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 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.

Evolution of the Spin Magnetic Moments and Atomic Valence of Vanadium in VCux+, VAgx+, and VAux+ Clusters (x = 3-14).

The atomic structures, bonding characteristics, spin magnetic moments, and stability of VCux+, VAgx+, and VAux+ (x = 3-14) clusters were examined using density functional theory. Our studies indicate that the effective valence of vanadium is size-dependent and that at small sizes some of the valence electrons of vanadium are localized on vanadium, while at larger sizes the 3d orbitals of the vanadium participate in metallic bonding eventually quenching the spin magnetic moment. The electronic stability of the clusters may be understood through a split-shell model that partitions the valence electrons in either a delocalized shell or localized on the vanadium atom. A molecular orbital analysis reveals that in planar clusters the delocalization of the 3d orbital of vanadium is enhanced when surrounded by gold due to enhanced 6s-5d hybridization. Once the clusters become three-dimensional, this hybridization is reduced, and copper most readily delocalizes the vanadium's valence electrons. By understanding these unique features, greater insight is offered into the role of a host material's electronic structure in determining the bonding characteristics and stability of localized spin magnetic moments in quantum confined systems.