Structures of disodium hydrogen citrate monohydrate, Na2HC6H5O7(H2O), and diammonium sodium citrate, (NH4)2NaC6H5O7, from powder diffraction data

The crystal structures of disodium hydrogen citrate monohydrate, Na2HC6H5O7(H2O), and diammonium sodium citrate, (NH4)2NaC6H5O7, have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. In NaHC6H5O7(H2O), the NaO6 coordination polyhedra share edges, forming zigzag layers lying parallel to the bc plane. The hydrophobic methylene groups occupy the interlayer spaces. The carboxylic acid group makes a strong charge-assisted hydrogen bond to the central carboxylate group. The hydroxyl group makes an intramolecular hydrogen bond to an ionized terminal carboxylate oxygen atom. Each hydrogen atom of the water molecule acts as a donor, to a terminal carboxylate and the hydroxyl group. Both the Na substructure and the hydrogen bonding differ from those of the known phase Na2HC6H5O7(H2O)1.5. In (NH4)2NaC6H5O7, the NaO6 coordination octahedra share corners, making double zigzag chains propagating along the b-axis direction. Each hydrogen atom of the ammonium ions acts as a donor in a discrete N—H...O hydrogen bond. The hydroxyl group forms an intramolecular O—H...O hydrogen bond to a terminal carboxylate oxygen atom.

Download Full-text

Structures of dipotassium rubidium citrate monohydrate, K2RbC6H5O7(H2O), and potassium dirubidium citrate monohydrate, KRb2C6H5O7(H2O), from laboratory X-ray powder diffraction data and DFT calculations

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989020011846 ◽

2020 ◽

Vol 76 (10) ◽

pp. 1566-1571

Author(s):

Andrew J. Cigler ◽

James A. Kaduk

Keyword(s):

Powder Diffraction ◽

Diffraction Data ◽

Metal Ion ◽

Density Functional ◽

Three Dimensional ◽

Hydroxyl Group ◽

Powder Diffraction Data ◽

Coordination Polyhedra ◽

X Ray ◽

Carboxylate Oxygen

The crystal structures of the isostructural compounds dipotassium rubidium citrate monohydrate, K2RbC6H5O7(H2O), and potassium dirubidium citrate monohydrate, KRb2C6H5O7(H2O), have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The compounds are isostructural to K3C6H5O7(H2O) and Rb3C6H5O7(H2O), but exhibit different degrees of ordering of the K and Rb cations over the three metal-ion sites. The K and Rb site occupancies correlate well to both the bond-valence sums and the DFT energies of ordered cation systems. The MO6 and MO7 coordination polyhedra share edges to form a three-dimensional framework. The water molecule acts as a donor in two strong charge-assisted O—H...O hydrogen bonds to carboxylate groups. The hydroxyl group of the citrate anion forms an intramolecular hydrogen bond to one of the central carboxylate oxygen atoms.

Download Full-text

Crystal structure of dilithium potassium citrate, Li2KC6H5O7 determined from powder diffraction data and DFT calculations

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989019002809 ◽

2019 ◽

Vol 75 (3) ◽

pp. 410-413 ◽

Cited By ~ 1

Author(s):

Andrew J. Cigler ◽

James A. Kaduk

Keyword(s):

Crystal Structure ◽

Powder Diffraction ◽

Diffraction Data ◽

Density Functional ◽

Potassium Citrate ◽

Hydroxyl Group ◽

Powder Diffraction Data ◽

Coordination Polyhedra ◽

Li Ion ◽

Citrate Anion

The crystal structure of poly[μ-citrato-dilithium(I)potassium(I)], [Li2K(C6H5O7)] n , has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The citrate anion triply chelates to the K+ cation through the hydroxyl group, the central carboxylate, and the terminal carboxylate. The KO7 coordination polyhedra share edges, forming chains parallel to the a axis. These chains share edges with one tetrahedral Li ion, and are bridged by edge-sharing pairs of the second tetrahedral Li ion, forming layers parallel to the ac plane.

Download Full-text

The crystal structure of sarmientite, Fe23+ (AsO4)(SO4)(OH)·5H2O, solved ab initio from laboratory powder diffraction data

Mineralogical Magazine ◽

10.1180/minmag.2014.078.2.08 ◽

2014 ◽

Vol 78 (2) ◽

pp. 347-360 ◽

Cited By ~ 3

Author(s):

F. Colombo ◽

J. Rius ◽

O. Vallcorba ◽

E. V. Pannunzio Miner

Keyword(s):

Crystal Structure ◽

Powder Diffraction ◽

Diffraction Data ◽

Rietveld Method ◽

Direct Methods ◽

Hydroxyl Group ◽

Monoclinic Space Group ◽

Powder Diffraction Data ◽

Patterson Function ◽

Unit Cell Dimensions

AbstractThe crystal structure of sarmientite, Fe23+ (AsO4)(SO4)(OH)·5H2O, from the type locality (Santa Elena mine, San Juan Province, Argentina), was solved and refined from in-house powder diffraction data (CuKα1,2 radiation). It is monoclinic, space group P21/n, with unit-cell dimensions a = 6.5298(1), b = 18.5228(4), c = 9.6344(3) Å, β = 97.444(2)º, V = 1155.5(5) Å3, and Z = 4. The structure model was derived from cluster-based Patterson-function direct methods and refined by means of the Rietveld method to Rwp = 0.0733 (X2 = 2.20). The structure consists of pairs of octahedral-tetrahedral (Fe−As) chains at (y,z) = (0,0) and (½,½), running along a. There are two symmetry-independent octahedral Fe sites. The Fe1 octahedra share two corners with the neighbouring arsenate groups. Both individual chains are related by a symmetry centre and joined by two symmetry-related Fe2 octahedra. Each Fe2 octahedron shares three corners with double-chain polyhedra (O3, O4 with arsenate groups; the O8 hydroxyl group with the Fe1 octahedron) and one corner (O11) with the monodentate sulfate group. The coordination of the Fe2 octahedron is completed by two H2O molecules (O9 and O10). There is also a complex network of H bonds that connects polyhedra within and among chains. Raman and infrared spectra show that (SO4)2− tetrahedra are strongly distorted.

Download Full-text

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

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989017000743 ◽

2017 ◽

Vol 73 (2) ◽

pp. 227-230 ◽

Cited By ~ 8

Author(s):

Alagappa Rammohan ◽

James A. Kaduk

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Powder Diffraction ◽

Diffraction Data ◽

Density Functional ◽

Three Dimensional ◽

Powder Diffraction Data ◽

Hydrogen Bond Donor ◽

X Ray ◽

Intramolecular Hydrogen

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 hydroxy group participates in an intramolecular hydrogen bond to the deprotonated central carboxylate group with graph-set motifS(5). The water molecule acts as a hydrogen-bond donor to both terminal and central carboxylate 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 hydrophobic methylene groups occupy channels along thebaxis.

Download Full-text

Crystal structure of prednicarbate, C27H36O8

Powder Diffraction ◽

10.1017/s0885715619000629 ◽

2019 ◽

Vol 34 (4) ◽

pp. 368-373 ◽

Cited By ~ 1

Author(s):

Zachary R. Butler ◽

James A. Kaduk ◽

Amy M. Gindhart ◽

Thomas N. Blanton

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Powder Diffraction ◽

Density Functional ◽

Ring System ◽

Hydroxyl Group ◽

Powder Diffraction Data ◽

Hydrogen Bond Donor ◽

Powder Diffraction File ◽

X Ray

The crystal structure of prednicarbate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Prednicarbate crystallizes in space group P212121 (#19) with a = 7.69990(3), b = 10.75725(3), c = 31.36008(11) Å, V = 2597.55(1) Å3, and Z = 4. In the crystal structure the long axis of the steroid ring system lies roughly parallel to the c-axis. The oxygenated side chains are orientated roughly perpendicular to the steroid ring system and are adjacent to each other, parallel to the ab-plane. The only traditional hydrogen bond donor in the prednicarbate molecule is the hydroxyl group O32–H33, but this does not participate in an O–H···O hydrogen bond. The nearest oxygen atoms to O32 are symmetry-related O32 at 4.495 Å, precluding the expected O–H···O hydrogen bond. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Download Full-text

Crystal structure of choline fenofibrate (Trilipix®), (C5H14NO) (C17H14ClO4)

Powder Diffraction ◽

10.1017/s0885715616000099 ◽

2016 ◽

Vol 31 (2) ◽

pp. 142-148

Author(s):

James A. Kaduk ◽

Kai Zhong ◽

Amy M. Gindhart ◽

Thomas N. Blanton

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Powder Diffraction ◽

Density Functional ◽

Hydroxyl Group ◽

Strong Hydrogen Bond ◽

Carboxylate Group ◽

Powder Diffraction Data ◽

Powder Diffraction File ◽

X Ray

The crystal structure of choline fenofibrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Choline fenofibrate crystallizes in space group Pbca (#61) with a = 12.341 03(2), b = 28.568 70(6), c = 12.025 62(2) Å, V = 4239.84(1) Å3, and Z = 8. The hydroxyl group of the choline anion makes a strong hydrogen bond to the ionized carboxylate group of the fenofibrate anion. Together with C–H···O hydrogen bonds, these link the cations and anions into layers parallel to the ac-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

Download Full-text

LiNaSiB3O7(OH) – novel structure of the new borosilicate mineral jadarite determined from laboratory powder diffraction data

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768107010130 ◽

2007 ◽

Vol 63 (3) ◽

pp. 396-401 ◽

Cited By ~ 5

Author(s):

Pamela S. Whitfield ◽

Yvon Le Page ◽

Joel D. Grice ◽

Chris J. Stanley ◽

Gary C. Jones ◽

...

Keyword(s):

Hydrogen Bond ◽

Ab Initio ◽

Rietveld Refinement ◽

Powder Diffraction ◽

Diffraction Data ◽

Laboratory Data ◽

Single Layer ◽

New Mineral ◽

Powder Diffraction Data ◽

Novel Structure

The structure of a new mineral jadarite, LiNaSiB3O7(OH) (IMA mineral 2006–36), has been determined by simulated annealing and Rietveld refinement of laboratory X-ray powder diffraction data. The structure contains a layer of corner-sharing, tetrahedrally coordinated Li, Si and B forming an unbranched vierer single layer, which is decorated with triangular BO3 groups. The Na ion is situated between the tetrahedral layers in a distorted octahedral site. As the very high boron content in this mineral makes obtaining neutron diffraction data very problematic, ab initio optimization using VASP was used to validate the structure and to better localize the H atom. The H atom is located on the apex of the triangular BO3 group and is involved in a weak intralayer hydrogen bond. The final Rietveld refinement agrees with the ab initio optimization with regard to a hydrogen bond between the H atom and one of the tetrahedral corner O atoms. The refined structure seems to be of a remarkably high quality given the complexity of the structure, the high proportion of very light elements and the fact that it was determined from relatively low-resolution laboratory data over a limited 2θ range (10–90° 2θ).

Download Full-text

Sodium dirubidium citrate, NaRb2C6H5O7, and sodium dirubidium citrate dihydrate, NaRb2C6H5O7(H2O)2

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989019003190 ◽

2019 ◽

Vol 75 (4) ◽

pp. 432-437 ◽

Cited By ~ 1

Author(s):

Andrew J. Cigler ◽

James A. Kaduk

Keyword(s):

Hydrogen Bond ◽

Hydrogen Atom ◽

Powder Diffraction ◽

Density Functional ◽

Three Dimensional ◽

Water Molecules ◽

Carboxylate Group ◽

Powder Diffraction Data ◽

X Ray ◽

Carboxylate Groups

The crystal structures of sodium dirubidium citrate {poly[μ-citrato-dirubidium(I)sodium(I)], [NaRb2(C6H5O7)] n } and sodium dirubidium citrate dihydrate {poly[diaqua(μ-citrato)dirubidium(I)sodium(I)], [NaRb2(C6H5O7)(H2O)2] n } have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. Both structures contain Na chains and Rb layers, which link to form different three-dimensional frameworks. In each structure, the citrate triply chelates to the Na+ cation. Each citrate also chelates to Rb+ cations. In the dihydrate structure, the water molecules are bonded to the Rb+ cations; the Na+ cation is coordinated only to citrate O atoms. Both structures contain an intramolecular O—H...O hydrogen bond between the hydroxy group and one of the terminal carboxylate groups. In the structure of the dihydrate, each hydrogen atom of the water molecules participates in a hydrogen bond to an ionized carboxylate group.

Download Full-text

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

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015000663 ◽

2015 ◽

Vol 71 (2) ◽

pp. 168-172 ◽

Cited By ~ 1

Author(s):

Atef Arfan ◽

Mwaffak Rukiah

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Crystal Structures ◽

Powder Diffraction ◽

Diffraction Data ◽

Crystal Packing ◽

Powder Diffraction Data ◽

X Ray ◽

Semicarbazide Hydrochloride

Crotonaldehyde semicarbazone {systematic name: (E)-2-[(E)-but-2-en-1-ylidene]hydrazinecarboxamide}, C5H9N3O, (I), and crotonaldehyde thiosemicarbazone {systematic name: (E)-2-[(E)-but-2-en-1-yldene]hydrazinecarbothioamide}, C5H9N3S, (II), show the sameEconformation around the imine C=N bond. Compounds (I) and (II) were obtained by the condensation of crotonaldehyde with semicarbazide hydrochloride and thiosemicarbazide, respectively. Each molecule has an intramolecular N—H...N hydrogen bond, which generates anS(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 thiosemicarbazide mean plane) is 9.12 (5)°. The crystal packing is different in the two compounds: in (I) intermolecular N—H...O hydrogen bonds link the molecules into layers parallel to thebcplane, while weak intermolecular N—H...S hydrogen bonds in (II) link the molecules into chains propagating in [110].

Download Full-text