Modeling of CyDs and Their Complexes

Molecular modeling is trendy and in a large number of studies of isolated molecules of small or medium size it can provide usefiil information using well-tested methods and established parameter sets. Calculations on large flexible molecules and supramolecular systems, in particular those involving CyDs, are much more problematic [1]. The situation is influenced by at least five factors. 

Cyclodextrins and Their Complexes. Edited by Helena Dodziuk Copyright 2006 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim ISBN 3-527-31280-3 

Another example showing the misinterpretation of experimental data is provided by the modeling of chiral recognition of ds-decalin invertomers by j8-CyD presented briefly below. In this case, the calculations [7] did not yield any reliable information and the authors misinterpreted our experimental results [8] to justify them. However, these calculations were dted [3] as one of numerous examples of the successful application of modeling in CyD studies. 

Before we discuss the calculations, it is appropriate to list the acronyms denoting methods used in this field. 

AMBER - molecular mechanics program and force field developed by Kollman s group [10] 

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Computational models. Easy access to computers and user-friendly program packages as well as the beauty of molecular models have resulted in a plethora of theoretical papers aiming at a rationalization of chiral recognition by CyDs. Computational studies of CyDs and their complexes, and in particular those referring to chiral recognition, are described in Chapter 11 in some detail. Here it should suffice to say that such calculations are mostly treated as operations on a... 

In the author s opinion the most useful application of molecular modeling and molecular mechanics calculations to enantioselective analyte-CyD interactions would be a computation of individual intermolecular forces based on the structure, dynamics, and population of the complexes determined by instrumental techniques. Researchers working on molecular modeling of enantioselective CyD-chiral analyte interactions may use CE as a very powerful experimental technique for evaluating the reliability of their calculations. This may significantly contribute to further refinement of calculation techniques. 

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