Use of the supermolecule approach to model the syn and anti conformations of solvated cyclic 3',5'-adenosine monophosphate

ACS Citation

Kirschner, K. N.; Sherer, E. C.; Shields, G. C. Use of the Supermolecule Approach to Model the Syn and Anti Conformations of Solvated Cyclic 3'€™,5'€™-adenosine Monophosphate. J. Phys. Chem. 1996, 100 (8), 3293-€“3298.


The supermolecule approach has been used to model the hydration of cyclic 3',5'-adenosine monophosphate, cAMP. Model building combined with PM3 optimizations predict that the anti conformer of cAMP is capable of hydrogen bonding to an additional solvent water molecule compared to the syn conformer. The addition of one water to the syn superstructure with concurrent rotation of the base about the glycosyl bond to form the anti superstructure leads to an additional enthalpy of stabilization of approximately -6 kcal/mol at the PM3 level. This specific solute-solvent interaction is an example of a large solvent effect, as the method predicts that cAMP has a conformational preference for the anti isomer in solution. This conformational preference results from a change in the number of specific solute-solvent interactions in this system. This prediction could be tested by NMR techniques. The number of waters predicted to be in the first hydration sphere around cAMP is in agreement with the results of hydration studies of nucleotides in DNA. In addition, the detailed picture of solvation about this cyclic nucleotide is in agreement with infrared experimental results.

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Journal of Physical Chemistry

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