Molecular mechanics of alkanes

To return to the present case, force fields have been devised that include a charge distribution in alkanes at the atomic level, and other force fields that are based on the assumption that the amount of charge distribution at the atomic level in alkanes is negligible for most purposes, and therefore electrostatics can be neglected in molecular mechanics calculations on alkanes. In our earliest molecular mechanics calculations we concluded that since charges in alkanes were certainly small, we would omit them until there was evidence that they needed to be included. It is true that alkanes do have very small dipole moments, for example, propane (0.083 and isobutane (0.132D). If one wishes to reproduce these in molecular mechanics, then one would have to include electrostatics. But to our knowledge, this is the only improvonent that electrostatics would make in the molecular mechanics of alkanes. The foreseeable improvement would be quite small, so we continue to omit electrostatics for alkanes. 

Wilkes H., Rabus R. Fischer Th., Armstroff A., Behrends A., Pierik A. J., and Widdel F. (2001). The anaerobic degradation of n-alkanes as pure substrates and in crude oil first direct insights into the molecular mechanism of the initial C-H-activation and the subsequent degradation... 

The final step in the molecular-mechanics calculation of molecular conformation involves the minimization of the energy Approximations are involved whose importance is not always clear. Usually, all first derivatives with respect to the various internal coordinates are set equal to zero - although these coordinates are often not independent (see Section 10.6). Furthermore, the final conformation obtained depends on the assumed initial structure. Therefore, (he method must be applied with care and a certain amount of chemical intuition. In spite of these uncertainties the molecular mechanics method has been employed with considerable success, particularly in the conformational analysis of branched alkanes. For molecules containing hetero-atoms, it can be applied, but with somewhat less confidence. 

The theoretician uses these programs to predict structure, either of single molecules or of assemblages of molecules, using X-ray or NMR data, when available, to test his predictions (13-15). It has been known for a long time that even the earlier molecular mechanics programs can predict the structures of certain types of molecules with excellent reliability. For the cyclic alkanes, an accuracy comparable to that of the best X-ray crystal structure analysis can be obtained. In fact, the method is more widely applicable since neither compound nor crystals are necessary (1 . 

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