Catalytic mechanism of 6-phosphogluconate dehydrogenase: a theoretical investigation

Density functional calculations are employed to theoretically explore the mechanism of all elementary reaction steps involved in the catalytic reaction of 6-phosphogluconate dehydrogenase (6PGDH). The model systems we choose for the enzyme contain the essential parts of the cofactor (NADP+), the substrate 6-phosphogluconate (6PG), and some key residues (Lys183 and Glu190) in the active site of sheep liver 6PGDH. The effect of the apoenzyme electrostatic environment on the studied reaction is treated by the self-consistent reaction-field method. Our calculations demonstrate that the first step of the catalytic reaction is the formation of a 3-keto 6PG intermediate, which proceeds through a concerted transition state involving a hydride transfer from 6PG to NADP+, and a proton transfer from 6PG to Lys183. The second step is the elimination of a CO2 molecule from 6-PG, concomitant with a proton transfer from Lys183 to 6-PG. In the final step, a concerted double proton transfer (one from Glu190 to the substrate, another from the substrate to Lys183) results in the final product, the keto form of ribulose 5-phosphate (Ru5P). The rate-limiting step is the formation of a 3-keto 6PG intermediate, with a free energy barrier of 22.7 kcal/mol at room temperature in the protein environment, and all three steps are calculated to be thermodynamically favorable. These results are in good agreement with the general acid/general base mechanism suggested from previous experiments for the 6PGDH reaction.     

Assembly of a heterobinuclear 2-D network: a rare example of endo- and exocyclic coordination of Pd(II)/Ag(I) in a single macrocycle

The S3O2 macrocycle L1 was synthesized by a dithiol-dihalide coupling reaction under high-dilution conditions. The reaction of L1 with K2PdCl4 afforded an exocoordinated complex 1, [cis-Cl2Pd(L1)], which can then be manipulated to provide a heterobinuclear complex 3, {[Pd(L1)Ag(NO3)(2.5)](NO3)(0.5)}n, utilizing endocyclic Pd(II) and exocyclic Ag(I) in a single macrocycle through a successive reaction with AgNO3. The network of 3 contains a unique honeycomb-like 2-D sheet made up of the repeating unit [Ag6(NO3)6].     

TEMPO-mediated oxidation of bacterial cellulose in a bromide-free system

A partially C6-carboxylated bacterial cellulose (BC) with a high carboxylate content was prepared in a bromide-free system by using 2,2,6,6-tetramethylpyperidine-1-oxyl (TEMPO) as a catalyst. ART-FTIR, X-ray diffraction, solid ¹³C-NMR, TEM analysis, and reaction kinetics measurements were performed to investigate the oxidation reaction of BC. Results show that C6 carboxylate was formed selectively on the microfiber surface without disrupting its highly ordered nanocrystalline structure. Given the extremely low accessibility of hydroxyl groups in d-anhydroglucopyranose units, the reaction can be described by second-order kinetics with very low reaction rate constants. pH exhibited a significant influence on the oxidation of BC and a higher activity at C6 was observed in a neutral medium.     

Photoacid-base reaction in ice via a mobile L-defect

A time-resolved emission technique was employed to study the photoprotolytic cycle of two photoacids 2-naphtol-6-sulfonate (2N6S) and 2-naphtol-6,8-disulfonate (2N68DS) in ice in the presence of a low concentration of a weak base fluoride ion. We found that an additional proton-transfer process occurs in ice doped with F- ions. This reaction takes place between a mobile L-defect (created by static F- ions) and the photoacid. We used a diffusion assisted reaction model, based on the Debye-Smoluchowski equation, to account for the direct reaction of the L-defect with the excited photoacid.     

Non-catalytic hydroamination of alkenes: a computational study

The detailed reaction profiles of the neutral-neutral as well as the cation-neutral direct hydroamination reactions between ethylene and ammonia are analyzed using MP2 (Full)/6-31++G(2df,2p) and B3LYP/6-31++G(2df,2p) methodologies. Analysis shows that both neutral-neutral, as well as the cation-neutral reactions are exothermic and the latter is >100 kJ/mol more exothermic than the former. Calculations show that a very large barrier height (>200 kJ/mol), and very large negative reaction entropy prevent the neutral-neutral reaction from proceeding in the forward direction. Analysis of the cation-neutral reaction, which is barrierless (the transition state is more stable than the reactants) and highly exothermic, indicates that the direct hydroamination reaction is thermodynamically attainable via a cation-neutral reaction pathway without a catalyst. Our calculations also suggest that although the cation-neutral direct hydroamination reaction is very fast, the cation of either ethylene or ammonia goes through a structural relaxation process before reacting with the other neutral reactant.     

A point mutation converts dihydroneopterin aldolase to a cofactor-independent oxygenase

Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (1) to 6-hydroxymethyl-7,8-dihydropterin (4) in the folate biosynthetic pathway. Substitution of a conserved tyrosine residue at the active site of DHNA by phenylalanine converts the enzyme to a cofactor-independent oxygenase, which generates mainly 7,8-dihydroxanthopterin (6) rather than 4. 6 is generated via the same enol intermediate as in the wild-type enzyme-catalyzed reaction, but this species undergoes an oxygenation reaction to form 6. The conserved tyrosine residue plays only a minor role in the formation of the enol reaction intermediate but a critical role in the protonation of the enol intermediate to form 4.     

硫代硫酸根插层水滑石的层间限域反应

将无机阴离子硫代硫酸根(S2O23-)限域在锌铝水滑石(LDH)层间,并研究了其在水滑石层板限域空间内被铁氰根(Fe(CN)63-)氧化的反应过程.通过X射线衍射(XRD)和傅里叶变换红外(FTIR)光谱仪对反应的中间产物和最终产物进行的表征发现,氧化产物连四硫酸根(S4O62-)进入到溶液中,还原产物亚铁氰根(Fe(CN)64-)则保留在水滑石层间.进一步系统研究了该反应的动力学过程,考察了硫代硫酸根插层水滑石用量、铁氰化钾浓度和温度对反应的影响.结果表明该氧化还原反应符合球体内扩散模型.根据温度对反应速率影响,得出了该反应的表观活化能为24.6kJ.mol-1,比相同条件下溶液中反应活化能降低了约13.7kJ.mol-1.采用分子动力学(MD)模拟计算了水分子含量对硫代硫酸根插层水滑石层间距大小的影响.计算表明:在水溶液环境中,水滑石微反应器的尺寸在特定方向具有可调控性.根据实验表征和理论计算对该层间反应的机理进行了探讨.因此,该类层状材料可以作为一种新型纳米级微反应器应用于调控化学反应.     

Mechanism of cysteine oxidation by a hydroxyl radical: a theoretical study.

Cysteine oxidation by HO(.) was studied at a high level of ab initio theory in both gas phase and aqueous solution. Potential energy surface scans in the gas phase performed for the model system methanethiol+HO(.) indicate that the reactants can form two intermediate states: a sulfur-oxygen adduct and a hydrogen bound reactant complex. However these states appear to play a minor role in the reaction mechanism as long as they are fast dissociating states. Thus the main reaction channel predicted at the QCISD(T)/6-311+G(2df,2pd) level of theory is the direct hydrogen atom abstraction. The reaction mechanism is not perturbed by solvation which was found to induce only small variations in the Gibbs free energy of different reactant configurations. The larger size reactant system cysteine+HO* was treated by the integrated molecular orbital+molecular orbital (IMOMO) hybrid method mixing the QCISD(T)/6-311+G(2df,2pd) and the UMP2/6-311+G(d,p) levels of theory. The calculated potential energy, enthalpy, and Gibbs free energy barriers are slightly different from those of methanethiol. The method gave a rate constant for cysteine oxidation in aqueous solution, k=2.4 x 10(9) mol(-1) dm(3) s(-1), which is in good agreement with the experimental rate constant. Further analysis showed that the reaction is not very sensitive to hydrogen bonding and electrical polarity of the molecular environment.     

Utilizing a copper MOF as a reagent in a solvent mediated reaction to form a topologically distinct MOF

Employing a semi-rigid di-1,2,4-triazole ligand leads to the formation of new MOFs [Cu(4)(L)(4)(SO(4))(4)]·4[Cu(H(2)O)(6)(SO(4))] (3) and [Cu(6)(L)(3)(SO(4))(5)(OH)(2)(H(2)O)(6)]·13H(2)O (4). The frameworks can be synthesized independently, but a reaction occurs in water wherein kinetic product 3 is used as a reagent to synthesize the topologically distinct thermodynamic product 4.     

Reaction of ketenyl radical with acetylene: a promising route for cyclopropenyl radical

The reaction of the ketenyl radical (HCCO) with acetylene (C(2)H(2)) is very relevant to the oxygen-acetylene flames and fuel-rich combustion process for nitrogen-containing compounds. Unfortunately, except for several rate constant measurements, the mechanism is completely unknown for this reaction. In this paper, detailed theoretical investigations are performed for the HCCO + C(2)H(2) reaction at the G3B3 level using the B3LYP/6-31G(d), B3LYP/6-311++G(d,p), and QCISD/6-31G(d) geometries. The exclusive fragmentation channel is the formation of the cyclopropenyl radical (c-C(3)H(3)) and carbon monoxide (CO) via the chainlike OCCHCHCH and three-membered ring OC-cCHCHCH intermediates. Thus, the mass spectroscopic peak of C(3)H(3)(+) in a previous experiment can be explained. The calculated overall reaction barrier is 4.4, 4.4, and 5.3 kcal/mol at the G3B3//B3LYP/6-31G(d), G3B3//B3LYP/6-311++G(d,p), and G3B3//QCISD/6-31G(d) levels, respectively. The title reaction may provide an effective route for generating the long-sought cyclopropenyl radical in the laboratory, which has been the long-standing subject of numerous theoretical studies as the simplest cyclic conjugate radical, and its bulky derivatives were already known. Future experimental investigations for the HCCO + C(2)H(2) reaction are greatly desired to test the predicted fragmentation channel. The implication of the present study in combustion and interstellar processes is discussed.     

阳离子表面活性剂存在下水/有机两相体系中双环戊二烯氢甲酰化

研究了在阳离子表面活性剂存在下水/有机两相中水溶性铑配合物RhCI(CO)(TPPTS)2(TPPTS:P(m-C6H4SO3Na)3)催化双环戊二烯氢甲酰化反应,考察了反应温度、催化剂浓度、不同水溶性膦配体TPPTS和TPPDS(C5H5P(m-C6H4SO3Na)2),以及表面活性剂结构对催化反应的影响.结果表明,...     

Simultaneous Determination of Samarium and Gadolinium by a Automated Stopped-flow Analyzer

The present paper contains the reaction mechanism of the rare earth complex with 2-(2-arsenophenylazo)-7-(2, 6-dichloro-4-fluoro-phenylazo)- 1, 8-dihydroxynaphthalene-3, 6-disulfonic acid (DCF-arsenazo) studied preliminarily with a fully automated stopped-flow analyzer. A method with a high sensitivity and selectivity is proposed for the simultaneous determination of samarium and gadolinium based on the differential kinetic reaction of the rare earth complex with DCF-arsenazo. Sm and Gd in their concentrated oxides were determined with the relative errors less than 6%.     

Antibody-catalyzed benzoin oxidation as a mechanistic probe for nucleophilic catalysis by an active site lysine

Aldolase antibody 24H6, which was obtained by reactive immunization against a 1,3-diketone hapten, is shown to catalyze additional reactions, including H/D exchange and oxidation reactions. Comparison of the H/D exchange reaction at the alpha-position of a wide range of aldehydes and ketones by 24H6 and by other aldolase antibodies, such as 38C2, pointed at the significantly larger size of the 24H6 active site. This property allowed for the catalysis of the oxidation of substituted benzoins to benzils by potassium ferricyanide. This reaction was used as a mechanistic probe to learn about the initial steps of the 24H6-catalyzed aldol condensation reaction. The Hammett correlation (rho=4.7) of log(k(cat)) versus the substituent constant, sigma, revealed that the reaction involves rapid formation of a Schiff base intermediate from the ketone and an active site lysine residue. The rate-limiting step in this oxidation reaction is the conversion of the Schiff base to an enamine intermediate. In addition, linear correlation (rho=3.13) was found between log(K(M)) and sigma, indicating that electronic rather than steric factors are dominant in the antibody-substrate binding phenomenon and confirming that the reversible formation of a Schiff base intermediate comprises part of the substrate-binding mechanism.     

Quantum Chemical Model of a Lysozyme+Substrate Complex and a Cooperative Process in It

This paper presents an ab initio (RHF/6-31G** and MP2(full)6-31G**) and density functional (DFT) study of the structure and energetics of formation of an intermolecular complex which is the simplest model of an active center lysozyme with a substrate. The calculated energy of complex formation is 41.4 (RHF), 53.4 (MP2), and 52.7 kcal/mole (DFT). The proton transfer reaction is a concerted reaction having an energy barrier of 41.1 (RHF), 31.6 (MP2), and 25.3 (DFT) kcal/mole.     

一种含假芪型偶氮生色团两亲性嵌段共聚物的合成与表征

利用原子转移自由基聚合（ATRP）合成了一种新型的含假芪型偶氮生色团的两亲性嵌段共聚物P（HEMA-b-6CNAzo）。首先,采用ATRP引发剂引发三甲基硅保护的羟乙基甲基丙烯酸酯（HEMA—TMS）聚合,得到大分子引发剂P（HEMA—TMS）;接着进一步引发单体甲基丙烯酸6-（N_甲基苯胺基）己酯进行ATRP反应,得...     

Asymmetric Diels-Alder reactions catalyzed by a triflic acid activated chiral oxazaborolidine

This paper reports a new method for the generation of chiral Lewis superacids by protonation of a non-Lewis acidic oxazaborolidine (1) with triflic acid. The resulting cationic species (3) are powerful and highly enantioselective catalysts for the Diels-Alder reaction of various 1,3-dienes with alpha,beta-enals. An optimization study (see Table 1) led to the selection of reaction conditions and catalysts (6A and 6B) which are very effective. The reactions are simple to conduct, reproducible, and economical, since only ca. 6 mol % of catalyst is required. In addition, the chiral catalyst precursor is readily recovered for reuse (>95% efficiency) and is commercially available. The broad scope of the process is documented by the 14 examples listed in Table 2. The absolute stereochemical course of the Diels-Alder reactions catalyzed by 6A and 6B was successfully predicted on the basis of the mechanistic principles which have recently been formulated for this type of catalytic enantioselective reaction involving re-face attack by the diene on complex 7. The mode of generation of Lewis superacids 6A and 6B allows an approximate comparison (or scale) connecting the catalytic power Lewis and protic acids.     

Synthesis and structural characterization of a series of lanthanide(II) amides: steric effect of amido ligand

The synthesis and structures of a series of lanthanide(II) and lanthanide(III) complexes supported by the amido ligand N(SiMe3)Ar were described. Several lanthanide(III) amide chlorides were synthesized by a metathesis reaction of LnCl3 with lithium amide, including {[(C6H5)(Me3Si)N]2YbCl(THF)}2.PhCH3 (1), [(C6H3-iPr2-2,6)(SiMe3)N]2YbCl(mu-Cl)Li(THF)3.PhCH3 (4), [(C6H3-iPr2-2,6)(SiMe3)N]YbCl2(THF)3 (6), and [(C6H3-iPr2-2,6)(SiMe3)N]2SmCl3Li2(THF)4 (7). The reduction reaction of 1 with Na-K alloy afforded bisamide ytterbium(II) complex [(C6H5)(Me3Si)N]2Yb(DME)2 (2). The same reaction for Sm gave an insoluble black powder. An analogous samarium(II) complex [(C6H5)(Me3Si)N]2Sm(DME)2 (3) was prepared by the metathesis reaction of SmI2 with NaN(C6H5)(SiMe3). The reduction reaction of ytterbium chloride 4 with Na-K alloy afforded monoamide chloride {[(C6H3-iPr2-2,6)(SiMe3)N]Yb(mu-Cl)(THF)2}2 (5), which is the first example of ytterbium(II) amide chloride, formed via the cleavage of the Yb-N bond. The same reduction reaction of 7 gave a normal bisamide complex [(C6H3-iPr2-2,6)(SiMe3)N]2Sm(THF)2 (8) via Sm-Cl bond cleavage. This is the first example for the steric effect on the outcome of the reduction reaction in lanthanide(II) chemistry. 5 can also be synthesized by the Na/K alloy reduction reaction of 6. All of the complexes were fully characterized including X-ray diffraction for 1-7.     

Signal enhancement for gene detection based on a redox reaction of [Fe(CN)(6)](4-) mediated by ferrocene at the terminal of a peptide nucleic acid as a probe with hybridization-amenable conformational flexibility

Electrochemically enhanced DNA detection was demonstrated by utilizing the couple of a synthesized ferrocene-terminated peptide nucleic acid (PNA) with a cysteine anchor and a sacrificial electron donor [Fe(CN)(6)](4-). DNA detection sensors were prepared by modifying a gold electrode surface with a mixed monolayer of the probe PNA and 11-hydroxy-1-undecanethiol (11-HUT), protecting [Fe(CN)(6)](4-) from any unexpected redox reaction. Before hybridization, the terminal ferrocene moiety of the probe was subject to a redox reaction due to the flexible probe structure and, in the presence of [Fe(CN)(6)](4-), the observed current was amplified based on regeneration of the ferrocene moiety. Hybridization decreased the redox current of the ferrocene. This occurred because hybridization rigidified the probe structure: the ferrocene moiety was then removed from the electrode surface, and the redox reaction of [Fe(CN)(6)](4-) was again prevented. The change in the anodic current before and after hybridization was enhanced 1.75-fold by using the electron donor [Fe(CN)(6)](4-). Sequence-specific detection of the complementary target DNA was also demonstrated.     

Synthesis of a novel macrocyclic ligand containing bipyridine units

The 6-hydroxymethyl-6'-tetrahydropyranyloxymethyl-2, 2'-bipyridine (2) was synthesized by the reaction of 6,6'-dihy-droxymethyl-2, 2'-bipyridine (1) with 3, 4-dihydropyran (DHP). 6-Tetrahydropyranyloxymethyl-6'-iodomethyl-2, 2'-bipyridine (5) was obtained from mesylate and iodizating reaction of compound 2. The coupling of 2 and 5 followed by hydrolysis gave bis(6'-hydroxymethyl-2,2'-bipyridme-6-methyl)ether (7) .The macrocydic ligand 8 was obtained by treating 7 and 6,6'-dibromomethyl-2,2'-bipyridine. The synthetic conditions of the intermediate 2 and macocyclic ligand 8 were discussed.     

Total synthesis of (+)-acanthodoral by the use of a Pd-catalyzed metal-ene reaction and a nonreductive 5-exo-acyl radical cyclization

[reaction: see text] The first total synthesis of the antibiotic acanthodoral (1) has been achieved from 3-methyl-2-cyclohexen-1-one in 19 steps in 2.1% overall yield. The synthesis features the use of a Pd-ene reaction in the presence of CO to form the endocyclic alkene 8, a nonreductive acyl radical cyclization reaction, and a ring contraction reaction by the Wolff rearrangement. (+)-Acanthodoral has also been synthesized starting from (+)-S-2,2-dimethyl-6-methylenecyclohexanecarboxylic acid.