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Polaron dynamics in anisotropic organic molecular semiconductors is theoretically investigated and simulated in the framework of a semi-classical Holstein-Peierls model. Our computational protocol is presented and applied to studies of a two-dimensional molecular crystal. The intermolecular (Peierls) parameters for a particular crystal direction are systematically changed in order to study the effect of anisotropy in the system. The usefulness of this methodology is highlighted by studying the polaron dynamics on a picosecond timescale, which provides a microscopic insight into the influence of the interplay between different intramolecular parameters on the charge transport mechanism. Our results show that the polaron mobility is substantially reduced in going from an anisotropic to an isotropic relationship between the Peierls parameters for different directions in the crystal. Interestingly, the molecular charge distribution presents three different signatures corresponding to a one-dimensional polaron, a two-dimensional polaron, and an intermediate state for which the polaron localization depends on the degree of anisotropy. Importantly, the two-dimensional polaron, which is present in the essentially isotropic system, is immobile whereas the other two types of polarons are mobile. This, in order for polaron transport to occur in a two-dimensional molecular based system, this system has to be anisotropic.

We present a study of mobility field and temperature dependence for C60 with Kinetic Monte Carlo simulations. We propose a new scheme to take into account polarization effects in organic materials through atomic induced dipoles on nearby molecules. This leads to an energy correction for the single site energies and to an external reorganization happening after each hopping. The inclusion of polarization allows us to obtain a good agreement with experiments for both mobility field and temperature dependence.

The influence of the interplay between symmetric and antisymmetric inter-molecular electron-phonon (e-ph) coupling mechanisms on the polaron stability and mobility in organic semiconductors has been theoretically investigated at a molecular level. A semi-empirical Holstein-Peierls model is used which in addition to the symmetric and antisymmetric inter-molecular e-ph interactions also includes an antisymmetric intra-molecular e-ph coupling. Our results show that the symmetric e-ph coupling plays the role of destabilizing the polaron as a result of temperature induced phonons that, via the symmetric coupling, affects the charge distribution of the polaron. Considering this kind of coupling, the parameter space for which the polaron is dynamically stable is strongly temperature-dependent. For the combination of symmetric e-ph coupling strength and temperature, which results in a stable polaron, the velocity of the polaron, and therefore also the charge carrier mobility, is not affected by the symmetric e-ph coupling strength.

A semi-empirical Holstein-Peierls model is used to study the temperature effects on the polaron stability in organic semiconductors at a molecular scale. The approach takes into account both intra- and inter-molecular electron-lattice interactions and is aimed at describing charge transport in the system. Particularly, we present a systematic numerical investigation to characterize the influence of both temperature and electric field on the stability as well as mobility of the polaron. It is found that the parameter space for which the polaron is dynamically stable is quite limited and the variations in some of these parameters strongly depend on the temperature. The electric field can play a role in further localizing the charge causing a compression of the lattice distortions associated with the polaron, increasing thereby its stability, up to a field strength of approximately 2.0 mV Å(-1). Considering field strengths higher than this critical value, the polaron is annihilated spreading charge through the lattice. Furthermore, we have studied the polaron mobility as a function of the anisotropy of the system, going from a one-dimensional system via a highly anisotropic two-dimensional system to a uniform two-dimensional system. There is a clearly observed mobility edge for the polaron; it exhibits a high mobility in the one-dimensional system but as the coupling in the second dimension is turned on the polaron slows down and becomes immobile in the uniform system. The results provided by this transport mechanism are in good agreement with experimental observations and may provide guidance to improve the charge transport in organic optoelectronic devices.

In this article, we analyze the electric field dependence of the hole mobility in disordered poly(p-phenylene vinylene). The charge carrier mobility is obtained from Monte Carlo simulations. Depending on the field strength three regions can be identified: the percolation region, the correlation region, and the inverted region. Each region is characterized by a different conduction mechanism and thus a different functional dependence of the mobility on the electric field. Earlier studies have highlighted that Poole-Frenkel law, which appears in the correlation region, is based on the type of correlation caused by randomly distributed electric dipoles. This behavior is thus observed in a limited range of field strengths, and by studying a broader range of electric fields, a more fundamental understanding of the transport mechanism is obtained. We identify the electric fields determining the transitions between the different conduction mechanisms in the material and we explain their physical origin. In principle, this allows us to characterize the mobility field dependence for any organic material. Additionally, we study the charge carrier trapping mechanisms due to diagonal and off-diagonal disorder, respectively.

Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and enthalpy at finite temperatures are challenging to determine with ensemble averaging alone. Here we report a method to directly record time-averaged equilibrium probability distributions by confining an individual molecule to a nanoscopic pore of a two-dimensional metal-organic nanomesh, using temperature-controlled scanning tunnelling microscopy. We associate these distributions with partition function projections to assess real-space-projected thermodynamic quantities, aided by computational modelling. The presented molecular dynamics-based analysis is able to reproduce experimentally observed projected microstates with high accuracy. By an in silico customized energy landscape, we demonstrate that distinct probability distributions can be encrypted at different temperatures. Such modulation provides means to encode and decode information into position-temperature space.

The field-induced dynamics of polarons in armchair graphene nanoribbons (GNRs) is theoretically investigated in the framework of a two-dimensional tight-binding model with lattice relaxation. Our findings show that the semiconductor behavior, fundamental to polaron transport to take place, depends upon of a suitable balance between the GNR width and the electron-phonon (e-ph) coupling strength. In a similar way, we found that the parameter space for which the polaron is dynamically stable is limited to an even narrower region of the GNR width and the e-ph coupling strength. Interestingly, the interplay between the external electric field and the e-ph coupling plays the role to define a phase transition from subsonic to supersonic velocities for polarons in GNRs.

The adsorption of organic molecules onto the close-packed facets of coinage metals is studied, and how accurately adsorption heights can be described by using recent advances of the van der Waals density functional (vdWDF), with optPBE/vdWDF, optB86b/vdWDF, vdWDF2, and rev/vdWDF2 functionals is illustrated. The adsorption of two prototypical aromatic hydrocarbons is investigated, and the calculated adsorption heights are compared to experimental literature values from normal incident X-ray standing wave absorption and a state-of-the-art semi-empirical method. It is shown that both the optB86b/vdWDF and rev/vdWDF2 functionals describe adsorption heights with an accuracy of 0.1 Å, compared to experimental values, and are concluded as reliable methods of choice for related systems., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Exciton dissociation in a donor-accepter polymer heterojunction has been simulated using a nonadiabatic molecular dynamics approach, which allows for the coupled evolution of the nuclear degrees of freedom and the electronic degrees of freedom described by multiconfigurational electronic wavefunctions. The simulations reveal important details of the charge separation process: the exciton in the donor polymer first dissociates into a "hot" charge transfer state, which is best described as a polaron pair. The polaron pair can be separated into free polaron charge carriers if a sufficiently strong external electric field is applied. We have also studied the effects of inter-chain interaction, temperature, and the external electric field strength. Increasing inter-chain interactions makes it easier for the exciton to dissociate into a polaron pair state, but more difficult for the polaron pair to dissociate into free charge carriers. Higher temperature and higher electric field strength both favor exciton dissociation as well as the formation of free charge carriers.

We computationally study the reaction mechanisms of halogen-based covalent self-assembly, a major route for synthesizing molecular nanostructures and nanographenes on surfaces. Focusing on biphenyl as a small model system, we describe the dehalogenation, recombination, and diffusion processes. The kinetics of the different processes are also investigated, in particular how diffusion and coupling barriers affect recombination rates. Trends across the periodic table are derived from three commonly used close-packed (111) surfaces (Cu, Ag, and Au) and two halogens (Br and I). We show that the halogen atoms can poison the surface, thus hindering long-range ordering of the self-assembled structures. Finally, we present core-level shifts of the relevant carbon and halogen atoms, to provide reference data for reliably detecting self-assembly without the need for atomic-resolution scanning tunneling microscopy.

In this work, a novel method to model off-diagonal disorder in organic materials has been developed. The off-diagonal disorder is taken directly from the geometry of the system, which includes both a distance and an orientational dependence on the constituent molecules, and does not rely on a parametric random distribution. The geometry of the system is generated by running molecular dynamics simulations on phenylene-vinylene oligomers packed into boxes. The effect of the kind of randomness generated in this way is then investigated by means of Monte Carlo simulations of the charge transport in these boxes and a comparison is made to the commonly used model of off-diagonal disorder, where only the distance dependence is accounted for. It is shown that this new refined way of treating the disorder has a significant impact on the charge transport, while still being compliant with previously published and confirmed results.

We simulate the interchain polaron recombination process in conjugated polymer systems using a nonadiabatic molecular dynamics method, which allows for the coupled evolution of the nuclear degrees of freedom and multiconfigurational electronic wavefunctions. Within the method, the appropriate spin symmetry of the electronic wavefunction is taken into account, thus allowing us to distinguish between singlet and triplet excited states. It is found that the incident polarons can form an exciton, form a bound interchain polaron pair, or pass each other, depending on the interchain interaction strength and the strength of an external electric field. Most importantly, we found that the formation of singlet excitons is considerably easier than triplet excitons. This shows that in real organic light emitting devices, the electroluminescence quantum efficiency can exceed the statistical limitation value of 25%, in agreement with experiments.

Charge transport in conjugated polymers has been investigated using Monte Carlo simulations implemented on top of the Marcus theory for donor-acceptor transition rates. In particular, polaron effects and the dependency of the mobility on the temperature and the applied electric field have been studied. The conclusions are that while the qualitative temperature dependence is similar to that predicted by Miller-Abrahams theory in the Gaussian disorder model (GDM), the electric field dependence is characterized by a crossover into the Marcus inverted region, not present in the GDM. Furthermore, available analytical approximations to describe the electric field dependence of the mobility in Marcus theory fail to fit the simulation data and hence cannot be used to directly draw conclusions about the importance of polaron effects for charge transport in conjugated polymers., (© 2011 American Institute of Physics)

We investigate the cooperative effects controlling the synthesis of a graphene nanoribbon on the Au(111) surface starting from an anthracene polymer using density functional calculations including van der Waals interactions. We focus on the high-temperature cyclodehydrogenation step of the reaction and find that the reaction proceeds by simultaneously transferring two H-atoms from the anthracene units to the Au surface, leaving behind a C-C bond in the process. This step is significantly more favorable than the three other potential reaction paths. Moreover, we find that successive dehydrogenations proceed from one end of the polyanthracene and propagate step-by-step through the polymer in a domino-like fashion.

By using the Su-Schrieffer-Heeger model modified to include electron-electron interactions, the Brazovskii-Kirova symmetry breaking term and an external electric field, we investigate the scattering process between a negative and a positive bipolaron in a system composed of two coupled polymer chains. Our results show that the Coulomb interactions do not favor the bipolaron recombination. In the region of weak Coulomb interactions, the two bipolarons recombine into a localized excited state, while in the region of strong Coulomb interactions they can not recombine. Our calculations show that there are mainly four channels for the bipolaron recombination reaction: (1) forming a biexciton, (2) forming an excited negative polaron and a free hole, (3) forming an excited positive polaron and a free electron, (4) forming an exciton, a free electron, and a free hole. The yields for the four channels are also calculated., (© 2011 American Institute of Physics)

A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assignment of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

Scattering process between a negative polaron and an exciton in a polymer chain is investigated by using the Su-Schrieffer-Heeger model modified to include electron-electron interactions, the Brazovskii-Kirova symmetry breaking term, and an external electric field. It is found that the scattering process is spin dependent. If the polaron and the exciton have parallel spins, the polaron can easily pass through the exciton as if it "do not see" the exciton. If the polaron and the exciton have antiparallel spins, there exist strong repulsion between them. The polaron may be bounced back, be dissociated or pass through the exciton depending on the strength of the external electric field. In any of these cases, the polaron cannot break the exciton.

A synthetic strategy was developed for the preparation of porphyrins containing between one and four stereogenic centers, such that their molecular weights vary only as a result of methyl groups which give the chiral forms. The low-dimensional nanoscale aggregates of these compounds reveal the profound effects of this varying molecular chirality on their supramolecular structure and optical activity. The number of stereogenic centers influences significantly the self-assembly and chiral structure of the aggregates of porphyrin molecules described here. A scanning tunneling microscopy study of monolayers on graphite shows that the degree of structural chirality with respect to the surface increases almost linearly with the number of stereogenic centers, and only one handedness is formed in the monolayers, whereas the achiral compound forms a mixture of mirror-image domains at the surface. In solution, four hydrogen bonds induce the formation of an H-aggregate, and circular dichroism measurements and theoretical studies indicate that the compounds self-assemble into helical structures. Both the chirality and stability of the aggregates depend critically on the number of stereocenters. The chiral porphyrin derivatives gelate methylcyclohexane at concentrations dependent on the number and position of chiral groups at the periphery of the aromatic core, reflecting the different aggregation forces of the molecules in solution. Increasing the number of stereogenic centers requires more material to immobilize the solvent, in all likelihood because of the greater solubility of the porphyrins. The vibrational circular dichroism spectra of the gels show that all compounds have a chiral environment around the amide bonds, confirming the helical model proposed by calculations. The morphologies of the xerogels (studied by scanning electron microscopy and scanning force microscopy) are similar, although more fibrous features are present in the molecules with fewer stereogenic centers. Importantly, the presence of only one stereogenic center, bearing a methyl group as the desymmetrizing ligand, in a molecule of considerable molecular weight is enough to induce single-handed chirality in both the one- and two-dimensional supramolecular self-assembled structures.

This tutorial review describes an atomistic simulation approach to studies of dynamics of charge transport in pi-conjugated molecular or polymer based materials. The approach, which is termed electron-lattice dynamics, is based on the Ehrenfest theorem and includes nonadiabatic transport processes. The equations of motion for both the electrons and the nuclei are solved simultaneously using a Runge-Kutta method. We show that for ideal systems without disorder and thermal fluctuations in the electronic coupling between the constituent elements that the electron transport can be described as an adiabatic polaron drift process. In the presence of thermal fluctuations caused by, e.g., phenyl ring torsions along a poly(paraphenylene vinylene) chain, there are extensive variations in the electronic coupling along the polymer chain which results in nonadiabatic hopping transport.

We have performed a study of charge transport in lambda-DNA using a recently developed model based on Marcus theory and dynamic Monte Carlo simulations. The model accounts for charge delocalization over multiple adjacent identical nucleobases. Such delocalized states are found to act as traps for charge transport and therefore have a negative impact on the charge carrier (hole) mobility. Both the electric field and temperature dependence of the mobility in lambda-DNA is reported in this paper. Furthermore, the detailed information produced by the simulation allow us to plot the progress of a hole propagating through the DNA sequence and this is used to identify the bottlenecks that limits the charge transport process.

A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallic substrates is systematically investigated within a joint scanning tunnelling microscopy/molecular modelling approach. The molecular conformation of TPP molecules, their adsorption on a gold surface and the growth of highly ordered TPP islands are modelled with a combination of density functional theory and dynamic force field methods. The results indicate a subtle interplay between different contributions. The molecule-substrate interaction causes a bending of the porphyrin core which also determines the relative orientations of phenyl legs attached to the core. A major consequence of this is a characteristic (and energetically most favourable) arrangement of molecules within self-assembled molecular clusters; the phenyl legs of adjacent molecules are not aligned parallel to each other (often denoted as pi-pi stacking) but perpendicularly in a T-shaped arrangement. The results of the simulations are fully consistent with the scanning tunnelling microscopy observations, in terms of the symmetries of individual molecules, orientation and relative alignment of molecules in the self-assembled clusters.

X-ray absorption spectra have been determined for ethylene and free base phthalocyanine at the carbon K-edge with use of the complex polarization propagator method combined with Kohn-Sham density functional theory and the Coulomb attenuated method B3LYP exchange-correlation functional. Apart from isolated molecules, the study includes pi-stacked systems of the phthalocyanine dimer and the ethylene dimer, trimer, tetramer, and pentamer. For ethylene, pi-stacking involves a reduction in transition energy of the valence pi( *)-band by some 70 meV and large spectral changes (regarding also shape and intensity) of the Rydberg bands. For phthalocyanine, there are large spectral changes in the entire valence pi( *)-part of the spectrum.

A model describing charge (hole) transport in DNA has been developed. The individual charge transfer steps in the transport process are described by Marcus theory modified to account for electron delocalization over adjacent identical nucleobases. Such a modification, as well as introducing a distance dependence in the reorganization energy, is necessary in order to reach an agreement with the observed transfer rates in well defined model systems to DNA. Using previously published results as a reference for the reorganization energy and with the delocalization described within the Huckel model we obtain an excellent agreement with experimental data.

The charge migration process in DNA is subject to a lively debate among researchers at the moment. We have performed calculations on poly(G)-poly(C) DNA which substantiate a recent report indicating bandlike conduction for this particular form of DNA. Our results show that both guanine and cytosine give rise to conducting channels along the DNA strands. The conductivity results from the overlap of the pi orbitals along the base stacks. We also demonstrate that the measured increase of the threshold voltage with temperature in poly(G)-poly(C) DNA is the result of electron localization due to the structural disorder following high temperature.

We report a new fullerenelike material consisting of cross-linked nano-onions of C and N. Growth of the onion shells takes place atom by atom on a substrate surface and yields thin solid films during magnetron sputter deposition. Electron microscopy and energy loss spectroscopy show that the core shell contains up to 20 at. % N corresponding to C(48)N(12) aza-fullerene composition. Nanoindentation of this nanostructured material gives high resilience with hardness 7 GPa, Young's modulus 37 GPa, and complete elastic recovery after loading with 0.5 mN to a depth of 75 nm. Total energy calculations show the stability of C(60-2n)N(2n) aza-fullerenes and suggest the existence of a novel C(48)N(12) molecule.

The motion of excitations such as polarons is believed to be of fundamental importance for the transport properties of conjugated polymers for the use in, e.g., polymer based LED's. We have investigated polaron dynamics in a system of coupled polymer chains in the presence of an external electric field. In particular, we focus on how a polaron migrates through the polymer lattice, i.e., the situation in which a polaron reaches a chain end and is scattered to the surrounding chains. We show that the outcome of this event strongly depends on the strength of the electric field, and we identify three different cases for the polaron migration.