粉末衍射技术解析青蒿素晶体结构方法学比对研究

以粉末X射线衍射技术(PXRD)表征有机物晶体结构为目的,选取我国第1个全新药物青蒿素(Artemisinin)验证粉晶解析有机物晶体结构方法的合理性。粉晶解析结果为正交晶系,P212121空间群,a=23.98223±0.01624,b=9.42480±0.00645,c=6.34589±0.00439,α=β=γ=90°,Z=4,V=1434.693;单晶解析结果为正交晶系,P212121空间群,a=23.9564(9),b=9.3224(5),c=6.3205(3),α=β=γ=90°,P212121,Z=4,V=1411.55(17)3;两者所确定分子非氢结构键长、键角、二面角的相关系数分别为0.9921、0.9833和0.9997,晶胞参数基本吻合,分子构型相似。结果表明,粉晶X射线衍射技术可以求得较为准确的青蒿素晶胞参数及晶胞内分子构型。     

Improving the Accuracy of Small-Molecule Crystal Structures Solved from Powder X-Ray Diffraction Data by Using External Sources

Structural analysis using powder X-ray diffraction data has overcome many obstacles and nowadays is readily applicable for structural analysis of all types of compounds and materials. Being less straightforward than single crystal diffraction, it requires significant users’ input and consequently, implementation of standardized tools to assess the accuracy of crystal structures. This article discusses potential errors in crystal structure solution and refinement of small-molecule structures obtained from PXRD data. Moreover, it proposes how accuracy of these structures can be improved by using high-quality PXRD data, complementary external analytical techniques, knowledge stored in crystal structure databases, as well as an approach to search the parameter space to avoid local minima in testing different sets of geometry restraints.     

Statistical Inference of Distribution of Crystal Size by X-Ray Powder Diffraction

We describe a method to calculate the distribution of sizes of fine crystals from pure powder-diffraction profile using a method of maximum entropy (MAXENT). We apply a Monte-Carlo technique of simulated annealing to seek a global minimum of the error surface in fitting this diffraction profile. We consider pure diffraction profile (instrument de-convoluted) of a powder specimen without lattice imperfection to a significant extent. Under these circumstances, the distribution of the pure diffraction profile can be attributed to the distribution of crystallite size. We applied this method to three cases of crystal sizes having a highly inhomogeneous distribution with certain noise-tolerance. The results agree well with synthetic data of diffraction.     

X-射线粉晶衍射谱图的计算机模拟

编写了一个FORTRAN程序,用于从单晶结构计算粉晶X射线衍射数据,并进一步用ORIGIN软件绘制出粉晶衍射图谱,选择了13个代表性经典化合物进行计算,结果与粉晶卡片上的实验数据相当一致,本文模拟方法,即可弥补粉晶图谱缺乏的不足,也可用于]校验粉晶衍射实验结果的可靠性。     

The Crystal Structures of two Anhydrous Magnesium Hydroxychloride Phases from in situ Synchrotron Powder Diffraction Data

The crystal structures of two members of the solid solution series Mg(OH)_xCl_y x+y = 2, Mg(OH)_1.7Cl_0.3 (P$\tilde {3}$ m1, a = 3.169(2) Å, c = 5.530(12), V = 48.1(1) ų at T = 365 °C) and MgOHCl (R$\tilde {3}$ m, a = 3.3877(4) Å, c = 17.534(4) Å, V = 174.27(6) ų at T = 625 °C) were determined from in situ synchrotron powder diffraction data at high temperature upon dehydration of 3Mg(OH)₂·MgCl₂·8H₂O (F3) and 5Mg(OH)₂·MgCl₂·8H₂O (F5) phases. The crystal structures of Mg(OH)_1.7Cl_0.3 (example of ss‐type‐OH) and MgOHCl (example of ss‐type‐Cl) can be related to the C19 (CdCl₂) and C6 (CdI₂) structure type, respectively, with the disordered chloride and hydroxide anions occupying the same crystallographic site in layers.     

Alkali‐Metal ortho‐Hydroxyphenolates: Syntheses and Crystal Structures from Powder X‐Ray Diffraction

Colorless and highly air‐ and moisture‐sensitive powders of M[o‐C₆H₄O(OH)] with M = K, Rb, or Cs have been synthesized from reaction mixtures of the appropriate alkali metal and catechol in thf. All compounds were structurally characterized by means of powder X‐ray diffraction using the Rietveld profile refinement technique including restraints for the C—C/C—O bond distances and the C—C—C angles. The atomic arrangements of M[o‐C₆H₄O(OH)] (K: monoclinic P2₁/c; Rb/Cs: orthorhombic Pbcm) are characterized by polymeric chains of [M₁^[4]O₂^[2]η⁶] units connected by hydrogen bonds, thereby making up layered structures similar to the one of catechol. The coordinatively unsaturated alkali metals are forming edge‐sharing MO₄ pyramids and exhibit asymmetrical η⁶‐interactions with the phenylene rings. The symmetry of the unit cells increases with increasing size of the cation, and this results in a decrease of the monoclinic angle from 118.5° (catechol) to 93.7° (K compound), eventually leading to orthorhombic cells for the Rb and Cs compounds.     

粉末衍射峰形拟合程序包CPOWDER

开发了一个Ｘ射线和中子粉末衍射峰形拟合程序包ＣＰＯＷＤＥＲ,它是由多个最小二乘峰形拟合程序与蒙特卡罗分峰程序组成的。最小二乘峰形拟合程序可用于约束条件下的峰形拟合分析,蒙特卡罗分峰程序可用于寻找全局最优解,为最小二乘拟合程序提供优质的峰形参数初始值,两者结合使用特别适合于多个严重重叠峰的分离。     

Low-Temperature Crystal Structure of S-camphor Solved from Powder Synchrotron X-ray Diffraction Data by Simulated Annealing

The ordered, low-temperature crystal structure of the pure enantiomer of camphor (C₁₀H₁₆O) has been solved from high-resolution powder synchrotron X-ray diffraction data. The structure is orthorhombic, space group P2₁2₁2₁, Z=8, with a=8.9277(2) Å, b=27.0359(5) Å, and c=7.3814(1) Å at 100 K. The structure was solved by autoindexing of the pattern, space group determination, and then optimization of the positions and orientations of the two independent molecules in the unit cell by simulated annealing. The molecular structure obtained from the restrained Rietveld refinement shows reasonable agreement with that optimized from ab initio molecular orbital calculations. In the crystal structure, the molecules are aligned antiferroelectrically and weak C-H…O hydrogen bonds link together the independent molecules.     

Crystal Structure Analysis by Neutron Diffraction II

This second part of the article “Crystal Structure Analysis by Neutron Diffraction” deals with the diffraction of neutrons by magnetically ordered crystals. Neutron diffraction is at present the only reliable method for the determination of the magnitude, direction, and spatial distribution of magnetic moments in crystalline substances. Since the magnetic moments are essentially due to the unpaired electrons, the distribution of these electrons in the crystal can be measured in this way.     

Alkali‐Metal meta‐Hydroxyphenolates: Syntheses and Crystal Structures from Powder X‐Ray Diffraction

M[m‐C₆H₄O(OH)] (M = Li—Cs) have been obtained as highly air‐ and moisture‐sensitive powders from reaction mixtures of the appropriate alkali metals and resorcinol in thf. Both the potassium and rubidium compounds were structurally characterized by means of powder X‐ray diffraction using the Simulated Annealing method and the Rietveld profile refinement technique including C—C/C—O bond distance and C—C—C angle restraints. K[m‐C₆H₄O(OH)] (orthorhombic P2₁2₁2₁) forms infinite alternating chains of meta‐hydroxyphenolate anions connected by K—O bonds and short charge‐assisted hydrogen bonds, thereby generating a three‐dimensional network of corrugated layers similar to the structure of pure resorcinol. The potassium cations are surrounded by a triangle of oxygen and, moreover, coordinated by six adjacent phenylene rings to form a distorted octahedron. The complex crystal structure of Rb[m‐C₆H₄O(OH)] (monoclinic Pa) is characterized by layers of hydrogen‐bonded meta‐hydroxyphenolate triple units separated by corrugated rubidium layers. The three crystallographically different Rb atoms are coordinated by three, four, and five oxygens with irregular polyhedra, and the rubidiums are also involved in further electrostatic interactions by up to eight phenylene rings.     

Unravelling Crystal Structures of Covalent Organic Frameworks by Electron Diffraction Tomography

Featuring the art of covalent chemistry on 2D and 3D with molecular precision, covalent organic frameworks (COFs) have attracted immense interests from inorganic, organic, polymer, materials and energy chemistry. However, due to the synthetic challenge of “crystallization problem”, structural determination of COFs has been the bottle‐neck in speeding up their discovery and design, as well as building up their structure‐ property relation. Electron diffraction tomography (EDT) has been developed to determine crystal structures of COFs with only sub‐micrometer sized single crystals, which enabled the ab initio determination of crystal structure, molecular connectivity, pore metrics, and host‐guest interaction at the atomic level. In this review, we summarized the recent developments of EDT for addressing challenges in structure determinations of such e‐beam sensitive, organic porous crystals, covering comprehensively automatic data collection, low dose, cryogenic protocols, structural solution method, powder X‐ray diffraction refinement, and high‐resolution transmission electron microscopy (HRTEM) imaging techniques. We do believe the EDT will propel this field into the new era of COF chemistry with atomic precision, and we envision the wide application of artificial intelligence will promote the structural determination and particle analysis of COFs and related materials.     

Evolving Opportunities in Structure Solution from Powder Diffraction Data—Crystal Structure Determination of a Molecular System with Twelve Variable Torsion Angles

The genetic algorithm approach , in which a population of trial structures is allowed to evolve subject to well-defined procedures for mating, mutation, and natural selection, was employed to solve the complex molecular crystal structure of Ph₂P(O)(CH₂)₇P(O)Ph₂ directly from powder diffraction data. The structure solution reveals an interesting (perhaps unexpected) molecular conformation (see picture), which emphasizes the importance of allowing complete conformational flexibility of the molecule in the structure solution calculation.     

The Crystal Structure of Trimethyl Borate by Neutron and X‐ray Powder Diffraction

The crystal structure of one of the simplest organoboron compounds, trimethyl borate does not appear to have been determined hitherto. The compound is of interest for the study of π‐donor ligands and their interaction with the π‐acceptor behavior of trigonal boron and the consequences of such interactions on molecular structure. We used powder neutron (with isotopically labeled material) and X‐ray diffraction to determine the crystal structure of trimethyl borate at 15 K and 200 K (neutron) and 200 K (X‐ray). The material is hexagonal (Z = 2) with a = b = 6.950(8) Å and c = 6.501(3) Å at 15 K. The unit cell volume is 272.00(1) ų. The space group is P6₃/m (SG 176) at 15 K and 200 K. This is the first crystal structure solved on the Neutron Powder Diffractometer (NPDF) at the Lujan Center.     

The Crystal Structure of Disodium Phosphonate,Na2HPO3

Anhydrous disodium phosphonate, Na₂HPO₃, was prepared by dehydration of its pentahydrate. The crystal structure of Na₂HPO₃ was solved from high resolution X‐ray powder diffraction data (P2₁/n; Z = 4; a = 9.6987(1), b = 6.9795(1), c = 5.0561(1) Å, β = 92.37(1)°; V = 341.97(1) ų). The crystal structure consists of two types of sodium‐oxygen polyhedra, which are connected via common edges and vertices forming layers perpendicular to [100]. These Na(1)‐ and Na(2)‐layers are interlinked via common edges, forming in a 3D‐framework. The resulting topology is providing oxygen arrangements that please the coordinative requirement of phosphorus(III).     

L-5-羟基色氨酸粉晶晶体结构解析

以50%甲醇溶液为提取溶剂,从加纳籽中提取L-5-羟基色氨酸(HTP),采用RP-HPLC获得纯度为99.5%样品,经80%甲醇溶液重结晶获得多晶粉末.利用X射线粉末衍射技术结合计算晶体学方法解析其粉晶晶体结构,模拟图谱与实验图谱的Rwp值为5.06%.结果表明:该晶体属单斜晶系,P2_1空间群,晶胞参数为a=13.69927 ±0.01967(A),b=5.34550 ±0.00756(A),c=7.88219±0.01129(A),a=y=90.00000°,β=86.25936±0.00359°,Z=2,V=579.973(A)~3,并在此基础上对其晶体生长特性进行了分析.     

Three Crystal Structures,One Chemical Formula – Barium Dihydrogen‐hypodiphosphate(IV)‐dihydrate,BaH2P2O6·2H2O

Three polymorphs of barium dihydrogen‐hypodiphosphate(IV)‐dihydrate, BaH₂P₂O₆ · 2H₂O ( A , B and C ), were obtained and structurally characterized by single‐crystal X‐ray diffraction. A crystallizes in the monoclinic space group P2₁/n (no. 14) with a = 7.459(1) Å, b = 8.066(1) Å, c = 12.460(2) Å, β = 91.27(1) ° and Z = 4. B crystallizes in the monoclinic space group C2/c (no. 15) with a = 11.049(8) Å, b = 6.486(3) Å, c = 10.956(6) Å, β = 106.89(5) ° and Z = 4. C crystallizes in the orthorhombic space group C222₁ (no. 20) with a = 9.193(3) Å, b = 6.199(2) Å, c = 12.888(4) Å and Z = 4. Discrete [H₂P₂O₆]^2– units, barium cations and water molecules, held together by intermolecular hydrogen bonds of the type O–H ··· O, build up the structures of the three polymorphs. The phase purity of A and C was verified by powder diffraction measurements.