Calculations molecular mechanics “strain

The calculations described here have been called strain calculations, molecular mechanics, or force field calculations. We prefer the latter term. For a discussion of historical developments and a literature survey of earlier work, which are not given here, the reader is referred to a number of other reviews (1-3). The present paper deals with the description of force field types, techniques of energy minimisation, and procedures for the determination of force field parameters, and with some applications, preferentially taken from our own field of interest. In accordance with the experiences of the author, the work of Lifson and coworkers is given special attention other authors are nevertheless well represented in the context of critical comparisons. We hope that this selection, although inevitably biased, will help to improve the consistency of the presentation of the subject. 

The molecular mechanics technique has been called by many different names, including Westheimer method, strain-energy method, conformational energy calculations, empirical potential energy calculations, atom-atom pair potential method, and force field calculations. Empirical force field is widely used, but somewhat long, and many authors omit empirical, leading to confusion with spectroscopic force field calculations. Molecular mechanics (11) now appears to be favored (10a) and is used (abbreviated as MM) throu out this chapter. 

Since molecular mechanics "strain energy" calculations (43, 44) have become a valuable tool in interpretation of molecular structure results from crystallographic studies, certain computing techniques used there will be mentioned. The method is simple in principle the strain energy of a particular conformation of a molecule is expressed as the sum of terms of several types, each related to certain structural parameters for example, bond length, non-bonded contacts, torsion angle. 

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

Once requiring minicomputers and worksta tions many molecular mechanics programs are avail able for personal computers The information that strain energy calculations can provide is so helpful... 

Make molecular models of the two chair conformations of cis 1 tert butyl 4 phenyl cyclohexane What is the strain energy calculated for each conformation by molecular mechanics Which has a greater preference for the equatorial onentation phenyl or tert butyD... 

The distorted structure can be replaced by a more reasonable structure using an empir ical molecular mechanics calculation This calculation which is invoked m Spartan Build by clicking on Minimize, automatically finds the structure with the smallest strain energy (m this case a structure with realistic bond distances and a boat conformation for the SIX membered ring)... 

An example of the application of molecular mechanics in the investigation of chemical reactions is a study of the correlation between steric strain in a molecule and the ease of rupture of carbon-carbon bonds. For a series of hexasubstituted ethanes, it was found that there is a good correlation between the strain calculated by the molecular mechanics method and the rate of thermolysis. Some of the data are shown in Table 3.3. 

Table 3.3. Correlation between Intramolecular Strain from Molecular Mechanics (MM) Calculations and Activation Energies for Dissociation of C—C Bonds in Substituted Ethanes"...

MicroEnv is calculated using standard approximations used in classical molecular mechanics (i.e., pair potentials and analytical expressions for strain energy190) ... 

Estimates of the ultimate shear strength r0 can be obtained from molecular mechanics calculations that are applied to perfect polymer crystals, employing accurate force fields for the secondary bonds between the chains. When the crystal structure of the polymer is known, the increase in the energy can be calculated as a function of the shear displacement of a chain. The derivative of this function is the attracting force between the chains. Its maximum value represents the breaking force, and the corresponding displacement allows the calculation of the maximum allowable shear strain. In Sect. 4 we will present a model for the dependence of the strength on time and temperature. In this model a constant shear modulus g is used, thus r0=gyb. 

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