Literature DB >> 15549851

Comparison of methods for finding saddle points without knowledge of the final states.

R A Olsen1, G J Kroes, G Henkelman, A Arnaldsson, H Jónsson.   

Abstract

Within the harmonic approximation to transition state theory, the biggest challenge involved in finding the mechanism or rate of transitions is the location of the relevant saddle points on the multidimensional potential energy surface. The saddle point search is particularly challenging when the final state of the transition is not specified. In this article we report on a comparison of several methods for locating saddle points under these conditions and compare, in particular, the well-established rational function optimization (RFO) methods using either exact or approximate Hessians with the more recently proposed minimum mode following methods where only the minimum eigenvalue mode is found, either by the dimer or the Lanczos method. A test problem involving transitions in a seven-atom Pt island on a Pt(111) surface using a simple Morse pairwise potential function is used and the number of degrees of freedom varied by varying the number of movable atoms. In the full system, 175 atoms can move so 525 degrees of freedom need to be optimized to find the saddle points. For testing purposes, we have also restricted the number of movable atoms to 7 and 1. Our results indicate that if attempting to make a map of all relevant saddle points for a large system (as would be necessary when simulating the long time scale evolution of a thermal system) the minimum mode following methods are preferred. The minimum mode following methods are also more efficient when searching for the lowest saddle points in a large system, and if the force can be obtained cheaply. However, if only the lowest saddle points are sought and the calculation of the force is expensive but a good approximation for the Hessian at the starting position of the search can be obtained at low cost, then the RFO approaches employing an approximate Hessian represent the preferred choice. For small and medium sized systems where the force is expensive to calculate, the RFO approaches employing an approximate Hessian is also the more efficient, but when the force and Hessian can be obtained cheaply and only the lowest saddle points are sought the RFO approach using an exact Hessian is the better choice. These conclusions have been reached based on a comparison of the total computational effort needed to find the saddle points and the number of saddle points found for each of the methods. The RFO methods do not perform very well with respect to the latter aspect, but starting the searches further away from the initial minimum or using the hybrid RFO version presented here improves this behavior considerably in most cases. Copyright 2004 American Institute of Physics.

Entities:  

Year:  2004        PMID: 15549851     DOI: 10.1063/1.1809574

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


  20 in total

1.  Simulation of surface processes.

Authors:  Hannes Jónsson
Journal:  Proc Natl Acad Sci U S A       Date:  2011-01-03       Impact factor: 11.205

2.  Learning to predict chemical reactions.

Authors:  Matthew A Kayala; Chloé-Agathe Azencott; Jonathan H Chen; Pierre Baldi
Journal:  J Chem Inf Model       Date:  2011-09-02       Impact factor: 4.956

3.  Theoretical prediction of the mechanisms for defect healing or oxygen doping in a hexagonal boron nitride (h-BN) sheet with nitrogen vacancies by NO2 molecules.

Authors:  Jing-wen Feng; Yue-Jie Liu; Jing-xiang Zhao
Journal:  J Mol Model       Date:  2014-05-29       Impact factor: 1.810

4.  Mapping saddles and minima on free energy surfaces using multiple climbing strings.

Authors:  Gourav Shrivastav; Eric Vanden-Eijnden; Cameron F Abrams
Journal:  J Chem Phys       Date:  2019-09-28       Impact factor: 3.488

5.  Silicon-doping in carbon nanotubes: formation energies, electronic structures, and chemical reactivity.

Authors:  Ruixin Bian; Jingxiang Zhao; Honggang Fu
Journal:  J Mol Model       Date:  2013-01-05       Impact factor: 1.810

6.  Chemical functionalization of graphene via aryne cycloaddition: a theoretical study.

Authors:  Jing-xiang Zhao; Hong-xia Wang; Bo Gao; Xiao-guang Wang; Qing-hai Cai; Xuan-zhang Wang
Journal:  J Mol Model       Date:  2011-11-30       Impact factor: 1.810

7.  Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods.

Authors:  Hua Deng; Shan Ke; Robert Callender; Gurusamy Balakrishnan; Thomas G Spiro; Eric R May; Charles L Brooks
Journal:  J Phys Chem B       Date:  2019-09-04       Impact factor: 2.991

8.  Stability and properties of the two-dimensional hexagonal boron nitride monolayer functionalized by hydroxyl (OH) radicals: a theoretical study.

Authors:  Hong-mei Wang; Yue-jie Liu; Hong-xia Wang; Jing-xiang Zhao; Qing-hai Cai; Xuan-zhang Wang
Journal:  J Mol Model       Date:  2013-10-05       Impact factor: 1.810

9.  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

Review 10.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Authors:  Fabio Sterpone; Simone Melchionna; Pierre Tuffery; Samuela Pasquali; Normand Mousseau; Tristan Cragnolini; Yassmine Chebaro; Jean-Francois St-Pierre; Maria Kalimeri; Alessandro Barducci; Yoann Laurin; Alex Tek; Marc Baaden; Phuong Hoang Nguyen; Philippe Derreumaux
Journal:  Chem Soc Rev       Date:  2014-04-23       Impact factor: 54.564

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.