Biomedical subjects

Mark A Ratner

Publications and source records attributed to Mark A Ratner.

At least 37 records · Page 2Linked to original sources

PubMed2006

Controlling the energy transfer in dipole chains.

Processing digital signals on the molecular scale is of great interest. In this paper, we discuss the control of pulselike energy propagation through one-dimensional arrays of dipoles. Three systems are explored. In the first system, a chain of coaxial dipoles is gated by two control dipoles. Changing the orientation of these control dipoles lets us control the transfer of energy in the chain. In the other two systems, the chain-branch system and the two-branch system, two chains are used as an input and the propagation of energy is controlled by sending one or two signals toward the junction. Both systems can operate as a logical AND port. Their geometrical configurations are key to a well-defined control and operation of the AND port.

Journal Article↗

PubMed2006

Molecular signatures in the transport properties of molecular wire junctions: what makes a junction "molecular"?

The simplest component of molecular electronics consists of a single-molecule transport junction: a molecule sandwiched between source and drain electrodes, with or without a third gate electrode. In this Concept article, we focus on how molecules control transport in metal-electrode molecular junctions, and where the molecular signatures are to be found. In the situation where the molecule is relatively short and the gap between injection energy and molecular eigenstates is large, transport occurs largely by elastic tunneling, stochastic switching is common, and the vibronic signature can be found using inelastic electron tunneling spectroscopy (IETS). As the energy gaps for injection become smaller, one begins to see stronger molecular signatures - these include Franck-Condon-like structures in the current/voltage characteristic and strong vibronic interactions, which can lead to hopping behavior at the polaron limit. Conformational changes induced by the strong electric field lead to another strong manifestation of the molecular nature of the junction. We overview some of this mechanistic landscape, focusing on significant effects of switching (both stochastic and controlled by the electric field) and of molecular vibronic coupling.

Crystallization↗

PubMed2006

Molecular transport junctions: Propensity rules for inelastic electron tunneling spectra.

We develop a series of propensity rules for interpreting inelastic electron tunneling (IET) spectra of single-molecule transport junctions. IETS has no selection rules, such as those seen in optical, infrared, and Raman spectra, because IETS features arise not from the field-dipole interaction characterizing these other spectroscopies but from vibronic modification of the electronic levels. Expansion of the Landauer-Imry formula in Taylor series in molecular normal coordinates gives a convenient, accurate perturbation-type formula for calculating both frequency and intensity of the IETS spectrum. Expansion in a Dyson-like form permits derivation of propensity rules, both symmetry-based and pathway-deduced, allowing correlation of structure and coupling geometry with the IETS spectrum. These propensity rules work very well for the calculated spectrum of five typical molecular bridges.

Computer Simulation↗

PubMed2005

Binding at molecule/gold transport interfaces. V. Comparison of different metals and molecular bridges.

The geometric and electronic structural properties of symmetric and asymmetric metal cluster-molecule-cluster' complexes have been explored. The metals include Au, Ag, Pd, and Al, and both benzenedithiol and the three isometric forms of dicyanobenzene are included as bridging molecules. Calculated properties such as cluster-molecule interface geometry, electronic state, degree of metal --> molecule charge transfer, metal-molecule mixing in the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy region, the HOMO-LUMO gap, cluster --> cluster' charge transfer as a function of external field strength and direction, and the form of the potential profile across such complexes have been examined. Attempts are made to correlate charge transport with the characteristics of the cluster-complex systems. Indications of rectification in complexes that are asymmetric in the molecule, clusters, and molecule-cluster interfaces are discussed. The results obtained here are only suggestive because of the limitations of the cluster-complex model as it relates to charge transport.

Journal Article↗

PubMed2005

Intermolecular charge transfer between heterocyclic oligomers. Effects of heteroatom and molecular packing on hopping transport in organic semiconductors.

For electron or hole transfer between neighboring conducting polymer strands or oligomers, the intrinsic charge-transfer rate is dictated by the charge-resonance integral and by the reorganization energy due to geometric relaxation. To explain conduction anisotropy and other solid-state effects, a multivariate, systematic analysis of bandwidth as a function of intermolecular orientations is undertaken for a series of oligoheterocycles, using first-principles methods. While cofacial oligomers show the greatest bandwidths at a given intermolecular C-C contact distance, for a fixed center-to-center intermolecular distance, tilted pi-stacking increases pi-overlap (particularly for LUMO orbitals) and decreases electrostatic repulsion, yielding optimum tilt angles for packing of approximately 40-60 degrees at small intermolecular separations. The calculations also reveal that bandwidths and intrinsic mobilities of holes and electrons in conjugated oligoheterocycles can be quite comparable.

Journal Article↗

PubMed2005

Absolute rates of hole transfer in DNA.

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclassical superexchange model. Site energies and charge-transfer integrals were calculated directly as the diagonal and off-diagonal matrix elements of the Kohn-Sham Hamiltonian, respectively, for all possible combinations of nucleobases. Taking into account the Coulomb interaction between the negative charge on the stilbenedicarboxamide linker and the hole on the DNA strand as well as effects of base pair twisting, the relative order of the experimental rates for hole transfer in different hairpins could be reproduced by tight-binding calculations. To reproduce quantitatively the absolute values of the measured rate constants, the effect of the reorganization energy was taken into account within the semiclassical superexchange model for charge transfer. The experimental rates could be reproduced with reorganization energies near 1 eV. The quantum chemical data obtained were used to discuss charge carrier mobility and hole-transport equilibria in DNA.

DNA↗

PubMed2005

High electron mobility in solution-cast and vapor-deposited phenacyl-quaterthiophene-based field-effect transistors: toward N-type polythiophenes.

New carbonyl-functionalized quaterthiophenes, 5,5' ''-diperfluorophenylcarbonyl-2,2':5',2' ':5' ',2' ''-quaterthiophene [DFCO-4T], 5,5' ''-diphenyl-2,2':5',2' ':5' ',2' ''-quaterthiophene [DPCO-4T], and a polymer having the same basic motif as DFCO-4T, poly{1,4-bis[(3'-n-octyl-2,2'-dithiophene)carbonyl]-2,3,5,6-tetrafluorobenzene} [P(COFCO-4T)], have been synthesized, characterized, and the crystal structures of the molecules determined. Field-effect transistors fabricated with vapor-deposited and solution-cast films of DFCO-4T exhibit very high Ion:Ioff current ratios (up to 108) and electron mobilities up to approximately 0.51 and approximately 0.25 cm2.V-1.s-1, respectively. Solution-cast blends of P(COFCO-4T) and DFCO-4T (1:1 weight ratio) exhibit an electron mobility of approximately 0.01 cm2.V-1.s-1 (Ion:Ioff = 104).

Journal Article↗

PubMed2005

Dissipative dynamics of a system passing through a conical intersection: ultrafast pump-probe observables.

The dynamics of a system incorporating a conical intersection, in the presence of a dissipative environment, is studied with the purpose of identifying observable ultrafast spectroscopic signatures. A model system consisting of two vibronically coupled electronic states with two nuclear degrees of freedom is constructed. Dissipation is treated by two different methods, Lindblad semigroup formalism and the surrogate Hamiltonian approach. Pump-probe experimental expectation values such as transient emission and transient absorption are calculated and compared to the adiabatic and diabatic population transfer. The ultrafast population transfer reflecting the conical intersection is not mirrored in transient absorption measurements such as the recovery of the bleach. Emission from the excited state can be suppressed on the ultrafast time scale, but the existence of a conical intersection is only one of the possible mechanisms that can provide ultrafast damping of emission.

Journal Article↗

PubMed2005

Multipolar excitation in triangular nanoprisms.

Theoretical studies on the optical properties of gold triangular prisms in solution are presented to determine how structural modifications affect the extinction spectrum. Well-defined trends in the particle extinction are found to depend on the triangular edge length and the prism thickness. Calculations performed on large, thin triangular prisms indicate multipolar excitation and display numerous peaks in the extinction spectrum. The dominant peaks are assigned to different in-plane modes corresponding to the lowest three orders of a multipole expansion. Vector polarization plots are presented to support the peak assignments. Altering the prisms by snipping off the points of the triangular cross section significantly blueshifts the dipole peak, but the higher-order modes are only slightly affected. Snipping off large volumes can lead to the suppression of high-order multipoles in the extinction spectrum.

Computer Simulation↗

PubMed2005

Synthesis and electrochemical characterization of a transition-metal-modified ligand-receptor pair.

The energetics of weak interactions (van der Waals forces, hydrogen bonding) are difficult to quantify in biological ligand-receptor pairs. Insight into the biochemical role these forces play is critical to an understanding of signal transduction events and the drug discovery process. Ruthenium pentaammine and iron tetracyano complexes modified with either biotin or desthiobiotin have been synthesized and characterized. These modified biological ligands bind to the protein avidin in a manner similar to that of native biotin. Experiments using redox mediators show that the avidin-bound complexes are electrochemically accessible.

Avidin↗

PubMed2005

Conformationally gated switching between superexchange and hopping within oligo-p-phenylene-based molecular wires.

We observe well-defined regions of superexchange and thermally activated hopping in the temperature dependence of charge recombination (CR) in a series of donor-bridge-acceptor (D-B-A) systems, where D = phenothiazine (PTZ), B = p-phenylene (Ph(n)), n = 1-4, and A = perylene-3,4:9,10-bis(dicarboximide) (PDI). A fit to the thermally activated CR rates of the n = 3 and n = 4 compounds yields activation barriers of 1290 and 2030 cm(-1), respectively, which match closely with theoretically predicted and experimentally observed barriers for the planarization of terphenyl and quaterphenyl. Negative activation of CR in the temperature regions dominated by superexchange charge transport is the result of a fast conformational equilibrium that increasingly depopulates the reactive state for CR as temperature is increased. The temperature dependence of the effective donor-acceptor superexchange coupling, V(DA), measured using magnetic field effects on the efficiency of the charge recombination process, shows that CR occurs out of the conformation with lower V(DA) via the energetically favored triplet pathway.

Crystallography, X-Ray↗

PubMed2005

A general formulation for magnetic exchange coupling within long-distance radical ion pairs.

A Hubbard model-based expression for the magnetic exchange interaction, 2J, between the spins of a radical ion pair is derived for a generic donor-bridge-acceptor (D-B(n)-A) system in terms of the superexchange coupling, t, between molecular orbitals of the donor, bridge, and acceptor and the energies, epsilon, and same-site Coulomb repulsions, U, of these orbitals. The formulation is used to predict 2J for the photophysically well-characterized series phenothiazine-p-(phenylene)n-perylene diimide, n = 2,3,4,5, where the superexchange coupling is calculated with multipathway, second- and third-order perturbation theory coupled with the extended Huckel formalism. U and epsilon are estimated through experimentally determined electrochemical potentials. Due to multiple interactions arising from the large distance between magnetic centers in these donor-bridge-acceptor systems, agreement with experiment was substantially improved when third-order corrections were included in the calculation of t and 2J.

Journal Article↗

PubMed2005

Structural behavior and self-assembly of Lennard-Jones clusters on rigid surfaces.

The phase behavior and surface pattern formation for intermediate size Lennard-Jones clusters on rigid surfaces are examined. We use a parallel tempering Monte Carlo algorithm, in the canonical ensemble. Tempering is done over the temperature domain in most of the calculations. A two-dimensional temperature and Hamiltonian tempering algorithm is also implemented, to examine its usefulness in investigating this type of problem. In general, we observe gas phase systems as they undergo a condensation transition on the surface, followed by a freezing transition. The final solid state pattern formed by the cluster on the surface is the result of a number of competing effects. First, there is a competition between attraction within the cluster and that between cluster and surface atoms. Second, a monolayer of Lennard-Jones atoms tends to pack in a hexadic geometry. This geometry is frustrated on a surface with a different symmetry. The molecular organization of the substrate has a serious impact on the cluster packing. The surface morphology and the size mismatch between cluster and surface atoms, along with the relative interaction strengths, determine which of the effects prevail. When the surface atoms are small enough, the interactions within the cluster determine the symmetry of the pattern. In such a case, the substrate behaves similarly to a continuous surface, and the low-temperature pattern is a hexadic monolayer. When the sizes of the surface and cluster atoms are comparable, the low-temperature adsorbed geometry mimics the substrate symmetry. On a face-centered cubic surface, face-centered cubic monolayers or droplets are obtained.

Journal Article↗

PubMed2005

Molecular electronics: some views on transport junctions and beyond.

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of "conduction as scattering" generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions.

Biological Transport↗

PubMed2005

Molecular transport junctions: asymmetry in inelastic tunneling processes.

Inelastic electron tunneling spectroscopy (IETS) measurements are usually carried out in the low-voltage ("Ohmic", i.e., linear) regime where the elastic conduction/voltage characteristic is symmetric to voltage inversion. Inelastic features, normally observed in the second derivative d(2)I/dV(2) are also symmetric (in fact antisymmetric) in many cases, but asymmetry is sometimes observed. We show that such asymmetry can occur because of different energy dependences of the two contact self-energies. This may be attributed to differences in contact density of states (different contact material) or different energy dependence of the coupling (STM-like geometry or asymmetric positioning of molecular vibrational modes in the junction). The asymmetry scales with the difference between the energy dependence of these self-energies and disappears when this dependence is the same for the two contacts. Our nonequilibrium Green function approach goes beyond proposed WKB scattering theory in properly accounting for Pauli exclusion, as well as providing a path to generalizations, including consideration of phonon dynamics and higher-order perturbation theory.

Journal Article↗

PubMed2005

Parametrization of an anharmonic Kirkwood-Keating potential for AlxGa1-xAs alloys.

We introduce a simple semiempirical anharmonic Kirkwood-Keating potential to model A(x)B(1-x)C-type semiconductors. The potential consists of the Morse strain energy and Coulomb interaction terms. The optical constants of pure components, AB and BC, were employed to fit the potential parameters such as bond-stretching and -bending force constants, dimensionless anharmonicity parameter, and charges. We applied the potential to finite temperature molecular-dynamics simulations on Al(x)Ga(1-x)As for which there is no lattice mismatch. The results were compared with experimental data and those of harmonic Kirkwood-Keating model and of equation-of-motion molecular-dynamics technique. Since the Morse strain potential effectively describes finite temperature damping, we have been able to numerically reproduce experimentally obtained optical properties such as dielectric functions and reflectance. This potential model can be readily generalized for strained alloys.

Journal Article↗

PubMed2005

Electron spin dynamics as a probe of molecular dynamics: temperature-dependent magnetic field effects on charge recombination within a covalent radical ion pair.

The electron spin-spin exchange interaction, 2J, in radical pairs (RPs) is exquisitely sensitive to the details of molecular structure and can thus serve as an important probe of structural dynamics in RPs of potential interest to photonic and electronic devices. Photoinitiated ultrafast two-step charge separation produces (1)(MeOAn(+)(*)-6ANI-NI(-)(*)), where MeOAn = p-methoxyaniline, 6ANI = 4-(N-piperidinyl)naphthalene-1,8-dicarboximide, and NI = naphthalene-1,8:4,5-bis(dicarboximide). Radical pair intersystem crossing subsequently produces (3)(MeOAn(+)(*)-6ANI-NI(-)(*)), and the total RP population decays with approximately 10 ns lifetime at 140 K, which increases to nearly 30 ns at 300 K in toluene. The activation energy observed for this process is negative and can be explained by a mechanism involving a conformational preequilibrium of the RP followed by charge recombination. Over the same temperature range, the magnetic field effect (MFE) on yield of the triplet recombination product, MeOAn-6ANI-(3)()NI, yields the magnitude of 2J, which directly monitors the superexchange electronic coupling for charge recombination. A single resonance in the MFE plot is observed at 300 K, which splits into two resonances at temperatures below 230 K, suggesting that there are two distinct groups of RP conformations at low temperature. The magnitude of 2J for the lower field resonance (10 mT) at 140 K is 5 times smaller than that of the high field resonance. At 300 K the equilibrium is shifted almost entirely to the set of conformers with the stronger electronic coupling. The motion that couples these two groups of conformations is the motion that most effectively gates the donor-acceptor electronic coupling.

Journal Article↗

PubMed2005

Electronic structure and band gaps in cationic heterocyclic oligomers. Multidimensional analysis of the interplay of heteroatoms, substituents, molecular length, and charge on redox and transparency characteristics.

Oxidative doping of extended pi-conjugated polymers and oligomers produces dramatic changes in optical and electrical properties, arising from polaron and soliton-derived midgap states. Despite the great importance of such changes for materials properties, far less is known about the cationic polaron states than about the neutral, semiconducting or insulating, undoped materials. The systematic, multifactor computational analysis of oligoheterocycles such as oligothiophenes, oligofurans, and oligopyrroles presented here affords qualitative and quantitative understanding of the interplay among skeletal substitution pattern, electronic structure, and the effective band gap reduction on p-doping. A simple linear relation is derived for predicting p-doped oligomer and polymer effective band gaps based on those of the neutral oligomers; this relationship confirms the effectiveness of a "fixed band" approximation and explains the counterintuitive increase of the effective band gap on p-doping of many small band gap oligomers. The present analysis also suggests new candidates for transparent conductive polymers and predicts limiting behavior of ionization potential, electron affinity, and other properties for various polyheterocyclic systems. The results yield insight into materials constraints in electrochromic polymers as well as on p- and n-type conductors and semiconductors.

Journal Article↗