Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation

A recently developed computational method, 'mining minima', is used to exam ine the hydrogen-bonding interactions of nucleic acid base-pairs and of the N-methylacetamide homodimer in chloroform. The mining minima algorithm agg ressively samples molecular conformations, identifies the most important lo cal minima, and computes their contributions to the overall free energy of the system. Here, the CHARMM 98 parameter set is used for the potential ene rgy and the generalized Born/surface area solvent model is used to account for the influence of the solvent. Good agreement with experiment is obtaine d for the non-covalent binding affinities of a series of complexes. The com putational approach used here is applicable to a range of molecular systems . (C) 1999 Elsevier Science B.V. All rights reserved.