Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data.

ABSTRACT: By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase. The anisotropic displacement parameters calculated from the MD simulations readily identified libration as the driving force behind the phase transition. Both the predicted crystal structure and the phase-transition mechanism were verified experimentally using TLS (translation, libration, screw) refinement against X-ray powder diffraction data.

SUBMITTER: van de Streek J

PROVIDER: S-EPMC6327187 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data.

van de Streek Jacco J Alig Edith E Parsons Simon S Vella-Zarb Liana L

IUCrJ 20190101 Pt 1

By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that ...[more]

PMID: 30713711

Similar Datasets

Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction

Project description:The structure of copper perchlorophthalocyanine (CuC32N8Cl16, Pigment Green 7) was solved from three-dimensional electron diffraction data (3D ED) and placed into the series of known copper phthalocyanine crystal structures. Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys.43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.

| S-EPMC8337017 | biostudies-literature

Crystal structure refinement of magnesium zinc divanadate, MgZnV<sub>2</sub>O<sub>7</sub>, from powder X-ray diffraction data.

Project description:The crystal structure of magnesium zinc divanadate, MgZnV2O7, was determined and refined from laboratory X-ray powder diffraction data. The title compound was synthesized by a solid-state reaction at 1023 K in air. The crystal structure is isotypic with Mn0.6Zn1.4V2O7 (C2/m; Z = 6) and is related to the crystal structure of thortveitite. The asymmetric unit contains two metal sites with statistically distributed magnesium and zinc atoms with the atomic ratio close to 1:1. One (Mg/Zn) metal site (M1) is located on Wyckoff position 8j and the other (M2) on 4h. Three V sites (all on 4i), and eight O (three 8j, four 4i, and one 2b) sites complete the asymmetric unit. The structure is an alternate stacking of V2O7 layers and (Mg/Zn) atom layers along [20]. It is distinct from other related structures in that each V2O7 layer consists of two groups: a V2O7 dimer and a V4O14 tetra-mer. Mixed-occupied M1 and M2 are coordinated by oxygen atoms in distorted trigonal bipyramidal and octa-hedral sites, respectively.

| S-EPMC8183434 | biostudies-literature

Crystal structures of two magnesium citrates from powder diffraction data.

Project description:The crystal structures of magnesium hydrogen citrate dihydrate, Mg(HC6H5O7)(H2O)2, (I), and bis-(di-hydrogen citrato)magnesium, Mg(H2C6H5O7)2, (II), have been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. In (I), the citrate anion occurs in the trans, trans-conformation, and triply chelates to the Mg cation. In (II), the citrate anion is trans, gauche, and doubly chelates to the Mg cation. In both compounds the Mg cation coordination polyhedron is an octa-hedron. In (I), the MgO6 coordination polyhedra are isolated, while in (II), they share edges to form chains. Strong O-H⋯O hydrogen bonds are prominent in the two structures, as well as in the previously reported magnesium citrate deca-hydrate.

| S-EPMC7534234 | biostudies-literature

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.

Project description:Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.

| S-EPMC5607859 | biostudies-literature

Crystal structure of Pigment Red 254 from X-ray powder diffraction data.

Project description:The crystal structure of Pigment Red 254 [P.R. 254, C18H10Cl2N2O2; systematic name: 3,6-bis-(4-chloro-phen-yl)-2,5-di-hydro-pyrrolo-[3,4-c]pyrrole-1,4-dione] was solved from laboratory X-ray powder diffraction data using the simulated annealing method followed by Rietveld refinement because the very low solubility of the pigment in all solvents impedes the growth of single crystals suitable for X-ray analysis. The mol-ecule lies across an inversion center. The dihedral angle between the benzene ring and the pyrrole ring in the unique part of the mol-ecule is 11.1 (2)°. In the crystal, mol-ecules are linked via N-H⋯O hydrogen bonds, forming chains along [110] incorporating R22(8) rings.

| S-EPMC5382609 | biostudies-literature

Cubic ZrW(1.75)Mo(0.25)O(8) from a Rietveld refinement based on neutron powder diffraction data.

Project description:The solid solution in the system Zr-Mo-W-O with composition ZrW(1.75)Mo(0.25)O(8) (zirconium tungsten molybdenum octa-oxide) was prepared by solid-state reactions as a polycrystalline material. Its structure has cubic symmetry (space group P2(1)3)?at room temperature. The structure contains a network of corner-sharing ZrO(6) octa-hedra (.3. symmetry) and MO(4) (M = W, Mo) tetra-hedra (.3. symmetry). Along the main threefold axis of the cubic unit cell, the MO(4) tetra-hedra are arranged in pairs forming M(2)O(8) units in which the M1O(4) tetra-hedra have larger distortions in terms of bond distances and angles than the M2O(4) tetra-hedra. These units are disordered over two possible orientations, with the M-O(terminal) vectors pointing to the [111] or [] directions. The reversal of the orientations of the M(2)O(8) units results from the concerted flips of these units. The time-averaged proportions of flipped and unflipped M(2)O(8) units were determined and the fraction of unflipped M(2)O(8) units is about 0.95. The order degree of the M(2)O(8) unit orientation is about 0.9. During the reversal process, the M-atom site has a migration about 0.93?Å, one of the O-atom sites has a 0.25?Å migration distance, whereas two other O-atom sites migrate marginally (? 0.08?Å). The results prove the constraint strategy to be a reasonable approach based on the ratcheting mechanism.

| S-EPMC2977542 | biostudies-literature

Modelling dynamics in protein crystal structures by ensemble refinement.

Project description:Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation-libration-screw (TLS) model. Modeling of 20 protein datasets at 1.1-3.1 Å resolution reduced cross-validated R(free) values by 0.3-4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a 'molten core' likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order-disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure-dynamics-function relationships.DOI:http://dx.doi.org/10.7554/eLife.00311.001.

| S-EPMC3524795 | biostudies-literature

Crystal structures of crotonaldehyde semicarbazone and crotonaldehyde thiosemicarbazone from X-ray powder diffraction data.

Project description:Crotonaldehyde semicarbazone {systematic name: (E)-2-[(E)-but-2-en-1-yl-idene]hydrazinecarboxamide}, C5H9N3O, (I), and crotonaldehyde thio-semi-carba-zone {systematic name: (E)-2-[(E)-but-2-en-1-yldene]hydra-zinecarbo--thio-amide}, C5H9N3S, (II), show the same E conformation around the imine C=N bond. Compounds (I) and (II) were obtained by the condensation of crotonaldehyde with semicarbazide hydro-chloride and thio-semicarbazide, respectively. Each mol-ecule has an intra-molecular N-H⋯N hydrogen bond, which generates an S(5) ring. In (I), the crotonaldehyde fragment is twisted by 2.59 (5)° from the semicarbazide mean plane, while in (II) the corresponding angle (with the thio-semicarbazide mean plane) is 9.12 (5)°. The crystal packing is different in the two compounds: in (I) inter-molecular N-H⋯O hydrogen bonds link the mol-ecules into layers parallel to the bc plane, while weak inter-molecular N-H⋯S hydrogen bonds in (II) link the mol-ecules into chains propagating in [110].

| S-EPMC4384554 | biostudies-literature

Crystal structures of spinel-type Na2MoO4 and Na2WO4 revisited using neutron powder diffraction.

Project description:Time-of-flight neutron powder diffraction data have been collected from Na2MoO4 and Na2WO4 to a resolution of sin?(?)/? = 1.25?Å(-1), which is substanti-ally better than the previous analyses using Mo K? 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.

| S-EPMC4459306 | biostudies-other

Exploring ligand dynamics in protein crystal structures with ensemble refinement.

Project description:Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.

| S-EPMC8329865 | 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