Optimizing transition states via kernel-based machine learning

The Journal of Chemical Physics
Zachary D PozunGraeme Henkelman

Abstract

We present a method for optimizing transition state theory dividing surfaces with support vector machines. The resulting dividing surfaces require no a priori information or intuition about reaction mechanisms. To generate optimal dividing surfaces, we apply a cycle of machine-learning and refinement of the surface by molecular dynamics sampling. We demonstrate that the machine-learned surfaces contain the relevant low-energy saddle points. The mechanisms of reactions may be extracted from the machine-learned surfaces in order to identify unexpected chemically relevant processes. Furthermore, we show that the machine-learned surfaces significantly increase the transmission coefficient for an adatom exchange involving many coupled degrees of freedom on a (100) surface when compared to a distance-based dividing surface.

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Citations

Jan 24, 2014·PLoS Computational Biology·Matthias RuppGisbert Schneider
Dec 18, 2013·The Journal of Chemical Physics·John C SnyderKieron Burke
Sep 4, 2015·The Journal of Chemical Physics·Raghunathan RamakrishnanO Anatole von Lilienfeld
Nov 18, 2015·Journal of Chemical Theory and Computation·Frank Noé, Cecilia Clementi
Jan 20, 2016·Scientific Reports·G PilaniaT Lookman
Apr 4, 2017·Physical Chemistry Chemical Physics : PCCP·Andrew J BallardDavid J Wales
Dec 8, 2017·Angewandte Chemie·O Anatole von Lilienfeld
Sep 17, 2020·Faraday Discussions·Jack WetherellLucia Reining
Sep 10, 2018·The Journal of Chemical Physics·Mohammad M Sultan, Vijay S Pande
Oct 13, 2017·Nature Communications·Felix BrockherdeKlaus-Robert Müller
Dec 6, 2018·Scientific Reports·Dipendra JhaAnkit Agrawal
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Mar 13, 2018·Journal of Nonlinear Science·Andreas BittracherChristof Schütte
Nov 22, 2014·Journal of Computational Chemistry·Emilio Martínez-Núñez
Mar 3, 2020·The Journal of Chemical Physics·Ralf Meyer, Andreas W Hauser
Mar 19, 2021·Journal of Chemical Theory and Computation·Christopher RobertsonScott Habershon
May 29, 2021·Nature Materials·Pascal FriederichAlán Aspuru-Guzik
Jun 4, 2021·Physical Chemistry Chemical Physics : PCCP·Marcos Del Cueto, Alessandro Troisi
Jul 17, 2021·The Journal of Chemical Physics·Małgorzata Z MakośElfi Kraka
Aug 12, 2021·Journal of Chemical Theory and Computation·Daniel Born, Johannes Kästner
Feb 8, 2019·The Journal of Physical Chemistry. B·Matthias FeldmaierRigoberto Hernandez
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Aug 13, 2013·Journal of Chemical Theory and Computation·Katja HansenKlaus-Robert Müller
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May 8, 2019·Journal of Chemical Information and Modeling·Gianmarc GrazioliCarter T Butts
Mar 4, 2020·The Journal of Physical Chemistry Letters·Pavlo O Dral

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Software Mentioned

libsvm
scikits
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