Combined QM/MM, machine learning path integral approach to compute free energy profiles and kinetic isotope effects in RNA cleavage reactions

TJ Giese, J Zeng, S Ekesan… - Journal of chemical theory …, 2022 - ACS Publications
We present a fast, accurate, and robust approach for determination of free energy profiles
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …

Pilgrim: A thermal rate constant calculator and a chemical kinetics simulator

D Ferro-Costas, DG Truhlar… - Computer Physics …, 2020 - Elsevier
Pilgrim is a program written in Python and designed to use direct dynamics in the calculation
of thermal rate constants of chemical reactions by the variational transition state theory …

Influence of multiple conformations and paths on rate constants and product branching ratios. thermal decomposition of 1-propanol radicals

D Ferro-Costas, E Martínez-Núñez… - The Journal of …, 2018 - ACS Publications
The potential energy surface involved in the thermal decomposition of 1-propanol radicals
was investigated in detail using automated codes (tsscds2018 and Q2DTor). From the …

[HTML][HTML] Equilibrium and kinetic isotope effects in heterogeneous catalysis: A density functional theory perspective

BWJ Chen - Catalysis Communications, 2023 - Elsevier
Isotopes are indispensable tools for elucidating catalytic reaction mechanisms. Yet,
computational isotopic studies in heterogeneous catalysis remain scarce, especially when …

Dual-level method for estimating multistructural partition functions with torsional anharmonicity

JL Bao, L Xing, DG Truhlar - Journal of Chemical Theory and …, 2017 - ACS Publications
For molecules with multiple torsions, an accurate evaluation of the molecular partition
function requires consideration of multiple structures and their torsional-potential …

New computational tools for chemical kinetics: the Cathedral Package

D Ferro-Costas, A Fernández-Ramos - Theoretical Chemistry Accounts, 2023 - Springer
The advent of recent technological developments in software engineering has enabled the
exploration of reaction mechanisms inside intricate reaction networks, thereby propelling the …

Role of microsolvation and quantum effects in the accurate prediction of kinetic isotope effects: The case of hydrogen atom abstraction in ethanol by atomic hydrogen …

S Kannath, P Adamczyk, D Ferro-Costas… - Journal of Chemical …, 2020 - ACS Publications
Hydrogen abstraction from ethanol by atomic hydrogen in aqueous solution is studied using
two theoretical approaches: the multipath variational transition state theory (MP-VTST) and a …

Temperature and pressure dependent rate constants of the reactions of OH• with cyclopentene from variational TST and SS-QRRK methods

JGS Monteiro, DCG Neves, ACPG Ventura… - The Journal of …, 2022 - pubs.aip.org
In this work, the pressure-and temperature-dependent reaction rate constants for the
hydrogen abstraction and addition of hydroxyl radicals to the unsaturated cyclopentene …

Differences in the torsional anharmonicity between reactant and transition state: the case of 3-butenal+ H abstraction reactions

MO Passos, IA Lins, MF Venâncio… - Physical Chemistry …, 2021 - pubs.rsc.org
Thermal rate coefficients for the hydrogen-abstraction reactions of 3-butenal by a hydrogen
atom were obtained applying multipath canonical variational theory with small-curvature …

High-temperature rate constants for CH3OCOH + OH reactions: the effects of multiple structures and paths

IA Lins, MO Passos, TV Alves - Theoretical Chemistry Accounts, 2020 - Springer
Rate constants for hydrogen abstraction reactions of methyl formate by hydroxyl radical are
computed with the one-well (1W) and multipath (MP) variational transition state theory with …