Making a molecular wire: charge and spin transport through para-phenylene oligomers

Functional molecular wires are essential for the development of molecular electronics. Charge transport through molecules occurs primarily by means of two mechanisms, coherent superexchange and incoherent charge hopping. Rates of charge transport through molecules in which superexchange dominates decrease approximately exponentially with distance, which precludes using these molecules as effective molecular wires. In contrast, charge transport rates through molecules in which incoherent charge hopping prevails should display nearly distance independent, wirelike behavior. We are now able to determine how each mechanism contributes to the overall charge transport characteristics of a donor-bridge-acceptor (D-B-A) system, where D = phenothiazine (PTZ), B = p-oligophenylene, and A = perylene-3,4:9,10-bis(dicarboximide) (PDI), by measuring the interaction between two unpaired spins within the system's charge separated state via magnetic field effects on the yield of radical pair and triplet recombination product.     

M-DNA: a self-assembling molecular wire for nanoelectronics and biosensing.

M-DNA is a complex between divalent metal ions such as Zn2+ and duplex DNA which forms at pH 8.5. Unlike B-DNA, M-DNA does not bind ethidium so that M-DNA formation can be monitored conveniently by an ethidium fluorescence assay. M-DNA was shown to be a better conductor than B-DNA by fluorometric measurements of electron transport in donor-acceptor labelled duplexes; by direct conductivity measurements of M-DNA bound between gold electrodes and by cyclic voltammetric studies on ferrocene labelled duplexes attached to gold microelectrodes. As is the case with B-DNA, M-DNA can self-assemble into a variety of structures and is anticipated to find widespread use in nanoelectronics and biosensing.     

Ferrocene-1,1'-dithiol as molecular wire between Ag electrodes: the role of surface defects

The interaction of ferrocene-1,1(')-dithiol (FDT) with two parallel Ag(111) surfaces has been theoretically studied at density-functional level. The effect of surface defects on the energetic and electronic structure was investigated. The electronic transport properties are studied with the nonequilibrium Green's function approach. The adsorption geometry has a strong effect on the electronic levels and conductivity. The presence of point defects strongly enhances the molecule-surface interaction but has a surprisingly small effect on the density of states near the Fermi energy. The FDT-surface bond is particularly strong near terraces or steps and leads to significant shifts of the molecular orbitals relative to the gas phase. For all considered defect types except the single adatom the electronic conductivity through the FDT molecule is decreased compared to adsorption on perfect surfaces.     

First-principles investigation of the asymmetric contact effect on current-voltage characteristics of a molecular device

The properties of electronic transport in an electronic device composed of a spatially symmetric phenyldithiolate molecule sandwiched between two gold electrodes with asymmetric contact are investigated by the first-principles study. It is found that the I-V and G-V characteristics of a device show significant asymmetry and the magnitudes of current and conductance depend remarkably on the variation of molecule-metal distance at one of the two contacts. Namely, an asymmetric contact would lead to the weak rectifying effects on the current-voltage characteristics of a molecular device. We also calculate self-consistently other microscopic quantities such as the local density of states, the total density of states, and the distribution of charges in the asymmetric molecular models under the applied bias. The results show that the highest-occupied molecular orbital (HOMO) is responsible for the resonant tunneling and the shifting of the HOMO due to the charging of the device under the bias voltage is the intrinsic origin of asymmetric I(G)-V characteristics.     

Charge transport through self-assembled monolayers of compounds of interest in molecular electronics

The electrical properties of self-assembled monolayers (SAMs) on metal surfaces have been explored for a series of molecules to address the relation between the behavior of a molecule and its structure. We probed interfacial electron transfer processes, particularly those involving unoccupied states, of SAMs of thiolates or arylates on Au by using shear force-based scanning probe microscopy (SPM) combined with current-voltage (i-V) and current-distance (i-d) measurements. The i-V curves of hexadecanethiol in the low bias regime were symmetric around 0 V and the current increased exponentially with V at high bias voltage. Different than hexadecanethiol, reversible peak-shaped i-V characteristics were obtained for most of the nitro-based oligo(phenylene ethynylene) SAMs studied here, indicating that part of the conduction mechanism of these junctions involved resonance tunneling. These reversible peaked i-V curves, often described as a negative differential resistance (NDR) effect of the junction, can be used to define a threshold tip bias, V(TH), for resonant conduction. We also found that for all of the SAMs studied here, the current decreased with increasing distance, d, between tip and substrate. The attenuation factor beta of hexadecanethiol was high, ranging from 1.3 to 1.4 A(-1), and was nearly independent of the tip bias. The beta-values for nitro-based molecules were low and depended strongly on the tip bias, ranging from 0.15 A(-1) for tetranitro oligo(phenylene ethynylene) thiol, VII, to 0.50 A(-1) for dinitro oligo(phenylene) thiol, VI, at a -3.0 V tip bias. Both the V(TH) and beta values of these nitro-based SAMs were also strongly dependent on the structures of the molecules, e.g. the number of electroactive substituent groups on the central benzene, the molecular wire backbone, the anchoring linkage, and the headgroup. We also observed charge storage on nitro-based molecules. For a SAM of the dintro compound, V, approximately 25% of charge collected in the negative scan is stored in the molecules and can be collected at positive voltages. A possible mechanism involving lateral electron hopping is proposed to explain this phenomenon.     

Inelastic insights for molecular tunneling pathways: bypassing the terminal groups

As an example of the use of inelastic transport to deduce structure in molecular transport junctions, we compute the orientation dependence of the Inelastic Electron Tunneling (IET) spectrum of the 1-pentane monothiolate. We find that upon increasing the tilting angle of the molecule with respect to the normal to the electrode the spectrum changes as the intensity of some vibrations is enhanced. These differences occur because for higher tilting angles the tunneling path that bypasses the terminal group grows in importance. IETS can therefore be used to establish the molecular orientation in junctions terminating with alkyl chains and to investigate experimentally the relative importance of the available tunneling paths.     

Theoretical study of a conjugated aromatic molecular wire

In this study, an organic conjugated molecule, 4,4′-[ethane-1,2-diylidenedi(nitrilo)] dibenzenthiol designed and is proposed as a molecular wire. Structural and electronic responses of this aromatic molecular wire to the static electric field with intensities −1.6 × 10⁻² to +1.6 × 10⁻² a.u., are studied using the DFT-B3LYP/6-31G* level of theory. Natural bond orbital atomic charge analysis shows that the imposition of static external electric field induces polarization—localization of charge on the two ends of molecule, especially on considered terminal contact sulfur atoms. The frontier molecular orbitals (MOs) energy levels including the highest occupied MO (HOMO) and the lowest unoccupied MO (LUMO) and the HOMO–LUMO gap (HLG) values are modified by the static electric field as well. The electric dipole moment and polarizability of the proposed molecular wire under the studied electric field strengths are considerably increased. The current–voltage characteristic curve is estimated for the proposed molecular wire.     

Synthesis of a head-to-tail-type cyclodextrin-based insulated molecular wire

We developed a new method for synthesizing an organic-soluble insulated molecular wire (IMW) using permethylated cyclodextrin (PMCD). The IMW obtained using this method is highly soluble in a variety of organic solvents and has a high covering ratio, regioregularity, rigidity, photoluminescence efficiency, and interchain hole mobility.     

Dithiocarbamate anchoring in molecular wire junctions: a first principles study

Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups.     

Polyether-bridged sexithiophene as a complexation-gated molecular wire for intramolecular photoinduced electron transfer

The porphyrin-sexithiophene-fullerene triad 2, where the two central thiophene units of the sexithiophene spacer are bridged with a crown-ether-like polyether chain, undergoes efficient intramolecular electron transfer from the photoexcited porphyrin moiety to the fullerene through the sexithiophene. However, complexation with a sodium cation in the crown ether ring causes complete suppression of electron transfer as a result of a drastic conformational change of the sexithiophene backbone. Furthermore, decomplexation resumes the photoinduced electron transfer. This on/off switching phenomenon indicates that the polyether-bridged sexithiophene can function as a complexation-gated molecular wire.     

Effect of electron-phonon coupling on the conductance of a one-dimensional molecular wire

The effect of inelastic scattering, particularly that of the electron-phonon interactions, on the current-voltage characteristics of a one-dimensional tight-binding molecular wire has been investigated. The wire has been modeled using the Su-Schreiffer-Heeger Hamiltonian and we compute the current using the Landauer's scattering formalism. Our calculations show that the presence of strong electron-lattice coupling in the wire can induce regions of negative differential resistance (NDR) in the I-V curves. The reasons for this can be traced back to the quasidegeneracy in few of the low-energy molecular levels in the presence of electron-phonon coupling and an external applied bias. The molecular levels become highly delocalized at the critical bias at which the NDR is seen, corresponding to the vanishing of the electron-phonon coupling with equal bond lengths.     

Electron hopping through the 15 A triple tryptophan molecular wire in DNA photolyase occurs within 30 ps

DNA photolyase is a photoactive flavoprotein that contains three tryptophan residues between the FAD cofactor and the protein surface, the solvent-exposed Trp being located 14.8 A from the flavin. Photoreduction of the neutral radical FADH. form to the catalytically active FADH- form occurs via electron transfer through this chain. The first step in this chain takes 30 ps, the second less than 4 ps. Using a combination of site-directed mutagenesis and femtosecond polarization spectroscopy to discriminate the spectroscopically indistinguishable Trp residues, we show that the third step occurs in less than 30 ps. This implies that the first photoreduction step is rate limiting and that the Trp chain effectively acts as molecular "wire" ensuring rapid and directed long-range charge translocation across the protein. This finding is important for the functioning of the large class of cryptochrome blue-light receptors, where the Trp chain is conserved. In DNA photolyase we make use of the natural photoactivation of the process, but more generally chains of aromatic amino acids may allow very fast long-range electron transfer also in nonphotoactive proteins.     

Investigation of the phase behavior of an embedded charge protein model through molecular simulation

The phase behavior of an embedded-charge model for lysozyme developed by Carlsson and co-workers (J. Phys. Chem. B 2001, 105, 9040) is investigated using grand canonical transition matrix Monte Carlo simulation. Within this model, protein-protein interactions are approximated through a combination of hard-sphere repulsion, isotropic hydrophobic attraction, and screened electrostatic interactions through a series of embedded point charges located at the positions of charged amino acid groups within lysozyme. Liquid-liquid phase diagrams are constructed for a wide range of solution conditions and compared with experimental data. Our results indicate that the model is generally capable of describing qualitative trends in the evolution of protein phase behavior with variation of pH and ionic strength. From a quantitative perspective, model estimates for both the change in critical temperature with variation of the solution conditions and the critical concentration do not agree with experimental results. We find the width of model coexistence curves to be independent of solution conditions and narrow relative to experimentally obtained phase envelopes. Connections between the value of the second virial coefficient evaluated at the critical temperature and the location of the liquid-liquid phase envelope are also examined.     

The role of molecular shape in bilayer elasticity and phase behavior

A previously developed molecular level model for lipid bilayers [G. Brannigan and F. L. H. Brown, J. Chem. Phys. 120, 1059 (2004)] is extended to allow for variations in lipid length and simulations under constant surface tension conditions. The dependence of membrane elasticity on bilayer thickness is obtained by adjusting lipid length at constant temperature and surface tension. Additionally, bilayer fluidity at various lipid lengths is quantified by analysis of a length versus temperature phase diagram at vanishing tension. Regions of solid, gel-like (hexatic) and fluid bilayer behavior are established by identification of phase boundaries. The main melting transition is found to be density driven; the melting temperature scales inversely with lipid length since thermal expansion increases with lipid aspect ratio.     

Polymer-nanoparticle interfacial behavior revisited: a molecular dynamics study

By tuning the polymer-filler interaction, filler size and filler loading, we use a coarse-grained model-based molecular dynamics simulation to study the polymer-filler interfacial structural (the orientations at the bond, segment and chain length scales, chain size and conformation), dynamic and stress-strain properties. Simulated results indicate that the interfacial region is composed of partial segments of different polymer chains, which is consistent with the experimental results presented by Chen et al. (Macromolecules, 2010, 43, 1076). Moreover, it is found that the interfacial region is within one single chain size (R(g)) range, irrespective of the polymer-filler interaction and the filler size, beyond which the bulk behavior appears. In the interfacial region, the orientation and dynamic behaviors are induced by the interfacial enthalpy, while the size and conformation of polymer chains near the filler are controlled by the configurational entropy. In the case of strong polymer-filler interaction (equivalent to the hydrogen bond), the innerest adsorbed polymer segments still undergo adsorption-desorption process, the transport of chain mass center in the interfacial region exhibits away from the glassy behavior, and no plastic-like yielding point appears in the stress-strain curve, which indicates that although the mobility of interfacial polymer chains is restricted, there exist no "polymer glassy layers" surrounding the filler. In addition, it is evidenced that the filler particle prefers selectively adsorbing the long polymer chains for attractive polymer-filler interaction, validating the experimental explanation of the change of the bound rubber (BR). In short, this work provides important information for further experimental and simulation studies of polymer-nanoparticle interfacial behavior.     

A new type of insulated molecular wire: a rotaxane derived from a metal-capped conjugated tetrayne

The platinum butadiynyl complex trans-(C(6)F(5))(p-tol(3)P)(2)Pt(C≡C)(2)H and a CuI adduct of a 1,10-phenanthroline based 33-membered macrocycle react in the presence of K(2)CO(3) and I(2) or O(2) to give a rotaxane (ca. 9%) in which the macrocycle is threaded by the sp carbon chain of trans,trans-(C(6)F(5))(p-tol(3)P)(2)Pt(C≡C)(4)Pt(Pp-tol(3))(2)(C(6)F(5)). The crystal structure and macrocycle/axle electronic interactions are analyzed in detail.     

Molecular-shape selectivity by molecular gel-forming compounds: bioactive and shape-constrained isomers through the integration and orientation of weak interaction sites

A molecular gel system was assembled on carrier particles and the integrated effect of weak interaction sites enabled highly efficient separation of the bioactive and shape-constrained isomers of tocopherols, β-carotene, and polycyclic aromatic hydrocarbons (PAHs) by multiple interaction mechanisms.     

Tunable phase‐separation behavior of thermoresponsive polyampholytes through molecular design

Here, we report that carboxylated poly‐l ‐lysine, a polyampholyte, shows lower critical solution temperature (LCST)‐type temperature‐responsive liquid–liquid phase separation and coacervate formation in aqueous solutions. The phase‐separation temperature of polyampholytes is strongly affected by the polymer concentration, balance between the carboxyl and amino groups, hydrophobicity of the side chain, and NaCl concentration in the solution. We concluded that the phase separation was caused by both electrostatic interactions between the carboxyl and amino groups and intermolecular hydrophobic interactions. The addition of NaCl weakened the electrostatic interactions, causing the two phases to remix. The introduction of the hydrophobic moiety decreased the phase‐separation temperature by making the molecular interactions stronger. Finally, temperature‐responsive hydrogels were prepared from the polyampholytes to explore their applicability as biomaterials and in drug delivery systems. The fine‐tuning of the phase‐separation temperature of poly‐l ‐lysine‐based polyampholytes through molecular design should open new avenues for their use in precisely controlled biomedical applications. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 876–884     

Transport behavior of oxygen and nitrogen through organasilicon-containing polystyrenes by molecular simulation

Molecular dynamics (MD) simulations have been used to study the transport properties of oxygen and nitrogen in the para-substituted polystyrenes which possess one to four Si atoms in each substituent. The Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to construct the polymers. Diffusion coefficients were obtained from molecular dynamics (NVT ensemble) with up to 3 ns simulation times. After molecular dynamic simulation, the trajectories of the small molecules in the polymer matrix were obtained. Then diffusion coefficients have been calculated from the Einstein relationship revealing a considerable agreement between the simulated and the experimental data. And solubility coefficients have been calculated by the Grand Canonical Monte Carlo (GCMC) method. The solubility of oxygen increased with increasing Si content in the polymer membrane. The para-substituted polystyrenes with a branched substituent at the alpha-position showed higher permeability than those of the nonbranched ones. The higher the glass transition temperature (T(g)) of the membrane, the larger the diffusion coefficients of oxygen and nitrogen obtained.