Cyclooctane.world File Reference

A cycloalkane with a 8 carbon loop. More...

Detailed Description

Introduction

Cyclooctane is a cyclic alkane used as an intermediate in production of plastics, fibers, adhesives, and coatings. It is also known as octomethylene.
The goal here is to compute an exhaustive map of all conformations that are compatible with the rigid-geometry hypothesis (fixed bond lengths and angles, variable torsion angles). To the best of our knowledge, a complete map of such conformations was not known so far. Other previous work on this molecule could only obtain low-energy conformers via sampling and/or local search techniques [Kolossvary and Guida 1993, Manocha and Zhu 1994, Rocha et al. 1998]. The map we provide is exhaustive (it contains all points of the conformational space) and may thus be used to determine its topology, or derive the whole (guaranteed) network of minimum-energy conformers and saddle point transitions between them.

The formulation provided here is not based on distances (as we did in Porta et al. 2007 but on rotation matrices and vectors (as in Porta et al. 2008). While with the former formulation we needed the help of the Marenostrum to get a fine discretization (one with 275000 boxes) of the configuration space, with the latter you can get a resonable approximation of the conformational space in few hours with a normal desktop computer (an approximation with 93000 boxes is obtained in about one hour in a Pentium 4 Core II Duo at 2.4 Ghz).

Note that the result is a two-dimensional manifold and therefore it is not worth to use tools such as cuiksort or cuikanimate on the solution file (these tools are basically aimed for zero or one-dimensional solution sest). Instead, you can obtain 3d projections of the conformational space using cuikplot3d.

References

I. Kolossvary and W. Guida, "Comprehensive conformational analysis of the four- to twelve-membered ring cycloalkanes: Identification of the complete set of interconversion pathways on the MM2 potential energy hypersurface," Journal of the American Chemical Society, vol. 115, pp. 2107-2119, 1993.
D. Manocha, Y. Zhu, "Kinematic Manipulation of Molecular Chains Subject to Rigid Constraints", Proc. 2nd Symposium on Molecular Biology , pp. 285-294, 1994.
J. M. Porta, L. Ros, F. Thomas, F. Corcho, J. Cantó,J. Pérez, "Complete Maps of Molecular Loop Conformational Spaces", Journal of Computation Chemistry, Vol. 28, pp. 2170-2189, 2007.
J. M. Porta, L. Ros, and F. Thomas, "A Linear Relaxation Technique for the Position Analysis of Multi-loop Linkages", IEEE Transactions on Robotics, accepted for publication, 2008.
W. R. Rocha, J. R. Pliego, S. M. Resende, H. F. Dos Santos, M. A. De Oliveira, and W. B. De Almeida, "Ab initio conformational analysis of cyclooctane molecule," Journal of Computational Chemistry, vol. 19, no. 5, pp. 524-534, 1998.

Definition in file Cyclooctane.world.