Decoding catalysis by terpene synthases

JN Whitehead, NGH Leferink, LO Johannissen… - ACS …, 2023 - ACS Publications
The review by Christianson, published in 2017 on the twentieth anniversary of the
emergence of the field, summarizes the foundational discoveries and key advances in …

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

S Maeda, Y Harabuchi, Y Ono… - … Journal of Quantum …, 2015 - Wiley Online Library
The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum
chemical analysis and prediction of the mechanism of chemical reactions. The IRC gives a …

Post-transition state bifurcations gain momentum–current state of the field

SR Hare, DJ Tantillo - Pure and Applied Chemistry, 2017 - degruyter.com
The existence of post-transition state bifurcations on potential energy surfaces for organic
and biological reaction mechanisms has been known for decades, but recently, new reports …

Direct chemical dynamics simulations

S Pratihar, X Ma, Z Homayoon… - Journal of the …, 2017 - ACS Publications
In a direct dynamics simulation, the technologies of chemical dynamics and electronic
structure theory are coupled so that the potential energy, gradient, and Hessian required …

Biosynthetic consequences of multiple sequential post-transition-state bifurcations

YJ Hong, DJ Tantillo - Nature chemistry, 2014 - nature.com
Selectivity in chemical reactions that form complex molecular architectures from simpler
precursors is usually rationalized by comparing competing transition-state structures that …

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

U Lourderaj, R Sun, SC Kohale, GL Barnes… - Computer Physics …, 2014 - Elsevier
The interface for VENUS and NWChem, and the resulting software package for direct
dynamics simulations are described. The coupling of the two codes is considered to be a …

Perspective: chemical dynamics simulations of non-statistical reaction dynamics

X Ma, WL Hase - … Transactions of the Royal Society A …, 2017 - royalsocietypublishing.org
Non-statistical chemical dynamics are exemplified by disagreements with the transition state
(TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic …

Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices

SR Hare, LA Bratholm, DR Glowacki… - Chemical science, 2019 - pubs.rsc.org
Most chemical transformations (reactions or conformational changes) that are of interest to
researchers have many degrees of freedom, usually too many to visualize without reducing …

Electrostatically Guided Dynamics The Root of Fidelity in a Promiscuous Terpene Synthase?

DT Major, M Weitman - Journal of the American Chemical Society, 2012 - ACS Publications
Terpene cyclases are responsible for the initial cyclization cascade in the multistep
synthesis of more than 60 000 known natural products. This abundance of compounds is …

[HTML][HTML] Dynamic behavior of rearranging carbocations–implications for terpene biosynthesis

SR Hare, DJ Tantillo - Beilstein Journal of Organic Chemistry, 2016 - beilstein-journals.org
This review describes unexpected dynamical behaviors of rearranging carbocations and the
modern computational methods used to elucidate these aspects of reaction mechanisms …