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Mark A Ratner

Publications and source records attributed to Mark A Ratner.

At least 55 records · Page 3Linked to original sources
PubMed2005

Wire-like charge transport at near constant bridge energy through fluorene oligomers.

The study of photoinitiated electron transfer in donor-bridge-acceptor molecules has helped elucidate the distance dependence of electron transfer rates and behavior of various electron transfer mechanisms. In all reported cases, the energies of the bridge electronic states involved in the electron transfer change dramatically as the length of the bridge is varied. We report here, in contrast, an instance in which the length of the bridge, and therefore the distance over which the electron is transferred, can be varied without significantly changing the energies of the relevant bridge states. A series of donor-bridge-acceptor molecules having phenothiazine (PTZ) donors, 2,7-oligofluorene (FL(n)) bridges, and perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptors was studied. Photoexcitation of PDI to its lowest excited singlet state results in oxidation of PTZ via the FL(n) bridge. In toluene, the rate constants for both charge separation and recombination as well as the energy levels of the relevant FL(n)(+.) bridge states for n = 1-4 are only weakly distance dependent. After the initial photo-generation of (1)(PTZ(+.)-FL(n)-PDI(-.)), radical pair intersystem crossing results in formation of (3)(PTZ(+.)-FL(n)-PDI(-.)) that recombines to give (3.)PDI. The dependence of the (3.)PDI yield on an applied magnetic field shows a resonance, which gives the singlet-triplet splitting, 2J, of the radical ion pair. The magnitude of 2J directly monitors the contribution of coherent charge transfer (superexchange) to the overall electron transfer rate. These data show that charge recombination through FL(n) is dominated by incoherent hopping at long distances.

Electron Transport↗
PubMed2005

Hopping transport in conductive heterocyclic oligomers: reorganization energies and substituent effects.

Molecular scale charge motion in disordered organic materials at ambient temperature occurs via a hopping-type mechanism with rates dictated both by the charge transfer integral and by the reorganization energy due to geometric relaxation. This contribution presents a systematic theoretical analysis of cation internal reorganization energies for a broad family of organic oligoheterocycles-variation of reorganization energy with oligomer chain length, heteroatom identity, and a range of heterocycle substituents provides key information on important structural properties governing internal reorganization energies. At room temperature, the range in reorganization energies induced by substituent variations corresponds to a >10(2)-fold variation in intrinsic hole transfer rate, suggesting that changes in reorganization energy dominate variations in charge-transfer rates for many semiconducting/conducting oligomers.

Journal Article↗
PubMed2005

Redox equilibria in hydroxylamine oxidoreductase. Electrostatic control of electron redistribution in multielectron oxidative processes.

We report results of continuum electrostatics calculations of the cofactor redox potentials, and of the titratable group pK(a) values, in hydroxylamine oxidoreductase (HAO). A picture of a sophisticated multicomponent control of electron flow in the protein emerged from the studies. First, we found that neighboring heme cofactors strongly interact electrostatically, with energies of 50-100 mV. Thus, cofactor redox potentials depend on the oxidation state of other cofactors, and cofactor redox potentials in the active (partially oxidized) enzyme differ substantially from the values obtained in electrochemical redox titration experiments. We found that, together, solvent-exposed heme 1 (having a large negative redox potential) and heme 2 (having a large positive redox potential) form a lock for electrons generated during the oxidation reaction The attachment of HAO's physiological electron transfer partner cytochrome c(554) results in a positive shift in the redox potential of heme 1, and "opens the electron gate". Electrons generated as a result of hydroxylamine oxidation travel to heme 3 and heme 8, which have redox potentials close to 0 mV versus NHE (this result is in partial disagreement with an existing experimental redox potential assignment). The closeness of hemes 3 and 8 from different enzyme subunits allows redistribution of the four electrons generated as a result of hydroxylamine oxidation, among the three enzyme subunits. For the multielectron oxidation process to be maximally efficient, the redox potentials of the electron-accepting cofactors should be roughly equal, and electrostatic interactions between extra electrons on these cofactors should be minimal. The redox potential assignments presented in the paper satisfy this general rule.

Bacterial Proteins↗
PubMed2005

Simplified charge separation energetics in a two-dimensional model for polymer-based photovoltaic cells.

An extension of our two-dimensional working model for photovoltaic behavior in binary polymer and/or molecular photoactive blends is presented. The objective is to provide a more-realistic description of the charge generation and charge separation processes in the blend system. This is achieved by assigning an energy to each of the possible occupation states, describing the system according to a simple energy model for exciton and geminate electron-hole pair configurations. The energy model takes as primary input the ionization potential, electron affinity and optical gap of the components of the blend. The underlying photovoltaic model considers a nanoscopic subvolume of a photoactive blend and represents its p- and n-type domain morphology, in terms of a two-dimensional network of donor and acceptor sites. The nearest-neighbor hopping of charge carriers in the illuminated system is described in terms of transitions between different occupation states. The equations governing the dynamics of these states are cast into a linear master equation, which can be solved for arbitrary two-dimensional donor-acceptor networks, assuming stationary conditions. The implications of incorporating the energy model into the photovoltaic model are illustrated by simulations of the short circuit current versus thickness of the photoactive blend layer for different choices of energy parameters and donor-acceptor topology. The results suggest the existence of an optimal thickness of the photoactive film in bulk heterojunctions, based on kinetic considerations alone, and that this optimal thickness is very sensitive to the choice of energy parameters. The results also indicate space-charge limiting effects for interpenetrating donor-acceptor networks with characteristic domain sizes in the nanometer range and high driving force for the photoinduced electron transfer across the donor-acceptor internal interface.

Journal Article↗
PubMed2005

Self-assembly on multiple length scales: a Monte Carlo algorithm with data augmentation.

We present a Monte Carlo algorithm that allows simulations where portions of the system of variable size are moved. The algorithm requires the definition of an augmented space that contains information on the bonding between components of the system and is updated as the simulation proceeds. With this method it is possible to incorporate, within the same simulation, processes involving motion of smaller and larger portions of a given system. The algorithm is presented in general terms and illustrated for a simple one-dimensional lattice model.

Journal Article↗
PubMed2005

Hysteresis, switching, and negative differential resistance in molecular junctions: a polaron model.

Within a simple mean-field model (self-consistent Hartree approximation) we discuss the possibility of polaron formation on a molecular wire as a mechanism for negative differential resistance (NDR), switching, and/or hysteresis in the I-V characteristic of molecular junctions. This mechanism differs from earlier proposed mechanisms of charging and conformational change. The polaron model captures the essential physics and provides qualitative correspondence with experimental data. The importance of active redox centers in the molecule is indicated.

Journal Article↗
PubMed2005

Interface geometry and molecular junction conductance: geometric fluctuation and stochastic switching.

Metal/molecule/metal transport junctions can transport charge in the elastic scattering (Landauer) regime if the injection gap is large and the molecule is relatively short. Stochastic switching and broad conduction peak distributions have been observed in such junctions. We examine the effect of altering interface geometry on transport, using density functional calculations. For most structures, variations in conductance of order 0-300% are found, but when an atomic wire of Au binds to the molecule, symmetry changes can modify currents by a factor of 10(3).

Journal Article↗
PubMed2004

An agent-based approach for modeling molecular self-organization.

Agent-based modeling is a technique currently used to simulate complex systems in computer science and social science. Here, we propose its application to the problem of molecular self-assembly. A system is allowed to evolve from a separated to an aggregated state following a combination of stochastic, deterministic, and adaptive rules. We consider the problem of packing rigid shapes on a lattice to verify that this algorithm produces more nearly optimal aggregates with less computational effort than comparable Monte Carlo simulations.

Algorithms↗
PubMed2004

Inelastic electron tunneling spectroscopy in molecular junctions: peaks and dips.

We study inelastic electron tunneling through a molecular junction using the nonequilibrium Green's function formalism. The effect of the mutual influence between the phonon and the electron subsystems on the electron tunneling process is considered within a general self-consistent scheme. Results of this calculation are compared to those obtained from the simpler Born approximation and the simplest perturbation theory approaches, and some shortcomings of the latter are pointed out. The self-consistent calculation allows also for evaluating other related quantities such as the power loss during electron conduction. Regarding the inelastic spectrum, two types of inelastic contributions are discussed. Features associated with real and virtual energy transfer to phonons are usually observed in the second derivative of the current I with respect to the voltage Phi when plotted against Phi. Signatures of resonant tunneling driven by an intermediate molecular ion appear as peaks in the first derivative dI/dPhi and may show phonon sidebands. The dependence of the observed vibrationally induced lineshapes on the junction characteristics, and the linewidth associated with these features are also discussed.

Journal Article↗
PubMed2004

The mechanism of aluminum-catalyzed Meerwein-Schmidt-Ponndorf-Verley reduction of carbonyls to alcohols.

The mechanistic details of the Meerwein-Schmidt-Ponndorf-Verley (MSPV) reduction of ketones to the corresponding alcohols were investigated both experimentally and computationally. Density functional theory (DFT) was used to assess the energetics of several proposed pathways (direct hydrogen transfer, hydridic, and radical). Our results demonstrate that a direct hydrogen transfer mechanism involving a concerted six-membered ring transition state is the most favorable pathway for all calculated systems starting from a small model system and concluding with the experimentally investigated BINOLate/Al/(i)PrOH/MePhC=O system. Experimental values for the activation parameters of acetophenone reduction using the BINOLate/Al/(i)PrOH system (DeltaG# = 21.8 kcal/mol, DeltaH# = 18.5 kcal/mol, DeltaS# = -11.7 au) were determined on the basis of kinetic investigation of the reaction and are in good agreement with the computational findings for this system. Calculated and experimental kinetic isotope effects support the concerted mechanism.

Journal Article↗
PubMed2004

Building blocks for n-type molecular and polymeric electronics. Perfluoroalkyl- versus alkyl-functionalized oligothiophenes (nT; n = 2-6). Systematics of thin film microstructure, semiconductor performance, and modeling of majority charge injection in field-effect transistors.

The solid-state properties and FET electrical behavior of several series of alpha,omega- and beta,beta'-fluorocarbon- and alkyl-substituted and unsubstituted oligothiophenes nTs (n = 2-6) are compared and contrasted. The thin films were grown by slow vacuum deposition over a range of substrate temperatures and/or by casting from solution and were investigated by X-ray diffraction and scanning electron microscopy. Our results indicate that vacuum deposition at 60-80 degrees C affords films with remarkably similar microstructures despite the extensive H --> F substitution. Trends in observed d spacing versus molecular core extension provide quantitative information on molecular orientation. Field-effect transistor measurements performed for all systems and having the same device structure, components, and fabrication conditions demonstrate that all nTs functionalized with fluorocarbon chains at the thiophene termini are n-type semiconductors, in contrast to the p-type activity of the remaining systems. One of these systems, alpha,omega-diperfluorohexyl-4T, exhibits a mobility of 0.22 cm2/(V s) and an Ion:Ioff ratio of 10(6), one of the highest so far reported for an n-type organic semiconductor. The effect of substitution regiochemistry on FET majority charge carrier was additionally studied, in the case of a 6T core, by shifting the fluorocarbon substituents from the terminal to the central thiophene units. Finally, we propose a simple theoretical model for electrode/organic interfacial carrier injection. The results suggest why modest substituent-induced changes in the injection barrier can produce working n-type materials.

Journal Article↗
PubMed2004

Building blocks for N-type molecular and polymeric electronics. Perfluoroalkyl- versus alkyl-functionalized oligothiophenes (nTs; n = 2-6). Systematic synthesis, spectroscopy, electrochemistry, and solid-state organization.

The synthesis, comparative physicochemical properties, and solid-state structures of five oligothiophene (nT) series differing in substituent nature and attachment, regiochemistry, and oligothiophene core length (n) are described. These five series include the following 25 compounds: (i) alpha,omega-diperfluorohexyl-nTs 1 (DFH-nTs, n = 2-6), (ii) beta,beta'-diperfluorohexyl-nTs 2 (isoDFH-nTs, n = 2-6), (iii) alpha,omega-dihexyl-nTs 3 (DH-nTs, n = 2-6), (iv) beta,beta'-dihexyl-nTs 4 (isoDH-nTs, n = 2-6), and (v) unsubstituted oligothiophenes 5 (alphanTs, n = 2-6). All new compounds were characterized by elemental analysis, mass spectrometry, and multinuclear NMR spectroscopy. To probe and address quantitatively how the chemistry and regiochemistry of conjugated core substitution affects molecular and solid-state properties, the entire 1-5 series was investigated by differential scanning calorimetry, thermogravimetric analysis, and optical absorption and emission spectroscopies. Single-crystal X-ray diffraction data for several fluorocarbon-substituted oligomers are also presented and compared. The combined analysis of these data indicates that fluorocarbon-substituted nT molecules strongly interact in the condensed state, with unit cell level phase separation between the aromatic core and fluorocarbon chains. Surprisingly, despite these strong intermolecular interactions, high solid-state fluorescence efficiencies are exhibited by the fluorinated derivatives. Insight into the solution molecular geometries and conformational behavior are obtained from analysis of optical and variable-temperature NMR spectra. Finally, cyclic voltammetry data offer a reliable picture of frontier MO energies, which, in combination with DFT computations, provide key information on relationships between oligothiophene substituent effects and electronic response properties.

Journal Article↗
PubMed2004

Structure changes in glassforming liquids upon cooling and compression.

Upon cooling and compression, both the thermodynamic and the kinetic properties of glassformers change. In fragile glassformers, these changes suggest changes in the local structure of the liquid. Thermodynamic data may then provide a measure of structure changes. Special criteria for structure changes in terms of energy and pressure fluctuations in the isochoric system are proposed; recent theoretical results allow one to rewrite the criteria in terms of long- and short-time thermodynamic characteristics of the liquid. Based on the proposed criteria, we discuss the changes in the local structure due to temperature and pressure variations.

Journal Article↗
PubMed2004

Solvent control of spin-dependent charge recombination mechanisms within donor-conjugated bridge-acceptor molecules.

We have shown recently that the oligomeric p-phenylene bridge within the PTZ-(Ph)n-PDI (PTZ = phenothiazine, Ph = phenyl, and PDI = perylenediimide) donor-bridge-acceptor system acts as a molecular wire in toluene, as shown by a change in the rate of radical ion pair (RP) recombination within PTZ+*-(Ph)n-PDI-* from an exponential distance dependence to a linear distance dependence as the bridge becomes longer. The population of the RP and its spin-selective recombination products are sensitive to the application of an external magnetic field, which can be used to directly measure the singlet-triplet splitting, 2J, within the RP. The value of 2J is a weighted sum of electronic coupling matrix elements that are to a good approximation directly proportional to VDA2, the effective coupling between the orbitals on the donor and acceptor sites. The dependence of RP population on magnetic field reveals the relative contributions of the singlet and triplet charge recombination (CR) pathways to overall RP decay. We have now observed an "inversion" of the MFE on the RP population within PTZ+*-(Ph)4-PDI-* and PTZ+*-(Ph)5-PDI-* upon a switch in solvent from toluene to 2-methyltetrahydrofuran (MTHF). We interpret the inversion of the MFE as a switch in the relative importance of the singlet and triplet charge recombination (CRS, CRT) pathways due to a stabilization of the RP state by more polar MTHF, making CRS more energetically favorable. This change in mechanism illustrates the sensitivity of molecular wire behavior to the surrounding environment.

Journal Article↗
PubMed2004

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.

Journal Article↗
PubMed2004

Application of evolutionary algorithm methods to polypeptide folding: comparison with experimental results for unsolvated Ac-(Ala-Gly-Gly)5-LysH+.

We present an evolutionary method for finding the low-energy conformations of polypeptides. The application, called FOLDAWAY,is based on a generic framework and uses several evolutionary operators as well as local optimization to navigate the complex energy landscape of polypeptides. It maintains two complementary representations of the structures and uses the CHARMM force field for evaluating the energies. The method is applied to unsolvated Met-enkephalin and Ac-(Ala-Gly-Gly)(5)-Lys(+)H(+). Unsolvated Ac-(Ala-Gly-Gly)(5)-Lys(+)H(+) has been the object of recent experimental studies using ion mobility measurements. It has a flat energy landscape where helical and globular conformations have similar energies. FOLDAWAY locates several large groups of structures not found in previous molecular dynamics simulations for this peptide, including compact globular conformations, which are probably present in the experiments. However, the relative energies of the different conformations found by FOLDAWAY do not accurately match the relative energies expected from the experimental observations.

Algorithms↗
PubMed2004

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties.

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.

Journal Article↗