Literature DB >> 16375464

Efficient methods for finding transition states in chemical reactions: comparison of improved dimer method and partitioned rational function optimization method.

Andreas Heyden1, Alexis T Bell, Frerich J Keil.   

Abstract

A combination of interpolation methods and local saddle-point search algorithms is probably the most efficient way of finding transition states in chemical reactions. Interpolation methods such as the growing-string method and the nudged-elastic band are able to find an approximation to the minimum-energy pathway and thereby provide a good initial guess for a transition state and imaginary mode connecting both reactant and product states. Since interpolation methods employ usually just a small number of configurations and converge slowly close to the minimum-energy pathway, local methods such as partitioned rational function optimization methods using either exact or approximate Hessians or minimum-mode-following methods such as the dimer or the Lanczos method have to be used to converge to the transition state. A modification to the original dimer method proposed by [Henkelman and Jonnson J. Chem. Phys. 111, 7010 (1999)] is presented, reducing the number of gradient calculations per cycle from six to four gradients or three gradients and one energy, and significantly improves the overall performance of the algorithm on quantum-chemical potential-energy surfaces, where forces are subject to numerical noise. A comparison is made between the dimer methods and the well-established partitioned rational function optimization methods for finding transition states after the use of interpolation methods. Results for 24 different small- to medium-sized chemical reactions covering a wide range of structural types demonstrate that the improved dimer method is an efficient alternative saddle-point search algorithm on medium-sized to large systems and is often even able to find transition states when partitioned rational function optimization methods fail to converge.

Year:  2005        PMID: 16375464     DOI: 10.1063/1.2104507

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  25 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-03       Impact factor: 11.205

3.  The kinetic Monte Carlo method as a way to solve the master equation for interstellar grain chemistry.

Authors:  H M Cuppen; L J Karssemeijer; T Lamberts
Journal:  Chem Rev       Date:  2013-11-04       Impact factor: 60.622

4.  Catalytic water dissociation by greigite Fe3S4 surfaces: density functional theory study.

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5.  Formation of the prebiotic molecule NH2CHO on astronomical amorphous solid water surfaces: accurate tunneling rate calculations.

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7.  Understanding potential-dependent competition between electrocatalytic dinitrogen and proton reduction reactions.

Authors:  Changhyeok Choi; Geun Ho Gu; Juhwan Noh; Hyun S Park; Yousung Jung
Journal:  Nat Commun       Date:  2021-07-16       Impact factor: 14.919

8.  Energetic and kinetic dataset on interaction of the vacancy and self-interstitial atom with the grain boundary in α-iron.

Authors:  Xiangyan Li; Wei Liu; Yichun Xu; C S Liu; B C Pan; Yunfeng Liang; Q F Fang; Jun-Ling Chen; G-N Luo; Guang-Hong Lu; Zhiguang Wang
Journal:  Data Brief       Date:  2016-03-19

9.  Microkinetics of alcohol reforming for H2 production from a FAIR density functional theory database.

Authors:  Qiang Li; Rodrigo García-Muelas; Núria López
Journal:  Nat Commun       Date:  2018-02-06       Impact factor: 14.919

10.  How Size Matters: Electronic, Cooperative, and Geometric Effect in Perovskite-Supported Copper Catalysts for CO2 Reduction.

Authors:  Drejc Kopač; Blaž Likozar; Matej Huš
Journal:  ACS Catal       Date:  2020-03-05       Impact factor: 13.084

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