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Metal-organic ruthenium-based dyes are often used as a source of photogenerated electrons in dye-sensitised solar cells and photocatalysis. Here, we study the relationship between adsorption geometry and electron injection properties of one of the most successful metal-organic dyes, N3 (cis-bis(isothiocyanato)-bis(4,4'-dicarboxy-2,2'-bipyridyl)-ruthenium(II)), on the TiO(2) rutile (110) surface. We systematically construct all possible adsorption configurations of the N3 molecule on this surface. By combining density-functional theory calculations and electron transfer calculations, we find that a large number of adsorption configurations are possible--more than ten structures, which differ in the number of carboxylic and thiocyanate groups adsorbed and in the adsorption mode of the carboxylic groups, have similar adsorption energies and similar electron injection times. Therefore, the observed fast electron injection from this dye may originate either from one adsorption configuration or from several co-existing configurations. Our results suggest that related substituted metal-organic dyes with fewer anchoring groups will also have good electron injection properties, even if only a small subset of adsorption configurations is available for them.

High-energy metal oxide surfaces are considered to be promising for applications involving surface-adsorbate electron transfer, such as photocatalysis and dye-sensitised solar cells. Here, we compare the efficiency of electron injection into different TiO(2) anatase surfaces. We model the adsorption of a carboxylic acid (formic acid) on anatase (101), (001), (100), (110) and (103) surfaces using density functional theory calculations, and calculate electron injection times from a model dye into these surfaces. We find that the different positions of the conduction band edge of these surfaces determine the rate of electron injection (which is faster for the surfaces with lower-lying conduction band, among them the most stable (101) surface). However, if the dye's injection energy is enforced to be at a fixed energy deep inside each surface's conduction band, then several anatase surfaces, such as the synthetically achievable (001) surface, show rates of injection comparable or faster than the (101) surface. Moreover, because of their higher-lying conduction bands, these minority surfaces are likely to offer higher open-circuit voltages in dye-sensitised solar cells. Therefore, synthetically accessible high-energy anatase surfaces, such as (001)-oriented nanostructures, may be promising candidates for use in dye-sensitised solar cells.

It is normally assumed that electrons and holes in organic solar cells are generated by the dissociation of excitons at the interface between donor and acceptor materials in strongly bound hole-electron pairs. We show in this contribution that excitons can dissociate tens of angstroms away from the interface and generate partially separated electrons and holes, which can more easily overcome their coulombic attraction and form free charges. We first establish under what conditions long-range exciton dissociation is likely (using a kinetic model and a microscopic model for the calculation of the long-range electron transfer rate). Then, defining a rather general model Hamiltonian for the donor material, we show that the phenomenon is extremely common in the majority of polymer:fullerene bulk heterojunction solar cells.

We developed a computational procedure to screen many different anchoring groups used or usable to connect a dye to the semiconducting surface in a dye-sensitized solar cell. The procedure leads to a clear identification of the anchoring groups that bind strongly to the surface and facilitate the electron injection at the same time, providing clear-cut indications for the design of new dyes. The complicated interplay of factors that determine the final results (preferred adsorption mode, the anchor's effect on the dye's electronic structure, and dye-semiconductor coupling) is illustrated through a few examples showing how chemical intuition can often be misleading in this problem.

Using a range of realistic interface geometries obtained from a molecular dynamics simulation we study the effects of different microscopic atomic arrangements on the electronic structure and charge transfer rates of the prototypical photovoltaic interface between P3HT (poly(3-hexylthiophene)) and PCBM ([6,6]-phenyl-C(61)-butyric acid methyl ester). The electronic structures of charge-transfer (CT) states belong to two groups that can be denoted as "charge-separated" and "charge-bridging" states. For the former group of structures, which may lead to fully separated charges, the ranges and the average values of internal reorganization energy, the electronic coupling and the charge separated states energy are evaluated. A range and distribution of absolute charge separation (CS) and recombination (CR) rates are computed using the Marcus-Levich-Jortner rate equation. Due to the variety of P3HT/PCBM interface structures, a very broad range of CS (7.7 × 10(9)-1.8 × 10(12) s(-1)) and CR (2.5 × 10(5)-1.1 × 10(10) s(-1)) "instantaneous" rates are computed. However, the energetic parameters affecting the rate evolve in time due to the dynamic nature of the interface with a characteristic timescale of about 10 ns. For this reason the slowest CR instantaneous rates are not observed and the minimum CR rate observed is determined by the rate of conformational rearrangement at the interface. The combination of these observations provides a more general framework for the interpretation of experimental spectroscopic data, suggesting that the analysis based on simple first order rates may be insufficient to describe charge transfer in organic solar cell interfaces.

Intramolecular structure and intermolecular packing in crystalline molecular semiconductors should have profound effects on the charge-carrier wave function, but simple drift mobility measurements are not very sensitive to this. Here we show that differences in the Hall resistance of two soluble pentacene derivatives can be explained with different degrees of carrier delocalization being limited by thermal lattice fluctuations. A combination of Hall measurements, optical spectroscopy, and theoretical simulations provides a powerful probe of structure-property relationships at a molecular level.

Charge carriers in organic crystals are often trapped in point defects. The persistence time of the charge in these defect states is evaluated by computing the escape rate from this state using non-adiabatic rate theory. Two cases are considered (i) the hopping between separate identical defect states and (ii) the hopping between a defect state and the bulk (delocalized) states. We show that only the second process is likely to happen with realistic defect concentrations and highlight that the inclusion of an effective quantum mode of vibration is essential for accurate computation of the rate. The computed persistence time as a function of the trap energy indicates that trap states shallower than ∼0.3 eV cannot be effectively investigated with some slow spectroscopic techniques such as THz spectroscopy or EPR commonly used to study the nature of excess charge in semiconductors.

A new family of optically pure tetrathiafulvalenium and tetraselenafulvalenium salts, D(3)[M(III)(S,S-EDDS)](2)·nH(2)O (where D = TTF, TSF; M = Co, Fe, Cr; EDDS = ethylenediaminedisuccinato), were synthesized electrochemically. These phases are semiconductors with conductivities between 6.9 × 10(-6) and 1.3 × 10(-5) S·cm(-1) (E(a)ca. 0.3 eV) for TTF and 2.8 × 10(-4) to 2.8 × 10(-5) S·cm(-1) (E(a)ca. 0.1 eV) for TSF compounds. While some crystals suffer from twinning, other well resolved structures consist of TTF/TSF stacks which, under the influence of the chiral anion, exhibit a periodic undulation described by an elliptical helix. The crystallographic data, along with computational work, indicate charge localization in the semiconducting motifs., (© 2011 American Chemical Society)

The theories developed since the fifties to describe charge transport in molecular crystals proved to be inadequate for the most promising classes of high mobility molecular semiconductors identified in the recent years, including for example pentacene and rubrene. After reviewing at an elementary level the classical theories, which still provide the language for the understanding of charge transport in these systems, this tutorial review outlines the recent experimental and computational evidence that prompted the development of new theories of charge transport in molecular crystals. A critical discussion will illustrate how very rarely it is possible to assume a charge hopping mechanism for high mobility organic crystals at any temperature. Recent models based on the effect of non-local electron-phonon coupling, dynamic disorder, coexistence of localized and delocalized states are reviewed. Additionally, a few more recent avenues of theoretical investigation, including the study of defect states, are discussed.

A semiclassical model to study charge transport in molecular semiconductors is extended from one to an arbitrary number of dimensions. The model is applied to the calculation of the charge mobility of the holes in the two dimensional plane of rubrene with the largest charge mobility. The absolute values of the computed mobility tensor, evaluated without adjustable parameters, are in excellent agreement with the experimental results of Podzorov et al. [Phys. Rev. Lett. 95, 226601 (2005)] and have the correct temperature dependence. The localization length and density of states determined by dynamic disorder are analyzed in detail and provide a global description of the charge transport process in agreement with the spectroscopic experiments. The effect of correlation in the modeling of dynamic disorder is also investigated.

Benzothiadiazines differently substituted at the sulfonamidic nitrogen atom, at the stereogenic carbon atom and at the anilinic nitrogen atom have been synthesized and fully characterized. Enantioseparation of these compounds has revealed rapid on-column enantiomerization. The recently developed software DCXplorer has been successfully applied to calculate enantiomerization kinetic parameters. Enantiomerization barriers of 3-phenyl substituted benzothiadiazines, calculated in this work, have indicated a higher enantiomerization rate suggesting that the aromatic substituent exerts a strong effect on the enantiomerization process. Methyl substitution on N(2) position led to higher free energy barriers of enantiomerization, suggesting negative influence of methyl in the N(2) position on enantiomerization kinetics. However, methylation on N(4) position increases the enantiomerization rates significantly. The results obtained have been employed to postulate an enantiomerization mechanism for chiral benzothiadiazine type compounds., ((c) 2010 Wiley-Liss, Inc.)

We analyze the relationship among the molecular structure, morphology, percolation network, and charge carrier mobility in four organic crystals: rubrene, indolo[2,3-b]carbazole with CH(3) side chains, and benzo[1,2-b:4,5-b']bis[b]benzothiophene derivatives with and without C(4)H(9) side chains. Morphologies are generated using an all-atom force field, while charge dynamics is simulated within the framework of high-temperature nonadiabatic Marcus theory or using semiclassical dynamics. We conclude that, on the length scales reachable by molecular dynamics simulations, the charge transport in bulk molecular crystals is mostly limited by the dynamic disorder, while in self-assembled monolayers the static disorder, which is due to the slow motion of the side chains, enhances charge localization and influences the transport dynamics. We find that the presence of disorder can either reduce or increase charge carrier mobility, depending on the dimensionality of the charge percolation network. The advantages of charge transporting materials with two- or three-dimensional networks are clearly shown.

We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.

The charge transport in organic materials, from molecular crystals to polymers, is determined by their degree of disorder. The dynamic disorder in ideal molecular crystals at room temperature and the static disorder in disordered polymers are just two limiting cases of the timescale of the fluctuations in the electronic Hamiltonian caused by nuclear motions. In fact, a very large number of important materials (e.g. liquid crystalline semiconductors) are actually in an intermediate regime where the disorder is neither purely static nor purely dynamic. This Minireview discusses the recent contribution of computational chemistry (molecular dynamics and quantum chemistry) to the characterization of these transport regimes and outlines the theoretical methods that can be used to relate the system characteristics to the measurable mobility.

A technique to predict the rate of electron transfer between a chromophore and the TiO(2) semiconductor surface in dye sensitized solar cells (DSSC) is presented. The rate is computed by partitioning the system into molecular and semiconductor states and computing the retarded Green's function for the system. A number of recently reported organic chromophores are considered and the results are rationalized in terms of the orbital shape and the energy alignment between molecular and semiconductor states. The method is designed to allow a rapid scanning of potential chromophores as the expensive components of the calculation (computing the density of states on the TiO(2) surface and the coupling between these states and the molecule) are performed once for all chromophores with similar adsorption chemistry. With this technique it is possible to predict the rate of injection of a new chromophore in a few hours using a desktop computer and routine quantum chemistry packages.

We model the two-dimensional self-assembly of planar molecules capable of complementary interactions (like hydrogen bonding) as a set of hexagonal tiles on a hexagonal lattice. We use Monte Carlo simulations to study the phase diagrams of three model systems. The phases are characterized using a variety of order parameters, and they are studied as a function of the strength of the complementary interaction energy. This simplified model is proven to be capable of reproducing the phases encountered in real systems, unifying within the same framework most of the structures encountered experimentally.

Fascinating packing patterns of identical spherical and discotic objects on curved surfaces occur readily in nature and science. Examples include C(60) fullerenes, (1, 2) 13-atom cuboctahedral metal clusters, (3) and S-layer proteins on outer cell membranes. (4) Numerous situations with surface-arranged objects of variable size also exist, such as the lenses on insect eyes, biomineralized shells on coccolithophorids, (5) and solid-stabilized emulsion droplets (6) and bubbles. (7) The influence of size variations on these packing patterns, however, is studied sparsely. Here we investigate the packing of nanosized silica particles on the surface of polystyrene latex particles fabricated by Pickering miniemulsion polymerization of submicrometer-sized armored monomer droplets. We are able to rationalize the experimental morphology and the nearest-neighbor distribution with the help of Monte Carlo simulations. We show that broadening of the nanoparticle size distribution has pronounced effects on the self-assembled equilibrium packing structures, with original 12-point dislocations or grain-boundary scars gradually fading out.

Agent-based simulations are rule-based models traditionally used for the simulations of complex systems. In this paper, an algorithm based on the concept of agent-based simulations is developed to predict the lowest energy packing of a set of identical rigid molecules. The agents are identified with rigid portions of the system under investigation, and they evolve following a set of rules designed to drive the system toward the lowest energy minimum. The algorithm is compared with a conventional Metropolis Monte Carlo algorithm, and it is applied on a large set of representative models of molecules. For all the systems studied, the agent-based method consistently finds a significantly lower energy minima than the Monte Carlo algorithm because the system evolution includes elements of adaptation (new configurations induce new types of moves) and learning (past successful choices are repeated).

Using classical molecular dynamics simulations and quantum chemical calculations, the structure and charge-transfer parameters in crystalline poly(3-hexylthiophene) (P3HT) are investigated. The changes in polymer structure with temperature are studied and, by performing DFT calculations on configurations found from MD, the changes in the charge-transfer characteristics are investigated. The system is found to adopt a structure consistent with X-ray diffraction experiments on the so-called type-II polymorph of the poly(3-alkylthiophenes). Upon increasing temperature, a conformational change in the polymer side chains occurs, which is found to lead to increased disorder in the interring torsions, which modulates the charge transfer along the polymer backbone. The intrachain transfer integrals are found to decrease slightly with temperature, while their distribution broadens considerably due to increased thermal motion of the rings. The interchain transfer integrals are found to be appreciable for both nearest and next-nearest neighbor rings. This, taken with the fact that the positions of rings on neighboring chains are strongly correlated, has consequences for the development of more accurate phenomenological charge-transport models, such as variable range hopping models.

A generic model Hamiltonian is proposed for the study of the transport in a quasi-one-dimensional semiconductor in the charge transport regime intermediate between dynamic localization and static localization due to structural disorder. This intermediate regime may be appropriate for many organic semiconductors, including polymers, discotic liquid crystals, and DNA. The dynamics of the charge carrier is coupled to classical Langevin oscillators whose spectral density can be adjusted to model experimental systems of interest. In the proposed model, the density of states is constant (at constant temperature) and the transition from dynamic to static disorder is controlled by a single parameter. This paper further clarifies that the density of states may not contain all the information needed to describe the charge transport in some materials.

Using dissipative particle dynamics simulations the relationship between molecular architecture and phase behaviour in model hairy-rod polymers is studied. In agreement with experimental and theoretical studies the phase behaviour is controlled by changes to the molecular structure, particularly the sidechain length and density, and the molecular interactions. For dense sidechains a lamellar structure is found, which becomes an inverted cylindrical phase when the sidechain density is lowered. The ordered phases become more stable on increasing sidechain length and on increasing the repulsion strength between the backbone and sidechains. In the absence of torsional potentials the structures are double-walled, i.e. layers are two polymer backbones thick, while single-walled structures are observed for polymers with torsional potentials.

In partially ordered organic semiconductors, the characteristic times of nuclear motion are comparable to those of charge carrier dynamics. It is impossible to describe charge transport using either static disorder models or temperature averaged electronic Hamiltonians. We build a model Hamiltonian which allows the study of charge transport whenever carrier and nuclear dynamics are not easily separable. Performing nanoseconds long molecular dynamics of a columnar mesophase of a discotic liquid crystal and evaluating electronic couplings, we identify realistic parameters of the Hamiltonian. All modes which are coupled to the electron dynamics can be described in the model Hamiltonian by a limited number of Langevin oscillators. This method can be applied to systems with both slow (nanoseconds) and fast (hundreds of femtoseconds) nuclear motions, i.e., with both dynamic and static disorder.

The charge carrier dynamics in organic semiconductors has been traditionally discussed with the models used in inorganic crystalline and amorphous solids but this analogy has severe limitations because of the more complicated role of nuclear motions in organic materials. In this perspective, we discuss how a new approach to the modelling of charge transport is emerging from the alliance between the conventional quantum chemical methods and the methods more traditionally used in soft-matter modelling. After describing the conventional limit cases of charge transport we discuss the problems arising from the comparison of the theory with the experimental and computational results. Several recent applications of numerical methods based on the propagation of the wavefunction or kinetic Monte Carlo methods on soft semiconducting materials are reviewed.

The inelastic electron tunnelling (IET) spectra of a series of molecules with the commonest functional groups are evaluated computationally. It is found that ether, secondary amine and thioether groups do not leave any characteristic signatures on the IET spectrum (in comparison with simple alkanes) and they cannot be used as 'tracers' for the tunnelling path of the electron. In contrast, carbonyl and ester groups modify the appearance of the IET spectrum considerably. The series of computations was also used to validate, for the case of saturated molecules, the propensity rules for IET spectroscopy proposed in the literature. It is found that totally symmetric vibrations give the largest contribution to the spectrum and that there is no correlation between IET and infrared or Raman absorption intensities.

Much current experimental research on transport in molecular junctions focuses on finite voltages, where substantial polarization-induced nonlinearities may result in technologically relevant device-type responses. Because molecules have strong polarization responses to changing charge state or external field, molecules isolated between electrodes can show strongly nonlinear current-voltage responses. For small applied voltages (up to approximately 0.3 volt), weak interaction between transporting electrons and molecular vibrations provides the basis for inelastic electron tunneling spectroscopy. At higher voltages and for certain time scale regimes, strong coupling effects occur, including Coulomb blockade, negative differential resistance, dynamical switching and switching noise, current hysteresis, heating, and chemical reactions. We discuss a general picture for such phenomena that arise from charging, strong correlation, and polarization (electronic and vibrational) effects in the molecule and at the interface.

We compare the low-temperature electron transport properties of alkyl monolayers which utilize different attachment strategies to gold. Inelastic electron tunneling spectroscopy (IETS) and current-voltage analysis were performed on molecular junctions incorporating alkyl-dithiocarbamate and alkanethiolate self-assembled monolayers of similar length. Alkyl-dithiocarbamate monolayers were formed by the condensation of dioctylamine or didecylamine with carbon disulfide in anhydrous ethanol and compared to alkanethiolate SAMs of 1-decanethiol and 1-dodecanethiol, respectively. The electron transport properties of each monolayer were examined using magnetically assembled microsphere junctions under high-vacuum conditions at low temperature. IETS was employed to differentiate the films on the basis of vibrational modes which are characteristic of each method of attachment. We use quantum chemical simulations of model compounds to calculate frequency and intensity of predicted signals arising from molecular vibrations to aid in the accurate assignment of the spectra. A qualitative comparison of our devices also reveals an increase in current density when utilizing dithiocarbamate attachment to gold compared to alkanethiolate molecules of similar length.

Using inelastic electron tunneling spectroscopy (IETS) to measure the vibronic structure of nonequilibrium molecular transport, aided by a quantitative interpretation scheme based on Green's function-density functional theory methods, we are able to characterize the actual pathways that the electrons traverse when moving through a molecule in a molecular transport junction. We show that the IETS observations directly index electron tunneling pathways along the given normal coordinates of the molecule. One can then interpret the maxima in the IETS spectrum in terms of the specific paths that the electrons follow as they traverse the molecular junction. Therefore, IETS measurements not only prove (by the appearance of molecular vibrational frequencies in the spectrum) that the tunneling charges, in fact, pass through the molecule, but also can be used to determine the transport pathways and how they change with the geometry and placement of molecules in junctions.

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.

Using a perturbative approach to simple model systems, we derive useful propensity rules for inelastic electron tunneling spectroscopy (IETS) of molecular wire junctions. We examine the circumstances under which this spectroscopy (that has no rigorous selection rules) obeys well defined propensity rules based on the molecular symmetry and on the topology of the molecule in the junction. Focusing on conjugated molecules of C(2h) symmetry, semiquantitative arguments suggest that the IETS is dominated by a(g) vibrations in the high energy region and by out of plane modes (a(u) and b(g)) in the low energy region. Realistic computations verify that the proposed propensity rules are strictly obeyed by medium to large-sized conjugated molecules but are subject to some exceptions when small molecules are considered. The propensity rules facilitate the use of IETS to help characterize the molecular geometry within the junction.

The study of charge transport through increasingly complex small molecules will benefit from a detailed understanding of how contaminants from the environment affect molecular conduction. This should provide a clearer picture of the electronic characteristics of molecules by eliminating interference from adsorbed species. Here we use magnetically assembled microsphere junctions incorporating thiol monolayers to provide insight into changing electron transport characteristics resulting from exposure to air. Using this technique, current-voltage analysis and inelastic electron tunnelling spectroscopy (IETS) demonstrate that the primary interaction affecting molecular conduction is rapid hydration at the gold-sulphur contacts. We use IETS to present evidence for changing mechanisms of charge transport as a result of this interaction. The detrimental effects on molecular conduction discussed here are important for understanding electron transport through gold-thiol molecular junctions once exposed to atmospheric conditions.

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.

In organic crystalline semiconductor molecular components are held together by very weak interactions and the transfer integrals between neighboring molecular orbitals are extremely sensitive to small nuclear displacements. We used a mixed quantum chemical and molecular dynamic methodology to assess the effect of nuclear dynamics on the modulation of the transfer integrals between close molecules. We have found that the fluctuations of the transfer integrals are of the same order of magnitude of their average value for pentacene and anthracene. Under these conditions the usual perturbative treatment of the electron-phonon coupling is invalid, the band description of the crystal breaks down and the charge carriers become localized. Organic crystals of pentacene and anthracene, even in the absence of defects, can be regarded as disordered media with respect to their charge transport properties. These results suggest that the dynamic electronic disorder can be the factor limiting the charge mobility in crystalline organic semiconductors.

We propose that the electron transport in crystalline organic semiconductors at room temperature (RT) is neither polaronic nor a combination of thermally activated hopping and polaronic transport, as previously thought. Thermal molecular motions cause large fluctuations in the intermolecular transfer integrals that, in turn, localize the charge carrier. This effect destroys the translational symmetry of the electronic Hamiltonian and makes the band description inadequate for RT organic crystals. We used a one-dimensional semiclassical model to compute the (temperature dependent) charge carrier mobility in the presence of thermal fluctuations of the electronic Hamiltonian. This transport mechanism explains several contrasting experimental observations pointing sometimes to a delocalized "bandlike" transport and sometimes to the existence of strongly localized charge carriers.

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.

The band structure of the four known polymorphs of pentacene is computed from first principles using the accurate molecular orbitals of the isolated molecule as the basis for the calculation of the crystalline orbitals. The computed bands are remarkably different for each polymorph, but their diversity can be easily rationalized using a simple analytical model that employs only three parameters. The effect of the electronic structure on the hole mobility was evaluated using a simple model based on the constant relaxation time approximation. It is found that the mobility tensor is highly anisotropic for three of the four considered polymorphs. The practical implication of this prediction on the technology of thin-film organic transistors is discussed.

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.

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., (2005 American Institute of Physics.)

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.

Control over the interchromophore separation, their angular relationship, and the spatial overlap of their electronic clouds in several ZnP-C(60) dyads (ZnP=zinc porphyrin) is used to modulate the rates of intramolecular electron transfer. For the first time, a detailed analysis of the charge transfer absorption and emission spectra, time-dependent spectroscopic measurements, and molecular dynamics simulations prove quantitatively that the same two moieties can produce widely different electron-transfer regimes. This investigation also shows that the combination of ZnP and C(60) consistently produces charge recombination in the inverted Marcus region, with reorganization energies that are remarkably low, regardless of the solvent polarity. The time constants of electron transfer range from the mus to the ps regime, the electronic couplings from a few tens to several hundreds of cm(-1), and the reorganization energies remain below 0.54 eV and can be as low as 0.16 eV.

A new approach for the design of a molecular rectifier is proposed. Using a simple model, we have shown that conformational changes induced by the electric field may lead to a rectifying junction. The simplest possible rectifier of this kind presents two almost isoenergetic conformations, with different conductances and dipole moments. A simple equation allows for the estimation of the range of molecular parameters and temperatures that lead to an effective rectification. Examples show that rectification based on this mechanism is also possible at room temperature.

More than a century after its initial synthesis, the static and dynamic geometry of 1,3,6,8-tetraazatricyclo [4.4.1.1(3,8)]dodecane (TTD), a fully saturated cage-like molecule, is finally established. Detection and modeling of the supersonic jet fluorescence excitation and emission spectra show that the molecule undergoes interconversion between two S(4) symmetry minima. The barrier at the D(2d) symmetric conformation is only 105 cm(-1), i.e., approximately 0.3 kcal mol(-1), and is overcome along a carbon-carbon torsional mode of a(2) symmetry. The presence of an S(4) conformation is corroborated by a Raman investigation. When excited to the first excited singlet state, the 3s Rydberg state, the molecule adopts a geometry with D(2d) symmetry. The satisfactory description of the spectroscopy of TTD obtained by a combination of quantum chemical and quantum mechanical models is discussed, and the apparent conflict between the present results and nuclear magnetic resonance and X-ray diffraction experiments is solved. Because of the close analogy between a Rydberg state and the ground state of the radical cation regarding geometry and spectroscopic properties, it is concluded that the radical cation is also of D(2d) symmetry.