Proton Transfer Isomerization of Pyrazole in the Ground State： σ vs π Mechanism and Water Assisting Effect

The proton transfer isomerization of pyrazole and the water assisting effect by looping 1 to 4 water molecules on the singlet state potential energy surface have been investigated by using hybrid density functional theory method （B3PW91） with a 6-311＋＋G^＊＊ basis set. Two mechanisms were proposed to explain the mono- and multi-water assisting effects, respectively. The reactants and products of all groups have been characterized on their potential energy surfaces. For the isomerizafion of monomolecule pyrazole, the isomeriz＇ation energy barrier is 46.4 kcal·mol^-1. For the monohydration assisting mechanism, the reactant complex is connected to the product complex via two saddle points. The corresponding isomerization barriers are 46.7and 23.0 kcal·mol^-1, respectively. As to the multihydration assisting mechanism, the isomerization barriers are 12.0, 10.9 and 13.14 kcal·mol^-1 accordingly, when the number of water molecules is 2, 3 and 4, respectively. The multihydration assisting isomerization can occur in water-dominated environments, for example, in the organism, and thereby is crucial to energy transference. The deproton and dehydrogen energies of monomolecule pyrazole and various hydrated pyrazoles were calculated and then found much bigger than the isomerization barriers of their relative complexes, suggesting the impossibility of deprotonation or dehydrogenation. The isomerization of pyrazole is a proton-coupling-electron-migration process, but two different mechanisms are noticed, viz. σ- and π-type mechanisms. The π-bond of pyrazole participates in isomerization in the π-type mechanism, whereas only o-electron takes part in isomerization in the σ-type mechanism.     

Proton Transfer Isomerization of Pyrazole in the Ground State:σν sπ Mechanism and Water Assisting Effect

The proton transfer isomerization of pyrazole and the water assisting effect by looping 1 to 4 water molecules on the singlet state potential energy surface have been investigated by using hybrid density functional theory method (B3PW91) with a 6-311++G** basis set. Two mechanisms were proposed to explain the mono- and multi-water assisting effects, respectively. The reactants and products of all groups have been characterized on their potential energy surfaces. For the isomerization of monomolecule pyrazole, the isomerization energy barrier is 46.4 kcal·mol-1. For the monohydration assisting mechanism, the reactant complex is connected to the product complex via two saddle points. The corresponding isomerization barriers are 46.7and 23.0 kcal(mol-1, respectively. As to the multihydration assisting mechanism, the isomerization barriers are 12.0, 10.9 and 13.14 kcal(mol-1 accordingly, when the number of water molecules is 2, 3 and 4, respectively. The multihydration assisting isomerization can occur in water-dominated environments, for example, in the organism, and thereby is crucial to energy transference. The deproton and dehydrogen energies of monomolecule pyrazole and various hydrated pyrazoles were calculated and then found much bigger than the isomerization barriers of their relative complexes, suggesting the impossibility of deprotonation or dehydrogenation. The isomerization of pyrazole is a proton-coupling-electron-migration process, but two different mechanisms are noticed, viz.σ- and π-type mechanisms. The π-bond of pyrazole participates in isomerization in the π-type mechanism, whereas only σelectron takes part in isomerization in the σ-type mechanism.     

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

Addition Mechanisms of Phenol toward Formaldehyde under Acidic Condition： a Theoretical Investigation

The reaction mechanisms of phenol with formaldehyde in the first and second addition at the ortho- and para-position in acid solution were theoretically investigated at the PW91/DNP level with solvent effects included. The reaction of phenol with protonated methanediol firstly forms an adduct intermediate, via a SN2 mechanism with a water molecule as the leaving group. From the adduct intermediate, there are two reaction channels involving a proton transfer to form the addition products. One is that a proton directly transfers via a four-membered ring transition state with a notable energy barrier (Four-member mechanism). Another mechanism involving a water molecule as catalyst to mediate the proton transfer (WCP mechanism), is a barrierless process, indicating that the formation of the adduct intermediate, the first reaction step, is rate-limiting. The reaction products are free hydroxymethyl phenols and/or hydroxybenzy carbocation (HOC6H4CH2+) which plays an important role in the following formation of methylene and methylene ether linkages. The second addition reactions between formaldehyde and hydroxymethyl phenol at all possible reaction sites of the phenol ring in acid solution were also investigated and discussed.     

Theoretical Study on the Reaction Mechanism of Ketene CH2CO with Isocyanate NCO Radical

The bimolecular single collision reaction potential energy surface of an isocyanate NCO radical with a ketene CH2CO molecule was investigated by means of B3LYP and QCISD（T） methods. The computed results indicate that two possible reaction channels exist on the surface. One is an addition-elimination reaction process, in which the CH2CO molecule is attacked by the nitrogen atom at its methylene carbon atom to lead to the formation of the intermediate OCNCH2CO followed by a C-C rupture channel to the products CH2NCO＋CO. The other is a direct hydrogen abstraction channel from CHzCO by the NCO radical to afford the products HCCO＋HNCO. Because of a higher barrier in the hydrogen abstraction reaction than in the addition-elimination reaction, the direct hydrogen abstraction pathway can only be considered as a secondary reaction channel in the reaction kinetics of NCO＋ CH2CO. The predicted results are in good agreement with previous experimental and theoretical investigations.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Selective 3,4-Polymerization Mechanism of Isoprene Catalyzed by Rare Earth Alkyl Complexes

The mechanism of selective 3,4-polymerization reaction of isoprene catalyzed by the rare earth lutecium（Ⅲ） alkyl complexes [2,6-Me2Ph-N-CH2-C（CH2SiMe3）=N-PhMe2-2,6]Lu（CH2SiMe3）2（THF）was investigated by means of the M06/sdd method with solvation effects taken into account.The results show that the structure of the catalyst core remained almost unchanged as the isoprene molecules were alternatively inserted into the complex at two opposite sides.The Gibbs free energies of the coordination complexes,transition state and intermediates indicate that all the isoprene molecules prefer to insert into the complex with the 3,4-polymerization selectivity as catalyzed by the catalyst,which is consistent with the experimental observations.It is found that the insertion reaction of each isoprene is exothermic,which comes mainly from the coordination of the isoprene molecule to the lutecium（Ⅲ） atom.The solvation effects were confirmed important in predicting the Gibbs free energies of the present reaction system.     

Theoretical Study on the Adsorption and Decomposition of Methanol over the Pt-Mo（111）/C Surface

The density functional theory(DFT) and self-consistent periodic calculation were used to investigate the methanol adsorption on the Pt-Mo(111)/C surface.The adsorption energies,equilibrium geometries and vibration frequencies of CH3OH on nine types of sites on the Pt-Mo(111)/C surface were predicted and the favorite adsorption site for methanol is the top-Pt site.Both sites of valence and conduction bands of doped system have been broadened,which are favorable for electrons to transfer to the cavity.The possible decomposition pathway was investigated with transition state searching and the calculation results indicate that the O-H bond is first broken,and then the methanol decomposes into methoxy.The activation barrier of O-H bond breaking with Pt-Mo catalyst is only 104.8 kJ mol-1,showing that carbon supported Pt-Mo alloys have promoted the decomposition of methanol.Comparing with the adsorption energies of CH3OH on the Pt(111)/C surface and that of CO,the adsorption energies of CO are higher,and Pt(111)/C is liable to be oxidized and loses the activity,which suggests that the catalyst Pt-Mo(111)/C is in favor of decomposing methanol and has better anti-poisoning ability than Pt(111)/C.     

Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water

The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate （NaBF4）/water mixture at room temperatures were studied with molecular dynamics simulation. Different concentrations of water （6.25%, 25.0%, 50.0%, 75.0%, 90.0%, and 99.6%） in NaBF4/water mixture were simulated to understand the structure and dynamics. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in both liquids. With increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift whereas the O-H stretch bands show blue shift, and the decay of the reorientation correlation function becomes slower. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the interor intra-molecular modes.     

Theoretical Studies on the Isomerization of Peroxynitrite to Nitrate Mediated by Peroxynitrous Acid

The conversion of peroxynitrite （ONOO-） to nitrate （NO3-） mediated by peroxynitrous acid （ONOOH） has been investigated at the CCSD/6-311G（d）//B3LYP/6-31 1＋G（d,p） level. Two kinds of pathways for the title reaction were found. The results show that the energy barrier of isomerization through pathway 1 is around 25 kcal/mol in the gas phase. This value is significantly lower than that of isomerization without any catalysts. Thus, it indicates that ONOOH definitely makes the conversion from ONOO- to NO3- feasible. Although pathway 2 does not decrease the energy barrier of this isomerization, peroxynitric acid （O2NOOH） was obtained; moreover, this is a new pathway for this formation. In view of the results that peroxynitrate anion can decompose into nitrite and dioxygen, we conclude that our results are consistent with the experimental observation that nitrate, nitrite, and dioxygen are the main final products of the decay of peroxynitrite around pH 7.     

Theoretical Study on the Mechanisms of Action of Sulfurand Nitrogen-containing Amino Acid Residues with Monofunctional Guanine Adduct Formed by Antitumor Drugs trans-[PtCl2（Am）（isopropylamine）] （Am = Isopropylamine,Dimethylamine and Propylamine） and Their cis Isomers

The mechanisms of action on monofunctional guanine adducts of analogues of transplatin with aliphatic amine ligands,such as trans-[Pt（Am）（isopropylamine）（G）（H2O）] where Am represents dimethylamine,propylamine or isopropylamine and their cis isomers reacting with sulfur- and nitrogen-containing amino acid residues,were explored. Histidine and lysine residues are chosen as the model ligands of nitrogen-containing amino acid residues of proteins; meanwhile,methionine and cysteine residues are chosen as the model ligands of sulfur-containing amino acid residues of proteins. A dominating preference for sulfur-containing ligand over nitrogen-containing ligand is established. The calculated smallest activation barrier for sulfur-containing ligand is 9.9,and 21.1 kcal/mol for nitrogen-containing ligand in aqueous solution,and both of them have trans configurations. The difference in activation energy is 11.2 kcal/mol,indicating the platination of sulfur-containing amino acid residues is faster by seven to eight orders of magnitude than that of nitrogen-containing amino acid residues.     

REFINED CRYSTAL STRUCTURE OF INSULIN AT 1.8A RESOLUTION——HYDROGEN BONDS AND BOUND WATER

The hydrogen bonds in insulin fall into three cases: the helical hydrogen bonds in α- or 3_(10)helices, the non-helical one formed by polar groups of insulin itself, and the hydrogen bondsformed between insulin and water. By using the information obtained, the results of a seriesof biochemical investigations on insulin analogs related to B-chain C-terminal peptide can beinterpreted and it can also be inferred that the complex behaviours of the aggregation ofinsulin may play a protective role for the unique conformation of the molecule. Water structure also appears in the refined model. About one third of the water in anasymmetric unit is hydrogen-bonded to insulin molecules or each other, which are referred toas bound water. The polar and charged groups of insulin all show the tendencies to bind towater molecules as many as possible, which is a significant factor for the stabilization of theunique conformation of the molecule. The binding way of water molecules to insulin mole-cules is also analysed.     

Characterization of Ultra Fine Solids（BS） in Athabasca Bitumen

The ultra fine (＜200 nm) inorganic solids (BS) were separated from bitumen which was washed by toluene and centrifugated at 2000 rpm. The result of PAS FTIR and image of TEM showed that the structure of BS particles was smiliar to that of kaolinite clay. On the surface of BS, both toluene insoluble organic matter and structural OH group are detected at the same time.The surface characteristics imparted a bi-wettable nature to the BS. As a result, the BS is able to stabilize fine water emulsion in the bitumen phase. The organic matter associated with BS is a possible factor of the fouling on catalyst and equipment.     

MONTE CARLO SIMULATION ON AQUEOUS SOLUTION OF BIOLOGICAL MOLECULES——ALANINE SOLUTION

The Monte Carlo simulation is performed for a cluster consisting of a neutral alanine molecule surrounded by 56 water molecules. The average water-water and alanine-water interaction energies are found. The space surrounding the alanine molecule is divided into three regions, where the central atoms are C' atom for the earboxyl group region, N atom for the amino group region and C~β atom for the methyl group region. The water-water and water-alanine interaction energies as functions of the distance between the oxygen atom in a water molecule and the central atom in each region are calculated. In each region the orientational correlation function for the dipole moments of water molecules, the radial distribution function for the oxygen and hydrogen atoms of water molecules are evaluated. In addition, the numbers of water molecules in the first solvation shells of each region and of entire alanine molecule are also counted.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Syntheses and Crystal Structures of [Na（H2O）1/2]X and NH2（CH2CH3）2X and Antioxidant Activity of the Former

In order to enhance the water-solubility and biological utilization rate of chrysin, sodium 5,7-dihydroxylflavone-8-sulfonate （1, [Na（H2O）1/2]X, X = C15H9OSO3, 5,7-dihydroxylfla- vone-8-sulfonate） was synthesized and its structure was identified on the basis of NMR, FT-IR and elemental analysis. The assembly of 5,7-dihydroxylflavone-8-sulfonate with diethylamide cation afforded diethylamide 5,7-dihydroxylflavone-8-sulfonate （2, NH2（CH2CH3）2X） which was characterized by FT-IR and elemental analysis. The crystal structures of 1 and 2 were determined by X-ray single-crystal diffraction analysis. The crystal of 1 is of triclinic system, space group P1, with a = 8.5628（13）, b = 12.8916（19）, c = 13.562（2） A, α = 82.494（1）, β = 78.601（2）, γ = 84.033（2）°, C30H20Na2O15S2, Z = 2, Mr = 730.59, V = 1450.3（4） A3, Dc = 1.673 g/cm3, F（000） = 748, p = 0.295 mm^-1, the final R = 0.0641 and wR = 0.1458. The crystal of 2 crystallizes in the triclinic system, space group Pi, with a = 7.689（2）, b = 11.184（3）, c = 11.734（3） A, α = 74.268（3）, βl = 81.751（4）, γ= 87.991（3）°, C19H21NO7S, Z = 2, Mr= 407.43, V= 961.2（4） A3, Dc = 1.408 g/cm3, F（000） = 428, p = 0.210 mm^-1, the final R = 0.0484 and wR = 0.1195. In 1, the three-dimensional structure is organized into organic and inorganic regions; the flavone skeletons are stacked into organic regions by π...π staeking interactions; inorganic regions are generated by Na-O coordination bonds among sulfonate groups, coordinated water molecules and NaI. The sulfonate groups play an important role as a bridge of inorganic and organic regions. One-dimensional chain structure of 2 is extended by N-H…O hydrogen bonds and π...π stacking interactions. Furthermore, the antioxidant activity of 1 was evaluated. The scavenging activity of 1 to DPPH free radical is better than that of the parent compound chrysin.     

Efficient transesterification 4-hydroxytetrahydropyran immobilized lipase resolution of 2-（4-chlorophenyl）- with magnetically separable

We report an efficient kinetic resolution of racemic 2-（4-chlorophenyl）-4-hydroxytetrahydro-pyran （CLP-4-HTHP） via Pseudomonas cepacia lipase （PSL）-catalyzed transesterification, where PSL is immobilized on a core-shell MnFe204@SiO2-（CH2）3-NH2 carrier and used as a magnetically separable catalyst. The as-synthesized PSL/MnFe204@SiO2-（CH2）3-NH2 catalyst exhibits enhanced catalytic activity for resolving racemic CLP-4-HTHP to the corresponding optically pure （2R,4S）-CLP-4-HTHP compared to the free PSL. The ees for the former is 2.3 times larger than that for the latter under optimized conditions （99.4% and 44.1%, respectively）, although the eep for them are same （99.2%）. Meanwhile, the PSL/MnFe204@SiO2-（CH2）3-NH2 catalyst possesses a high saturate magnetization of 59.7 emu/g and could be easily recovered by magnetic separation and reused. The catalytic activity in six recycling tests did not significantly decrease, suggesting its great potential for industrial applications.     

Crystal Structure, Thermal Decomposition Behavior and the Standard Molar Enthalpy of Formation of a Novel 3D Hydrogen- Bonded Supramolecular [Co（HnicO）2·（H2O）2]

Hydrothermal synthesis and X-ray characterized 3D supramolecular networks were constructed by [Co（HnicO）2·（H2O）2] （HnicOH=2-hydroxynicofinic acid） （1） as building block via abundant dimeric homomeric （N--H…O） and unusually cyclic tetrameric heteromeric （O-H…O） hydrogen-bonds. It is noted that there exist unusually linear metal-water chains comprised of tetrameric units linked by vertexes sharing cobalt centers through hydrogen-bonding. TG-DTG curves illustrated that thermal decomposition was completed by two steps, one is the loss of two terminal water molecules in the range of 156--234℃, and the other is the pyrolysis of HnicO ligand in the range of 234--730 ℃. The standard molar enthalpy of formation of the complex was determined to be （-1845.43± 2.77） kJ·mol^-1 by a rotary-bomb combustion calorimeter.     

Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and 'free' water molecules emerge at the concentration of around 54%.     

A DFT Study of Thiophene Adsorption on the Rh（111） Surfaces

Thiophene adsorption on the Rh(111) surfaces has been investigated by density functional theory.The results show that the adsorption at the hollow and bridge sites is the most stable.The molecular plane of the thiophene ring is distorted,the C=C bond is stretched to 1.448  and the C-C bond is shortened to 1.390.The C-H bonds tilt 22～42oaway from the surface.The calculated adsorption geometries are in reasonable agreement with population analysis and density of states.The thiophene molecule obtains 0.74 electrons,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.The reaction paths and transition states for desulfurization of the molecule have been investigated.The bridge adsorption structure of thiophene leads to a thiol via an activated reaction with an energetic barrier of 0.30 eV.This second step is slightly difficult,and dissociation into a C4H4 fragment and a sulfur atom is possible,with an energetic barrier of 0.40 eV.