Semi-empirical insertion probability for hard-spheres and hard-sphere chains

In spite of its simplicity and a well-defined theoretical basis, the Flory–Guggenheim approach is conventionally regarded as inapplicable to off-lattice system since the insertion probability of the approach does not account for the excluded region, existing in the off-lattice system. In this work, we propose the insertion probability accounting for the excluded region of off-lattice fluids and derive a new version of equation of state (EOS) for hard-sphere chains basing on the Flory–Guggenheim approach. To investigate the behavior of the excluded regions, a Monte Carlo sampling was performed for hard disks and the various excluded regions were found to have different density dependence. On the basis of the simulation result, we formulated the insertion probability for hard-sphere and that of hard-sphere chain which accounts for the effect of chain-connectivity on the monomer insertion. The proposed insertion probability was found to correctly predict the simulation data for monomer and correctly correlate the simulation data for chain fluids. The resulting EOS was found to meet closed-packed limit and predict the simulation data of compressibility factor for monomer and chains with a reasonable degree of accuracy. When compared with other off-lattice based EOS, it shows a comparable or better result. For second virial coefficient of chain molecules, the model was found to reasonably predict the simulation data.     

Prediction of hydrogen solubility in heavy hydrocarbons over a range of temperatures and pressures using molecular dynamics simulations

Using the method of molecular dynamics (MD), we have estimated the solubility of hydrogen in heavy hydrocarbons for a range of temperatures and pressures. Heavy hydrocarbon systems are known to be challenging not only for experimental measurements but also for reliable estimations using traditional equations of state (EOS). The simulation system used was designed with semi-permeable membranes to mimic actual experimental studies of gas solubility. Binary interaction parameters between the solute gas and the solvent (heavy hydrocarbons) components were adjusted when necessary to improve agreement with experimental results and then used in subsequent multi-component studies. Temperature and pressure ranges studied included higher temperatures and pressures which are especially difficult to investigate experimentally. Simulation results were finally used to adjust the binary interaction parameters (BIP) in simulation packages (e.g. Aspen) to enable quick and reliable predictions.     

Surface diffusion in reversed-phase liquid chromatography

More than 40 years ago, Giddings pointed out in “Dynamics of Chromatography” that surface diffusion should become an important research topic in the kinetics of chromatographic phenomena. However, few studies on surface diffusion in adsorbents used in chromatography were published since then. Most scientists use ordinary rate equations to study mass transfer kinetics in chromatography. They take no account of surface diffusion and overlook the significant contributions of this mass transfer process to chromatographic behavior and to column efficiency at high mobile phase flow rate. Only recently did the significance of surface diffusion in separation processes begin to be recognized in connection with the development of new techniques of fast flow, high efficiency chromatography. In this review, we revisit the reports on experimental data on surface diffusion and introduce a surface-restricted molecular diffusion model, derived as a first approximation for the mechanism of surface diffusion, on the basis of the absolute rate theory. We also explain how this model accounts for many intrinsic characteristics of surface diffusion that cannot properly be explained by the conventional models of surface diffusion.     

Metal-organic chains constructed from pre-organized N2S2 donor ligands

Three new N₂S₂ donor ligands 1,1′-((2-(2-(phenylthio)phenylthio)phenyl)methylene)bis(3,5-R-1H-pyrazole), R = H (L^H), R = Me (L^Me), R = i-Pr (L^i-Pr) have been prepared and characterized. These bifunctional ligands incorporate two distinct chelate donor systems, by virtue of the presence of bispyrazole and bisthioether functions. The preferred conformation of these ligands is such that the N₂ and S₂ donor moieties may be oriented in opposite directions, thus favoring the formation of molecular chains when treated with AgBF₄. The X-ray structures of Ag(I) complexes show that, depending on the steric hindrance present on the pyrazole rings, these ligands behave as κ⁴-SSNN-μ bridging tetradentate (when R = H), or κ³-SNN-μ bridging tridentate (when R = Me, i-Pr). Interestingly, [Ag(L^H)]BF₄ crystallizes in the chiral space group P4₁, with the molecular chain that is folded around the 4₁ screw axis.     

Evaluation of selective composite cryogel for bromate removal from drinking water

Bromate, which is a potential carcinogen, should be removed from drinking water to levels of less than 10 μg/L. A chitosan‐based molecularly imprinted polymer (MIP) and a sol–gel ion‐exchange double hydrous oxide (Fe₂O₃·Al₂O₃·xH₂O) adsorbent (inorganic adsorbent) were prepared for this purpose. The sorption behavior of each adsorbent including sorption kinetics, isotherms, effect of pH and selective sorption were investigated in detail. Sorption experimental results showed that the MIP adsorbents had better selectivity for bromate, even in the presence of high concentrations of nitrate, as compared to the inorganic adsorbent. It was found that pH does not affect the adsorption of bromate when using the inorganic adsorbent. Additionally, both adsorbents were immobilized in a polymeric cryogel inside plastic carriers to make them more practical for using in larger scale. Regeneration of the cryogels either containing MIP or inorganic adsorbents were carried out by 0.1 M NaOH and 0.1 M NaCl, respectively. It was found that the regenerated MIP and inorganic adsorbents could be used at least three and five times, respectively, without any loss in their sorption capacity.     

Vibrational Spectra and Density Functional Theory Calculations of Metallo-tetra-(tert-butyl)-tetra-azaporphyrines

The infrared absorption and 514.5 nm excited Raman spectra were measured for the metallo-tetra-(tert-butyl)-tetraazaporphyrin (MT(tBu)TAP, M=Cu, Co, Ni, Zn). The ground-state structures and vibrational spectra of MT(tBu)TAPs have been calculated at the B3LYP level of theory. The observed Raman and IR bands have been assigned based on the calculation results and by comparing with the normal metalloporphyrins. The relationship between the Raman/IR frequencies and the structures of TAP ring was investigated. The results show that the frequencies of C_βC_β′ stretch (A_g), asymmetric C_αN_m stretch (A_g), and symmetric C_αN_m stretch (B_g) modes increase linearly with the decrease of the core-sizes of TAP ring.Among the three modes, the later two are more sensitive to the core-size change.     

Molecular Dynamic Simulation on the Absorbing Process of Isolating and Coating of α-olefin Drag Reducing Polymer

The absorbing process in isolating and coating process of α-olefin drag reducing polymer was studied by molecular dynamic simulation method, on basis of coating theory of α-olefin drag reducing polymer particles with polyurethane as coating material. The distributions of sodium laurate, sodium dodecyl sulfate, and sodium dodecyl benzene sulfonate on the surface of α-olefin drag reducing polymer particles were almost the same, but the bending degrees of them were obviously different. The bending degree of SLA molecules was greater than those of the other two surfactant molecules. Simulation results of absorbing and accu-mulating structure showed that, though hydrophobic properties of surfactant molecules were almost the same, water density around long chain sulfonate sodium was bigger than that around alkyl sulfate sodium. This property goes against useful absorbing and accumulating on the surface of α-olefin drag reducing polymer particles; simulation results of interactions of different surfactant and multiple hydroxyl compounds on surface of particles showed that, interactions of different surfactant and one kind of multiple hydroxyl compound were similar to those of one kind of surfactant and different multiple hydroxyl compounds. These two contrast types of interactions also exhibited the differences of absorbing distribution and closing degrees to surface of particles. The sequence of closing degrees was derived from sim-ulation; control step of addition polymerization interaction in coating process was absorbing mass transfer process, so the more closed to surface of particle the multiple hydroxyl com-pounds were, the easier interactions with isocyanate were. Simulation results represented the compatibility relationship between surfactant and multiple hydroxyl compounds. The isolating and coating processes of α-olefin drag reducing polymer were further understood on molecule and atom level through above simulation research, and based on the simulation, a referenced theoretical basis was provided for practical optimal selection and experimental preparation of α-olefin drag reducing polymer particles suspension isolation agent.     

Molecular Dynamics Simulation of Ester‐Linked Hen Egg White Lysozyme Reveals the Effect of Missing Backbone Hydrogen Bond Donors on the Protein Structure

The three‐dimensional structure of a protein is stabilized by a number of different atomic interactions. One of these is hydrogen bonding. Its influence on the spatial structure of the hen egg white lysozyme is investigated by replacing peptide bonds (except those of the two proline residues) by ester bonds. Molecular dynamics simulations of native and ester‐linked lysozyme are compared with the native crystal structure and with NOE distance bounds derived from solution NMR experiments. The ester‐linked protein shows a slight compaction while losing its native structure. However, it does not unfold completely. The structure remains compact due to its hydrophobic core and a changed network of hydrogen bonds involving side chains.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.