Geometric Parameters in Nucleic Acids:  Nitrogenous Bases

Clowney, Lester; Jain, Shri C.; Srinivasan, A. R.; Westbrook, John D.; Olson, Wilma K.; Berman, Helen M.

doi:10.1021/ja952883d

Cited by 181 publications

(155 citation statements)

References 10 publications

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“…The experimental geometries of nucleobases were employed. 34 While the structure of nucleobases deforms upon trapping of an excess electron, 25-27 this effect was not accounted for in the present calculations.…”

Section: B Geometry Of Dimersmentioning

confidence: 88%

Estimates of electronic coupling for excess electron transfer in DNA

Voityuk

2005

The Journal of Chemical Physics

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Electronic coupling V da is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of V da for hole transfer, estimates of electronic couplings for excess electron transfer ͑ET͒ in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a stack. Two approaches are considered. First, we employ the diabatic-state ͑DS͒ method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine ͑AT͒ and guanine-cytosine ͑GC͒. In this approach, similar values of V da are obtained with the standard 6-31G * and extended 6-31+ + G ** basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals ͑LUMOs͒ of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of V da are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements V da for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.

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Section: B Geometry Of Dimersmentioning

confidence: 88%

Estimates of electronic coupling for excess electron transfer in DNA

Voityuk

2005

The Journal of Chemical Physics

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“…61 Experimental idealized atomic coordinates of the four bases (adenine, cytosine, guanine, and thymine) taken from high-resolution X-ray and neutron studies were used for generating the structures. 62 The mutual positions of the nucleobases in the models studied correspond to a regular DNA structure with a rise of 3.38 Å and a twist of 36°. In addition, four one-strand symmetrical structures GG, AA, TT, and CC with a twist of 0°were considered.…”

Section: Methodsmentioning

confidence: 97%

Electronic Coupling for Charge Transfer and Transport in DNA

et al. 2000

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We calculated electronic matrix elements for hole transfer between adjacent nucleobases in DNA. Calculations of the matrix elements for intrastrand and interstrand transfer were performed at the Hartree-Fock level employing the 6-31G* and 6-311G** basis sets. The matrix elements for intrastrand hole transfer, for which a wealth of experimental solution data is available, are almost independent of the basis set and exhibit an exponential interbase distance dependence, sensitivity to the donor-acceptor geometry, and dependence on 5′ f 3′ direction base sequence. The calculated intrastrand hole transfer matrix elements between adjacent thymines, v + (T,T) ) 0.16 eV, is in good agreement with the experimental estimate, v + (T,T) ) 0.18 eV, inferred from hole hopping in G + (T) m GGG (m ) 1-3). The features of the nucleobase bridge specificity for superexchange-induced hole hopping between guanines in G + XY...G (X,Y ) T or A) were elucidated, with the prediction of enhanced efficiency of thymine relative to adenine as mediator. Information on superexchangemediated intrastrand and direct interstrand hole hopping between guanine bases was also inferred. Our results for interstrand, adjacent G + G coupling predict the existence of zigzagging pathways for hole hopping, in line with experiment.

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“…4 Experimental idealized atomic coordinates of the four bases taken from high-resolution X-ray and neutron studies were used for generating the structures. 39 The mutual positions of the nucleobases in the models studied correspond to the intra-strand arrangement in a regular (ideal) B-DNA structure, with a distance of 3.38 Å between the planes of the rings. The geometries of the systems were constructed with the program SCHNArP 40 and are given in the supplementary material.…”

Section: Methodsmentioning

confidence: 99%

Exciton delocalization, charge transfer, and electronic coupling for singlet excitation energy transfer between stacked nucleobases in DNA: An MS-CASPT2 study

Blancafort

Voityuk

2014

The Journal of Chemical Physics

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Articles you may be interested inFragment transition density method to calculate electronic coupling for excitation energy transfer J. Chem. Phys. 140, 244117 (2014) Exciton delocalization and singlet excitation energy transfer have been systematically studied for the complete set of 16 DNA nucleobase dimers in their ideal, single-strand stacked B-DNA conformation, at the MS-CASPT2 level of theory. The extent of exciton delocalization in the two lowest (π ,π * ) states of the dimers is determined using the symmetrized one-electron transition density matrices between the ground and excited states, and the electronic coupling is calculated using the delocalization measure and the energy splitting between the states [see F. Plasser, A. J. A. Aquino, W. L. Hase, and H. Lischka, J. Phys. Chem. A 116, 11151-11160 (2012)]. The calculated couplings lie between 0.05 eV and 0.14 eV. In the B-DNA conformation, where the interchromophoric distance is 3.38 Å, our couplings deviate significantly from those calculated with the transition charges, showing the importance of orbital overlap components for the couplings in this conformation. The calculation of the couplings is based on a two-state model for exciton delocalization. However, in three stacks with a purine in the 5 position and a pyrimidine in the 3 one (AT, GC, and GT), there is an energetically favored charge transfer state that mixes with the two lowest excited states. In these dimers we have applied a three-state model that considers the two locally excited diabatic states and the charge transfer state. Using the delocalization and charge transfer descriptors, we obtain all couplings between these three states. Our results are important in the context of DNA photophysics, since the calculated couplings can be used to parametrize effective Hamiltonians to model extended DNA stacks. Our calculations also suggest that the 5 -purine-pyrimidine-3 sequence favors the formation of charge transfer excited states.

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Geometric Parameters in Nucleic Acids: Nitrogenous Bases

Cited by 181 publications

References 10 publications

Estimates of electronic coupling for excess electron transfer in DNA

Estimates of electronic coupling for excess electron transfer in DNA

Electronic Coupling for Charge Transfer and Transport in DNA

Exciton delocalization, charge transfer, and electronic coupling for singlet excitation energy transfer between stacked nucleobases in DNA: An MS-CASPT2 study

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