Electronic Characteristics and Charge Transport Mechanisms for Large Area Aromatic Molecular Junctions

This paper reports the electron transport characteristics of carbon/molecule/Cu molecular junctions, where aromatic molecules (azobenzene or AB and nitroazobenzene or NAB) are employed as the molecular component. It is shown that these devices can be made with high yield (>90%), display excellent reproducibility, and can withstand at least 1.5 × 10 9 potential cycles and temperatures of at least 180°C. Transport mechanisms are investigated by analysis of current density/voltage (J-V) curves as a function of the molecular layer thickness and temperature. Results show that J decreases exponentially with thickness, giving a measured value for the low-bias attenuation factor ( ) of 2.5 ( 0.1 nm -1 for AB and NAB. In addition, it is shown that transport is not thermally activated over a wide range of temperatures (5-450 K) and that the appearance of a thermally "activated" region at higher temperatures can be accounted for by the effect of temperature on the distribution of electrons around the Fermi level of the contact(s). These results indicate that quantum mechanical tunneling is likely the mechanism for charge transport in these junctions. Although application of the Simmons tunneling model leads to transport parameters consistent with nonresonant tunneling, the parameters obtained from fitting experimental data indicate that the barrier height and/or shape, effective mass, and dielectric constant (ε) can all change with thickness. Experimental measurements of ε and density functional theory (DFT) calculations of molecular energy levels and polarizability support these conclusions. Finally, the implications of the transport mechanisms are discussed from the viewpoint of designing functional molecular electronic devices

Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination

Processive transcription antitermination requires the assembly of the complete antitermination complex, which is initiated by the formation of the ternary NusB–NusE–BoxA RNA complex. We have elucidated the crystal structure of this complex, demonstrating that the BoxA RNA is composed of 8 nt that are recognized by the NusB–NusE heterodimer. Functional biologic and biophysical data support the structural observations and establish the relative significance of key protein–protein and protein–RNA interactions. Further crystallographic investigation of a NusB–NusE–dsRNA complex reveals a heretofore unobserved dsRNA binding site contiguous with the BoxA binding site. We propose that the observed dsRNA represents BoxB RNA, as both single-stranded BoxA and double-stranded BoxB components are present in the classical lambda antitermination site. Combining these data with known interactions amongst antitermination factors suggests a specific model for the assembly of the complete antitermination complex

Predictive multiscale modeling of properties and interaction of macro/bio molecules in solvents and mixtures

Over the past few decades nanoscience and molecular biology has shown a strong growth worldwide in many areas of research and proved their significance in todays ́ competitive environment. However, there still remains an enormous potential for further development which could revolutionize every area of human life. Unfortunately, in some cases, that potential is screened out by complexity and multilevel character of systems and processes at a nanometer scale. The success of future applications in a high-tech industry requires deep understanding of fundamental mechanisms on different levels of description and their communication. That could be provided only by appropriate combination of experimental study with predictive theoretical modeling. Nowadays, more and more scientists in different fields of chemistry and biology are using computational modeling methods in their research, either as a technique per se, or as a complement to experimental work. However, despite the in- creasing attention to computational nanoscience and biology the specificity of application of standard theoretical and computational modeling in nanotechnology and bioscience is complicated due to complexity of the systems of interest and needs to be discussed separately, especially in the view of multilevel representation of systems and pro- cesses on nanoscale. One of most important and demanding applications in computational chemistry is multiscale modeling of properties and interaction of macro/bio molecules in solvents and mixtures. The presentation will address different aspects of theoretical and computational approaches and their combination at the different time and length scales to model impact of solvents on physicochemical properties of molecules as geometry, conforma- tional equilibria, reaction rates, as well as their UV-vis, IR, or NMR spectra. It will focus on the combination of statistical-mechanical molecular theory of liquids (3D reference interaction site model, known as 3D-RISM) with density functional theory (DFT) which provides the accurate and efficient way to predict the electronic properties of molecular system in different solvents and mixtures with high level of accuracy comparable with simulations but with less computational cost [1]. Similar to explicit solvent simulations, 3D-RISM properly accounts for chemical and physical activity of both solute and solvent molecules, such as hydrogen bonding and hydrophobic forces, by yielding the 3D site density distributions of the solvent. Moreover, it readily provides, via analytical expressions, the solvation thermodynamics, including the solvation free energy, its energetic and entropic decomposition, and partial molar volume and compressibility. Recently the number of new approaches and approximations was de- veloped in order to increase efficiency of 3D-RISM and DFT combination. They could be subdivided into two main groups focused on the optimization of 3D-RISM algorithm (memory optimization, parallelization, etc.) and methodology improvements [2]. I will present a review and analysis of latest achievements focused on improves of accuracy and applicability the combination. Some examples will be also discussed. References [1] GusarovS., ZieglerT., KovalenkoA., Self-Consistent Combination of the Three-Dimensional RISM Theory of Molecular Solvation with Analytical Gradients and the Amsterdam Density Functional Package, JPCA 110, 1, pp. 6083-6090 (2006). [2] Gusarov S., Bhalchandra P., Kovalenko A., Efficient treatment of solvation shells in 3D molecular theory of solvation, , J. Comp. Chem, 33, 1, pp. 1478-1494 (2012).Non UBCUnreviewedAuthor affiliation: National Institute for NanotechnologyFacult

Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package

The three-dimensional reference interaction site model with the closure relation by Kovalenko and Hirata (3D-RISM-KH) in combination with the density functional theory (DFT) method has been implemented in the Amsterdam density functional (ADF) software package. The analytical first derivatives of the free energy with respect to displacements of the solute nuclear coordinates have also been developed. This enables study of chemical reactions, including reaction coordinates and transition state search, with the molecular solvation described from the first principles. The method yields all of the features available by using other solvation approaches, for instance infrared spectra of solvated molecules. To evaluate the accuracy of the present method, test calculations have been carried out for a number of small molecules, including four glycine conformers, a set of small organic compounds, and carbon nanotubes of various lengths in aqueous solution. Our predictions for the solvation free energy agree well with other approaches as well as experiment. This new development makes it possible to calculate at modest computational cost the electronic properties and molecular solvation structure of a solute molecule in a given molecular liquid or mixture from the first principles.Peer reviewed: YesNRC publication: Ye

Efficient treatment of solvation shells in 3D molecular theory of solvation

We developed a technique to decrease memory requirements when solving the integral equations of three-dimensional (3D) molecular theory of solvation, a.k.a. 3D reference interaction site model (3D-RISM), using the modified direct inversion in the iterative subspace (MDIIS) numerical method of generalized minimal residual type. The latter provides robust convergence, in particular, for charged systems and electrolyte solutions with strong associative effects for which damped iterations do not converge. The MDIIS solver (typically, with 2 7 10 iterative vectors of argument and residual for fast convergence) treats the solute excluded volume (core), while handling the solvation shells in the 3D box with two vectors coupled with MDIIS iteratively and incorporating the electrostatic asymptotics outside the box analytically. For solvated systems from small to large macromolecules and solid\u2013liquid interfaces, this results in 6- to 16-fold memory reduction and corresponding CPU load decrease in MDIIS. We illustrated the new technique on solvated systems of chemical and biomolecular relevance with different dimensionality, both in ambient water and aqueous electrolyte solution, by solving the 3D-RISM equations with the Kovalenko\u2013Hirata (KH) closure, and the hypernetted chain (HNC) closure where convergent. This core\u2013shell-asymptotics technique coupling MDIIS for the excluded volume core with iteration of the solvation shells converges as efficiently as MDIIS for the whole 3D box and yields the solvation structure and thermodynamics without loss of accuracy. Although being of benefit for solutes of any size, this memory reduction becomes critical in 3D-RISM calculations for large solvated systems, such as macromolecules in solution with ions, ligands, and other cofactors.Peer reviewed: YesNRC publication: Ye

The Effect of Molecular Structure and Environment on the Miscibility and Diffusivity in Polythiophene-Methanofullerene Bulk Heterojunctions: Theory and Modeling with the RISM Approach

Although better means to model the properties of bulk heterojunction molecular blends are much needed in the field of organic optoelectronics, only a small subset of methods based on molecular dynamics- and Monte Carlo-based approaches have been hitherto employed to guide or replace empirical characterization and testing. Here, we present the first use of the integral equation theory of molecular liquids in modelling the structural properties of blends of phenyl-C61-butyric acid methyl ester (PCBM) with poly(3-hexylthiophene) (P3HT) and a carboxylated poly(3-butylthiophene) (P3BT), respectively. For this, we use the Reference Interaction Site Model (RISM) with the Universal Force Field (UFF) to compute the microscopic structure of blends and obtain insight into the miscibility of its components. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived by the Density Functional Theory (DFT) methods. We also run Molecular Dynamics (MD) simulation to compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively. A remarkably good agreement with available experimental data and results of alternative modelling/simulation is observed for PCBM in the P3HT system. We interpret this as a step in the validation of the use of our approach for organic photovoltaics and support of its results for new systems that do not have reference data for comparison or calibration. In particular, for the less-studied P3BT, our results show that expectations about its performance in binary blends with PCBM may be overestimated, as it does not demonstrate the required level of miscibility and short-range structural organization. In addition, the simulated mobility of PCBM in P3BT is somewhat higher than what is expected for polymer blends and falls into a range typical for fluids. The significance of our predictive multi-scale modelling lies in the insights it offers into nanoscale morphology and charge transport behaviour in multi-component organic semiconductor blends

Using on-top pair density for construction of correlation functionals for multideterminant wave functions

The value of the two-particle density function at coalescence is frequently used as an additional variable for formulating approximate exchange-correlation or correlation functionals. Here, its applications as one of the key variables for the construction of new DFT (preferably multi-determinant) functionals is investigated. The basic formalism is presented and it is shown that this replacement avoids some difficulty to construct a Fock matrix in a ROKS (restricted open-shell Kohn-Sham) method and also to reduce the 'double counting' of correlation energy in CASDFT (complete active space density functional theory) calculations. Calculations of excitation energies for transition metals and dissociation curves for diatomic molecules are presented as an example

Modeling of bitumen fragment adsorption on Cu+ and Ag+ exchanged zeolite nanoparticles

We investigate bitumen desulfurisation on zeolite chabazite nanoparticles that contain Ag+ and Cu+ by using periodic density functional theory. The large bitumen molecules that contain thiophene derivative impurities and useful aromatic hydrocarbons cannot enter into zeolite pores but adsorb on the outer surface of the zeolite. The zeolite nanoparticle surface can be optimised for efficient impurities removal and bitumen upgrading, as we have shown recently. On chabazite nanoparticle surface, Ag+ that reside near the main channel enhance the bitumen fragment adsorption in the order benzene < thiophene < benzothiophene < dibenzothiophene. For Cu+, the bitumen fragment adsorption strength increases in the order benzene < dibenzothiophene < benzothiophene < thiophene. The different trends arise from the spatial constraint of the surface termination and the smaller ionic radius of Cu+ relative to Ag+. Our results show that zeolite surface modifications allow for stronger adsorption of thiophenes relative to hydrocarbons. Our results can be applied toward the rational design of zeolite nanoparticles for bitumen upgrading. We conclude that the preferred configurations of organic macromolecules adsorbed on zeolite outer surfaces can be safely predicted by using Fukui functions.Peer reviewed: YesNRC publication: Ye