Alkane Conformation Hunt

Jonathan M Goodman
Department of Chemistry, Lensfield Road, Cambridge

First presented at:
Chemistry Webmasters 3

Unbranched alkanes (C_nH_2n+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:

What is the global minimum conformation of an unbranched alkane, length N ?

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?

Can humans beat computers?

The low energy structures listed here were designed by hand, before the energies were calculated using MacroModel. Many computational procedures are available for the generation of low energy structures, including Monte Carlo, Molecular Dynamics and Genetic Algorithms. These three methods have been applied to this problem, but they have not generated lower energy structures than those designed without such computational methods. For longer alkanes, they have done significantly worse. It would appear that human brains can beat computers at this puzzle, at least for the moment! The internet provides a mechanism for many people to work in parallel to find solutions to the puzzle.

Are these calculations useful?

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.