Graph-set R22 Research Articles

Proposed crystal structure of carbadox, C11H10N4O4

A model for the crystal structure of carbadox has been generated and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Carbadox crystallizes in space group P21 (#4) with a = 13.8155(3), b = 21.4662(1), c = 16.3297(3) Å, β = 110.0931(7)°, V = 4548.10(3) Å3, and Z = 16. The crystal structure is characterized by approximately parallel stacking of the eight independent carbadox molecules parallel to the bc-plane. There are two different molecular configurations of the eight carbadox molecules; five are in the lower-energy configuration and three are in a ~10% higher-energy configuration. This arrangement likely achieves the lowest-energy crystalline packing via hydrogen bonding. Hydrogen bonds link the molecules both within and between the planes. Each of the amino groups forms a N–H⋯O hydrogen bond to an oxygen atom of the 1,4-dioxidoquinoxaline ring system of another molecule. The result is four pairs of hydrogen-bonded molecules, which form rings with graph set R2,2(14). Variation in specimen preparation can affect the preferred orientation of particles considerably. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

N-Methyl-2-{3-methyl-2-[(2Z)-pent-2-en-1-yl]cyclo-pent-2-en-1-yl-idene}hydrazinecarbo-thio-amide.

The equimolar and hydro-chloric acid-catalysed reaction between cis-jasmone and 4-methyl-thio-semicarbazide in ethano-lic solution yields the title compound, C13H21N3S (common name: cis-jasmone 4-methyl-thio-semicarbazone). Two mol-ecules with all atoms in general positions are present in the asymmetric unit. In one of them, the carbon chain is disordered [site occupancy ratio = 0.821 (3):0.179 (3)]. The thio-semicarbazone entities [N-N-C(=S)-N] are approximately planar, with the maximum deviation from the mean plane through the selected atoms being -0.0115 (16) Å (r.m.s.d. = 0.0078 Å) for the non-disordered mol-ecule and 0.0052 (14) Å (r.m.s.d. = 0.0031 Å) for the disordered one. The mol-ecules are not planar, since the jasmone groups have a chain with sp 3-hybridized carbon atoms and, in addition, the thio-semicarbazone fragments are attached to the respective carbon five-membered rings and the dihedral angles between them for each mol-ecule amount to 8.9 (1) and 6.3 (1)°. In the crystal, the mol-ecules are connected through pairs of N-H⋯S and C-H⋯S inter-actions into crystallographically independent centrosymmetric dimers, in which rings of graph-set motifs R 2 2(8) and R 2 1(7) are observed. A Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are from H⋯H (70.6%), H⋯S/S⋯H (16.7%), H⋯C/C⋯H (7.5%) and H⋯N/N⋯H (4.9%) inter-actions [considering the two crystallographically independent mol-ecules and only the disordered atoms with the highest s.o.f. for the evaluation].

A second crystalline modification of 2-{3-methyl-2-[(2Z)-pent-2-en-1-yl]cyclo-pent-2-en-1-yl-idene}hydrazinecarbo-thio-amide.

A second crystalline modification of the title compound, C12H19N3S [common name: cis-jasmone thio-semicarbazone] was crystallized from tetra-hydro-furane at room temperature. There is one crystallographic independent mol-ecule in the asymmetric unit, showing disorder in the cis-jasmone chain [site-occupancy ratio = 0.590 (14):0.410 (14)]. The thio-semicarbazone entity is approximately planar, with the maximum deviation from the mean plane through the N/N/C/S/N atoms being 0.0463 (14) Å [r.m.s.d. = 0.0324 Å], while for the five-membered ring of the jasmone fragment, the maximum deviation from the mean plane through the carbon atoms amounts to 0.0465 (15) Å [r.m.s.d. = 0.0338 Å]. The mol-ecule is not planar due to the dihedral angle between these two fragments, which is 8.93 (1)°, and due to the sp 3-hybridized carbon atoms in the jasmone fragment chain. In the crystal, the mol-ecules are connected by N-H⋯S and C-H⋯S inter-actions, with graph-set motifs R 2 2(8) and R 2 1(7), building mono-periodic hydrogen-bonded ribbons along [010]. A Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are H⋯H (67.8%), H⋯S/S⋯H (15.0%), H⋯C/C⋯H (8.5%) and H⋯N/N⋯H (5.6%) [only non-disordered atoms and those with the highest s.o.f. were considered]. This work reports the second crystalline modification of the cis-jasmone thio-semicarbazone structure, the first one being published recently [Orsoni et al. (2020 ▸). Int. J. Mol. Sci. 21, 8681-8697] with the crystals obtained in ethanol at 273 K.

2-{3-Methyl-2-[(2Z)-pent-2-en-1-yl]cyclo-pent-2-en-1-yl-idene}-N-phenylhydrazinecarbo-thio-amide.

The hydro-chloric acid-catalyzed equimolar reaction between cis-jasmone and 4-phenyl-thio-semicarbazide yielded the title compound, C18H23N3S (common name: cis-jasmone 4-phenyl-thio-semicarbazone). Concerning the hydrogen bonding, an N-H⋯N intra-molecular inter-action is observed, forming a ring with graph-set motif S(5). In the crystal, the mol-ecules are connected into centrosymmetric dimers by pairs of N-H⋯S and C-H⋯S inter-actions, forming rings of graph-set motifs R 2 2(8) and R 2 1(7), with the sulfur atoms acting as double acceptors. The thio-semicarbazone entity is approximately planar, with the maximum deviation from the mean plane through the N/N/C/S/N atoms being 0.0376 (9) Å (the r.m.s.d. amounts to 0.0234 Å). The mol-ecule is substantially twisted as indicated by the dihedral angle between the thio-semicarbazone fragment and the phenyl ring, which amounts to 56.1 (5)°, and because of the jasmone fragment, which bears a chain with sp 3-hybridized carbon atoms in the structure. The Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are: H⋯H (65.3%), H⋯C/C⋯H (16.2%), H⋯S/S⋯H (10.9%) and H⋯N/N⋯H (5.5%).

Boron-π interactions in two 3-(dihydroxyboryl)anilinium salts analyzed by crystallographic studies and supported by the noncovalent interactions (NCI) index theoretical approach.

In the title compounds, 3-(dihydroxyboryl)anilinium bisulfate monohydrate, C6H9BNO2+·HSO4-·H2O (I), and 3-(dihydroxyboryl)anilinium methyl sulfate, C6H9BNO2+·CH3SO4- (II), the almost planar boronic acid molecules are linked by pairs of O-H...O hydrogen bonds, forming centrosymmetric motifs that can be described by the graph-set R22(8) motif. In both crystals, the B(OH)2 group acquires a syn-anti conformation (with respect to the H atoms). The presence of the hydrogen-bonding functional groups B(OH)2, NH3+, HSO4-, CH3SO4- and H2O generates three-dimensional hydrogen-bonded networks, in which the bisulfate (HSO4-) and methyl sulfate (CH3SO4-) counter-ions act as the central building blocks within the crystal structures. Furthermore, in both structures, the packing is stabilized by weak boron-π interactions, as shown by noncovalent interactions (NCI) index calculations.

Crystal structure of elvitegravir Form II, C23H23ClFNO5

The crystal structure of elvitegravir Form II has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Elvitegravir Form II crystallizes in space group P21 (#4) with a = 11.54842(7), b = 14.04367(5), c = 13.33333(8) Å, β = 90.0330(6)°, V = 2162.427(14) Å3, and Z = 4. The crystal structure consists of alternating layers of parallel molecules perpendicular to the b-axis. The mean planes of the oxoquinoline ring systems in molecules 1 and 2 are 1(22)-1 and -1(22)1. Between the stacks are layers of the halogenated phenyl rings. These exhibit herringbone stacking. In each molecule, the carboxylic acid group forms a strong intramolecular O–H⋯O hydrogen bond to the nearby carbonyl group. The hydroxyl group of each molecule forms a strong hydrogen bond to the carbonyl group of the carboxylic acid of the other molecule. These O–H⋯O hydrogen bonds link the molecules into dimers, with a graph set R2,2(18) > a > c. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Crystal structure of oxibendazole, C12H15N3O3

The crystal structure of oxibendazole has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Oxibendazole crystallizes in space group C2/c (#15) with a = 23.18673(22), b = 5.35136(5), c = 19.88932(13) Å, β = 97.0876(9)°, V = 2449.018(17) Å3, and Z = 8. The structure consists of hydrogen-bonded layers of planar molecules parallel to the bc-plane. Strong N–H⋯N hydrogen bonds link the molecules into dimers, with a graph set R2,2(8). N–H⋯O hydrogen bonds further link these dimers into layers parallel to the bc-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Crystal structure of vismodegib, C19H14Cl2N2O3S

The crystal structure of vismodegib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Vismodegib crystallizes in space group P21/a (#14) with a = 16.92070(20), b = 10.20235(4), c = 12.16161(10) Å, β = 108.6802(3)°, V = 1988.873(9) Å3, and Z = 4. The crystal structure consists of corrugated layers of molecules parallel to the bc-plane. There is only one classical hydrogen bond in the structure, between the amide nitrogen atom and the N atom of the pyridine ring. Pairs of these hydrogen bonds link the molecules into dimers, with a graph set R2,2(14) > a > a. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Crystal structure of diclazuril, C17H9Cl3N4O2

The crystal structure of diclazuril has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Diclazuril crystallizes in space group P21/a (#14) with a = 27.02080(18), b = 11.42308(8), c = 5.36978(5) Å, β = 91.7912(7)°, V = 1656.629(15) Å3, and Z = 4. The crystal structure consists of layers of molecules parallel to the ac-plane. A strong N–H⋯O hydrogen bond links the molecules into dimers along the a-axis with a graph set R2,2(8). The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

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.

Crystal structure of baricitinib, C16H17N7O2S

The crystal structure of baricitinib has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Baricitinib crystallizes in space group I2/a (#15) with a = 11.81128(11), b = 7.06724(6), c = 42.5293(3) Å, β = 91.9280(4)°, V = 3548.05(5) Å3, and Z = 8. The crystal structure is characterized by hydrogen-bonded double layers parallel to the ab-planes. The dimers form a graph set R2,2(8). The sulfone ends of the molecules reside in the interlayer regions. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Insights on structure and interactions of 2-amino-4-methoxy-6-methylpyrimidinium salts with 4-aminosalicylate and 5-chlorosalicylate: a combined experimental and theoretical charge-density analysis.

The proton-transfer complexes 2-amino-4-methoxy-6-methylpyrimidinium (2A4M6MP) 4-aminosalicylate (4AMSA), C6H10N3O+·C7H6NO3-, I, and 5-chlorosalicylate (5ClSA), C6H10N3O+·C7H4ClO3-, II, were synthesized by slow evaporation and crystallized. The crystal structures of both I and II were determined by single-crystal X-ray structure analysis. The crystal structures of both salts exhibit O-H...O, N-H...O, N-H...N and C-H...O interactions in their crystals. The 4AMSA and 5ClSA anions in combination with the 2A4M6MP cations form distinct synthons, which are represented by the graph-set notations R22(8), R42(8) and R22(8). Furthermore, the ΔpKa values were calculated and clearly demonstrate that 2A4M6MP is a good salt former when combined with carboxylic acids. Hirshfeld surface analysis was used to quantify the weak and strong interactions in the solid state, and energy framework calculations showed the stability of the hydrogen-bonding interactions. QTAIM (quantum theory of atoms in molecules) analysis revealed the nature of the chemical bonding in I and II, and the charge-density distribution in the intermolecular interactions in the crystal structures.

Crystal structure of brigatinib Form A (Alunbrig®), C29H39ClN7O2P

The crystal structure of brigatinib Form A has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Brigatinib Form A crystallizes in space group P-1 (#2) with a = 9.59616(20), b = 10.9351(3), c = 14.9913(6) Å, α = 76.1210(13), β = 79.9082(11), γ = 74.0802(6)°, V = 1458.497(15) Å3, and Z = 2. Structure solution was complicated by the lowest cost factor solution having an unreasonable conformation of the dimethylphosphoryl group. The second-best structure yielded a better refinement. The crystal structure is characterized by alternating layers of aliphatic and aromatic portions of the molecules along the b-axis. Strong N–H⋯N hydrogen bonds link the molecules into pairs, with a graph set R2,2(8). There is a strong intramolecular N–H⋯O hydrogen bond to the phosphoryl group, which determines the orientation of this group. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Crystal structure of 9,9-di-ethyl-9H-fluorene-2,4,7-tricarbaldehyde.

The title compound, C20H18O3, crystallizes in the space group P21/c with one mol-ecule in the asymmetric unit of the cell. The fluorene skeleton is nearly planar and the crystal structure is composed of mol-ecular layers extending parallel to the (302) plane. Within a layer, one formyl oxygen atom participates in the formation of a Carene-H⋯O bond, which is responsible for the formation of an inversion symmetric supra-molecular motif of graph set R 2 2(10). A second oxygen atom is involved in an intra-molecular Carene-H⋯O hydrogen bond and is further connected with a formyl hydrogen atom of an adjacent mol-ecule. A Hirshfeld surface analysis indicated that the most important contributions to the overall surface are from H⋯H (46.9%), O⋯H (27.9%) and C⋯H (17.8%) inter-actions.

Crystal structure of palbociclib isethionate Form B, (C24H30N7O2)(C2H5O4S)

The crystal structure of palbociclib isethionate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Palbociclib isethionate crystallizes in space group P-1 (#2) with a = 8.71334(4), b = 9.32119(6), c = 17.73725(18) Å, α = 80.0260(5), β = 82.3579(3), γ = 76.1561(1)°, V = 1371.282(4) Å3, and Z = 2. The crystal structure is dominated by cation⋯anion and cation⋯cation hydrogen bonds, which result in layers roughly parallel to the (104) plane. Both hydrogen atoms on the protonated nitrogen atom of the pyrimidine ring participate in strong hydrogen bonds to the anions. One proton binds to the sulfonate group, while the other bonds to the hydroxyl group of the isethionate anion. The hydroxyl group of the anion acts as a donor to a ketone oxygen atom in the cation. There are also strong N–H⋯N hydrogen bonds, which occur in pairs linking the cations into dimers with rings having a graph set R2,2(8). The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Combined DFT calculation, Hirshfeld surface analysis, and Energy framework study of non-covalent interactions in the crystal structure of (Z)-5-ethylidene-2-thiohydantoin determined by powder X-ray diffraction

The thiohydantoin core is used in the synthesis and development of new drugs. Furthermore, the study of these materials allows us to analyze the role that non-covalent interactions play in their supramolecular structure and how they can influence their pharmacological properties. Herein, a novel thiohydantoin compound, namely (Z)-5-ethylidene-2-thiohydantoin was synthesized and characterized by FT-IR, 1H-NMR, and 13C-NMR spectroscopy. Its crystal structure was determined and refined by powder X-ray diffraction techniques. This material crystallizes in the monoclinic system with space group P21/c, Z=4. The crystal packing is controlled by N–H···O, N–H···S and C–H···O hydrogen bond interactions, forming infinite two-dimensional sheets with graph-set motifs R22(8), R12(7), and R66(26). NCI calculations, Hirshfeld surface analysis, and the Energy framework study reproduce in good agreement the crystal packing exhibited by the X-ray diffraction study.

Crystal structure of a methanol solvate of a macrocycle bearing two flexible side-arms.

Di-tert-butyl N,N'-{[13,15,28,30,31,33-hexa-ethyl-3,10,18,25,32,34-hexa-aza-penta-cyclo-[25.3.1.15,8.112,16.120,23]tetra-triaconta-1(31),3,5,7,9,12(33),13,15,18,20,22,24,27,29-tetra-deca-ene-14,29-di-yl]bis-(methyl-ene)}dicarbamate methanol disolvate, C52H72N8O4·2CH3OH, was found to crystallize in the space group P21/c with one half of the macrocycle (host) and one mol-ecule of solvent (guest) in the asymmetric unit of the cell, i.e. the host mol-ecule is located on a crystallographic symmetry center. Within the 1:2 host-guest complex, the solvent mol-ecules are accommodated in the host cavity and held in their positions by O-H⋯N and N-H⋯O bonds, thus forming ring synthons of graph set R 2 2(7). The connection of the 1:2 host-guest complexes is accomplished by C-H⋯O, C-H⋯N and C-H⋯π inter-actions, which create a three-dimensional supra-molecular network.

Crystal structure of ipratropium bromide monohydrate, C20H30NO3Br(H2O)

The crystal structure of ipratropium bromide monohydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Ipratropium bromide monohydrate crystallizes in the space group P21/c (#14) with a = 8.21420(7) Å, b = 10.54617(13) Å, c = 24.0761(39) Å, β = 99.9063(7) °, V = 2054.574(22) Å3, and Z = 4. Both hydrogen atoms of the water molecule act as donors to the bromide cation, forming a ring with the graph set R2,4(8). The hydroxyl group also acts as a donor to Br. Several C–H⋯Br hydrogen bonds are present. The water molecule acts as an acceptor in two C–H⋯O hydrogen bonds from methyl groups. The ketone acts as an acceptor in C–H⋯O hydrogen bonds from methyl groups, a methylene group, and a methyne group. The hydroxyl group acts as an acceptor in a C–H⋯O hydrogen bond from a phenyl carbon atom. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1611.

Hypervalent organoselenium compounds stabilized by intramolecular coordination: synthesis and crystal structures.

Two novel hypervalent selenium(IV) compounds stabilized by intramolecular interactions, namely 6-phenyl-6,7-dihydro-5H-2,3-dioxa-2aλ4-selenacyclopenta[hi]indene, C14H12O2Se, 14, and 5-phenyl-5,6-dihydro-4H-benzo[c][1,2]oxaselenole-7-carbaldehyde, C14H12OSe2, 15, have been synthesized by the reaction of 2-chloro-1-formyl-3-(hydroxymethylene)cyclohexene with in-situ-generated disodium diselenide (Na2Se2). The title compounds were characterized by FT-IR spectroscopy, ESI-MS, and single-crystal X-ray diffraction studies. For 14, there is whole-molecule disorder, with occupancies of 0.605 (10) and 0.395 (10), a double bond between C and Se, and the five-membered selenopentalene rings are coplanar. The packing is stabilized by π-π stacking interactions involving one of the five-membered Se/C/C/C/O rings [centroid-centroid (Cg...Cg) distance = 3.6472 (18) Å and slippage = 1.361 Å], as well as C-H...π interactions involving a C-H group and the phenyl ring. In addition, there are bifurcated C-H...Se,O interactions which link the molecules into ribbons in the c direction. For 15, the C-Se bond lengths are longer than those of 14. The two five-membered rings are coplanar. There are no π-π or C-H...π interactions; however, molecules are linked by C-H...O interactions into centrosymmetric dimers, with graph-set notation R22(16).

Chiral one-dimensional hydrogen-bonded architectures constructed from single-enantiomer phosphoric triamides.

The two single-enantiomer phosphoric triamides N-(2,6-difluorobenzoyl)-N',N''-bis[(S)-(-)-α-methylbenzyl]phosphoric triamide, [2,6-F2-C6H3C(O)NH][(S)-(-)-(C6H5)CH(CH3)NH]2P(O), denoted L-1, and N-(2,6-difluorobenzoyl)-N',N''-bis[(R)-(+)-α-methylbenzyl]phosphoric triamide, [2,6-F2-C6H3C(O)NH][(R)-(+)-(C6H5)CH(CH3)NH]2P(O), denoted D-1, both C23H24F2N3O2P, have been investigated. In their structures, chiral one-dimensional hydrogen-bonded architectures are formed along [100], mediated by relatively strong N-H...O(P) and N-H...O(C) hydrogen bonds. Both assemblies include the noncentrosymmetric graph-set motifs R22(10), R21(6) and C22(8), and the compounds crystallize in the chiral space group P1. Due to the data collection of L-1 at 120 K and of D-1 at 95 K, the unit-cell dimensions and volume show a slight difference; the contraction in the volume of D-1 with respect to that in L-1 is about 0.3%. The asymmetric units of both structures consist of two independent phosphoric triamide molecules, with the main difference being seen in one of the torsion angles in the OPNHCH(CH3)(C6H5) part. The Hirshfeld surface maps of these levo and dextro isomers are very similar; however, they are near mirror images of each other. For both structures, the full fingerprint plot of each symmetry-independent molecule shows an almost asymmetric shape as a result of its different environment in the crystal packing. It is notable that NMR spectroscopy could distinguish between compounds L-1 and D-1 that have different relative stereocentres; however, the differences in chemical shifts between them were found to be about 0.02 to 0.001 ppm under calibrated temperature conditions. In each molecule, the two chiral parts are also different in NMR media, in which chemical shifts and P-H and P-C couplings have been studied.