Spacing of molecules

The Monte Carlo and molecular dynamics simulation methods can be used to explor the conformational space of molecules. During such a simulation the system is able t... 

Leach, A. Methods for searching the conformational space of molecules. In Reviews in Computational Chemistry, lipkowitz, K. B., Boyd, D. B. (eds.),... 

Siegbahn has also argued that in some cases C35, Cjp, and Cla type orbitals should be included in the active space of molecules containing these atoms. This is also supported by the ethylene calculations of Sunil et which demonstrate that additional n and n orbitals must be included in the active space for an adequate description of the low-lying excited states. 

The dynamic method for selection of active conformers appears to be useful in this venture. Its first step is a procedure for generation of 3D isomers, representing the conformational space of molecules. Although the 3DGEN algorithm is used in the OASIS system, most of the other algorithms for conformational space search (after minor modifications) could be used for that purpose. Next, a method for conformer screening is nsed, based on a hierarchical set ofmles, in an attempt to find the active conformers. 

A very important source of error is the basis set superposition error if the basis used for molecule A is inadequate, the virtual orbitals of molecule B may be able to improve the description of A in a way which has nothing to do with the interaction, and this leads to a spurious stabilization. It is conventional to correct for it by means of the functional counterpoise method [22] in which reference calculations are performed for each molecule in the presence of the basis functions, but not the electrons or nuclei, of the other. This procedure overcorrects for the effect, since it makes available to molecule A the occupied space of molecule B as well as the virtual space. It is possible to carry out a reference calculation for A in which the occupied orbitals of B are projected out of the basis[23], but although this gives better results than the normal procedure it is probably too cumbersome for routine use. Note that the function counterpoise method demands a separate reference calculation for each of the interacting molecules at every relative position, since the basis extension error varies with the position of the orbitals of the other molecule, and the procedure is therefore very time-consuming. 

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