Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis

The Journal of Chemical Physics
Scott Habershon

Abstract

Automatically generating chemical reaction pathways is a significant computational challenge, particularly in the case where a given chemical system can exhibit multiple reactants and products, as well as multiple pathways connecting these. Here, we outline a computational approach to allow automated sampling of chemical reaction pathways, including sampling of different chemical species at the reaction end-points. The key features of this scheme are (i) introduction of a Hamiltonian which describes a reaction "string" connecting reactant and products, (ii) definition of reactant and product species as chemical connectivity graphs, and (iii) development of a scheme for updating the chemical graphs associated with the reaction end-points. By performing molecular dynamics sampling of the Hamiltonian describing the complete reaction pathway, we are able to sample multiple different paths in configuration space between given chemical products; by periodically modifying the connectivity graphs describing the chemical identities of the end-points we are also able to sample the allowed chemical space of the system. Overall, this scheme therefore provides a route to automated generation of a "roadmap" describing chemical reactivity. Th...Continue Reading

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Citations

Mar 5, 2016·Journal of Chemical Theory and Computation·Scott Habershon
Aug 27, 2016·Molecular Simulation·Xiya LuQiang Cui
Oct 13, 2016·Faraday Discussions·Jonny ProppeMarkus Reiher
Feb 17, 2017·Journal of Chemical Theory and Computation·Alain C Vaucher, Markus Reiher
Nov 15, 2017·Journal of Computational Chemistry·Satoshi MaedaYuriko Ono
Mar 6, 2018·Journal of Computational Chemistry·Toshiyuki Takayanagi, Taiki Nakatomi
Sep 25, 2018·Journal of Computational Chemistry·Aurelio RodríguezEmilio Martínez-Núñez
Aug 21, 2018·Chemistry : a European Journal·Ewa N Szlapa, Jeremy N Harvey
Feb 7, 2019·Physical Chemistry Chemical Physics : PCCP·Kanami SugiyamaSatoshi Maeda
Feb 28, 2020·Annual Review of Physical Chemistry·Jan P Unsleber, Markus Reiher
Dec 6, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Saulo A VázquezEmilio Martinez-Nunez
Feb 23, 2021·Journal of Computational Chemistry·Christopher Robertson, Scott Habershon
Mar 19, 2021·Journal of Chemical Theory and Computation·Christopher RobertsonScott Habershon
Apr 30, 2021·The Journal of Physical Chemistry. a·Toshiyuki Takayanagi
Jun 25, 2021·Chemical Science·Elisa PieriTodd J Martínez
Aug 12, 2021·Journal of the American Chemical Society·Xiaowei XieKristin A Persson
Aug 14, 2021·Journal of Computational Chemistry·Emilio Martínez-NúñezSaulo A Vazquez
Mar 23, 2019·The Journal of Physical Chemistry. a·Idil IsmailScott Habershon
Mar 13, 2019·Journal of Chemical Theory and Computation·Satoshi Maeda, Yu Harabuchi
Jul 26, 2019·The Journal of Physical Chemistry Letters·Li ZhuTimothy A Strobel
Oct 31, 2017·Journal of Chemical Theory and Computation·Gregor N Simm, Markus Reiher
Feb 1, 2020·Journal of Chemical Theory and Computation·Marshall HutchingsLee-Ping Wang
Dec 7, 2018·Journal of Chemical Theory and Computation·Jonny Proppe, Markus Reiher
Nov 14, 2018·The Journal of Physical Chemistry. a·Gregor N SimmMarkus Reiher

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