Strain energy calculations molecular mechanics

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. 

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... 

Molecular Mechanics Models. Methods for structure, conformation and strain energy calculation based on bond stretching, angle bending and torsional distortions, together with Non-Bonded Interactions, and parameterized to fit experimental data. 

Some examples from our recent study of opiate analgesic structures (8,24) serve to illustrate further the types of information which a combined approach can provide. The approach used in this study was 1) accumulate accurate crystal structure results on representative compounds by literature search and performing crystal structure determinations, then 2) develop and verify molecular mechanics potential parameters for use with analgesics, and 3) perform strain energy calculations to find active conformations by comparing different chemical structural types which act at a common receptor. The object of the study was to 1) better define the three-dimensional requirements of opiate analgesics, and 2) better understand the opiate receptor itself by indirectly investigating it. 

Molecular mechanics (MM2(85)) calculations were carried out to assess the strain energy and ring-opening equilibria of a number of cyclic disulfides, including 1,2-dithiocane (9), 3,4,7,8-tetra-hydro-l,2-dithiocin (10), and l,2,5,6-tetrahydro-3,4-benzodithiocin (11) <90JA6296>. In response to... 

For molecules with many bonds about which rotation can occur and many conformations that might be populated at room temperature, the POP and TOR corrections can be significant. For relatively rigid molecules, however, these terms are less important, and the strain energies calculated from molecular mechanics can more closely approximate those that would be determined with consideration of POP and TOR. For example, consider the results of a molecular mechanics calculation for puckered cyclobutane, the final portion of which is reproduced here. 

The molecular mechanics approach to conformational analysis has the virtue of describing molecular properties in terms that are physically easily understood. Moreover, the use of carefully chosen potential functions can give highly precise information as to the relative energies of various molecular arrangements. Certainly the quality of the strain-energy calculations performed on hydrocarbons testifies to the capabilities of classical mechanics in simple systems. Concurrent with the improvement in the methodology of molecular mechanical calculations has been the development of approaches to conformational analysis based on molecular orbital... 

In this section, we will show that although molecular mechanics does not calculate the precise thermodynamic energies for the conformations of butane, it will give strain energies that predict the order of stability correctly. We will also investigate the difference between a local minimum and a global minimum. 

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. 

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)... 

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

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