Principles of Nucleic Acid Structure
- W. Saenger
- Springer, New York
Full geometry optimizations using the PM3, AMl, 3-21G*/HF and 6-31G*/HF levels of theory were conducted on the syn and anti conformations of cyclic 3’,5’-adenosine monophosphate (CAMP). Comparison of the anti crystal structures with the semiempirical and ab initio results revealed that the ab initio results agree well with the experimental results. The results of semiempirical calculations are in qualitative agreement with experimental and ab initio values, with the exception of the glycosyl torsion angle for the anti conformer. Sugar puckering, which is not handled properly by semiempirical methods for unconstrained sugars, nucleosides, nucleotides and nucleotide base pairs, is modeled reasonably well by the semiempirical methods for CAMP. This improvement results from the constraints introduced by the cyclization of AMP to form the phosphodiester.