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PubMed2003

Preparation of protein nanocrystals and their characterization by solid state NMR.

Preparation of proteins in their crystalline state has been found to be important in producing stable therapeutic protein formulations, cross-linked enzyme crystals for application in industrial processes, generating novel porous media for separations, and of course in structure elucidation. Of these applications only X-ray crystallography requires large crystals, defined here as being crystals 100s of microns or greater in size. Smaller crystals have attractive attributes in many instances, and are just as useful in structure determination by solid state NMR (ssNMR) as are large crystals. In this paper we outline a simple set of procedures for preparing nanocrystalline protein samples for ssNMR or other applications and describe the characterization of their crystallinity by ssNMR and X-ray powder diffraction. The approach is demonstrated in application to five different proteins: ubiquitin, lysozyme, ribonuclease A, streptavidin, and cytochrome c. In all instances the nanocrystals produced are found to be highly crystalline as judged by natural abundance 13C ssNMR and optical and electron microscopy. We show for ubiquitin that nanocrystals prepared by rapid batch crystallization yield equivalent 13C ssNMR spectra to those of larger X-ray diffraction quality crystals. Single crystal and powder X-ray diffraction measurements are made to compare the degree of order present in polycrystalline, nanocrystalline, and lyophilized ubiquitin. Solid state 13C NMR is also used to show that ubiquitin nanocrystals are thermally robust, giving no indication of loss of local order after repeated temperature cycling between liquid nitrogen and room temperature. The methods developed are rapid and should scale well from the tenths of milligram to multi-gram scales, and as such should find wide utility in the preparation of protein nanocrystals for applications in catalysis, separations, and especially in sample preparation for structural studies using ssNMR.

Crystallization↗
PubMed2006

Crystallinity of plant epicuticular waxes: electron and X-ray diffraction studies.

The crystal structure of the epicuticular waxes of 35 plant species has been examined by electron diffraction and X-ray powder diffraction. The waxes include the most common morphological wax types such as platelets, tubules, films and rodlets. Most of them were prepared with a special mechanical isolation method, which preserves the original crystal structure. Solvent-extracted recrystallized plant waxes were compared with mechanically isolated samples. The waxes were found to occur in three different crystal structures. Most of the waxes exhibited an orthorhombic structure which is the most common for aliphatic compounds. Tubules containing mainly secondary alcohols showed diffraction reflections of a triclinic phase; broad reflection peaks indicated a significant disorder. Ketones, in particular beta-diketone tubules, displayed the reflections of a hexagonal structure. Mixtures of different phases could be identified. For most of the waxes, the 'long spacing' diffraction reflections indicated a layer structure with the characteristics of the major component. Others showed no 'long spacing' reflections indicating a strong disorder of the molecular layers.

Crystallization↗
PubMed2004

Nonpolymeric hydrogelator derived from N-(4-pyridyl)isonicotinamide.

A series of pyridyl amides derived from isonicotinic acid, nicotinic acid, and benzoic acid have been synthesized. Only N-(4-pyridyl)isonicotinamide 1 is found to be an efficient hydrogelator with a minimum gelator concentration of 0.37 wt %. A wide range of concentrations (0.37-20 wt %) could be used to form hydrogels. The other amides, namely, N-(3-pyridyl)isonicotinamide 2, N-(2-pyridyl)isonicotinamide 3, N-(phenyl)isonicotinamide 4, N-(4-pyridyl)nicotinamide 5, N-(3-pyridyl)nicotinamide 6, and N-(4-pyridyl)benzamide 7, did not show any gelation properties. Fourier transform infrared spectroscopy, variable temperature 1H NMR, single-crystal diffraction and X-ray powder diffraction (XRPD), and scanning electron microscopy have been used to characterize the gel. Single-crystal diffraction and XRPD studies indicate that the morph responsible for gel formation is different from that in its bulk solid and xerogel.

Amides↗
PubMed2003

(3 + 1)-dimensional structure refinement of the fresnoite framework-structure type compound Ba(2)TiGe(2)O(8).

The incommensurately modulated structure of the fresnoite framework-structure type compound Ba(2)TiGe(2)O(8) has been solved using a (3 + 1)-dimensional superspace approach. The structure is orthorhombic and adopts the superspace group Cmm2(0,beta,1/2)s00 with beta approximately 0.635 at room temperature. The refinement was based on neutron powder diffraction data obtained from a powdered single crystal grown by Czochralski pulling. The modulation parameters that were obtained support the idea that frozen-in rigid-unit modes cause the modulation. The modulation is mainly manifested by positional displacements of O atoms. Barium ions are either eightfold, ninefold or tenfold coordinated in the one-dimensional modulated structure. A significant improvement of the bond-valence sum for both barium positions is achieved by the introduction of the positional modulation. This finding strongly suggests that underbonded barium positions are critically involved in provoking the incommensurate modulation in Ba(2)TiGe(2)O(8).

Journal Article↗
PubMed2003

Recent results from the in situ study of hydrothermal crystallisations using time-resolved X-ray and neutron diffraction methods.

We present new time-resolved powder diffraction data measured in situ during the hydrothermal crystallisation of two families of crystalline inorganic materials. In the first study, we have used time-resolved energy-dispersive X-ray diffraction (EDXRD) to follow the formation of zeolitic zinc phosphates from amine phosphates and zinc oxide in acidic solutions at 60-150 degrees C. The advantage of this method is the ability to penetrate a laboratory-sized reaction vessel and to measure data in short (< 1 min) time intervals. Integration of the Bragg peak intensities during the crystallisation of the product allows accurate crystallisation curves to be produced. In addition, in a number of cases, we observe the formation of transient crystalline intermediate phases which can be identified by use of a new three-element detector that allows a large amount of diffraction data to be measured during the experiment. We are thus able to show that three-dimensional zinc phosphate architectures often form via low-dimensional chain and layered phases, which is consistent with a recent aufbau model proposed for their formation. In the second study, we focus on the hydrothermal formation of ferroelectric barium titanate from TiO2 and barium salts in alkaline solution using time-resolved neutron diffraction. Although the time resolution of the neutron diffraction experiment is lower than the EDXRD experiment (data are measured in intervals of 5 min), we are able to penetrate reaction mixtures that are highly absorbing towards X-rays, and thus can measure data in a large volume reaction cell. Neutron diffraction data were collected on one of the highest-flux/highest detector-coverage diffractometers currently available; the GEM diffractometer at ISIS, UK. These experiments reveal that BaTiO3 crystallises after a large amount of TiO2 has been consumed; this implies that a dissolution crystallisation mechanism predominates. Additional mechanistic information is inferred by the observation of transient crystalline phases under certain reaction conditions.

Journal Article↗
PubMed2006

Molecular versus crystal symmetry in tri-substituted triazine, benzene and isocyanurate derivatives.

The crystal structures of triethyl-1,3,5-triazine-2,4,6-tricarboxylate (I), triethyl-1,3,5-benzenetricarboxylate (II) and tris-2-hydroxyethyl isocyanurate (III) have been determined from conventional laboratory X-ray powder diffraction data using the differential evolution structure solution technique. The determination of these structures presented an unexpectedly wide variation in levels of difficulty, with only the determination of (III) being without complication. In the case of (I) structure solution resulted in a Rietveld refinement profile that was not ideal, but was subsequently rationalized by single-crystal diffraction as resulting from disorder. Refinement of structure (II) showed significant variation in side-chain conformation from the initial powder structure solution. Further investigation showed that the structure solution optimization had indeed been successful, and that preferred orientation had a dramatic effect on the structure-solution R-factor search surface. Despite the presence of identical side chains in (I) and (II), only the triazine-based system retains threefold molecular symmetry in the crystal structure. The lack of use of the heterocyclic N atom as a hydrogen-bond acceptor in this structure results in the formation of a similar non-centrosymmetric network to the benzene-based structure, but with overall three-dimensional centrosymmetry. The hydrogen-bonded layer structure of (III) is similar to that of other isocyanurate-based structures of this type.

Benzene Derivatives↗
PubMed1988

Physical characterization of two oxyphenbutazone pseudopolymorphs.

Two pseudopolymorphic forms of oxyphenbutazone, a benzene solvate (Solvate B) and a cyclohexane solvate (Solvate C), were prepared by recrystallization from benzene and cyclohexane, respectively. The forms were characterized by means of differential scanning calorimetry, thermogravimetry, infrared spectrophotometry, X-ray powder diffraction, and thermomicroscopy, as well as powder and intrinsic dissolution rates. The dissolution rates of the two pseudopolymorphs were shown to be superior to those of the anhydrate, hemihydrate, and monohydrate which were previously reported. A brief stability report is included.

Calorimetry, Differential Scanning↗
PubMed2005

Structure determination of CdS and ZnS nanoparticles: direct modeling of synchrotron-radiation diffraction data.

We introduce a modified method of powder-diffraction data analysis to obtain precise structural information on freestanding ZnS and CdS nanoparticles with diameters well below 5 nm, i.e., in a range where common bulk-derived approaches fail. The method is based on the Debye equation and allows us to access the crystal structure and the size of the particles with high precision. Detailed information on strain, relaxation effects, stacking faults, and the shape of the particles becomes available. We find significant size differences between our new results and those obtained by established methods, and conclude that a mixed zinc-blende/wurtzite stacking and significant lattice distortions occur in our CdS nanoparticles. Our approach should have direct impact on the understanding and modeling of quantum size effects in nanoparticles.

Journal Article↗
PubMed2001

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.

Journal Article↗
PubMed2003

High-resolution and high-intensity powder diffractometer at BL15XU in SPring-8.

A new ultra-high-resolution powder diffractometer for synchrotron radiation has been constructed at beamline BL15XU, SPring-8. The two-axis diffractometer is optimized for high-flux and high-coherent X-ray beams, which are provided by combining a planar undulator and a large offset rotated-inclined Si(111) double-crystal monochromator. The optics design of the diffractometer is based on transmission geometry, which employs a capillary specimen and reflection geometries using a flat-plate specimen. The intensity data are collected using a 2theta step-scan technique in both geometries. The diffractometer can be arranged in a variety of optical configurations, e.g. simple receiving slits, flat crystal analyzer of Ge(111) or Si(111), and in-vacuum-type long horizontal parallel slits. A minimum full width at half-maximum against 2theta was 0.00572 degrees at lambda = 0.63582 A for the (200) reflections from Si powder in the transmission geometry employing the Ge(111) crystal analyzer. A wide temperature range (32-900 K), which is controlled by a He/N(2) gas stream system, is available. 288 structure parameters of a zeolite ZSM-5 sample have been demonstrated to successfully refine with a R(wp) value of 6.96% by a Rietveld analysis of the high-resolution powder diffraction data from a 1 mm-diameter capillary specimen.

Crystallization↗
PubMed2001

Vibrational spectra and normal coordinate analysis of a weak ligand complex, Co(p-DMABA)2Cl2 x 2H2O.

The complex Co(p-DMABA)2Cl2 x 2H2O (p-dimethylaminobenzaldehyde, p-DMABA) was prepared from the solid-state reaction of a weak ligand p-DMABA and CoCl2 x 6H2O at lower heating temperature (60 degrees C). It is very difficult to obtain the title complex using solution reaction method, less than isolating single crystals. In order to determine the crystal structure of the title compound, we have to rely on the X-ray powder diffraction data. That is, the crystal structure can be solved directly from powder data, which crucial step is to constitute the structure model. Indirect spectroscopic methods, such as infrared and Raman spectroscopes, and further vibrational assignments made with the aid of normal coordinate calculations by using a modified Urey-Bradley force field, were analyzed to proposed molecular structure. One hundred and fifty-seven internal coordinates were established and 129 theoretical vibrational frequencies were calculated. An appropriate set of internal coordinates and force constants in the course of calculation were introduced, so that the calculated vibration frequencies are good agreement with the observed values. The average difference and the maximum deviation between theoretic and experimental frequencies are 2.44 and 8.0 cm(-1), respectively. Thus the normal coordinate analysis is a powerful tool to the molecular structure. Other structural and spectral properties are also discussed in this paper. The purpose of the present paper is to obtain a good structural model. This model was used as starting model for crystal structure determination from powder X-ray diffraction (XRD) data.

Crystallization↗
PubMed2005

Homoleptic, sigma-bonded octahedral superelectrophilic metal carbonyl cations of iron(II), ruthenium(II), and osmium(II). Part 2: Syntheses and characterizations of [M(CO)(6)][BF(4)](2) (M = Fe, Ru, Os).

As the first examples of homoleptic, sigma-bonded superelectrophilic metal carbonyl cations with tetrafluoroborate [BF(4)](-) as the counter anions three thermally stable salts of the composition [M(CO)(6)][BF(4)](2) (M = Fe, Ru, Os) have been synthesized and extensively characterized by thermochemical, structural, and spectroscopic methods. A common synthetic route, the oxidative carbonylation of either Fe(CO)(5) (XeF(2) as the oxidizer) or M(3)(CO)(12) (M = Ru, Os) (F(2) as the oxidizer) in the conjugate Bronsted-Lewis superacid HF/BF(3), was employed. The thermal behavior of the three salts, studied by differential scanning calorimetry (DSC) and gas-phase IR spectroscopy of the decomposition products, has been compared to that of the corresponding [SbF(6)](-) salts. The molecular structures of [M(CO)(6)][BF(4)](2) (M = Fe, Os) were obtained by single-crystal X-ray diffraction at 100 K. X-ray powder diffraction data for [M(CO)(6)][BF(4)](2) (M = Ru, Os) were obtained between 100 and 300 K in intervals of 50 K. All three salts are isostructural and crystallized in the tetragonal space group I4/m (No. 87). As for the corresponding [M(CO)(6)][SbF(6)](2) salts (M = Fe, Ru, Os), similar unit cell parameters and vibrational fundamentals were also found for the three [BF(4)](-) compounds. For the structurally characterized salts [M(CO)(6)][BF(4)](2) (M = Fe, Os), very similar bond parameters for both cations and anions were found. Hence, the invariance of structural and spectroscopic properties of [M(CO)(6)](2+) cations (M = Fe, Ru, Os) extended from the fluoroantimonates [Sb(2)F(11)](-) and [SbF(6)](-) as counteranions also to [BF(4)](-).

Journal Article↗
PubMed2002

Crystal structure of neotame anhydrate polymorph G.

PURPOSE: To determine the crystal structure of the neotame anhydrate polymorph G and to evaluate X-ray powder diffractometry (XRPD) with molecular modeling as an alternative method for determining the crystal structure of this conformationally flexible dipeptide. METHODS: The crystal structure of polymorph G was determined by single crystal X-ray crystallography (SCXRD) and also from the X-ray powder diffraction (XRPD) pattern using molecular modeling (Cerius2, Powder Solve module). RESULTS: From SCXRD, polymorph G crystals are orthorhombic with space group of P2(1)2(1)2(1) with Z = 4, unit cell constants: a = 5.5999(4), b = 11.8921(8), c = 30.917(2) A, and one neotame molecule per asymmetric unit. The XRPD pattern of polymorph G, analyzed by Cerius2 software, led to the same P2(1)2(1)2(1) space group and almost identical unit cell dimensions. However, with 13 rigid bodies defined, Cerius2 gives a conformation of the neotame molecule, which is different from that determined by SCXRD. CONCLUSIONS: For neotame anhydrate polymorph G, the unit cell dimensions calculated from XRPD were almost identical to those determined by SCXRD. However, the crystal structure determined by XRPD closely resembled that determined by SCXRD, only when the correct conformation of the neotame molecule had been chosen before detailed analysis of the XRPD pattern.

Crystallization↗
PubMed2003

First-principles calculations as a tool for structure validation in electron crystallography.

The crystal structures of Ti(11)Se(4) [Weirich, Ramlau, Simon, Hovmöller & Zou (1996). Nature (London), 382, 144-146] and Ti(45)Se(16) [Weirich (2001). Acta Cryst. A57, 183-191] determined previously from selected-area electron diffraction (SAED) data have been checked for their correctness by means of total energy calculations within the non-local density functional theory. The reliability of the used method was verified by test calculations carried out for the structurally related compound Ti(8)Se(3), which is well known from single-crystal X-ray diffraction [Weirich, Pöttgen & Simon (1996). Z. Kristallogr. 212, 929-930]. For Ti(8)Se(3), structural models from both experiment and calculation show a perfect match (average agreement 0.01 A). This proves that the geometrical optimized models from first-principles calculation can be used as a reliable alternative when good-quality X-ray results cannot be obtained. Calculations carried out for the two structures determined from electron crystallography yielded average improvement of the atomic coordinates of 0.04 and 0.09 A for Ti(11)Se(4) and Ti(45)Se(16), respectively. The optimized cell parameters of the monoclinic structures (both space group C2/m, No. 12) are a = 25.51, b = 3.43, c = 19.19 A, beta = 117.9 degrees for Ti(11)Se(4) and a = 36.31, b = 3.45, c = 16.59 A, beta = 92.1 degrees for Ti(45)Se(16). These results prove that crystals that are too small for single-crystal X-ray diffraction and are difficult to solve by powder diffraction may nevertheless be amenable to accurate structure determination by electron diffraction structure analysis using data from standard SAED and the assumption of quasi-kinematical scattering. Moreover, this study shows that geometry optimization by first-principles calculations is the perfect tool for validation and improvement of complex structural models, which are suspected to have errors owing to the poor quality of experimental data.

Journal Article↗
PubMed2004

Determination of depth-dependent diffraction data: a new approach.

A direct method for determining powder diffraction data at specific depths from angle-dependent diffraction data is described. The method is non-destructive and only traditional data collections, where the angle of incidence is varied, are required. These angle-dependent spectra are transformed to give diffraction data arising from different depths, which may then be exploited using any conventional method. This is a novel approach as traditional methods are forced to tolerate the inherent depth averaging of grazing-angle diffraction, or only examine specific structural characteristics. In order to obtain depth-dependent X-ray diffraction data, a Fredholm integral equation of the first kind is solved using regularization techniques. The method has been validated by the generation of pseudo-experimental data having known depth profiles and solving the Fredholm integral equation to recover the solution. The method has also been applied to experimental data from a number of thin film systems.

Journal Article↗
PubMed2006

Monetite formed in mixed solvents of water and ethylene glycol and its transformation to hydroxyapatite.

Agglomerated nanorods of hydroxyapatite have been synthesized using monetite as a precursor in a NaOH solution. Monetite consisting of nanosheets has been successfully synthesized by a one-step microwave-assisted method using CaCl(2).2.5H(2)O, NaH(2)PO(4), and sodium dodecyl sulfate (SDS) in water/ethylene glycol (EG) mixed solvents. The effects of the molar ratio of water to EG and the reaction time on the products were investigated. The products were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier transform infrared spectrometry (FTIR).

Calcium Phosphates↗
PubMed2005

The use of softer X-rays in the structure elucidation of microporous materials.

Microporous materials, such as zeolites and aluminophosphates, have many applications as molecular sieves and shape-selective catalysts. This is due to their three-dimensional frameworks, which contain regular pores and channels, to their high acidity, arising from Brønsted and Lewis acid active sites, and to the incorporation of transition metal atoms into framework sites. This review firstly provides an introduction into the nature and properties of these materials, and their important applications; the difficulties in their full characterization and possible methods of elucidating their structures are then outlined; finally, methods of characterization, utilizing 'softer X-rays' are introduced. The first method is the determination of low concentrations of transition metals, incorporated into the frameworks using single crystal anomalous dispersion crystallography; synchrotron radiation is used to tune to the absorption edge of the metal atom in question, in order to change its signal relative to that of the rest of the structure, thereby allowing the pinpointing of its positions and the determination of its concentration at each site in the framework. Secondly, the use of longer wavelengths in powder diffraction studies is described, which, by stretching out the powder pattern, thereby reduces the overlapping of the diffraction peaks, thus allowing the structure to be solved by conventional direct methods. Finally, the use of X-ray absorption spectroscopy to determine the metal incorporation and the nature of coordination at the metal atom sites, in Mn silicalite-1 and FAPO-36, are described.

Ceramics↗
PubMed2006

The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's beta-amyloid polypeptide.

Alzheimer's beta-amyloid diphenylalanine motif has previously been shown to self-assemble into discrete and extraordinary stiff nanotubes; these nanotubes were initially thought to be distinct from the single crystal structure of diphenylalanine, but it is now shown that the X-ray powder diffraction pattern of the nanotubes is identical to the simulated pattern for the single crystal structure, affording a new foundation for understanding and rationalizing the properties of this remarkable organic material.

Amyloid beta-Peptides↗