ChemInform Abstract: Reactions of Sodium Clusters with Oxygen Molecules.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

Kinetics of CO oxidation on the surface of heterophase catalysts. Modeling by the Monte Carlo method

The Monte Carlo method has been used to simulate CO oxidation on a lattice consisting of various alternating patches: M1, where s(CO)>s(O₂) and M2, where s(CO)2). The reaction is shown to proceed over all the surface at low temperature as CO_ads spillover from M1 to M2 and backwards.     

苯乙烯在顺1,4-聚丁二烯上的接枝共聚反应动力学的Monte Carlo模拟

用ＭｏｎｔｅＣａｒｌｏ模拟方法对苯乙烯在顺１，４－聚丁二烯上的接枝反应动力学进行了研究。模拟结果表明，对于不同的橡胶浓度，接枝的和均聚的聚苯乙烯的数均聚合度、接枝效率与苯乙烯在顺１，４－聚丁二烯上的接枝共聚反应的动力学的解析解十分吻合，证明本方法能够有效地应用于自由基型接枝共聚合反应体系。     

Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 Å from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.     

A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor

Summary A novel pharmacophore definition procedure is described, which uses a Monte Carlo method to superimpose molecules. Pharmacophore space is searched by a technique similar to high temperature annealing. Subsequent refinement of candidate pharmacophores by energy minimization produces low-energy conformations that may be involved in receptor binding. The method has been applied to compounds that bind to the human platelet-activating factor (PAF) receptor. Alternative binding site models for the PAF receptor are presented and discussed.A preliminary account of this work has been published elsewhere [1].     

Application of kinetic Monte Carlo method to equilibrium systems: vapour-liquid equilibria

Kinetic Monte Carlo (kMC) simulations were carried out to describe the vapour-liquid equilibria of argon at various temperatures. This paper aims to demonstrate the potential of the kMC technique in the analysis of equilibrium systems and its advantages over the traditional Monte Carlo method, which is based on the Metropolis algorithm. The key feature of the kMC is the absence of discarded trial moves of molecules, which ensures larger number of configurations that are collected for time averaging. Consequently, the kMC technique results in significantly fewer errors for the same number of Monte Carlo steps, especially when the fluid is rarefied. An additional advantage of the kMC is that the relative displacement probability of molecules is significantly larger in rarefied regions, which results in a more efficient sampling. This provides a more reliable determination of the vapour phase pressure and density in case of non-uniform density distributions, such as the vapour-liquid interface or a fluid adsorbed on an open surface. We performed kMC simulations in a canonical ensemble, with a liquid slab in the middle of the simulation box to model two vapour-liquid interfaces. A number of thermodynamic properties such as the pressure, density, heat of evaporation and the surface tension were reliably determined as time averages.     

3D Monte Carlo Simulations of Diffusion Limited Cluster Aggregation up to the Sol-Gel Transition: Structure and Kinetics

Three-dimensional (3D) Monte Carlo simulations of diffusion limited cluster aggregation at different concentrations () show a crossover from a flocculation regime at short times to a percolation regime close to the gel time (t_g). Contrary to suggestions in the literature t_g is independent of the system size (L) for large L. The structural and temporal crossovers between flocculation and percolation take place at characteristic values of the cluster mass (m_c) and the time (t_c) which depend on . After normalisation by these characteristic values the crossovers are independent of except for very small clusters and at short times. The concentration dependence of m_c and t_c indicates that the crossover takes place at a given cumulated volume fraction of the clusters independent of . At low concentrations the -dependence of t_g is determined by the cluster growth in the flocculation regime.     

On Coarse-Graining by the Inverse Monte Carlo Method: Dissipative Particle Dynamics Simulations Made to a Precise Tool in Soft Matter Modeling

We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD) simulations, which are then used in coarse-grained dissipative particle dynamics (DPD) simulations. Here, the effective potentials were obtained by applying the inverse Monte Carlo method [Lyubartsev and Laaksonen, Phys. Rev. E. 52, 3730 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. In our first application of the method, the effective potentials were used in DPD simulations of aqueous NaCl solutions. With the same computational effort we were able to simulate systems of one order of magnitude larger than the MD simulations. The results from the MD and DPD simulations are in excellent agreement.     

Modeling the structure of amorphous MoS3: a neutron diffraction and reverse Monte Carlo study

A model for the structure of amorphous molybdenum trisulfide, a-MoS3, has been created using reverse Monte Carlo methods. This model, which consists of chains of MoS6 units sharing three sulfurs with each of its two neighbors and forming alternate long, nonbonded, and short, bonded, Mo-Mo separations, is a good fit to the neutron diffraction data and is chemically and physically realistic. The paper identifies the limitations of previous models based on Mo3 triangular clusters in accounting for the available experimental data.     

Monte Carlo simulation of RRKM unimolecular decomposition in molecular beam experiments. III. Application to angular distributions and branching fractions for the system K + CsF

The experiments on the reactive systems K + CsF and K + RbF by Stolte et al. are unique in that product angular distributions and branching fractions with variation of both translational and rotational energies have been obtained. The results for the reaction K + CsF with translational energy variation have now been re-evaluated using an algorithm recently published by us. A satisfactory fit to the experimental data is found by a long-lived collision complex model including strict angular momentum conservation in both the reactive and the non-reactive channels. No “osculating” behaviour has to be added to the model. Angular momentum limits have to be included in the model to reach agreement with the measured branching fractions and cross sections. This indicates that the internal dynamics of the complexes is important. The calculation shows that the reactants giving reactive complexes have large rotational and vibrational energies, while their translational energy is nearly average. The internal energy of reactive pairs of molecules decreases with increasing translational energy. The question how rapidly the branching fraction varies with translational energy is thus more complicated to answer than believed previously.     

Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid

The paper reports a Monte Carlo technique for estimation of the free energies of fluids by sampling on distributions designed for this purpose, rather than on the usual Boltzmann distribution. As an illustration of its use, the free energy of a Lennard-Jones fluid in the liquid-vapour coexistence region has been estimated by relating it to that of the inverse-twelve (soft sphere) fluid, which itself shows no condensation.     

A combined pressure-controlled scanning calorimetry and Monte Carlo determination of the Joule-Thomson inversion curve. Application to methane

A combination of a pressure-controlled scanning calorimetry (PCSC) and Monte Carlo simulations (MCS) is presented for an unequivocal determination of the Joule-Thomson inversion curve (JTIC) with high accuracy over wide ranges of pressure and temperature. The MCS performed with the fluctuation method are fast and easy to operate, but the results can vary significantly depend on the set of primary molecular data needed for the calculations. The PCSC is an experimental and more laborious technique, but supplies data of high quality. Thus, it can be used to check the MCS data and to verify the molecular parameters used for the calculations. Such a combined procedure was used in the present study for determination of the JTIC for methane, for which a correlation equation was established valid from 302.9 to 586.5 K. A combination of a direct experimental technique with molecular simulations permits also to better understand the complex behavior of the Joule-Thomson inversion phenomenon over wide ranges of pressure and temperature.     

Monte Carlo Simulation of the Topology and Conformational Behavior of Hyperbranched Molecules: Pd–Diimine‐Catalyzed Polyethylene

A kinetic Monte Carlo model was developed to simulate the polymerization of ethylene with palladium–α‐diimine catalyst wherein hyperbranched molecules are formed through a chain‐walking mechanism. The total degree of branching and the distribution of short branches obtained with the model agree well with reported ¹³C NMR experimental results. Different chain topologies were generated by varying the probability of chain walking, P_w , which controls the competition between chain‐walking and monomer insertion. Molecular Monte Carlo simulations were subsequently conducted to study the conformations of isolated molecules (created by the kinetic Monte Carlo scheme) to relate molecular shape and topology. Our results provide evidence that the topology varies from predominantly linear with many short branches at low P_w to a densely branched, globular structure at high P_w . In contrast to experimental observations, our results for the molecular weight (N) dependence of the radius of gyration (R_g ∝ N^v) indicate that the branching topology has an effect on this relation, i. e., high‐P_w molecules have a smaller scaling exponent v. The simulated N‐dependence of the second virial coefficient exhibits a similar behavior. We also discuss the unusual conformational behavior of highly branched polymers obtained when P_w → 1.     

Theoretical Investigation on the Charge Transport Properties of 2,5-Di(cyanovinyl)-thiophene/furan with the Kinetic Monte Carlo Method

Exploring, designing, and synthesizing novel organic field-effect transistor(OFET) materials have kept an important and hot issue in organic electronics. In the current work, the charge transport properties for 2,5-di(cyanovinyl)thiophene/furan crystal associating two pentafluorophenyl units linked via the azomethine bond, CTE and CFE have been theoretically investigated by means of density functional theory(DFT) calculations coupled with the incoherent charge-hopping mechanism and the kinetic Monte Carlo simulation. Results show that these two compounds possess remarkably low-lying HOMO(–7.0 eV) and LUMO(–4.0 e V) levels, as well as large electron affinities( 3.0 e V), which indicate their high stability exposed to air as promising OFET materials. However, the μh value at room temperature(T = 300 K) is predicted to be 2.058×10~(-7) cm~2·V~(-1)·s~(-1), and the μe is as low as 9.834×10~(-8) cm~2·V~(-1)·s~(-1) for CFT crystal. Meanwhile, these two values are 7.561 × 10~(-8) and 8.437 × 10~(-8) cm~2·V~(-1)·s~(-1) for the CFE crystal, respectively. Furthermore, the simulation of angle-dependent mobility in the a-b, a-c, and b-c crystal planes shows that the charge transport in CTE and CFE crystals is remarkably anisotropic, which maybe is helpful for the fabrication of high-performance OFET devices.     

Monte Carlo simulation for inhomogeneous chemical kinetics: Application to the Belousov–Zhabotinskii reaction

A Monte Carlo algorithm, capable of simulating numerically the time and space dependence of chemical concentrations in a reacting system, is presented. This method is used to study the phenomenon of trigger waves in the Oregonator model of the Belousov–Zhabotinskii reaction, including the diffusion of species X and Y in one dimension. The results show that a small disturbance in a homogeneous mixture can grow into a chemical (trigger) wave propagating in space at constant velocity. The dependence of this velocity on several factors is studied, namely, initial concentrations, the diffusion of Y, and the stoichiometry of the autocatalytic step of the model. A comparison of the Monte Carlo results with a previous simulation also is discussed.     

Monte Carlo investigations of dense copolymer systems. III. Properties of triblock copolymers in good and theta solvent

The present article gives an analysis of XYX triblock copolymers in a good solvent and in a theta solvent, the segments of type X and type Y being repulsive for each other. The results are compared to homopolymers as well as to copolymers in a selective solvent that is a good one for the outer blocks and a theta solvent for the inner one and vice versa, the strength of repulsion between blocks being the same as in the present types of copolymers. A lattice model is used for the investigations and the concentration ranges from a volume fraction phi = 0 up to phi = 0.8. In the limit phi --> 0 the triblocks in good solvent are slightly more expanded than homopolymers and in theta solvent mean square dimensions of triblocks are considerably increased compared to homopolymers due to the repulsion between blocks. With increasing concentration the dimensions decrease but then they increase again and for large concentrations they become similar for all types of copolymers studied, as the effect of the solvent levels off making the repulsive interaction between blocks the dominant interaction. This leads to an orientation effect and as a consequence to microphase separation which is demonstrated by the concentration dependence of various quantities as well as by visualization of snapshots.     

Thermal Analysis and Kinetics of Solid-State Reactions Its Application to Education in Chemistry

In an attempt to show the importance of preparing extensively teaching materials for comprehensive education in thermal analysis at an undergraduate level, the significance of the teaching materials concerning the thermal analysis and kinetics of the solid-state reactions is discussed by reviewing our teaching activities at Hiroshima University. Application of the thermoanalytical techniques to thermal decomposition of basic copper(II) salts is appropriate for an introductory experiment to thermal analysis. Microscopic observations of the textural change during the thermal dehydration of inorganic salt hydrates are suitable for introducing the kinetics of solid-state reactions. A computer practice of drawing the experimental master plot enables students to understand the kinetic theory. This revised version was published online in August 2006 with corrections to the Cover Date.