Conductance and configuration of molecular gold-water-gold junctions under electric fields.

Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.

Charge splitters and charge transport junctions based on guanine quadruplexes.

Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.

Dynamics of charged excitons in electronically and morphologically homogeneous single-walled carbon nanotubes.

The trion, a three-body charge-exciton bound state, offers unique opportunities to simultaneously manipulate charge, spin, and excitation in one-dimensional single-walled carbon nanotubes (SWNTs) at room temperature. Effective exploitation of trion quasi-particles requires fundamental insight into their creation and decay dynamics. Such knowledge, however, remains elusive for SWNT trion states, due to the electronic and morphological heterogeneity of commonly interrogated SWNT samples, and the fact that transient spectroscopic signals uniquely associated with the trion state have not been identified. Here, we prepare length-sorted SWNTs and precisely control charge-carrier-doping densities to determine trion dynamics using femtosecond pump-probe spectroscopy. Identification of the trion transient absorptive hallmark enables us to demonstrate that trions (i) derive from a precursor excitonic state, (ii) are produced via migration of excitons to stationary hole-polaron sites, and (iii) decay in a first-order manner. Importantly, under appropriate carrier-doping densities, exciton-to-trion conversion in SWNTs can approach 100% at ambient temperature. Our findings open up possibilities for exploiting trions in SWNT optoelectronics, ranging from photovoltaics and photodetectors to spintronics.

Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes.

Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The molecular conductance was found to vary by 12 to 13 times with the change in backbone. Computational studies show that the molecular conductance differences between nucleic acids of different backbones correlate with differences in backbone structural flexibility. The molecular conductance was also measured for duplexes connected to the electrode through two different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker causes an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the electrical conductance with backbone composition are preserved. The highest molecular conductance value, 0.06G0, was measured for aeg-PNA duplexes with a base stack linker. These findings reveal an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.

Engineering nanometre-scale coherence in soft matter.

Electronic delocalization in redox-active polymers may be disrupted by the heterogeneity of the environment that surrounds each monomer. When the differences in monomer redox-potential induced by the environment are small (as compared with the monomer-monomer electronic interactions), delocalization persists. Here we show that guanine (G) runs in double-stranded DNA support delocalization over 4-5 guanine bases. The weak interaction between delocalized G blocks on opposite DNA strands is known to support partially coherent long-range charge transport. The molecular-resolution model developed here finds that the coherence among these G blocks follows an even-odd orbital-symmetry rule and predicts that weakening the interaction between G blocks exaggerates the resistance oscillations. These findings indicate how sequence can be exploited to change the balance between coherent and incoherent transport. The predictions are tested and confirmed using break-junction experiments. Thus, tailored orbital symmetry and structural fluctuations may be used to produce coherent transport with a length scale of multiple nanometres in soft-matter assemblies, a length scale comparable to that of small proteins.

Dexter energy transfer pathways.

Energy transfer with an associated spin change of the donor and acceptor, Dexter energy transfer, is critically important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Dexter transfer between chemically linked donors and acceptors is bridge mediated, presenting an enticing analogy with bridge-mediated electron and hole transfer. However, Dexter coupling pathways must convey both an electron and a hole from donor to acceptor, and this adds considerable richness to the mediation process. We dissect the bridge-mediated Dexter coupling mechanisms and formulate a theory for triplet energy transfer coupling pathways. Virtual donor-acceptor charge-transfer exciton intermediates dominate at shorter distances or higher tunneling energy gaps, whereas virtual intermediates with an electron and a hole both on the bridge (virtual bridge excitons) dominate for longer distances or lower energy gaps. The effects of virtual bridge excitons were neglected in earlier treatments. The two-particle pathway framework developed here shows how Dexter energy-transfer rates depend on donor, bridge, and acceptor energetics, as well as on orbital symmetry and quantum interference among pathways.

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system-environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (

Modeling of the Sub-Tg Relaxation Spectrum of Pd42.5Ni7.5Cu30P20 Metallic Glass.

We study the mechanical relaxation spectrum of Pd42.5Ni7.5Cu30P20 metallic glass. The effect of aging on the relaxation behavior is analyzed by measuring the internal friction during consecutive heating runs. The mechanical relaxation of the well-annealed glass state is modeled by fitting susceptibility functions to the primary and secondary relaxations of the system. The model is able to reproduce the mechanical relaxation spectrum below the glass transition temperature (sub-Tg region) in the frequency-temperature ranges relevant for the high temperature physical properties and forming ability of metallic glasses. The model reveals a relaxation spectrum composed by the overlapping of primary and secondary processes covering a wide domain of times but with a relatively narrow range of activation energies.

Conformationally Gated Charge Transfer in DNA Three-Way Junctions.

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.

Charge transfer in dynamical biosystems, or the treachery of (static) images.

CONSPECTUS: The image is not the thing. Just as a pipe rendered in an oil painting cannot be smoked, quantum mechanical coupling pathways rendered on LCDs do not convey electrons. The aim of this Account is to examine some of our recent discoveries regarding biological electron transfer (ET) and transport mechanisms that emerge when one moves beyond treacherous static views to dynamical frameworks. Studies over the last two decades introduced both atomistic detail and macromolecule dynamics to the description of biological ET. The first model to move beyond the structureless square-barrier tunneling description is the Pathway model, which predicts how protein secondary motifs and folding-induced through-bond and through-space tunneling gaps influence kinetics. Explicit electronic structure theory is applied routinely now to elucidate ET mechanisms, to capture pathway interferences, and to treat redox cofactor electronic structure effects. Importantly, structural sampling of proteins provides an understanding of how dynamics may change the mechanisms of biological ET, as ET rates are exponentially sensitive to structure. Does protein motion average out tunneling pathways? Do conformational fluctuations gate biological ET? Are transient multistate resonances produced by energy gap fluctuations? These questions are becoming accessible as the static view of biological ET recedes and dynamical viewpoints take center stage. This Account introduces ET reactions at the core of bioenergetics, summarizes our team's progress toward arriving at an atomistic-level description, examines how thermal fluctuations influence ET, presents metrics that characterize dynamical effects on ET, and discusses applications in very long (micrometer scale) bacterial nanowires. The persistence of structural effects on the ET rates in the face of thermal fluctuations is considered. Finally, the flickering resonance (FR) view of charge transfer is presented to examine how fluctuations control low-barrier transport among multiple groups in van der Waals contact. FR produces exponential distance dependence in the absence of tunneling; the exponential character emerges from the probability of matching multiple vibronically broadened electronic energies within a tolerance defined by the rms coupling among interacting groups. FR thus produces band like coherent transport on the nanometer length scale, enabled by conformational fluctuations. Taken as a whole, the emerging context for ET in dynamical biomolecules provides a robust framework to design and interpret the inner workings of bioenergetics from the molecular to the cellular scale and beyond, with applications in biomedicine, biocatalysis, and energy science.

Biological charge transfer via flickering resonance.

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 ≲ 15 Šdoes not necessarily prove a tunneling mechanism.

(Nd(1.5)Mg(0.5))Ni7-based compounds: structural and hydrogen storage properties.

The structural and hydrogen storage properties of (Nd(1.5)Mg(0.5))Ni(7)-based alloys (i.e., A(2)B(7)-type) with a coexistence of two structures (hexagonal 2H and rhombohedral 3R) are investigated in this study. In both 2H- and 3R-type A(2)B(7) structures, Mg atoms occupy Nd sites of Laves-type AB(2) subunits rather than those of AB(5) subunits because Mg substitution for Nd in the AB(2) subunits more significantly strengthens the ionic bond in the system. An increase in the A-atomic radius or the B-atomic radius stabilizes the 2H structure, but a decrease in the A-atomic radius or the B-atomic radius is favorable for formation of the 3R structure. The 2H-A(2)B(7) and 3R-A(2)B(7) phases in each alloy have quite similar equilibrium pressures upon hydrogen absorption and desorption, which show a linear relationship with the average subunit volume. The hydriding enthalpy for the (Nd(1.5)Mg(0.5))Ni(7) compound is about -29.4 kJ/mol H(2) and becomes more negative with partial substitution of La for Nd and Co/Cu for Ni but less negative with partial substitution of Y for Nd.

Strong up-conversion emissions in ZnO:Er3+, ZnO:Er(3+)-Yb3+ nanoparticles and their surface modified counterparts.

ZnO:Er(3+) and ZnO:Er(3+)-Yb(3+) nanoparticles (NPs) are fabricated by a sol-gel method, afterwards parts of which are separated and surface modified in Mo(NO(3))(3) solution. Analyses on phase and structure based on X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) techniques indicate that Er(3+) and Yb(3+) are incorporated into the ZnO lattice successfully and after Mo treatment, a thin layer of MoO(3) forms on the NPs surface, forming core/shell structures. Raman scattering spectra reveal the existence of ZnMoO(4) in the shell part. Visible up-conversion (UC) is observed in all the samples, with Mo treated and untreated ZnO:Er(3+) emitting dominant but relatively weak red light, corresponding to (4)F(9/2)-(4)I(15/2) transition of Er(3+). In Yb(3+)-codoping systems, the integral UC intensity is enhanced obviously though red emission still dominates the UC spectra before surface modification. In the Mo treated system, ZnO:Er(3+)-Yb(3+)/MoO(3), green emission is increased while the red is suppressed in comparison to ZnO:Er(3+)-Yb(3+), with the intensity of green to red ratio (GRR) changing from 0.25 to 8. A novel phenomenon is discovered that the green emissions in our samples involve three-photon processes.