Original scientific paper

Application of Cluster Analysis in Search of Low-energy Conformations by the Overlapping Spheres Method

Nenad Raos ; Institute for Medical Research and Occupational Health, Ksaverska c. 2, P.O.B. 291, 10001 Zagreb, Croatia
Lora Žuža-Mak ; Institute for Medical Research and Occupational Health, Ksaverska c. 2, P.O.B. 291, 10001 Zagreb, Croatia

Abstract

In order to achieve a general procedure for molecular fragmentation in the overlapping spheres (OS) method, aimed to search for low-energy conformations, cluster analysis (Ward’s method) was applied. The center of the central sphere was situated at the geometrical center of the larger of two clusters, i.e., molecular fragments. The new procedure was tested on three aliphatic hydrocarbon molecules with various degrees of branching, and on three diastereomers of copper(II) bis-chelates with 1-[N-(tert-butoxycarbonyl)amino]-2-hydroxymethylcyclopropane-1-carboxylic acid. The newly proposed procedure is more efficient than the old one (based on topological fragmentation) and is suitable for automation. However, Ward’s method offers little or no advantage for molecules possessing some kind of symmetry, yielding virtually identical fragments.

Keywords

cluster analysis; Ward’s method; conformational analysis; global optimization; amino acids; copper(II) complexes

Hrčak ID:

102645

URI

https://hrcak.srce.hr/102645

Publication date:

31.5.2004.

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