Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The prog...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-04-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/24/9/1653 |
| _version_ | 1818519790149435392 |
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| author | Aurélien de la Lande Aurelio Alvarez-Ibarra Karim Hasnaoui Fabien Cailliez Xiaojing Wu Tzonka Mineva Jérôme Cuny Patrizia Calaminici Luis López-Sosa Gerald Geudtner Isabelle Navizet Cristina Garcia Iriepa Dennis R. Salahub Andreas M. Köster |
| author_facet | Aurélien de la Lande Aurelio Alvarez-Ibarra Karim Hasnaoui Fabien Cailliez Xiaojing Wu Tzonka Mineva Jérôme Cuny Patrizia Calaminici Luis López-Sosa Gerald Geudtner Isabelle Navizet Cristina Garcia Iriepa Dennis R. Salahub Andreas M. Köster |
| author_sort | Aurélien de la Lande |
| collection | DOAJ |
| description | deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born−Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton. |
| first_indexed | 2024-12-11T01:28:47Z |
| format | Article |
| id | doaj.art-19533e8d49134635b184ea2901a19bf2 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-11T01:28:47Z |
| publishDate | 2019-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-19533e8d49134635b184ea2901a19bf22022-12-22T01:25:25ZengMDPI AGMolecules1420-30492019-04-01249165310.3390/molecules24091653molecules24091653Molecular Simulations with in-deMon2k QM/MM, a Tutorial-ReviewAurélien de la Lande0Aurelio Alvarez-Ibarra1Karim Hasnaoui2Fabien Cailliez3Xiaojing Wu4Tzonka Mineva5Jérôme Cuny6Patrizia Calaminici7Luis López-Sosa8Gerald Geudtner9Isabelle Navizet10Cristina Garcia Iriepa11Dennis R. Salahub12Andreas M. Köster13Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, FranceLaboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, FranceLaboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, FranceLaboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, FranceLaboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, FranceMatériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM) Montpellier CEDEX 5, 34090 Montpellier, FranceLaboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 4, FrancePrograma de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, MexicoDepartamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, MéxicoDepartamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, MéxicoLaboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, FranceLaboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, FranceDepartment of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4, CanadaPrograma de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, MexicodeMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born−Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.https://www.mdpi.com/1420-3049/24/9/1653QM/MM simulationsDFTelectron and nuclear dynamics |
| spellingShingle | Aurélien de la Lande Aurelio Alvarez-Ibarra Karim Hasnaoui Fabien Cailliez Xiaojing Wu Tzonka Mineva Jérôme Cuny Patrizia Calaminici Luis López-Sosa Gerald Geudtner Isabelle Navizet Cristina Garcia Iriepa Dennis R. Salahub Andreas M. Köster Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review Molecules QM/MM simulations DFT electron and nuclear dynamics |
| title | Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review |
| title_full | Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review |
| title_fullStr | Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review |
| title_full_unstemmed | Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review |
| title_short | Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review |
| title_sort | molecular simulations with in demon2k qm mm a tutorial review |
| topic | QM/MM simulations DFT electron and nuclear dynamics |
| url | https://www.mdpi.com/1420-3049/24/9/1653 |
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