Abstract: MATH/CHEM/COMP 2002, Dubrovnik, June 24-29, 2002

 

 

OVERLAPPING SPHERE (OS) METHOD AS A TOOL FOR THE SEARCH OF THE LOW-ENERGY CONFORMATIONS

 

Nenad Raos

 

Institute for Medical Research and Occupational Health, P. O. B. 291, HR-1001 Zagreb, Croatia

 

 

Overlapping sphere (OS)1 method introduces a new concept of conformational energy. The conformational energy is not related to the contributions due to bonding, non-bonding, etc. interactions, as in the molecular-mechanics approach, but to the potential due to penetration of the van der Waals spheres of atoms into the central sphere. The sphere has radius, Rv, usually in the range of 0.3 to 0.6 nm, and is centered at the geometrical center of molecule or molecular fragment, or at another characteristic point (e. g. apical position for planar coordination compounds).

The first application of OS method was aimed to estimate the gain in conformational energy due to interactions of chalate rings in molecules of copper(II) complexes with N-alkylated amino acids, and accordingly to estimate the conformational energy of bis-complexes from the energy of the parent mono-complexes.2 The next application was generation of low-energy conformations (of alkanes, cycloalkanes, and copper(II) mono-, and bis-chelates3). The generation was performed by steepest-descent minimization of the common overlap volume of central sphere and neighbouring atoms, followed by standard molecular-mechanics procedure of geometrical optimization. The center of central sphere was situated either at the geometrical center of the molecule,4 or its fragment.5 Also, the moving sphere approach, where central sphere is moving during the minimization step from the geometrical center of the molecule to the sterically most crowded atom, was also checked on alkanes. It was shown to be more efficient than the method of molecular fragmentation.

The efficiency of OS method depends mostly on molecular constitution. Symmetric, less branched, as well as molecules with long alyphatic chains are very suitable for application of OS method; other factors like size of the molecule and its cyclization seems not to play a dominant role.

 

1 N. Raos, Kem. Ind. 48 (1999) 385-390.

2 N. Raos, Croat. Chem. Acta 70 (1997) 913-924.

3 N. Raos, L. Zuza, Croat. Chem. Acta (submitted).

4 N. Raos, Croat. Chem. Acta 72 (1999) 727-736.

5 N. Raos, J. Comput. Chem. 21 (2000) 1353-1360.