Local Molecular Mechanics MM

The elementary empirical tool for the molecular modelling of polyatomic systems is the method of molecular mechanics (MM) [2,3]. It explicitly employs intuitively transparent features of molecular electronic structure like localization of chemical bonds and groups. The basic assumption of the MM is the possibility to directly parameterize molecular PES in the form of a sum of contributions (force fields) relevant to bonds, their interactions, and to interactions of non-bonded atoms ... 

Molecular mechanics (MM) and dynamics (MD) are useful tools to investigate the conformational properties of organic molecules. (75) In particular, the combined use of MM and MD can be very effective in sampling the potential energy hypersurface (PES) when structurally constrained molecules are considered. In the present work, the PES has been described using the MM+ forcefield (16) and MM optimizations were followed by short MD runs (10 ps) carried out at different temperature (from 300 to 700 K) in order to sample the PES efficiently. Usually, due to the steric properties of the molecules investigated, no more than 10 MM/MD cycles were necessary to localize all the relevant energy minimum structures. 

There are many processes in large systems where the electronically active part is quite localized, for example chemical reactions in a well-defined active site or electronic excitations in a chromophore. In such cases, hybrid methods may be appropriate where the electronically active region is described by quantum mechanics (QM) and the environment by molecular mechanics (MM). These QM/MM methods offer a versatile approach that can be tailored to the specific systems studied, by a suitable choice of the QM/MM partitioning and of the QM and MM methods employed. 

The vibrations are generally treated at the classical level, in terms of local deformation coordinates. The local deformation functions are of the same type of those used in molecular mechanics (MM) methods. Nowadays, MM treats geometry changes for molecules of any dimension and chemical composition. 

Hartree-Fock, DFT or CCSD levels. Because they can reproduce such quantities, APMM procedures should account for an accurate description of the interactions including polarization cooperative effects and charge transfer. They should also enable the reproduction of local electrostatic properties such as dipole moments an also facilitate hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) embeddings. 

The coupled DFT/MM formalism can be regarded as an intermediate approximation between ab initio molecular dynamics, and classical molecular mechanics. Being so, the range of its applicability extends to problems not treatable by molecular mechanics, chemical reactions for instance. The possibility of restricting quantum-mehcanical treatment to well-localized regions also makes it computationally advantageous over supermolecule ab initio simulations. It is important to note that this formalism does not differ whether applied to study biochemical reactions or to study reactions taking place in an other microscopic environment. This makes it possible to test any implementation on problems for which there... 

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