Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystal structure of dicesium hydrogen citrate from laboratory single-crystal and powder X-ray diffraction data and DFT comparison.

ABSTRACT: The crystal structure of dicesium hydrogen citrate, 2Cs⁺·C₆H₆O₇^2-, has been solved using laboratory X-ray single-crystal diffraction data, refined using laboratory powder X-ray data, and optimized using density functional techniques. The Cs⁺ cation is nine-coordinate, with a bond-valence sum of 0.92 valence units. The CsO₉ coordination polyhedra share edges and corners to form a three-dimensional framework. The citrate anion is located on a mirror plane. Its central hy-droxy/carboxyl-ate O-H?O hydrogen bond is short, and (unusually) inter-molecular. The centrosymmetric end-end carboxyl-ate hydrogen bond is exceptionally short (O?O = 2.416?Å) and strong. These hydrogen bonds contribute 16.5 and 21.7 kcal mol^-1, respectively, to the crystal energy. The hydro-phobic methyl-ene groups occupy pockets in the framework.

SUBMITTER: Rammohan A

PROVIDER: S-EPMC5290572 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystal structure of dicesium hydrogen citrate from laboratory single-crystal and powder X-ray diffraction data and DFT comparison.

Rammohan Alagappa A Sarjeant Amy A AA Kaduk James A JA

Acta crystallographica. Section E, Crystallographic communications 20170120 Pt 2

The crystal structure of dicesium hydrogen citrate, 2Cs+·C6H6O72-, has been solved using laboratory X-ray single-crystal diffraction data, refined using laboratory powder X-ray data, and optimized using density functional techniques. The Cs+ cation is nine-coordinate, with a bond-valence sum of 0.92 valence units. The CsO9 coordination polyhedra share edges and corners to form a three-dimensional framework. The citrate ...[more]

PMID: 28217349

Similar Datasets

Crystal structure of dirubidium hydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of dirubidium hydrogen citrate, 2Rb+·HC6H5O72-, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The un-ionized carb-oxy-lic acid group forms helical chains of very strong hydrogen bonds (O⋯O ∼ 2.42 Å) along the b axis. The hy-droxy group participates in a chain of intra- and inter-molecular hydrogen bonds along the c axis. These hydrogen bonds result in corrugated hydrogen-bonded layers in the bc plane. The Rb+ cations are six-coordinate, and share edges and corners to form layers in the ab plane. The inter-layer contacts are composed of the hydro-phobic methyl-ene groups.

| S-EPMC5209781 | biostudies-literature

Crystal structure of caesium di-hydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of caesium di-hydrogen citrate, Cs+·H2C6H5O7-, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The coordination polyhedra of the nine-coordinate Cs+ cations share edges to form chains along the a-axis. These chains are linked by corners along the c-axis. The un-ionized carb-oxy-lic acid groups form two different types of hydrogen bonds; one forms a helical chain along the c-axis, and the other is discrete. The hy-droxy group participates in both intra- and inter-molecular hydrogen bonds.

| S-EPMC5290550 | biostudies-literature

Crystal structure of trirubidium citrate from laboratory X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of trirubidium citrate, 3Rb+·C6H5O73-, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb+ cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra-molecular one between the hy-droxy group and the central carboxyl-ate, with graph set S(5). The hydro-phobic methyl-ene groups lie in pockets in the framework.

| S-EPMC5290576 | biostudies-literature

Crystal structure of anhydrous tripotassium citrate from laboratory X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of anhydrous tripotassium citrate, [K3(C6H5O7)] n , has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The three unique potassium cations are 6-, 8-, and 6-coordinate (all irregular). The [KO n ] coordination polyhedra share edges and corners to form a three-dimensional framework, with channels running parallel to the c axis. The only hydrogen bond is an intra-molecular one involving the hy-droxy group and the central carboxyl-ate group, with graph-set motif S(5).

| S-EPMC4971862 | biostudies-literature

Crystal structure of trirubidium citrate monohydrate from laboratory X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of the title compound, 3Rb+·C6H5O73-·H2O, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The hy-droxy group participates in an intra-molecular hydrogen bond to the deprotonated central carboxyl-ate group with graph-set motif S(5). The water mol-ecule acts as a hydrogen-bond donor to both terminal and central carboxyl-ate O atoms. The three independent rubidium cations are seven-, six- and six-coordinate, with bond-valence sums of 0.84, 1.02, and 0.95, respectively. In the extended structure, their polyhedra share edges and corners to form a three-dimensional network. The hydro-phobic methyl-ene groups occupy channels along the b axis.

| S-EPMC5290571 | biostudies-literature

Crystal structure of penta-sodium hydrogen dicitrate from synchrotron X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of penta-sodium hydrogen dicitrate, Na5H(C6H5O7)2, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Each of the two independent citrate anions is joined into a dimer by very strong centrosymmetric O-H⋯O hydrogen bonds, with O⋯O distances of 2.419 and 2.409 Å. Four octa-hedrally coordinated Na+ ions share edges to form open layers parallel to the ab plane. A fifth Na+ ion in trigonal-bipyramidal coordination shares faces with NaO6 octahedra on both sides of these layers.

| S-EPMC5290583 | 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

Crystal structure of calcium perchlorate anhydrate, Ca(ClO4)2, from laboratory powder X-ray diffraction data.

Project description:The crystal structure of calcium perchlorate anhydrate was determined from laboratory X-ray powder diffraction data. The title compound was obtained by heating hydrated calcium perchlorate [Ca(ClO4)2·xH2O] at 623?K in air for 12?h. It crystallizes in the ortho-rhom-bic space group Pbca and is isotypic with Ca(AlD4)2. The asymmetric unit contains one Ca, two Cl and eight O sites, all on general sites (Wyckoff position 8c). The crystal structure consists of isolated ClO4- tetra-hedra and Ca2+ cations. The Ca2+ cation is coordinated by eight O atoms of eight symmetry-related ClO4- tetra-hedra within a distorted square-anti-prismatic environment.

| S-EPMC5946979 | biostudies-literature

Crystal structures of eight mono-methyl alkanes (C26-C32) via single-crystal and powder diffraction and DFT-D optimization.

Project description: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.

| S-EPMC4547817 | biostudies-other

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

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