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.     

New Approaches for Solving Crystal Structures from Powder Diffraction Data

The determination of crystal structures from single crystal diffraction data can generally be carried out routinely and straightforwardly. However, many crystalline solids can be obtained only as microcrystalline powders and are not suitable for investigation by conventional single crystal diffraction methods. In the past, this problem has limited the ability to elucidate the structural properties of such materials. For the wide range of materials in this category, there is clearly a pressing need to develop and exploit techniques that allow crystal structures to be solved from powder diffraction data. Although traditional techniques for structure solution from powder diffraction data have been applied successfully in several cases, these techniques have certain intrinsic limitations, and for the case of organic molecular crystals the challenges that must be overcome are particularly severe. For these reasons, our recent research has focused on the development and implementation of new methodologies for structure solution from powder diffraction data, leading to new “direct-space” techniques for structure solution in which a hypersurface based on the profile R-factor is searched using Monte Carlo or Genetic Algorithm techniques. This paper presents a brief overview of the problems and challenges associated with structure solution from powder diffraction data. The foundations of the techniques that we have developed are described, and illustrative examples (from the field of organic molecular crystals) are given to highlight the application of these techniques.     

N-(1-萘基)-琥珀酰亚胺化合物晶体结构的理论预测

用Materials Studio软件对N-(1-萘基)-琥珀酰亚胺多晶粉末的X射线衍射数据进行衍射峰指标化、晶胞参数优化和空间群搜索等理论计算, 可以确定晶体结构所属的晶系和空间群, 并初步给出和多晶粉末衍射数据相近的晶胞参数; 在已确定空间群范围内, 以密度泛函理论计算得到的最低能量构象作为初始分子结构, 对N-(1-萘基)-琥珀酰亚胺多晶进行晶体结构理论预测, 给出一系列假定的晶胞参数, 从中可以找到和经上述计算给出的晶胞参数一致的晶体结构；对其进行晶胞参数优化后, 得到晶体结构具有和多晶粉末X射线衍射数据相近的衍射曲线, 并与已有的单晶数据相吻合.     

Crystallographic modelling

Summary The project on crystallographic modelling aims at extending the application of interactive graphics to inorganic structures. Starting from the available expertise in organic and protein modelling, the symmetry of the crystal structure is used not only to draw fixed models of many unit cells of the structure, which as an entity can be interactively manipulated, but also to change details of the structures interactively with retention of the original symmetry. Real-time shifts of atom positions are automatically applied to all symmetryequivalent atoms given the symmetry constraints. This also applies to translations and rotations of groups of atoms. In order to get feedback about these structural changes one can simulate powder diffraction patterns in real-time mode and compare them with the experimental powder patterns. These features are crucial in truly crystallographic modelling, but have not been implemented before in other programs. The program can be used in combination with standard molecular modelling programs and is also interfaced to the Inorganic Crystal Structure Database. Before describing the realization of these features on state-of-the-art hardware, we will review the expertise in molecular modelling and discuss an MS-DOS program to study inorganic crystal structures.     

Physico-chemical characterization of an active pharmaceutical ingredient

The physico-chemical properties and polymorphism of a new active pharmaceutical ingredient entity has been analyzed and the gain of knowledge during the chemical development of the substance is described. Initial crystallization revealed an anhydrous crystal form with good crystallinity and a single, sharp DSC melting peak at 171°C and a straightforward development of this crystal form seemed possible. However, during polymorphism screening, new crystalline forms were detected that were often analyzed as mixtures of crystal forms. The process of characterization and identification of the different crystalline forms and its thermodynamical relationship has been supported by a combination of experimental and computational work including determination of the three-dimensional structures of the crystal forms. The crystal structure of one polymorphic form was solved by single crystal X-ray structure analysis. Unfortunately, Mod B resisted in formation of suitable single crystals, but its structure could be solved by high resolution powder diffraction data analysis using synchrotron radiation. Calculation of the theoretical X-ray powder diffraction pattern from three dimensional crystal coordinates allowed an unambiguous identification of the different crystalline forms. Two polymorphic crystal forms of the API-CG3, named Mod A and Mod B, are enantiotropic whereas Mod B is the most stable polymorph at room temperature up to about 50°C and Mod A at temperatures above 50°C. The mechanism of the solid-solid transition can be explained by analyzing the molecular packing information gained from the single crystal structures. A third crystalline form with the highest melting peak turned out to be not a polymorphic or pseudopolymorphic crystal modification of our API-CG3 but a chemically different substance. This revised version was published online in July 2006 with corrections to the Cover Date.     

Atomic sublattices: Problems of indexing powder patterns, structural model determination

The second basic theorem of lattice crystallography (by N. V. Belov) underlies the theory of atomic sublattices characteristic of the overwhelming majority of crystal structures we have studied. By the example of structures of particular inorganic compounds (involving mercury chalcohalides) it is illustrated that a priory knowledge of cationic and anionic sublattices typical of a given class of compounds may provide useful information for analyzing powder diffraction patterns of substances with unknown crystal structures. It has been shown that complicated structures can be analyzed “in parts” by identifying their individual components discernable in powder diffraction patterns.     

A solid-state NMR method for solution of zeolite crystal structures

Since zeolites are notoriously difficult to prepare as large single crystals, structure determination usually relies on powder X-ray diffraction (XRD). However, structure solution (i.e., deriving an initial structural model) directly from powder XRD data is often very difficult due to the diffraction phase problem and the high degree of overlap between the individual reflections, particularly for materials with the structural complexity of most zeolites. Here, we report a method for structure determination of zeolite crystal structures that combines powder XRD and nuclear magnetic resonance (NMR) spectroscopy in which the crucial step of structure solution is achieved using solid-state (29)Si double-quantum dipolar recoupling NMR, which probes the distance-dependent dipolar interactions between naturally abundant (29)Si nuclei in the zeolite framework. For two purely siliceous zeolite blind test samples, we demonstrate that the NMR data can be combined with the unit cell parameters and space group to solve structural models that refine successfully against the powder XRD data.     

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。     

How to determine structures when single crystals cannot be grown: opportunities for structure determination of molecular materials using powder diffraction data

Many crystalline solids cannot be prepared as single crystals of sufficient size and/or quality for structure determination to be carried out using single crystal X-ray diffraction techniques. In such cases, when only polycrystalline powders of a material are available, it is necessary instead to tackle structure determination using powder X-ray diffraction. This article highlights recent developments in the opportunities for determining crystal structures directly from powder diffraction data, focusing on the case of molecular solids and giving particular attention to the most challenging stage of the structure determination process, namely the structure solution stage. In particular, the direct-space strategy for structure solution is highlighted, as this approach has opened up new opportunities for the structure determination of molecular solids. The article gives an overview of the current state-of-the-art in structure determination of molecular solids from powder diffraction data. Relevant fundamental aspects of the techniques in this field are described, and examples are given to highlight the application of these techniques to determine crystal structures of molecular materials.     

Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose Iβ

Previous studies of calculated diffraction patterns for cellulose crystallites suggest that distortions that arise once models have been subjected to molecular dynamics (MD) simulation are the result of both microfibril twisting and changes in unit cell dimensions induced by the empirical force field; to date, it has not been possible to separate the individual contributions of these effects. To provide a better understanding of how twisting manifests in diffraction data, the present study demonstrates a method for generating twisted and linear cellulose structures that can be compared without the bias of dimensional changes, allowing assessment of the impact of twisting alone. Analysis of unit cell dimensions, microfibril volume, hydrogen bond patterns, glycosidic torsion angles, and hydroxymethyl group orientations confirmed that the twisted and linear structures collected with this method were internally consistent, and theoretical powder diffraction patterns for the two were shown to be effectively indistinguishable. These results indicate that differences between calculated patterns for the crystal coordinates and twisted structures from MD simulation can result entirely from changes in unit cell dimensions, and not from microfibril twisting. Although powder diffraction patterns for models in the 81-chain size regime were shown to be unaffected by twisting, suggesting that a modest degree of twist is not inconsistent with available crystallographic data, it may be that other diffraction techniques are capable of detecting this structural difference. Until such time as definitive experimental evidence comes to light, the results of this study suggest that both twisted and linear microfibrils may represent an appropriate model for cellulose Iβ.     

Characterization of complicated new polymorphs of chlorothalonil by X-ray diffraction and computer crystal structure prediction

A simultaneous experimental and computational search for polymorphs of chlorothalonil (2,4,5,6-tetrachloro-1,3-benzenedicarbonitrile) has been conducted, leading to the first characterization of forms 2 and 3. The crystal structure prediction study, using a specifically developed anisotropic atom-atom potential for chlorothalonil, gave as the global minimum in the lattice energy a structure that was readily refined against powder diffraction data to the known form 1 (P2(1)/a). The structure of form 2 was solved and refined from powder diffraction data, giving a disordered structure in the Rm (166) space group (Z = 3). It could also be refined against a P1 ordered model, starting from a low-energy hypothetical sheet structure found in the computational search. This shows that the disorder could be associated with the stacking of ordered sheets. The disordered structure for form 2 was later confirmed by single-crystal X-ray diffraction. The structure of form 3, determined from single-crystal diffraction, contains three independent molecules in the asymmetric unit in P2(1) (4) (Z = 6). Powder diffraction showed that this single-herringbone structure was similar to two low-energy structures found in the search. Further analysis confirmed that form 3 has a similar lattice energy and contains elements from both these predicted structures, which can be considered as good approximations to the form 3 structure.     

Understanding the structural properties of a dendrimeric material directly from powder X-ray diffraction data

Complete structure determination of an early-generation dendrimeric material has been carried out directly from powder X-ray diffraction data, using the direct-space genetic algorithm technique for structure solution followed by Rietveld refinement. This work represents the first application of modern direct-space techniques for structure determination from powder X-ray diffraction data in the case of a dendrimeric material and paves the way for the future application of this approach to enable complete structure determination of other dendrimeric materials that cannot be prepared as single crystal samples suitable for single crystal X-ray diffraction studies.     

Structure determination from powder diffraction

The review surveys modern methods for the determination of unknown crystal structures of organic and inorganic compounds from powder diffraction data. The main stages of this process, from the preparation of the specimen to a search for the structural motif followed by the Rietveld refinement, are considered. The results obtained on different diffractometers using X-ray, synchrotron, and neutron radiations are demonstrated to be well reproducible. Examples of successful structure solution are cited, which provide evidence that powder diffraction is a reliable tool in establishing structures of a wide range of compounds for which single crystals are unavailable.     

The solvation of poly(vinyl alcohol)

The possible incorporation of water molecules within the crystal structure of poly(vinyl alcohol) is discussed. Modelling of the crystal structure suggested that water could be incorporated without severe disruption, and the effect on the X-ray powder diffraction trace was simulated. The effect of variation in tacticity is discussed in terms of the nature of the hydrogen bonding. Simulated traces are compared with experimental data from atactic samples in which a change in the diffraction peak intensities is observed for samples crystallised with water present. This is compared with samples produced from nonaqueous solutions.     

Contemporary Advances in the Use of Powder X-Ray Diffraction for Structure Determination

Many crystalline solids cannot be prepared in the form of single crystals of sufficient size and/or quality for investigation using single-crystal X-ray diffraction techniques, and the opportunity to carry out structure determination using powder diffraction data is therefore essential to understand the structural properties of such materials. Although the refinement stage of the structure determination process can be carried out fairly routinely from powder diffraction data using the Rietveld profile refinement technique, solving crystal structures directly from powder data is associated with several intrinsic difficulties. Nevertheless, substantial progress has been made in recent years in the scope and potential of techniques in this field. This article aims to highlight the types of structural problems for which structure determination may now be tackled directly from powder diffraction data, and contemporary applications across several chemical disciplines are presented. A brief survey of the underlying methodologies is given, with some emphasis on recently developed techniques for carrying out the structure-solution stage of the structure-determination process.     

Demonstrating structural deformation in an inorganic nanotube

There is much current interest in nanostructured materials (nanotubes, nanobelts, nanospheres, etc.). Their crystal structures can differ from those of the equivalent bulk materials. Determining these differences is important in understanding how the properties of nanomaterials differ from those of the bulk. Established methods of X-ray structure determination become increasingly difficult or impossible to apply on reducing the dimensions to a few nanometers. Here we show that, by combining the Debye equation for X-ray scattering (which relates an ensemble of atoms to their diffraction pattern without recourse to symmetry) with a model of the crystal structure, generated by folding the ideal crystal structure into a nanotube, the severely broadened/distored powder diffraction pattern may be described. This procedure reveals the significant structural deformations necessary to accommodate the nanotube shape. The importance of knowing the (deformed) crystal structure is discussed.     

Structural understanding of a molecular material that is accessed only by a solid-state desolvation process: the scope of modern powder X-ray diffraction techniques

Many molecular materials cannot be prepared as a "pure" (nonsolvate) crystalline phase by conventional crystal growth from solution due to the facile formation of solvate structures. In such cases, it may be possible to obtain the pure phase by a solid-state desolvation process, although such processes are generally associated with loss of crystal integrity, yielding a microcrystalline powder of the pure phase. This paper demonstrates the utility of modern powder X-ray diffraction techniques for obtaining structural understanding in such cases, focusing on a particular member of a structural family that is of wider relevance within the context of crystal engineering and design.     

H2Pc-VOPc二元体系的制备和表征

八十年代,国外Canon,IBM,HP,Ricoh,Xerox等公司开发出由计算机控制、数字扫描、激光成像的高分辨激光打印机,并逐渐占领市场。这种激光打印机具有印刷质量高、寿命长、印刷速度快、版面可任意调制、噪音小等特点。     

Second order incommensurate phase transition in 25L-Ta2O5

A new structural state 25L-Ta₂O₅, obtained from sintering and annealing treatments of a Ta₂O₅ powder, is identified both by electron diffraction and high resolution imaging on a transmission electron microscope (TEM). According to general rules for the different L-Ta₂O₅ structures proposed by Grey et al. (J. Solid State Chem. 178 (2005) 3308), a structural model is derived from their crystallographic data on 19L-Ta₂O₅. This model yields simulated images in agreement with high resolution TEM observations of the structure oriented along its [001] zone axis, but only for a very thin crystal thickness of less than 1.2 nm. Such a limitation is shown to be due to a modulation of the structure along its [001] axis. Actually, from an analysis of a diffuse scattering and of its evolution into satellites reflections as a function of the cooling rate, a second order incommensurate phase transition can be assumed to occur in this compound. The property of single phase samples observed by TEM is also verified by X-ray powder diffraction. In a discussion about studies performed by different authors on incommensurate structures in the system Ta₂O₅-WO₃, it is noticed that TEM results, similar to ours, indicate that phase transitions could be expected in these structures.