Biomedical subjects

Alessandro Troisi

Publications and source records attributed to Alessandro Troisi.

13 recordsLinked to original sources

PubMed2006

Propensity rules for inelastic electron tunneling spectroscopy of single-molecule transport junctions.

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.

Journal Article↗

PubMed2006

Effects of hydration on molecular junction transport.

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.

Electrochemistry↗

PubMed2006

Dynamics of the intermolecular transfer integral in crystalline organic semiconductors.

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.

Journal Article↗

PubMed2006

Charge-transport regime of crystalline organic semiconductors: diffusion limited by thermal off-diagonal electronic disorder.

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.

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

Band structure of the four pentacene polymorphs and effect on the hole mobility at low temperature.

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.

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↗

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

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study.

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.

Journal Article↗

PubMed2003

Modulating charge-transfer interactions in topologically different porphyrin-C60 dyads.

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.

Journal Article↗

PubMed2002

Molecular rectification through electric field induced conformational changes.

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.

Journal Article↗

PubMed2002

Structure and photophysics of an old, new molecule: 1,3,6,8-tetraazatricyclo[4.4.1.1(3,8)]dodecane.

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.

Journal Article↗