Determination of complex reaction mechanisms. Analysis of chemical, biological and genetic networks

We present several methods of determining, not guessing, complex chemical reaction mechanisms and their functions. One method is based on the theory of correlation functions of measured time series of concentrations of chemical species; another is on measurements of temporal responses of concentrations to various perturbations of arbitrary magnitude; a third deals with the analysis of oscillatory systems; a fourth is on the use of genetic algorithms to determine functions of chemical reaction networks. All methods are applicable to chemical, biochemical, and biological reaction systems and to genetic networks and systems biology. The methods depend on the design of appropriate experiments on the whole system and corresponding theories for interpretation that lead to information on the causal chemical connectivity of species, on reaction pathways, on reaction mechanisms, on control centers in the system, and on functions of the system. The first three methods require no assumption of a model or hypothesis, nor extensive calculations, unlike the interpretation of measurements made on a gene network at only one time.     

Different approaches to legal requirements on validation of test methods for official control of foodstuffs and of veterinary drug residues and element contaminants in the EC

 In order to ensure food consumer protection as well as to avoid barriers to trade and unnecessary duplications of laboratory tests and to gain mutual recognition of results of analyses, the quality of laboratories and test results has to be guaranteed. For this purpose, the EC Council and the Commission have introducedprovisions – on measures for quality assurance for official laboratories concerning the analyses of foodstuffs on the one hand and animals and fresh meat on the other, – on the validation of test methods to obtain results of sufficient accuracy. This article deals with legal requirements in the European Union on basic principles of laboratory quality assurance for official notification to the EC Commission and on method validation concerning official laboratories. Widespread discussions and activities on measurement uncertainty are in progress, and the European validation standards for official purposes may serve as a basis for world-wide efforts on quality harmonization of analytical results. Although much time has already been spent, definitions and requirements have to be revised and further additions have to be made.     

A Comparative Study of Electrochemical Reduction of 4‐Nitrophenyl Covalently Grafted on Gold and Carbon

4‐Nitrophenyl layers were grafted on gold and glassy carbon surfaces by electrochemical reductive adsorption of the corresponding diazonium salt. Electrochemical conversion efficiencies of 4‐nitrophenyl moieties to 4‐aminophenyl moieties on gold versus on glassy carbon in a protic medium were investigated using X‐ray photoelectron spectroscopy (XPS). In total contrast to all previous comparative studies showing greater electrochemical reactivity of aryl diazonium salt‐derived layers on gold than on glassy carbon, a much lower rate of conversion to 4‐aminophenyl was observed on gold than on glassy carbon by both cyclic voltammetry (CV) and chronoamperometry (CA) methods. The lower electron transfer rate during conversion observed on gold versus glassy carbon was proposed to be due to a mechanism related to the molecular structure rearrangement of 4‐nitrophenyl during the process on glassy carbon. However, whilst complete conversion of 4‐nitrophenyl to 4‐aminophenyl on gold by chronoamperometry was achieved, on glassy carbon complete reduction could not be achieved under the same conditions.     

Dewetting of liquids on ceramic surfaces at high temperatures.

The influence of surface structure and chemistry on high-temperature dewetting of silicate liquids on ceramic surfaces has been investigated. Model systems based on well-defined crystallography and known chemistry have been used to illustrate the effect of surface roughness and chemistry on the dewetting process. Reconstructed ceramic surfaces provide ideal substrates to study effects of surface roughness. It has been shown that the morphology of dewet droplets depend on the length scale and the crystallography of the facets on the surface. Complex pattern formation due to solute redistribution during dewetting is illustrated in the case of SiO2 dewetting on (001) rutile substrates. The role of kinetics on the dewetting process has also been clarified.     

溶菌酶蛋白在聚合物防污膜表面的吸附

采用分子动力学模拟方法比较了溶菌酶蛋白在两种典型聚合物防污材料聚乙二醇(PEG)和聚二甲基硅氧烷(PDMS)表面的吸附行为, 在微观上探讨了聚合物膜表面性质对蛋白质吸附的影响. 根据蛋白质与聚合物膜之间的相互作用、能量变化及表面水化层分子的动力学行为, 解释了PEG防污涂层相对于PDMS表面具有更佳防污效果的原因: (1) 相比PDMS涂层, 蛋白质与PEG涂层的结合能量较低, 使其结合更加疏松; (2) 蛋白质吸附到材料表面要克服表面水化层分子引起的能障, PEG表面与水分子之间结合紧密, 结合水难于脱附, 造成蛋白质在其表面的吸附需要克服更高的能量, 不利于蛋白质的吸附.     

Role of the Fermi surface in adsorbate-metal interactions: an energy decomposition analysis

We present the result of a fragment-based energy decomposition analysis on some molecule-surface interactions. The analysis allows us to quantify the Pauli repulsion, its relief, and the attractive orbital interaction energy. In a metal, the existence of incompletely occupied energy bands causes significant relief of the Pauli repulsion due to escape of antibonding electrons to unoccupied states at the Fermi energy. This is the key electronic structure feature of metals that causes metal-molecule bond energies to be stronger and dissociation barriers of chemisorbed molecules to be much lower than those in comparable systems with no or one metal atom. As examples, we discuss the energy decomposition for the activated dissociation of hydrogen on the Cu surface and its unactivated dissociation on Pd, and for the (activated) chemisorption of N2 on W. We show that in all cases the relief of Pauli repulsion is of crucial importance for the chemisorption energy and for the low (or nonexistent) dissociation barriers. The barrier to the chemisorption well for nitrogen on tungsten is clearly related to a late relief of the Pauli repulsion. The relief of Pauli repulsion is important in lowering the barrier to dissociation of H2 on both Cu and Pd, but the difference in barrier heights for Cu and Pd appears to not be due to stronger relief of Pauli repulsion on Pd but primarily to the Pauli repulsion itself being stronger on Cu than on Pd, the relief energy being quite comparable on the two metals.     

The electroreduction of formaldehyde on tin and indium

The electrochemical behavior of formaldehyde on tin and indium cathodes has been studied over a wide range of pH (0.4–13), concentrations (1×10^?3 to 6×10^?1M) and potentials. Potentiostatic, potentiodynamic, ac impedance and photoe mission techniques were used to determine the kinetics of the reaction and to postulate a mechanism. The behavior on indium is similar to that reported on mercury cathodes. Tafel slopes are about 65 to 80 mV/decade. This value indicates that protonation of a reaction intermediate is the rate determining step of the reaction. The value of the slope depends slightly on concentration and pH because of adsorption under Temkin conditions. The reaction order with respect to formaldehyde is close to 1 in the limiting current region, but smaller in the Tafel region. The effect of formaldehyde on tin in neutral and alkaline solutions is to decrease the hydrogen overpotential by about 0.5 V, without affecting the Tafel slope. The rate of formaldehyde reduction is very slow. An explanation for this catalytic effect is postulated, based on the adsorption of formaldehyde-related species on the electrode surface. Formation of bridge-type complexes is also postulated. The exact nature of the adsorbed species is unknown. Preliminary results indicate that the behavior of formaldehyde on lead is similar to that on tin. The influence of this species on the reduction of formic acid on tin and lead is discussed.     

Ru—Co—Mo／Al2O3还原催化剂：CO和NO吸附的红外光谱研究

本文采用CO、NO作为探针分子,应用红外光谱法对其在还原态Mo/Al_2O_3,Co-Mo/Al_2O_3,Ru-Mo/Al_2O_3,Ru-Co-Mo/Al_2O_3系列催化剂上的吸附态进行了表征。CO和NO在Mo,Co,Ru中心上的吸附峰随着它们的担载量增加而增强。Co和Ru作为助剂对Mo中心的吸附能力产生显著不同的影响,增加Co担载量大大减少了Mo中心的吸附NO量,并且NO在Co中心上的吸附红外谱带1775,1860 cm~(-1)位移到1800,1879 cm~(-1);而增加Ru担载量则加强了CO和NO在Mo中心上的吸附量,并使得NO在Mo中心上的吸附红外谱带1706,1812 cm~(-1)红移至1679,1801 cm~(-1)。根据实验结果,本文分别对Co和Ru的助剂功能进行了讨论。     

Spectroscopic analysis of L-histidine adsorbed on gold and silver nanoparticle surfaces investigated by surface-enhanced Raman scattering

The adsorption of l-histidine on gold (Au) and silver (Ag) nanoparticle surfaces has been comparatively analyzed by means of surface-enhanced Raman scattering (SERS). The SERS spectra of l-histidine on Ag were found to be quite different from those on Au, indicating dissimilar adsorption structures depending on metal substrates. Most peaks of l-histidine on Ag appeared to be due to coordination via the carboxylate (COO(-)) group with an imidazole ring of fairly upright geometry, whereas on Au it was assumed to adsorb with a rather flat geometry. A density functional theory (DFT) calculation was performed at the level of B3LYP/LANL2DZ to estimate the energetic stability of the binding of the imidazole ring and the carboxylate group of l-histidine with the Ag and Au atoms, respectively. Based on the DFT calculation, the carboxylate group of l-histidine was predicted to bind more favorably to Ag than to Au, and this was in line with our SERS spectral analysis.     

CO adsorption on Ag(100) and Ag/MgO(100)

Theoretical studies of CO adsorption on a two-layer Ag(100) film and on a two-layer Ag film on a MgO(100) support are reported. Ab initio calculations are carried at the configuration interaction level of theory using embedding methods to treat the metal-adsorbate region and the extended ionic solid. The metal overlayer is considered in two different structures: where Ag-Ag distances are equal to the value in the bulk solid, and for a slightly expanded lattice in which the Ag-Ag distances are equal to the O-O distance on the MgO(100) surface. The calculated adsorption energy of Ag(100) on MgO(100) is 0.58 eV per Ag interfacial atom; the Ag-O distance is 2.28 A. A small transfer of electrons from MgO to Ag occurs on deposition of the silver overlayer. CO adsorption at an atop Ag site is found to be the most stable for adsorption on the two-layer Ag film and also for adsorption on Ag deposited on the oxide; CO adsorption energies range from 0.12 to 0.19 eV. The CO adsorption energy is reduced for the Ag/MgO system compared to adsorption on the unsupported metal film thereby providing evidence for a direct electronic effect of the oxide support at the metal overlayer surface. Expansion of the Ag-Ag distance in the two-layer system also reduces the adsorption energy.     

Interfacial behavior of tetrapyridylporphyrin monolayer arrays

The behavior of monolayer films of free base 5,10,15,20-tetrapyridylporphinato (TPyP) and 5,10,15,20-tetrapyridylporphinato zinc(II) (ZnTPyP) on pure water, 0.1 M CdCl2, and 0.1 M CuCl2 subphases was investigated by surface pressure-area isotherms, specular X-ray reflectometry, and polarized total reflection X-ray absorption spectroscopy (PTRXAS). Surface pressure-area isotherms showed significant differences in the area per molecule on pure water compared to that on salt subphases, with a marked increase in the area observed on the salt solutions. This behavior was noted for both forms of the porphyrin and both salts investigated. Modeling of specular X-ray reflectometry data indicated that thinner and more electron dense layers on salt subphases best fit the observed profiles. These data suggest that the porphyrin macrocycle is oriented parallel to the interface on salt subphases and takes on a tilted conformation on pure water. In the case of ZnTPyP, PTRXAS was used to determine the orientation of the porphyrin moiety relative to the surface and to probe the coordination of the central Zn ion. In agreement with the pressure-area isotherms and reflectometry, the PTRXAS data indicate a change in orientation on the salt subphases.     

甲醇与氧在银钯合金上的吸附和反应

本文运用UPS、超高真空程序升温反应谱(TPRS)研究了氧和甲醇在银钯合金上的吸附和反应。实验结果表明, 合金表面存在两种分别与Ag和Pd原子有关的活性位; 少量钯原子的存在, 一方面提供了甲醇分解反应的活性中心, 另一方面通过与银之间的电子相互作用, 削弱了氧与银的结合, 增强了表面吸附氧的反应活性, 从而改变了甲醇氧化反应的选择性。     

Cell docking inside microwells within reversibly sealed microfluidic channels for fabricating multiphenotype cell arrays

We present a soft lithographic method to fabricate multiphenotype cell arrays by capturing cells within an array of reversibly sealed microfluidic channels. The technique uses reversible sealing of elastomeric polydimethylsiloxane (PDMS) molds on surfaces to sequentially deliver various fluids or cells onto specific locations on a substrate. Microwells on the substrate were used to capture and immobilize cells within low shear stress regions inside channels. By using an array of channels it was possible to deposit multiple cell types, such as hepatocytes, fibroblasts, and embryonic stem cells, on the substrates. Upon formation of the cell arrays on the substrate, the PDMS mold could be removed, generating a multiphenotype array of cells. In addition, the orthogonal alignment and subsequent attachment of a secondary array of channels on the patterned substrates could be used to deliver fluids to the patterned cells. The ability to position many cell types on particular regions within a two dimensional substrate could potentially lead to improved high-throughput methods applicable to drug screening and tissue engineering.     

Ionic reaction of halogens with terminal alkenes: the effect of electron-withdrawing fluorine substituents on the bonding of halonium ions

Ionic reactions of terminal alkenes with chlorine (Cl(2)), bromine (Br(2)), and iodine monochloride (ICl) are sensitive to the alkyl substituents, and the positions and number of vinyl fluorine atoms. These perturbations influence the symmetry of the halonium ion intermediates, which can be determined by the distribution of the Markovnikov to anti-Markovnikov products. A vinyl fluorine on the number-2 carbon favors an unsymmetrical intermediate with greater charge on the number-2 carbon unless the alkyl group is electron withdrawing. A vinyl fluorine on the terminal number-1 carbon favors positive charge development on that carbon unless a resonance stabilizing group is on the number-2 carbon. The symmetry of halonium ions with vinyl fluorines on both carbons-1 and -2 depends primarily on the characteristics of the alkyl substituent. Intermediates range from open-ions with the positive charge on carbon-2, to various bridged species, to open-ions on the terminal carbon.     

Effect of capillary condensation on friction force and adhesion

Friction force measurements have been conducted with a colloid probe on mica and silica (both hydrophilic and hydrophobized) after long (24 h) exposure to high-humidity air. Adhesion and friction measurements have also been performed on cellulose substrates. The long exposure to high humidity led to a large hysteresis between loading and unloading in the friction measurements with separation occurring at large negative applied loads. The large hysteresis in the friction-load relationship is attributed to a contact area hysteresis of the capillary condensate which built up during loading and did not evaporate during the unloading regime. The magnitude of the friction force varied dramatically between substrates and was lowest on the mica substrate and highest on the hydrophilic silica substrate, with the hydrophobized silica and cellulose being intermediate. The adhesion due to capillary forces on cellulose was small compared to that on the other substrates, due to the greater roughness of these surfaces.     

溶菌酶蛋白在聚合物防污膜表面的吸附

采用分子动力学模拟方法比较了溶菌酶蛋白在两种典型聚合物防污材料聚乙二醇(PEG)和聚二甲基硅氧烷(PDMS)表面的吸附行为,在微观上探讨了聚合物膜表面性质对蛋白质吸附的影响.根据蛋白质与聚合物膜之间的相互作用、能量变化及表面水化层分子的动力学行为,解释了PEG防污涂层相对于PDMS表面具有更佳防污效果的原因:(1)相比PDMS涂层,蛋白质与PEG涂层的结合能量较低,使其结合更加疏松;(2)蛋白质吸附到材料表面要克服表面水化层分子引起的能障,PEG表面与水分子之间结合紧密,结合水难于脱附,造成蛋白质在其表面的吸附需要克服更高的能量,不利于蛋白质的吸附.     

Reverse nonequilibrium molecular dynamics simulation of thermal conductivity in nanoconfined polyamide-6,6

A new molecular dynamics simulation method, with coupling to external baths, is used to perform equilibrium simulations on polyamide-6,6 trimers nanoconfined between graphene surfaces, in equilibrium with the bulk polymer. The method is coupled with the reverse nonequilibrium molecular dynamics simulation technique to exchange heat in the direction normal to the surfaces. To be able to study the effect of confinement on the heat conductance in nanoconfined pores, in this work a number of simulations on systems with different pore sizes are done. It is concluded that the coefficient of heat conductivity depends on the degree of polymer layering between the surfaces and on the pore width. Our results further indicate a considerable temperature drop at the interface between the surfaces and polymer. The calculated Kapitza lengths depend on the intersurface distance and on the layering of the polymer nanoconfined between the surfaces.     

THEORY OF GAS-PHASE ACIDITY(Ⅰ)CORRELATION OF DEPROTONATION ENERGY WITH HYDROGEN CHARGE

The charge distributions of various acids and their conjugate bases are calculated by using CNDO/2 and MNDO with full geometry optimization.The deprotonation energy is found to be better correlated with the charge on the acidic hydrogen than with the charge on the atom linking to the hydrogen and with the charge on the nucleophilic atom of the conjugate base.This shows that the charge on the acidic hydrogen has an important effect on acidity,whereas the effect of the charge on the linking atom and on the nucleophilic atom of the conjugate base is not important.It can thus be deduced that the view of stabilization of the anio'n due to dispersion of the negative charge is not a significant explanation of acidity.     

NiO nanocone as a CO sensor: DFT investigation

Adsorption properties of CO molecule on NiO nanocone were investigated using density functional approach in terms of adsorbed energy, structural, and electronic properties. The results of the present study reveal that the favorable adsorption site for CO molecule is to the oxygen atom on the apex of NiO nanocone. The adsorbed energy on the apex of oxygen atom in nanocone is found to be ?8.432 eV. The average variation in the energy gap is found to be 50 % for CO adsorption on apex of oxygen atom. The Mulliken population analysis and density of states also confirm the adsorption of CO on to the oxygen atom in the apex of nanocone. The present result provides the insight to fine-tune the sensing properties of CO on to the NiO nanocone and enhance the sensing properties.