Ravindra Venkatramani

Steering Electrons on Moving Pathways

Electron transfer (ET) reactions provide a nexus among chemistry, biochemistry, and physics. These reactions underpin the power plants and power grids of bioenergetics, and they challenge us to understand how evolution manipulates structure to control ET kinetics. Ball-and-stick models for the machinery of electron transfer, however, fail to capture the rich electronic and nuclear dynamics of ET molecules: these static representations disguise, for example, the range of thermally accessible molecular conformations. The influence of structural fluctuations on electron-transfer kinetics is amplified by the exponential decay of electron tunneling probabilities with distance, as well as the delicate interference among coupling pathways. Fluctuations in the surrounding medium can also switch transport between coherent and incoherent ET mechanisms--and may gate ET so that its kinetics is limited by conformational interconversion times, rather than by the intrinsic ET time scale. Moreover, preparation of a charge-polarized donor state or of a donor state with linear or angular momentum can have profound dynamical and kinetic consequences. In this Account, we establish a vocabulary to describe how the conformational ensemble and the prepared donor state influence ET kinetics in macromolecules. This framework is helping to unravel the richness of functional biological ET pathways, which have evolved within fluctuating macromolecular structures. The conceptual framework for describing nonadiabatic ET seems disarmingly simple: compute the ensemble-averaged (mean-squared) donor-acceptor (DA) tunneling interaction, , and the Franck-Condon weighted density of states, rho(FC), to describe the rate, (2pi/variant Plancks over 2pi)rho(FC). Modern descriptions of the thermally averaged electronic coupling and of the Franck-Condon factor establish a useful predictive framework in biology, chemistry, and nanoscience. Describing the influence of geometric and energetic fluctuations on ET allows us to address a rich array of mechanistic and kinetic puzzles. How strongly is a proteins fold imprinted on the ET kinetics, and might thermal fluctuations wash out signatures of structure? What is the influence of thermal fluctuations on ET kinetics beyond averaging of the tunneling barrier structure? Do electronic coupling mechanisms change as donor and acceptor reposition in a protein, and what are the consequences for the ET kinetics? Do fluctuations access minority species that dominate tunneling? Can energy exchanges between the electron and bridge vibrations generate vibronic signatures that label some of the D-to-A pathways traversed by the electron, thus eliminating unmarked pathways that would otherwise contribute to the DA coupling (as in other which way or double-slit experiments)? Might medium fluctuations drive tunneling-hopping mechanistic transitions? How does the donor-state preparation, in particular, its polarization toward the acceptor and its momentum characteristics (which may introduce complex rather than pure real relationships among donor orbital amplitudes), influence the electronic dynamics? In this Account, we describe our recent studies that address puzzling questions of how conformational distributions, excited-state polarization, and electronic and nuclear dynamical effects influence ET in macromolecules. Indeed, conformational and dynamical effects arise in all transport regimes, including the tunneling, resonant transport, and hopping regimes. Importantly, these effects can induce switching among ET mechanisms.

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.

Optimizing Single-Molecule Conductivity of Conjugated Organic Oligomers with Carbodithioate Linkers

In molecular electronics, the linker group, which attaches the functional molecular core to the electrode, plays a crucial role in determining the overall conductivity of the molecular junction. While much focus has been placed on optimizing molecular core conductivity, there have been relatively few attempts at designing optimal linker groups to metallic or semiconducting electrodes. The vast majority of molecular electronic studies use thiol linker groups; work probing alternative amine linker systems has only recently been explored. Here, we probe single-molecule conductances in phenylene-ethynylene molecules terminated with thiol and carbodithioate linkers, experimentally using STM break-junction methods and theoretically using a nonequilibrium Greens function approach. Experimental studies demonstrate that the carbodithioate linker augments electronic coupling to the metal electrode and lowers the effective barrier for charge transport relative to the conventional thiol linker, thus enhancing the conductance of the linker-phenylene-ethynylene-linker unit; these data underscore that phenylene-ethynylene-based structures are more highly conductive than originally appreciated in molecular electronics applications. The theoretical analysis shows that the nature of sulfur hybridization in these species is responsible for the order-of-magnitude increased conductance in carbodithioate-terminated systems relative to identical conjugated structures that feature classic thiol linkers, independent of the mechanism of charge transport. Interestingly, in these systems, the tunneling current is not dominated by the frontier molecular orbitals. While barriers >k(B)T to produce the low beta values seen in our experiments. Taken together, these experimental and theoretical studies indicate a promising role for carbodithioate-based connectivity in molecular-scale electronics applications involving metallic and semiconducting electrodes.

Evidence for a Near-Resonant Charge Transfer Mechanism for Double-Stranded Peptide Nucleic Acid

We present evidence for a near-resonant mechanism of charge transfer in short peptide nucleic acid (PNA) duplexes obtained through electrochemical, STM break junction (STM-BJ), and computational studies. A seven base pair (7-bp) PNA duplex with the sequence (TA)(3)-(XY)-(TA)(3) was studied, in which XY is a complementary nucleobase pair. The experiments showed that the heterogeneous charge transfer rate constant (k(0)) and the single-molecule conductance (σ) correlate with the oxidation potential of the purine base in the XY base pair. The electrochemical measurements showed that the enhancement of k(0) is independent, within experimental error, of which of the two PNA strands contains the purine base of the XY base pair. 7-bp PNA duplexes with one or two GC base pairs had similar measured k(0) and conductance values. While a simple superexchange model, previously used to rationalize charge transfer in single stranded PNA (Paul et al. J. Am. Chem. Soc. 2009, 131, 6498-6507), describes some of the experimental observations, the model does not explain the absence of an enhancement in the experimental k(0) and σ upon increasing the G content in the duplexes from one to two. Moreover, the superexchange model is not consistent with other studies (Paul et al. J. Phys. Chem. B 2010, 114, 14140), that showed a hopping charge transport mechanism is likely important for PNA duplexes longer than seven base pairs. A quantitative computational analysis shows that a near-resonant charge transfer regime, wherein a mix of superexchange and hopping mechanisms are expected to coexist, can rationalize all of the experimental results.

Role of Nucleobase Energetics and Nucleobase Interactions in Single-Stranded Peptide Nucleic Acid Charge Transfer

Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven nucleotides (TTTXTTT), a C-terminus cysteine, and an N-terminus ferrocene redox group were formed on gold electrodes. The PNA monomer group (X) was selected to be either cytosine (C), thymine (T), adenine (A), guanine (G), or a methyl group (Bk). The charge transfer rate through the oligonucleotides was found to correlate with the oxidation potential of X. Kinetic measurements and computational studies of the ss-PNA fragments show that a nucleobase mediated charge transport mechanism in the deep tunneling superexchange regime can explain the observed dependence of the kinetics of charge transfer on the PNA sequence. Theoretical analysis suggests that the charge transport is dominantly hole-mediated and takes place through the filled bridge orbitals. The strongest contribution to conductance comes from the highest filled orbitals (HOMO, HOMO-1, and HOMO-2) of individual bases, with a rapid drop off in contributions from lower lying filled orbitals. Our studies further suggest that the linear correlation observed between the experimental charge transfer rates and the oxidation potential of base X arises from weak average interbase couplings and similar stacking geometries for the four TTTXTTT systems.

The Single-Molecule Conductance and Electrochemical Electron-Transfer Rate Are Related by a Power Law

This study examines quantitative correlations between molecular conductances and standard electrochemical rate constants for alkanes and peptide nucleic acid (PNA) oligomers as a function of the length, structure, and charge transport mechanism. The experimental data show a power-law relationship between conductances and charge transfer rates within a given class of molecules with the same bridge chemistry, and a lack of correlation when a more diverse group of molecules is compared, in contrast with some theoretical predictions. Surprisingly, the PNA duplexes exhibit the lowest charge-transfer rates and the highest molecular conductances. The nonlinear rate-conductance relationships for structures with the same bridging chemistries are attributed to differences in the charge-mediation characteristics of the molecular bridge, energy barrier shifts and electronic dephasing, in the two different experimental settings.

Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes

Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.

Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus.

We study the effect of the oxidative lesion 8‐oxoguanine (8oxoG) on the preorganization of the active site for DNA replication in the closed (active) state of the Bacillus fragment (BF), a Klenow analog from Bacillus stearothermophilus. Our molecular dynamics and free energy simulations of explicitly solvated model ternary complexes of BF bound to correct dCTP/incorrect dATP opposite guanine (G) and 8oxoG bases in DNA suggest that the lesion introduces structural and energetic changes at the catalytic site to favor dATP insertion. Despite the formation of a stable Watson‐Crick pairing in the 8oxoG:dCTP system, the catalytic geometry is severely distorted to possibly slow down catalysis. Indeed, our calculated free energy landscapes associated with active site preorganization suggest additional barriers to assemble an efficient catalytic site, which need to be overcome during dCTP incorporation opposite 8oxoG relative to that opposite undamaged G. In contrast, the catalytic geometry for the Hoogsteen pairing in the 8oxoG:dATP system is highly organized and poised for efficient nucleotide incorporation via the “two‐metal‐ion” catalyzed phosphoryl transfer mechanism. However, the free energy calculations suggest that the catalytic geometry during dATP incorporation opposite 8oxoG is considerably less plastic than that during dCTP incorporation opposite G despite a very similar, well organized catalytic site for both systems. A correlation analysis of the dynamics trajectories suggests the presence of significant coupling between motions of the polymerase fingers and the primary distance for nucleophilic attack (i.e., between the terminal primer O3′ and the dNTP Pα. atoms) during correct dCTP incorporation opposite undamaged G. This coupling is shown to be disrupted during nucleotide incorporation by the polymerase with oxidatively damaged DNA/dNTP substrates. We also suggest that the lesion affects DNA interactions with key polymerase residues, thereby affecting the enzymes ability to discriminate against non‐complementary DNA/dNTP substrates. Taken together, our results provide a unified structural, energetic, and dynamic platform to rationalize experimentally observed relative nucleotide incorporation rates for correct dCTP/incorrect dATP insertion opposite an undamaged/oxidatively damaged template G by BF. Proteins 2008.

Computational delineation of the catalytic step of a high-fidelity DNA polymerase

The Bacillus fragment, belonging to a class of high‐fidelity polymerases, demonstrates high processivity (adding ∼115 bases per DNA binding event) and exceptional accuracy (1 error in 106 nucleotide incorporations) during DNA replication. We present analysis of structural rearrangements and energetics just before and during the chemical step (phosphodiester bond formation) using a combination of classical molecular dynamics, mixed quantum mechanics molecular mechanics simulations, and free energy computations. We find that the reaction is associative, proceeding via the two‐metal‐ion mechanism, and requiring the proton on the terminal primer O3′ to transfer to the pyrophosphate tail of the incoming nucleotide before the formation of the pentacovalent transition state. Different protonation states for key active site residues direct the system to alternative pathways of catalysis and we estimate a free energy barrier of ∼12 kcal/mol for the chemical step. We propose that the protonation of a highly conserved catalytic aspartic acid residue is essential for the high processivity demonstrated by the enzyme and suggest that global motions could be part of the reaction free energy landscape.

Molecular electronics: general discussion

Fred Wudl answered: Thank you for the question, Prof. Lemmer. Those days were about 20 or more years before the advent of “nano”, and the materials available were very tiny, brittle crystals. Prof. Qichun Zhang from NTU in Singapore has been relatively successful in obtaining nanoscale objects of TCNQ charge transfer salts. The heyday of charge transfer salts was also before the introduction of the important concept of supramolecular control, the way that Prof. Perepichkas paper shows it.