Estimates of electronic coupling for excess electron transfer in DNA

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study

The genome-the source of life and platform of evolution-is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent-solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

The 2Ih and OXOG Proximity Consequences on Charge Transfer through ds-DNA: Theoretical Studies of Clustered DNA Damage

Genetic information is continuously exposed to harmful factors, both intra- and extracellular. Their activity can lead to the formation of different types of DNA damage. Clustered lesions (CDL) are problematic for DNA repair systems. In this study, the short ds-oligos with a CDL containing (R) or (S) 2Ih and ^OXOG in their structure were chosen as the most frequent in vitro lesions. In the condensed phase, the spatial structure was optimized at the M062x/D95**:M026x/sto-3G level of theory, while the electronic properties were optimized at the M062x/6-31++G** level. The influence of equilibrated and non-equilibrated solvent-solute interactions was then discussed. It was found that the presence of (R)2Ih in the ds-oligo structure causes a greater increase in structure sensitivity towards charge adoption than (S)2Ih, while ^OXOG shows high stability. Moreover, the analysis of charge and spin distribution reveals the different effects of 2Ih diastereomers. Additionally, the adiabatic ionization potential was found as follows for (R)-2Ih and (S)-2Ih in eV: 7.02 and 6.94. This was in good agreement with the AIP of the investigated ds-oligos. It was found that the presence of (R)-2Ih has a negative influence on excess electron migration through ds-DNA. Finally, according to the Marcus theory, the charge transfer constant was calculated. The results presented in the article show that both diastereomers of 5-carboxamido-5-formamido-2-iminohydantoin should play a significant role in the CDL recognition process via electron transfer. Moreover, it should be pointed out that even though the cellular level of (R and S)-2Ih has been obscured, their mutagenic potential should be at the same level as other similar guanine lesions found in different cancer cells.

First-principles investigation of band offset and charge transfer characteristics at the PE/fluorinated layer interface

Polymers, especially polyethylene (PE), are widely employed as insulating materials in electrical power transmission systems. However, the insulation still faces the problem of space charge, which distorts the electric field distribution and accelerates electrical aging. Experimental results show that after the fluorination process, less charge injection occurs compared with pure PE. To clarify the mechanism, classical molecular dynamics was employed to build a PE/fluorinated layer interfacial model and first principles calculation was utilized to get the band offset at the interface. The results calculated by both the bulk plus band lineup method and the layer-decomposed density of states method show that the energy band of the fluorinated PE layer is overall lower than that of the PE side, and the band offsets are around 2 eV. Charge transport results based on Marcus theory and kinetic Monte Carlo simulations also show that charge can easily accumulate at the interfacial area under an electric field and the band offset can suppress charge injection. The conduction band offset acts as an energy barrier for the excess electrons at the fluorinated layer side to cross the interface, while the valence band offset has the same effect on hole transport because of the energy barrier caused by the inverted region. Our findings provide a fundamental and theoretical basis for material modification and space charge inhibition.

Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion

In condensed solids, triplet exciton migration and succeeding triplet-triplet annihilation (TTA) are major bottleneck processes for efficient photon upconversion (UC) using sunlight excitation. We theoretically investigated the reaction times of TTA and the triplet-triplet energy transfer (TTET) as the elementary processes of triplet exciton migration in organic crystals of two molecular species: 9,10-diphenylanthracene (DPA) and its double-strapped alkyl  derivative (C7-sDPA) as the models of a recently reported crystalline system of TTA-UC by Kamada et al. The reaction times calculated based on Marcus theory clarified that the dimensionality of TTET and synergetic effects of TTA and TTET are responsible for the high UC quantum yield as well as their triplet lifetimes.

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.

DFT-based Green's function pathways model for prediction of bridge-mediated electronic coupling

New LMO-GFM methodology enables intuitive understanding of electron tunneling in terms of through-bond and through-space interactions.

A multi-state fragment charge difference approach for diabatic states in electron transfer: extension and automation

The electron transfer (ET) rate prediction requires the electronic coupling values. The Generalized Mulliken-Hush (GMH) and Fragment Charge Difference (FCD) schemes have been useful approaches to calculate ET coupling from an excited state calculation. In their typical form, both methods use two eigenstates in forming the target charge-localized diabatic states. For problems involve three or four states, a direct generalization is possible, but it is necessary to pick and assign the locally excited or charge-transfer states involved. In this work, we generalize the 3-state scheme for a multi-state FCD without the need of manual pick or assignment for the states. In this scheme, the diabatic states are obtained separately in the charge-transfer or neutral excited subspaces, defined by their eigenvalues in the fragment charge-difference matrix. In each subspace, the Hamiltonians are diagonalized, and there exist off-diagonal Hamiltonian matrix elements between different subspaces, particularly the charge-transfer and neutral excited diabatic states. The ET coupling values are obtained as the corresponding off-diagonal Hamiltonian matrix elements. A similar multi-state GMH scheme can also be developed. We test the new multi-state schemes for the performance in systems that have been studied using more than two states with FCD or GMH. We found that the multi-state approach yields much better charge-localized states in these systems. We further test for the dependence on the number of state included in the calculation of ET couplings. The final coupling values are converged when the number of state included is increased. In one system where experimental value is available, the multi-state FCD coupling value agrees better with the previous experimental result. We found that the multi-state GMH and FCD are useful when the original two-state approach fails.

Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation

Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist.

Stabilization of radical anion states of nucleobases in DNA

Trapping of an electron by DNA leads to the formation of radical anion states of pyrimidine bases. Because these states play an important role in biological and chemical processes, their computational treatment is of particular interest. We show that simple electrostatic and quantum chemical models can accurately reproduce the adiabatic electron affinities (EAs) of short DNA stacks recently derived from high-level ab initio calculations (M. Kobylecka, J. Leszczynski, and J. Rak, J. Am. Chem. Soc., 2008, 130, 15683). The electrostatic interaction of an excess electron localized on cytosine or thymine with intra- and inter-strand adjacent nucleobases is found to strongly affect the energy of the radical anions. This interaction is the main origin of the dependence of EA of nucleobases on the nature of neighboring base pairs. In particular, the states XT(-)Y and XC(-)Y, where X and Y = C, T, are, by ca. 0.7 eV, more stable than radical anions GT(-)G and GC(-)G. We find that second-neighbor effects can also significantly modulate EAs, although being smaller than the effects of adjacent bases. The strongest destabilizing effect is found for 5'-GC and 3'-GC, while the 5'-AT base pair stabilizes the radical anion states. Using a combined QM/MD approach, we consider how structural fluctuations of DNA influence the stability of the radical anion states. Despite large dispersions of the stabilization energies due to conformational dynamics of DNA, there are only few thermally accessible structures where GT(-)G and GC(-)G are energetically more favorable than the corresponding pyrimidine triplets. Although stabilization energies calculated for stacks of regular structure are in qualitative agreement with the QM/MD results, structural fluctuations of pi stacks should be taken into account for more accurate description of the excess electron trapped by DNA. The results obtained in this study suggest that simple electrostatic models, in combination with MD simulations, can be very helpful to explore the long time scale behavior of radical anions in DNA.

Pathways of excess electron transfer in phenothiazine-tethered DNA containing single-base mismatches

The effects of local structural disorder on excess electron transfer (EET) in DNA were investigated by evaluating photoinduced electron transfer in phenothiazine (PTZ)-modified oligodeoxynucleotides bearing single-base mismatches. Unexpectedly, more efficient electron transfer was observed for the mismatched duplexes than for the complementary DNA, suggesting that distraction of hydrogen bond interaction at the mismatch site enables electron injection or hopping beyond the mismatch sites. It was also anticipated that water accessibility of the mismatched nucleobases could affect EET because protonation of the electron-captured pyrimidine intermediates became competitive to EET, especially at the mismatch sites.

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.

Charge-transfer excitons in DNA

There have been a number of theoretical treatments of excitons in DNA, most neglecting both the intrachain and interchain wavefunction overlaps of the electron and hole, treating them as Frenkel excitons. Recently, the importance of the intrachain and interchain coupling has been highlighted. Experiments have shown that in (dA)n oligomers and in duplex (dA)n.(dT)n, to be abbreviated (A/T), where A is adenine and T is thymine, the exciton wavefunction is delocalized over several bases. In duplexes it is possible to have charge-transfer (CT) excitons. Theoretical calculations have suggested that CT excitons in DNA may have lower energy than single chain excitons. In all the calculations of excitons in DNA, the polarization of the surrounding water has been neglected. Calculations have shown, however, that polarization of the water by an excess electron or a hole in DNA lowers its energy by approximately 1/2 eV, causing it to become a polaron. It is therefore to be expected that polarization charge induced in the surrounding water has a significant effect on the properties of the exciton. In what follows, we present calculations of some properties CT excitons would have in an A/T duplex taking into account the wavefunction overlaps, the effect of the surrounding water, which results in the electron and hole becoming polarons, and the ions in the water. As expected, the CT exciton has lowest energy when the electron and hole polarons are directly opposite each other. By appropriate choice of the dielectric constant, we can obtain a CT exciton delocalized over the number of sites found in photoinduced absorption experiments. The absorption threshold that we then calculate for CT exciton creation in A/T is in reasonable agreement with the lowest singlet absorption deduced from available data.

Estimation of electronic coupling in pi-stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of V(da) because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a pi stack, where donor and acceptor are separated by a bridging unit, can be obtained as V(da) = (E(2)-E(1))mu(12)R(da) + (2E(3)-E(1)-E(2))2mu(13)mu(23)R(da) (2), where E(1), E(2), and E(3) are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, mu(ij) is the transition dipole moments between the states i and j, and R(da) is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model.

MS-CASPT2 calculation of excess electron transfer in stacked DNA nucleobases

Calculations using the complete active space self-consistent field (CASSCF) and complete active space second-order perturbation (CASPT2) methods, and the multistate formulation of CASPT2 (MS-CASPT2), are performed for the ground and excited states of radical anions consisting of two pi-stacked nucleobases. The electronic couplings for excess electron transfer (EET) in the pi-stacks are estimated by using the generalized Mulliken-Hush approach. We compare results obtained within the different methods with data derived using Koopmans' theorem approximation at the Hartree-Fock level. The results suggest that although the one-electron scheme cannot be applied to calculate electron affinities of nucleobases, it provides reasonable estimates for EET energies. The electronic couplings calculated with KTA lie between the CASPT2 and the MS-CASPT2 based values in almost all cases.

Electronic Coupling Mediated by Stacked [Thymine-Hg-Thymine] Base Pairs

Very recently it has been shown that stable metal-mediated base pairs [Thymine-Hg-Thymine] can form in DNA. To estimate the effect of such pairs on the efficiency of charge transfer through DNA, we carry out quantum mechanical calculations of double-stranded pi-stacks GXG, GXXG, and GXXXG, where X = [Thymine-Hg-Thymine] and stacks GT(n)G of canonical base pairs. The charge-transfer efficiency in short duplexes GXG and GTG is found to be similar. However, the donor-acceptor coupling in GXXG and GXXXG is stronger by a factor of 2.5-3.0 than that in GT(n)G (n = 2 and 3), respectively. It is shown that the valence orbitals of Hg atoms do not essentially participate in mediating the electronic coupling for hole transfer; however, they may play an important role in excess electron transfer.