Uncovering reaction sequences on surfaces through graphical methods

Physical Chemistry Chemical Physics : PCCP
Mina Jafari, Paul M Zimmerman

Abstract

ZStruct is a graph-based model that generates an ensemble of plausible reaction pathways starting from a given initial state, without requiring prior knowledge of reaction intermediates. In this article, a surface-reaction oriented implementation (S-ZStruct) is introduced for unimolecular and bimolecular reactions, including sampling of different binding sites and adsorption orientations. To test the unimolecular reaction generation ability and angle sampling feature of S-ZStruct, the propanoic acid to ethylene dissociation network is studied. Starting from multiple initial orientations of two key intermediates, multiple unique reaction pathways, each with different activation energies, were discovered. Atomic layer deposition of TiN on Si(100)-involving a challenging reaction mechanism-is also studied as an example of bimolecular reactions. In addition to locating a number of expected pathways, S-ZStruct found that the little-understood step of reduction of Ti(iv) to Ti(iii) likely occurs through β-hydride transfer between diamido ligands on neighboring Ti centers. These results suggest that S-ZStruct is a powerful tool for exploring surface chemistry, which will permit discoveries of reaction mechanisms in a wide variety of e...Continue Reading

References

Oct 15, 1996·Physical Review. B, Condensed Matter·G Kresse, J Furthmüller
Nov 1, 1993·Physical Review. B, Condensed Matter·G Kresse, J Hafner
May 2, 2002·Journal of Computational Chemistry·Michael Hirsch, Wolfgang Quapp
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Jul 15, 2003·Physical Review Letters·Marcella IannuzziMichele Parrinello
Jul 23, 2004·The Journal of Chemical Physics·Semen A Trygubenko, David J Wales
Feb 24, 2006·Accounts of Chemical Research·Bernd EnsingMichael L Klein
Oct 11, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Dec 16, 2011·The Journal of Chemical Physics·Andrew BehnMartin Head-Gordon
Mar 20, 2013·Journal of Computational Chemistry·Paul M Zimmerman
May 8, 2014·ACS Applied Materials & Interfaces·Delphine LongrieChristophe Detavernier
Jan 13, 2015·Journal of Computational Chemistry·Paul M Zimmerman
Jun 10, 2015·Journal of the American Chemical Society·Alex J NettJohn Montgomery
Nov 18, 2015·Journal of Chemical Theory and Computation·Yury V Suleimanov, William H Green
Jul 9, 2013·Journal of Chemical Theory and Computation·Paul Zimmerman
Aug 9, 2011·Journal of Chemical Theory and Computation·Satoshi Maeda, Keiji Morokuma
Feb 5, 2016·The Journal of Physical Chemistry. a·Maxwell W LiPaul M Zimmerman
Apr 28, 2016·Nature·Jacob R LudwigCorinna S Schindler
Dec 13, 2016·Organic & Biomolecular Chemistry·Amanda L Dewyer, Paul M Zimmerman
Jan 29, 2017·Journal of Computational Chemistry·Mina Jafari, Paul M Zimmerman

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Citations

Oct 16, 2019·Journal of Chemical Theory and Computation·Eric D HermesJudit Zádor
Feb 25, 2020·Journal of Chemical Information and Modeling·Joshua A KammeraadPaul M Zimmerman
Feb 6, 2020·The Journal of Physical Chemistry. a·Ethan R CurtisPaul M Zimmerman

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Software Mentioned

SE
Open Babel
ZStruct
Atomic Simulation Environment 38 ( ASE )
Vienna Ab Initio Simulation Package ( VASP )
GSM
VASP

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