scholarly journals Crystal structure of aqua(citric acid)(hydrogen citrato)calcium monohydrate, [Ca(HC6H5O7)(H3C6H5O7)(H2O)]·H2O, from synchrotron X-ray powder data, and DFT-optimized crystal structure of existing calcium hydrogen citrate trihydrate, [Ca(HC6H5O7)(H2O)3]

2020 ◽  
Vol 76 (10) ◽  
pp. 1689-1693
Author(s):  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Citric Acid ◽  
Density Functional ◽  
Dft Calculation ◽  
The Other ◽  
Powder Diffraction Data ◽  
Hydrogen Atoms ◽  
Acta Cryst ◽  
Coordination Polyhedra ◽  
X Ray

The crystal structure of `aquabis(dihydrogen citrato)calcium hydrate', better formulated as aqua(citric acid)(hydrogen citrato)calcium monohydrate, (I), has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. The CaO8 coordination polyhedra are isolated, but occur in layers parallel to the ab plane. Both the Rietveld-refined and DFT-optimized structures indicate that one citrate is doubly ionized and that the other is citric acid. All of the active hydrogen atoms participate in strong (11–16 kcal mol−1) hydrogen bonds. Hydrogen atoms were added to the existing calcium hydrogen citrate trihydrate structure [Sheldrick (1974). Acta Cryst. B30, 2056–2057; CSD refcode: CAHCIT], (II), and a DFT calculation was carried out to assess the hydrogen bonding and compare it to this optimized structure.

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

2016 ◽  
Vol 72 (8) ◽  
pp. 1159-1162 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Three Dimensional ◽  
Carboxylate Group ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Graph Set

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 [KOn] coordination polyhedra share edges and corners to form a three-dimensional framework, with channels running parallel to thecaxis. The only hydrogen bond is an intramolecular one involving the hydroxy group and the central carboxylate group, with graph-set motifS(5).

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

2017 ◽  
Vol 73 (2) ◽  
pp. 250-253 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Three Dimensional ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Methylene Groups ◽  
Graph Set

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 intramolecular one between the hydroxy group and the central carboxylate, with graph setS(5). The hydrophobic methylene groups lie in pockets in the framework.

Crystal structure of strontium hydrogen citrate monohydrate, Sr(HC6H5O7)(H2O)

2021 ◽  
pp. 1-9
Author(s):  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Water Molecules ◽  
Powder Diffraction Data ◽  
Unknown Compound ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Carboxylic Acid Groups ◽  
Triclinic Unit Cell

The crystal structure of strontium hydrogen citrate monohydrate has been solved using laboratory X-ray powder diffraction data, refined using both laboratory and synchrotron data, and optimized using density functional techniques. Strontium hydrogen citrate monohydrate crystallizes in space group C2/c (#15) with a = 25.15601(17), b = 10.90724(6), c = 6.37341(4) Å, β = 91.9846(6)°, V = 1747.704(12) Å3, and Z = 8. The Sr coordination and the hydrogen bonding result in a layered structure. The SrO8 coordination polyhedra share edges to form corrugated layers parallel to the bc-plane. Hydrogen bonds between the carboxylic acid groups and water molecules link the layers. Intermolecular hydroxyl–carboxyl hydrogen bonds also link the layers in a ring pattern with a graph set symbol R2,2(12). After storage for 2 years, partial re-crystallization occurred, to an as-yet unknown compound with a triclinic unit cell.

scholarly journals A second polymorph of sodium dihydrogen citrate, NaH2C6H5O7: structure solution from powder diffraction data and DFT comparison

2016 ◽  
Vol 72 (6) ◽  
pp. 854-857 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Commercial Sample ◽  
Acta Cryst ◽  
Coordination Polyhedra ◽  
Structure Solution ◽  
Sodium Dihydrogen

The crystal structure of a second polymorph of sodium dihydrogen 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 [Gluskeret al.(1965).Acta Cryst.19, 561–572; refcode NAHCIT]. In this polymorph, the [NaO7] coordination polyhedra form edge-sharing chains propagating along theaaxis, while in NAHCIT the octahedral [NaO6] groups form edge-sharing pairs bridged by two hydroxy groups. The most notable difference is that in this polymorph one of the terminal carboxyl groups is deprotonated, while in NAHCIT the central carboxylate group is deprotonated, as is more typical.

Accurate unrestrained DDM refinement of crystal structures from highly distorted and low-resolution powder diffraction data

2016 ◽  
Vol 72 (5) ◽  
pp. 738-743 ◽  
Author(s):  
Leonid A. Solovyov
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Acta Cryst ◽  
Functional Theory ◽  
Interatomic Distances ◽  
X Ray ◽  
Anisotropic Displacement Parameters ◽  
Xrpd Pattern

The structure of benzene:ethane co-crystal at 90 K is refined with anisotropic displacement parameters without geometric restraints from high-resolution synchrotron X-ray powder diffraction (XRPD) data using the derivative difference method (DDM) with properly chosen weighting schemes. The average C—C bond precision achieved is 0.005 Å and the H-atom positions in ethane are refined independently. A new DDM weighting scheme is introduced that compensates for big distortions of experimental data. The results are compared with density functional theory (DFT) calculations reported by Maynard-Caselyet al.[(2016).IUCrJ,3, 192–199] where a rigid-body Rietveld refinement was also applied to the same dataset due to severe distortions of the powder pattern attributable to experimental peculiarities. For the crystal structure of 2-aminopyridinium fumarate–fumaric acid formerly refined applying 77 geometric restraints by Donget al.[(2013).Acta Cryst.C69, 896–900], an unrestrained DDM refinement using the same XRPD pattern surprisingly gave two times narrower dispersion of interatomic distances.

scholarly journals Crystal structure of caesium dihydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison

2017 ◽  
Vol 73 (2) ◽  
pp. 133-136 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Helical Chain ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Different Types

The crystal structure of caesium dihydrogen 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 thea-axis. These chains are linked by corners along thec-axis. The un-ionized carboxylic acid groups form two different types of hydrogen bonds; one forms a helical chain along thec-axis, and the other is discrete. The hydroxy group participates in both intra- and intermolecular hydrogen bonds.

Reinterpretation of the monohydrate of clarithromycin from X-ray powder diffraction data as a trihydrate

2012 ◽  
Vol 68 (9) ◽  
pp. o369-o372 ◽  
Author(s):  
Jacco van de Streek
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Original Data ◽  
Water Molecules ◽  
Powder Diffraction Data ◽  
Acta Cryst ◽  
X Ray

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst.(2012), E68, o667–o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X-ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules. After successful location of the two additional water molecules, the Rietveld refinement still showed minor problems. These were resolved by noticing that one of the chiral centres in the molecule had been inverted. The corrected crystal structure of clarithromycin trihydrate, refined against the original data, is now reported. Dispersion-corrected density functional theory calculations were used to check the final crystal structure and to position the H atoms.

Powder X-ray diffraction data for dimethylarsinic acid, (CH3)2AsO(OH)

2021 ◽  
pp. 1-6
Author(s):  
Joel W. Reid
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Density Functional ◽  
Dimethylarsinic Acid ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Functional Theory ◽  
X Ray ◽  
Synchrotron Powder Diffraction

Synchrotron powder diffraction data is presented for the monoclinic polymorph of dimethylarsinic acid, (CH3)2AsO(OH) (DMAV). Rietveld refinement with GSASII yielded lattice parameters of a = 15.9264(15) Å, b = 6.53999(8) Å, c = 11.3401(9) Å, and β = 125.8546(17)° (Z = 8, space group C2/c). The Rietveld-refined structure was compared with both a density functional theory (DFT)-optimized structure and the published, low-temperature single-crystal structure, and all three structures exhibited excellent agreement. The triclinic polymorph of DMAV was also DFT optimized with CRYSTAL17 to determine the positions of the hydrogen atoms. Monoclinic DMAV forms zigzag chains parallel to the b-axis with adjacent DMAV molecules connected by an O–H⋯O bond, whereas triclinic DMAV forms dimers connected by two O–H⋯O bonds.

Crystal structures of tricalcium citrates

2018 ◽  
Vol 33 (2) ◽  
pp. 98-107 ◽  
Author(s):  
James A. Kaduk
Keyword(s):  
Crystal Structures ◽  
Density Functional ◽  
Three Dimensional ◽  
Water Molecules ◽  
Calcium Citrate ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Calcium Supplements ◽  
Dimensional Network

The crystal structures of calcium citrate hexahydrate, calcium citrate tetrahydrate, and anhydrous calcium citrate have been solved using laboratory and synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Both the hexahydrate and tetrahydrate structures are characterized by layers of edge-sharing Ca coordination polyhedra, including triply chelated Ca. An additional isolated Ca is coordinated by water molecules, and two uncoordinated water molecules occur in the hexahydrate structure. The previously reported polymorph of the tetrahydrate contains the same layers, but only two H2O coordinated to the isolated Ca and two uncoordinated water molecules. Anhydrous calcium citrate has a three-dimensional network structure of Ca coordination polyhedra. The new polymorph of calcium citrate tetrahydrate is the major crystalline phase in several commercial calcium supplements.

Crystal structure of bretylium tosylate (Bretylol®), C18H24BrNO3S

2018 ◽  
Vol 33 (4) ◽  
pp. 298-302
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
X Ray ◽  
Polar Interactions ◽  
Normal Hydrogen

The crystal structure of bretylium tosylate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Bretylium tosylate crystallizes in space group C2/c (#15) with a = 32.6238(4), b = 12.40353(14), c = 9.93864(12) Å, β = 101.4676(10), V = 3941.39(5) Å3, and Z = 8. The sample exhibited visible decomposition in the X-ray beam. The unusual displacement ellipsoid of the Br atom probably indicates that the decomposition in the beam involves the Br atom. The crystal structure can be viewed as layered parallel to the bc plane. The layers are double, the center consisting of the cation/anion polar interactions and the outer surface of the double layers consists of hydrocarbon interactions. In the absence of normal hydrogen bond donors, the only hydrogen bonds in the bretylium tosylate structure are C–H…O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

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