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

Aurélien de la Lande (1) , Aurelio Alvarez-Ibarra (1) , Karim Hasnaoui (1) , Fabien Cailliez (1) , Xiaojing Wu (2, 3, 1) , Tzonka Mineva (4) , Jérôme Cuny (5) , Patrizia Calaminici (6, 7) , Luis López-Sosa (7) , Gerald Geudtner (7) , Isabelle Navizet (8) , Cristina Garcia-Iriepa (8) , Dennis R. Salahub (9, 10) , Andreas M Köster (6, 7)

1 LCPO - Laboratoire de Chimie Physique D'Orsay
2 IBPC (FR_550) - Institut de biologie physico-chimique
3 LBT (UPR_9080) - Laboratoire de biochimie théorique [Paris]
4 ICGM - Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier
5 MAD - Modélisation, Agrégats, Dynamique (LCPQ)
6 CINVESTAV - Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional
7 Departamento de Quimica - Cinvestav
8 MSME - Laboratoire de Modélisation et Simulation Multi Echelle
9 Department of Chemistry, Centre for Molecular Simulation
10 Henan University of Science and Technology

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.

Mots clés: QM/MM simulations; DFT; electron and nuclear dynamics

Domaines: Chimie théorique et/ou physique

Aurélien de la Lande, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, et al.. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review. Molecules, 2019, 24 (9), pp.1653. ⟨10.3390/molecules24091653⟩. ⟨hal-02129887⟩