021 - ACS Publications
Neural network (NN) potential energy surfaces (PESs) have been widely used in atomistic
simulations with ab initio accuracy. While constructing NN PESs, their training data points …

Predictive a priori pressure-dependent kinetics

AW Jasper, KM Pelzer, JA Miller, E Kamarchik… - Science, 2014 - science.org
The ability to predict the pressure dependence of chemical reaction rates would be a great
boon to kinetic modeling of processes such as combustion and atmospheric chemistry. This …

Kinetics of the reaction of methyl radical with hydroxyl radical and methanol decomposition

AW Jasper, SJ Klippenstein, LB Harding… - The Journal of …, 2007 - ACS Publications
The CH3+ OH bimolecular reaction and the dissociation of methanol are studied
theoretically at conditions relevant to combustion chemistry. Kinetics for the CH3+ OH …

Predictive theory for the combination kinetics of two alkyl radicals

SJ Klippenstein, Y Georgievskii… - Physical Chemistry …, 2006 - pubs.rsc.org
An ab initio transition state theory based procedure for accurately predicting the combination
kinetics of two alkyl radicals is described. This procedure employs direct evaluations of the …

Sulfuric acid as autocatalyst in the formation of sulfuric acid

M Torrent-Sucarrat, JS Francisco… - Journal of the American …, 2012 - ACS Publications
Sulfuric acid can act as a catalyst of its own formation. We have carried out a computational
investigation on the gas-phase formation of H2SO4 by hydrolysis of SO3 involving one and …

Comparison of Quantum Dynamics and Quantum Transition State Theory Estimates of the H + CH4 Reaction Rate

S Andersson, G Nyman, A Arnaldsson… - The Journal of …, 2009 - ACS Publications
Thermal rate constants are calculated for the H+ CH4→ CH3+ H2 reaction employing the
potential energy surface of Espinosa-García (Espinosa-García, JJ Chem. Phys. 2002, 116 …