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