Abstract
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.
Highlights
The hybrid quantum mechanical/molecular mechanical (QM/MM) scheme is a computationally efficient approach to simulate physicochemical phenomena with adaptive levels of accuracy [1,2,3].As pointed out by Warshel, Karplus and Levitt in the 1970s [1,2,3], processes involving key modifications of electronic structures must be modeled by quantum mechanical approaches while the environment can be well approximated by classical molecular mechanical approaches
In this article we focus on the internal QM/MM module that does not involve an interface with an external MM package but evaluates all energy terms internally
During MetaD simulations, Born–Oppenheimer Molecular Dynamics (BOMD) trajectories are biased by introducing a time-dependent external potential V (X, t) where R represents the atomic coordinates of the system
Summary
The hybrid quantum mechanical/molecular mechanical (QM/MM) scheme is a computationally efficient approach to simulate physicochemical phenomena with adaptive levels of accuracy [1,2,3]. DeMon2k is a program specialized in Kohn–Sham [16] density functional theory (DFT) within the Auxiliary DFT framework [17] The latter permits remarkably fast evaluation of energies, potentials and properties. Link atoms [20] and capping potentials have been incorporated to deal with QM/MM frontiers that cut covalent bonds Both Born–Oppenheimer molecular dynamics (MD) simulations [21,22,23] and Ehrenfest non-adiabatic MD simulations are available. A first aim of this article is to provide users with a consistent description of the QM/MM methodology implemented in deMon2k at the dawn of 2019 This is the object of Part I. simulations with respect to 2015 review paper [19]
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