Article

Local Aromaticity in Natural Nucleobases and Their Size-Expanded Benzo-Fused Derivatives

Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avenida Diagonal 643, 08028, Barcelona, Spain, Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, Center for Nanophase Material Sciences and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831-6494, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, 08028 Barcelona, Spain, Unidad de Modelización Molecular y Bioinformática, Parc Científic de Barcelona, Josep Samitier 1−6, 08028 Barcelona, Spain, Computacional Biology Program, Barcelona Supercomputing Center. Edificio Nexus II. Barcelona 08028, Spain, and Institut de Química Computacional and Departament de Química, Universitat de Girona, 17071 Girona, Spain
J. Phys. Chem. A, 2006, 110 (44), pp 12249–12258
DOI: 10.1021/jp063790t
Publication Date (Web): October 17, 2006
Copyright © 2006 American Chemical Society

Abstract

The influence of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is examined. To this end, the local aromaticity of the six- and five-membered rings in both the natural bases and their benzoderivatives is determined using HOMA, NICS, aromatic fluctuation index (FLU), and para-delocalization index (PDI) descriptors. In general, there is a good correspondence between the different indices, so that ring moieties with more negative NICS values also have larger HOMA and PDI measures and lower FLU indices. The results also point out notable differences in the aromatic character of the natural and size-expanded bases, which generally are hardly affected upon hydrogen bonding. The differences in the highest occupied molecular orbital−lowest unoccupied molecular orbital (HOMO−LUMO) gap determined for the size-expanded nucleobases show an inverse correlation with the aromaticity of the fused benzene ring, so that the larger the HOMO−LUMO gap is, the lower the destabilization experienced by the benzene upon insertion/addition to the natural bases. This finding suggests that the introduction of suitable chemical modifications in the benzene ring might be useful to modulate the HOMO−LUMO gap while enabling the design of modified DNA duplexes that are able to act as molecular wires.

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Received 18 June 2006
Published online 17 October 2006
Published in print 1 November 2006
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