2‐Amino‐5‐iodopyridinium bromide hemihydrate and 2‐amino‐5‐iodopyridinium chloride monohydrate

The hydrobromide and hydrochloride salts of 2‐amino‐5‐iodopyridine were prepared from aqueous solutions. The hydrobromide salt, C₅H₆IN₂⁺·Br⁻·0.5H₂O, crystallizes as a hemihydrate, and exhibits hydrogen bonding and π‐stacking which stabilize the crystal structure. The hydrochloride salt, C₅H₆IN₂⁺·Cl⁻·H₂O·0.375HCl, crystallized as the hydrate and exhibits similar hydrogen bonding and π‐stacking in the lattice. The most interesting feature of the hydrochloride salt is the presence of an additional fractional HCl molecule which introduces disorder in the location of the water molecule. The additional proton from the fractional HCl molecule is accounted for by the presence of a partial hydronium ion on one of the water sites.     

SMFs-supported Pd nanocatalysts in selective acetylene hydrogenation: Pore structure-dependent deactivation mechanism

In the present study, CNFs, ZnO and Al₂O₃ were deposited on the SMFs panels to investigate the deactivation mechanism of Pd-based catalysts in selective acetylene hydrogenation reaction. The examined supports were characterized by SEM, NH₃-TPD and N₂ adsorption-desorption isotherms to indicate their intrinsic characteristics. Furthermore, in order to understand the mechanism of deactivation, the resulted green oil was characterized using FTIR and SIM DIS. FTIR results confirmed the presence of more unsaturated constituents and then, more branched hydrocarbons formed upon the reaction over alumina-supported catalyst in comparison with the ones supported on CNFs and ZnO, which in turn, could block the pores mouths. Besides the limited hydrogen transfer, N₂ adsorption-desorption isotherms results supported that the lowest pore diameters of Al₂O₃/SMFs close to the surface led to fast deactivation, compared with the other catalysts, especially at higher temperatures.     

Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.     

Handling of Environmental and Biological Samples via Pre-Column Technologies

Abstract

Sample handling is still a weak point in chromatography and in analytical chemisty in general. One consideration is the automation potential of new procedures. Solid-liquid extraction techniques in combination with pre-column technology are particularly promising in this regards. The construction and geometry of pre-columns both for conventional and narrow-bore HPLC are of major importance, since band broadening should be kept at a minimum for an optimal functioning of the analytical system. The various operations that can be carried out with such a pre-column are trace-enrichment, clean-up of the sample which depends on the type of adsorbents used in the precolumn, i.e., polar or apolar materials, ion exchangers or metal covered surfaces, etc., protection of the analytical column, field sampling and storage of samples and as a substrate for on-column chemical derivatizations. These various operations are demonstrated with practical examples from the fields of environmental and biological analysis. The selectivity can be further enhanced by coupling precolumn technology with selective detection modes such as diode array UV, electrochemical or fluorescence detection. This enables the construction of optimal and integrated analysis sytems which are fully automated and microprocessor controlled. They can also be made compatible with miniaturized LC-technology.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Construction of a portable sample preparation device with a magnetic poly(methacrylic acid‐co‐ethylene dimethacrylate) monolith as the extraction medium and its application in the enrichment of UV filters in water samples

A portable sample preparation device with a magnetic polymer monolith as the extraction medium was constructed. The monolith was synthesized by polymerizing methacrylic acid and ethylene dimethacrylate around a cylindrical magnet. In this way, the monolith with a magnetic core could be readily attached to the extraction device by magnetism. The constructed device was evaluated for the enrichment of UV filters in water samples, followed by high‐performance liquid chromatographic analysis. The extraction efficiency for the targets was satisfactory with no matrix interference. Good linearities were obtained for the UV filters with the correlation coefficients >0.9986. The limits of detection and quantification for the UV filters were 0.3–0.8 and 1.0–2.4 ng/mL, respectively. The recoveries of the UV filters from the spiked water samples at the concentration of 100 ng/mL were 95.3–101.7%, with relative standard deviations <10%. Accordingly, the proposed portable device was demonstrated to be suitable for on‐site simultaneous sampling, purification, and preconcentration within a single step.     

Probing the Role of the Conserved Arg174 in Formate Dehydrogenase by Chemical Modification and Site-Directed Mutagenesis

The reactive adenosine derivative, adenosine 5′-O-[S-(4-hydroxy-2,3-dioxobutyl)]-thiophosphate (AMPS-HDB), contains a dicarbonyl group linked to the purine nucleotide at a position equivalent to the pyrophosphate region of NAD⁺. AMPS-HDB was used as a chemical label towards Candida boidinii formate dehydrogenase (CbFDH). AMPS-HDB reacts covalently with CbFDH, leading to complete inactivation of the enzyme activity. The inactivation kinetics of CbFDH fit the Kitz and Wilson model for time-dependent, irreversible inhibition (K_D = 0.66 ± 0.15 mM, first order maximum rate constant k₃ = 0.198 ± 0.06 min⁻¹). NAD⁺ and NADH protects CbFDH from inactivation by AMPS-HDB, showing the specificity of the reaction. Molecular modelling studies revealed Arg174 as a candidate residue able to be modified by the dicarbonyl group of AMPS-HDB. Arg174 is a strictly conserved residue among FDHs and is located at the Rossmann fold, the common mononucleotide-binding motif of dehydrogenases. Arg174 was replaced by Asn, using site-directed mutagenesis. The mutant enzyme CbFDHArg174Asn was showed to be resistant to inactivation by AMPS-HDB, confirming that the guanidinium group of Arg174 is the target for AMPS-HDB. The CbFDHArg174Asn mutant enzyme exhibited substantial reduced affinity for NAD⁺ and lower thermostability. The results of the study underline the pivotal and multifunctional role of Arg174 in catalysis, coenzyme binding and structural stability of CbFDH.     

HZSM-5分子筛中邻近酸中心上的协同催化作用

总结了HZSM-5分子筛中邻近的酸中心协同催化作用的研究进展, 包括布朗斯特酸(B酸)和路易斯酸 (L酸)的协同催化、 B酸和B酸的协同催化作用. 综述了通过多种表征手段下协同催化作用机理的研究进展, 以及实验与理论计算相结合并相互验证的研究结果, 对邻近酸中心协同作用下反应分子的共同吸附、 活化与转化路径的特点进行了分析与总结, 提出了对邻近酸中心协同催化作用进行深入研究的关键科学问题和可能的解决方案.     

Inhibition of two Cu(II) and Mn(II) coordination polymers on the surgical site infections by inhibiting the bacterial biofilm formation

Within this work, two novel Cu(II) and Mn(II)-based coordination polymers (CPs) along with chemical compositions of {[Cu₂(L¹)(1,4-NDC)₂]·3H₂O}_n (1, 1,4-H₂NDC = Naphthalene-1,4-dicarboxylic acid, L¹ ​= ​di(1H-imidazole-1-yl)methane) and [Mn₃(L²)₂(H₂O)₂(1,4-NDC)₂]_n (2, L² ​= ​1,4-di(1H-imidazole-1-yl)benzene) have been completed in success via related metal salts reaction with 1,4-H₂NDC ligand in existence of various N-donor co-ligands. We discovered its application values on the surgical site infections (SSI) along with corresponding mechanism in the interim. We evaluated inflammatory cytokines released into the urine through ELISA detection kit after compound treatment. Then, we discovered the inhibitory effect of compound on the bacterial biofilm formation via real time RT-PCR.     

FER分子筛中铝原子的受限落位

分子筛是一类具有规则孔道或笼状结构的多孔材料,因其独特的结构和可调的酸性而广泛用于石油化工、精细化学品合成、现代煤化工等诸多行业.2006年Iglesia等在具有8元环孔道结构/侧口袋的FER和MOR分子筛上实现了无卤素添加、无贵金属存在条件下,由二甲醚羰基化合成乙酸甲酯的反应.乙酸甲酯通过进一步加氢可实现煤基乙醇的绿色生产.MOR分子筛通常具有较高的催化活性,但失活迅速;FER分子筛表现出良好的催化稳定性,但活性较低.如何在保证FER分子筛稳定性的前提下,进一步提升其羰基化活性是目前研究的热点.前期理论和实验研究发现,二甲醚羰基化反应活性与分子筛8元环孔道中的Br?nsted酸位密度存在正相关.因此,通过优化合成条件,选择性调控铝原子分布在"ferrierite"笼中,可以提高FER分子筛的羰基化反应活性.尽管研究者已在调节FER分子筛铝分布方面进行了大量研究,但对于不同T位上Al原子的精准识别以及对应Br?nsted酸位的可接触性还缺少系统和深入的认识.本文选取了几种代表性模板剂,分别在碱性和含氟体系下制备了系列FER分子筛样品,利用Rietveld精修和模拟退火算法,在原子水平揭示了模板剂种类以及合成介质变化对Al原子在不同T位分布的影响,并结合二甲醚羰基化反应进行了结构和性能的关联.首先选取不同尺寸大小的环状胺(环己胺、哌啶、吡啶、吡咯烷)和链状胺(乙二胺)合成了具有相似形貌、孔结构、酸密度的系列FER分子筛样品.以CHA-Na-FER为例,PXRD精修结果显示,Na+(平衡35％的骨架负电荷)分布在10元环孔道中与O1形成氢键,质子化的环己胺分布在"ferrierite"笼中,并且环己胺上的N与O3形成氢键.这说明与O1相连的T3位以及与O3相连的T1位都有可能是Al富集的位置.为了进一步验证该结论,本文还精修了吸附探针分子吡啶的样品CHA-Na-FER-Py-60h.原粉以及吸附吡啶样品的精修结果表明,T1位和T3位是样品中铝富集的位置.随后,运用相同方法研究了Py-Na-FER,PI-Na-FER,En-Na-FER和Pyrr-HF-FER样品中的Al落位,发现T1/T3位均是样品中Al富集的位置.此外,理论计算结果表明T1/T3位上Al原子的取代能较低,说明Al优先取代T1/T3位上的Si,这与精修结果相一致.前期理论模拟结果表明,FER分子筛中T2-O5和T4-O7位点的CO插入反应能垒较低,是二甲醚羰基化反应的活性位.本文吡啶吸附实验、热重分析以及PXRD精修结果表明,FER分子筛中大部分Al富集在T1/T3位,与T2/T4位相关的Br?nsted酸约占18％～30％.最后,对各样品进行了二甲醚羰基化反应评价,结果显示PI-Na-FER,Py-Na-FER,En-Na-FER和CHA-Na-FER催化剂的乙酸甲酯生成速率相近,约为0.10 mol/(mol H+?h).Pyrr-HF-FER催化剂的乙酸甲酯生成速率最高,可达到0.16 mol/(mol H+?h),这可能是由于Pyrr-HF-FER催化剂具有更多T2/T4位相关的Br?nsted酸.虽然Pyrr-HF-FER催化剂的乙酸甲酯生成速率较其他四个催化剂有一定提升,但其仍远低于MOR分子筛上乙酸甲酯生成速率(0.40 mol/(mol H+·h)).综上,有机模板剂的选择与合成介质的改变对FER分子筛中Al分布的调控作用是有限的,即Al原子总是优先分布于T1/T3位.而与T1和T3位相关的Br?nsted酸位不是二甲醚羰基化反应的活性位点.因此与MOR相比,FER分子筛在二甲醚羰基化反应中表现出较低的催化活性.