Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations
We present a method for the automatic determination of transition states (TSs) that is based on Grimme’s RMSD-PP semiempirical tight binding reaction path method (J. Chem. Theory Comput. 2019, 15, 2847–2862), where the maximum energy structure along the path serves as an initial guess for DFT TS sea...
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doaj-4c5bab8ab33d4fdeab33a70691b946182020-11-25T03:39:22ZengPeerJ Inc.PeerJ Physical Chemistry2689-77332020-09-012e1510.7717/peerj-pchem.15Fast and automatic estimation of transition state structures using tight binding quantum chemical calculationsMaria H. Rasmussen0Jan H. Jensen1Department of Chemistry, University of Copenhagen, Copenhagen, DenmarkDepartment of Chemistry, University of Copenhagen, Copenhagen, DenmarkWe present a method for the automatic determination of transition states (TSs) that is based on Grimme’s RMSD-PP semiempirical tight binding reaction path method (J. Chem. Theory Comput. 2019, 15, 2847–2862), where the maximum energy structure along the path serves as an initial guess for DFT TS searches. The method is tested on 100 elementary reactions and located a total of 89 TSs correctly. Of the 11 remaining reactions, nine are shown not to be elementary reactions after all and for one of the two true failures the problem is shown to be the semiempirical tight binding model itself. Furthermore, we show that the GFN2-xTB RMSD-PP barrier is a good approximation for the corresponding DFT barrier for reactions with DFT barrier heights up to about 30 kcal/mol. Thus, GFN2-xTB RMSD-PP barrier heights, which can be estimated at the cost of a single energy minimisation, can be used to quickly identify reactions with low barriers, although it will also produce some false positives.https://peerj.com/articles/pchem-15.pdfTransition states |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Maria H. Rasmussen Jan H. Jensen |
spellingShingle |
Maria H. Rasmussen Jan H. Jensen Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations PeerJ Physical Chemistry Transition states |
author_facet |
Maria H. Rasmussen Jan H. Jensen |
author_sort |
Maria H. Rasmussen |
title |
Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations |
title_short |
Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations |
title_full |
Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations |
title_fullStr |
Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations |
title_full_unstemmed |
Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations |
title_sort |
fast and automatic estimation of transition state structures using tight binding quantum chemical calculations |
publisher |
PeerJ Inc. |
series |
PeerJ Physical Chemistry |
issn |
2689-7733 |
publishDate |
2020-09-01 |
description |
We present a method for the automatic determination of transition states (TSs) that is based on Grimme’s RMSD-PP semiempirical tight binding reaction path method (J. Chem. Theory Comput. 2019, 15, 2847–2862), where the maximum energy structure along the path serves as an initial guess for DFT TS searches. The method is tested on 100 elementary reactions and located a total of 89 TSs correctly. Of the 11 remaining reactions, nine are shown not to be elementary reactions after all and for one of the two true failures the problem is shown to be the semiempirical tight binding model itself. Furthermore, we show that the GFN2-xTB RMSD-PP barrier is a good approximation for the corresponding DFT barrier for reactions with DFT barrier heights up to about 30 kcal/mol. Thus, GFN2-xTB RMSD-PP barrier heights, which can be estimated at the cost of a single energy minimisation, can be used to quickly identify reactions with low barriers, although it will also produce some false positives. |
topic |
Transition states |
url |
https://peerj.com/articles/pchem-15.pdf |
work_keys_str_mv |
AT mariahrasmussen fastandautomaticestimationoftransitionstatestructuresusingtightbindingquantumchemicalcalculations AT janhjensen fastandautomaticestimationoftransitionstatestructuresusingtightbindingquantumchemicalcalculations |
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1724539287767089152 |