Hapticity-dependent charge transport through carbodithioate-terminated [5,15-bis(phenylethynyl)porphinato]zinc(II) complexes in metal-molecule-metal junctions.

Single molecule break junction experiments and nonequilibrium Green's function calculations using density functional theory (NEGF-DFT) of carbodithioate- and thiol-terminated [5,15-bis(phenylethynyl)-10,20-diarylporphinato]zinc(II) complexes reveal the impact of the electrode-linker coordination mode on charge transport at the single-molecule level. Replacement of thiolate (-S(-)) by the carbodithioate (-CS2(-)) anchoring motif leads to an order of magnitude increase of single molecule conductance. In contrast to thiolate-terminated structures, metal-molecule-metal junctions that exploit the carbodithioate linker manifest three distinct conductance values. We hypothesize that the magnitudes of these conductances depend upon carbodithoate linker hapticity with measured conductances across Au-[5,15-bis(4'-(dithiocarboxylate)phenylethynyl)-10,20-diarylporphinato]zinc(II)-Au junctions the greatest when both anchoring groups attach to the metal surface in a bidentate fashion. We support this hypothesis with NEGF-DFT calculations, which consider the electron transport properties for specific binding geometries. These results provide new insights into the origin of molecule-to-molecule conductance heterogeneity in molecular charge transport measurements and the factors that optimize electrode-molecule-electrode electronic coupling and maximize the conductance for charge transport.

Single-molecule sensing of environmental pH--an STM break junction and NEGF-DFT approach.

Sensors play a significant role in the detection of toxic species and explosives, and in the remote control of chemical processes. In this work, we report a single-molecule-based pH switch/sensor that exploits the sensitivity of dye molecules to environmental pH to build metal-molecule-metal (m-M-m) devices using the scanning tunneling microscopy (STM) break junction technique. Dyes undergo pH-induced electronic modulation due to reversible structural transformation between a conjugated and a nonconjugated form, resulting in a change in the HOMO-LUMO gap. The dye-mediated m-M-m devices react to environmental pH with a high on/off ratio (≈100:1) of device conductivity. Density functional theory (DFT) calculations, carried out under the non-equilibrium Green's function (NEGF) framework, model charge transport through these molecules in the two possible forms and confirm that the HOMO-LUMO gap of dyes is nearly twice as large in the nonconjugated form as in the conjugated form.

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.

TiO(2)/LiCl-based nanostructured thin film for humidity sensor applications.

A simple and straightforward method of depositing nanostructured thin films, based on LiCl-doped TiO(2), on glass and LiNbO(3) sensor substrates is demonstrated. A spin-coating technique is employed to transfer a polymer-assisted precursor solution onto substrate surfaces, followed by annealing at 520°C to remove organic components and drive nanostructure formation. The sensor material obtained consists of coin-shaped nanoparticles several hundred nanometers in diameter and less than 50 nm thick. The average thickness of the film was estimated by atomic force microscopy (AFM) to be 140 nm. Humidity sensing properties of the nanostructured material and sensor response times were studied using conductometric and surface acoustic wave (SAW) sensor techniques, revealing reversible signals with good reproducibility and fast response times of about 0.75 s. The applicability of this nanostructured film for construction of rapid humidity sensors was demonstrated. Compared with known complex and expensive methods of synthesizing sophisticated nanostructures for sensor applications, such as physical vapor deposition (PVD) and chemical vapor deposition (CVD), this work presents a relatively simple and inexpensive technique to produce SAW humidity sensor devices with competitive performance characteristics.

Photoinduced electron transfer occurs between 2-aminopurine and the DNA nucleic acid monophosphates: results from cyclic voltammetry and fluorescence quenching.

2-Aminopurine (2AP) is a fluorescent adenine analogue that is useful in part because its substantial fluorescence quantum yield is sensitive to base stacking with native bases in ss- and ds-DNA. However, the degree of quenching is sequence dependent and the mechanism of quenching is still a matter of some debate. Here we show that the most likely quenching mechanism in aqueous solution involves photoinduced electron transfer (PET), as revealed by cyclic voltammetry (CV) performed in aprotic organic solvents. These potentials were used with spectroscopic data to obtain excited-state reduction and oxidation potentials. Stern-Volmer (S-V) experiments using the native base monophosphate nucleotides (NMPs) rGMP, rAMP, rCMP, and dTMP were performed in aqueous solution to obtain quenching rate constants kq. The results suggest that 2AP* can act as either an electron donor or an electron acceptor depending on the particular NMP but that PET proceeds for all NMPs tested.

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 Green's 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.

Differential fluorescence quenching of fluorescent nucleic acid base analogues by native nucleic acid monophosphates.

Fluorescent nucleic acid base analogues (FBAs) are used widely as probes of DNA and RNA structure and dynamics. Of increasing utility are the pteridone adenosine analogues (6MAP, DMAP) and pteridine guanosine analogues (3MI, 6MI). These FBAs (collectively referred to as PTERs) are useful, in part, because their fluorescence quantum yields, Phi(f), are modulated by base stacking with native bases (NBs), making them sensitive reporters of DNA structure. The quenching mechanism has been hypothesized to be photoinduced electron transfer following selective excitation of the FBA, but hard evidence for this has been lacking. The degree of quenching shows some dependence on the neighboring bases, but there has been no real determination as to whether FBA*:NB complexes satisfy the basic thermodynamic requirement for spontaneous PET: a negative free energy for the electron transfer reaction. Indeed, quenching may result from entirely different mechanisms. To address these questions, Stern-Volmer (S-V) experiments were performed using the native-base monophosphate nucleotides (NMPs) GMP, AMP, CMP, and dTMP in aqueous solutions as quenchers to obtain quenching rate constants, k(q). Cyclic voltammetry (CV) and optical absorption and emission data of the PTERS were obtained in aprotic organic solvents. These data were used to obtain excited-state redox potentials from which electron transfer free energies were derived using the Rehm-Weller equation. The reorganization energies for PET were obtained using the Scandola-Balzani equation, taking into account the free energy contribution due to water. 6MAP*, DMAP*, and 3MI* gave negative free energies between -0.1 and -0.2 eV and reorganization energies of about 0.13 eV. They all displayed ET activation energies below the accessible thermal energy (0.038 eV = 3/2k(B)T, where k(B) is Boltzmann's constant) for all NMPs with the exception of CMP, whose activation barrier was only about 35% higher (approximately 0.05 eV). Thus, we conclude that these PTERs act as electron acceptors and promote NMP oxidation. However, 6MI* had positive ET free energies for all NMPs with the exception of GMP (and then only for nucleobase oxidation). The magnitudes of these free energies (> or = 0.45 eV for AMP, CMP, and dTMP) suggest that 6MI* may not quenched by PET.

An STM study of the pH dependent redox activity of a two-dimensional hydrogen bonding porphyrin network at an electrochemical interface.

Studying electron transfer reactions of porphyrin molecules is important for a wide range of applications including biology, molecular devices, artificial photosynthesis, information storage, and fuel cells. It is known that porphyrins adsorbed in a self-assembled monolayer at an electrochemical interface may lose their electrochemical activity. However, the mechanism of the suppressed electrochemical activity is not clear. In this article, the electrochemical behavior of the two-dimensional network structures of 5,10,15,20-tetrakis(4-carboxylphenyl)-21H,23H-porphyrin (TCPP) molecules, formed via intermolecular hydrogen bonding on Au(111), was investigated by electrochemical scanning tunneling microscopy (EC-STM). Three types of domains, including a square network with molecules trapped inside, square packing, and hexagonal close-packing structures have been observed under various pH conditions. The difference in STM contrast between oxidized and reduced TCPP allows the slow electrochemical reduction of adsorbed TCPP to be visualized by STM. For the first time, the pH dependent reduction of porphyrins was imaged by EC-STM, revealing the mechanism of porphyrin slow reduction at electrochemical interfaces. TCPP reduction can be accelerated either by tuning the working electrode potential to a more negative value or by lowering the H(+) concentration. A redox reaction model was proposed based on the pH dependent reduction of TCPP to elucidate the fundamental aspects of porphyrin redox reactions.

Specificity and sensitivity of fluorescence labeling of surface species.

FLOSS (fluorescence labeling of surface species) enables one to identify and quantify very low concentrations of surface functional groups. Unlike most surface analytical techniques, FLOSS can provide absolute, as well as relative, surface coverage determination. However, as with any other surface derivatization technique, FLOSS provides a lower limit to surface coverage. The specificity of FLOSS for a particular functional group is the key to this application. In one FLOSS protocol, amine-modified dyes are used to label surface aldehyde groups. However, amine-modified dyes, in principle, can bind to both aldehyde and carboxyl groups, limiting specificity. In this paper, we report that the FLOSS protocol devised results in less than 0.5 % of the carboxyl-modified dyes binding to the surface amine groups. Therefore, the presence of carboxyl groups on the surface should have a limited effect on the detection of aldehyde groups by amine-modified dye. Quenching of fluorescence can potentially affect quantitative measurements. To address this issue, the densities of surface functional groups of CHO-, NH2-, and epoxy-coated glass surfaces were quantified using FLOSS and compared to surface densities estimated by other methods. The FLOSS technique was extended to glass surfaces by using visible absorbing and emitting dyes. The lower detection limit is on the order of 10(9) groups/cm2.