PyFrag 2019—Automating the exploration and analysis of reaction mechanisms

We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment‐based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrin...

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Published in:Journal of computational chemistry Vol. 40; no. 25; pp. 2227 - 2233
Main Authors: Sun, Xiaobo, Soini, Thomas M., Poater, Jordi, Hamlin, Trevor A., Bickelhaupt, F. Matthias
Format: Journal Article
Language:English
Published: Hoboken, USA John Wiley & Sons, Inc 30.09.2019
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ISSN:0192-8651, 1096-987X, 1096-987X
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Abstract We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment‐based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time‐consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc. PyFrag 2019 is a user‐friendly python program that resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: (1) the management of multiple parallel calculations to automatically find a reaction path; (2) the real‐time monitoring of the entire computational process; and (3) the analysis and presentation of these data in a clear and informative way to rationalize the characteristics of the reaction profile in terms of intrinsic properties of the reactant species by means of the activation strain model (ASM) and an energy decomposition analysis (EDA, when using ADF).
AbstractList We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment‐based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time‐consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment‐based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time‐consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc. PyFrag 2019 is a user‐friendly python program that resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: (1) the management of multiple parallel calculations to automatically find a reaction path; (2) the real‐time monitoring of the entire computational process; and (3) the analysis and presentation of these data in a clear and informative way to rationalize the characteristics of the reaction profile in terms of intrinsic properties of the reactant species by means of the activation strain model (ASM) and an energy decomposition analysis (EDA, when using ADF).
We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment‐based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time‐consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
Author Bickelhaupt, F. Matthias
Soini, Thomas M.
Sun, Xiaobo
Poater, Jordi
Hamlin, Trevor A.
AuthorAffiliation 1 Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling Vrije Universiteit Amsterdam De Boelelaan 1083, 1081 HV Amsterdam Netherlands
3 ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain and Departament de Química Inorgànica i Orgànica & IQTCUB Universitat de Barcelona 08028 Barcelona Catalonia Spain
4 Institute for Molecules and Materials Radboud University Heyendaalseweg 135, 6525 AJ Nijmegen Netherlands
2 Software for Chemistry & Materials B.V. De Boelelaan 1083, 1081 HV Amsterdam Netherlands
AuthorAffiliation_xml – name: 2 Software for Chemistry & Materials B.V. De Boelelaan 1083, 1081 HV Amsterdam Netherlands
– name: 3 ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain and Departament de Química Inorgànica i Orgànica & IQTCUB Universitat de Barcelona 08028 Barcelona Catalonia Spain
– name: 4 Institute for Molecules and Materials Radboud University Heyendaalseweg 135, 6525 AJ Nijmegen Netherlands
– name: 1 Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling Vrije Universiteit Amsterdam De Boelelaan 1083, 1081 HV Amsterdam Netherlands
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Issue 25
Keywords energy decomposition analysis
reaction mechanisms
density functional calculations
automation
program
activation strain model
Language English
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2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
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Snippet We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment‐based activation strain analysis along a...
We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a...
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Index Database
Enrichment Source
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StartPage 2227
SubjectTerms activation strain model
Automation
Computational chemistry
Decomposition reactions
density functional calculations
energy decomposition analysis
Exploration
Organic chemistry
Potential energy
program
Reaction mechanisms
Software and Updates
Strain analysis
Workflow
Title PyFrag 2019—Automating the exploration and analysis of reaction mechanisms
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fjcc.25871
https://www.ncbi.nlm.nih.gov/pubmed/31165500
https://www.proquest.com/docview/2268285384
https://www.proquest.com/docview/2268574429
https://pubmed.ncbi.nlm.nih.gov/PMC6771738
Volume 40
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