Topological coordinates for nanotubes Original Research Article

The topological coordinate method is a simple and effective approach for generating good initial coordinates for fullerene and nanotube carbon structures in molecular mechanics calculations. In this method some special eigenfunctions, the bi-lobal eigenfunctions of the Hückel Hamiltonian, or the adjacency matrix are used. It is based on a special connection between the electronic and geometric structure of fullerenes and nanotubes. We have found that the most efficient nanotube initial coordinates can be obtained with the four bi-lobal eigenvector method. The three bi-lobal eigenvector method gave relative good initial coordinates only if the two ends of the tube were closed. In both cases the scaling factors based on the Schrödinger equation of a particle in a rectangular box gave the best result.