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Simplified representation of crystal structures : cholic acid host frameworks as a case study

Organization of molecules in crystals is governed by a myriad of different types of interactions which are responsible for intermolecular contacts. The networks of these interactions in the crystal are quite often very complicated. In trying to rationalize the topology and connectivity of these networks it is necessary to somehow reduce their complexity. This is also important in comparing networks from different molecules or polymorphs of the same molecule. For this purpose there are already many different simplification schemes that have more or less mathematical and graph theory background.1 It is very often the case that the organization of intermolecular bonds in the crystal is obscured by molecules themselves. Therefore, for the simplified description of the networks, it is necessary to discard all the unimportant parts and concentrate on the interactions that are responsible for the network connectivity. This means that the number of atoms in the molecule has to be reduced in some way paying special attention to the “ contact” atoms. Cholic acid (CA) molecules, due to their unique amphiphilic form, are suitable for forming host frameworks that can include various guest molecules.2 These host frameworks fall into several categories depending on the orientation and connectivity of oxygen atoms. To make automatic classification and to visualize these frameworks a set of scripts was written in python programming language making use a Computational crystallography toolbox (cctbx) for general crystallographic calculations and PyMol visualization package for the presentation.

cholic acid; host-guest chemistry; python programming

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