Molecular mechanics methodology

The relative importance of these components is seen in Table 20, which contains a sampling of the calculated and observed data for 1,2-dichloroethane142. Many additional examples for this and other dihalides, as well as for haloketones and haloethers are available142,149. It is seen that benzene and xylene behave as solvents more polar than their dielectric constants would indicate this is observed in other cases, too. The quadrupole effect is clearly important and partly counteracts the dipole effect, while the polar effect is almost negligible. These principles have been incorporated into the molecular mechanics methodology, apparently with promising results150,151. 

Monard, G. and Merz, K.M. (1999). Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc. Chem. Res. 32, 904-911... 

Monard, G., Merz, K. M., Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems, Aec. Chem. Res. 1999, 32, 904-911. 

Representation of effects operating in molecular mechanics (left). An example of binding of a copper complex to a phosphate group on the backbone of a DNA strand optimised using molecular mechanics methodology appears at right. 

The most extensive use of multibody potentials for the simulation of materials by means of ionic pair potentials has been the addition of bond angle bending terms to two-body potentials used to describe silicate and framework structured materials. - s jn addition, harmonic planarity restraining terms have been employed in the simulation of polyatomic anions (in, e.g., inorganic carbonates). Here, as in the organic molecular mechanics methodology described latei structural distortions about an expected geometry are realized at an enei etic cost. 

Zhang X, Lu G. Quantum mechanics/molecular mechanics methodology for metals based on oibital- ee density fimctional theory. Phys. Rev. B 2007 76 245111. 

Within the molecular mechanics methodology a molecule is considered as a collection of atoms joined together as springs which are atterr5)ting to restore the natural or ideal geometric features within the molecule. The stretching of a bond, for example, is often described by a harmonic potential as shown in Equation 5.6. 

Sauers, R. R., Scimone, A., and Shams, H., Synthesis and photochemistry of some new pentacy-cloundecan-8-ones probes for hydrogen abstraction in the Jt-plane, /. Org. Chem., 53,6084, 1988. Sauers, R. R. and Krogh-Jesperson, K., Anal) is of Norrish type 11 reactions by molecular mechanics methodology. Tetrahedron Lett., 30, 527,1989. 

Sauers, R. R. and Huang, S.-Y, Analysis of Norrish type II reactions by molecular mechanics methodology cyclodecanone. Tetrahedron Lett., 31, 5709,1990. 

---