Electron spectroscopy with excited atoms and photons.: X. Halogen-substituted methanes and methyl amines

Electron binding energy spectra have been measured for CH₃Cl, CH₃Br, CH₃I, CFCl₃, CF₂Cl₂, CF₃Cl, CF₄, CH₃NH₂, (CH₃)₂ NH and (CH₃)₃N. Measurements have been made using 584 Å (21.22 eV) photons as well as with 2³S(19.82 eV) and 2¹S(20.62 eV) metastable helium atoms. Relative spectral intensities are compared for photoionization and Penning ionization.     

Rate coefficients for the reactions CH3 + Br2 (224–358 K), CH3CO + Br2 (228 and 298 K), and Cl + Br2 (228 and 298 K)

Rate coefficients for the reactions of CH₃ + Br₂ (k₂), CH₃CO + Br₂ (k₃), and Cl + Br₂ (k₅) were measured using the laser‐pulsed photolysis method combined with detection of the product Br atoms using resonance fluorescence. For the reactions involving organic radicals, the rate coefficients were observed to increase with decreasing temperature and within the temperature range explored, were adequately described by Arrhenius‐like expressions: k₂ (224–358 K) = 1.83 × 10^?11 exp(252/T) and k₃ (228–298 K) = 2.92 × 10^?11 exp(361/T) cm³ molecule^?1 s^?1. The total, temperature‐independent uncertainty for each reaction (including possible systematic errors in Br₂ concentration measurement) was estimated as ～7% for k₂ and 10% for k₃. Accurate data on k₅ was obtained at 298 K, with a value of 1.88 × 10^?10 cm³ molecule^?1 s^?1 obtained (with an associated error of 6%). A limited data set at 228 K suggests that k₅ is, within experimental uncertainty, independent of temperature. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 575–585, 2010     

Determination of the adsorption isotherm of methanol on the surface of ice. An experimental and grand canonical Monte Carlo simulation study

The adsorption isotherm of methanol on ice at 200 K has been determined both experimentally and by using the Grand Canonical Monte Carlo computer simulation method. The experimental and simulated isotherms agree well with each other; their deviations can be explained by a small (about 5 K) temperature shift in the simulation data and, possibly, by the non-ideality of the ice surface in the experimental situation. The analysis of the results has revealed that the saturated adsorption layer is monomolecular. At low surface coverage, the adsorption is driven by the methanol-ice interaction; however, at full coverage, methanol-methanol interactions become equally important. Under these conditions, about half of the adsorbed methanol molecules have one hydrogen-bonded water neighbor, and the other half have two hydrogen-bonded water neighbors. The vast majority of the methanols have a hydrogen-bonded methanol neighbor, as well.     

Absorption cross section and photolysis of OIO

Pulsed laser photolysis combined with transient absorption spectroscopy and resonance fluorescence was used to examine the photolysis of OIO at a number of wavelengths corresponding to absorption bands in its visible spectrum between approximately 530 and 570 nm. Photolysis at 532 nm was found to result in substantial depopulation of the absorbing ground state, enabling an estimate for the absorption cross section of OIO at 610.2 nm of (6 +/- 2) x 10(-18) cm2 molecule(-1) to be obtained. No evidence was found for I atom formation following photolysis of OIO at 532, 562.3, 567.9 and 573.8 nm, enabling an upper limit to the I atom quantum yield of < 0.05 (560-580 nm) and < 0.24 (532 nm) to be established.     

The reaction of IO with CH3SCH3: products and temperature dependent rate coefficients by laser induced fluorescence

The technique of pulsed laser photolysis was coupled to laser induced fluorescence detection of iodine oxide (IO) to measure rate coefficients, k(1)(T), for the title reaction IO + CH3SCH3 --> products (R1). A value of k1(298 K) = (1.44 +/- 0.15) x 10(-14) cm3 molecule(-1) s(-1) was obtained, independent of bath gas pressure (50 < P((N2 or air))/Torr < 300). The expression k1(T) = (3.2 +/- 1.4)x 10(-13)exp[(-925 +/- 136)/T)] adequately described the data over the range of temperatures (256 < T/K < 341) covered. Uncertainties (2sigma) in the 298 K rate coefficient and the pre-exponential factor include an estimate of systematic error. The conventional Arrhenius behaviour of k1(T) and the lack of pressure dependence are suggestive of an abstraction mechanism, characterised by an energy barrier of E approximately 8 kJ mol(-1). The product yield for production of I-atoms was determined indirectly to be close to unity, indicating that the reaction proceeds via transfer of the O-atom from IO to CH3SCH3 to form CH3S(O)CH3. In general, the values of k1(T) measured in this work indicate that has little impact on the chemistry of the atmosphere.     

New faster CHARMM molecular dynamics engine

We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. © 2013 Wiley Periodicals, Inc.     

Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ

The Family 7 cellobiohydrolase (Cel7A) from Trichoderma reesei consists of a carbohydrate-binding module (CBM) joined by a linker to a catalytic domain. Cellulose hydrolysis is limited by the accessibility of Cel7A to crystalline substrates, which is perceived to be primarily mediated by the CBM. Here, the binding of CBM to the cellulose Iβ fiber is characterized by combined Brownian dynamics (BD) and molecular dynamics (MD) simulations. The results confirm that CBM prefers to dock to the hydrophobic than to the hydrophilic fiber faces. Both electrostatic (ES) and van der Waals (VDW) interactions are required for achieving the observed binding preference. The VDW interactions play a more important role in stabilizing the CBM-fiber binding, whereas the ES interactions contribute through the formation of a number of hydrogen bonds between the CBM and the fiber. At long distances, an ES steering effect is also observed that tends to align the CBM in an antiparallel manner relative to the fiber axis. Furthermore, the MD results reveal hindered diffusion of the CBM on all fiber surfaces. The binding of the CBM to the hydrophobic surfaces is found to involve partial dewetting at the CBM-fiber interface coupled with local structural arrangements of the protein. The present simulation results complement and rationalize a large body of previous work and provide detailed insights into the mechanism of the CBM-cellulose fiber interactions.     

Standardization for oxygen isotope ratio measurement - still an unsolved problem

Numerous organic and inorganic laboratory standards were gathered from nine European and North American laboratories and were analyzed for their delta(18)O values with a new on-line high temperature pyrolysis system that was calibrated using Vienna standard mean ocean water (VSMOW) and standard light Antartic precipitation (SLAP) internationally distributed reference water samples. Especially for organic materials, discrepancies between reported and measured values were high, ranging up to 2 per thousand. The reasons for these discrepancies are discussed and the need for an exact and reliable calibration of existing reference materials, as well as for the establishment of additional organic and inorganic reference materials is stressed. Copyright 1999 John Wiley & Sons, Ltd.     

Quantification of collagen organization and extracellular matrix factors within the healing ligament

Ligament healing of a grade III injury (i.e., a complete tear) involves a multifaceted chain of events that forms a neoligament, which is more scar-like in character than the native tissue. The remodeling process may last months or even years with the injured ligament never fully recovering pre-injury mechanical properties. With tissue engineering and regenerative medicine, understanding the normal healing process in ligament and quantifying it provide a basis to create and assess innovative treatments. Ligament fibroblasts produce a number of extracellular matrix (ECM) components, including collagen types I and III, decorin and fibromodulin. Using a combination of advanced histology, molecular biology, and nonlinear optical imaging approaches, the early ECM events during ligament healing have been better characterized and defined. First, the dynamic changes in ECM factors after injury are shown. Second, the factors associated with creeping substitution are identified. Finally, a method to quantify collagen organization is developed and used. Each ECM factor described herein as well as the temporal quantification of fiber organization helps elucidate the complexity of ligament healing.