DNA Electron Transfer Processes: Some Theoretical Notions

Berlin, Yu. A.; Kurnikov, Igor V.; Beratan, David N.; Ratner, Mark A.; Burin, Alexander L.; Berggruen, Senta

doi:10.1007/b94471

Cited by 116 publications

(147 citation statements)

References 94 publications

Supporting

Mentioning

144

Contrasting

Order By: Relevance

“…A large body of experimental data indicates two regimes of DNA charge transfer: a regime with strong (exponential) dependence of the rate/yield on distances up to ∼3-7 bp and a much weaker dependence for longer distances (35). Theoretical models have focused on describing short-distance transport with a tunneling model and longer-distance transport with a multistep or multirange hopping approach (36,37). This framework has challenges associated with understanding transient B population in an apparent tunneling regime and with describing the transition between strong and weak distancedependent regimes (SI Text, section S1 and refs.…”

Section: Correlated Vs Uncorrelated Site Energy Fluctuationsmentioning

confidence: 99%

Biological charge transfer via flickering resonance

Zhang¹,

Liu²,

Balaeff³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

153

263

View full text Add to dashboard Cite

Biological electron-transfer (ET) reactions are typically described in the framework of coherent two-state electron tunneling or multistep hopping. However, these ET reactions may involve multiple redox cofactors in van der Waals contact with each other and with vibronic broadenings on the same scale as the energy gaps among the species. In this regime, fluctuations of the molecular structures and of the medium can produce transient energy level matching among multiple electronic states. This transient degeneracy, or flickering electronic resonance among states, is found to support coherent (ballistic) charge transfer. Importantly, ET rates arising from a flickering resonance (FR) mechanism will decay exponentially with distance because the probability of energy matching multiple states is multiplicative. The distance dependence of FR transport thus mimics the exponential decay that is usually associated with electron tunneling, although FR transport involves real carrier population on the bridge and is not a tunneling phenomenon. Likely candidates for FR transport are macromolecules with ET groups in van der Waals contact: DNA, bacterial nanowires, multiheme proteins, strongly coupled porphyrin arrays, and proteins with closely packed redox-active residues. The theory developed here is used to analyze DNA charge-transfer kinetics, and we find that charge-transfer distances up to three to four bases may be accounted for with this mechanism. Thus, the observed rapid (exponential) distance dependence of DNA ET rates over distances of K K K K15 Å does not necessarily prove a tunneling mechanism.vibronic coupling | resonant tunneling pathways | superexchange | coherence | gated transport C hemical structure and, importantly, structural fluctuations determine the mechanism and kinetics of charge transfer. Redox energy fluctuations are of particular significance when transport barrier heights and the energy fluctuations are of similar magnitude. Indeed, the sensitivity of biological electrontransfer (ET) rates to conformational fluctuations and consequent (transient) delocalization is the topic of intense interest (1-3). Resonant enhancement of biological ET rates is consistent with a growing body of physical and structural data found in DNA ET through stacked nucleobases (4), extended delocalized structures of bacterial photosynthesis (including the special pair, bridging chlorophyll and pheophytin) (5), the polaronic states of oxidized porphyrin arrays up to seven porphyrin diameters in spatial extent (6), micrometer-scale bacterial nanowires (7, 8), multiheme oxidoreductases (9, 10), amino acid side chains in ribonucleotide reductase (11), engineered protein-based hopping-chains (12), and centimeter-scale charge-transport chains in filamentous bacteria (13). Here, we describe a transient or flickering resonance (FR) mechanism for ET. The FR mechanism arises when thermal fluctuations produce geometries that enable charge delocalization across the entire structure by bringing the donor (D), bridge (B), and acceptor (...

show abstract

Section: Correlated Vs Uncorrelated Site Energy Fluctuationsmentioning

confidence: 99%

Biological charge transfer via flickering resonance

Zhang¹,

Liu²,

Balaeff³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

153

263

View full text Add to dashboard Cite

show abstract

“…Theoretical and computational studies provide very useful results which allow one to elucidate the role of electronic, structural, and dynamic factors in ET through stacks. 3,4 The effective coupling of donor and acceptor V da is a key parameter which determines the efficiency of the ET reactions, and therefore quantummechanical calculations of this parameter is of wide interest. 5,6 The application of different computational schemes to estimate V da in DNA stacks has been discussed recently.…”

Section: Introductionmentioning

confidence: 99%

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

Voityuk

2006

The Journal of Chemical Physics

View full text Add to dashboard Cite

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 stack, where donor and acceptor are separated by a bridging unit, can be obtained, where E 1 , E 2 , and E 3 are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, 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.

show abstract

“…Elementary steps for charge transfer in DNA were considered by Berlin et al 9 General aspects of charge-transfer modeling in DNA have recently been considered in an excellent review. 10 The electronic coupling of donor and acceptor V da is a key characteristic which controls the rate of charge transfer and mainly determines its sensitivity to the arrangement of donor and acceptor. There are several studies on estimation and analysis of electronic couplings for hole transfer in DNA.…”

Section: Introductionmentioning

confidence: 99%

Estimates of electronic coupling for excess electron transfer in DNA

Voityuk

2005

The Journal of Chemical Physics

View full text Add to dashboard Cite

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.

show abstract

DNA Electron Transfer Processes: Some Theoretical Notions

Cited by 116 publications

References 94 publications

Biological charge transfer via flickering resonance

Biological charge transfer via flickering resonance

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

Estimates of electronic coupling for excess electron transfer in DNA

Contact Info

Product

Resources

About