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Open AccessArticle

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

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Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France
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CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, 75005 Paris, France
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Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM) Montpellier CEDEX 5, 34090 Montpellier, France
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Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 4, France
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Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico
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Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
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Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France
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Department 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, Canada
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College of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, China
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Authors to whom correspondence should be addressed.
We dedicate this manuscript to the memory of Annick Goursot who passed away in April 2017. Annick initiated the in-deMon2k QM/MM project on which all the results presented here are built.
Academic Editor: Antonio Monari
Molecules 2019, 24(9), 1653; https://doi.org/10.3390/molecules24091653
Received: 1 March 2019 / Revised: 11 April 2019 / Accepted: 12 April 2019 / Published: 26 April 2019
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. View Full-Text
Keywords: QM/MM simulations; DFT; electron and nuclear dynamics QM/MM simulations; DFT; electron and nuclear dynamics
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de la Lande, A.; Alvarez-Ibarra, A.; Hasnaoui, K.; Cailliez, F.; Wu, X.; Mineva, T.; Cuny, J.; Calaminici, P.; López-Sosa, L.; Geudtner, G.; Navizet, I.; Garcia Iriepa, C.; Salahub, D.R.; Köster, A.M. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review. Molecules 2019, 24, 1653.

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