Energy minimization, empirical force fields

It is important to realize that for any arrangement of more than two atoms the strain energy minimized structure does not have ideal (zero strain) distances and angles. This is demonstrated in the case of ethane (Fig. 2.2), where, due to the repulsion of the protons, the experimentally determined C-C distance in ethane of 1.532 A, which is well reproduced by empirical force field calculations, is slightly longer than the ideal C-C separation of 1.523 A used in the MM2 force field1. Further examples are presented in Table 2.1. With increasing substitution of the carbon atoms the C-C separation increases up to 1.611 A in tris(t-butyl)methane. 

Molecular modeling applied to polymers is, in principle, an extension of the concepts applied to small molecules. Readers familiar with energy minimization with empirical force fields (MM2, etc.), Monte Carlo, or molecular dynamics techniques for simulations already know a significant part of what is required to model polymer systems. What we present here is a description of the various techniques available for the simulation of polymers. The discussion is mostly limited to homopolymers, although we briefly mention some exciting topics outside this area. 

Another important zeolite-catalyzed chemical reaction is the decomposition of NO. Cu-exchanged zeolites, especially Cu-ZSM-5, have been shown to catalyze the decomposition of NO in the presence of hydrocarbons and excess oxygen. The increasing awareness of the detrimental effects of automobile exhaust has prompted several theoretical studies on the active site and reaction mechanism. ° Cu-ZSM-5 was described using an empirical force field and energy minimization to locate the copper ions in ZSM-5. Isolated copper atoms and copper clusters were found in the micropores, mostly associated with framework aluminium species. A cluster of two copper ions bridged via an OH species not part of the zeolite framework ( extra-framework ) was proposed as the active site. Quantum mechanical cluster calculations were carried out to study the elementary steps in the NO decomposition. A single T-site model was used to represent the zeolite framework. 

There is a tendency to use the term molecular mechanics (MM) as opposite to quantum mechanics, therefore including all classical dynamics methods, such as energy minimization, Monte Carlo, and molecular dynamics. Sometimes it is used to describe only the energy minimization method using empirical force field (potential) or it is even used to refer to the quantum mechanical method specifically, emphasizing its use for molecular motion. Nevertheless, we will focus on the second definition of molecular mechanics (43-45). In this approach, a molecule is viewed as a collection of particles (atoms) held together by simple harmonic or elastic forces. Such forces are defined in terms of potential energy... 

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