Convergence in the QM‐only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

We report systematic quantum mechanics‐only (QM‐only) and QM/molecular mechanics (MM) calculations on an enzyme‐catalyzed reaction to assess the convergence behavior of QM‐only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2‐SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single‐point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model ( M3a , with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4 . QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a , but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate‐limiting in the QM/MM calculations with M3a ( M4 ). QM‐only gas‐phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM‐only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single‐point QM‐only and QM/MM calculations (MAD typically about 1–2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1–2 kcal/mol.Copyright © 2013 Wiley Periodicals, Inc.     

巯基功能化介孔材料高效锚定钯负载型催化剂的制备及其苯酚加氢催化性能

以含巯基官能团有机硅烷修饰的介孔材料MCM-41和SBA-15为载体, 采用浸渍-氢气还原法制备了高分散和高活性的负载型Pd催化剂. X射线衍射、N₂吸附-脱附和透射电子显微镜表征结果显示, 所制Pd催化剂Pd-SH-MCM-41和Pd-SH-SBA-15具有很好的长程有序结构、分布均匀的孔径、高比表面积及高度分散的Pd颗粒. 苯酚加氢反应结果表明, 以Pd-SH-MCM-41和Pd-SH-SBA-15为催化剂时, 在80℃, 1.0MPa反应1h, 苯酚转化率达99%以上, 环己酮选择性为98%. 它们的催化活性为商业Pd/C催化剂的5倍, Pd/MCM-41和Pd/SBA-15催化剂的3倍. 这可归因于介孔材料表面修饰的巯基官能团对Pd的锚定作用, 避免了Pd颗粒的团聚, 使其高度分散在介孔材料上.     

辉光放电电解等离子体引发合成高吸水性树脂

以淀粉、丙烯酸和腐殖酸钠为原料,以N,N-亚甲基双丙烯酰胺为交联剂,采用辉光放电电解等离子体在水溶液中引发聚合制备淀粉-聚丙烯酸/腐殖酸钠复合高吸水树脂。考察了放电电压、放电时间,单体与淀粉质量比、腐殖酸钠含量、交联剂、温度及中和度对树脂吸水率的影响。用红外光谱和热重分析分别对树脂进行了结构表征和稳定性测试,结果表明,在优化合成条件下,所得的复合树脂具有较高的吸水性和耐盐性,常温下对蒸馏水吸收量为862g/g,对0.9%NaCl溶液的吸收量为69g/g。     

双功能配体促进的钯催化不对称醚化和胺化反应（英文）

研究双亚砜膦配体(BiSO-P)亚砜基团的Bronsted碱性在协同催化反应中的作用.1H NMR研究表明双亚砜膦与醇和胺等质子试剂形成氢键;并将此类配体应用于钯催化的不对称醚化和胺化反应,最高获得99%ee.研究发现氢键的存在能有效提高反应的ee值,配体亚砜基团在反应过程中同时起着Lewis和Bronsted碱的作用.     

Synthesis and Properties of Oval‐Shaped Iron Oxide/Ethylene Glycol Mesostructured Nanosheets

We have demonstrated a new and facile bottom‐up protocol for the effective synthesis of oval‐shaped iron oxide/ethylene glycol (FeO_x/EG) mesostructured nanosheets. Deprotonated ethylene glycol molecules are intercalated into iron oxide layers to form an interlayer distance of 10.6 Å. These materials display some peculiar magnetic properties, such as the low Morin temperature T_M and ferromagnetism below this T_M value. CdSe/ZnS nanoparticles can be loaded onto these mesostructured nanosheets to produce nanocomposites that combine both magnetic and fluorescence functions. In addition, iron oxide/propanediol (or butanediol) mesostructured materials with increased interlayer distances can also be synthesized. The developed synthetic strategy may be extended toward the creation of other ultrathin mesostructured nanosheets.     

滑动弧电极放电等离子体作用甲烷制C2烃的工艺

采用刀片式不锈钢电极放电反应器,以Ar气为稀释气,研究了等离子体作用下甲烷转化制C2烃的工艺条件。考察了CH4流量、高频电源输入电压和电极间距等参数对甲烷转化率、C2烃选择性、收率和反应表观能耗的影响。结果表明,增加CH4流量,表观能耗随之降低;当输入电压和电极间距较小时,甲烷转化率随输入电压和电极间距的增大而增大,但输入电压和电极间距过大时,C2烃收率明显下降,积碳严重。在CH4流量14 mL/min、Ar气流量60 mL/min、高频电源输入电压22 V、电流0.44 A、电极间距4 mm的优化条件下,甲烷最高转化率为43.1%,C2烃收率、选择性和表观能耗分别为40.1%、93.2%和2.41 MJ/mol。C2烃中不饱和烃的体积分数可达95%以上。     

A novel efficient protocol for preparation of 3-formyl-2-arylbenzo[b]furan derivatives

An efficient method for preparation of 3-formyl-2-arylbenzo[b]furan derivatives 4 from 3-chloro-2-(2-methoxyaryl)-1-arylprop-2-en-1-one 2 was developed, and the desired product was obtained in good to excellent yields. By converting 2-(2-methoxyphenyl)-3-oxo-3-phenylpropanal 1 to 2, the regioselectivity problem occurring in the reaction when using 1 as the starting material was successfully avoided. Furthermore, a one-pot procedure for the successive demethylation, cyclization, and hydrolysis was evolved, although the intermediate 3-(dibromomethyl)-2-phenylbenzo[b]furan 3a could be isolated. A plausible mechanism was proposed based on some in situ investigations.     

Extraction kinetics of Uranium(VI) and Thorium(IV) with Tri-iso-amyl phosphate from nitric acid using a Lewis Cell

The extraction kinetics of uranium(VI) and thorium(IV) with Tri-iso-amyl phosphate (TiAP) from nitric acid medium has been investigated using a Lewis Cell. Especially, dependences of the extraction rate on stirring speed, temperature, interfacial area were firstly measured to elucidate the extraction kinetics regimes. The experimental results demonstrated that extraction kinetic of U(VI) is governed by chemical reactions at interface with an activation energy, E_a, of 43.41 kJ/mol, while the rate of Th(IV) extraction is proved to be intermediate controlled, of which the E_a is 23.20 kJ/mol. Reaction orders with respect to the influencing parameters of the extraction rate are determined, and the rate equations of U(VI) and Th(IV) at 293 K have been proposed as $$ {\text{r}} = - {\text{dcUO}}_{ 2} \left( {{\text{NO}}_{ 3} } \right)_{ 2} /{\text{dt}} = 1. 80 \times 10^{ - 3} \left[ {{\text{UO}}_{ 2} \left( {{\text{NO}}_{ 3} } \right)_{ 2} } \right]^{ 1.0 1} \left[ {\text{TiAP}} \right]^{0. 5 5} , $$ $$ {\text{r}} = - {\text{dcTh }}\left( {{\text{NO}}_{ 3} } \right)_{ 4} /{\text{dt}} = 1. 8 8\times 10^{ - 3} \left[ {{\text{Th }}\left( {{\text{NO}}_{ 3} } \right)_{ 4} } \right]^{ 1.0 4} \left[ {\text{TiAP}} \right]^{ 1. 7 7} \left[ {{\text{HNO}}_{ 3} } \right]^{0. 3 8} , $$ respectively.     

Determination of tritium in Li–Pb alloy irradiated by thermal neutrons with quantitatively analyzing the byproduct 4He

The mass of the tritium produced in ⁶Li(n,α)T reaction was obtained by quantitatively analyzing the byproduct ⁴He with mass spectrometer. The self-expending seal method was employed to quantitatively prepare the Li–Pb alloy targets in room temperature. They were irradiated for 2 h in two rabbit irradiation channels in Xi’an pulsed reactor and measured after cooling 15 days. A sample purifying unit was set up to get rid of the hydrogen isotopes to remarkably reduce the interference to helium isotopes when measuring. And the sample disposal platform including purifying unit was testified with simulative gas and nature atmosphere. The targets were melted at 700 °C to release most of the ⁴He atoms which were measured by adding dilution gas ³He. And it was testified that ⁴He had released completely by repetitiously melting the targets. This approach had solved the problem that the tritium couldn’t be accurately determined by directly analyzing it because of non-complete releasing from lithium alloy.     

Simultaneous determination of atropine,scopolamine, and anisodamine from Hyoscyamus niger L. in rat plasma by high‐performance liquid chromatography with tandem mass spectrometry and its application to a pharmacokinetics study

In order to investigate the pharmacokinetics of tropane alkaloids in Hyoscyamus niger L., a sensitive and specific high‐performance liquid chromatography with tandem mass spectrometry method for the simultaneous determination of atropine, scopolamine, and anisodamine in rat plasma is developed and fully validated, using homatropine as an internal standard. The separation of the four compounds was carried out on a BDS Hypersil? C₁₈ column using a mobile phase consisting of acetonitrile and water (containing 10 mmol ammonium acetate). Calibration curves were linear from 0.2 to 40 ng/mL for atropine, scopolamine, and from 0.08 to 20 ng/mL for anisodamine. The precision of three analytes was <5.89% and the accuracy was between ?1.04 to 2.94%. This method is successfully applied to rat pharmacokinetics analysis of the three tropane alkaloids after oral administration of H. niger extract. The maximum concentration of these three tropane alkaloids was reached within 15 min, and the maximum concentrations were 31.36 ± 7.35 ng/mL for atropine, 49.94 ± 2.67 ng/mL for scopolamine, and 2.83 ± 1.49 ng/mL for anisodamine. The pharmacokinetic parameters revealed areas under the curve of 22.76 ± 5.80, 16.80 ± 3.08, and 4.31 ± 1.21 ng/h mL and mean residence times of 2.08 ± 0.55, 1.19 ± 0.45, and 3.28 ± 0.78 h for atropine, scopolamine, and anisodamine, respectively.