Journal ArticleDOI
Intrinsic reaction coordinate: Calculation, bifurcation, and automated search
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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
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Reaction mechanism of benzene alkylation with propylene catalyzed by HZSM-5 zeolite and H-Beta zeolite
TL;DR: In this paper, two possible alkylation mechanisms (i.e., consecutive and associative mechanisms) of benzene and propylene to produce cumene were investigated by the density functional theory (DFT) using the B3LYP functional of the Gaussian 09 package with the 8 T model of HZSM-5 zeolite.
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A DFT mechanistic and kinetic study on the reaction of phloroglucinol with •OH in different media: Hydrogen atom transfer versus oxidation
TL;DR: A theoretical study on the reaction of phloroglucinol with •OH has been performed with the aim of elucidating the geometric, energetic and kinetic properties of the reaction as well as identifying... as discussed by the authors.
Journal ArticleDOI
Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems.
TL;DR: A multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems and gave lower reaction energy profiles than the QM/MM‐ONIOM‐microiteration method over the entire reaction paths with comparable computational costs.
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.
Journal ArticleDOI
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.
Journal ArticleDOI
An Introduction to the Bootstrap
TL;DR: Statistical theory attacks the problem from both ends as discussed by the authors, and provides optimal methods for finding a real signal in a noisy background, and also provides strict checks against the overinterpretation of random patterns.
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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