Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

• Published in: Journal of computational chemistry Vol. 37; no. 1; pp. 83 - 92
• Main Authors: Petraglia, Riccardo, Nicolaï, Adrien, Wodrich, Matthew D., Ceriotti, Michele, Corminboeuf, Clemence
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 05-01-2016; Wiley Subscription Services, Inc; John Wiley and Sons Inc
• Subjects: ab initio molecular dynamics; Alignment; Binding energy; Catalysis; Chemistry; Computational chemistry; computational organic chemistry; Computer simulation; Density; density functional tight binding; Dynamical systems; Electronic structure; Electronics; Empirical analysis; Exchanging; Exploration; Isomerization; Molecular dynamics; Molecular structure; Molecules; Organic chemicals; Organic chemistry; Pictures; Potential energy; replica exchange molecular dynamics; Software; Systems analysis; Temperature; ab initio molecular dynamics; computational organic chemistry; density functional tight binding; replica exchange molecular dynamics
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.24025

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica‐exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature‐dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD‐DFTB methodology at the heart of this study is powered by i‐PI, which efficiently handles the interface between the DFTB and REMD codes. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Replica‐exchange molecular dynamics (REMD) is combined with density functional tight binding (DFTB) and applied to organic chemical problems. REMD@DFTB permits thorough exploration of the potential energy surface and reveals new insights and chemistry that likely would be missed using static electronic structure computations.