Structure, density and viscosity of water

We analyzed the possibilities of the use of the cluster model of water to assess its viscosity. The Nemethy-Scheraga model was used in our study. In a simplified version, this model implies the presence of water cluster that are linked by hydrogen bonds as well as individual molecules (monomolecules) interacting only by van der Waals forces. The paper gives an estimation of average cluster size. Based on the experimental temperature dependences of viscosity and density, the content of monomolecules in water was approximately determined. In the first case, the ratio of the viscosity of water to monomolecules was estimated from the inverse Arrhenius temperature dependence of viscosity by considering experimental activation energy ~18.6 kJ mol–1 (0÷300C) and energy of dispersion interactions ~7.4 kJ mol–1. Then, the volumetric content of monomolecules was estimated by using the inverse Betchelor's formula, which relates the viscosity of the suspension (clusters) and dispersion medium (monomolecules) to their ratio. On the other hand, a similar estimation was performed based on the density of water, clusters that were considered similar to ice floes, and the estimated density of monomolecules. Both estimates showed that the volumetric content of water not bound into clusters does not exceed 9%. It was concluded that the structure of water most likely corresponds to the clathrate model, according to which some of the H2O molecules move into the middle of ice-like clusters, and vacancies are stabilized by H3O+–OH– pairs.

A Mechanism Based Probe for Visualising Chromatinmodifying Enzyme Lysine-Specific Histone Demethylase 1

Lysine-specific demethylase 1 (LSD1), the first histone demethylase to be identified, catalyses specifically the demethylation of the mono and dimethyl groups of histone 3 (H3) lysine 4 (K4), and its dysregulation is thought to contribute to the development of cancer. GlaxoSmithKline (GSK) and Oryzon Genomics (ORY) have submitted numerous N-alkylated phenylcyclopropylamine (PCPA) molecules to phase II clinical trials against several different cancers. Eight probes have been designed and synthesised with alkyne and azide tags from PCPA. Their inhibitory values have been investigated towards Monoamine Oxidase (MAO) and LSD1, showing over two times the increase in selectivity towards LSD1. Probe 1 has been subject to cell treatment and its ability to inhibit LSD1 confirmed using NTERA2 cells. Furthermore, these synthesised probes are conjugated to a peptide to successfully guide the probes into the cell. The addition of the peptide causes an increase in the inhibitory values towards LSD1 by on average seven fold. Chiral separation was undertaken on probe 7 to explore the potential inhibition differences of the two enantiomers. Single Crystal X-Ray Diffraction analysis and 1H NMR Nuclear Overhauser effect (nOe) confirmed the chiral separation, with inhibitory data showing (1 R – 2 S)-probe 7 is a more potent inhibitor of LSD1 than its enantiomer. In addition to this, N-alkylation of probe 4 achieved a successfully increase of potency towards LSD1 over PCPA. The mechanistic inhibition pathway for PCPA inhibiting LSD1 is currently unknown. Here, DFT is used on cluster models of Flavin Adenine Dinucleotide (FAD) and the active site of LSD1 (135 atoms and 218 atoms) to investigate the mechanistic inhibition pathway for PCPA inhibiting the FAD cofactor. The calculated energy of the potential rate determining step was 45.3 kcal mol-1 which is 23.5 kcal mol-1 greater than the experimental activation energy for the inhibition of LSD1.

DISSOLUTION KINETICS OF GOLD IN SYSTEM THIOUREA–THIOSULFATE WITH OXIDANT OF Fe(III)EDTA

Cyanidation remains the predominant technology for the dissolution of gold from mineral raw materials. Environmental and technological disadvantages in the use of cyanides are the cause of the development of alternative systems, which include reagent-oxidant and reagent-complexant. A special place is occupied by the solvents, in which the formation of heteroligand complexes of gold is possible. Thus due to the formation of more durable compounds the rate of dissolution of the metal increases. In this work, as the ligands the thiourea and the ions of thiosulfate in the form of sodium salt were used, as the oxidant – complex of the iron (III) and EDTA. The influence of the mixed solvent composition on the kinetic characteristics and the reaction mechanism was studied by the rotating disc method. To confirm the role of different ligand complexes, the dependence of the dissolution rate of gold by the mixed system – thiosulphate and thiourea in the isomolar series, was determined. With a constant total ligands concentration, the molar ratio of reagents was changing. On the basis of the data obtained, a mathematical model of the process of oxidative dissolution of gold is proposed. A characteristic feature of the calculated results is a substantial increase in the reaction constants for the formation of heteroligand complexes, which confirms their role in the process of gold oxidation. The influence of pH and concentration of oxidant and ligand-forming substances on the kinetics of gold dissolution is established. To elucidate the mechanism of the limiting stage of the heterophase process, the experimental activation energy is calculated and the effect of the disk rotation frequency on the dissolution rate is studied. The experimental activation energy is 28.1 kJ/mol. The order by the disk rotation frequency is 0.35. Evaluation of the contribution of the diffusion and kinetic components of rate is estimated on the basis of the modified Levich equation for the mixed regime. Diffusion component of rate is almost an order of magnitude smaller than the kinetic one. Calculation of the diffusion flux of the supplied reagents showed that the only process that inhibits mass transfer is the diffusion of the reaction products from the surface of the rotating disc. The formation of more durable heteroligand complexes and a greater equilibrium constant of the oxidation reaction lead to an increase in the concentration of products at the surface and, consequently, to an increase in the rate of diffusion of the metal into the solution. An important factor affecting the oxidation of gold in the system studied is the formation of intermediate solid reaction products on the metal surface. To identify solid products, IR spectra of reflection of polished gold surface after etching in the system studied were obtained. A strong absorption band in the 808-762 cm-1 region is observed on the spectra. Absorption in this region is associated with valence symmetrical vibrations of the bond of the –C = S group adsorbed or chemically bound to the surface of the molecules of thiourea and its oxidation products. Depending on the composition of the solution and the temperature, the maximum of the peak shifts, and its intensity also changes. This can be explained by a change in the composition of the adsorbed compounds. The efficiency of regeneration of the oxidant Fe(III)EDTA by oxygen in thiourea-thiosulfate solution has been showed.

A DFT study on the mechanism of reaction between 2, 4-diisocyanatotolune and cellulose

The reaction mechanisms between 2, 4-Diisocyanatotolune (2, 4-TDI) and cellulose have been investigated using the density functional theory at the B3LYP/6-31[Formula: see text]G (d, p) level. The calculations show that the direct addition of 2, 4-TDI and cellulose possesses an unrealistically high barrier of 32–34[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. With a neighboring [Formula: see text]-d-glucose serving as a proton transporter by forming a flexible six-membered ring transition state, the energy barrier of the reaction is significantly reduced to 16–18 kcal[Formula: see text]mol[Formula: see text], which is in a good accordance with the experimental activation energy of 13.9–16.7[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is indicated that the reaction between 2, 4-TDI and cellulose is auto-catalyzed with a neighboring [Formula: see text]-d-glucose acting as a reactive catalyst.

Lithium Dendrite Inhibition on Post-Charge Anode Surface: The Kinetics Role

ABSTRACTWe report experiments and molecular dynamics calculations on the kinetics of electrodeposited lithium dendrites relaxation as a function of temperature and time. We found that the experimental average length of dendrite population decays via stretched exponential functions of time toward limiting values that depend inversely on temperature. The experimental activation energy derived from initial rates as Ea∼ 6-7 kcal/mole, which is closely matched by MD calculations, based on the ReaxFF force field for metallic lithium. Simulations reveal that relaxation proceeds in several steps via increasingly larger activation barriers. Incomplete relaxation at lower temperatures is therefore interpreted a manifestation of cooperative atomic motions into discrete topologies that frustrate monotonic progress by ‘caging’.

Ion Irradiated Amorphous Silicon: A Model Approach to Dynamics of Defect Creation and Annihilation

ABSTRACTThe dynamics of defect annihilation and creation in amorphous silicon (a-Si) are measured in detail using defect-related changes in the electrical conductivity of a-Si A model is proposed which for the first time can track the complete time evolution of defect population across the activation energy spectrum with explicit dependence on irradiation and annealing parameters. The model is based upon experimental activation energy spectrum, bimolecular recombination kinetics, and on the notion of a maximum density of defect states beyond which no additional defects can be supported. The new model predicts transient dynamics in defect population and describes structure of the defect population in detail. Its predictions are in good qualitative agreement, and in reasonable quantitative agreement with experimental data.

The kinetic study of the addition of tetrachloromethane to styrene in the presence of copper complexes

Kinetics of the addition of tetrachloromethane to styrene catalyzed by copper-amine complexes was studied. The pseudo-first order kinetics in respect to styrene and the catalyst was observed at an excess of tetrachloromethane. The reaction mechanism involving a catalytic cycle compatible with the kinetic observations is proposed. The experimental activation energy, being about 104 kJ mol-1, indicates a catalytic mechanism.

Alkaline hydrolysis of monomethyl esters of maleic and fumaric acids

The kinetics of alkaline hydrolysis of maleic and fumaric acids monomethyl esters were studied as function of the temperature, ionic strength, and relative permittivity of the reaction medium. Electrostatic and nonelectrostatic contributions of the interaction energies of reacting species were calculated from the measured data and compared with the experimental activation energy values. The dependence of the rate constant on the temperature brings an evidence for the mutual compensation of the electrostatic and nonelectrostatic effects.

The carbon monoxide/nitrous oxide reaction. Kinetics of catalysis on TiO2 (anatase) and ZnO and activity correlations for the first-row transition metal oxides

The catalytic reaction between carbon monoxide and nitrous oxide on titanium dioxide (anatase) and zinc oxide has been examined in a continuous flow reactor at atmospheric pressure. The experimental activation energy was 144 ± 4 kJ mol−1 from 723 to 793 K on TiO2 and 121 ± 4 kJ mol−1 from 543 to 653 K on ZnO. Analyses of kinetic results indicated that a transient carbonate-like species may be involved in catalysis on both oxides. Relationships between the experimental activation energies for the CO/N2O reaction on first-row transition metal oxides and (i) activation energies for isotopic oxygen exchange, (ii) heats of carbonate formation, and (iii) the charge/radius ratio of the cation are interpreted in terms of the influence on catalysis of the cohesive properties of the metal/oxygen bonds in the oxide surfaces.

Reorientation of thiophene molecules in a benzene lattice

Benzene and thiophene are known to form solid solutions over the entire composition range; the present work demonstrates the orientational freedom of thiophene molecules in solid solution with excess perdeuterobenzene, through measurements of spin–lattice relaxation times. In addition, the atom–atom approximation to intermolecular forces yielded a potential energy profile for in-plane rotation of a thiophene molecule, embedded in a benzene lattice, which is consistent with the experimental activation energy for the relaxation. The second moment of the absorption signal for thiophene in perdeuterobenzene at 80 K was determined to be 0.66 G2, compared with a value of 0.42 G2 computed as the intramolecular contribution only for in-plane rotation