Journal ArticleDOI
Intrinsic reaction coordinate: Calculation, bifurcation, and automated search
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TLDR
The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions as mentioned in this paper, which gives a unique connection from a given transition structure to local minima of the reactant and product sides.Abstract:
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 unique connection from a given transition structure to local minima of the reactant and product sides. This allows for easy understanding of complicated multistep mechanisms as a set of simple elementary reaction steps. In this article, three topics concerning the IRC approach are discussed. In the first topic, the first ab initio study of the IRC and a recent development of an IRC calculation algorithm for enzyme reactions are introduced. In the second topic, cases are presented in which dynamical trajectories bifurcate and corresponding IRC connections can be inaccurate. In the third topic, a recent development of an automated reaction path search method and its application to systematic construction of IRC networks are described. Finally, combining these three topics, future perspectives are discussed. © 2014 Wiley Periodicals, Inc.read more
Citations
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Dynamics study of the post-transition-state-bifurcation process of the (HCOOH)H+ → CO + H3O+/HCO+ + H2O dissociation: application of machine-learning techniques.
TL;DR: In this article , the phase information of the vibrational motions at the transition state of formic acid was studied using ring-polymer molecular dynamics (RPMD), classical MD, and quasi-classical trajectory (QCT).
Journal ArticleDOI
Dynamic Effects in Intramolecular Schmidt Reactions: Entropy, Electrostatic Drag, and Selectivity Prediction
Qing Sun,Xin Lu,Dean J. Tantillo +2 more
TL;DR: In this paper, the authors characterized the electrostatic drag in the Schmidt reaction of azidopropylcyclohexanones using density functional theory (DFT) calculations and direct dynamics simulations.
Journal ArticleDOI
Limonene: A scented and versatile tropospheric free radical deactivator
TL;DR: In this article , the density functional theory was used to investigate the reactions of limonene with various free radicals (•OCH3, •OBr, •SH, •OOH, and •OOCH3) along the 273.15-312.15 K temperature range.
Journal ArticleDOI
A Dataset of Computational Reaction Barriers for the Claisen Rearrangement: Chemical and Numerical Analysis.
Hiroaki Okada,Satoshi Maeda +1 more
TL;DR: In this paper, a dataset of reaction barriers of size ∼100000 was generated to evaluate various implementations of an optimization algorithm such as GA and BO, which can be used to quickly evaluate the performance of an algorithm.
References
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Book
An introduction to the bootstrap
Bradley Efron,Robert Tibshirani +1 more
TL;DR: This article presents bootstrap methods for estimation, using simple arguments, with Minitab macros for implementing these methods, as well as some examples of how these methods could be used for estimation purposes.
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A climbing image nudged elastic band method for finding saddle points and minimum energy paths
TL;DR: In this article, a modification of the nudged elastic band method for finding minimum energy paths is presented, where one of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point.
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An Introduction to the Bootstrap
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Journal ArticleDOI
An improved algorithm for reaction path following
TL;DR: In this article, a second order algorithm for finding points on a steepest descent path from the transition state of the reactants and products is presented. But the points are optimized so that the segment of the reaction path between any two adjacent points is given by an arc of a circle, and the gradient at each point is tangent to the path.
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