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. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Photochromic Torsional Switch (PTS): a light-driven actuator for the dynamic tuning of π-conjugation extension

“…The geometrical conformations of both 1. trans and 1. cis , were determined by replica-exchange molecular dynamic (REMD) computations performed at the density functional tight binding (DFTB) level (REMD@DFTB). 44 Several minima were identified and optimized statically at the density functional theory level (see ESI for details†). The lowest-lying structures revealed that when the azobenzene is in its extended trans conformation ( 1. trans ), the bithiophene unit is forced to twist out of coplanarity with a dihedral angle ( θ ) of 55° (Fig.…”

i-PI 2.0: A universal force engine for advanced molecular simulations

“…If a move is rejected, both ensembles are restored to their initial state. The i-PI implementation of replica exchange has already been used to sample organic chemical reactions and conformational transitions with den-sity functional tight binding [33]. Here, we provide a simple demonstration that illustrates the power of this approach using both classical and path integral REMD.…”

“…• replica exchange MD (R. Petraglia, R. Meissner, M. Ceriotti) [33]; accelerated convergence of averages by performing Monte Carlo exchanges of configurations between parallel calculations…”

Hierarchical parallelization of divide‐and‐conquer density functional tight‐binding molecular dynamics and metadynamics simulations

“…[ 43–45 ] The efficiency of DFTB‐MD for large systems has been greatly improved by combination with fragment molecular orbital [ 46–49 ] or divide‐and‐conquer (DC) techniques. [ 50,51 ] Enhanced sampling methods have been recently applied to DFTB‐MD, resulting in novel DFTB‐REMD, [ 52 ] DFTB‐REUS, [ 53,54 ] and DFTB‐MetaD methods. [ 55,56 ]…”