A theoretical study of structures and electron affinities of radical anions of guanine‐cytosine, adenine‐thymine, and hypoxanthine‐cytosine base pairs
- 29 March 2004
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 25 (8), 1047-1059
- https://doi.org/10.1002/jcc.20020
Abstract
Adiabatic electron affinities (AEA) and structural perturbations due to addition of an excess electron to each of the neutral guanine-cytosine (G-C), adenine-thymine (A-T), and hypoxanthine-cytosine (HX-C) base pairs were studied using the self-consistent charge, density functional tight-binding (SCC-DFTB-D) method, augmented by the empirical London dispersion energy term. Performance of the SCC-DFTB-D method was examined by comparing the calculated results using it with those obtained from experiment as well as ab initio and other different density functional theoretical studies. An excellent agreement between the SCC-DFTB-D results and those obtained by the other calculations regarding the structural modifications, hydrogen bonding, and dissociation energies of the neutral and radical anion base pairs was found. It is shown that adiabatic electron affinity can be better predicted by considering reaction enthalpies of formation of the respective neutral and anionic base pairs from their respective molecular components instead of taking the difference between their total energies. The calculated AEAs of the base pairs were compared with those obtained by the bracketing method from Schaefer and coworkers, where a satisfactory agreement was found. It shows applicability of the SCC-DFTB-D method to study charged DNA models at a highly economical computational cost. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1047–1059, 2004Keywords
This publication has 94 references indexed in Scilit:
- A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large BiomoleculesPhysica Status Solidi (b), 2000
- Electron Transfer Between Bases in Double Helical DNAScience, 1999
- A proposed model for electron conduction in DNA based upon pairwise anion π stacking: electron affinities and ionization potentials of the hydrogen bonded base pairsBioelectrochemistry and Bioenergetics, 1998
- EPR and ENDOR Studies of X-Irradiated Single Crystals of Deoxycytidine 5‘-Phosphate Monohydrate at 10 and 77 KThe Journal of Physical Chemistry A, 1998
- The Electron Affinities of the Radicals Formed by the Loss of an Aromatic Hydrogen Atom from Adenine, Guanine, Cytosine, Uracil, and ThymineBiochemical and Biophysical Research Communications, 1998
- Mutations caught in the actNature, 1995
- The determination of absolute electron affinities of the purines and pyrimidines in DNA and RNA from reversible reduction potentialsBiochemical and Biophysical Research Communications, 1991
- Elementary prediction of linear combination of atomic orbitals matrix elementsPhysical Review B, 1979
- RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrateJournal of Molecular Biology, 1976
- RNA double-helical fragments at atomic resolution: I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrateJournal of Molecular Biology, 1976