The structure of vitamin B 12 V. The structure of the air-dried crystals of vitamin B 12

Abstract

The refinement of the positions found in air-dried B 12 crystals in the Oxford and Princeton investigations has been carried out through four cycles of structure factor and electron density calculations, on the basis of the Princeton data. Owing to the disordered character of the dried crystal and consequent limitations on the X-ray data, no high precision of atom placing can be achieved; preferred parameters are listed for 93 atoms of the B 12 molecule and 15 water molecules with an additional 7 less well-defined water molecule sites. Certain interesting features of molecular geometry have appeared during structure refinement. The two planes of the benziminazole ring and inner atoms of the corrin nucleus, around which the molecule is constructed, lie at an angle of 80° to one another—the angle of tilt seems to be required by the close contact between the benziminazole nitrogen atom and the methyl group attached at the direct junction between two of the five-membered rings of the corrin nucleus. The projected position of the benziminazole ring across the nucleus also seems to be determined largely by packing considerations within the molecule; various small distortions occur which increase otherwise too short contacts. The latest difference density maps somewhat strengthen the identification as methyl groups of the various single atom substituents to the nucleus; they show small peaks at many of the possible hydrogen atom positions. Of the 18 water molecules indicated by the crystal density, the major part are in definite positions, hydrogen bonded to one another and to active groups on the molecular surface, the remainder are somewhat disordered by the crystal drying and are probably stranded at different positions in different unit cells, among the possible sites listed.