title: Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry.
abstract: 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.
authors.affiliation: Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Petraglia
authors.affiliation: Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
authors.forename: Adrien
authors.initials: A
authors.lastname: Nicolaï
authors.affiliation: Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Wodrich
authors.affiliation: Laboratory of Computational Science and Modelling, Institut des Materiaux, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
authors.forename: Michele
authors.initials: M
authors.lastname: Ceriotti
authors.affiliation: Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
authors.forename: Clemence
authors.initials: C
authors.lastname: Corminboeuf
keywords: ab initio molecular dynamics; computational organic chemistry; density functional tight binding; replica exchange molecular dynamics