Wild-type and molten globular chorismate mutase achieve comparable catalytic rates using very different enthalpy/entropy compensations

The origin of the catalytic power of enzymes with a meta-stable native state,e.g.molten globular state,is an unsolved challenging issue in biochemistry.To help understand the possible differences between this special class of enzymes and the typical ones,we report here computer simulations of the catalysis of both the well-folded wild-type and the molten globular mutant of chorismate mutase.Using the ab initio quantum mechanical/molecular mechanical minimum free-energy path method,we determined the height of reaction barriers that are in good agreement with experimental measurements.Enzyme-substrate interactions were analyzed in detail to identify factors contributing to catalysis.Computed angular order parameters of backbone N–H bonds and side-chain methyl groups suggested site-specific,non-uniform rigidity changes of the enzymes during catalysis.The change of conformational entropy from the ground state to the transition state revealed distinctly contrasting entropy/enthalpy compensations in the dimeric wild-type enzyme and its molten globular monomeric variant.A unique catalytic strategy was suggested for enzymes that are natively molten globules:some may possess large conformational flexibility to provide strong electrostatic interactions to stabilize the transition state of the substrate and compensate for the entropy loss in the transition state.The equilibrium conformational dynamics in the reactant state were analyzed to quantify their contributions to the structural transitions enzymes needed to reach the transition states.The results suggest that large-scale conformational dynamics make important catalytic contributions to sampling conformational regions in favor of binding the transition state of substrate.     

STUDIES ON THE STRUCTURE OF FORKED CONJUGATIVE SYSTEMS——THE CRYSTAL STRUCTURE AND CONFORMATION OF 2-BENZOYLTHIOPHENE

The crystal structure and the conformational properties of the title compound have been investigated by means of X-ray single diffraction and the PCILO methods. C_(11)H_8OS belongs to the orthorhombic system, the space group is P2_12_12_1, a=11.945(4), b 10.236(7), c=7.649(4), Z=4, D_c-1.37g/cm~3. The molecule is not planar structure because of steric hindrance. The thiophene ring and the phenyl ring make dihedral angles of 21°(θ_1) and 32°(θ_2) with the carbonyl frame plane, respectively. The lowestenergy conformation obtained by PCILO calculation is in agreement with the crystallinestatc conformation. In this paper, the molecular structure, the influence of steric hindrance and the groups' abilities to conjugate upon the conformation and the variations of the potential energy of the isolated molecule in the whole conformational space are discussed.     

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.     

Conformational Properties of Comb-shaped Polyelectrolytes with Negatively Charged Backbone and Neutral Side Chains Studied by a Generic Coarse-grained Bead-and-Spring Model

A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit counterions.The agreement on the radius of gyration of the PCEs with experiments shows that our model can be useful in studying the equilibrium sizes of PCEs in solution.The effects of ionic strength,side-chain number,and side-chain length on the conformational behavior of PCEs in solution are explored.Single-chain equilibrium properties,including the radius of gyration,end-to-end distance and persistenee length of the polymer backbone,shape-asphericity parameter,and the mean span dimension,are determined.It is found that with the increase of ionic strength,the equilibrium sizes of the polymers decrease only slightly,and a linear dependenew of the persistence length of backbone on the Debye screening length is found,in good agreement with the theory developed by Dobrynin.Increasing side-chain numbers and/or side-chain lengths increases not only the equilibrium sizes(radius of gyration and mean span)of the polymer as a whole,but also the persistence length of the backbone due to excluded volume interactions.     

PHOTOCHROMIC PROPERTIES OF (E)-DICYCLOPROPYLMETHYLENE-(2,5-DIMETHYL-3-FURYLETHYLIDENE)-SUCCINIC ANHYDRIDE DOPED IN POLYSTYRENE THIN FILMS

Fulgide 1-E doped in polystyrene polymer films was heated at various annealing temperatures.Upon irradiation with UV light(366 nm),fulgide 1-E undergoes a conrotatory ring closure to the pink colored closed form 1-C.The later color was switched back to the original color when the films were irradiated with white light.The kinetics of photocoloration and photobleaching processes were followed spectrophotometrically by monitoring the absorbance of the ring closed product 1-C at itsλ_(max) of 525 nm.The fir...     

SYNTHESIS OF POLY ( ETHER-URETHANE) CONTAINING PENDANT AMINO GROUP

This paper is concerned with the synthesis of poly (ether-urethane) with pendant amino groups. The copolyether produced by ring opening copolymerization of tetrahydrofuran and epibromohydrin was treated with sodium azide in dimethylformamide to form azido substituted copolyether. The poly (ether-urethane) made from it was subjected to reduction reaction to convert azido group to amino group. The stress-strain behavior and dynamic-mechanical properties of poly (ether-urethane) containing pendant amino groups were studied.     

A molecular dynamics and computational study of human KAT3 involved in KYN pathway

Kynurenine aminotransferases (KATs) catalyze the transamination of kynurenine (KYN) pathway and endogenous KYNs have been suggested to highly correlate to abnormal brain diseases. HKAT3 is a key member of KAT family, while the binding mechanism of KYN and cofactor with HKAT3 has not been determined yet. In this study, we focus on the structure-function relationship among KYN, cofactor and HKAT3. The binding models of KYN complex and KYN&cofactor complex were obtained and were studied by molecular dynamics (MD) simulations. We identified several critical residues and influence of conformational changes in human kynurenine aminotransferase 3 (HKAT3) complexes. The cofactor may contribute largely not only to the catalysis, but also to the binding. In addition, a hypothesis is proposed that a strong hydrophobic interaction between Tyr159 and Lys280 may influence the binding mode and the binding region of the substrate and the cofactor. Our results will be a good starting point for further determination of the biological role.     

Zn/Al/Tyr摩尔比对Tyr/Zn-Al-LDH纳米复合物的影响

The intercalation of amphoteric amino acid tyrosine （Tyr） into LDH by co-precipitation method was systematically studied. The influence of initial molar ratios （R） of LDH to Tyr has also been examined. Powder X-ray diffraction, Fourier transform infrared spectroscopy, specific surface areas and pore size distributions, and thermal analysis have been employed for the characterization of the nanocomposites. The nanohybrids were found to have an expanded layered structure except the samples prepared with low R values, indicating that the biomolecules were intercalated into the gallery as anions. The intercalation of amino acids resulted in the increase of the surface areas and pore volumes, and the value of surface areas and pore volumes increased with enhancement of biomolecules intercalated. TEM analysis revealed that with increasing biomolecules into the gallery, the nanohybrids were changed from hexagonal particles to spherical ones. Moreover, the configuration of Tyr anions was varied under different R values, changed from monolayer to bilayers with more biomolecules intercalating into the gallery.     

In situ Synthesis of Oligonucleotides on Plasma Treated Polypropylene Microporous Membrane

Polypropylene microporous membranes were treated with plasma in a mixture of N2 and H2 (1:2 in volume). Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and ultra-violet (UV) spectra demonstrated the success of grafting amino groups. The density of the polar amino groups on the membrane surface is about 0.59 μmol/cm^2. The as-treated membranes were successively applied to the in situ synthesis of oligonucleotides and an average coupling yield was more than 98%. The surface feature of the treated membrane is suggested to be responsible for its advantage over a glass slide.     

Synthesis,Characterization,Biological and Docking Simulations of 4-(Benzylideneamino) Benzoic Acids

The present research paper presents the synthesis, characterization, biological and computational studies of 4-(benzylideneamino) benzoic acid derivatives(3a~3g). Derivatives 3a~3c displayed best antidiabetic potential with a glucose-lowering effect compared to the reference drug Glibenclamide. Biochemical parameters including plasma glucose, serum triglycerides, cholesterol, alanine amino transferase and aspartate amino transferase levels showed significant alterations in concentrations relative to the control. Similarly, the derivatives 3a, 3d and 3e displayed potent in vitro antibacterial potential. Molecular docking simulations delineated that the ligands and complexes were stabilized at the active site by electrostatic and hydrophobic forces, consistent with the corresponding experimental results. In silico study of the binding pattern predicted that the synthesized ligands, 3d and 3a could serve as a potential surrogate for hit-to-lead generation and the design of novel antibacterial drugs.     

二氧化碳和丙烯直接合成甲基丙烯酸的NiPMo/TiO2催化剂的研究

用溶胶-凝胶法以磷钼酸(MPA)的镍盐溶液水解钛酸四丁酯制备了NiPMo/TiO2催化剂.使用ICP、 XRD、 TG-DTA、 IR、 TPD-MS和微反应技术研究了催化剂的化学组成、热稳定性、化学吸附性质和催化反应性能.杂多钼酸盐与TiO2通过O2-在TiO2表面发生了键合.在623 K下,杂多阴离子仍保持原有的Keggin结构.CO2在Lewis酸位Ni(Ⅱ)和Lewis碱位Ni-O-Mo的桥氧协同作用下生成CO2卧式吸附态Ni(Ⅱ)←O-(CO)←(O--Ni).丙烯有多种吸附态在催化剂上吸附.在563 K、 1 MPa和空速1500 h-1的反应条件下,丙烯的摩尔转化率为3.2%,产物MAA选择性为95%.     

Synthesis of 1-benzyloxypyrazin-2(1H)-one derivatives

Different approaches for the synthesis of 1-benzyloxypyrazin-2(1H)-one derivatives from simple amino acids have been investigated. A library of 33 precursors for the preparation of N-hydroxy pyrazinones was obtained in moderate to good yields.     

Toward new camptothecins. Part 6: Synthesis of crucial ketones and their use in Friedländer reaction

In the context of the preparation of camptothecin and luotonin A analogs, the synthesis of some key keto-precursors and their use in Friedländer condensation are described. This paper also focuses on the stability of these keto intermediates and emphasizes the major differences between indolizinones and pyrroloquinazolinones series. Noteworthy is also the report of some original structures isolated as by-products of some experiments.     

CoFe2O4自形成磁性液体场致结构化对磁化的影响

The Langevin paramagnetic theory can’t describe the relation between magnetization of ferrofluids and applied magnetic field. The structuralization of ferrofluids, which is considered the main influence factor of the magnetization, is regarded. The part of magnetization works is deposited when the structure is forming. This action influences the magnetization of ferrofluids directly or indirectly. On the base of the “compressing” model, the Langevin function that usually describes the magnetization of ferrofluid is modified, and a well-fitted curve is obtained. An equation of the relation between the equivalent volume fraction after being “compressed” and the intensity of magnetic field is discovered, which approximately describes the process of magnetization. The relation between the approximate initial susceptibility and the volume fraction can be obtained from modified formula.     

Highly regioselective Buchwald–Hartwig amination at C-2 of 2,4-dichloropyridine enabling a novel approach to 2,4-bisanilinopyridine (BAPyd) libraries

The highly regioselective Buchwald–Hartwig amination at C-2 of the cheap and readily accessible reagent, 2,4-dichloropyridine with a range of anilines and heterocyclic amines is described. This new methodology is robust and provides a facile access to 4-chloro-N-phenylpyridin-2-amines on 0.25 mol scale. These intermediates undergo a further Buchwald–Hartwig amination at higher temperature to enable rapid exploration of the chemical space at C-4 and to provide a library of 2,4-bisaminopyridines.     

KMnO4-mediated oxidative CN bond cleavage of tertiary amines: Synthesis of amides and sulfonamides

KMnO₄-mediated oxidative CN bond cleavage of tertiary amines producing secondary amine was introduced, which was trapped by electrophiles (acyl chloride and sulfonyl chloride) to form amides and sulfonamides. The reaction could take place at mild condition, tolerating a wide range of function groups and affording products in moderate to excellent yields.     

Chemistry of heterocyclic compounds at the A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, over 50 years (Review)

The review contains a concise historical account and information on the most significant researches undertaken by the staff at the A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences on the Chemistry of Heterocyclic Compounds. Dedicated to Academician of the Russian Academy of Sciences B. A. Trofimov on his 70th jubilee. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1443–1502, October, 2008.     

A general and convenient synthesis of 4-(tosylmethyl)semicarbazones and their use in amidoalkylation of hydrogen,heteroatom, and carbon nucleophiles

A general synthesis of previously unknown semicarbazone-based α-amidoalkylating reagents, 4-(tosylmethyl)semicarbazones, has been developed. The synthesis involved three-component condensation of semicarbazones of aliphatic or aromatic aldehydes with the same or other aldehydes and p-toluenesulfinic acid. The scope and limitations of this reaction were investigated. The compounds obtained were demonstrated to be an efficient α-(4-semicarbazono)alkylating agents. They were reacted with H- (sodium borohydride), O- (sodium methylate), S- (sodium phenylthiolate), N- (pyrrolidine, sodium succinimide), P- (trialkyl phosphites), and C-nucleophiles (sodium diethyl malonate) to give the corresponding products of the tosyl group substitution, 4-substituted semicarbazones, including analogues of nitrofurazone. Among the prepared compounds tested in vitro for antibacterial and antifungal activity, three nitrofuryl-containing semicarbazones exhibited high biological activities with minimum inhibitory concentration (MIC) values of 8–32 μg/mL.     

Sulfur-directed metal-free and regiospecific methyl C(sp3)–H imidation of thioanisoles

Regiospecific and direct imidation of the methyl C(sp³)–H bond of thioanisoles is realized under mild and metal-free conditions with N-fluorobis(benzenesulfonyl)imide as an oxidant and nitrogen source. Proposed mechanism suggests that thionium ion intermediates and a Pummerer-type reaction are involved. The imidation has advantages such as high step-economy, excellent functionality tolerance, and regiospecificity, giving structurally diverse imidation products.     

Synthesis of novel chiral bidentate hydroxyalkyl-N-heterocyclic carbene ligands and their application in palladium-catalyzed Mizoroki–Heck couplings and asymmetric addition of diethylzinc to benzaldehyde

A small library of new chiral bidentate hydroxyalkyl-imidazolium salts 1 is conveniently synthesized on multi-gram scale from inexpensive and commercially available chiral pool amino acids. The corresponding carbenes, generated by deprotonation of imidazolium salts 1, in combination with palladium(II) chloride were tested in the Mizoroki–Heck coupling reaction. The most significant results in terms of yields and reactivities were achieved with low catalyst loading. The catalytic activities of these imidazolium salts were also investigated in the asymmetric addition of diethylzinc to benzaldehyde. The use of MgO nanoparticles as an additive in conjunction with these ligands played a crucial role in increasing the efficiency of these reactions.