Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm
Article first published online: 5 SEP 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 29, pages 2502–2513, 5 November 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 2502–2513. DOI: 10.1002/jcc.23408, .
- Issue published online: 24 SEP 2013
- Article first published online: 5 SEP 2013
- Manuscript Accepted: 21 JUL 2013
- Manuscript Revised: 20 JUN 2013
- Manuscript Received: 15 MAY 2013
- Ontario Centers of Excellence and GasTOPS
- energy landscape exploration;
- molecular systems;
- conformational changes;
- Hessian matrix eigenvectors;
- transition state energies
The Transition Rapidly exploring Random Eigenvector Assisted Tree (TRREAT) algorithm is introduced to perform searches along low curvature pathways on a potential energy surface (PES). The method combines local curvature information about the PES with an iterative Rapidly exploring Random Tree algorithm (LaValle, Computer Science Department, Iowa State University, 1998, TR98–11) that quickly searches high-dimensional spaces for feasible pathways between local minima. Herein, the method is applied to identifying conformational changes of molecular systems using Cartesian coordinates while avoiding a priori definition of collective variables. We analyze the pathway identification problem for alanine dipeptide, cyclohexane and glycine using nonreactive and reactive forcefields. We show how TRREAT-identified pathways can be used as valuable input guesses for double-ended methods such as the Nudged Elastic Band when ascertaining transition state energies. This method can be utilized to improve/extend the reaction databases that lie at the core of automatic chemical reaction mechanism generator software currently developed to build kinetic models of chemical reactions. © 2013 Wiley Periodicals, Inc.