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The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change
Much chemical insight ultimately comes down to finding out which fragment of a total system behaves like the total system, in terms of an energy profile. A simple example is that of the water dimer, where this system is regarded as held together by a hydrogen bond. The hydrogen bond consists of two...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979521/ https://www.ncbi.nlm.nih.gov/pubmed/32025197 http://dx.doi.org/10.1007/s00214-017-2113-z |
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author | Thacker, Joseph C. R. Popelier, Paul L. A. |
author_facet | Thacker, Joseph C. R. Popelier, Paul L. A. |
author_sort | Thacker, Joseph C. R. |
collection | PubMed |
description | Much chemical insight ultimately comes down to finding out which fragment of a total system behaves like the total system, in terms of an energy profile. A simple example is that of the water dimer, where this system is regarded as held together by a hydrogen bond. The hydrogen bond consists of two atoms (H···O), which energetically behave similarly to the total system (H(2)O)(2). However, from a quantum mechanical point of view, each atom in the total system interacts with any other atom. Thus, the view that the hydrogen bond by itself governs the energetic stability of the water dimer needs rigorous justification. In this work, we propose a method that provides such a justification, in general, but only illustrated on the water dimer here. This method is based on the topological energy partitioning method called interacting quantum atoms (IQA). The method is implemented in the program ANANKE, which calculates correlations between the energy profile of the total system and those of subsystems (or fragments). ANANKE acts on the IQA energy contributions obtained for a sequence of full-system geometries controlled by a coordinate of interest (e.g. the O···H distance in the water dimer). Although applied only for the water dimer in this work, the method is general and able to explain the gauche effect, the torsional barrier in biphenyl, the arrow-pushing scheme of an enzymatic reaction (peptide hydrolysis in the HIV-1 Protease active site), and halogen-alkane nucleophilic substitution (S(N)2) reactions. Those applications will appear elsewhere as separate and elaborated case studies; here we focus on the details of the ANANKE method and its justification, using the water dimer as a concrete case. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00214-017-2113-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6979521 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-69795212020-02-03 The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change Thacker, Joseph C. R. Popelier, Paul L. A. Theor Chem Acc Regular Article Much chemical insight ultimately comes down to finding out which fragment of a total system behaves like the total system, in terms of an energy profile. A simple example is that of the water dimer, where this system is regarded as held together by a hydrogen bond. The hydrogen bond consists of two atoms (H···O), which energetically behave similarly to the total system (H(2)O)(2). However, from a quantum mechanical point of view, each atom in the total system interacts with any other atom. Thus, the view that the hydrogen bond by itself governs the energetic stability of the water dimer needs rigorous justification. In this work, we propose a method that provides such a justification, in general, but only illustrated on the water dimer here. This method is based on the topological energy partitioning method called interacting quantum atoms (IQA). The method is implemented in the program ANANKE, which calculates correlations between the energy profile of the total system and those of subsystems (or fragments). ANANKE acts on the IQA energy contributions obtained for a sequence of full-system geometries controlled by a coordinate of interest (e.g. the O···H distance in the water dimer). Although applied only for the water dimer in this work, the method is general and able to explain the gauche effect, the torsional barrier in biphenyl, the arrow-pushing scheme of an enzymatic reaction (peptide hydrolysis in the HIV-1 Protease active site), and halogen-alkane nucleophilic substitution (S(N)2) reactions. Those applications will appear elsewhere as separate and elaborated case studies; here we focus on the details of the ANANKE method and its justification, using the water dimer as a concrete case. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00214-017-2113-z) contains supplementary material, which is available to authorized users. Springer Berlin Heidelberg 2017-07-05 2017 /pmc/articles/PMC6979521/ /pubmed/32025197 http://dx.doi.org/10.1007/s00214-017-2113-z Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Regular Article Thacker, Joseph C. R. Popelier, Paul L. A. The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change |
title | The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change |
title_full | The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change |
title_fullStr | The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change |
title_full_unstemmed | The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change |
title_short | The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change |
title_sort | ananke relative energy gradient (reg) method to automate iqa analysis over configurational change |
topic | Regular Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979521/ https://www.ncbi.nlm.nih.gov/pubmed/32025197 http://dx.doi.org/10.1007/s00214-017-2113-z |
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