Molecular configurations method

Molecules. The electronic configurations of molecules can be built up by direct addition of atomic orbitals (LCAO method) or by considering molecular orbitals which occupy all of the space around the atoms of the molecule (molecular orbital method). 

The molecular orbital approach to chemical bonding rests on the notion that as elec trons m atoms occupy atomic orbitals electrons m molecules occupy molecular orbitals Just as our first task m writing the electron configuration of an atom is to identify the atomic orbitals that are available to it so too must we first describe the orbitals avail able to a molecule In the molecular orbital method this is done by representing molec ular orbitals as combinations of atomic orbitals the linear combination of atomic orbitals molecular orbital (LCAO MO) method... 

An N-atom molecular system may be described by 3N Cartesian coordinates. Six independent coordinates (five for linear molecules, three for a single atom) describe translation and rotation of the system as a whole. The remaining coordinates describe the molecular configuration and the internal structure. Whether you use molecular mechanics, quantum mechanics, or a specific computational method (AMBER, CNDO, etc.), you can ask for the energy of the system at a specified configuration. This is called a single point calculation. 

The van der Waals volume and area are characterizing parameters relating molecular configurations. Bondi describes group contribution methods for their calculatiou. 

Molecular dynamics, in contrast to MC simulations, is a typical model in which hydrodynamic effects are incorporated in the behavior of polymer solutions and may be properly accounted for. In the so-called nonequilibrium molecular dynamics method [54], Newton s equations of a (classical) many-particle problem are iteratively solved whereby quantities of both macroscopic and microscopic interest are expressed in terms of the configurational quantities such as the space coordinates or velocities of all particles. In addition, shear flow may be imposed by the homogeneous shear flow algorithm of Evans [56]. 

The examples cited above are of molecules which are not strictly speaking noorigid, although they have more than one well-defined equilibrium configuration. The 1,2-dichloroetbane molecule discussed above is a classic example. With the aid of computer programs that have been developed to treat this problem, it has become possible to calculate wifi) confidence the equilibrium conformations of such molecules, as well as the energy differences and the tunneling barriers between them. It is appropriate here to summarize briefly the so-called molecular mechanics method that is currently employed to obtain these results. 

Molecular Dynamics Methods. In contrast to the MC method, both kinetic and structural properties of a molecular system can be evaluated from MD studies. These properties are evaluated as averages over configurations generated during time. In microcanonical ensemble studies with the MD method, the properties which are controlled... 

Water Potentials. The ST2 (23), MCY (24), and CF (2J5) potentials are computationally tractable and accurate models for two-body water-water interaction potentials. The ST2, MCY and CF models have five, four, and three interaction sites and have four, three and three charge centers, respectively. Neither the ST2 nor the MCY potentials allow OH or HH distances to vary, whereas bond lengths are flexible with the CF model. While both the ST2 and CF potentials are empirical models, the MCY potential is derived from ab initio configuration interaction molecular orbital methods (24) using many geometrical arrangements of water dimers. The MCY+CC+DC water-water potential (28) is a recent modification of the MCY potential which allows four body interactions to be evaluated. In comparison to the two-body potentials described above, the MCY+CC+DC potential requires a supercomputer or array processor in order to be computationally feasible. Therefore, the ST2, MCY and CF potentials are generally more economical to use than the MCY+CC+DC potential. 

Computational quantum chemistry has emerged in recent years as a viable tool for the elucidation of molecular structure and molecular properties, especially for the prediction of geometrical parameters, kinetics and thermodynamics of highly labile compounds such as nitrosomethanides. However, they are difficult objects for both experimental (high toxicity, redox lability, high reactivity, explosive character etc.) and computational studies, even with today s sophisticated techniques (e.g. NO compounds are often species with open-shell biradical character which requires the application of multi-configuration methods). 

In the cluster analysis, local molecular configurations of low energy in the equilibrium are presumed to be clusters. The cluster distribution is obtained using the equilibrium snapshots, when the following function F( n, ) is a minimum. We calculated F( n, ) and determined the cluster distribution using the Metropolis method. 

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