pKa,MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step

The acylation step of the catalytic mechanism of beta-lactamases and penicillin-binding proteins (PBPs) has been studied with various approaches. The methods applied range from molecular dynamics (MD) simulations to multiple titration calculations using the Poisson-Boltzmann approach to quantum mechanical (QM) methods. The mechanism of class A beta-lactamases was investigated in the greatest detail. Most approaches support the critical role of Glu-166 and hydrolytic water in the acylation step of the enzymatic catalysis in class A beta-lactamases. The details of the catalytic mechanism have been revealed by the QM approach, which clearly pointed out the critical role of Glu-166 acting as a general base in the acylation step with preferred substrates. Lys-73 shuffles a proton abstracted by Glu-166 O(epsilon ) to the beta-lactam nitrogen through Ser-130 hydroxyl. This proton is transferred from O(gamma) of the catalytic Ser-70 through the bridging hydrolytic water to Glu-166 O(epsilon ). Then the hydrogen is simultaneously passed through S(N)2 inversion mechanism at Lys-73 N(zeta) to Ser-130 O(gamma), which loses its proton to the beta-lactam nitrogen. The protonation of beta-lactam nitrogen proceeds with an immediate ring opening and collapse of the first tetrahedral species into an acyl-enzyme intermediate. However, the studies that considered the effect of solvation lower the barrier for the pathway, which utilizes Lys-73 as a general base, thus creating a possibility of multiple mechanisms for the acylation step in the class A beta-lactamases. These findings help explain the exceptional efficiency of these enzymes. They emphasize an important role of Glu-166, Lys-73, and Ser-130 for enzymatic catalysis and shed light on details of the acylation step of class A beta-lactamase mechanism. The acylation step for class C beta-lactamases and six classes of PBPs were also considered with continuum solvent models and MD simulations.     

The utilization of modified BCR three-step sequential extraction procedure for the fractionation of Cd, Cr, Cu, Ni, Pb and Zn in soil reference materials of different origins

A modified three-step sequential extraction procedure for the fractionation of heavy metals, proposed by the Commission of the European Communities Bureau of Reference (BCR) has been applied to the Slovak reference materials of soils (soil orthic luvisols, soil rendzina and soil eutric cambisol), which represent pedologically different types of soils in Slovakia. Analyses were carried out by flame or electrothermal atomic absorption spectrometry (FAAS or ETAAS). The fractions extracted were: exchangeable (extraction step 1), reducible-iron/manganese oxides (extraction step 2), oxidizable-organic matter and sulfides (extraction step 3). The sum of the element contents in the three fractions plus aqua-regia extractable content of the residue was compared to the aqua-regia extractable content of the elements in the origin soils. The accuracy obtained by comparing the determined contents of the elements with certified values, using BCR CRM 701, certified for the extractable contents (mass fractions) of Cd, Cr, Cu, Ni, Pb and Zn in sediment following a modified BCR-three step sequential extraction procedure, was found to be satisfactory.     

Direct access to marine pyrrole-2-aminoimidazoles, oroidin, and derivatives, via new acyl-1,2-dihydropyridin intermediates

[reaction: see text] A short synthesis of the C(11)N(5) oroidin derivatives is reported. The key step of the strategy is a one-pot oxidative bromine-mediated addition of protected guanidines to the N-acyl-1,2-dihydropyridines 9a-c. The new N-acyl-1,2-dihydropyridines were prepared directly from pyridine and pyrrole-2-carbonyl chloride by reduction with borohydride reagent in one step.     

N,N-二(对氟苄基)-N'-(2',3'-二脱氧-3'-硫代胞苷)甲脒水解反应的理论研究

采用密度泛函理论方法B3LYP/6-31++G(d,p)//B3LYP/6-31G(d,p)和导体极化连续模型B3LYP/CPCM/6-31++G(d,p)方法对苯环对位上有F取代的N,N-二(对氟苄基)-N′-(2′,3′-二脱氧-3′-硫代胞苷)甲脒(FBFA-3TC)水解反应机理和溶剂效应进行了研究. 考虑两条可能反应途径: 水分子首先进攻C=N双键的途径(Path A)和先进攻C-N单键的途径(Path B). 计算结果表明, 气相和水中两条途径的第一步都是速率控制步骤, Path A 比Path B 更有利. 对优势途径Path A的第二步反应的进一步研究发现, 中间体的羟基H原子转移到双键N比单键N更容易, 从而形成2′,3′-二脱氧-3′-硫代胞苷(3TC)的最终水解产物.     

Kinetics and mechanism of oxidation of fumarate,acrylate, cinnamate,and maleate anions by hexavalent manganese in aqueous alkaline medium

Kinetics of oxidation of fumarate, acrylate, cinnamate, and maleate anions by hexavalent manganese has been studied in aqueous alkaline medium. The order in [oxidant] was unity while that in [substrate] was fractional. The order of reactivity of anions is fumarate → acrylate → cinnamate → maleate. The reactions followed Michaelis–Menten kinetics suggesting the formation of a cyclic intermediate between Mn(VI) and the substrate followed by its disproportionation in a slow step. The equilibrium constant (K) for the preequilibrium step and the rate constant (k) for the slow disproportionation step have been calculated from the intercept and the slope values of the linear plot of 1/k_obs versus 1/[substrate]. Activation parameters are also presented and discussed. A convenient iodometric method is reported for the estimation of Mn(VI).     

Rapid determination of ascorbic acid, dehydroascorbic acid, and total vitamin C by electrochemiluminescence with a thin-layer electrochemical cell

This paper reports on a rapid and sensitive method for the simultaneous determination of ascorbic acid (H₂A), dehydroascorbic acid (DHA), and total vitamin C by electrochemiluminescence (ECL) using a thin-layer electrochemical cell. Significant ECL signals can be generated by the anodic oxidation of Ru(bpy)₃ ²⁺ in the presence of H₂A or DHA in pH 8.8 phosphate buffer solution. Because of the extremely small dead volume of the thin-layer cell (approximately 1.5 μL), almost all amount of H₂A is assumed to be completely oxidized to DHA with a short pre-electrolysis step. As a result, it is possible to determine the reductive vitamin C (H₂A) by square wave voltammetry before the pre-electrolysis step, while total vitamin C (sum of H₂A and DHA) is able to be determined at a subsequent ECL step. The method was employed for the determination of vitamin C in commercial beverages with the analytical results in good agreement with the certified values.

Carbenoid chain reactions through proton, deuteron, or bromine transfer from unactivated 1-bromo-1-alkenes to organolithium compounds

The deceptively simple vinylic substitution reactions Alk2C=CA-Br + RLi --> Alk2C=CA-R + LiBr (A = H, D, or Br) occur via an alkylidenecarbenoid chain mechanism (three steps) without transition metal catalysis. 2-(Bromomethylidene)-1,1,3,3-tetramethylindan (Alk2C=CH-Br, 2a) is deprotonated (step 1) by phenyllithium (PhLi) to give the Br,Li-alkylidenecarbenoid Alk2C=CLi-Br (3). In the ensuing chain cycle, 3 and PhLi (step 2) form the observable alkenyllithium intermediate Alk2C=CLi-Ph that characterizes the carbenoid mechanism in Et2O and is able to propagate the chain (step 3) through deprotonation of 2a, furnishing carbenoid 3 and the product Alk2C=CH-Ph. The related 2-(dibromomethylidene)-1,1,3,3-tetramethylindan (Alk2C=CBr2, 2c) and methyllithium (MeLi) generate carbenoid 3 (step 1), which incorporates MeLi (step 2) to give Alk2C=CLi-CH3, which reacts with 2c by bromine transfer producing Alk2C=CBr-CH3 and carbenoid 3 (step 3). PhCCLi cannot carry out step 1, but MeLi can initiate (step 1) the carbenoid chain cycle (steps 2 and 3) of 2c with PhC[triple bond]CLi leading to Alk2C=CBr-C[triple bond]C-Ph. Reagent 2a may perform both proton and bromine transfer toward Alk2C=CLi-CH3, feeding two coupled carbenoid chain processes in a ratio that depends on the solvent and on a primary kinetic H/D isotope effect.     

Thermally polymerizable bisaryloxy-bisimido-bisphthalonitriles containing dimethylsilane,hexafluoroisopropylidene, ether,and keto groups: Synthesis,characterization, and NMR study

A proton-NMR study of the condensation reaction (step 1) of 4-(3′-aminophenoxy)phthalonitrile (4-3′APPN) ( I ) in an aprotic solvent with various aromatic dianhydrides demonstrated the formation of the corresponding bisamic acid within 5–10 min. There was no effect of the electron affinity of the used aromatic dianhydrides on the time of the condensation reaction and also no charge-transfer complex formation was indicated. Proton-NMR study of the synthesized bisaryloxy-bisimido-bisphthalonitriles at 250.1 MHz has revealed general findings for their NMR characterization. The coupling constant (J) value for the ortho-coupled protons of the phthalonitrile ring of the 4–3′-APPN portion is 8.8 ± 0.05 Hz and that for the ortho-coupled protons of the aminophenoxy ring of 4–3′-APPN is 8.1 ± 0.05 Hz. The coupling constant (J) values for ortho-coupled protons of the dianhydride portion range from 8.1 to 7.5 Hz. Various thermally polymerizable bisaryloxybisimido-bisphthalonitriles (BBBP) ( X, XI, XII , and XIII ) containing dimethylsilane, hexafluoroisopropylidene, ether, and keto groups, suitable for the development of thermooxidative stable, void-free composites, were synthesized by two methods. In method 1,4–3′-APPN ( I ) in N,N-dimethylacetamide (DMAC) was condensed (step 1) with bis(3,4-dicarboxyphenyl)dimethylsilane dianhydride (SIDA) ( II ), 4, 4′-hexafluoroisopropylidenediphthalic anhydride (6FDA) ( III ), bis(3,4-dicarboxyphenyl)ether dianhydride (ODPA) ( IV ), and 3,4,3′,4′-benzophenonetetracarboxylic dianhydride (BTDA) ( V ), respectively, to give the corresponding bisamic acids. Thermal cyclodehydration of the intermediate bisamic acid at 160°C gave the bisphthalonitriles. In method 2, the second step of thermal cyclodehydration was performed in situ in refluxing toluene. The characterization of the synthesized bisaryloxy-bisimido-bisphthalonitriles (BBBP) was performed using FT-IR, ¹H-NMR, ¹³C-NMR, mass spectroscopy, and elemental analysis. A preliminary study indicated that thermal-polymerization of these bisphthalonitriles (BBBP) gave tough, thermosetting polymers, useful for high-temperature applications. © 1993 John Wiley & Sons, Inc.     

Total synthesis of macrosphelides A, B, and E: first application of ring-closing metathesis for macrosphelide synthesis

A new synthetic route for macrosphelides A, B, and E based on ring-closing metathesis (RCM) was established. The substrates for RCM could be synthesized starting from commercially available chiral materials, methyl (S)-lactate and methyl (S)- or (R)-3-hydroxybutyrate, in good overall yields. In the investigation of the key RCM step, it was found that the steric factor around the reaction site significantly affected the reaction rate of macrocyclization. A detailed account regarding this synthetic study is described herein.     

Syntheses of (+)-cytisine, (-)-kuraramine, (-)-isokuraramine, and (-)-jussiaeiine A

Total syntheses of (+)-cytisine, (-)-kuraramine, (-)-isokuraramine, and (-)-jussiaeiine A were achieved via a samarium diiodide-promoted reductive deamination reaction, followed by simultaneous recyclization of a proline derivative to give the corresponding delta-lactam derivative, as a key step.     

Combining atom‐transfer radical polymerization and ring‐opening polymerization through bifunctional initiators derived from hydroxy benzyl alcohol—Preparation and characterization of initiators,macroinitiators, and block copolymers

A simple, one‐step procedure has been developed for the preparation of bifunctional initiators capable of polymerizing monomers suitable for atom‐transfer radical polymerization (ATRP) and ring‐opening polymerization (ROP). These bifunctional initiators were employed for making narrow disperse poly(styrene) macroinitiators, which were subsequently used for the ROP of various lactides to yield poly(styrene‐block‐lactide) copolymers. Thermogravimetric analysis (TGA) of these block copolymers are interesting in that it shows a two‐step degradation curve with the first step corresponding to the degradation of poly(lactide) segment and the second step associated with the poly(styrene) segment of the block copolymer. This nature of the block copolymer makes it possible to estimate the block copolymer content by TGA in addition to the ¹H NMR spectroscopic analysis. Thus, this study for the first time highlights the possibility of making porous materials by thermal means which are otherwise obtained by base hydrolysis. The bifunctional initiators were prepared by the esterification of 3‐hydroxy, 4‐hydroxy, and 3,5‐dihydroxy benzyl alcohols with α‐bromoisobutyryl bromide and 2‐bromobutyryl bromide. A mixture of products was obtained, which were purified by column chromatography. The esterified benzyl alcohols were employed in the polymerization of styrene under copper (Cu)‐catalyzed ATRP conditions to yield macroinitiators with low polydispersity. These macroinitiators were subsequently used in the ROP of L ‐, DL ‐, and mixture of lactides. The formation of block copolymers was confirmed by gel permeation chromatography (GPC), spectroscopic and thermal characterizations. The molecular weight of the block copolymers was always higher than the macroinitiator, and the GPC chromatogram was symmetrical indicating the uniform initiation of ROP by the macroinitiators. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 102–116, 2008     

Functionality,Effectiveness, and Mechanistic Evaluation of a Multicatalyst‐Promoted Reaction Sequence by Electrospray Ionization Mass Spectrometry

A multicatalytic three‐step reaction consisting of epoxidation, hydrolysis, and enantioselective monoacylation of cyclohexene was studied by using mass spectrometry (MS). The reaction sequence was carried out in a one‐pot reaction using a multicatalyst. All reaction steps were thoroughly analyzed by electrospray ionization (ESI) MS (and MS/MS), as well as high‐resolution MS for structure elucidation. These studies allow us to shed light on the individual mode of action of each catalytic moiety. Thus, we find that under the epoxidation conditions, the catalytically active N‐methyl imidazole for the terminal acylation step is partially deactivated through oxidation. This observation helps to explain the lower efficiency of the catalyst in the last step compared to the monoacylation performed separately. All reactive intermediates and products of the reaction sequence, as well as of the side‐reactions, were monitored, and we present a working mechanism of the reaction.     

Transketolase and fructose-1,6-bis-phosphate aldolase, complementary tools for access to new ulosonic acid analogues

A new approach to the synthesis of ulosonic acids KDO and DAH is described. The key step is the C₅-C₆ bond formation catalysed by fructose-1,6-bisphosphate aldolase (for KDO) or transketolase (for DAH) using substituted acrylonitrile α-hydroxyaldehyde. All asymmetric carbon configurations are determined in an enzymatic step by the means of deshydrogenase or lipase. This strategy, using a non-metabolism pathway, allows access to novel precursors of KDO, DAH and analogues.     

One-pot, two-step conversion of aldehydes to phosphonyl- and sulfonylpyrazoles using bestmann-ohira reagent

A one-pot, two-step, three-component method for the conversion of commercially available aldehydes to phosphonylpyrazoles has been developed, demonstrating, for the first time, the dual reactivity of the Bestmann-Ohira reagent (BOR) in a single-pot transformation. This method, extended to the synthesis of sulfonylpyrazoles by employing BOR in the first step and a diazomethyl sulfone in the second step, is complementary, with regard to regioselectivity, to the previous methods for the synthesis of such functionalized pyrazoles.     

1,4,7,10-四氮杂环十二院的合成研究

多氮杂环化合物及其衍生物近年来愈来愈显示出其重要而广泛的用途,譬如：可作为人体内结石的清除药物［‘·’j,作为MnSOD的模拟物可抑制心肌缺血性再灌注引起的损伤［’j,且具有抗爱滋病活性等;尤其是在制造磁共振成像（MRI）、X射线CT、超声成像等医学影像技术的造影剂以及恶性肿瘤的放射性治疗药物方面［‘－’‘,多氨杂环烷烃特别是1,4,7,10一四氮染环十二烷（Cyclen,环楞胺）及其衍生物显示出极其重要的应用价值．多氨杂环烷烃及其衍生物可因具体情况有不同的合成方法,环楞胺最初由乙二胶二乙酸氯与乙二胺在高度稀释条…     

Enantiospecific total synthesis of (-)-bakkenolide III and formal total synthesis of (-)-bakkenolides B, C, H, L, V, and X

A concise enantiospecific synthesis of (-)-bakkenolide III was accomplished from (S)-(+)-carvone. The key step involved radical cyclization of an iodoketone intermediate which afforded the cis-hydrindanone skeleton. Further synthetic transformations generated bakkenolide III, which also constitutes the formal total synthesis of (-)-bakkenolides, B, C, H, L, V, and X.     

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function

A symplectic multiple-time-step (MTS) algorithm has been developed for the united-residue (UNRES) force field. In this algorithm, the slow-varying forces (which contain most of the long-range interactions and are, therefore, expensive to compute) are integrated with a larger time step, termed the basic time step, and the fast-varying forces are integrated with a shorter time step, which is an integral fraction of the basic time step. Based on the split operator formalism, the equations of motion were derived. Separation of the fast- and slow-varying forces leads to stable molecular dynamics with longer time steps. The algorithms were tested with the Ala(10) polypeptide chain and two versions of the UNRES force field: the current one in which the energy components accounting for the energetics of side-chain rotamers (U(rot)) can lead to numerically unstable forces and a modified one in which the the present U(rot) was replaced by a numerically stable expression which, at present, is parametrized only for polyalanine chains. With the modified UNRES potential, stable trajectories were obtained even when extending the basic time step to 15 fs and, with the original UNRES potentials, the basic time step is 1 fs. An adaptive multiple-time-step (A-MTS) algorithm is proposed to handle instabilities in the forces; in this method, the number of substeps in the basic time step varies depending on the change of the magnitude of the acceleration. With this algorithm, the basic time step is 1 fs but the number of substeps and, consequently, the computational cost are reduced with respect to the MTS algorithm. The use of the UNRES mesoscopic energy function and the algorithms derived in this work enables one to increase the simulation time period by several orders of magnitude compared to conventional atomic-resolution molecular dynamics approaches and, consequently, such an approach appears applicable to simulating protein-folding pathways, protein functional dynamics in a real molecular environment, and dynamical molecular recognition processes.     

Two-step chromatographic purification of recombinant human thyrotrophin and its immunological, biological, physico-chemical and mass spectral characterization

A purification strategy for rapidly obtaining recombinant human thyrotropin (rhTSH) was designed based on size exclusion and reversed-phase high-performance liquid chromatographic (HPLC) analysis, carried out on hTSH-secreting CHO cell conditioned medium. These analyses permitted the identification of the main contaminants to be eliminated. Considering that hTSH is highly hydrophobic and elutes only with the addition of organic solvents, hydrophobic interaction chromatography was adopted as the first purification step; this resulted in the elimination of, among others, the major contaminant. A second purification step, based on size exclusion chromatography, was then utilized, being effective in the elimination of other previously identified contaminating proteins. Useful purity, as high as 99% at the chemical reagent level, and recoveries (37%) were obtained by adopting this two step strategy, which also provided adequate material for physico-chemical, immunological and biological characterization. This included matrix-assisted laser desorption ionization time-of-flight mass spectral analysis (MALDI-TOF-MS), Western blotting analysis, in vivo biological assay, size-exclusion HPLC (HPSEC) and reversed-phase HPLC (RP-HPLC) analysis, which confirmed the integrity and bioactivity of our rhTSH in comparison with the only two reference preparations available at the milligram level of native (hTSH-NIDDK) and recombinant (Thyrogen) hTSH. Thyrogen and rhTSH-IPEN, when compared to pit-hTSH-NIDDK, presented more than twice as much biological activity and about 7% increased molecular mass by MALDI-TOF-MS analysis, an accurate heterodimer mass determination providing the Mr values of 29,611, 29,839 and 27,829, respectively. The increased molecular mass of the two recombinant preparations was also confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and HPSEC analysis. Comparing the two recombinant preparations, minor though interesting physico-chemical and biological differences were also observed.     

Biosynthesis of violacein: a genuine intermediate, protoviolaceinic acid, produced by VioABDE, and insight into VioC function

A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE was elucidated to be 5-(5-hydroxy-1H-indol-3-yl)-3-(1H-indol-3-yl)-1H-pyrrole-2-carboxylic acid, named protoviolaceinic acid, indicating that VioC, responsible for the final biosynthetic step, works to oxygenate at the 2-position of the right side indole ring, and that the oxygenation reaction to form the central pyrrolidone core proceeds in a non-enzymatic fashion.