Evaluation of molecular mechanics calculated binding energies for isolated and monolayer organic molecules on graphite

The calculated molecule-surface binding energy, E(cal)( *), for physical adsorption was determined using molecular mechanics MM2 parameters for a model graphite surface and various organic molecules. The results for E(cal)( *) were compared to published experimental binding energy values, E( *), from gas chromatography (GC) or thermal desorption (TD). The binding energies from GC were for isolated molecules in the Henry's law region of adsorption, and the binding energies from TD were for molecules in monolayer coverage on a highly oriented pyrolytic graphite (HOPG). A simple desorption model was used to allow the calculation of monolayer coverage to include both molecule-surface and molecule-molecule interactions and then the results were compared to experimental values. For the 14 TD organic adsorbates (polyaromatic hydrocarbons, alcohols, benzene, substituted benzenes, methane, chloroalkanes, N,N-dimethylformamide, and C(60) Buckyball), the experimental versus calculated binding energies were E( *)=1.1193E(cal)( *) and r(2)=0.967. The GC E( *) values were also well correlated by calculated E(cal)( *) values for a set of 11 benzene and methyl substituted benzenes and for another set of 10 alkanes and haloalkanes. The TD E(cal)( *) mechanics computation provides a useful comparison to the one for GC data since adsorbate-adsorbate interactions as well as adsorbate-surface must be considered.     

Adsorption energies for a nanoporous carbon from gas-solid chromatography and molecular mechanics

Gas-solid chromatography was used to obtain second gas-solid virial coefficients, B2s, in the temperature range 342-613 K for methane, ethane, propane, butane, 2-methylpropane, chloromethane, chlorodifluoromethane, dichloromethane, and dichlorodifluoromethane. The adsorbent used was Carbosieve S-III (Supelco), a carbon powder with fairly uniform, predominately 0.55 nm slit width pores and a N2 BET surface area of 995 m2/g. The temperature dependence of B2s was used to determine experimental values of the gas-solid interaction energy, E*, for each of these molecular adsorbates. MM2 and MM3 molecular mechanics calculations were used to determine the gas-solid interaction energy, E*(cal), for each of the molecules on various flat and nanoporous model surfaces. The flat model consisted of three parallel graphene layers with each graphene layer containing 127 interconnected benzene rings. The nanoporous model consisted of two sets of three parallel graphene layers adjacent to one another but separated to represent the pore diameter. A variety of calculated adsorption energies, E*(cal), were compared and correlated to the experimental E* values. It was determined that simple molecular mechanics could be used to calculate an attraction energy parameter between an adsorbed molecule and the carbon surface. The best correlation between the E*(cal) and E* values was provided by a 0.50 nm nanoporous model using MM2 parameters.     

有机硅活性中间体的研究 II. 一些含环丙基的有机硅化合物的合成及其结构

用锂有机物的方法合成了四种含有环丙基有机硅化合物,对上述每种化合物中可能存在着的立体异构进行了分离和和构型测定。     

Binding energies for alkane molecules on a carbon surface from gas-solid chromatography and molecular mechanics

Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for 12 alkanes (10 branched and 2 cyclic) interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 393 to 623 K with each alkane measured at 5 or 6 different temperatures. The temperature variations of the gas-solid virial coefficients were used to find the experimental adsorption energy or binding energy values (E( *)) for each alkane. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (E(cal)( *)) using augmented MM2 parameters. The surface model consisted of three parallel graphene layers with each layer containing 127 interconnected benzene rings and two separated nanostructures each containing 17 benzene rings arranged in a linear strip. As the parallel nanostructures are moved closer together, the surface roughness increases and molecule-surface interactions are enhanced. A comparison of the experimental and calculated binding energies showed excellent agreement with an average difference of 3.8%. Linear regressions of E( *) versus E(cal)( *) for the current data set and a combined current and prior alkane data set both gave excellent correlations. For the combined data set with 18 linear, branched and cyclic alkanes; a linear regression of E( *)=0.9848E(cal)( *) and r(2)=0.976 was obtained. The results indicate that alkane-surface binding energies may be calculated from MM2 parameters for some gas-solid systems.     

The microwave heating of two-dimensional slabs with small Arrhenius absorptivity

The microwave heating of two-dimensional slabs in a long rectangularwaveguide propagating the TE₁₀ mode is examined. The temperaturedependency of the electrical conductivity and the thermal absorptivityis assumed to be governed by the Arrhenius law, while both theelectrical permittivity and the magnetic permeability are assumedconstant. The governing equations are the forced heat equationand the steady-state version of Maxwell's equation while theboundary conditions take into account both convective and radiativeheat loss. Approximate analytical solutions, valid for smallthermal absorptivity, are found for the temperature and theelectric-field amplitude using the Galerkin method. As the Arrheniuslaw is not amenable analytically, it is approximated by a rational-cubicfunction. At the steady state the temperature versus power relationshipis found to be multivalued; at the critical power level thermalrunaway occurs when the temperature jumps from the lower (cool)temperature branch to the upper (hot) temperature branch ofthe solution. In the steady-state limit the approximate analyticalsolutions are compared with the numerical solutions of the governingequations for various special cases. These are the limits ofsmall and large heat loss and an intermediate case involvingradiative heat loss. Results are also presented for a case wheredifferential cooling occurs on the different sides on the slab.An alternative heating scenario, where one end of the waveguideis blocked by a short, is also considered. The approximate solutionsare found for this geometry and compared in the small Biot-numberlimit to Kriegsmann (1997). Also, a control process is presented,which allows thermal runaway to be avoided and the desired finalsteady state to be reached. Various special cases of the feedbackparameters associated with the control process are examined.     

Bi-directional modulation of AMPA receptor unitary conductance by synaptic activity

Background  

Knowledge of how synapses alter their efficiency of communication is central to the understanding of learning and memory. The most extensively studied forms of synaptic plasticity are long-term potentiation (LTP) and its counterpart long-term depression (LTD) of AMPA receptor-mediated synaptic transmission. In the CA1 region of the hippocampus, it has been shown that LTP often involves a rapid increase in the unitary conductance of AMPA receptor channels. However, LTP can also occur in the absence of any alteration in AMPA receptor unitary conductance. In the present study we have used whole-cell dendritic recording, failures analysis and non-stationary fluctuation analysis to investigate the mechanism of depotentiation of LTP.     

Predicting second gas-solid virial coefficients using calculated molecular properties on various carbon surfaces

Gas-solid chromatography was used to obtain values of the second gas-solid virial coefficient, B2s, in the temperature range from 343 to 493 K for seven adsorbate gases: methane, ethane, propane, chloromethane, chlorodifluoromethane, dimethyl ether, and sulfur hexafluoride. Carboxen-1000, a 1200 m2/g carbon molecular sieve (Supelco Inc.), was used as the adsorbent. These data were combined with earlier work to make a combined data set of 36 different adsorbate gases variously interacting with from one to four different carbon surfaces. All B2s values were extrapolated to 403 K to create a set of 65 different gas-solid B2s values at a fixed temperature. The B2s value for a given gas-solid system can be converted to a chromatographic retention time at any desired flow rate and can be converted to the amount of gas adsorbed at any pressure in the low-coverage, Henry's law region. Beginning with a theoretical equation for the second gas-solid virial coefficient, various quantitative structure retention relations (QSRR) were developed and used to correlate the B2s values for different gas adsorbates with different carbon surfaces. Two calculated adsorbate molecular parameters (molar refractivity and connectivity index), when combined with two adsorbent parameters (surface area and a surface energy contribution to the gas-solid interaction), provided an effective correlation (r2 = 0.952) of the 65 different B2s values. The two surface parameters provided a simple yet useful representation of the structure and energy of the carbon surfaces and thus our correlations considered variation in both the adsorbate gas and the adsorbent solid.     

Twisting DNA: single molecule studies

Over the past 10 years a number of new techniques have emerged that allow the manipulation of single DNA molecules and other biopolymers (RNA, proteins, etc.). These experiments have permitted the measurement of the DNA stretching and twisting elasticity and have consequently revealed the essential role played by the DNA mechanical properties in its interactions with proteins. We shall first describe the different methods used to stretch and twist single DNA molecules. We will then focus on its behaviour under torsion, especially by discussing the different methods used to estimate its torsional modulus.     

PROMOT: A Modeling Tool for Chemical Processes

The novel process modeling tool PROMOT supports the object-oriented modeling of chemical processes for the simulation environment DIVA. In PROMOT, differential-algebraic process models can be built by aggregating structural and behavioral modeling entities that represent the topological structure or the dynamic and steady-state behavior, respectively, of the investigated chemical processes. Process models and their modeling entities may be defined either in an object-oriented modeling language or with a graphical user interface. This paper discusses the modeling concept, the modeling language, the knowledge representation aspects, and the implementation of PROMOT.     

Determining molecule-carbon surface adsorption energies using molecular mechanics and graphene nanostructures

Five model surfaces were developed using molecular mechanics with MM2 parameters. A smooth, flat model surface was constructed of three parallel graphene layers where each graphene layer contained 127 interconnected benzene rings. Four rough surfaces were constructed by varying the separation between a pair of graphene nanostructures placed on the topmost layer of graphene. Each nanostructure contained 17 benzene rings arranged in a linear strip. The parallel nanostructures were moved closer together to increase the surface roughness and to enhance the molecule-surface interaction. Experimental adsorption energy values from the temperature variation of second gas-solid virial coefficients values were available for 16 different alkanes, haloalkanes, and ether molecules adsorbed on Carbopack B (Supelco, 100 m(2)/g). For each of the five different surface models, sets of 16 calculated adsorption energies, E(cal)( *), were determined and compared to the available experimental adsorption energies, E( *). The best linear regression correlation between E( *) and E(cal)( *) was found for a 1.20 nm internuclei separation of the surface nanostructures, and for this surface model the calculated gas-solid interaction energies closely matched the experimental values (E( *)=1.018E(cal)( *), r(2)=0.964).