| pubmed-article:1474397 | pubmed:abstractText | A novel, CPU-time inexpensive two-bond drive technique, called 'ValleyScan' [1], is described. It makes it possible to omit the chemically nonrelevant points of high energy, which are normally part of a two-dimensional (2D) grid calculation. The new procedure works well for the calculation of the ring inversion of cyclic molecules, but should also be useful for other 'two-bond' problems e.g. side-chain movements in larger molecules (e.g. proteins). The algorithm is based upon pseudocode description and can easily be included in any molecular modelling software with an open user interface. Starting from an energy minimum, the calculation scans the potential surface in all directions up to a user-defined energy limit. With this strategy, attention is paid only to the area close to the stationary points - energetically higher structures do not have to be calculated. We applied the procedure to the test molecules 1,3-cyclohexadiene (4), 2H-pyran (5) and 6H-dibenzo[b,d]pyran (6). The extension of this method to the variation of more than two dihedral angles for more complex problems, e.g. sterically more hindered rotation, is in progress. | lld:pubmed |
