Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Indomethacin Polymorph δ Revealed To Be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47-Year-Old Misunderstanding.

ABSTRACT: Indomethacin is a clinically classical non-steroidal anti-inflammatory drug that has been marketed since 1965. The third polymorph, Form δ, was discovered by both melt and solution crystallization in 1974. δ-indomethacin cannot be cultivated as large single crystals suitable for X-ray crystallography and, therefore, its crystal structure has not yet been determined. Here, we report the structure elucidation of δ-indomethacin by 3D electron diffraction and reveal the truth that melt-crystallized and solution-crystallized δ-indomethacin are in fact two polymorphs with different crystal structures. We propose to keep the solution-crystallized polymorph as Form δ and name the melt-crystallized polymorph as Form θ. Intriguingly, both structures display plastic flexibility based on a slippage mechanism, making indomethacin the first drug to have two plastic polymorphs. This discovery and correction of a 47-year-old misunderstanding signify that 3D electron diffraction has become a powerful tool for polymorphic structural studies.

SUBMITTER: Lightowler M

PROVIDER: S-EPMC9306882 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Quantifiable stretching-induced fluorescence shifts of an elastically bendable and plastically twistable organic crystal.

Project description:Organic crystals with mechanical stimulus-response properties are being developed increasingly nowadays. However, the studies involving tensile-responsive crystals are still lacking due to the strict requirement of crystals with good flexibility. In this work, an organic crystal with the ability of elastic bending and plastic twisting upon loading stress and shearing force, respectively, is reported. The deformability in different directions enables the crystal to be a model for tensile-responsive study. Indeed, blue shifts of fluorescence were observed when the tensile forces loaded upon the needle-shaped crystal were stretched to a certain degree. The mathematical correlation between emission wavelength changes and stretching strain was obtained for the first time, which proves that the crystal has a potential application for tension sensors. In addition, a low detection limit and high sensitivity enabled the crystal to have the ability to detect tension variations in precision instruments. Theoretical calculations and X-ray crystal structure analyses revealed the mechanism of emission wavelength shifts caused by molecular movement during the stretching process. The presented crystal successfully overcame the limitations of traditional mechanochromic organic crystals, which have difficulty in responding to tensile forces.

| S-EPMC8635174 | biostudies-literature

On the reliability of powder diffraction Line Profile Analysis of plastically deformed nanocrystalline systems.

Project description:An iron-molybdenum alloy powder was extensively deformed by high energy milling, so to refine the bcc iron domain size to nanometer scale (~10?nm) and introduce a strong inhomogeneous strain. Both features contribute to comparable degree to the diffraction peak profile broadening, so that size and strain contributions can be easily separated by exploiting their different dependence on the diffraction angle. To assess the reliability of Line Profile Analysis, results were compared with evidence from other techniques, including scanning and transmission electron microscopy and X-ray small angle scattering. Results confirm the extent of the size broadening effect, whereas molecular dynamics simulations provide insight into the origin of the local atomic, inhomogeneous strain, pointing out the role of dislocations, domain boundaries and interactions among crystalline domains.

| S-EPMC4748273 | biostudies-literature

Polymorph evolution during crystal growth studied by 3D electron diffraction.

Project description:3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order ? < ? < ?. The least stable ? polymorph forms within the first 3?min, but this begins to yield the ?-form after only 1?min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20?s on crystals of thickness ?100?nm. Even though the ?-form is thermodynamically the most stable polymorph, kinetics favour the ?-form, which dominates after prolonged standing. In the same sample, some ? and one crystallite of the ? polymorph were also observed.

| S-EPMC6949601 | biostudies-literature

Macromolecular phasing using diffraction from multiple crystal forms.

Project description:A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms - crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.

| S-EPMC7842209 | biostudies-literature

Correcting the linear and nonlinear distortions for atomically resolved STEM spectrum and diffraction imaging.

Project description:Specimen and stage drift as well as scan distortions can lead to a mismatch between true and desired electron probe positions in scanning transmission electron microscopy (STEM) which can result in both linear and nonlinear distortions in the subsequent experimental images. This problem is intensified in STEM spectrum and diffraction imaging techniques owing to the extended dwell times (pixel exposure time) as compared to conventional STEM imaging. As a consequence, these image distortions become more severe in STEM spectrum/diffraction imaging. This becomes visible as expansion, compression and/or shearing of the crystal lattice, and can even prohibit atomic resolution and thus limits the interpretability of the results. Here, we report a software tool for post-correcting the linear and nonlinear image distortions of atomically resolved 3D spectrum imaging as well as 4D diffraction imaging. This tool improves the interpretability of distorted STEM spectrum/diffraction imaging data.

| S-EPMC6025237 | biostudies-literature

Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme.

Project description:Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.

| S-EPMC6400191 | biostudies-literature

Solid-State Forms of β-Resorcylic Acid: How Exhaustive Should a Polymorph Screen Be?

Project description:An extensive experimental screen, coupled with a computational study, revealed seven new solid-state forms of β-resorcylic acid. The known, stable polymorph II° shows a reversible phase transformation to the new, kinetically stable, probably disordered high temperature form I. The study provides a consistent picture of the solid-state of β-resorcylic acid.

| S-EPMC3015459 | biostudies-literature

Understanding and misunderstanding randomized controlled trials.

Project description:Randomized Controlled Trials (RCTs) are increasingly popular in the social sciences, not only in medicine. We argue that the lay public, and sometimes researchers, put too much trust in RCTs over other methods of investigation. Contrary to frequent claims in the applied literature, randomization does not equalize everything other than the treatment in the treatment and control groups, it does not automatically deliver a precise estimate of the average treatment effect (ATE), and it does not relieve us of the need to think about (observed or unobserved) covariates. Finding out whether an estimate was generated by chance is more difficult than commonly believed. At best, an RCT yields an unbiased estimate, but this property is of limited practical value. Even then, estimates apply only to the sample selected for the trial, often no more than a convenience sample, and justification is required to extend the results to other groups, including any population to which the trial sample belongs, or to any individual, including an individual in the trial. Demanding 'external validity' is unhelpful because it expects too much of an RCT while undervaluing its potential contribution. RCTs do indeed require minimal assumptions and can operate with little prior knowledge. This is an advantage when persuading distrustful audiences, but it is a disadvantage for cumulative scientific progress, where prior knowledge should be built upon, not discarded. RCTs can play a role in building scientific knowledge and useful predictions but they can only do so as part of a cumulative program, combining with other methods, including conceptual and theoretical development, to discover not 'what works', but 'why things work'.

| S-EPMC6019115 | biostudies-literature

A second polymorph of sodium di-hydrogen citrate, NaH2C6H5O7: structure solution from powder diffraction data and DFT comparison.

Project description:The crystal structure of a second polymorph of sodium di-hydrogen citrate, Na(+)·H2C6H5O7 (-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The powder pattern of the commercial sample used in this study did not match that corresponding to the known crystal structure [Glusker et al. (1965). Acta Cryst. 19, 561-572; refcode NAHCIT]. In this polymorph, the [NaO7] coordination polyhedra form edge-sharing chains propagating along the a axis, while in NAHCIT the octa-hedral [NaO6] groups form edge-sharing pairs bridged by two hy-droxy groups. The most notable difference is that in this polymorph one of the terminal carboxyl groups is deprotonated, while in NAHCIT the central carboxyl-ate group is deprotonated, as is more typical.

| S-EPMC4908552 | biostudies-literature

A Mechanistic Perspective on Plastically Flexible Coordination Polymers.

Project description:Mechanical flexibility in single crystals of covalently bound materials is a fascinating and poorly understood phenomenon. We present here the first example of a plastically flexible one-dimensional (1D) coordination polymer. The compound [Zn(μ-Cl)2 (3,5-dichloropyridine)2 ]n is flexible over two crystallographic faces. Remarkably, the single crystal remains intact when bent to 180°. A combination of microscopy, diffraction, and spectroscopic studies have been used to probe the structural response of the crystal lattice to mechanical bending. Deformation of the covalent polymer chains does not appear to be responsible for the observed macroscopic bending. Instead, our results suggest that mechanical bending occurs by displacement of the coordination polymer chains. Based on experimental and theoretical evidence, we propose a new model for mechanical flexibility in 1D coordination polymers. Moreover, our calculations propose a cause of the different mechanical properties of this compound and a structurally similar elastic material.

| S-EPMC7155097 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data