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IUCrJ Sep 2015The crystal structures of eight mono-methyl alkanes have been determined from single-crystal or high-resolution powder X-ray diffraction using synchrotron radiation....
The crystal structures of eight mono-methyl alkanes have been determined from single-crystal or high-resolution powder X-ray diffraction using synchrotron radiation. Mono-methyl alkanes can be found on the cuticles of insects and are believed to act as recognition pheromones in some social species, e.g. ants, wasps etc. The molecules were synthesized as pure S enantiomers and are (S)-9-methylpentacosane, C26H54; (S)-9-methylheptacosane and (S)-11-methylheptacosane, C28H58; (S)-7-methylnonacosane, (S)-9-methylnonacosane, (S)-11-methylnonacosane and (S)-13-methylnonacosane, C30H62; and (S)-9-methylhentriacontane, C32H66. All crystallize in space group P21. Depending on the position of the methyl group on the carbon chain, two packing schemes are observed, in which the molecules pack together hexagonally as linear rods with terminal and side methyl groups clustering to form distinct motifs. Carbon-chain torsion angles deviate by less than 10° from the fully extended conformation, but with one packing form showing greater curvature than the other near the position of the methyl side group. The crystal structures are optimized by dispersion-corrected DFT calculations, because of the difficulties in refining accurate structural parameters from powder diffraction data from relatively poorly crystalline materials.
PubMed: 26306191
DOI: 10.1107/S2052252515010271 -
Data in Brief Sep 2016The data presented in this article are related to the production of 1:1 Caffeine:Glutaric Acid cocrystals as part of the research article entitled "Green production of...
The data presented in this article are related to the production of 1:1 Caffeine:Glutaric Acid cocrystals as part of the research article entitled "Green production of cocrystals using a new solvent-free approach by spray congealing" (Duarte et al., 2016) [1]. More specifically, here we present the thermal analysis and the X-ray powder diffraction data for pure Glutaric Acid, used as a raw material in [1]. We also include the X-ray powder diffraction and electron microscopy data obtained for the 1:1 Caffeine:Glutaric Acid cocrystal (form II) produced using the cooling crystallization method reported in "Operating Regions in Cooling Cocrystallization of Caffeine and Glutaric Acid in Acetonitrile" (Yu et al., 2010) [2]. Lastly, we show the X-ray powder diffraction data obtained for assessing the purity of the 1:1 Caffeine:Glutaric cocrystals produced in [1].
PubMed: 27331096
DOI: 10.1016/j.dib.2016.04.074 -
Journal of Synchrotron Radiation May 2015Powder X-ray diffraction techniques largely benefit from the superior beam quality provided by high-brilliance synchrotron light sources in terms of photon flux and...
Powder X-ray diffraction techniques largely benefit from the superior beam quality provided by high-brilliance synchrotron light sources in terms of photon flux and angular resolution. The High Resolution Powder Diffraction Beamline P02.1 at the storage ring PETRA III (DESY, Hamburg, Germany) combines these strengths with the power of high-energy X-rays for materials research. The beamline is operated at a fixed photon energy of 60 keV (0.207 Å wavelength). A high-resolution monochromator generates the highly collimated X-ray beam of narrow energy bandwidth. Classic crystal structure determination in reciprocal space at standard and non-ambient conditions are an essential part of the scientific scope as well as total scattering analysis using the real space information of the pair distribution function. Both methods are complemented by in situ capabilities with time-resolution in the sub-second regime owing to the high beam intensity and the advanced detector technology for high-energy X-rays. P02.1's efficiency in solving chemical and crystallographic problems is illustrated by presenting key experiments that were carried out within these fields during the early stage of beamline operation.
PubMed: 25931084
DOI: 10.1107/S1600577515002222 -
Journal of Research of the National... 1996The Powder Diffraction file has been the primary reference for Powder Diffraction Data for more than half a century. The file is a collection of about 65 000 reduced...
The Powder Diffraction file has been the primary reference for Powder Diffraction Data for more than half a century. The file is a collection of about 65 000 reduced powder patterns stored as sets of / data along with the appropriate crystallographic, physical and experimental information. This paper reviews the development and growth of the PDF and discusses the role of the ICDD in the maintenance and dissemination of the file.
PubMed: 27805163
DOI: 10.6028/jres.101.027 -
Acta Crystallographica. Section E,... Jun 2015Time-of-flight neutron powder diffraction data have been collected from Na2MoO4 and Na2WO4 to a resolution of sin (θ)/λ = 1.25 Å(-1), which is substanti-ally...
Time-of-flight neutron powder diffraction data have been collected from Na2MoO4 and Na2WO4 to a resolution of sin (θ)/λ = 1.25 Å(-1), which is substanti-ally better than the previous analyses using Mo Kα X-rays, providing roughly triple the number of measured reflections with respect to the previous studies [Okada et al. (1974 ▶). Acta Cryst. B30, 1872-1873; Bramnik & Ehrenberg (2004 ▶). Z. Anorg. Allg. Chem. 630, 1336-1341]. The unit-cell parameters are in excellent agreement with literature data [Swanson et al. (1962 ▶). NBS Monograph No. 25, sect. 1, pp. 46-47] and the structural parameters for the molybdate agree very well with those of Bramnik & Ehrenberg (2004 ▶). However, the tungstate structure refinement of Okada et al. (1974 ▶) stands apart as being conspicuously inaccurate, giving significantly longer W-O distances, 1.819 (8) Å, and shorter Na-O distances, 2.378 (8) Å, than are reported here or in other simple tungstates. As such, this work represents an order-of-magnitude improvement in precision for sodium molybdate and an equally substantial improvement in both accuracy and precision for sodium tungstate. Both compounds adopt the spinel structure type. The Na(+) ions have site symmetry .-3m and are in octa-hedral coordination while the transition metal atoms have site symmetry -43m and are in tetra-hedral coordination.
PubMed: 26090129
DOI: 10.1107/S2056989015008774 -
AAPS PharmSciTech 2008Practical examples of preformulation support of the form selected for formulation development are provided using several drug substances (DSs). The examples include... (Review)
Review
Practical examples of preformulation support of the form selected for formulation development are provided using several drug substances (DSs). The examples include determination of the solubilities vs. pH particularly for the range pH 1 to 8 because of its relationship to gastrointestinal (GI) conditions and dissolution method development. The advantages of equilibrium solubility and trial solubility methods are described. The equilibrium method is related to detecting polymorphism and the trial solubility method, to simplifying difficult solubility problems. An example of two polymorphs existing in mixtures of DS is presented in which one of the forms is very unstable. Accelerating stability studies are used in conjunction with HPLC and quantitative X-ray powder diffraction (QXRD) to demonstrate the differences in chemical and polymorphic stabilities. The results from two model excipient compatibility methods are compared to determine which has better predictive accuracy for room temperature stability. A DSC (calorimetric) method and an isothermal stress with quantitative analysis (ISQA) method that simulates wet granulation conditions were compared using a 2 year room temperature sample set as reference. An example of a pH stability profile for understanding stability and extrapolating stability to other environments is provided. The pH-stability of omeprazole and lansoprazole, which are extremely unstable in acidic and even mildly acidic conditions, are related to the formulation of delayed release dosage forms and the resolution of the problem associated with free carboxyl groups from the enteric coating polymers reacting with the DSs. Dissolution method requirements for CR dosage forms are discussed. The applicability of a modified disintegration time (DT) apparatus for supporting CR dosage form development of a pH sensitive DS at a specific pH such as duodenal pH 5.6 is related. This method is applicable for DSs such as peptides, proteins, enzymes and natural products where physical observation can be used in place of a difficult to perform analytical method, saving resources and providing rapid preformulation support.
Topics: Calorimetry, Differential Scanning; Chemistry, Pharmaceutical; Chromatography, High Pressure Liquid; Crystallography, X-Ray; Delayed-Action Preparations; Drug Stability; Excipients; Hydrogen-Ion Concentration; Powder Diffraction; Solubility; Technology, Pharmaceutical; Temperature; Time Factors
PubMed: 18431656
DOI: 10.1208/s12249-008-9067-3 -
IUCrJ Mar 2014The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals,...
The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365-378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called 'shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.
PubMed: 25075327
DOI: 10.1107/S2052252514002838 -
Journal of Applied Crystallography Dec 2021A key step in the analysis of powder X-ray diffraction (PXRD) data is the accurate determination of unit-cell lattice parameters. This step often requires significant...
A key step in the analysis of powder X-ray diffraction (PXRD) data is the accurate determination of unit-cell lattice parameters. This step often requires significant human intervention and is a bottleneck that hinders efforts towards automated analysis. This work develops a series of one-dimensional convolutional neural networks (1D-CNNs) trained to provide lattice parameter estimates for each crystal system. A mean absolute percentage error of approximately 10% is achieved for each crystal system, which corresponds to a 100- to 1000-fold reduction in lattice parameter search space volume. The models learn from nearly one million crystal structures contained within the Inorganic Crystal Structure Database and the Cambridge Structural Database and, due to the nature of these two complimentary databases, the models generalize well across chemistries. A key component of this work is a systematic analysis of the effect of different realistic experimental non-idealities on model performance. It is found that the addition of impurity phases, baseline noise and peak broadening present the greatest challenges to learning, while zero-offset error and random intensity modulations have little effect. However, appropriate data modification schemes can be used to bolster model performance and yield reasonable predictions, even for data which simulate realistic experimental non-idealities. In order to obtain accurate results, a new approach is introduced which uses the initial machine learning estimates with existing iterative whole-pattern refinement schemes to tackle automated unit-cell solution.
PubMed: 34963768
DOI: 10.1107/S1600576721010840 -
Journal of Applied Crystallography Dec 2022The quantitative phase analysis using X-ray diffraction of pyrite ore concentrate samples extracted from the Thackaringa mine is problematic due to poor particle...
The quantitative phase analysis using X-ray diffraction of pyrite ore concentrate samples extracted from the Thackaringa mine is problematic due to poor particle statistics, microabsorption and preferred orientation. The influence of sample preparation on these issues has been evaluated, with ball milling of the powder found most suitable for accurate and precise quantitative phase analysis. The milling duration and other aspects of sample preparation have been explored, resulting in accurate phase reflection intensities when particle sizes are below 5 µm. Quantitative phase analysis on those samples yielded precise phase fractions with standard deviations below 0.3 wt%. Some discrepancy between the elemental composition obtained using X-ray powder diffraction data and that determined using wavelength-dispersive X-ray fluorescence was found, and is thought to arise from unaccounted for crystalline phase substitution and the possible presence of an amorphous phase. This study provides a methodology for the precise and accurate quantitative phase analysis of X-ray powder diffraction data of pyrite ore concentrate from the Thackaringa mine and a discussion of the limitations of the method. The optimization process reveals the importance of confirming reproducibility on new samples, with as much prior knowledge as possible.
PubMed: 36570660
DOI: 10.1107/S1600576722009888 -
Acta Crystallographica. Section A,... Sep 2022A prototype application for machine-readable literature is investigated. The program is called pyDataRecognition and serves as an example of a data-driven literature...
A prototype application for machine-readable literature is investigated. The program is called pyDataRecognition and serves as an example of a data-driven literature search, where the literature search query is an experimental data set provided by the user. The user uploads a powder pattern together with the radiation wavelength. The program compares the user data to a database of existing powder patterns associated with published papers and produces a rank ordered according to their similarity score. The program returns the digital object identifier and full reference of top-ranked papers together with a stack plot of the user data alongside the top-five database entries. The paper describes the approach and explores successes and challenges.
Topics: Databases, Factual; Powder Diffraction; Powders; Publications
PubMed: 36047395
DOI: 10.1107/S2053273322007483