Structural analysis using the program of conformational code for organic molecules (CCOM)

Abstract

Many software programs visualizing organic molecules such as GaussView can easily represent chirality by one-button operation. However, there is no program to describe the conformations of organic molecules such as trans and +gauche automatically. For the determination of absolute configuration of chiral organic molecules using vibrational circular dichroism (VCD) spectroscopy, the accurate conformational information is necessary, and especially in the case of pharmaceutical candidates, a lot of conformations must be arranged to narrow down the stable conformers. The program of conformational code for organic molecules (CCOM) was applied to VCD conformational analysis of pravastatin sodium. The output of CCOM was arranged as the sdf file format containing the information of conformational codes and Gibbs free energies (if calculated). The auto-selection of the Gaussian outputs using conformational code to exclude the same optimized geometries for the population-weighted VCD spectra was also carried out by using this program. Further, the characteristic conformational 3D fragments of mevastatin in X-ray structure can be easily retrieved together with other molecules in combination with Simplified Molecular Input Line Entry Specification syntax (SMILES) and SMiles ARbitrary Target Specification (SMARTS) strings.