An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

Didier Gigmes; Yoelvis Orozco-Gonzalez; Madushanka Manathunga; María del Carmen Marín; Damianos Agathangelou; Kwang-Hwan Jung; Federico Melaccio; Nicolas Ferré; Stefan Haacke; Kaline Coutinho; Sylvio Canuto; Massimo Olivucci

doi:10.1021/acs.jctc.7b00860

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An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

Didier Gigmes ¹ Yoelvis Orozco-Gonzalez Madushanka Manathunga María del Carmen Marín Damianos Agathangelou Kwang-Hwan Jung Federico Melaccio ² Nicolas Ferré ¹ Stefan Haacke ³ Kaline Coutinho Sylvio Canuto ⁴ Massimo Olivucci ⁵

1 ICR - Institut de Chimie Radicalaire

2 UNISI - Università degli Studi di Siena = University of Siena

3 IPCMS - Institut de Physique et Chimie des Matériaux de Strasbourg

4 IFSC-USP - Instituto de Física de São Carlos

5 Dipartimento di Chimica

Didier Gigmes ¹ AuthorId : 1026661
Author

Yoelvis Orozco-Gonzalez AuthorId : 1427867
Author

Madushanka Manathunga AuthorId : 1427847
Author

María del Carmen Marín AuthorId : 11182255
Author

Damianos Agathangelou AuthorId : 11182256
Author

Kwang-Hwan Jung AuthorId : 11182257
Author

Federico Melaccio ² AuthorId : 1427861
Author

Nicolas Ferré ¹ AuthorId : 1427852
Author IdHAL : nicolas-ferre ORCID : https://orcid.org/0000-0002-5583-8834 ResearcherId : http://www.researcherid.com/rid/K-8228-2012

Stefan Haacke ³ AuthorId : 234409
Author

Kaline Coutinho AuthorId : 11182258
Author

Sylvio Canuto ⁴ AuthorId : 1263002
Author

Massimo Olivucci ⁵ AuthorId : 1427835
Author

1 ICR - Institut de Chimie Radicalaire (Avenue Escadrille Normandie-Niemen Service D42 13397 Marseille cedex 20 - France) StructId : 258556

INC - Institut de Chimie du CNRS (3 Rue Michel-Ange 75 016 Paris - France) StructId : 341038
CNRS - Centre National de la Recherche Scientifique : UMR7273 (France) StructId : 441569
AMU - Aix Marseille Université : UMR7273 (Aix-Marseille Université Jardins du Pharo 58 Boulevard Charles Livon 13284 Marseille cedex 7 - France) StructId : 198056

2 UNISI - Università degli Studi di Siena = University of Siena (Rettorato - Via Banchi di Sotto 55 - 53100 Siena - Italy) StructId : 105124

3 IPCMS - Institut de Physique et Chimie des Matériaux de Strasbourg (23 rue du Loess - BP 43 - 67034 Strasbourg Cedex 2 - France - France) StructId : 93794

UNISTRA - Université de Strasbourg (4 rue Blaise Pascal - CS 90032 - 67081 Strasbourg cedex - France) StructId : 199013
CNRS - Centre National de la Recherche Scientifique : UMR7504 (France) StructId : 441569
FMNGE - Matériaux et nanosciences d'Alsace (France) StructId : 529627
- INC - Institut de Chimie du CNRS (3 Rue Michel-Ange 75 016 Paris - France) StructId : 341038
- UNISTRA - Université de Strasbourg : FR3627 (4 rue Blaise Pascal - CS 90032 - 67081 Strasbourg cedex - France) StructId : 199013
- Université de Haute-Alsace (UHA) - Université de Haute-Alsace (UHA) Mulhouse - Colmar (2, rue des Frères Lumière F-68093 Mulhouse Cedex - France) StructId : 237692
- INSERM - Institut National de la Santé et de la Recherche Médicale (101, rue de Tolbiac, 75013 Paris - France) StructId : 303623
- CNRS - Centre National de la Recherche Scientifique : FR3627 (France) StructId : 441569
Réseau nanophotonique et optique (France) StructId : 529628
- CNRS - Centre National de la Recherche Scientifique (France) StructId : 441569
- UNISTRA - Université de Strasbourg : FR3678 (4 rue Blaise Pascal - CS 90032 - 67081 Strasbourg cedex - France) StructId : 199013
- Université de Haute-Alsace (UHA) - Université de Haute-Alsace (UHA) Mulhouse - Colmar (2, rue des Frères Lumière F-68093 Mulhouse Cedex - France) StructId : 237692

4 IFSC-USP - Instituto de Física de São Carlos (Avenida Trabalhador São-carlense, nº 400, CEP 13566-590 - São Carlos – São Paulo – Brasil - Brazil) StructId : 119113

USP - Universidade de São Paulo (Cidade Universitaria - 05508-090 São Paulo - Brazil) StructId : 7119

5 Dipartimento di Chimica (Italy) StructId : 227188

UNISI - Università degli Studi di Siena = University of Siena (Rettorato - Via Banchi di Sotto 55 - 53100 Siena - Italy) StructId : 105124

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Journal articles

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Chemical Sciences

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https://hal-amu.archives-ouvertes.fr/hal-01768448
Contributor : Didier Gigmes Connect in order to contact the contributor
Submitted on : Tuesday, April 17, 2018 - 11:41:28 AM
Last modification on : Friday, January 7, 2022 - 3:53:31 AM

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HAL Id : hal-01768448, version 1
DOI : 10.1021/acs.jctc.7b00860

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UNIV-AMU | CNRS | INC-CNRS | SITE-ALSACE

Citation

Didier Gigmes, Yoelvis Orozco-Gonzalez, Madushanka Manathunga, María del Carmen Marín, Damianos Agathangelou, et al.. An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. Journal of Chemical Theory and Computation, American Chemical Society, 2017, 13 (12), pp.6391 - 6404. ⟨10.1021/acs.jctc.7b00860⟩. ⟨hal-01768448⟩

An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

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An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

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