Biologically relevant phosphoranes: structural characterization of a nucleotidyl phosphorane

The first successful crystal structures of biorelevant nucleoside and carbohydrate-based phosphoranes are reported. Employing thymidine, a nucleotidyl phosphorane was synthesized in 90% yield and was shown by X-ray analysis to possess a trigonal bipyramidal geometry. With the use of 1,2-O-isopropylidene-alpha-d-glucofuranose, a carbohydrate-based phosphorane was formed and similarly found to have a trigonal bipyramidal geometry. NMR studies demonstrated the existence of isomerism in solution associated with the nucleotidyl phosphorane and rapid exchange for the carbohydrate-based phosphorane. The geometrical representations reported here are expected to have significant applications associated with active site mechanisms of phosphoryl transfer enzymes, for example, in DNA, RNA, c-AMP, and others.