Molecular mechanics strain energy

Molecular mechanics strain energies have another use They can also be used to com pare the energies of models that share the same molecular formula that is models that are either stereoisomers or different conformations of a single molecule (allowed com parisons are shown here)... 

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. 

The first four terms of the function are commonly found in molecular mechanics strain energy functions, and they are modified Hooke s law functions. The last term has been added to insure the proper stereochemistry about asymmetric atoms. A model is refined by minimizing the highly nonlinear strain energy function with respect to the atomic coordinates. An adaptive pattern search routine is used for the strain energy minimization because it does not require analytical derivatives. The time necessary to obtain good molecular models depends on the number of atoms in the molecule, the flexibility of the structure, and the quality of the starting model. 

Chang et al. [29] 2005 Analytical molecular mechanics, potential energy — — 1-5 Critical buckling strain under axial compression... 

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)... 

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

---