A density functional theory (DFT) calculation of the geometry and vibrational spectrum of natural product, ginkgolide B

A quantum chemistry calculation at DFT-B3LYP/6-31G* level on the geometry and IR spectrum of ginkgolide B was performed. The fully optimised geometry of ginkgolide B was found to be consistent with X-ray crystal structure. In addition, some important thermodynamic parameters were provided. The predicted vibrational bands of ginkgolide B scaled by a scaling factor of 0.945 were perfectly aligned to the experimental IR spectrum. Normal mode analysis on all 156 predicted bands showed that the stretching of O-H bonds of alcohol hydroxyl groups correspond to modes 156, 155 and 154 (from 3501 to 3443 cm(-1)). The stretching of C=O bonds of carbonyl groups result in modes 132, 131 and 130 (from 1788 to 1764 cm(-1)). These assigned results were in accordance with what had been assigned in experiment based on IR spectroscopy. However, our normal mode analyses on the bands below 1192 cm(-1) (mode 97) showed that none of these bands could be simply assigned to the stretching of a C-O bond. These bands are the results of coupling between the breathing of condensed ring structure and some other vibrations, such as the stretching of C-O bond or the rocking of C-H bond. Some of the bands that had been assigned to the stretching of C-O bond in experiment could be partly contributed by the vibration of C-O bonds. Furthermore, this study result showed that the stretching of C-H bond, and the rocking of t-Bu, methyl and methenyl groups can be located at the bands around 2900 and 1460 cm(-1), respectively. (C) 2000 Elsevier Science B.V. All rights reserved.