The Effect of Oxygen Heteroatoms on the Single Molecule Conductance of Saturated Chains

Single molecule conductance measurements on alkanedithiols and alkoxydithiols (dithiolated oligoethers) were performed using the STM-controlled break junction method in order to ascertain how the oxygen heteroatoms in saturated linear chains impact the molecular conductance. The experimental results show that the difference in conductance increases with chain length, over the range studied. Comparisons with electronic structure calculations and previous work on alkanes indicate that the conductance of the oligoethers is lower than that of alkane chains with the same length. Electronic structure calculations allow the difference in the conductance of these two families of molecules to be traced to differences in the spatial distribution of the molecular orbitals that contribute most to the conductance. A pathway analysis of the electronic coupling through the chain is used to explain how the difference in conductance between the alkane and oligoether molecules depends on the chain length

Molecular Conductance of Nicked Nucleic Acid Duplexes

This work investigates how the conductance of a nucleic acid duplex with a “nick” in its backbone compares with that of a duplex with a fully covalent backbone. Statistical analyses of the single-molecule conductance properties reveal that molecular junctions with a nicked duplex have an average conductance close to that found for non-nicked structures but exhibit greater variability in the molecular conductance. This effect is shown for both DNA homoduplexes and DNA/PNA heteroduplexes, with the heteroduplexes showing a greater average molecular conductance and a smaller degree of variability. The average molecular conductance of the heteroduplexes is also shown to be affected by their PNA content; the conductance of duplexes increases as the ratio of PNA to DNA increases. These observations suggest that the charge-transfer properties of nucleic acid-based assemblies can support complex functions

Luminescence Quenching by Photoinduced Charge Transfer between Metal Complexes in Peptide Nucleic Acids

A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru­(Bpy)₃]²⁺ donor to a bis­(8-hydroxyquinolinate)₂ copper [CuQ₂] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru­(Bpy)₃]^2+* donor is quenched by electron transfer to the [CuQ₂] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru­(Bpy)₃]²⁺ can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru­(Bpy)₃]^2+* is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates

A Three-Step Kinetic Model for Electrochemical Charge Transfer in the Hopping Regime

Single-step nonadiabatic electron tunneling models are widely used to analyze electrochemical rates through self-assembled monolayer films (SAMs). For some systems, such as nucleic acids, long-range charge transfer can occur in a “hopping” regime that involves multiple charge transfer events and intermediate states. This report describes a three-step kinetic scheme to model charge transfer in this regime. Some of the features of the three-step model are probed experimentally by changing the chemical composition of the SAM. This work uses the three-step model and a temperature dependence of the charge transfer rate to extract the charge injection barrier for a SAM composed of a 10-mer peptide nucleic acid that operates in the hopping regime

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

Charge Transfer through Modified Peptide Nucleic Acids

We studied the charge transfer properties of bipyridine-modified peptide nucleic acid (PNA) in the absence and presence of Zn­(II). Characterization of the PNA in solution showed that Zn­(II) interacts with the bipyridine ligands, but the stability of the duplexes was not affected significantly by the binding of Zn­(II). The charge transfer properties of these molecules were examined by electrochemistry for self-assembled monolayers of ferrocene-terminated PNAs and by conductive probe atomic force microscopy for cysteine-terminated PNAs. Both electrochemical and single molecular studies showed that the bipyridine modification and Zn­(II) binding do not affect significantly the charge transfer of the PNA duplexes

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