Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

Uranyl ion‐specific DNAzyme : A DNAzyme (lower strand) cleaves the substrate (upper strand) in the presence of the uranyl ion. The enzyme folds into a bulged three‐way‐junction structure with catalytically important nucleotides residing in the bulge. A highly conserved G?A mismatch is also crucial for the enzyme's activity.

     

The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme

DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.     

NO Formation by Neuronal NO‐Synthase can be Controlled by Ultrafast Electron Injection from a Nanotrigger

Synchronized catalysis in native enzyme : We used a photoactive nanotrigger (NT) to study the initial electron transfer to FAD in native neuronal NOS catalysis. Modeling and fluorescence spectroscopy showed that selective NT binding to NADPH sites is able to override Phe1395 regulation, thus permitting ultrafast injection of electrons into the protein electron pathway. That NT initiation of flavoenzyme catalysis led to the formation of NO is promising for time‐resolved X‐ray and other cellular applications.

     

Structural Studies on the Reaction of Isopenicillin N Synthase with a Sterically Demanding Depsipeptide Substrate Analogue

Isopenicillin N synthase (IPNS) is a nonheme iron(II)‐dependent oxidase that catalyses the central step in penicillin biosynthesis, conversion of the tripeptide δ‐L ‐α‐aminoadipoyl‐L ‐cysteinyl‐D ‐valine (ACV) to isopenicillin N (IPN). This report describes mechanistic studies using the analogue δ‐(L ‐α‐aminoadipoyl)‐(3S‐methyl)‐L ‐cysteine D ‐α‐hydroxyisovaleryl ester (A^SmCOV), designed to intercept the catalytic cycle at an early stage. A^SmCOV incorporates two modifications from the natural substrate: the second and third residues are joined by an ester, so this analogue lacks the key amide of ACV and cannot form a β‐lactam; and the cysteinyl residue is substituted at its β‐carbon, bearing a (3S)‐methyl group. It was anticipated that this methyl group will impinge directly on the site in which the co‐substrate dioxygen binds. The novel depsipeptide A^SmCOV was prepared in 13 steps and crystallised with IPNS anaerobically. The 1.65 Å structure of the IPNS–Fe^II–A^SmCOV complex reveals that the additional β‐methyl group is not oriented directly into the oxygen binding site, but does increase steric demand in the active site and increases disorder in the position of the isovaleryl side chain. Crystals of IPNS–Fe^II–A^SmCOV were incubated with high‐pressure oxygen gas, driving substrate turnover to a single product, an ene‐thiol/C‐hydroxylated depsipeptide. A mechanism is proposed for the reaction of A^SmCOV with IPNS, linking this result to previous crystallographic studies with related depsipeptides and solution‐phase experiments with cysteine‐methylated tripeptides. This result demonstrates that a (3S)‐methyl group at the substrate cysteinyl β‐carbon is not in itself a block to IPNS activity as previously proposed, and sheds further light on the steric complexities of IPNS catalysis.     

Unexpected oxidation of a depsipeptide substrate analogue in crystalline isopenicillin N synthase

Isopenicillin N synthase (IPNS) is a non-heme iron(ii)-dependent oxidase that is central to penicillin biosynthesis. Herein, we report mechanistic studies of the IPNS reaction in the crystalline state, using the substrate analogue delta-(L-alpha-aminoadipoyl)-(3R)-methyl-L-cysteine D-alpha-hydroxyisovaleryl ester (AmCOV) to probe the early stages of the catalytic cycle. The X-ray crystal structure of the anaerobic IPNS:Fe(II):AmCOV complex was solved to 1.40 A resolution, and it reveals several subtle differences in the active site relative to the complex of the enzyme with its natural substrate. The crystalline IPNS:Fe(II):AmCOV complex was then exposed to oxygen gas at high pressure; this brought about reaction to give what appears to be a hydroxymethyl/ene-thiol product. A mechanism for this reaction is proposed. These results offer further insight into the delicate interplay of steric and electronic effects in the IPNS active site and the mechanistic intricacies of this remarkable enzyme.     

The effects of ligand exchange and mobility on the peroxidase activity of a bacterial cytochrome c upon unfolding

The effect on the heme environment upon unfolding Paracoccus versutus ferricytochrome c-550 and two site-directed variants, K99E and H118Q, has been assessed through a combination of peroxidase activity increase and one-dimensional NMR spectroscopy. At pH 4.5, the data are consistent with a low- to high-spin heme transition, with the K99E mutation resulting in a protein with increased peroxidase activity in the absence of or at low concentrations of denaturant. Furthermore, the mobility of the polypeptide chain at pH 4.5 for the wild-type protein has been monitored in the absence and presence of denaturant through heteronuclear NMR experiments. The results are discussed in terms of local stability differences between bacterial and mitochondrial cytochromes c that are inferred from peroxidase activity assays. At pH 7.0, a mixture of misligated heme states arising from protein-based ligands assigned to lysine and histidine is detected. At low denaturant concentrations, these partially unfolded misligated heme forms inhibit the peroxidase activity. Data from the K99E mutation at pH 7.0 indicate that K99 is not involved in heme misligation, whereas histidine coordination is proven by the data from the H118Q variant.     

结晶动力学研究进展

综述了溶液结晶动力学及聚合物结晶动力学的现状及进展,并对其研究中存在的缺陷与不足进行了评述.     

聚苯乙烯在空气中热降解的化学动力学研究

研究了聚苯乙烯在空气中的热降解化学动力学机理。实验结果显示,聚苯乙烯在空气中热降解存在两个失重阶段:第一阶段,温度范围从250.59℃开始至397.41℃,在此范围内,大约有85%的聚苯乙烯发生了分解;第二阶段为397.41～515.29℃,大约有15%的聚苯乙烯发生分解。动力学计算拟合结果表明,聚苯乙烯的主要失重阶段(第一阶段)的热解符合二级化学反应方程,其平均表观活化能Ea值为166.19kJ/mol,lnA值为32.15。     

The kinetics and mechanism of polyethylene photo-oxidation

The kinetics of the natural and accelerated photo-oxidation of low-denisty polyethylene (LDPE) films have been studied; different geographical locations have been selected for the natural tests, and a range of temperatures used in the accelerated experiments in a specially built temperature-controlled ultraviolet radiation enclosure. A meaningful correlation between natural and accelerated weathering results was established, by means of an adequate superposition of the effects of UV radiation exposure and temperature. Reasonably detailed and accurate, lumped-parameter, kinetic models of the photo-oxidation process have also been developed, to interpret and predict the results of measurements of carbonyl, hydroperoxide and vinyl absorbances as functions of time and temperature; the models predict the general experimental behaviour, and also that both the formation of hydroperoxides and carbonyl Norrish-I reactions are important initiation steps. More complex models have the potential of interpreting other fine details of the degradation behaviour, namely the generation of other chemical species, and the chain scission and cross-linking process which are directly related to changes in the mechanical properties.     

On the mechanism of the copper‐catalysed hydro‐genation; a reinterpretation of published data

The copper‐catalysed hydrogenation of triglyceride oils differs from the nickel‐catalysed reaction in that copper catalysts only hydrogenate double bonds in methylene interrupted polyunsaturated fatty acid moieties. Accordingly, the copper‐catalysed reaction stops when the triglycerides present in the reaction mixture are only monounsaturated fatty acids and polyunsaturated fatty acids in which the double bonds are separated by more than one methylene group. Copper catalysts thus exhibit a very high oleic acid selectivity. This observation has been explained in the literature by assuming that copper catalysts can only catalyse the hydrogenation of conjugated polyenes and that they are also capable of catalysing the conjugation of methylene interrupted polyenes. Accordingly, the hydrogenation of linolenic acid and linoleic acid moieties starts with their conjugation which is then followed by hydrogen addition to these conjugated acids. For both reactions (conjugation and hydrogenation) the literature assumes the Horiuti‐Polanyi mechanism stipulating the addition of a hydrogen atom to a double bond as the first step. Reinterpretation of the literature data now leads to the hypothesis that the first step in the conjugation mechanism could well be the abstraction of a hydrogen atom from an allylic methylene group rather than the addition of a hydrogen atom to a doubly bonded carbon atom. A conjugated double bond system then results from the addition of a hydrogen atom to the allylic radical formed by the foregoing hydrogen abstraction.     

TiO2光催化降解2,4-二氯酚动力学及机理的研究

以TiO2作为催化剂,500 W汞灯作为光源,对水体中2,4-二氯酚（2,4-DCP）的光催化降解特性进行了研究。实验结果表明,TiO2光催化降解2,4-DCP效果较好,降解的最佳pH为7,催化剂的最佳投加量为200 mg·L-1。2,4-DCP的初始浓度越小,光催化的效率越高。在初始浓度为5 mg·L-1时,光催化1 h的降解率达90%。在实验的四种不同初始浓度（5 mg·L-1、10 mg·L-1、20 mg·L-1、40 mg·L-1）下,2,4-DCP的光降解速率常数近似与其初始质量浓度成一级反应动力学关系。结合高效液相色谱、气相色谱-质谱的测定结果以及Cl-、COD的变化,认为2,4-DCP的主要降解过程为：脱氯-开环-矿化、中间产物相互作用-进一步矿化。     

The Mathematical Models of the Initial Stage of the Thermal Degradation of Poly(Vinyl Chloride)

Abstract

The mathematical models of the initial stage of the thermal dehydrochlorination of PVC are proposed. It is shown that abnormal unstable fragments having constants of rates of degradation equal to 10^?3–10^?4sec^?1 have the greatest influence on the thermal degradation of PVC at 180–200°C. The groups having chlorine near tertiary carbon and chloroallylic groups may be such fragments.     

Vinyl acetate monomer—a pilot plant study

The kinetics of the reaction of acetic acid and acetylene over zinc acetate-activated carbon catalyst was investigated over a wide range of process variables in a pilot reactor. Although various catalytic reaction mechanisms were postulated, the rate of reaction was most satisfactorily correlated by a mechanism of surface reaction between charged adsorbed acetic acid and acetylene, which assumes that the rate controlling step was the irreversible charged adsorption of acetylene and acetic acid.     

The leaching kinetics and mechanism of potassium from phosphorus-potassium associated ore in hydrochloric acid at low temperature

The leaching kinetics of potassium from phosphorus-potassium associated ore in hydrochloric acid/fluorite (CaF₂) system was studied. HCl concentration, liquor/solid ratio, CaF₂ dosage, and temperature were found to be the main factors. The leaching rate of potassium can be reached more than 92% under the optimum operation conditions. A classic shrinking core model with the mixed chemically diffusion as the rate-controlling step was successfully modeled the leaching kinetics of potassium, and the activation energy was found to be 30.7 kJ·mol^?1. The leaching mechanism of potassium was also elucidated based on the experimental results.     

明胶的酶降解反应动力学研究——Ⅱ.动力学规律和机理

根据文献[1]中的实验数据,结合化学反应动力学的基础理论,计算了明胶的酶降解反应的反应级数、表观活化能、指前因子等有关动力学参数值。得到反应的总速率方程。所求得的反应速率常数与温度的关系表明,在实验温度范围内,符合Arrhenius公式。最后提出了该反应的酶催化反应机理,实验结果与所推得的机理动力学方程相吻合。     

Curing kinetics of a rigid polyurethane foam formulation

The curing kinetics of a typical commercial formulation used in the manufacture of rigid polyurethane foams has been studied. The adiabatic temperature rise method was used, taking into account corrections for heat losses. A polymeric isocyanate was reacted with a stoichiometric amount of a polyether polyol, using dibutyltin dilaurate (DBTDL) as catalyst. For DBTDL < 2.6 mol m^?3, a strong inhibition of the catalyst took place, and the uncatalysed reaction played a major role. Second order kinetics gave a good fit for the whole conversion range. For DBTDL > 2.6 mol m^?3, the catalysed reaction took place. Second order kinetics were applicable up to the gel point, but then the rate slowed down severely. A first order dependence on the initial catalyst concentration was observed in the pre-gel region. The kinetics are discussed in terms of a modified version of the Van der Weij's mechanism. The heat of reaction was 17.6 kcal/NCO equivalent.     

Fast pyrolysis of glucose‐based carbohydrates with added NaCl part 1: Experiments and development of a mechanistic model

Sodium ions, one of the natural inorganic constituents in lignocellulosic biomass, significantly alter pyrolysis behavior and resulting chemical speciation. Here, experiments were conducted using a micropyrolyzer to investigate the catalytic effects of NaCl on fast pyrolysis of glucose‐based carbohydrates (glucose, cellobiose, maltohexaose, and cellulose), and on a major product of cellulose pyrolysis, levoglucosan (LVG). A mechanistic model that addressed the significant catalytic effects of NaCl on the product distribution was developed. The model incorporated interactions of Na⁺ with cellulosic chains and low molecular weight species, reactions mediated by Na⁺ including dehydration, cyclic/Grob fragmentation, ring‐opening/closing, isomerization, and char formation, and a degradation network of LVG in the presence of Na⁺. Rate coefficients of elementary steps were specified based on Arrhenius parameters. The mechanistic model for cellulose included 768 reactions of 222 species, which included 252 reactions of 150 species comprising the mechanistic model of glucose decomposition in the presence of NaCl. © 2015 American Institute of Chemical Engineers AIChE J, 62: 766–777, 2016     

Critical initiation-energy density as a function of single-crystal size in explosive decomposition of silver azide

The dependence of the critical initiation-energy density of explosive decomposition of silver azide on the sample size was studied experimentally for the first time. The dependence of the critical energy density was found to be determined by the diffusion of the reactants to the crystal surface, where their recombination rate far exceeds the bulk rate. The diffusion coefficient and the rate constant of bulk electron-hole recombination obtained for the explosive decomposition agree within the experimental error with those determined earlier in photoconductivity studies. __________ Translated from Fizika Goreniya i Vzryva, Vol. 44, No. 2, pp. 76–78, March–April, 2008.