Literature DB >> 22168681

Efficient exploration of reaction paths via a freezing string method.

Andrew Behn1, Paul M Zimmerman, Alexis T Bell, Martin Head-Gordon.   

Abstract

The ability to efficiently locate transition states is critically important to the widespread adoption of theoretical chemistry techniques for their ability to accurately predict kinetic constants. Existing surface walking techniques to locate such transition states typically require an extremely good initial guess that is often beyond human intuition to estimate. To alleviate this problem, automated techniques to locate transition state guesses have been created that take the known reactant and product endpoint structures as inputs. In this work, we present a simple method to build an approximate reaction path through a combination of interpolation and optimization. Starting from the known reactant and product structures, new nodes are interpolated inwards towards the transition state, partially optimized orthogonally to the reaction path, and then frozen before a new pair of nodes is added. The algorithm is stopped once the string ends connect. For the practical user, this method provides a quick and convenient way to generate transition state structure guesses. Tests on three reactions (cyclization of cis,cis-2,4-hexadiene, alanine dipeptide conformation transition, and ethylene dimerization in a Ni-exchanged zeolite) show that this "freezing string" method is an efficient way to identify complex transition states with significant cost savings over existing methods, particularly when high quality linear synchronous transit interpolation is employed.
© 2011 American Institute of Physics

Entities:  

Year:  2011        PMID: 22168681     DOI: 10.1063/1.3664901

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


  9 in total

1.  Generating conformational transition paths with low potential-energy barriers for proteins.

Authors:  Minh Khoa Nguyen; Léonard Jaillet; Stéphane Redon
Journal:  J Comput Aided Mol Des       Date:  2018-08-01       Impact factor: 3.686

2.  Selective removal of alkali metal cations from multiply-charged ions via gas-phase ion/ion reactions using weakly coordinating anions.

Authors:  Carl A Luongo; Jiexun Bu; Nicole L Burke; Joshua D Gilbert; Boone M Prentice; Steven Cummings; Christopher A Reed; Scott A McLuckey
Journal:  J Am Soc Mass Spectrom       Date:  2015-01-06       Impact factor: 3.109

Review 3.  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Authors:  Tatiana Maximova; Ryan Moffatt; Buyong Ma; Ruth Nussinov; Amarda Shehu
Journal:  PLoS Comput Biol       Date:  2016-04-28       Impact factor: 4.475

4.  Gas phase formation of c-SiC3 molecules in the circumstellar envelope of carbon stars.

Authors:  Tao Yang; Luke Bertels; Beni B Dangi; Xiaohu Li; Martin Head-Gordon; Ralf I Kaiser
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-01       Impact factor: 11.205

5.  A benchmark dataset for Hydrogen Combustion.

Authors:  Xingyi Guan; Akshaya Das; Christopher J Stein; Farnaz Heidar-Zadeh; Luke Bertels; Meili Liu; Mojtaba Haghighatlari; Jie Li; Oufan Zhang; Hongxia Hao; Itai Leven; Martin Head-Gordon; Teresa Head-Gordon
Journal:  Sci Data       Date:  2022-05-17       Impact factor: 8.501

6.  Fast exploration of an optimal path on the multidimensional free energy surface.

Authors:  Changjun Chen
Journal:  PLoS One       Date:  2017-05-18       Impact factor: 3.240

Review 7.  Reaction prediction via atomistic simulation: from quantum mechanics to machine learning.

Authors:  Pei-Lin Kang; Zhi-Pan Liu
Journal:  iScience       Date:  2020-12-30

8.  Spin-Forbidden Carbon-Carbon Bond Formation in Vibrationally Excited α-CO.

Authors:  Jessalyn A DeVine; Arnab Choudhury; Jascha A Lau; Dirk Schwarzer; Alec M Wodtke
Journal:  J Phys Chem A       Date:  2022-04-05       Impact factor: 2.944

Review 9.  Accelerated Multiphosphorylated Peptide Synthesis.

Authors:  Dana Grunhaus; Estefanía Rossich Molina; Roni Cohen; Tamar Stein; Assaf Friedler; Mattan Hurevich
Journal:  Org Process Res Dev       Date:  2022-07-12       Impact factor: 3.858

  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.