(p-95)PRINCIPLE OF DIHEDRAL ANGLE CALCULATION FOR STEREOCHEMISTRY

Tadashi Nemoto¹, Ken-ichi Fujita², Yasuko Ishizuka¹ and Hiroshi Nakanishi¹

¹National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, MITI, Tsukuba, Ibaraki 305-8566, Japan.
²Electron Optic Instruments Engineering Department, JEOL Datum Ltd. Akishima, Tokyo 196-0022, Japan.

Dihedral angle calculation is remarkably fast comparing to other methods. Proteins and peptides are good targets to elucidate their 3-D structures. On the other, 3-D structures of other biomolecules including sugar and terpenoids are still not fully elucidated. General protocol for chirality analysis by dihedral angle calculation is as follows:
1. Measure nuclear magnetic resonance spectrum with appropriate pulse programs and all protons should be assigned.
2.Prepare library. Two dimensional structure will be drawn. Run MM2 calculation to build 3-d structure. Define rotational bonds. Make library file (.lib). Make sequence file (.seq). Make molecular file (.mol).
3.Generate stereoisomers from molecular file.
4.Extract constraints from NMR spectrum.
5.Run dihedral angle calculation.
6.Analyze log file, molecular view, distances and angles.
7.Refinement (loop to 4). For example, calculation time for acoradiene including 19 nOe based constraints required less than 1s on SGI Indigo XZ4000 graphic workstation. Fundamental information about dihedral angle calculation on semiochemicals will be presented.