Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase

Combined QM(PM3)/MM molecular dynamics simulations together with QM(DFT)/MM optimizations for key configurations have been performed to elucidate the enzymatic catalysis mechanism on the detoxification of paraoxon by phosphotriesterase (PTE). In the simulations, the PM3 parameters for the phosphorous atom were reoptimized. The equilibrated configuration of the enzyme/substrate complex showed that paraoxon can strongly bind to the more solvent‐exposed metal ion Zn_β, but the free energy profile along the binding path demonstrated that the binding is thermodynamically unfavorable. This explains why the crystal structures of PTE with substrate analogues often exhibit long distances between the phosphoral oxygen and Zn_β. The subsequent S_N2 reaction plays the key role in the whole process, but controversies exist over the identity of the nucleophilic species, which could be either a hydroxide ion terminally coordinated to Zn_α or the μ‐hydroxo bridge between the α‐ and β‐metals. Our simulations supported the latter and showed that the rate‐limiting step is the distortion of the bound paraoxon to approach the bridging hydroxide. After this preparation step, the bridging hydroxide ion attacks the phosphorous center and replaces the diethyl phosphate with a low barrier. Thus, a plausible way to engineer PTE with enhanced catalytic activity is to stabilize the deformed paraoxon. Conformational analyses indicate that Trp131 is the closest residue to the phosphoryl oxygen, and mutations to Arg or Gln or even Lys, which can shorten the hydrogen bond distance with the phosphoryl oxygen, could potentially lead to a mutant with enhanced activity for the detoxification of organophosphates. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Analysis of XPS and XES of diamond and graphite by DFT calculations using model molecules

X‐ray photoelectron and emission spectra (XPS and XES) of diamond and graphite have been analyzed by deMon density‐functional theory (DFT) calculations using the model adamantane derivative (C₁₀H₁₂(CH₃)₄) and pyrene (C₁₆H₁₀) molecules, respectively. The theoretical valence photoelectron and C Kα X‐ray emission spectra for the allotrope are in good accordance with the experimental ones. The combined analysis of the valence XPS and C Kα XES enables us to divide the valence electronic distribution into the individual contributions for pσ‐, and pπ‐bonding MOs of the diamond and graphite, respectively. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 102–108, 2001     

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H(3)N-H-NH(3)](+) using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential.     

硅胶-氰丙基复合固相萃取柱分离原油中饱和烃及芳烃组分

探讨了硅胶-氰丙基(SiO2/C3-CN,(1 g/0.5 g,6 mL))复合固相萃取柱分离与净化原油中饱和烃和芳烃组分的方法。结果表明:SiO2/C3-CN复合固相萃取柱较单一硅胶(SiO2)小柱的分离效果好,仅使用4.5 mL正己烷和4.5 mL正己烷-二氯甲烷(1∶1)洗脱即可实现饱和烃和芳烃组分的完全分离与满意回收(回收率分别为98%和99%);而单一硅胶小柱存在低环数芳烃化合物(如萘及其甲基系列、苊等)与饱和烃组分的共洗脱现象。通过对原油实物样品的测定,饱和烃和芳烃组分在硅胶-氰丙基复合柱上经正己烷、正己烷-二氯甲烷(体积比1∶1)的洗脱行为与标准混合液完全一致,该方法实用可靠、流程简单、试剂消耗少、精密度良好(RSD为4.2%～8.5%),适用于石油样品中饱和烃和芳烃组分的定量分析。     

Mass‐Spectrometric Observation of Counter Anion Production in SU‐8 Exposed to UV Light and its Use for Dill C Parameter Determination

Photopolymerization is a phenomenon that is the basis of much of today's microfabrication technology and intense research is conducted to improve its control and the characteristics of end products for a variety of applications. The design of microscopic structures often relies on the accurate knowledge and modeling of photopolymer's behavior upon exposure, i.e. the Dill parameters, for each radiation species of interest and therefore the development of flexible characterization techniques is of great importance. SU‐8 is a popular compound that is representative of a whole class that relies on cationic polymerization, where an acid is obtained via photolysis of an onium salt during exposure. Here we report on the observation of SbF₆^? via laser desorption mass spectrometry on SU‐8 exposed to UV light at the wavelength of 365 nm and demonstrate that the yield of this counter‐anion as a function of exposure is consistent with the Dill C parameter value available in the literature. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 967–972     

XH-NH3(X=F,Cl,Br)质子传递的溶剂效应:簇模型,连续介质模型和离散-连续组合模型的比较

分别采用分子簇模型、连续介质模型和离散-连续组合模型研究了XH-NH3(X=F,Cl,Br)分子内质子传递的溶剂效应．结果表明,对于弱酸性化合物FH-NH3,其溶剂效应主要为短程作用,3个H2O分子即可使其发生质子传递,而简单的连续介质模型得到的仍为分子化合物形式,需进一步包含溶剂效应短程作用．对于强酸性化合物ClH-NH3和BrH-NH3,较弱的溶剂效应即可促使其发生质子传递,分子簇模型和连续介质模型均可合理描述,且与离散-连续组合模型的结果相近．离散-连续组合模型既在从头算水平考虑了溶质分子和第一溶剂化层中溶剂分子间的短程作用,又包含了溶剂效应的长程静电作用,能更准确地描述溶剂化作用,且对弱酸性化合物和强酸性化合物体系均适用．     

Solvent effects on the asymmetric Diels–Alder reaction between cyclopentadiene and (−)-menthyl acrylate revisited with the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method

The construction of the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method is detailed. This method is specifically devoted to the study of the reactivity of large chemical systems in solution. The solvent, modeled by a polarizable continuum, surrounds the whole solute molecule. Solute–solvent interactions are taken into account by means of the self-consistent reaction field approach. The solute system is treated by both quantum and molecular mechanics, the former being principally applied to the reactive part, i.e., the part undertaking bond forming or breaking, the latter being reserved for the ancillary encumbering groups. The connection between the molecular mechanics and the quantum mechanics part is accomplished by a strictly localized bond orbital that remains frozen within the local self-consistent field framework. As a test system, the asymmetric Diels–Alder reaction between cyclopentadiene and (–)-menthyl acrylate is studied for the first time with steric interactions and electrostatic solvent effects taken into account simultaneously. The results indicate that the coupling of both interactions leads to conclusions that could not have been guessed from separate calculations.Proceedings of the 11th International Congress of Quantum chemistry satellite meeting in honour of Jean-Louis Rivail     

偶合反应化学发光法测定痕量银的研究

本将Ａｇ（Ⅰ）催化Ｓ２Ｏ＾２－８氧化Ｍｎ（Ⅱ）生成ＭｎＯ＾－４的催化反应与ＬｕｍｉｎｏｌＭｎＯ＾－４－ＯＨ＾－的化学发光反应相偶合，建立起一种新的灵敏测定痕量银的化学发光分析法，在所研究的优化条件下，该法测定银的选择性较好，检测限达到３．２×１０＾－１２ｇ／ｍＬＡｇ线性浓度范围为１．０×１０＾－１１－１．０×１０＾－５ｇ／ｍＬＡｇ，用于水样分析，结果较为满意。     

负载型纳米TiO2复合载体及其CoMo催化剂的酸性及孔特性的研究

总结了复载不同纳米尺度的复合载体及其CoMo催化剂的表面酸性及孔结构特性的表征结果。结果表明，负载型纳米TiO2与基载体γ-Al2O3存在着相互作用。当负载比较少量的纳米TiO2时，复合载体的总酸量随着TiO2含量的增加而增加，超过γ-Al2O3的酸量，但当 TiO2的含量比较高时复合载体的酸量又降低，纳米TiO2优先负载在γ-Al2O3的强酸中心位；负载了CoMo活性组分后酸量增加。不同粒径的纳米TiO2对复合载体和催化剂的酸分布没有明显影响，但对总酸量有影响。对不同尺度TiO2，随着TiO2负载量的增加以及负载金属活性组分的增加，表面积、孔容和最可几孔径均有不同程度的减少。     

用双过渡金属复合催化剂制备长链支化聚乙烯

乙烯聚合;原位共聚合;用双过渡金属复合催化剂制备长链支化聚乙烯