Modeling the kinetics of bimolecular reactions

A Fernández-Ramos, JA Miller, SJ Klippenstein… - Chemical …, 2006 - ACS Publications
This review is concerned with the theoretical and computational modeling of bimolecular
reactions, especially with generally applicable methods for kinetics (ie, overall rates as …

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

SCL Kamerlin, A Warshel - Proteins: Structure, Function, and …, 2010 - Wiley Online Library
Enzymes play a key role in almost all biological processes, accelerating a variety of
metabolic reactions as well as controlling energy transduction, the transcription, and …

[HTML][HTML] Mapping transcriptomic vector fields of single cells

X Qiu, Y Zhang, JD Martin-Rufino, C Weng… - Cell, 2022 - cell.com
Summary Single-cell (sc) RNA-seq, together with RNA velocity and metabolic labeling,
reveals cellular states and transitions at unprecedented resolution. Fully exploiting these …

[图书][B] Essentials of computational chemistry: theories and models

CJ Cramer - 2013 - books.google.com
Essentials of Computational Chemistry provides a balanced introduction to this dynamic
subject. Suitable for both experimentalists and theorists, a wide range of samples and …

QM/MM: what have we learned, where are we, and where do we go from here?

H Lin, DG Truhlar - Theoretical Chemistry Accounts, 2007 - Springer
This paper briefly reviews the current status of the most popular methods for combined
quantum mechanical/molecular mechanical (QM/MM) calculations, including their …

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

A Warshel, RP Bora - The Journal of chemical physics, 2016 - pubs.aip.org
Enzymes control chemical reactions that are key to life processes, and allow them to take
place on the time scale needed for synchronization between the relevant reaction cycles. In …

Quantum mechanical methods for enzyme kinetics

J Gao, DG Truhlar - Annual Review of Physical Chemistry, 2002 - annualreviews.org
▪ Abstract This review discusses methods for the incorporation of quantum mechanical
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …

[图书][B] Isotope effects in chemistry and biology

A Kohen, HH Limbach - 2005 - taylorfrancis.com
The field of isotope effects has expanded exponentially in the last decade, and researchers
are finding isotopes increasingly useful in their studies. Bringing literature on the subject up …

Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: a tutorial review

S Ahmadi, L Barrios Herrera… - … Journal of Quantum …, 2018 - Wiley Online Library
Exemplars of the state of the art in modeling enzymes are reviewed through a selection of
works from leading schools using QM‐only cluster models, QM/MM models and QM/MM/MD …

The diabatic picture of electron transfer, reaction barriers, and molecular dynamics

T Van Voorhis, T Kowalczyk, B Kaduk… - Annual review of …, 2010 - annualreviews.org
Diabatic states have a long history in chemistry, beginning with early valence bond pictures
of molecular bonding and extending through the construction of model potential energy …