Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3''-monophosphate.

Semi-empirical conformational energy calculations were performed for the mononucleotides 5'-AMP, NMN+ and 3'-AMP. Only intramolecular forces are considered. Essentially all conformational states were explored to investigate the population distribution likely to be found in a non-crystalline environment. The calculations suggest that 5'-AMP and 3'-AMP are relatively flexible and a mixture of conformational states is expected. In contrast, the results for NMN+ suggest that a strong electrostatic interaction between the positively charged nicotinamide nitrogen atom and negatively charged phosphate oxygen is possible, stabilizing a few specific states. This interaction will be most significant in a solvent-free situation or an apolar environment.