Effects of Sugar Ring Puckering, Anti-Syn Interconversion and Intramolecular Interactions on N-Glycosidic Bond Cleavage in 3-Methyl-2'-deoxyadenosine and 2'-Deoxyadenosine

The effects of structural parameters and intramolecular interactions on N-glycosidic bond length in 3-methyl-2'-deoxyadenosine (3MDA) and 2'-deoxyadenosine (DA) were investigated employing quantum mechanical methods. All calculations were performed at B3LYP/6-311++G** level in the gas phase. The N-glycosidic bond length strongly depends on sugar configuration; it is shorter in syn conformation relative to anti in many cases where they have the same sugar ring configuration. The sugar conformation can influence the N-glycosidic bond through interaction with the O4' atom. The impact of intramolecular improper hydrogen bonds and H-H bonding interactions on N-glycosidic bond length was investigated in DA and 3MDA and their modeled structures. Improper hydrogen bonds decrease N-glycosidic bond length while H-H bonding interactions increase it.