Molecular mechanics valence bond systems

For this reason, there has been much work on empirical potentials suitable for use on a wide range of systems. These take a sensible functional form with parameters fitted to reproduce available data. Many different potentials, known as molecular mechanics (MM) potentials, have been developed for ground-state organic and biochemical systems [58-60], They have the advantages of simplicity, and are transferable between systems, but do suffer firom inaccuracies and rigidity—no reactions are possible. Schemes have been developed to correct for these deficiencies. The empirical valence bond (EVB) method of Warshel [61,62], and the molecular mechanics-valence bond (MMVB) of Bemardi et al. [63,64] try to extend MM to include excited-state effects and reactions. The MMVB Hamiltonian is parameterized against CASSCF calculations, and is thus particularly suited to photochemistry. 

Quantum mechanics provide many approaches to the description of molecular structure, namely valence bond (VB) theory (8-10), molecular orbital (MO) theory (11,12), and density functional theory (DFT) (13). The former two theories were developed at about the same time, but diverged as competing methods for describing the electronic structure of chemical systems (14). The MO-based methods of calculation have enjoyed great popularity, mainly due to the availability of efficient computer codes. Together with geometry optimization routines for minima and transition states, the MO methods (DFT included) have become prevalent in applications to molecular structure and reactivity. 

Internal coordinate systems include normal coordinates which are symmetry adapted and used in spectroscopy, and coordinate systems based on interatomic distances ( bond lengths ), three-center angles ( valence angles ) and four-center angles ( torsion angles ). In the latter case a Z-matrix of the form shown in Table 3.1 defines the structure of a molecule. The input and output files of nearly all molecular mechanics programs are in cartesian coordinates. 

Polymers differ from other substances by the size of their molecules which, appropriately enough, are referred to as macromolecules, since they consist of thousands or tens of thousands of atoms (molecular weight up to 106 or more) and have a macroscopic rectilinear length (up to 10 4 cm). The atoms of a macromolecule are firmly held together by valence bonds, forming a single entity. In polymeric substances, the weaker van der Waals forces have an effect on the components of the macromolecules which form the system. The structure of polymeric systems is more complicated than that of low-molecular solids or liquids, but there are some common features the atoms within a given macromolecule are ordered, but the centres of mass of the individual macromolecules and parts of them are distributed randomly. Remarkably, the mechanical response of polymeric systems combines the elasticity of a solid with the fluidity of a liquid. Indeed, their behaviour is described as viscoelastic, which is closely connected with slow (relaxation time to 1 sec or more) relaxation processes in systems. 

Qualitative valence-bond (VB) descriptions of the electronic structures of molecules are often able to provide "primitive patterns of understanding" [1] of the origin of various molecular properties. In this chapter, we shall give consideration to VB structures for some molecular systems that involve four active-space orbitals. The discussion will include VB formulations of the electronic structures of isolated molecules, reaction mechanisms, and types of "metallic orbitals" that can be used in VB representations for electron conduction in metallic lithium. For the latter topic, the results of STO-6G VB calculations are reported in order to make a provisional comparison of two conduction mechanisms. 

Solvent effects can significantly influence the function and reactivity of organic molecules.1 Because of the complexity and size of the molecular system, it presents a great challenge in theoretical chemistry to accurately calculate the rates for complex reactions in solution. Although continuum solvation models that treat the solvent as a structureless medium with a characteristic dielectric constant have been successfully used for studying solvent effects,2,3 these methods do not provide detailed information on specific intermolecular interactions. An alternative approach is to use statistical mechanical Monte Carlo and molecular dynamics simulation to model solute-solvent interactions explicitly.4 8 In this article, we review a combined quantum mechanical and molecular mechanical (QM/MM) method that couples molecular orbital and valence bond theories, called the MOVB method, to determine the free energy reaction profiles, or potentials of mean force (PMF), for chemical reactions in solution. We apply the combined QM-MOVB/MM method to... 

---