X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用

自然界中的材料,比如无机材料,有机材料,生物材料等等,均有其独特的物理和化学性质。而材料的性能又与材料的结构息息相关,只有充分了解了材料的结构,才能更加深入的研究材料性质。因此,材料结构的确定在化学、物理、生物等学科中的显得尤为重要。X射线晶体学作为传统的结构解析技术仍然是目前最重要的结构解析手段,但是对于复杂结构,X射线衍射晶体学解析结构也存在一些不足,往往需要其他技术手段相补充才能完成复杂结构的结构解析。电子晶体学虽然起步比X射线晶体学晚,但是,经过近几十年的发展,已经是结构解析领域一个非常重要的手段。本文将主要介绍X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用。     

合成氨装置101D堵塞物中晶体定性分析

基于Boentgen、Laue与Ewald、W.H.Bragg及W.L.Bragg、Friedrich和Knipping等前辈X射线及其晶体学的研究与发现,X射线晶体结构分析已成为研究原子或离子在晶体点阵中结合、鉴定晶体化合物空间结构的可靠方法.Debye-Scherrer粉晶X射线衍射法(XRPD)在合成氨装置101D工况技术分析中,比较有意义的实际应用是解决由不同单质或化合物组成的复杂混合堵塞物中晶体的鉴定问题.采用XRPD定性分析了合成氨装置101D堵塞物样品中的主要晶体成分.实验结果表明:本法对合成氨装置101D工况技术分析具有重要的意义.     

卡文迪什实验室的创建及其对化学的重要贡献

通过对卡文迪什实验室成立百年诺贝尔奖获得情况的分析可知,物理学等学科的发展能为化学的发展开创新领域或为化学问题的解决提供新方法,如电子、质子和中子的发现使化学认识从宏观到微观,X射线晶体学为晶体结构研究提供了新手段。化学的发展不是独立的,而是根植于整个自然科学发展的土壤中。     

分子模型及其在手性识别机理研究上的应用

介绍了近十几年来在色谱手性识别机理研究中的分子模型。在这些模型中,采用量子力学、分子力学和分子动力学等方法计算了手性选择试剂与对映体之间的相互作用,并借助X射线晶体学、核磁共振技术和计算机模拟等技术建立了各种分子模型,研究在手性化合物分离过程中的手性识别机理。     

扫描电镜与能谱仪

<正>扫描电镜利用精细聚焦电子束照射在样品表面,该电子束可以是静止或在样品表面作光栅扫描。在这个过程中,电子束与样品相互作用产生各种信号,其中包括二次电子、背散射电子、俄歇电子、特征X射线和不同能量的光子等,这些信号来自样品中的特定区域,分别利用探测器接收,可以提供样品的各种信息,用于研究材料的微观形貌、晶体学特征和微区化学成分。X射线能谱仪是扫描电镜附带的附件,通过检测从样品出射的特征X射线的波长或能量,测定样品元素的组成、相对含量以及分布。     

基于小波支持向量机的蛋白质同源寡聚体分类研究

蛋白质具有的功能在很大程度上取决于其空间结构,因此对蛋白质空间结构的研究有着重要的意义.目前,蛋白质空间结构的解析主要有X射线晶体学方法、多维核磁共振法和基于结构知识的蛋白质结构预测方法.     

钆、铽、铒、铥的乙酰丙酮三水络合物的晶体结构和分子结构

报导了用X射线衍射法测定的钆、铽、铒、铥的四种乙酰丙酮三水络合物的晶体结构。确定了它们的晶体学参数与原子在晶胞中的分数坐标。讨论了晶体结构与分子结构的特征。     

外延X射线吸收精细结构(EXAFS)谱——一种结构测定新技术

一、引言X 射线结晶学从二十年代以来,一直作为物质结构研究中的一个重要工具。但是,随着科学技术的发展,越来越要求对像无定形材料、多相催化剂、催化剂载体及化学性质不稳定的原子簇等的结构有精确的了解。而对这些一般难以获得单晶的物质,X 射线结晶学所能提供的结构信息是极其有限的。近年发展起来的新     

X射线晶体学和电子晶体学在分子筛结构表征中的应用

分子筛是一类具有规则孔道或笼结构的晶态微孔材料, 在吸附、 分离和催化中都表现出了优异的性能. 为了探索其结构与性质的关系, 在原子尺度上研究分子筛的微观结构是十分必要的. 本综述介绍了一系列与X射线晶体学和电子晶体学相关的表征技术（倒易空间和正空间）在分子筛结构表征中的应用. 随后, 基于分子筛的结构表征方法和化学组成, 对2007年之后发现的85种新分子筛进行了系统总结, 对其中9种具有独特合成方法或结构特征的分子筛进行了详细介绍.     

化学家的有力工具——X射线单晶结构分析

X 射线单晶结构分析(简称 X 结构分析)是通过单晶对 X 射线的衍射效应来测定物质内部构造的实验方法。在晶体中原子、分子在空间周期性地排列,这为研究物质的内部构造提供了非常有利的条件。自1912年劳埃(Laue)发现晶体的 X 射线衍射效应后,X 结构分析为我们积累了大量键长、键角、构型、构象等十分有     

Nucleic acid X-ray crystallography via direct selenium derivatization

X-ray crystallography has proven to be an essential tool for structural studies of bio-macromolecules at the atomic level. There are two major bottle-neck problems in the macromolecular crystal structure determination: phasing and crystallization. Although the selenium derivatization is routinely used for solving novel protein structures through the MAD phasing technique, the phase problem is still a critical issue in nucleic acid crystallography. The background and current progress of using direct selenium-derivatization of nucleic acids (SeNA) to solve the phase problem and to facilitate nucleic acid crystallization for X-ray crystallography are summarized in this tutorial review.     

Syntheses and structures of isomeric [6.6]- and [8.8]cyclophanes with 1,4-dioxabut-2-yne and 1,6-dioxahexa-2,4-diyne bridges

All three isomers (ortho, meta, and para) of [8.8]cyclophane bearing 1,6-dioxahexa-2,4-diyne bridges have been synthesized and structually characterized by single-crystal X-ray crystallography to determine the conformation of the cyclophanes and their cavity dimensions. The three isomeric [6.6]cyclophanes bearing 1,4-dioxabut-2-yne bridges have also been synthesized from but-2-yne-1,4-diol ditosylate and the isomeric dihydroxybenzenes. The [6.6]orthocyclophane has been structurally characterized by single-crystal X-ray crystallography. The energy-minimized structures from the semiempirical AM1 calculations of these cyclophanes compare very well with the structures obtained by X-ray crystallography.     

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination

X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's [15N-1H]-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.     

Sulfoxide carbon-sulfur bond activation

The alkynylsulfoxide, TMSCCSO(p-tolyl) (TMS = trimethylsilyl, tolyl = C6H4Me), undergoes reaction with (eta5-C5H5)Co(PPh3)2 at room temperature to give the cobaltosulfoxide complex, (C5H5)Co(PPh3)(eta1-CCTMS)[eta1-(S)-SO(p-tolyl)], which was characterized by X-ray crystallography. Exposure of this cobaltosulfoxide complex to oxygen gas leads to the formation of the corresponding metallosulfone complex, (C5H5)Co(PPh3)(eta1-CCTMS)[eta1-(S)-SO2(p-tolyl)], which was characterized by X-ray crystallography. Alternatively, in solution at room temperature, the metallosulfoxide is converted to a 1:4 mixture of the equatorial-equatorial and equatorial-axial bridging cobalt-thiolato dimers, {(C5H5)Co[mu-S(p-tolyl)]}2, respectively. The equatorial-equatorial isomer was characterized by X-ray crystallography.     

Absolute Configuration of Small Molecules by Co-Crystallization

The most reliable method to determine the absolute configuration of chiral molecules is X-ray crystallography, but small molecules can be difficult to crystallize. We report rapid co-crystallization of tetraaryladamantanes with small molecules as different as n-decane to nicotine to produce crystals for X-ray analysis and the assignment of absolute configuration when the molecules are chiral. A screen of 52 diverse compounds gave inclusion in co-crystals for 88 % of all cases and a high-resolution structure in 77 % of cases. Furthermore, starting from three milligrams of analyte, a combination of NMR spectroscopy and X-ray crystallography produced a full structure in less than three days using an adamantane crystallization chaperone that encapsulates the analyte at room temperature.     

Synthesis and characterization of a biphenyl-linked hemicryptophane and an endohedral cobalt(II) complex

Hemicryptophanes are covalent molecular cages, constructed from a cyclotriveratrylene-based host unit and a functional unit linked by covalent spacers, which have been designed to accommodate endohedral functionalities in the cavity. In this study, the synthesis and characterization of the rigid, biphenyl-linked hemicryptophane 1 were investigated by NMR, ESI-MS, and X-ray crystallography. The structure of the inclusion complex, in which a dichloromethane molecule was constructed encapsulated within 1, was characterized by X-ray crystallography. An endohedral, cobalt(II) hemicryptophane complex 2 was also synthesized and characterized ESI-MS and X-ray crystallography. The X-ray crystal structure of 2 showed that the biphenyl-linked hemicryptophane had three components—a molecule each of chloroform and acetonitrile, and a cobalt(II) ion—within its cavity.     

Tailor-made naphthyridines: Self-assembling multiple hydrogen-bonded supramolecular architectures from dimer to helix

Stepwise changes of functional oxo and amino groups in 1,8-naphthyridines to modify the supramolecular architecture have been carried out. The first example of a naphthyridine helix has been found and its structure established by X-ray crystallography. The design is based on hydroxy and amido tautomeric naphthyridines which crystallize in dimers or catemers, one of them attaining helicity. The most stable tautomer present in all the compounds discussed in this paper, as well as the formation of hydrogen-bonded dimers or catemers, was established by X-ray crystallography and rationalized with theoretical calculations.     

Preparation of large crystals of photoactive yellow protein for neutron diffraction and high resolution crystal structure analysis

The exact positions of all the hydrogen atoms in photoactive yellow protein (PYP) is important for understanding the molecular mechanism of the photoreaction because the protonation/deprotonation of certain amino acid residues and rearrangements in the hydrogen bond network are involved in the conformational changes of PYP. Neutron crystallography is one of the most effective methods to determine the hydrogen positions. However, a large crystal is required for neutron crystallography because a neutron-incident flux is quite limited. In addition, the crystal should be grown from heavy water to reduce the incoherent background from hydrogen. We prepared a large crystal of PYP (dimensions: 1.5 x 0.7 x 0.7 mm3) for neutron crystallography using ammonium sulfate with sodium chloride. The obtained large crystal gave X-ray diffraction spots up to 0.84 angstroms. Although some of the hydrogen atoms could be observed in the high resolution X-ray crystal structure, functionally important hydrogen atoms were impossible to see, indicating the importance of neutron crystallography. Thus, we optimized the crystallization conditions with heavy water and successfully obtained neutron diffraction spots up to 2.1 angstroms with the crystal in D2O.     

7-Bromo-5-phenyl-1,2-dihydro-3H-1,3,5-benztriazepin-2-one

7-Bromo-5-phenyl-1,2-dihydro-3H-1,4-benztriazepin-2-one was obtained by thermolysis of the syn-4-phenylsemicarbazone of 2-aminobenzophenone. Its molecular and crystal structure were established by X-ray crystallography. The nature of the hydrogen bonds between molecules of the compound in solution and in the crystalline state was determined by IR spectroscopy and X-ray crystallography.