Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism

Herein, we present results from MD simulations of the Michaelis complex formed between the B. cereus zinc-beta-lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the specific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methylazetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molecular-mechanics representations of the prereactive complex and transition state configurations docked into the active site. Linear-scaling semiempirical calculations coupled with a continuum solvent model were then performed on these static models. We propose that the experimental rate data for the B. cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta-lactam substrates in which His210 acts as a proton donor.     

超离子导体CaF2中的Ca2+亚晶格和F-亚晶格

CaF_2在熔化以前为超离子导体相。一些实验和理论的研究表明,在超离子导体相中,Ca~(2+)仍维持原有的面心立方骨架,而F~-则在Ca~(2+)骨架中运动。早期的分子动力学模拟结果表明Ca~(2+)的均方根位移仅约0.3A,而F~-的扩散系数可达2.6×10~(-5)cm·s~(-1),已是熔盐扩散系数量级。近年来的中子散射实验表明在扩散离子和近邻离子间存在着某种动力学相关。为解释这些事实,新近Gillan的分子动力学模拟表明扩散离子伴随着F~-亚晶格变形,而Kaneko和Ueda的分子动力学模拟则表明扩散离子伴随着近邻离子在同一运动方向的相关运动。进一步的研究尚待进行。八十年代初,Nelson等人提出了描述晶体、非晶和液态中键取向的键球谐函数方法。     

蜜蜂外激素9－ODA和9－HDA的合成

６－溴－２－己酮在Ｌｉ２ｃｕＣｌ４催化下与γ－溴代巴豆酸甲酯进行格氏偶联，合成了蜂王物质９－羰基－（Ｅ）－２－癸烯酸（９－ＯＤＡ），将其还原得到另一蜂王物质９－羟基－（Ｅ）－２－癸烯酸（９－ＨＤＡ）。该法是合成９－ＯＤＡ和９－ＨＤＡ的新路线。     

甲醇／丙烷在ZSM－5分子筛上偶合转化过程的研究

考察了甲醇／低碳烷烃在ＺＳＭ－５分子筛上偶合转化为芳烃和低碳烯烃的反应过程。对特定的催化体系，存在一最佳原料配比，使反应的热效应近似为零。偶合转化时甲醇完全转化，低碳烷烃的转化率低；不同催化剂上偶合转化产物分布差别极大，与ＨＺＳＭ－５相比，Ｇａ改性后可获得较高的芳烃和低碳烯烃收率。     

Intramolecular hydrogen abstraction. Iodosobenzene diacetate,an efficient and convenient reagent for alkoxy radical generation

Photolysis of several hydroxy compounds in presence of iodosobenzene diacetate and iodine leads to alkoxy radical derivatives which undergo intramolecular hydrogen abstraction to produce cyclic ethers in good yield.     

Synthesis of 8,9-dialkoxy-substituted tetrahydrobenz[h] isoquinolines

6,7-Dimethoxy-2-naphthylethylamine, prepared by the diborane reduction of 6,7-dimethoxy-2-naphtlialeneacetamide, underwent a Pictet-Spengler cyclization to form 8,9-dimethoxy-1,2,3,4-tetrahydrobenz[h]isoquinoline. This compound is identical with that obtained by reduction of the corresponding dihydrobenzisoquinoline prepared from formamide cyclization. 6,7-Dialkoxy-2-naphthaleneacetic acids, the key intermediates for the preparation of these amides, were obtained from 6,7-dialkoxy-2-acetonaphthones by a modified Willgerodt reaction.     

Geometries,vibrational frequencies,and electron affinities of X2Cl (X=C,Si,Ge) clusters

Ab initio quantum chemical calculations have been performed on X₂Cl^? and X₂Cl (X = C, Si, Ge) clusters. The geometrical structures, vibrational frequencies, electronic properties and dissociation energies are investigated at the Hartree–Fock (HF), Møller–Plesset second‐ and fourth‐order (MP2, MP4), CCSD(T) level with the 6‐311+G(d) basis set. The X₂Cl (X = C, Si, Ge) and X₂Cl^? (X = Si, Ge) take a bent shape obtained at the ground state, while C₂Cl^? has a linear structure. The impact on internal electron transfer between the X₂Cl and the corresponding anional clusters is studied. The three different types of electron affinities (EAs) at the CCSD(T) are reported. The most reliable adiabatic electronic affinities, obtained at the CCSD(T)/cc‐pvqz level of theory, are predicted to be 3.30, 2.62, and 1.98 eV for C₂Cl, Si₂Cl, and Ge₂Cl, respectively. The calculated EAs of C₂Cl and Ge₂Cl are in good agreement with theoretical results reported. The correlation effects and basis sets effects on the geometrical structures and dissociation energies are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Design, synthesis, and binding affinities of pyrrolinone-based somatostatin mimetics

[structure: see text] Tetrapyrrolinone somatostatin (SRIF) mimetics (cf. 1), based on a heterochiral (D,L-mixed) pyrrolinone scaffold, were designed, synthesized, and evaluated for biological activity. The iterative synthetic sequence, incorporating the requisite functionalized coded and noncoded amino acid side chains, comprised a longest linear synthetic sequence of 23 steps. Binding affinities at two somatostatin receptor subtypes (hsst 4 and 5) reveal micromolar activity, demonstrating that the d,l-mixed pyrrolinone scaffold can be employed to generate functional mimetics of peptide beta-turns.     

Investigation of efflorescence of inorganic aerosols using fluorescence spectroscopy

The phase transition is one of the most fundamental phenomena affecting the physical and chemical properties of atmospheric aerosols. Efflorescence, in particular, is not well understood, partly because the molecular interactions between the solute and water molecules of saturated or supersaturated solution droplets have not been well characterized. Recently, we developed a technique that combines the use of an electrodynamic balance and a fluorescence dye, 8-hydroxyl-1,3,6-pyrenetrisulfonate (pyranine), to study the distributions of solvated and free water in aqueous droplets (Choi, M. Y.; Chan, C. K.; Zhang, Y. H. J. Phys. Chem. A 2004, 108, 1133). We found that the equality of the amounts of solvated and free water is a necessary but not sufficient condition for efflorescence. For efflorescing compounds such as Na2SO4, (NH4)2SO4, and a mixture of NaCl and Na2SO4, the amount of free water decreases, while that of solvated water is roughly constant in bulk measurements and decreases less dramatically than that of free water in single-particle measurements as the relative humidity (RH) decreases. Efflorescence of the supersaturated droplets of these solutions occurs when the amounts of free and solvated water are equal, which is consistent with our previous observation for NaCl. For nonefflorescing compounds in single-particle levitation experiments such as MgSO4 and Mg(NO3)2, the amounts of free and solvated water are equal at a water-to-solute molar ratio of about 6, at which spectral changes due to the formation of contact ion pairs between magnesium and the anions occur as shown by Raman spectroscopy. Fluorescence imaging shows that the droplets of diluted Mg(NO3)2 (at 80% RH) and MgSO4 are homogeneous but those of NaCl, Na2SO4, (NH4)2SO4, and supersaturated Mg(NO3)2 (at 10% RH) are heterogeneous in terms of the solvated-to-free water distribution. The solvated-to-free water ratios in NaCl, Na2SO4, and (NH4)2SO4 droplets are higher in the outer regions by about half a radius deep than at the center of the droplets.     

Microfluidic synthesis of high-valence programmable atom-like nanoparticles for reliable sensing

Synthesis of programmable atom-like nanoparticles (PANs) with high valences and high yields remains a grand challenge. Here, a novel synthetic strategy of microfluidic galvanic displacement (μ-GD) coupled with microfluidic DNA nanoassembly is advanced for synthesis of single-stranded DNA encoder (SSE)-encoded PANs for reliable surface-enhanced Raman scattering (SERS) sensing. Notably, PANs with high valences (e.g., n-valence, n = 12) are synthesized with high yields (e.g., >80%) owing to the effective control of interfacial reactions sequentially occurring in the microfluidic system. On the basis of this, we present the first demonstration of a PAN-based automatic analytical platform, in which sensor construction, sample loading and on-line monitoring are carried out in the microfluidic system, thus guaranteeing reliable quantitative measurement. In the proof-of-concept demonstration, accurate determination of tetracycline (TET) in serum and milk samples with a high recovery close to 100% and a low relative standard deviation (RSD) less than 5.0% is achieved by using this integrated analytical platform.

A novel synthetic strategy is presented for microfluidic preparation of programmable atom-like nanoparticles with high valences and high yields.