X射线晶体学和电子晶体学在分子筛结构表征中的应用（英文）

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.     

现代晶体学与化学

晶体学在自身发展的过程中对化学等学科的促进堪称自然科学中诸学科相互渗透而相得益彰的典范。本文提出了现代晶体学研究方法的几个前沿领域,以及这些研究方法对化学发展的巨大影响。讨论了测定晶体静态结构以研究分子化学反应所取得的成果。说明了现代晶体学已为人们提供了一个认识原子三维空间结构的强有力手段,它与合成化学配合正对人类改造自然和促进社会发展作出令人瞩目的贡献。     

关于晶体学的一些概念

大学化学编辑部约我写篇文章,讨论一些晶体学的基本概念和表述方法。我想藉此机会写一些学习体会,和读者交流,就教于读者。1晶体的周期结构和点阵晶体是由原子或分子按照一定的周期性在空间排列形成的固体。在晶体内部三维空间中,原子的排列按周期规律隔一定距离重复出现,每个重复的单位具有相同的化学组成、相同的化学结构、相同的空间取向和相同的周围环境。这种重复的基本结构内容叫结构基元。为了研究晶体中结构基元排列的周期性,将每个结构基元抽象成一个几何上的点表示,而不考虑结构基元的内容和结构,这些点形成点阵。点阵是在空间任…     

在化学系进行晶体学教学的经验与方案

澳大利亚昆士兰大学C.H.L.Kennard博士是国际晶体学会IUCr教育委员会的顾问.他在晶体学、晶体化学的教学与科研方面都有丰富的经验.这篇短文是他在“晶体学及其教学夏季研讨班”(IUCr教育委员会主办,1988年9月15-24日,天津)上讲演的主要内容.其中所介绍的课程设置方案中,三门课程分低、中、高三个层次,学时虽少,讲课、实习、实验几方面的内容匹配甚好.课程中已将晶体学教学与微型计算机的应用密切结合起来.他的经验值得我国从事晶体学、结构化学教学工作者借鉴.     

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。     

X射线晶体学在高等教育中的通识性

X射线晶体学是一门研究物质晶体结构的科学,X射线衍射技术已成为当今化学、材料、生命等众多科学领域中对物质结构研究的必要手段与方法。本文从X射线晶体学的诞生、发展和迅速普及的角度,谈谈X射线晶体学的发展历程对人类文明的贡献,以及X射线晶体学在当今高等教育中的重要性,从而阐述在高等学校通识教育中加强与推广X射线晶体学的必要性与可行性。     

天花粉蛋白2.6分辨率的晶体学修正

本文报道了用溶剂过滤法改善电子密度图,依据Collins提出的一级结构,重新建立天花粉蛋白分子模型。使用2.6分辨率衍射强度数据和约束参数最小二乘法,对处于晶体学不对称单元中两个天花粉蛋白分子(共3828个非氢原子)进行晶体学修正。修正结果,偏离因子R=0.223,键长根均方误差r.m.s=0.023,新的分子模型和以2F_0-F_o为系数的电子密度图符合甚好。     

主族金属氨基酸配合物的晶体学研究进展

主族金属配合物的研究是配位化学的重要主题之一. 相对于过渡金属和稀土金属配合物而言, 主族金属配合物的研究比较薄弱, 其主要原因在于: 主族金属的闭壳层电子层结构、有限的价电子数和较少的氧化态等特点, 使得主族金属与有机配体的相互作用较弱, 作用模式较为单一. 但近年来, 随着合成技术与分析检测技术的不断提升, 具有新颖结构并具有与过渡金属配合物相似的优良性能的主族金属配合物也不断地进入了人们的视野. 作为生物体的基本结构单元的氨基酸是一类良好的功能配体, 主族金属氨基酸配合物的研究具有重要的学术价值和应用价值, 也是化学、生物、医药和材料等众多学科领域中的共同的基本问题. 解决基本问题的一个切入点可能是研究这些新型主族金属氨基酸配合物的分子结构与物质结构. 因此, 本工作基于2000年以后发表的主族金属氨基酸配合物的晶体结构, 从X射线晶体学的研究视角, 分析了新型的主族金属氨基酸配合物的结构多样性, 包括当前热门的MOF类的结构; 综述了主族金属氨基酸配合物的研究进展; 展望了未来这一领域的发展方向; 提出了以功能为导向系统地开展主族金属氨基酸的配位化学和超分子化学的研究思路. 谨以此文献给2014年国际晶体学年.     

白鲢鱼胰岛素的晶体学研究

本实验获得了白鲢鱼胰岛素的单晶体并收集了2.8A分辨率的强度数据.确定晶体所属空间群为 P2_12_12_1,晶胞参数是a=96.73(8)A,b=57.74(7)A,c=53.88(9)A.每个不对称单位含有6个胰岛素分子.用旋转函数法揭示出非晶体学三重轴和二重轴的取向,并说明了白鲢鱼胰岛素具有与三方二锌猪胰岛素相似的空间结构和聚合状态.本文讨论了一级结构的变化对胰岛素的结晶行为和堆积方式的影响。     

钛硅介孔分子筛

综述了钛硅介孔分子筛的合成、表征及其应用研究进展.评述了钛硅介孔分子筛的合成方法与合成条件对分子筛结构性能、钛物种的配位状态和催化性能的影响.介绍了鉴定钛硅介孔分子筛内骨架钛原子的多种波谱学方法以及钛硅介孔分子筛在选择氧化、光催化、酸催化反应中的应用,并指出钛硅介孔分子筛是一种非常有应用前景的环境友好的多相催化剂.     

六方硫化钒晶体的空间群推演

晶体空间群推演是晶体结构描述和表达的关键环节,也是理论印证实验晶体结构的手段。因涉及数学方法、物理技术和图形软件,所以不仅是晶体结构教学的重点也是难点。本文基于六方硫化钒晶体结构测定的基本结构数据,用自编晶体学程序cryst 2015在图形软件上再现硫化钒的晶体结构。在点空间和三维实向量空间中,由线性映射表达平移和非平移对称操作,得到硫化钒的空间群和对应的矩阵表示群。由生成元的幂次连乘导出空间群群元素的生成顺序,以及由空间群导致的晶体学分类。这种借助实例的连贯推演方法,有助于建立晶体学知识结构框架,尤其能帮助初学者理解晶体学的科学思想体系。     

NMR crystallography of zeolites: How far can we go without diffraction data?

Nuclear magnetic resonance (NMR) crystallography—an approach to structure determination that seeks to integrate solid-state NMR spectroscopy, diffraction, and computation methods—has emerged as an effective strategy to determine structures of difficult-to-characterize materials, including zeolites and related network materials. This paper explores how far it is possible to go in determining the structure of a zeolite framework from a minimal amount of input information derived only from solid-state NMR spectroscopy. It is shown that the framework structure of the fluoride-containing and tetramethylammonium-templated octadecasil clathrasil material can be solved from the 1D ²⁹Si NMR spectrum and a single 2D ²⁹Si NMR correlation spectrum alone, without the space group and unit cell parameters normally obtained from diffraction data. The resulting NMR-solved structure is in excellent agreement with the structures determined previously by diffraction methods. It is anticipated that NMR crystallography strategies like this will be useful for structure determination of other materials, which cannot be solved from diffraction methods alone.     

Enabling Efficient Folding and High-Resolution Crystallographic Analysis of Bracelet Cyclotides

Cyclotides have attracted great interest as drug design scaffolds because of their unique cyclic cystine knotted topology. They are classified into three subfamilies, among which the bracelet subfamily represents the majority and comprises the most bioactive cyclotides, but are the most poorly utilized in drug design applications. A long-standing challenge has been the very low in vitro folding yields of bracelets, hampering efforts to characterize their structures and activities. Herein, we report substantial increases in bracelet folding yields enabled by a single point mutation of residue Ile-11 to Leu or Gly. We applied this discovery to synthesize mirror image enantiomers and used quasi-racemic crystallography to elucidate the first crystal structures of bracelet cyclotides. This study provides a facile strategy to produce bracelet cyclotides, leading to a general method to easily access their atomic resolution structures and providing a basis for development of biotechnological applications.     

Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in FeIV=O Formation

Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (Fe^IV=O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the Fe^III and Fe^IV=O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.     

Fast quantum crystallography

Typical contemporary X-ray crystallography delivers the geometries and, at best, the electron densities of molecules or periodic systems in the crystalline phase. Energies, electron momentum densities, and information relating to the pair density such as electron delocalization measures—all crucial to chemistry—are simply missed. Quantum crystallography (QCr) is an emerging line of research aimed at filling this gap by solving the crystallographic problem under the constraints of quantum mechanics. In this way, not only geometries and electron densities become experimentally accessible but also the entire panoply of quantum mechanical properties that are in the output of any quantum chemical software package. However, QCr remains limited to smaller systems (small molecules or small unit cells) due to the exponential bottleneck that plagues quantum mechanical calculations. When combined with a fragmentation technique, termed the “kernel energy method (KEM)”, QCr's reach to larger molecules is extended considerably to almost “any size”, that is, systems of up to many hundreds of thousands of atoms. KEM has made this doable with any chemical model and is capable of providing the entire quantum mechanics of large molecular systems. The smallness of the R-factor adjudicates the accuracy of the quantum mechanics extracted from the crystallography.     

Generating Skeletal Diversity from the C19‐Diterpenoid Alkaloid Deltaline: A Ring‐Distortion Approach

The development of new drugs calls for large collections of diverse molecules with considerable complexity. Ring distortion of natural products provides an efficient and facile approach to access new architectures with intriguing biological activities, by harnessing their inherent complexity. In this study, such a strategy has been explored on an abundant C₁₉‐diterpenoid alkaloid, deltaline, enabling the synthesis of 32 new derivatives bearing a broad spectrum of unique scaffolds. Extensive spectroscopic studies including X‐ray crystallographic analyses strongly supported the structures of the obtained novel skeletons, which present comparable opportunities with the great contributions made by nature for discovery of new lead compounds.     

Exploring the Potential of Multinuclear Solid-State 1H, 13C,and 35Cl Magnetic Resonance To Characterize Static and Dynamic Disorder in Pharmaceutical Hydrochlorides

Crystallographic disorder, whether static or dynamic, can be detrimental to the physical and chemical stability, ease of crystallization and dissolution rate of an active pharmaceutical ingredient. Disorder can result in a loss of manufacturing control leading to batch-to-batch variability and can lengthen the process of structural characterization. The range of NMR active nuclei makes solid-state NMR a unique technique for gaining nucleus-specific information about crystallographic disorder. Here, we explore the use of high-field ³⁵Cl solid-state NMR at 23.5 T to characterize both static and dynamic crystallographic disorder: specifically, dynamic disorder occurring in duloxetine hydrochloride ( 1 ), static disorder in promethazine hydrochloride ( 2 ), and trifluoperazine dihydrochloride ( 3 ). In all structures, the presence of crystallographic disorder was confirmed by ¹³C cross-polarization magic-angle spinning (CPMAS) NMR and supported by GIPAW-DFT calculations, and in the case of 3 , ¹H solid-state NMR provided additional confirmation. Applying ³⁵Cl solid-state NMR to these compounds, we show that higher magnetic fields are beneficial for resolving the crystallographic disorder in 1 and 3 , while broad spectral features were observed in 2 even at higher fields. Combining the data obtained from ¹H, ¹³C, and ³⁵Cl NMR, we show that 3 exhibits a unique case of disorder involving the ⁺N−H hydrogen positions of the piperazinium ring, driving the chloride anions to occupy three distinct sites.     

Structures of the chain metaphosphates NaM(PO3)3 (M = Ca or Sr)

Solid-state (23)Na and (31)P magic-angle spinning nuclear magnetic resonance spectroscopy and X-ray crystallography have been used to study the structures of the chain metaphosphates NaCa(PO(3))(3) and NaSr(PO(3))(3). The compounds are isostructural and crystallise in space group P(-1) with the following parameters: NaCa(PO(3))(3), a = 6.711 A, b = 6.934 A, c = 7.619 A, alpha = 83.44 degrees , beta = 81.41 degrees , gamma = 82.80 degrees ; NaSr(PO(3))(3)a = 6.805 A, b = 7.133 A, c = 7.720 A and alpha = 83.71 degrees , beta = 80.48 degrees , gamma = 82.87 degrees . Both structures contain anionic metaphosphate chains of (PO(3))(n) (n) with ionic contacts to Na(+) ions in distorted octahedral sites and Ca(2+) (or Sr(2+)) in distorted dodecahedral sites. (31)P and (23)Na NMR are entirely consistent with the crystallographic data and an empirical method for assigning (31)P resonances to particular crystallographically unique P atoms is described.     

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.