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.

The purpose of this communication is two-fold. We introduce the fragment charge difference (FCD) method to estimate the electron transfer matrix element HDA between a donor D and an acceptor A, and we apply this method to several aspects of hole transfer electronic couplings in π-stacks of DNA, including systems with several donor–acceptor sites. Within the two-state model, our scheme can be simplified to recover a convenient estimate of the electron transfer matrix element HDA=(1−Δq2)1/2(E2−E1)/2 based on the vertical excitation energy E2–E1 and the charge difference Δq between donor and acceptor. For systems with strong charge separation, Δq≳0.95, one should resort to the FCD method. As favorable feature, we demonstrate the stability of the FCD approach for systems which require an approach beyond the two-state model. On the basis of ab initio calculations of various DNA related systems, we compared three approaches for estimating the electronic coupling: the minimum splitting method, the generalized Mulliken–Hush (GMH) scheme, and the FCD approach. We studied the sensitivity of FCD and GMH couplings to the donor–acceptor energy gap and found both schemes to be quite robust; they are applicable also in cases where donor and acceptor states are off resonance. In the application to π-stacks of DNA, we demonstrated for the Watson–Crick pair dimer [(GC),(GC)] how structural changes considerably affect the coupling strength of electron hole transfer. For models of three Watson–Crick pairs, we showed that the two-state model significantly overestimates the hole transfer coupling whereas simultaneous treatment of several states leads to satisfactory results.

A partially incoherent rate theory of long-range charge transfer in deoxyribose nucleic acid Electronic matrix elements for hole transfer between Watson-Crick pairs in desoxyribonucleic acid ͑DNA͒ of regular structure, calculated at the Hartree-Fock level, are compared with the corresponding intrastrand and interstrand matrix elements estimated for models comprised of just two nucleobases. The hole transfer matrix element of the GAG trimer duplex is calculated to be larger than that of the GTG duplex. ''Through-space'' interaction between two guanines in the trimer duplexes is comparable with the coupling through an intervening Watson-Crick pair. The gross features of bridge specificity and directional asymmetry of the electronic matrix elements for hole transfer between purine nucleobases in superstructures of dimer and trimer duplexes have been discussed on the basis of the quantum chemical calculations. These results have also been analyzed with a semiempirical superexchange model for the electronic coupling in DNA duplexes of donor ͑nuclobases͒-acceptor, which incorporates adjacent base-base electronic couplings and empirical energy gaps corrected for solvation effects; this perturbation-theory-based model interpretation allows a theoretical evaluation of experimental observables, i.e., the absolute values of donoracceptor electronic couplings, their distance dependence, and the reduction factors for the intrastrand hole hopping or trapping rates upon increasing the size of the nucleobases bridge. The quantum chemical results point towards some limitations of the perturbation-theory-based modeling.

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The extension of the MNDO formalism to d orbitals is outlined. MNDO/d parameters are reported for Na, Mg, Al, Si, P, S, Cl, Br, I, Zn, Cd, and Hg. According to extensive test calculations covering more than 600 molecules and several properties, MNDO/d provides significant improvements over established semiempirical methods, especially for hypervalent compounds. The mean absolute error in MNDO/d heats of formation amounts to 5.4 kcal/mol for the complete validation set of 575 molecules and is identical for the subsets of 508 normal valent and 67 hypervalent compounds. In addition to the statistical evaluations, several specific applications are briefly discussed to illustrate the performance of MNDO/d in selected areas and to comment on problematic cases.

We explore the relationship between the electronic-nuclear level structure, the electronic couplings, and the dynamics of hole hopping transport in DNA. We utilized the electronic coupling matrix elements for hole transfer between nearest-neighbor nucleobases in DNA [Voityuk, A. A.; Jortner, J.; Bixon, M.; Rösch, N. J. Chem. Phys. 2001, 114, 5614] to evaluate intrastrand and interstrand superexchange electronic couplings, which determine hole hopping rates within the framework of a semiempirical quantum mechanical-kinetic model. Calculations of the exponential distance (R) dependence of the superexchange mediated intrastrand electronic couplings |V super|2 ∝ exp(−βR) between guanines (G) in “short” G+(T−A) n G (n ≲ 3) duplexes result in β = 0.8−0.9 Å-1. We interpret the experimental data on time-resolved hole transport in the presence of a site-specifically bound methyl transferase mutant in DNA [Wagenknecht, H.-A.; Rajski, S. R.; Pascally, M.; Stemp, E. D. A.; Barton, J. K. J. Am. Chem. Soc. 2001, 123, 4400] in terms of composite sequential, interstrand and intrastrand superexchange mediated, and direct interstrand hole hopping. This mechanism accounts for the rate determining step, for the weak duplex size dependence of the rate, and for the long-range charge transport induced by interstrand superexchange via short (T−A) bridges, containing a single mediating nucleobase. For hole transfer via longer (T−A) n (n ≳ 3) bridges, the superexchange mechanism is replaced by the parallel mechanism of thermally induced hole hopping (TIH) via long (A) n chains. A kinetic analysis of the experimental data for hole transport through seven GG pairs separated by (T−A) n (n = 2−5) bridges across the 3‘−5‘ strand of the DNA duplex [Sartor, V.; Boone, E.; Schuster, G. B. J. Phys. Chem. B, 2001, 105, 11057] reveals that the superexchange−TIH crossover occurs at n = n x = 3. The explorations of the range of applicability and the breakdown of the superexchange mechanism in DNA lay the foundations for the scrutiny of the universality and system specificity of this mechanism in large-scale chemical and biophysical systems.

The relative energies of radical cation states on nucleobases in DNA are considerably affected by the local distribution of water molecules and counterions. In fact, fluctuations of ΔG are large enough to render electron‐hole transfer from G+ to A energetically feasible, thus allowing a changeover from the generally accepted G‐hopping mechanism to A‐hopping (see picture).

CASSCF and CAS-PT2 calculations are performed for the ground and excited states of radical cations consisting of two and three nucleobases. The generalized Mulliken-Hush approach is employed for estimating electronic couplings for hole transfer in the pi-stacks. We compare the CASSCF results with data obtained within Koopmans' approximation. The calculations show that an excess charge in the ground and excited states in the systems is quite localized on a single base both at the CASSCF level and in Koopmans' picture. However, the CASSCF calculations point to a larger degree of localization and, in line with this, smaller transition dipole moments. The agreement between the CAS-PT2 corrected energy gaps and the values estimated with Koopmans' theorem is better, with the CAS-PT2 calculations giving somewhat smaller gaps. Overall, both factors result in smaller CASSCF/CAS-PT2 couplings, which are reduced by up to 40% of the couplings calculated using Koopmans' approximation. The tabulated data can be used as benchmark values for the electronic couplings of stacked nucleobases. For the base trimers, comparison of the results obtained within two- and three-state models show that the multistate treatment should be applied to derive reliable estimates. Finally, the superexchange approach to estimate the donor acceptor electronic coupling in the stacks GAG and GTG is considered.