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In this contribution we advance and explore the thermally induced hopping (TIH) mechanism for long-range charge transport (CT) in DNA and in large-scale chemical systems. TIH occurs in donor-bridge-acceptor systems, which are characterized by off-resonance donor-bridge interactions (energy gap DeltaE > 0), involving thermally activated donor-bridge charge injection followed by intrabridge charge hopping. We observe a "transition" from superexchange to TIH with increasing the bridge length (i.e., the number N of the bridge constituents), which is manifested by crossing from the exponential N-dependent donor-acceptor CT rate at low N (< N(X)) to a weakly (algebraic) N-dependent CT rate at high N (>N(X)). The "critical" bridge size N(X) is determined by the energy gap, the nearest-neighbor electronic couplings, and the temperature. Experimental evidence for the TIH mechanism was inferred from our analysis of the chemical yields for the distal/proximal guanine (G) triplets in the (GGG)(+)TTXTT(GGG) duplex (X = G, azadine (zA), and adenine (A)) studied by Nakatani, Dohno and Saito [J. Am. Chem. Soc. 2000, 122, 5893]. The TIH sequential model, which involves hole hopping between (GGG) and X, is analyzed in terms of a sequential process in conjunction with parallel reactions of (GGG)(+) with water, and provides a scale of (free) energy gaps (relative to (GGG)(+)) of Delta = 0.21-0.24 eV for X = A, Delta = 0.10-0.14 eV for X = zA, and Delta = 0.05-0.10 eV for X = G. We further investigated the chemical yields for long-range TIH in (G)l(+)Xn(G)l (l = 1-3) duplexes, establishing the energetic constraints (i.e., the donor - bridge base (X) energy gap Delta), the bridge structural constraints (i.e., the intrabridge X-X hopping rates k(m)), and the kinetic constraints (i.e., the rate k(d) for the reaction of with water). Effective TIH is expected to prevail for Delta less than or approximately equal to 0.20 eV with a "fast" water reaction (k(d)/k(m) approximately 10(-3)) and for Delta < 0.30 eV with a "slow" water reaction (k(d)/k(m) approximately 10(-5)). We conclude that (T)n bridges (for which Delta approximately equals 0.6 eV) cannot act in TIH of holes. From an analysis based on the energetics of the electronic coupling matrix elements in G(+)(T-A)n(GGG) duplexes we conclude that the superexchange mechanism is expected to dominate for n = 1-4. For long (A)n bridges (n > or approximately equal to 4) the TIH prevails, provided that the water side reaction is slow, raising the issue of chemical control of TIH through long (A)n bridges in DNA attained by changing the solution composition.

We explore charge migration in DNA, advancing two distinct mechanisms of charge separation in a donor (d)-bridge ([Bj])-acceptor (a) system, where [Bj] = B1,B2, . , BN are the N-specific adjacent bases of B-DNA: (i) two-center unistep superexchange induced charge transfer, d*[Bj]a --> d[Bj]a+/-, and (ii) multistep charge transport involves charge injection from d* (or d+) to [Bj], charge hopping within [Bj], and charge trapping by a. For off-resonance coupling, mechanism i prevails with the charge separation rate and yield exhibiting an exponential dependence approximately exp(-betaR) on the d-a distance (R). Resonance coupling results in mechanism ii with the charge separation lifetime tau approximately Neta and yield Y approximately (1 + Neta)-1 exhibiting a weak (algebraic) N and distance dependence. The power parameter eta is determined by charge hopping random walk. Energetic control of the charge migration mechanism is exerted by the energetics of the ion pair state dB1+/-B2 . BNa relative to the electronically excited donor doorway state d*B1B2 . BNa. The realization of charge separation via superexchange or hopping is determined by the base sequence within the bridge. Our energetic-dynamic relations, in conjunction with the energetic data for d*/d- and for B/B+, determine the realization of the two distinct mechanisms in different hole donor systems, establishing the conditions for "chemistry at a distance" after charge transport in DNA. The energetic control of the charge migration mechanisms attained by the sequence specificity of the bridge is universal for large molecular-scale systems, for proteins, and for DNA.

Abstract: The theory of thermally induced hopping (TIH) in donor–bridge–acceptor systems for hole transport in DNA duplexes in solution is extended to include energetic theoretical data for the effects of inter-nucleobase interactions. The extended theory incorporates the site specificity of the energetic stabilization of the radical cation of guanine (G), which acts as a resting site for the hole, and of the radical cations of adenine (A), which are accessible by thermal excitation from G+ (Δ =0.20–0.25eV). The modified TIH model properly accounts for the flat bridge size dependence of the relative chemical yields for hole transport in G(A–T) n GGG duplexes (n =4–16). This flat, non-ohmic, bridge length dependence is attributed to an energetic gating mechanism, which is induced by energy barriers (∼0.1eV) exerted by the proximal and by the terminal edge A groups in the (A) n bridge, while the interior A groups act as shallow traps for the hole. Our ‘molecular polaron’ model for incoherent, hopping charge transport in solvated DNA is supported by independent theoretical evidence for hole localization induced by intrabase configurational distortions and by polar solvent effects. [Copyright &y& Elsevier]

We present a kinetic–quantum model for the mechanisms of hole transport in DNA duplexes, which involves a sequence of hole hopping processes between adjacent guanines (G) and/or hole hopping/trapping via GG or GGG, all of which are separated by thymine (T)–adenine (A) bridges. Individual hole hopping processes between G sites fall into two distinct parallel mechanisms, i.e., unistep superexchange mediated hopping via `short'' (T–A)n bridges and thermally induced hopping (TIH) via `long'' (T–A)n (n>3–4) bridges. The bridge specificity for TIH via (A)n chains pertains to the energetics, with the G+A energy gap Δ=0.20±0.05 eV being sufficiently low to warrant endothermic hole excitation from G+ to (A)n, and to the electronic couplings, with the nearest-neighbor A–A couplings being unique in the sense that the intrastrand and interstrand couplings are close and large (V(A–A)≃0.30–0.060 eV). Accordingly, both effective intrastrand and interstrand (zigzagging) hole transport via (A)n chains will prevail, being nearly invariant with respect to the nucleobases ordering within the (T–A)n duplex. We treated the `transition'' between the superexchange and the TIH mechanism in 5′-G+(T–A)nG-3′ duplexes to predict that the crossover occurs at nx≃3–4, with nx exhibiting a moderate bridge specificity and energy gap dependence. nx is in accord with the experimental data of Giese et al. [Nature 412, 318, 2001]. We assert that the kinetic–quantum mechanical model for the chemical yields and elementary rates cannot be reconciled with the experimental TIH data, with respect to the very weak bridge size dependence of the relative chemical yields and the ratios of the rates. Configurational relaxation accompanying endothermic hole injection from G+ to (A)n may result in the gating (switching-off) of the backrecombination, providing a reasonable description of TIH dynamics and very long-range hole transport in long (A)n chains. [Copyright &y& Elsevier]

Electronic matrix elements for hole transfer between Watson-Crick pairs in desoxyribonucleic acid (DNA) 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 (nuclobases)-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 donor-acceptor 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. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]