Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

Vacuum-ultraviolet induced oxidation of the polymers polyethylene and polypropylene

The emission from low-pressure microwave plasmas in the vacuum-ultraviolet (VUV) region (λ < 200 nm) was investigated in order to use these plasmas as light sources for the study of the VUV photochemistry of polyethylene (PE) and polypropylene (PP) as part of the study of plasma-polymer interaction. These polymers, immersed in low-presure oxygen, were exposed to radiation with wavelengths down to 112 nm, the cut off of magnesium fluoride used as a window to separate the polymer specimen from the plasma light source. Total oxygen incorporation in the surface [O], and the formation of hydroxyl, carbonyl, and carboxyl groups were measured using XPS in combination with chemical derivatizations, particularly their dependence upon the radiation spectrum and the oxygen pressure around the sample. In most experiments the surface oxygen concentration [O] attained a constant value that appears to be related to the initial oxidation rate; this suggests a competition between oxygen incorporation and chain scission reactions, followed by the removal of volatile oxidation products. PE is usually oxidized to a higher level than PP, the latter appearing to be more susceptible to reaction with atomic oxygen than PE. A general initiation mechanism for the VUV experiments is proposed that allows us to explain the observed differences in behavior between PE and PP, and the results obtained under different irradiation conditions. The nature of oxidation products is in both cases very similar to what is observed after direct plasma treatment of the polymers. We conclude that short wavelength radiation contributes very appreciably to the observed surface modification effects during plasma treatment of PE and PP. © 1995 John Wiley & Sons, Inc.     

Hydrogels in aqueous phases of polyvinylalcohol (PVA), surfactants and clay minerals

Aqueous solutions of synthetic clay minerals have been studied in the presence of surfactants and water-soluble polyvinylalcohol (PVA). The PVAs (PVA 1, PVA 2) had a molecular weight of about 10⁵ Dalton and a degree of hydrolysis of 82%. The PVA-samples were surface active and lowered the surface tension to 43 mN/m. As a consequence of their amphiphilic nature the PVA molecules bind strongly to clay mineral particles. On saturation the clay mineral particles adsorb the fivefold weight of PVA of their own weight. It is concluded that the thickness of the adsorbed layers on both sides of the clay mineral is in the range of the hydrodynamic diameter of the PVA-coils in the bulk phase.When the clay mineral particles are not saturated with PVA, they act as cross-linking agents for the PVA. The whole systems are physically cross-linked and assume gel-like properties. Rheological measurements show that samples behave like soft matter with a yield stress value. All of them have a frequency independent storage modulus which is an order of magnitude larger than the loss modulus. The hydrogels become stronger as PVA concentration increases.Small amounts of cationic surfactants bind on the clay mineral. The interface of the clay mineral becomes more hydrophobic and the binding of the PVA on the clay mineral is strengthened. With rising concentration of the surfactant the surfactant molecules bind on PVA and the PVA becomes hydrophilic. As a consequence the PVA can no longer bind on the clay mineral and the gels transform to viscous and turbid solutions. Small amounts of cationic surfactants therefore stiffen the hydrogels while larger amounts cause phase separation and a solution with low viscosity. Anionic surfactants like SDS do not bind on the clay mineral, but strongly on the PVA. With increasing SDS concentration, the hydrogels become stiffer at first but thereafter they break and transform to viscous fluids.In PVA-solutions without the clay minerals both cationic and anionic surfactants bind to the PVAs in the aqueous solution. With increasing concentration of surfactant, the viscosities of the solutions pass over a maximum. In this respect the PVAs behave like hydrophobically modified water soluble polymers. The surfactants bind to the hydrophobic microdomain and thereby crosslink the polymer molecules. On saturation the polyvinyl alcohol with anionic surfactant become hydrophilic and the network character disappears to a certain extent.     

Elastic behavior of non-Gaussian polymethylene chains

In this paper, elastic behaviors of non-Gaussian polymethylene (PM) chains with chain length N=100 are investigated by rotational isomeric state model. Here the tetrahedral lattice of PM chain and the non-local interaction of Sutherland potential are adopted. In the metropolis movement of PM chain, a four-bond movement model is used. The average energy and average Helmholtz free energy with various elongation ratios λ are calculated by Monte Carlo simulation method. The average energy increases with elongation ratio λ and the average Helmholtz free energy decreases with elongation ratio λ. The elastic force f and the energy contribution to elastic force f_u can be obtained from f=∂〈A〉/∂r and f=∂〈U〉/∂r. We find that the elastic force f increases with elongation ratio λ and the energy contribution f_u decreases with elongation ratio λ, and f_u is less than zero. The ratio f_u/f is close to −0.21 for λ?1.25, and −0.04 to −0.35 for λ>1.25 at T=364 K. In our calculation, the rubber elasticity may be discussed in terms of the chemical structure of polymer chains.     

Measurement of attachment force of microbial cells

A parallel-plate flow chamber consisting of two transparent electro-conductive glass plates was constructed. The two glass plates were set parallel to each other and connected to a potentiostat apparatus to regulate the strength of the electric field between the plates. A microbial cell suspension was flowed through the chamber. This system enabled the application of an electrostatic force to suspend charged particles, e.g. microbial cells, existing between the two plates. The time course of the cell attachment of Pseudomonas syringae pv. atropurpurea NIAES 1309 suspended in 10 mM phosphate buffer solution (pH 7.0) to the glass plate was investigated at various electric field strengths ranging from −4.2 to +4.1 V cm⁻¹. The attachment rate and the maximum number of attached cells increased linearly with the increase in the strength of the positive electric field. In contrast, the rate and the number of cells decreased linearly with the decrease in the strength of the negative electric field. These linear relations gave a specific value for the strength of the electric field (−5.9 ± 0.7 V cm⁻¹) where the electrostatic repulsion and the microbial attachment force were thought to be equal, resulting in no cell attachment. From this value, the electrostatic repulsion, i.e. the microbial attachment force, was calculated to be 5.0 × 10⁻¹¹ N cell⁻¹ for cells of average size.     

Reaction paths of some open-shell reactive intermediates

The intermolecular interaction energy for reacting systems in singlet, triplet and doublet states was partitioned by the perturbation expansion method into the chemically meaningful five interaction terms: the Coulomb, exchange-repulsion, induction, dispersion, and charge-transfer energies. In the local ZDO approximation, these energy terms were evaluated for the dimerization of methylenes (^1,3CH₂), the additions of carbenes (^1,3CH₂ and^1,3CF₂) as well as amino radicals (²NH₂ and²NF₂) toward ethylene, and the hydrogen abstractions by methylenes (^1,3CH₂), nitrene (³NH), and hydroxyl radical (²OH) from methane. It has been found that the reaction path is much influenced by the spinmultiplicity, and that the charge-transfer and exchange-repulsion terms play a dominant role in determining the course of reactions.     

Ab initio SCF investigation of the intramolecular hydrogen bonding in δ-aminopentanoic acid

The potential energy surface of the neutral form of-aminopentanoic acid was investigated by means of ab initio 4-31G SCF calculations. Four symmetry unique local minima are stabilized by an intramolecular O-H NH₂ hydrogen bond. The geometries, energies, and wave numbers of these conformers are reported. The hydrogen bond is discussed with respect to all reactions of these conformers and in comparison with the homologues glycine,-alanine, and-aminobutyric acid and also with the bimolecular adducts between formic acid, acetic acid, and propionic acid, on the one hand, and ammonia, methylamine, and ethylamine, on the other hand.     

探究Cu/ZnO相互作用对CO2加氢制甲醇反应性能的影响

Using renewable green hydrogen and carbon dioxide (CO₂) to produce methanol is one of the fundamental ways to reduce CO₂ emissions in the future, and research and development related to catalysts for efficient and stable methanol synthesis is one of the key factors in determining the entire synthesis process. Metal nanoparticles stabilized on a support are frequently employed to catalyze the methanol synthesis reaction. Metal-support interactions (MSIs) in these supported catalysts can play a significant role in catalysis. Tuning the MSI is an effective strategy to modulate the activity, selectivity, and stability of heterogeneous catalysts. Numerous studies have been conducted on this topic; however, a systematic understanding of the role of various strengths of MSI is lacking. Herein, three Cu/ZnO-SiO₂ catalysts with different strengths of MSI, namely, normal precipitation Cu/ZnO-SiO₂ (Nor-CZS), co-precipitation Cu/ZnO-SiO₂ (Co-CZS), and reverse precipitation Cu/ZnO-SiO₂ (Re-CZS), were successfully prepared to determine the role of such interactions in the hydrogenation of CO₂ to methanol. The results of temperature-programmed reduction (H₂-TPR) and X-ray photoelectron spectroscopy (XPS) characterization illustrated that the MSI of the catalysts was considerably affected by the precipitation sequence. Fourier transform infrared reflection spectroscopy (FT-IR) results indicated that the Cu species existed as CuO in all cases and that copper phyllosilicate was absent (except for strong Cu-SiO₂ interaction). Transmission electron microscopy (TEM), X-ray diffraction (XRD), and N₂O chemical titration results revealed that strong interactions between the Cu and Zn species would promote the dispersion of Cu species, thereby leading to a higher CO₂ conversion rate and improved catalytic stability. As expected, the Re-CZS catalyst exhibited the highest activity with 12.4% CO₂ conversion, followed by the Co-CZS catalyst (12.1%), and the Nor-CZS catalyst (9.8%). After the same reaction time, the normalized CO₂ conversion of the three catalysts decreased in the following order: Re-CZS (75%) > Co-CZS (70%) > Nor-CZS (65%). Notably, the methanol selectivity of the Re-CZS catalyst was found to level off after a prolonged period, in contrast to that of Co-CZS and Nor-CZS. Investigation of the structural evolution of the catalyst with time on stream revealed that the high methanol selectivity of the catalyst was caused by the reconstruction of the catalyst, which was induced by the strong MSI between the Cu and Zn species, and the migration of ZnO onto Cu species, which caused an enlargement of the Cu/ZnO interface. This work offers an alternative strategy for the rational and optimized design of efficient catalysts.     

On the factors affecting the enhanced resonance light scattering signals of the interactions between proteins and multiply negatively charged chromophores using water blue as an example

Electrostatic interactions of proteins, including bovine serum albumin (BSA), human serum albumin (HSA), γ-globulin (γ-IgG), α-chymotrypsin (Chy), lysozyme (Lys) and cellulase (Cel), with multiply negatively charged chromophores were investigated based on the measurements of the enhanced resonance light scattering (RLS) signals. Using triply negatively charged water blue (WB) as an example, the factors were discussed that affect the enhanced resonance light scattering signals of the interactions between proteins and the negatively charged chromophores. It was found that the enhanced RLS signals with the maximum light scattering peak at 346.0 nm in these interacting systems are strongly dependent on the isoelectric points of proteins and show adverse linear relationships with increasing ionic strength depending on the positive charges of the inorganic metal ions used to control the ionic strength of the medium, sufficiently disclosing that the electrostatic attraction performs an important role in the combination of proteins with WB. Linear responses were discovered between the enhanced RLS signals and the protein molecular weights (M_w), displaying the dimensions of scattered particles formed by proteins and WB make a key contribution to the RLS enhancements. An empirical equation is proposed which possibly displays the factors affecting the enhanced RLS signals of the interactions between proteins with negatively charged chromophores.     

基于非生物折叠体的分子识别

利用分子自组装的方法控制大分子量的线性有机分子的构象是物理有机化学一个富于挑战性的研究课题. 近年来, 化学家已经成功利用不同的分子内非共价键作用力如氢键和疏溶剂作用等诱导线性分子的折叠乃至螺旋构象的产生. 综述了近年来这种新的非生物二级结构形式在分子识别研究中的应用.