An automated method to find transition states using chemical dynamics simulations

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study.

Related collections

Most cited references 89

Record: found
Abstract: not found
Article: not found

Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points

Graeme Henkelman, Hannes Jónsson (2000)

0 comments Cited 1297 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

James J. P. Stewart (2007)

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol−1. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol−1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol−1. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta6Cl12]2+ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0233-4) contains supplementary material, which is available to authorized users.

0 comments Cited 527 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

Escaping free-energy minima

M. Parrinello, A Laio (2002)

We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

0 comments Cited 526 times – based on 0 reviews

Preprint

     Review now

Bookmark

All references

Author and article information

Journal

Title: Journal of Computational Chemistry

Abbreviated Title: J. Comput. Chem.

Publisher: Wiley

ISSN: 01928651

Publication date Created: February 05 2015

Publication date (Print): February 05 2015

Publication date (Electronic): November 21 2014

Volume: 36

Issue: 4

Pages: 222-234

Affiliations

[1 ]Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares; Campus Vida, Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain