ISSN:
0192-8651
Keywords:
Computational Chemistry and Molecular Modeling
;
Biochemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
We compare the electrostatic potential surrounding several natural and synthetic nucleic acid bases calculated using an atom-centered multiple expansion (ACME) derived from integration of the charge distribution with that from potential-derived charges (PDCs) obtained using the CHELPG procedure. When the multipole expansions are carried out to octapoles, the root mean square (rms) error in the potential is always less than that from PDCs. Electrostatic interactions in pairs of these nucleic acid bases were also evaluated using ACMEs up to octapoles and PDCs. The electrostatic interaction energies from ACMEs were found always to be larger than those from PDCs or the total self-consistent field (SCF) interaction energy. The value of the electrostatic energy differs by as much as approximately 19 or as little as approximately 8 kJ/mol between the ACME and PDC methods. The rank ordering provided by the electrostatic models is grossly similar but differs in the ranking of systems with two and three hydrogen bonds. A rigid twist about the N—H ⃛ N axis of the pairs was examined using SCF calculations and the electrostatic models. It was found that with ACMEs the energy required for a 90-degree rotation was always higher than that found from SCF calculations. With PDCs, similar results are obtained, except with the adenine/thymine and 9-methyl-adenine/1-methyl-thymine pairs. In these instances, the barrier is about 4 kJ/mol lower than that found with SCF calculations. These results demonstrate that integration of the charge density can provide convergent multipole expansions that provide a more accurate description of the electrostatic potential than the commonly used PDC model. In addition, the description of electrostatic interactions during twisting of AT and mAmT given by this model is shown to be somewhat anomalous. © 1995 by John Wiley & Sons, Inc.
Additional Material:
5 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/jcc.540160613
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