Molecular mechanics force field correlated methods

Cartesian coordinates system for locating points in space based on three coordinates, which are usually given the symbols x, y, z or i, j, k CBS (complete basis set) an ah initio method CC (coupled cluster) a correlated ah initio method CFF (consistent force field) a class of molecular mechanics force fields CFMM (continuous fast multipole method) a method for fast DFT calculations on large molecules... 

Besides the classical techniques for structural determination of proteins, namely X-ray diffraction or nuclear magnetic resonance, molecular modelling has become a complementary approach, providing refined structural details [4—7]. This view on the atomic scale paves the way to a comprehensive smdy of the correlations between protein structure and function, but a realistic description relies strongly on the performance of the theoretical tools. Nowadays, a full size protein is treated by force fields models [7-10], and smaller motifs, such as an active site of an enzyme, by multiscale approaches involving both quantum chemistry methods for local description, and molecular mechanics for its environment [11]. However, none of these methods are ab initio force fields require a parameterisation based on experimental data of model systems DPT quantum methods need to be assessed by comparison against high level ab initio calculations on small systems. 

The possibility of consideration of atoms as elementary subunits of the molecular systems is a consequence of Born-Oppenheimer or adiabatic approximation ( separation of electron and nuclear movements) aU quantum chemistry approaches start from this assumption. Additivity (or linear combination) is a common approach to construction of complex functions for physical description of the systems of various levels of complexity (cf orbital approximation, MO LCAO approximation, basis sets of wave functions, and some other approximations in quantum mechanics). The final justification of the method is good correlation of the results of its applications with the available experimental data and the potential to predict the characteristics of molecular systems before experimental data become available. It can be achieved after careful parameter adjustment and proper use of the force field in the area of its validity. The contributions not considered explicitly in the force field formulae are included implicitly into parameter values of the energy terms considered. 

The philosophical transition from the atomic prejudice to a view of intermolecular interaction in terms of diffuse electron density has its proper computational counterpart in full quantum mechanical calculations, which, however, cannot at present provide complete intermolecular energies because of limitations in the treatment of electron correlation, a major ingredient of the intermolecular interaction recipe. In a different perspective, the classical atom-atom force-field approach is widely applicable but entirely parametric and of scarce adherence to physical principles. The need is felt for an extension to represent in a more realistic manner the effects of diffuse electron clouds. This is done in the so-called semi-classical density sums (SCDS) or briefly. Pixel approach [9], which will now be described. The Pixel method is based on numerical integrations over molecular electron densities, and allows a separation of the total intermolecular cohesion energy into coulombic, polarization, dispersion, and repulsion contributions. 

ACES II Anharmonic Molecular Force Fields Bench-mark Studies on Small Molecules Complete Active Space Self-consistent Field (CASSCF) Second-order Perturbation Theory (CASPT2) Configuration Interaction Core-Valence Correlation Effects Coupled-cluster Theory Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field G2 Theory Heats of Formation Hybrid Methods Hydrogen Bonding 1 M0ller-Plesset Perturbation Theory NMR Data Correlation with Chemical Structure Photochemistry Proton Affinities r 2 Dependent Wave-functions Rates of Chemical Reactions Reaction Path Following Reaction Path Hamiltonian and its Use for Investigating Reaction Mechanisms Spectroscopy Computational... 

---