Lattice models for hydrogen-bonded solvents

A class of lattice models for a binary mixture is defined by assuming that one of the components may form bonds to neighboring molecules of the same species. It is assumed that the fugacity of a molecule depends on the number of bonds which connect the molecule to other molecules. If no molecule is allowed to be connected by more than two bonds to other molecules, then no phase transition occurs, while phase transition can occur if more than two bonds are allowed. If only two or no bonds are allowed, then the model can be solved rigorously for certain planar lattices by transforming it to a dimer covering problem; this model shows behavior similar to the Ising model in zero magnetic field.Work supported by National Science Foundation grant GP-26526.On leave of absence from Corpus Christi College, Cambridge, England.On leave from the University of Copenhagen.     

On the selective catalytic behaviour of the Cu-NI alloy surface

The selective catalytic behaviour of the Cu_xNi_1?x alloy surface is studied. The concentration dependence of the catalytic activity with respect to chemical reactions involving cracking and non-cracking of C-C bonds is calculated for a simple model for C-C bonds. Surface segregation and local environment effects on chemisorption both calculated from a microscopic electronic theory using tight-binding approximation are taken into account.     

Kinetic models of a binary alloy at zero temperature

We study theoretically two types of kinetic models of a binary alloy at zero temperature. In the phase separation model, a nearest-neighbor interchange can occur if the fraction of AB bonds (where A and B denote distinct species of atoms in a binary alloy) is thereby decreased. The crystallization model is defined by the opposite evolution rule. We examine these models in one dimension and obtain exact analytical results for the densities of domain walls, defects, and for a number of other correlators. Nonergodic zero-temperature dynamics leads to final states strongly dependent on initial conditions. For generalized models, in which nearest-neighbor interchange is also performed if the portion of AB bonds is not changed, a very rich kinetic behavior is observed.     

Pd-Mo-K/Al2O3催化剂的结构及合成醇性能

采用ＸＲＤ、ＥＸＡＦＳ技术研究了不同Ｐｄ含量的Ｐｄ－Ｍｏ－Ｋ／Ａｌ２Ｏ３催化剂结构,并关联其合成低碳混合醇性能。结果表明,在氧化态Ｍｏ－Ｋ／Ａｌ２Ｏ３催化剂体系中添加Ｐｄ后,“Ｋ－Ｍｏ”物相晶粒变小,分散度提高,说明钯可能和钾钼物种发生了较强的相互作用。经硫化还原处理后,发生了氧硫交换,钼主要以ＭｏＳ２物种形式存在,其粒度随着Ｐｄ含量的增加而明显减小。尺寸的显著变化可能导致ＭｏＳ２与载体作用形式的     

Microspectroscopic soft X-ray analysis of keratin based biofibers

Scanning soft X-ray transmission microspectroscopy (STXM) and transmission electron microscopy (TEM) have been employed for a high-resolution morphological and chemical analysis of hair fibers from human, sheep and alpaca. STXM allows optimum contrast imaging of the main hair building blocks due to tuneable photon energy. Chemical similarities and deviations for the human hair building blocks as well as for the three investigated species are discussed on the basis of the local near-edge X-ray absorption fine structure (NEXAFS). The spectra of melanosomes corroborate the state-of-the-art model for the chemical structure of eumelanin. Complementary TEM micrographs reveal the occurrence of cortex sectioning in alpaca hair to some extent. A spectroscopic analysis for human hair cortex indicates low mass loss upon soft X-ray irradiation, but transformation of chemical species with decreasing amount of peptide bonds and increasing NEXAFS signal for unsaturated carbon–carbon bonds.     

Random channel kinetics for reaction-diffusion systems

A random channel approach is developed for reaction-diffusion processes in disordered systems. Although the starting point of our research is the kinetic study of the decay and preservation of marine organic carbon, our approach can be used for describing other disordered kinetic catalytic processes with random pathways. We consider a generic catalytic mechanism with two species: (a) a catalyst, which is continuously produced by a variable number of independent sources randomly distributed in space; this catalyst diffuses from the sources and is degrading according to a first order kinetic law; the generation, the degradation and the diffusion of the catalyst balance each other out and a stationary concentration field is generated; (b) an active species, which decays according to a second order kinetic law; the decay rate is proportional to the product of the concentrations of the catalyst and the concentration of the active species. We show that the catalyst concentration field can be represented by the sum of a random number of Yukawa-like potentials. The average value of the survival function of the active species can be expressed as a grand canonical average of a nonlinear functional of the catalyst field and can be evaluated exactly. We show that a good approximation is given by a nearest neighbor approach, where only the contribution of the closest source is taken into account for the computation of the random concentration field of the catalyst. We discuss the application of the model to the problem of decay and preservation of marine organic carbon. With minor adaptation the model can be applied to other problems of disordered kinetics, such as spatially distributed heterogeneous catalytic processes.     

Interactions of triiodide cluster ion with solvents

An equilibrium molecular dynamics model is developed to investigate the interactions of triiodide cluster ion with solvents. The internal dynamics of the triiodide ion is described by a valence bond model which responds to the field of the classical solvent molecules. The solvent molecules were described by standard classical models with rigid molecules, fixed partial charges on atomic sites and site-site Lennard-Jones interactions. One finds the solvent effects on the I^-₃ are unusually strong as it is a very polarizable species. Protic solvents such as water, ethanol, and methanol that can form hydrogen bonds to lead to the I^-₃ geometry with two unequal bonds and an asymmetric distribution of charges. But for the solvents such as xenon, tetrahydrofuran, methyltetrahydrofuran, and acetonitrile, the I^-₃ only illustrates a geometry with two equal bonds. We find that structure changing is induced by local electrostatic attraction between solvent molecules.     

Impact of Mercury(II) on proteinase K catalytic center: investigations via classical and Born-Oppenheimer molecular dynamics

Mercury(II) has a strong affinity for the thiol groups in proteins often resulting in the disruption of their biological functions. In this study we present classical and first-principles, DFT-based molecular dynamics (MD) simulations of a complex of Hg(II) and proteinase K, a well-known serine protease with a very broad and diverse enzymatic activity. It contains a catalytic triad formed by Asp39, His69, and Ser224, which is responsible for its biological activity. It was found previously by X-ray diffraction experiments that the presence of Hg(II) inhibits the enzymatic action of proteinase K by affecting the stereochemistry of the triad. Our simulations predict that (i) the overall structure as well as the protein backbone dynamics are only slightly affected by the mercury cation, (ii) depending on the occupied mercury site, the hydrogen bonds of the catalytic triad are either severely disrupted (both bonds for mercury at site 1, and the His69–Ser224 contact for mercury at site 2) or slightly strengthened (the Asp39–His69 bond when mercury is at site 2), (iii) the network of hydrogen bonds of the catalytic triad is not static but undergoes constant fluctuations, which are significantly modified by the presence of the Hg(II) cation, influencing in turn the triad’s ability to carry out the enzymatic function—these facts explain the experimental findings on the inhibition of proteinase K by Hg(II).     

Comparison of the process of deactivation of homogeneous catalysts by the example of copper(II) compounds in the presence of some additives in various solvents

For a model reaction of tetralylhydroperoxide decomposition, kinetic data for evaluating the catalytic activity of Cu(II) complexes in solvents of different natures were obtained. The experiments were performed using chlorobenzene (aprotic solvent), ethanol (capable of forming intermolecular hydrogen bonds), and ethyl acetate (having no movable proton). The passivation of the catalysts in the presence of benzoic acid and N,N'-bis(o-hydroxybenzoyl) hydrazine (inhibitor) in these solvents was studied. It was found that the tested additives produce different effects on the catalytic activity of the initial and reaction-modified forms of Cu(II).     

Modeling of size and shape dependent band gap,dielectric constant and phonon frequency of semiconductor nanosolids

A bond theory model is extended to study the size and shape dependent optoelectronics properties of semiconductors solids at nanoscale. On structural miniaturization down to nano scale, the optical parameters no longer remain stable but become tunable. The fraction of surface atoms and the dangling bonds on the surface affects the properties of semiconductors at nanoscale. The theory is applied to study the size and shape dependent energy band gap, dielectric constant and phonon frequency of TiO₂, CdS, CdSe, Si and GaN semiconductor nanosolids. We incorporated the relaxation factor, defined as the ratio of dangling bonds and the total bonds of atoms at nano scale. It is predicted that as the energy band increases with decrease in size, the effect becomes more when shape changes from spherical to tetrahedral. The model projects a decrease in phonon frequency and dielectric constants of semiconductor nanostructured materials with decrease in particle size. A good agreement between predicted results and the available experimental data is projected.     

Chemical reactions of chlorine on a vicinal Si(100) surface studied by ESDIAD

The reaction of Cl₂ on a vicinal Si(100) surface has been studied by ESDIAD. This type of surface possesses two types of sites: pairs of dangling bonds on Si---Si terrace dimers, and single dangling bonds on the 2-atom layer high steps. The reactivity of these two sites is compared. For low coverages the step dangling bonds are identified as the preferred Cl bonding site after 673 K-annealing. Upon higher temperature annealing and SiCl₂(g) desorption, the terrace-site Cl species are depleted more rapidly than the step-site Cl species. Extensive isothermal etching under a continuous Cl₂ flux at 800 K is found to produce a disordered surface structure. Heating to 1123 K causes a reordering of the surface.     

Interaction of methanol with ZnO surfaces at low temperatures

Adsorption and condensation of methanol on polar (0001) faces of zinc oxide were studied by XPS and UPS. The results indicate that adsorbed CH₃OH is partly transformed to a precursor of a methoxy species at temperatures at low as 105 K. Adsorption saturates only at a coverage of about two monolayers. This double layer seems to become oriented by the structural influence of the (0001) face and stabilized by hydrogen bridge bonds. The sticking coefficient is of the order of 10^?2 while the condensation coefficient on top of the oriented double layer is as low as 10^?3. TDS on a polycrystalline ZnO film supports this model. No other species than CH₃OH occurred in desorption.     

Uncertainty quantification in the catalytic partial oxidation of methane

This work focuses on uncertainty quantification of eight random parameters required as input for 1D modelling of methane catalytic partial oxidation within a highly dense foam reactor. Parameters related to geometrical properties, reactor thermophysics and catalyst loading are taken as uncertain. A widely applied 1D heterogeneous mathematical model that accounts for proper transport and surface chemistry steps is considered for the evaluation of deterministic samples. The non-intrusive spectral projection approach based on polynomial chaos expansion is applied to determine the stochastic temperature and species profiles along the reactor axial direction as well as their ensemble mean and error bars with a confidence interval of 95%. Probability density functions of relevant variables in specific reactor sections are also analysed. A different contribution is noticed from each random input to the total uncertainty range. Porosity, specific surface area and catalyst loading appear as the major sources of uncertainty to bulk gas and surface temperature and species molar profiles. Porosity and the mean pore diameter have an important impact on the pressure drop along the whole reactor as expected. It is also concluded that any trace of uncertainty in the eight input random variables can be almost dissipated near the catalyst outlet section for a long-enough catalyst, mainly due to the approximation to thermodynamic equilibrium.     

Triple-period partial misfit dislocations at the InN/GaN (0001) interface: A new dislocation core structure for III-N materials

The lattice-misfit InN/GaN (0001) interface supports a triangular network of α-core 90° partial misfit dislocations. These misfit dislocations provide excellent strain relief. However, in their unreconstructed form the dislocation contains numerous high-energy N dangling bonds, which must be eliminated by reconstructing the dislocation core. Existing single-period (SP) and double-period (DP) dislocation reconstruction models eliminate these dangling bonds via a like-atom dimerization, such as N-N dimers. However, we show that these N–N dimers are unstable for the III-N materials, so an entirely new reconstruction mechanism is needed. A “triple-period” (TP) structural model is developed which eliminates N dangling bonds via the formation of N vacancies instead of N-N dimers. The model contains no N–N (or III–III) bonds, fully bonds all N atoms to four group-III neighboring atoms, and satisfies the “electron counting rule” by transferring charge from In dangling bonds to Ga dangling bonds.     

Chemically powered nanodimers

Self-propelled motion of a chemically powered nanodimer is discussed. The nanodimer comprises two linked spheres, one of which has equal interactions with A and B solvent species but catalyzes the reaction A-->B. The other sphere is not chemically active but interacts differently with the two species. The nonequilibrium concentration gradient generated at the catalytic end, in conjunction with the force difference at the noncatalytic end, leads to directed motion. The model mimics features of experimentally studied synthetic nanorod motion. Particle-based simulations and analytical estimates of the velocity provide insight into the nature of nanomotor directed motion.     

Bond theory model to study cohesive energy,thermal expansion coefficient and specific heat of nanosolids

The fraction of surface atoms and the dangling bonds on the surface affect the thermodynamical properties of the nanostructured solids. A bond theory model is extended to study the size dependent thermodynamical properties at nanoscale. The theory is applied to analysis the size and shape dependence of cohesive energy, thermal expansion coefficient and specific heat of Ag, Au, Cu and Se nanosolids. The relaxation factor is incorporated at low dimension of nanosolids, which is expressed as the ratio of dangling bonds and the total bonds of atoms. It is predicted that the cohesive energy decreases with decrease in particle size. On the same ground, the model is proposed to analyze the thermal expansion coefficient and specific heat of the nanomaterials. It is reported that the thermal expansion coefficient and specific heat increase as particle size decreases. The predictions agree well with available experimental or simulation results.     

General theories and features of interfacial thermal transport

A clear understanding and proper control of interfacial thermal transport is important in nanoscale devices. In this review, we first discuss the theoretical methods to handle the interfacial thermal transport problem, such as the macroscopic model, molecular dynamics, lattice dynamics, and quantum transport theories. Then we discuss various effects that can significantly affect the interfacial thermal transport, such as the formation of chemical bonds at interface, defects, interface roughness, strain, substrates, atomic species, mass ratios, and structural orientations. Then importantly, we analyze the role of inelastic scattering at the interface, and discuss its application in thermal rectifications. Finally, the challenges and promising directions are discussed.     

Hydrogen bonding in different pyrimidine–methanol clusters probed by polarized Raman spectroscopy and DFT calculations

We report on the hydrogen bonding between pyrimidine (Pd) and methanol (M) as H‐donor in this study. Hydrogen bonds between pyrimidine and methanol molecules as well as those between different methanol molecules significantly influence the spectral features at high dilution. The ring‐breathing mode ν₁ of the reference system Pd was chosen as a marker band to probe the degree of hydrogen bonding. Polarized Raman spectra in the region 970–1020 cm⁻¹ for binary mixtures of (pyrimidine + methanol) at 28 different mole fractions were recorded. A Raman line shape analysis of the isotropic Raman line profiles at all concentrations revealed three distinct spectral components at mole fractions of Pd below 0.75. The three components are attributed to three distinct groups of species: ‘free Pd’ (pd), ‘Pd with low methanol content’ (pd1) and ‘Pd with high‐methanol content’ (pd2). The two latter species differ considerably in the pattern and the strengths of the hydrogen bonds. The results of density functional theory calculations on structures and vibrational spectra of neat Pd and eight Pd/M complexes with varying methanol content support our interpretations of the experimental results. A nice spectra–structure correlation for the different cluster subgroups was obtained, similar to earlier results obtained for Pd and water. Apart from N···H and O···H hydrogen bonds between pyrimidine and methanol, O···H hydrogen bonds formed among the methanol molecules in the cluster at high methanol content also play a crucial role in the interpretation of the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Heavy-atom skeleton quantization and proton tunneling in "intermediate-barrier" hydrogen bonds

Quantum effects on proton transfer through barriers of several kcal/mol in hydrogen bonds are investigated theoretically in malonaldehyde. Such "intermediate-barrier" proton transfer processes play a key role in the catalytic activity of some enzymes. Tunneling is shown to be significant in this reaction even at room temperature. More importantly, the quantum nature of the heavy molecular frame atoms is found to substantially enhance proton tunneling. These findings have far-reaching implications for common modeling strategies of proton transfer in complex systems such as biomolecules.     

A multi-fluid stagnation-flow plasma model with self-consistenttreatment of the collisional sheath

A two-temperature, multifluid model of a plasma in stagnation flow against a cooled, electrically biased surface is presented. The model couples bulk fluid motion, species diffusion and convection, electron and bulk energy equations, and net finite-rate ionization with Poisson's equation for the electric field in a generalized formulation. Application of the model to argon flow reveals important interactions between thermal, hydrodynamic, chemical and electrical boundary layers, with implications for current-limiting regimes of arcjet operation. The response of a planar Langmuir probe in contact with a collisional, flowing plasma is examined. Determinations of current-voltage behavior compare well with simple theory, including dependence on incident plasma velocity. Departures from this theory arise from boundary-layer perturbations near the electrode surface, away from free-stream conditions. The computational model incorporates a finite-rate catalytic recombination of ions and electrons at the electrode surface together with a specified current