First presented at:
Chemistry Webmasters 3
Unbranched alkanes (CnH2n+2) are well described by molecular mechanics force fields. Even within the limits of the molecular mechanics models, some of their properties are still mysterious. In particular, there is no general answer to the question:
If N is small, then the answer is that the extended conformation corresponds to the global minimum. If N is greater than about eighteen, folded conformations are lower in energy than the extended conformation, because of favourable van der Waals interactions between adjacent methylene units. Can you find the global minima?
The conformational properties of peptides, nucleotides, polyhydroxybutyrates and other bio-polymers are of great importance, and many new analogs are being developed (see, for example, Chemical and Engineering News June 16th, 1997, page 32). Force fields are necessary to calculate the conformational properties of such large systems, but force field parameters are not 100 % accurate. Any calculation of the properties of such systems will face two difficulties: (i) The parameters are not completely reliable (ii) The conformation space is very large. The parameters are probably most precise for alkanes, and so investigation of the conformation space of alkane polymers and oligomers will minimise the effect of the first problem, so that the second may be thoroughly investigated. Such studies may, therefore, play an important role in the development of procedures for studying biopolymers with more immediate applications. Comparison of the lowest energy structures that are known for C10H22, C18H22, C39H22, and C200H22 suggests that alkanes can develop secondary and tertiary structures in a manner analogous to that of proteins.