Effect of proton transfer on the electronic coupling in DNA

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries

We present benchmark calculations of nine selected points on potential energy surfaces describing proton transfer process in three model systems, H(5)O(2) (+), CH(3)OH…H(+)…OH(2), and CH(3)COOH…OH(2). The calculated relative energies of these geometries are compared to those calculated by various wave function and density functional methods, including the polarized molecular orbital (PMO) model recently developed in our research group and other semiempirical molecular orbital methods. We found that the SCC-DFTB and PMO methods (the latter available so far only for molecules consisting of only O and H and therefore only for the first of the three model systems) give results that are, on average, within 2 kcal/mol of the benchmark results. Other semiempirical molecular orbital methods have mean unsigned errors (MUEs) of 3 to 8 kcal/mol, local density functionals have MUEs in the range 0.7 to 3.7 kcal/mol, and hybrid density functionals have MUEs of only 0.3 to 1.0 kcal/mol, with the best density functional performance obtained by hybrid meta-GGAs, especially M06 and PW6B95.

Theoretical study of the tautomerism in the one-electron oxidized guanine-cytosine base pair

Ionizing radiation on DNA mainly generates one-electron oxidized guanine-cytosine base pair (G(+·):C), and in the present paper we study all possible tautomers of G(+·):C by using ab initio approaches. Our calculations reveal that the tautomeric equilibrium follows a peculiar path, characterized by a stepwise mechanism: first the proton in the central hydrogen bond N1(G)-H1-N3(C) migrates from guanine to cytosine, and then the cytosine cation releases one proton from its amino group. During this second step, water acts as a proton acceptor, localizing the positive charge on one of the water molecules interacting with the guanine radical. In agreement with experimental findings, the computed energy barriers show that the deprotonation of the cytosine cation is the speed-limiting step in the tautomeric equilibrium. The influence of the number of water molecules incorporated in the theoretical model is analyzed in detail. The evolution of electronic properties along the reaction path is also discussed on the basis of partial atomic charges and spin density distributions. This work demonstrates that water indeed plays a crucial role in the tautomeric equilibra of base pairs.

Influence of hydration on proton transfer in the guanine-cytosine radical cation (G*+-C) base pair: a density functional theory study

Upon one-electron oxidation, all molecules including DNA bases become more acidic in nature. For the GC base pair, experiments suggest that a facile proton transfer takes place in the G(*+)-C base pair from N(1) of G(*+) to N(3) of cytosine. This intrabase pair proton-transfer reaction has been extensively considered using theoretical methods for the gas phase, and it is predicted that the proton transfer is slightly unfavorable, in disagreement with experiment. In the present study, we consider the effect of the first hydration layer on the proton-transfer reaction in G(*+)-C by the use of density functional theory (DFT) using B3LYP/6-31+G** calculations of the G(*+)-C base pair in the presence of 6 and 11 water molecules. Under the influence of hydration of 11 waters, a facile proton transfer from N(1) of G(*+) to N(3) of C is predicted. The zero-point energy (ZPE)-corrected forward and backward energy barriers, for the proton transfer from N(1) of G(*+) to N(3) of C, was found to be 1.4 and 2.6 kcal/mol, respectively. The proton-transferred G(*)-(H(+))C + 11H(2)O was found to be 1.2 kcal/mol more stable than G(*+)-C + 11H(2)O, in agreement with experiment. The present calculation demonstrates that the inclusion of the first hydration shell around the G(*+)-C base pair has an important effect on the internal proton-transfer energetics.

PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms

The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles of hole donor and acceptor, separated by a bridge of two adenine bases, was analyzed using combined molecular dynamics (MD) and quantum-chemical methods. Surprisingly, electronic structure calculations on individual MD snapshots show significant frontier orbital electronic population on the bridge in approximately 10% of the structures. Electron-density delocalization to the bridge is found to be gated by fluctuations of the covalent conjugated bond structure of the aromatic rings of the nucleic bases. It is concluded, therefore, that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments. PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.