CSD Refcode Research Articles

X-ray powder diffraction data for mosapride dihydrogen citrate dihydrate

The previously unindexed laboratory X-ray powder diffraction data of mosapride dihydrogen citrate dihydrate, an API used to stimulate gastrointestinal motility, has been recorded at room temperature. Using these data, the crystal structure of this API has been refined in space group P21/c (No. 14) with a = 18.707(4) Å, b = 9.6187(1) Å, c = 18.2176(4) Å, β = 114.164(1)°, V = 2990.74(8) Å3, and Z = 4. The structure of this material corresponds to the phase associated with CSD Refcode LUWPOL determined at 93 K. The Rietveld refinement, carried out with TOPAS-Academic, proved the single nature of the sample and the quality of the data recorded.

A novel Co(II) complex with sulfamethoxazole ligand: Isostructuralism, non-covalent interactions, Hirshfeld surfaces, crystal voids and energy calculations

The crystal structure of [Co(H2O)6][Co(SMX)3]2 complex (SMX = sulfamethoxazole), hereafter CoSMXW, has been solved by X-ray diffraction methods. The complex CoSMXW was characterized by Infrared (IR), Raman, and UV-Vis spectroscopies. A comparison with the analogous Mn(II) complex, [Mn(H2O)6][Mn(SMX)3]2 (CSD refcode AJIFUW), indicates 3D isostructurality and packing similarity, as evident from X-ray diffraction and geometric descriptors such as dissimilarity index (X = 2.0 from XPac) and packing similarity (PSab = 0.3070 from CrystalCMP), respectively. This represents the first case of isostructurality observed among eleven metal complexes of sulfamethoxazole reported in the literature. A study of non-covalent interactions shows presence of structural motifs involving N-H…O and N-H…S (Motif I), N-H…O (Motif II), O-H…O and O-H…N (Motif III) H-bonds, as well as C-H…π contacts (Motif IV) for [Co(H2O)6][Co(SMX)3]2 and AJIFUW. Energy analysis using CrystalExplorer indicates that the strongest dimer involves Motifs I and II with total energy of -70.3 kcal/mol for CoSMXW, which is only 2.1 kcal/mol longer than that for AJIFUW. Hirshfeld surface (HS) analysis reveals meaningless effect of metal replacement on the intermolecular contacts, confirming the energetic results. The volume of the crystal voids and the percentage of free space were calculated as 862.35 Å3 and 11.8 % for CoSMXW, and 911.42 Å3 and 12.2 % for AJIFUW. 3D topology and hierarchy of interactions were analyzed with energy framework diagrams. Further, structural motifs, HS, crystal voids and intermolecular energies for the SMX free ligand (CSD refcode SLFNMB08) were also studied. Finally, the present study was complemented with DFT calculations to evaluate the strength and nature of the non-covalent interactions by using the quantum theory of atoms in molecules (QTAIM) and NCIplots computational tools. In addition, we have used the potential energy density predictor obtained from QTAIM analysis to investigate the relative contribution of each interaction to the formation of the assemblies.

Insights into the structural investigation of metal-complexes with 1,3-diamino-2-hydroxypropanetetraacetic acid: Inputs from X-ray and computational studies

A new 1,3-diamino-2-hydroxypropanetetraacetate copper complex (1) [{Cu(Hpdta)}{Cu(H2O)6}] has been synthesized and structurally characterized by single crystal X-ray diffraction and compared with a similar cobalt complex (2) of H4Hpdta (H4Hpdta = 1,3-diamino-2-hydroxypropanetetraacetic acid) retrieved from CSD (CSD ref code: TELBAN) with a detailed analysis of intermolecular interactions. X-ray crystallography reveals that both complexes are stabilized through C−H⋯O and O−H⋯O interactions generating different supramolecular networks. Detailed analysis of Hirshfeld surfaces and 2D fingerprint plot has been carried out for the title complexes to quantify the intermolecular interactions. Further, the noncovalent interactions are characterized through the Bader’s theory of ‘Atoms in Molecules’ (AIM) and noncovalent interaction (NCI) plot index. At the bond critical point (BCP), the electron density (ρBCP) and the Laplacian of electron density (∇2(ρBCP)) differ significantly for strong and weak noncovalent interactions. The dissociation energies are evaluated for validating the intermolecular interactions required to stabilize the complexes. The analysis of topological parameters extracted from AIM calculation characterized the interactions as closed-shell interactions.

Powder X-ray diffraction of pazopanib hydrochloride Form 1, C21H24N7O2SCl

The crystal structure of pazopanib hydrochloride Form 1 has been refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pazopanib hydrochloride crystallizes in space group P-1 (#2) with a = 8.45008(6), b = 8.71310(12), c = 16.05489(35) Å, α = 79.5996(9), β = 86.4784(5), γ = 87.3764(3)°, V = 1159.724(9) Å3, and Z = 2. The crystal structure is essentially identical to that of CSD Refcode CEVYEK. There are four strong N–H⋯Cl hydrogen bonds to the chloride anion. Several additional weaker N–H⋯Cl and C–H⋯Cl hydrogen bonds are also present. A variety of C–H⋯O, C–H⋯N, and N–H⋯S hydrogen bonds also contribute to the lattice energy. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Regarding configuration and hydrogen atom placement in “Development of new L-Serine Squarate single crystal” [Tyagi et al., J. Mol. Struct. 1224 (2021) 129190

The crystal structure of L-serinium hydrogensquarate (CSD refcode: HUQNIT), published in this journal very recently [Tyagi et al., J. Mol. Struct. 1224 (2021) 129190], is revised. Problems arise from the assignment of the absolute configuration of the serinium cation and the positioning of disordered hydrogen atoms of the hydrogensquarate anion. The correct structure of L-serinium hydrogensquarate was published more than 20 years ago [CSD refcode: PAZCUO; Kolev et al., Z. Kristallogr. NCS 213 (1998) 169-170].

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.

Phenol hemihydrate: redetermination of the crystal structure by neutron powder diffraction, Hirshfeld surface analysis and characterization of the thermal expansion.

Phenol hemihydrate, C5H5OH·0.5H2O, crystallizes in the space group Pbcn, Z = 8. The previously published crystal structure [CSD refcode PHOLHH; Meuthen & von Stackelberg (1960 ▸). Z. Elektrochem. 64, 387-390] is shown to be incorrect. Pairs of phenol mol-ecules, related by an inversion centre, are bridged by one water mol-ecule via O-H⋯O hydrogen bonds; an extended R 4 4(8) hydrogen-bonded motif links these inversion dimers into chains parallel to the c axis. Packing of the chains is achieved by weaker T-shaped C-H⋯π inter-actions between nearest neighbour phenol mol-ecules in the bc plane. Analysis of the thermal expansion and parameterization with a Debye model in terms of the linear elastic moduli shows that the c axis is ∼3 times stiffer than the two orthogonal directions.

Crystal structure of cloxacillin sodium monohydrate, C19H17ClN3O5SNa(H2O)

The crystal structure of cloxacillin sodium monohydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Cloxacillin sodium monohydrate crystallizes in space group P212121 (#19) with a = 7.989 36(12), b = 10.918 09(10), c = 25.559 3(6) Å, V = 2229.50(5) Å3, and Z = 4. The crystal structure is characterized by corner-sharing chains of irregular NaO5 polyhedra along the a-axis. The carboxylate group chelates to the Na and bridges two Na cations. The coordination sphere is completed by the water molecule and a carbonyl group. The Na–O bonds are mostly ionic but have some covalent character. The bond valence sum of the Na is 1.14. The water molecule acts as a donor to the carboxylate group and a carbonyl oxygen. It is an acceptor in C–H⋯O hydrogen bonds from a methyl group and a ring carbon. The crystal structure of cloxacillin sodium monohydrate is very similar to that of the fluorinated derivative (CSD Refcode BEBCAM), reflecting the similarity of the lattice parameters. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

Crystal structure of N-(p-methylbenzylidene)-p-bromoaniline

The asymmetric unit of the title compound C14H12BrN (systematic name (E)-N-(4-bromophenyl)-1-(p-tolyl)methanimine) contains one half-molecule: a crystallographic center of inversion is located at the midpoint of the bridging N=C bond. The central HC=N unit makes dihedral angles of 15.7(3)° and 15.2(4)° with bromobenzene and methylbenzene ring systems, respectively. The C and N atoms of the HC=N central unit are disordered over two sites in a 50:50 ratio. The Br atom of the 4-bromoaniline ring and the methyl atom of the 4-methylbenzilidene ring systems are also 50% disordered. In the crystal, molecules are linked by C–H⋯π interactions forming slabs parallel to the bc plane. The atomic coordinates are not available for the previously reported crystal structure of the title compound: CSD refcode MBZCLE. The reported R factor of 0.103 for the analysis in the space group P21/a is much higher than in the present analysis, which gives 0.033 in the space group P21/c.

The phase transition in bis(methyl(2-phenylethyl)ammonium) tetrabromidocuprate(II)

Bis(methyl(2-phenylethyl)ammonium) tetrachloridocuprate(II) is a well-known thermochromic compound that exhibits an abrupt color change (from green to yellow) at 353 K that is caused by a change in coordination geometry from square planar to flattened tetrahedral [1]. As part of a reinvestigation of established thermochromic chloridocuprate(II) and their related compounds, the bromide analog [bis(methyl(2-phenylethyl)ammonium) tetrabromidocuprate(II)] has been studied anew. The structure redetermination at ambient temperature agrees with the original [2] (CSD refcode: FUTTIX), i.e. alternating layers of flattened tetrahedral tetrabromidocuprate(II) complexes and of organic cations stacked along the a-axis of the monoclinic C2/c unit cell. A DSC scan from ambient temperature to 183 K reveals an exothermic peak (and corresponding endothermic peak upon heating) at 215 K. Single crystal structures, determined from ambient temperature to 120 K in steps of ~20 K, track a steady increase in b-axis length on cooling to the transition temperature. Across the transition temperature abrupt 1.1% and 0.74% increases in lengths of the b- and c-axes, respectively. and a 0.23% decrease in the a-axis length are observed with no change in space group. Slight changes of the organic cation phenyl group conformation are observed across the transition temperature that cause the organic layer to spread out and become thinner so that neighbouring layers are stacked more closely together along a. However, the flattened tetrahedral geometry of the tetrabromidocuprate(II) complex remains essentially unchanged across the transition.

Polymorphs, enantiomorphs, chirality and helicity in [Rh{N,O}(η4-cod)] complexes with {N,O} = salicylaldiminato Schiff base or aminocarboxylato ligands

The dimeric complex acetato(eta4-cycloocta-1,5-diene)rhodium(I), [Rh(O2CMe)(eta4-cod)]2 (cod = cycloocta-1,5-diene) reacts with N,O-chelating Schiff-base ligands or with N-phenylglycine to afford the diminato- or aminocarboxylato(4-cycloocta-1,5-diene)rhodium(I) complexes [{Rh(eta4-cod)}2(salen)] (1), [{Rh(eta4-cod)}2(salophen)] (2), [Rh((S)-N-phenylglycinato)(eta4-cod)] (3S), [Rh(rac-N-phenylglycinato)(eta4-cod)] (3rac), [Rh((R)-N-(4-methoxphenyl)ethyl-2-oxo-1-naphthaldiminato)(eta4-cod)] (4) and [Rh(N-(o-tolyl)-2-oxo-1-naphthaldiminato)(eta4-cod)] (5) [salen2- = N,N-ethylene-bis(salicylaldiminato), salophen2- = N,N-(1,2-phenylene)-bis(salicylaldiminato)]. The complexes are characterized by IR-, UV/Vis-, 1H/13C-NMR- and mass-spectroscopy. Complexes 1, 2, 4 and 5 contain six-membered metallaaromatic Rh-(N-CCC-O)-chelate rings which accept C-H...pi contacts. The crystal structure of 2 presents a polymorph (dimorph) (2a) to a previously reported structure (2b, CSD refcode SCLIRB10). Polymorphic forms 2a and 2b are traced to a different interlocking of adjacent dinuclear molecules with their corrugated van der Waals surface. The achiral N-phenylglycine ligand gives a chiral N-phenylglycinato complex [Rh(O2C-CH2-NHPh)(eta4-cod)] (3) with the nitrogen atom becoming the stereogenic center upon metal coordination. Complex 3 can crystallize as the enantiomorph 3S in the tetragonal, chiral space group P41 in a spontaneous resolution of the racemic mixture into homo-chiral helix-enantiomers due to inter-molecular N-H...O hydrogen bonding which connects only molecules of the same (S-) configuration into (right-handed or P-) 41-helical chains. Variation of the crystallization conditions gives 3 as a racemic polymorphic 3rac. R- and S-complexes 3 assemble in the polymorph 3rac in parallel chains along the 21-axes through N-HO hydrogen bonding. Again, only molecules of the same configuration are combined into a chain, albeit neighboring chains have complexes of opposite configuration. The chiral enantiomeric naphthaldiminato complex 4 displays a herring-bone arrangement. Achiral compound 5 crystallizes in the non-centrosymmetric polar space group Cc where all molecules show the same orientation.

Crystal structure of 2-phenylsulfinyl-cyclohexanone,C12H14O2

C12H14O2S, monoclinic, P121/a1 (no. 14), a = 10.787(1) A, b = 10.3955(9) A, c = 10.888(1) A, = 108.928(5)°, V = 1154.9 A, Z = 4, Rgt(F) = 0.047, wRref(F) = 0.142, T = 293 K. Source of material The starting 2-phenylsulfanyl-cyclohexanone was prepared from the reactionof 2-chloro-cyclohexanone and thiophenol [1].A solution of SeO2 (0.2 g, 1.8mmol) and 30%aqueous solution ofH2O2 (0.8 mL, 7.27 mmol) in CH3OH (5 mL) was added dropwise, at 273 K, to a solution of 2-phenylsulfanylcyclohexanone (1.5 g, 7.27 mmol) in CH3OH (10 mL) [2]. The reaction mixture was stirred at 273 K for 3 hours and at room temperature for 2 hours. After completion of the reaction a saturated aqueous NaCl solution (40 mL) was added, the aqueous layer was extracted with CH2Cl2 (60 mL) and the organic solution was dried over anhydrous MgSO4. After solvent evaporation under reduced pressure 1.2 g (5.39 mmol, yield 74 %; m.p. 364-367 K) of the crude 2phenylsulfinyl-cyclohexanonewas obtained (m.p. 377-378K [3]). The oxidation afforded amixture of 2:1 [C(R)S(S)/C(S)S(R)] and [C(R)S(R)/C(S)S(S)] diastereomeric sulfoxides, respectively, (cf. stereogenic centers C2 and S) determined from HNMRspectra of the crude product. From n-hexane/acetone fractional crystallization the pure [C(R)S(S)/C(S)S(R)] diastereomer was obtained as a white solid (m.p. 366-367K). Suitable crystals for X-ray analysis of the referred diastereomer were obtained by vapor diffusion from n-hexane/acetone at 298 K. Elemental analysis – found: C, 64.48 %; H, 6.26 %; calc. for C12H14O2S: C, 64.83 %; H, 6.35 %. Discussion The cyclohexanone ring is in a slightly distorted chair conformation, the Cremer and Pople’s [4] ring-puckering parameters being: q2 = 0.0603(4) A, q3 = 0.530(5) A, 2 = 117(4)°, 2 = 6.5(4)° and Q = 0.533(5) A. The dihedral angle between the phenyl ring and the OSCph moiety amounts of 4.7(3)° and that of 4-t-butyl-2(ptolylsulfinyl)cyclohexanone [5] (CSD ref code HAFCEW) is 0.98°. The S Odistance of 1.497(3)A is in the range found in the CSD [6], mean of 1.4875 A. The molecules are arranged via C–H···O hydrogen bonds in a threedimensional framework. First the molecules form centrosymmetric dimers: d(C3···O1) = 3.387(5) A, C3–H3···O1 = 131°, giving rise to a twelve-membered ring. They are, in turn, related in an helical fashion through: d(C7···O1) = 3.271(4)A, C7–H7···O1 = 163°; d(C11···O2) = 3.586(6) A, C11–H11B···O2 = 152° (symmetry operations: i: 1–x,1–y,–z; ii: x–1⁄2,1⁄2–y,z). Z. Kristallogr. NCS 221 (2006) 311-312 / DOI 10.1524/ncrs.2006.0088 311 © by Oldenbourg Wissenschaftsverlag, Munchen Crystal: colorless irregular plate, size 0.08 × 0.10 × 0.12 mm Wavelength: Mo K radiation (0.71073 A) : 2.58 cm−1 Diffractometer, scan mode: Nonius CAD4, /2 2 max: 50.94° N(hkl)measured, N(hkl)unique: 2251, 2136 Criterion for Iobs, N(hkl)gt: Iobs > 2 (Iobs), 985 N(param)refined: 136 Programs: SIR92 [7], SHELXL-97 [8], PARST [9], PLATON [10], ORTEP-3 [11], WinGX [12] Table 1. Data collection and handling.

4-Ethoxycarbonyl-3-furoic acid

The title compound, (I), represents the first example of a crystal structure of a mono-ester of furoic acid. Previous related crystal structures observed in the Cambridge Structural Database (CSD, Version 5.26; Allen, 2002) include the cyclohexane (CSD refcode CIHNIQ; Baldwin et al., 1997) and methyl (CSD refcode FURCAM; Okada et al., 1971) diesters, and the diacid (CSD refcode FURDCB and derivatives), although there has been some discussion as to the correct space group of this compound (Williams & Rundle, 1964; Semmingsen et al., 1986).

Polymorphism and pseudo-polymorphism in the crystal structures of [ML2]2[{M(mnt)2}2] (M = Fe or Co, L = Cp or Cp*)

The salts [ML2]2[{M′(mnt)2}2] {M = Co, L = Cp; M = Fe or Co, L = Cp* (Cp* = η-C5Me5); M′ = Fe or Co; mnt = [S2C2(CN)2]2−} have been prepared and structurally characterised to investigate the effects of cation size, metal d-electron configuration and the packing of pseudo-spherical cations with ellipsoidal dianions. By comparing the structures of [CoCp2]2[{M′(mnt)2}2] (M′ = Fe 1 or Co 2) with those of [FeCp*2]2[{M′(mnt)2}2] (M′ = Fe 3 or Co 4) the effect of cation size and magnetic character on the crystal lattice is investigated. Two polymorphs of 3 were identified, α-3 and β-3, both of which crystallise in the space group P21/n. The structures of 1, 2, and α-3 are similar with columns of anion dimers separated by cations lying perpendicular to the anion stacks, whereas β-3 comprises mixed, face-to-face ⋯cation⋯cation⋯anion⋯ stacks. Two forms of 4 were characterised, namely the polymorph α-4, which is isostructural with α-3, and the dichloromethane-solvated pseudo-polymorph 4S2. The structure of 4S2 is analogous to that of β-3 in comprising face-to-face stacks of mixed ions. Three related structures are known, namely [FeCp*2]2[{Co(mnt)2}2] [denoted γ-4 (CSD refcode ZAXJAJ)] and the two pseudo-polymorphs [FeCp*2]2[{M′(mnt)2}2]·MeCN [M′ = Fe 3S1 (ZAXJEN) or Co 4S1 (ZAXHUB)]. These are included for comparison with the structures determined here. The packing coefficients, k, varied in the range 0.59(3) (for 4S2) to 0.73(1) (for β-3).

A diamondoid supramolecular crystal lattice maintained entirely by sixfold phenyl embraces

Crystalline [Cu{P(C6H4-4-OCH3)3}3]+ClO4− (CSD refcode VIVPUL) possesses a diamondoid net, in which multiple phenyl embraces are the supramolecular linkages between [Cu{P(C6H4-4-OCH3)3}3]+ molecules. Each complex forms three sixfold phenyl embraces (6PE) and one enlarged sixfold phenyl embrace (E6PE): the 4-substitution of the phenyl rings does not interfere, and three rings per complex are used in both 6PE and E6PE. The space group of VIVPUL is R, and the E6PE lie on the threefold axes: there is slight threefold compression of the diamondoid net. The ClO4− ions occupy the centres of the pseudo-adamantanoid cages that comprise the net. Calculated intermolecular energies are −14.0 kcal mol−1 per (PAr3)2 for each 6PE and −15.3 kcal mol−1 per (PAr)6 in the E6PE. The VIVPUL lattice is also a more sophisticated version of the HA6PE (hexagonal array of sixfold phenyl embraces) net previously described, in the sense that more phenyl rings are involved in embraces, and the net is expanded: this structure type is therefore named super-HA6PE.

P1 or P\bar 1? Corrigendum

The structure of bis((phenyl-O,N,N-azoxy)oxy)methane, C_{13}H_{12}N_4O_4, originally reported as triclinic, space group P1 [Zyuzin et al. (1997). Isz. Akad. Nauk SSSR Ser. Khim. pp. 1486–1492; CSD refcode NIXQAM] was recently revised to monoclinic, space group C2 [Marsh (1999). Acta Cryst. B55, 931–936]. It is properly described as orthorhombic, space group Fdd2.