Omadacycline dihydrate, C29H40N4O7·2H2O, from X-ray powder diffraction data.

The crystal structure of the title compound {systematic name: (4S,4aS,5aR,12aR)-4,7-bis-(di-methyl-amino)-9-[(2,2-di-methyl-propyl-amino)-meth-yl]-1,10,11,12a-tetra-hydroxy-3,12-dioxo-4a,5,5a,6-tetra-hydro-4H-tetra-cene-2-carb-oxamide dihydrate, C29H40N4O7·2H2O} has been solved and refined using synchrotron X-ray powder diffraction data: it crystallizes in space group R3 with a = 24.34430 (7), c = 14.55212 (4) Å, V = 7468.81 (2) Å3 and Z = 9. Most of the hydrogen bonds are intra-molecular, but two classical N-H⋯O inter-molecular hydrogen bonds (along with probable weak C-H⋯O and C-H⋯N hydrogen bonds) link the mol-ecules into a three-dimensional framework. The framework contains voids, which contain disordered water mol-ecules. Keto-enol tautomerism is apparently important in this mol-ecule, and the exact mol-ecular structure is ambiguous.

An Improved Model for Biogenic Ammonium Urate.

The pathological crystallization of ammonium urate inside the urinary tract is a well-documented medical condition; however, structural studies of the biogenic material have proven challenging owing to its propensity to precipitate as a powder and to exhibit diffraction patterns with widely varying intensities. Using block Rietveld refinement methods of powder diffraction data, here we identify ammonium urate hydrate (AUH) as a likely component in natural uroliths. AUH has a planar 2-D hydrogen-bonded organic framework of urate ions separated by ammonium ions with water molecules residing in bisecting channels. AUH is stable up to 150 °C for short time periods but begins to decompose with prolonged heating times and/or at higher temperatures. Changes in the solid-state structure and composition of synthetic material over a temperature range from 25 to 300 °C are elucidated through thermogravimetric and spectroscopic data, combustion analysis, and time-resolved synchrotron powder X-ray diffraction studies. We contend that biogenic ammonium urate is more accurately modeled as a mixture of AUH and anhydrous ammonium urate, in ratios that can vary depending on the growth environment. The similar but not identical diffraction patterns of these two forms likely account for much of the variability seen in natural ammonium urate samples.

Organo-Functionalized Lacunary Double Cubane-Type Oxometallates: Synthesis, Structure, and Properties of [(MII Cl)2 (VIV O)2 {((HOCH2 CH2 )(H)N(CH2 CH2 O))(HN(CH2 CH2 O)2 )}2 ] (M=Co, Zn).

Organofunctionalized tetranuclear clusters [(MII Cl)2 (VIV O)2 {((HOCH2 CH2 )(H)N(CH2 CH2 O))(HN(CH2 CH2 O)2 )}2 ] (1, M=Co, 2: M=Zn) containing an unprecedented oxometallacyclic {M2 V2 Cl2 N4 O8 } (M=Co, Zn) framework have been prepared by solvothermal reactions. The new oxo-alkoxide compounds were fully characterized by spectroscopic methods, magnetic susceptibility measurement, DFT and ab initio computational methods, and complete single-crystal X-ray diffraction structure analysis. The isostructural clusters are formed of edge-sharing octahedral {VO5 N} and trigonal bipyramidal {MO3 NCl} units. Diethanolamine ligates the bimetallic lacunary double cubane core of 1 and 2 in an unusual two-mode fashion, unobserved previously. In the crystalline state, the clusters of 1 and 2 are joined by hydrogen bonds to form a three-dimensional network structure. Magnetic susceptibility data indicate weakly antiferromagnetic interactions between the vanadium centers [Jiso (VIV -VIV )=-5.4(1); -3.9(2) cm-1 ], and inequivalent antiferromagnetic interactions between the cobalt and vanadium centers [Jiso (VIV -CoII )=-12.6 and -7.5 cm-1 ] contained in 1.

Crystal structure of 2,5-di-hydroxy-terephthalic acid from powder diffraction data.

The crystal structure of anhydrous 2,5-dhy-droxy-terephthalic acid, C8H6O6, was solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The published structure of 2,5-di-hydroxy-terephthalic acid dihydrate was also optimized. The carb-oxy-lic acid groups form strong hydrogen bonds, which form centrosymmetric rings with graph set R 2 2(8). These hydrogen bonds link the mol-ecules into chains along [011]. There is an intra-molecular O-H⋯O hydrogen bond between the hydroxyl group and the carbonyl group of the carb-oxy-lic acid. The hydrogen bonding in the dihydrate is very different. Although the intra-molecular hy-droxy/carb-oxy-lic acid hydrogen bond is present, the water mol-ecule acts as an acceptor to the carb-oxy-lic acid and a donor to two other oxygen atoms. The carb-oxy-lic acid groups do not inter-act with each other directly.

Structures of dicobalt and dinickel 4,4'-bi-phenyldi-carboxyl-ate di-hydroxide, M 2(O2CC6H4C6H4CO2)(OH)2, M = Co and Ni, and di-ammonium 4,4'-bi-phenyldi-carboxyl-ate from powder diffraction data.

The triclinic structures of poly[(µ4-4,4'-bi-phenyldi-carboxyl-ato)di-µ-hydroxido-dicobalt], [Co2(C14H8O4)(OH)2] n , and poly[(µ4-4,4'-bi-phenyldi-carboxyl-ato)di-µ-hydroxido-dinickel], [Ni2(C14H8O4)(OH)2] n , were established using laboratory X-ray powder diffraction data. These structures, as well as that of poly[(µ4-4,4'-bi-phenyldi-carboxyl-ato)di-µ-hydroxido-dimanganese], [Mn2(C14H8O4)(OH)2] n , were optimized using density functional techniques. The structure of di-ammonium 4,4'-bi-phenyldi-carboxyl-ate, 2NH4 +·C14H8O4 2-, was also solved using laboratory powder data. The Mn and Co compounds are isostructural: the octa-hedral MO6 groups share edges to form chains running parallel to the c-axis. These chains share corners (OH groups) to link into layers lying parallel to the bc plane. The hydroxyl groups do not participate in hydrogen bonds. The structure of (NH4)2BPDC consists of alternating layers of BPDC and ammonium ions lying parallel to the ab plane. Each hydrogen atom of the ammonium ions in (NH4)2BPDC participates in a strong N-H⋯O hydrogen bond.

Crystal structures of dimetal terephthalate di-hydroxides, M 2(C8H4O4)(OH)2 (M = Co, Ni, Zn) from powder diffraction data and DFT calculations.

The crystal structure of poly[di-hydroxido(µ6-terepthalato)dizinc], [Zn2(C8H4O4)(OH)2] n , was solved and refined using synchrotron powder data, and the structures of the isostructural Co and Ni analogues were refined using laboratory powder X-ray data. The structure of [Co2(C8H4O4)(OH)2] n has been reported previously in space group C2/m, which yields disordered terephthalate anions. Doubling the c-axis of that cell results in an ordered model in space group C2/c. The octa-hedral MO6 coordination polyhedra of the metal cations share edges, forming chains running parallel to the b-axis direction. These chains share corners (hydroxyl groups), forming layers lying perpendicular to the a-axis direction.

Cynarine monohydrate from synchrotron powder X-ray diffraction data.

The crystal structure of cynarine monohydrate (systematic name: 1,3-bis{[(E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid monohydrate), C25H24O12·H2O, has been solved and refined using synchrotron powder X-ray diffraction data, and optimized using density functional techniques. Despite being purchased as anhydrous, cynarine crystallizes as a monohydrate and the crystal structure is characterized by alternating layers of hydrocarbon and hydrogen-bonding interactions parallel to the bc plane. Hydrogen bonds are significant in the crystal structure. The carboxylic acid group forms a strong intermolecular hydrogen bond to a hydroxy group of the quinic acid ring. Most of the hydroxy groups act as donors in O-H...O hydrogen bonding to carbonyl O atoms. One hydroxy group participates in bifurcated hydrogen bonds, one to a hydroxy group on the quinic acid ring and the other, an intramolecular interaction, to another hydroxy group. The powder pattern has been submitted to the International Centre for Diffraction Data (ICDD) for inclusion in the Powder Diffraction File (PDF-4).

Psilocybin: crystal structure solutions enable phase analysis of prior art and recently patented examples.

Psilocybin {systematic name: 3-[2-(dimethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate} is a zwitterionic tryptamine natural product found in numerous species of fungi known for their psychoactive properties. Following its structural elucidation and chemical synthesis in 1959, purified synthetic psilocybin has been evaluated in clinical trials and has shown promise in the treatment of various mental health disorders. In a recent process-scale crystallization investigation, three crystalline forms of psilocybin were repeatedly observed: Hydrate A, Polymorph A, and Polymorph B. The crystal structure for Hydrate A was solved previously by single-crystal X-ray diffraction. This article presents new crystal structure solutions for the two anhydrates, Polymorphs A and B, based on Rietveld refinement using laboratory and synchrotron X-ray diffraction data, and density functional theory (DFT) calculations. Utilizing the three solved structures, an investigation was conducted via Rietveld method (RM) based quantitative phase analysis (QPA) to estimate the contribution of the three different forms in powder X-ray diffraction (PXRD) patterns provided by different sources of bulk psilocybin produced between 1963 and 2021. Over the last 57 years, each of these samples quantitatively reflect one or more of the hydrate and anhydrate polymorphs. In addition to quantitatively evaluating the composition of each sample, this article evaluates correlations between the crystal forms present, corresponding process methods, sample age, and storage conditions. Furthermore, revision is recommended on characterizations in recently granted patents that include descriptions of crystalline psilocybin inappropriately reported as a single-phase `isostructural variant.' Rietveld refinement demonstrated that the claimed material was composed of approximately 81% Polymorph A and 19% Polymorph B, both of which have been identified in historical samples. In this article, we show conclusively that all published data can be explained in terms of three well-defined forms of psilocybin and that no additional forms are needed to explain the diffraction patterns.

Tribarium dicitrate penta-hydrate, [Ba3(C6H5O7)2(H2O)4]·H2O.

The crystal structure of tribarium dicitrate penta-hydrate, [Ba3(C6H5O7)2(H2O)4]·H2O, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. The BaO9 and BaO10 coordination polyhedra share edges and corners to form a three-dimensional network. All of the active hydrogen atoms act as donors in O-H⋯O hydrogen bonds. Most of the acceptors are carboxyl-ate oxygen atoms, but there are also water⋯water hydrogen bonds. Both of the citrate hydroxyl groups form intra-molecular O-H⋯O hydrogen bonds to terminal carboxyl groups.

Lithium dipotassium citrate monohydrate, LiK2C6H5O7(H2O).

The crystal structure of dilithium potassium citrate monohydrate, Li+·2K+·C6H5O7 3-·H2O or LiK2C6H5O7·H2O, has been solved by direct methods and refined against laboratory X-ray powder diffraction data, and optimized using density functional techniques. The complete citrate trianion is generated by a crystallographic mirror plane, with two C and three O atoms lying on the reflecting plane, and chelates to three different K cations. The KO8 and LiO4 coordination polyhedra share edges and corners to form layers lying parallel to the ac plane. An intra-molecular O-H⋯O hydrogen bond occurs between the hydroxyl group and the central carboxyl-ate group of the citrate anion as well as a charge-assisted inter-molecular O-H⋯O link between the water mol-ecule and the terminal carboxyl-ate group. There is also a weak C-H⋯O hydrogen bond.

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.

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 mol-ecule acts as a donor in two strong charge-assisted O-H⋯O hydrogen bonds to carboxyl-ate groups. The hydroxyl group of the citrate anion forms an intra-molecular hydrogen bond to one of the central carboxyl-ate oxygen atoms.

Structures of disodium hydrogen citrate mono-hydrate, Na2HC6H5O7(H2O), and di-ammonium sodium citrate, (NH4)2NaC6H5O7, from powder diffraction data.

The crystal structures of disodium hydrogen citrate monohydrate, Na2HC6H5O7(H2O), and di-ammonium 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 hydro-phobic methyl-ene groups occupy the inter-layer spaces. The carb-oxy-lic acid group makes a strong charge-assisted hydrogen bond to the central carboxyl-ate group. The hydroxyl group makes an intra-molecular hydrogen bond to an ionized terminal carboxyl-ate oxygen atom. Each hydrogen atom of the water mol-ecule acts as a donor, to a terminal carboxyl-ate 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 octa-hedra 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 intra-molecular O-H⋯O hydrogen bond to a terminal carboxyl-ate oxygen atom.

Crystal structures of two magnesium citrates from powder diffraction data.

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.

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].

The crystal structure of 'aquabis-(di-hydrogen 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.

Crystal structures of two isostructural compounds: a second polymorph of dipotassium hydrogen citrate, K2HC6H5O7, and potassium rubidium hydrogen citrate, KRbHC6H5O7.

The crystal structures of a new polymorph of dipotassium hydrogen citrate, 2K+·HC6H5O72-, and potassium rubidium hydrogen citrate, K+·Rb+·HC6H5O72-, have been solved and refined using laboratory powder X-ray diffraction and optimized using density functional techniques. In the new polymorph of the dipotassium salt, KO7 and KO8 coordination polyhedra share corners and edges to form a three-dimensional framework with channels parallel to the a axis and [111]. The hydrophobic methylene groups face each other in the channels. The un-ionized carboxylic acid group forms a strong charge-assisted hydrogen bond to the central ionized carboxylate group. The hydroxy group forms an intermolecular hydrogen bond to a different central carboxylate group. In the potassium rubidium salt, the K+ and Rb+ cations are disordered over two sites, in approximately 0.72:0.28 and 0.28:0.72 ratios. KO8 and RbO9 coordination polyhedra share corners and edges to form a three-dimensional framework with channels parallel to the a axis. The un-ionized carboxylic acid group forms a strong charge-assisted hydrogen bond to an ionized carboxylate group. The hydroxy group forms an intermolecular hydrogen bond to the central carboxylate group. Density functional theory (DFT) calculations on the ordered cation structures suggest that interchange of K+ and Rb+ at the two cation sites changes the energy insignificantly.

Di-ammonium potassium citrate, (NH4)2KC6H5O7.

The crystal structure of di-ammonium potassium citrate, 2NH4 +·K+·C6H5O7 3-, has been solved and refined using laboratory X-ray powder diffraction data and optimized using density functional theory. The KO7 coordination polyhedra are isolated. The ammonium cations and the hydro-phobic methyl-ene sides of the citrate anions occupy the spaces between the coordination polyhedra. Each hydrogen atom of the ammonium ions acts as a donor in a charge-assisted N-H⋯O, N-H⋯(O,O) or N-H⋯(O,O,O) hydrogen bond. There is an intra-molecular O-H⋯O hydrogen bond in the citrate anion between the hydroxide group and one of the terminal carboxyl-ate groups.

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

The crystal structures of sodium dirubidium citrate {poly[µ-citrato-dirubi-dium(I)sodium(I)], [NaRb2(C6H5O7)] n } and sodium dirubidium citrate dihydrate {poly[di-aqua-(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 mol-ecules are bonded to the Rb+ cations; the Na+ cation is coordinated only to citrate O atoms. Both structures contain an intra-molecular O-H⋯O hydrogen bond between the hy-droxy group and one of the terminal carboxyl-ate groups. In the structure of the dihydrate, each hydrogen atom of the water mol-ecules participates in a hydrogen bond to an ionized carboxyl-ate group.

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

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 carboxyl-ate, and the terminal carboxyl-ate. The KO7 coordination polyhedra share edges, forming chains parallel to the a axis. These chains share edges with one tetra-hedral Li ion, and are bridged by edge-sharing pairs of the second tetra-hedral Li ion, forming layers parallel to the ac plane.

Sodium rubidium hydrogen citrate, NaRbHC6H5O7, and sodium caesium hydrogen citrate, NaCsHC6H5O7: crystal structures and DFT comparisons.

The crystal structure of sodium rubidium hydrogen citrate, NaRbHC6H5O7 or [NaRb(C6H6O7)] n , has been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. This compound is isostructural to NaKHC6H5O7. The Na atom is six-coordinate, with a bond-valence sum of 1.16. The Rb atom is eight-coordinate, with a bond-valence sum of 1.17. The distorted [NaO6] octa-hedra share edges to form chains along the a-axis direction. The irregular [RbO8] coordination polyhedra share edges with the [NaO6] octa-hedra on either side of the chain, and share corners with other Rb atoms, resulting in triple chains along the a-axis direction. The most prominent feature of the structure is the chain along [111] of very short, very strong hydrogen bonds; the O⋯O distances are 2.426 and 2.398 Å. The Mulliken overlap populations in these hydrogen bonds are 0.140 and 0.143 electrons, which correspond to hydrogen-bond energies of about 20.3 kcal mol-1. The crystal structure of sodium caesium hydrogen citrate, NaCsHC6H5O7 or [NaCs(C6H6O7)] n , has also been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. The Na atom is six-coordinate, with a bond-valence sum of 1.15. The Cs atom is eight-coordinate, with a bond-valence sum of 0.97. The distorted trigonal-prismatic [NaO6] coordination polyhedra share edges to form zigzag chains along the b-axis direction. The irregular [CsO8] coordination polyhedra share edges with the [NaO6] polyhedra to form layers parallel to the (101) plane, unlike the isolated chains in NaKHC6H5O7 and NaRbHC6H5O7. A prominent feature of the structure is the chain along [100] of very short, very strong O-H⋯O hydrogen bonds; the refined O⋯O distances are 2.398 and 2.159 Å, and the optimized distances are 2.398 and 2.347 Å. The Mulliken overlap populations in these hydrogen bonds are 0.143 and 0.133 electrons, which correspond to hydrogen-bond energies about 20.3 kcal mol-1.

Dilithium (citrate) crystals and their relatives.

New compounds of the type LiMHC6H5O7 (M = Li, Na, K, Rb) have been prepared from the metal carbonates and citric acid in solution. The crystal structures have been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. The compounds crystallize in the triclinic space group P-1 and are nearly isostructural. The structures are lamellar, with the layers in the ab plane. The boundaries of the layers consist of hydrophobic methylene groups and very strong intermolecular O-H...O hydrogen bonds. The O...O distances range from 2.666 Šfor M = Li to 2.465 Šfor M = Rb. The Li-O bonds exhibit significant covalent character, while the heavier M-O bonds are ionic. The Li atoms are four-, five-, or six-coordinate, while the coordination numbers of the larger cations are higher, i.e. eight for Na and nine for K and Rb. The citrate anion occurs in the trans,trans conformation, one of the two low-energy conformations of an isolated citrate anion. The crystal structure of LiRbHC6H5O7·H2O was also solved and refined. It consists of the same layers as in the anhydrous M = Rb compound, with interlayer water molecules and a different hydrogen-bonding pattern.