First-principles calculation on the conductance of a single 1,4-diisocyanatobenzene molecule with single-walled carbon nanotubes as the electrodes

The conductance of a single 1,4-diisocyanatobenzene molecule sandwiched between two single-walled carbon nanotube (SWCNT) electrodes are studied using a fully self-consistent ab initio approach which combines nonequilibrium Green's function formalism with density functional theory calculations. Several metallic zigzag and armchair SWCNTs with different diameters are used as electrodes; dangling bonds at their open ends are terminated with hydrogen atoms. Within the energy range of a few eV of the Fermi energy, all the SWCNT electrodes couple strongly only with the frontier molecular orbitals that are related to nonlocal pi bonds. Although the chirality of SWCNT electrodes has significant influences on this coupling and thus the molecular conductance, the diameter of electrodes, the distance, and the torsion angle between electrodes have only minor influences on the conductance, showing the advantage of using SWCNTs as the electrodes for molecular electronic devices.     

Equilibrium calculations of viscosity and thermal conductivity across a solid-liquid interface using boundary fluctuations

We calculate viscosity and thermal conductivity in systems of Lennard-Jones particles consisting of coexisting solid and liquid with different interface wetting properties using the recently developed equilibrium boundary fluctuation theory. We compare the slip length and equivalent liquid length obtained from these calculations with those obtained from nonequilibrium molecular dynamics. The equilibrium and nonequilibrium calculations of the slip length and the sum of the thermal equivalent lengths are in good agreement. We conclude that for both interfacial properties, the nonequilibrium simulations were probing the linear response. The significant dependence of the intrinsic equivalence length on the interfacial temperature difference used to generate the thermal gradient is explained as a consequence of the different thermodynamic states of the two interfaces.     

Molecular-level functionalization of electrode surfaces. An overview

Electrochemical reactions occur at electrode/electrolyte interfaces. Hence, manipulation and design of electrochemical interfaces accompanied by surface modifications have assumed vital importance. Molecular level modification, either at the monolayer or multilayer level of electrode surfaces and leading to functionalization of electrodes, is being actively pursued by researchers. Modification based on the self-assembled monolayer approach has enabled electrodes to acquire molecular recognition and molecular electronic characteristics. Functionalization of electrode surfaces using polymeric materials and enzymes has facilitated electrodes in exhibiting properties like catalysis, molecular recognition, electrochromism and birefringence. The results of such molecular level functionalization studies of electrode surfaces carried out recently in our laboratories are presented in this overview. Besides, some representative results reported from elsewhere are also included.     

Gate-induced switching and negative differential resistance in a single-molecule transistor: emergence of fixed and shifting states with molecular length

The quantum transport of a gated polythiophene nanodevice is analyzed using density functional theory and nonequilibrium Green's function approach. For this typical molecular field effect transistor, we prove the existence of two main features of electronic components, i.e., negative differential resistance and good switching. Ab initio based explanations of these features are provided by distinguishing fixed and shifting conducting states, which are shown to arise from the interface and functional molecule, respectively. The results show that proper functional molecules can be used in conjunction with metallic electrodes to achieve basic electronics functionality at molecular length scales.     

Surface conservation laws at microscopically diffuse interfaces

In studies of interfaces with dynamic chemical composition, bulk and interfacial quantities are often coupled via surface conservation laws of excess surface quantities. While this approach is easily justified for microscopically sharp interfaces, its applicability in the context of microscopically diffuse interfaces is less theoretically well-established. Furthermore, surface conservation laws (and interfacial models in general) are often derived phenomenologically rather than systematically. In this article, we first provide a mathematically rigorous justification for surface conservation laws at diffuse interfaces based on an asymptotic analysis of transport processes in the boundary layer and derive general formulae for the surface and normal fluxes that appear in surface conservation laws. Next, we use nonequilibrium thermodynamics to formulate surface conservation laws in terms of chemical potentials and provide a method for systematically deriving the structure of the interfacial layer. Finally, we derive surface conservation laws for a few examples from diffusive and electrochemical transport.     

Calculating fifth-order Raman signals for various molecular liquids by equilibrium and nonequilibrium hybrid molecular dynamics simulation algorithms

The fifth-order two-dimensional (2D) Raman signals have been calculated from the equilibrium and nonequilibrium (finite field) molecular dynamics simulations. The equilibrium method evaluates response functions with equilibrium trajectories, while the nonequilibrium method calculates a molecular polarizability from nonequilibrium trajectories for different pulse configurations and sequences. In this paper, we introduce an efficient algorithm which hybridizes the existing two methods to avoid the time-consuming calculations of the stability matrices which are inherent in the equilibrium method. Using nonequilibrium trajectories for a single laser excitation, we are able to dramatically simplify the sampling process. With this approach, the 2D Raman signals for liquid xenon, carbon disulfide, water, acetonitrile, and formamide are calculated and discussed. Intensities of 2D Raman signals are also estimated and the peak strength of formamide is found to be only five times smaller than that of carbon disulfide.     

Miniature organic transistors with carbon nanotubes as quasi-one-dimensional electrodes

As the dimensions of electronic devices approach those of molecules, the size, geometry, and chemical composition of the contact electrodes play increasingly dominant roles in device functions. It is shown here that single-walled carbon nanotubes (SWNT) can be used as quasi-one-dimensional (1D) electrodes to construct organic field effect transistors (FET) with molecular scale width ( approximately 2 nm) and channel length (1-3 nm). An important feature owing to the quasi-1D electrode geometry is the favorable gate electrostatics that allows for efficient switching of ultra-short organic channels. This affords room temperature conductance modulation by orders of magnitude for organic transistors that are only several molecules in length, with switching characteristics superior to similar devices with lithographically patterned metal electrodes. With nanotubes, covalent carbon-carbon bonds could be utilized to form contacts to molecular materials. The unique geometrical, physical, and chemical properties of carbon nanotube electrodes may lead to various interesting molecular devices.     

Specifics of localization of carbon black at the interface between polymeric phases

The thermodynamic and kinetic factors that determine the localization of carbon black particles at interfaces in polymer blends were established. Substantial differences in particle localization conditions at the interfaces of two high-molecular-mass or low-molecular-mass liquids were revealed; these differences are manifested in the determining effect of the sequence of mixing of the filler with the polymeric components of the blend on the localization. The effect is explained in terms of nonequilibrium positions of carbon black particles at the interface. This nonequilibrium distribution is primarily due to a high energy of desorption of macromolecules from the solid surface.     

Comparison of transmissive permeable and reflective impermeable interfaces between electrode and electrolyte

This article described the basic concepts of the permeable boundary (PB) and impermeable boundary (IPB) conditions between electrode and electrolyte that are essential in studying diffusion and migration of ions through the electrode for electrochemical devices. The transmission line models (TLMs) were introduced to explain the boundary conditions at the electrode/electrolyte interfaces. The impedance data were simulated based upon the TLMs for PB and IPB conditions, giving attention to the different behaviors of low-frequency impedance. In addition, this article explained that the electrodes used for fuel cells and batteries can be classified according to the PB and IPB conditions.     

Comparison of transmissive permeable and reflective impermeable interfaces between electrode and electrolyte

This article described the basic concepts of the permeable boundary (PB) and impermeable boundary (IPB) conditions between electrode and electrolyte that are essential in studying diffusion and migration of ions through the electrode for electrochemical devices. The transmission line models (TLMs) were introduced to explain the boundary conditions at the electrode/electrolyte interfaces. The impedance data were simulated based upon the TLMs for PB and IPB conditions, giving attention to the different behaviors of low-frequency impedance. In addition, this article explained that the electrodes used for fuel cells and batteries can be classified according to the PB and IPB conditions.

     

Angstrom-Scale Electrochemistry at Electrodes with Dimensions Commensurable and Smaller than Individual Reacting Species

In nature and technologies, many chemical reactions occur at interfaces with dimensions approaching that of a single reacting species in nano- and angstrom-scale. Mechanisms governing reactions at this ultimately small spatial regime remain poorly explored because of challenges to controllably fabricate required devices and assess their performance in experiment. Here we report how efficiency of electrochemical reactions evolves for electrodes that range from just one atom in thickness to sizes comparable with and exceeding hydration diameters of reactant species. The electrodes are made by encapsulating graphene and its multilayers within insulating crystals so that only graphene edges remain exposed and partake in reactions. We find that limiting current densities characterizing electrochemical reactions exhibit a pronounced size effect if reactant's hydration diameter becomes commensurable with electrodes’ thickness. An unexpected blockade effect is further revealed from electrodes smaller than reactants, where incoming reactants are blocked by those adsorbed temporarily at the atomically narrow interfaces. The demonstrated angstrom-scale electrochemistry offers a venue for studies of interfacial behaviors at the true molecular scale.     

Nematic-isotropic interfaces under shear: a molecular-dynamics simulation

We present a large-scale molecular-dynamics study of nematic-paranematic interfaces under shear. We use a model of soft repulsive ellipsoidal particles with well-known equilibrium properties, and consider interfaces which are oriented normal to the direction of the shear gradient (common stress case). The director at the interface is oriented parallel to the interface (planar). A fixed average shear rate is imposed with moving periodic boundary conditions, and the heat is dissipated with a profile-unbiased thermostat. First, we study the properties of the interface at one particular shear rate in detail. The local interfacial profiles and the capillary wave fluctuations of the interfaces are calculated and compared with those of the corresponding equilibrium interface. Under shear, the interfacial width broadens and the capillary wave amplitudes at large wavelengths increase. The strain is distributed inhomogeneously in the system (shear banding), the local shear rate in the nematic region being distinctly higher than in the paranematic region. Surprisingly, we also observe (symmetry-breaking) flow in the vorticity direction, with opposite direction in the nematic and the paranematic state. Finally, we investigate the stability of the interface for other shear rates and construct a nonequilibrium phase diagram.     

Small Systems and Limitations on the Use of Chemical Thermodynamics

Limitations on using chemical thermodynamics to describe small systems are formulated. These limitations follow from statistical mechanics for equilibrium and nonequilibrium processes and reflect (1) differences between characteristic relaxation times in momentum, energy, and mass transfer in different aggregate states of investigated systems; (2) achievements of statistical mechanics that allow us to determine criteria for the size of smallest region in which thermodynamics can be applied and the scale of the emergence of a new phase, along with criteria for the conditions of violating a local equilibrium. Based on this analysis, the main thermodynamic results are clarified: the phase rule for distorted interfaces, the sense and area of applicability of Gibbs’s concept of passive forces, and the artificiality of Kelvin’s equation as a result of limitations on the thermodynamic approach to considering small bodies. The wrongness of introducing molecular parameters into thermodynamic derivations, and the activity coefficient for an activated complex into the expression for a reaction rate constant, is demonstrated.     

A theoretical study of molecular conduction. III. A nonequilibrium-Green's-function-based Hartree-Fock approach

Many recent experimental and theoretical studies have paid attention to the conductivity of single molecule transport junctions, both because it is fundamentally important and because of its significance in the development of molecular-based electronics. In this paper, we discuss a nonequilibrium Green's function (NEGF)-based Hartree-Fock (HF) approach; the NEGF method can appropriately accommodate charge distributions in molecules connected to electrodes. In addition, we show that a NEGF-based density matrix can reduce to an ordinary HF density matrix for an isolated molecule if the molecule does not interact with electrodes. This feature of the NEGF-based density matrix also means that NEGF-based Mulliken charges can be reduced to ordinary Mulliken charges in those cases. Therefore, the NEGF-based HF approach can directly compare molecules that are connected to electrodes with isolated ones, and is useful in investigating complicated features of molecular conduction. We also calculated the transmission probability and conduction for benzenedithiol under finite electrode biases. The coupling between the electrodes and molecule causes electron transfer from the molecule to the electrodes, and the applied bias modifies this electron transfer. In addition, we found that the molecule responds capacitively to the applied bias, by shifting the molecular orbital energies.     

Computing the Soret coefficient in aqueous mixtures using boundary driven nonequilibrium molecular dynamics

We have computed the Soret coefficient in aqueous mixtures using a boundary driven nonequilibrium molecular dynamics algorithm and standard molecular force fields. The choice of this specific approach is justified by the nature of the mixtures studied here. Four aqueous solutions, including methanol, ethanol, acetone, and dimethyl-sulfoxide (DMSO) have been studied at ambient conditions for different compositions. The experimental behavior of water-alcohol mixtures was reproduced, including the change of sign of the Soret coefficient with composition, in excellent agreement with existing experimental data. The methodology has been applied to obtain pure predictions for water-acetone and water-DMSO where no experimental data are accessible. A change of sign is also observed in the same range of composition as in water-alcohol mixtures. It is suggested that the nature and strength of the molecular interactions, rather than the mass or shape ratio of the components, dominates the behavior of the Soret coefficient versus composition for the aqueous associating mixtures studied here.     

Lower size boundary for the applicability of thermodynamics

The problem of the lower boundary of the intrinsic linear size of the range in which the thermodynamic approach is applicable is considered. It is established that a natural constraint of any thermodynamic approach is the discrete structure of a substance at the atomic-molecular level. It is shown that with a reduction in the size of a substance, the fraction of surface particles compared to their total amount grows and spontaneous density fluctuations increase. The molecular theory of density fluctuation in small systems is discussed. Drop radii below which thermodynamic approaches cannot be used, and for which thermodynamic approaches can be used when both the discreteness of a substance and the contributions from spontaneous fluctuations can be ignored, are estimated. The consequences of the molecular theory of curved vapor-liquid interfaces are examined within the lattice gas model for spherical drops in the vapor phase. The limitations and conditions for considering corrections for density fluctuations in macrophases are discussed.     

Modeling the measurements of cellular fluxes in microbioreactor devices using thin enzyme electrodes

An analytic approach to the modeling of stop-flow amperometric measurements of cellular metabolism with thin glucose oxidase and lactate oxidase electrodes would provide a mechanistic understanding of the various factors that affect the measured signals. We divide the problem into two parts: (1) analytic formulas that provide the boundary conditions for the substrate and the hydrogen peroxide at the outer surface of the enzyme electrode layers and the electrode current expressed through these boundary conditions, and (2) a simple diffusion problem in the liquid compartment with the provided boundary conditions, which can be solved analytically or numerically, depending on the geometry of the compartment. The current in an amperometric stop-flow measurement of cellular glucose or lactate consumption/excretion is obtained analytically for two geometries, corresponding to devices developed at the Vanderbilt Institute for Integrative Biosystems Research and Education: a multianalyte nanophysiometer with effective one-dimensional diffusion and a multianalyte microphysiometer, for which plentiful data for metabolic changes in cells are available. The data are calibrated and fitted with the obtained time dependences to extract several cellular fluxes. We conclude that the analytical approach is applicable to a wide variety of measurement geometries and flow protocols.