Systematic Name Research Articles

Solvent influence on the crystal packing of 6-aminothiocytosine.

The crystal structures of 6-aminothiocytosine (systematic name: 4,6-diamino-1,2-dihydropyrimidine-2-thione, DAPMT, C4H6N4S), its hemihydrate (0.5H2O) and its dimethylformamide (DMF, C3H7NO) monosolvate were compared, and the influence of the type of solvent on the supramolecular motifs was analysed. In all three crystal structures, there are two symmetry-independent molecules (A and B), and these molecules are connected by three relatively short and directional hydrogen bonds to form chains of alternating A and B molecules. A further organization of these chains is dependent on the nature of the solvent molecule. In the unsolvated form, two orientations of the neighbouring chains are observed, and similar motifs - but only one per structure - can be observed in the solvated structures. These two different motifs can be connected by two different kinds of contacts, i.e. either π-π (hemihydrate) or staple-supported S...S (DMF). In the crystal structures, the O atoms of the solvent molecules are double acceptors of the same type of hydrogen bonds and bind the chains of DAPMT molecules into different motifs (dimeric or infinite chains). A Hirshfeld fingerprint analysis was used for visualization and additional interpretation of these results.

Structure determination of a new cocrystal of carbamazepine and DL-tartaric acid by synchrotron powder X-ray diffraction.

The crystal structure of a new cocrystal of carbamazepine (systematic name: 5H-dibenzo[b,f]azepine-5-carboxamide, C15H12N2O) and DL-tartaric acid (C4H6O6), obtained by liquid-assisted grinding, was solved by powder X-ray diffraction (PXRD). The high-resolution PXRD pattern of this new phase was recorded at room temperature thanks to synchrotron experiments at the European Synchrotron Radiation Facility (Grenoble, France). The starting structural model was generated by a Monte-Carlo simulated annealing method. The final structure was obtained through Rietveld refinement and an energy minimization simulation was used to estimate the H-atom positions. The stability of the proposed structure as a function of temperature was also assessed from molecular dynamics simulations. The symmetry is monoclinic (space group P21/c) and contains eight molecules per unit cell, namely, four DL-tartaric acid and four carbamazepine molecules.

Crystal structure and Hirshfeld surface analysis of the methanol solvate of sclareol, a labdane-type diterpenoid.

The title compound, C20H36O2·CH3OH [systematic name: (3S)-4-[(S)-3-hy-droxy-3-methyl-pent-4-en-1-yl]-3,4a,8,8-tetra-methyl-deca-hydro-naphthalen-3-ol methanol monosolvate], is a methanol solvate of sclareol, a diterpene oil isolated from the medicinally important medicinal herb Salvia sclarea, commonly known as clary sage. It crystallizes in space group P1 (No. 1) with Z' = 2. The sclareol mol-ecule comprises two trans-fused cyclo-hexane rings, each having an equatorially oriented hydroxyl group, and a 3-methyl-pent-1-en-3-ol side chain. In the crystal, Os-H⋯Os, Os-H⋯Om, Om-H⋯Os and Om-H⋯Om (s = sclareol, m = methanol) hydrogen bonds connect neighboring mol-ecules into infinite [010] chains. The title compound exhibits weak anti-leishmanial activity (IC50 = 66.4 ± 1.0 µM ml-1) against standard miltefosine (IC50 = 25.8 ± 0.2 µM ml-1).

The crystal structure of the first synthetic copper(II) tellurite arsenate, CuII5(TeIVO3)2(AsVO4)2.

Crystals of the first synthetic copper tellurite arsenate, CuII5(TeIVO3)2(AsVO4)2 [systematic name pentacopper(II) bis-oxotellurate(IV) bis-oxoarsenate(V)], were grown by the chemical vapour transport method and structurally determined using single-crystal X-ray diffraction. CuII5(TeIVO3)2(AsVO4)2 possesses a novel structure type including a new topological arrangement of CuII and O atoms. CuII5(TeIVO3)2(AsVO4)2 is formed from a framework of two types of Jahn-Teller distorted [CuIIO6] octahedra (one of which is considerably elongated) and [CuIIO5] square pyramids, which are linked by edge-sharing to form chains and dimers and by corner-sharing to complete a three-dimensional framework. [AsVO4] tetrahedra and [TeIVO5] polyhedra bridge the edges of channels along the a-axis direction, with void space remaining for the TeIV stereoactive 5s2 lone pairs. A comparison is made between the crystal structure of CuII5(TeIVO3)2(AsVO4)2 and those of known compounds and minerals, in particular fumarolitic Cu minerals.

Crystal structure of a tripeptide biphenyl hybrid C50H56N6O10·0.5H2O.

A peptide biphenyl hybrid compound {systematic name: dimethyl 2,2'-[((2S,2'S)-2,2'-{[(2S,2'S)-1,1'-([1,1'-biphen-yl]-2,2'-dicarbon-yl)bis-(pyrrolidine-1,2-diyl-2-carbon-yl)]bis-(aza-nedi-yl)}bis-(3-phenyl-propano-yl))bis-(aza-nedi-yl)](2S,2'S)-dipropionate hemihydrate}, C50H56N6O10·0.5H2O, was prepared by coupling of [1,1'-biphen-yl]-2,2'-dicarbonyl dichloride, tri-ethyl-amine and the tripeptide Pro-Phe-Ala in CH2Cl2 at 273 K under an N2 atmosphere. In the crystal, the asymmetric unit contains the peptide biphenyl hybrid accompanied by one-half of a water mol-ecule. A C atom of one of the proline rings is disordered between two positions in a 0.746 (11):0.254 (11) ratio. An important structural aspect of peptide compounds is their capacity to self-associate mediated by inter-molecular and intra-molecular hydrogen bonding. This characteristic can be useful in understanding the inter-actions between peptides and biomacromolecular targets, as well as to explain peptide properties.

An unusually short inter-molecular N-H⋯N hydrogen bond in crystals of the hemi-hydro-chloride salt of 1-exo-acetamido-pyrrolizidine.

The title compound [systematic name: (1R*, 8S)-2-acetamidoocta-hydro-pyrrol-izin-4-ium chloride-N-[(1R, 8S)-hexa-hydro-1H-pyrrolizin-2-yl)acetamide (1/1)], 2(C9H16N2O)·HCl or C9H17N2O+·Cl-·C9H16N2O, arose as an unexpected product when 1-exo-acetamido-pyrrolizidine (AcAP; C9H16N2O) was dissolved in CHCl3. Within the AcAP pyrrolizidine group, the unsubstituted five-membered ring is disordered over two orientations in a 0.897 (5):0.103 (5) ratio. Two AcAP mol-ecules related by a crystallographic twofold axis link to H+ and Cl- ions lying on the rotation axis, thereby forming N-H⋯N and N-H⋯Cl⋯H-N hydrogen bonds. The first of these has an unusually short N⋯N separation of 2.616 (2) Å: refinement of different models against the present data set could not distinguish between a symmetrical hydrogen bond (H atom lying on the twofold axis and equidistant from the N atoms) or static or dynamic disorder models (i.e. N-H⋯N + N⋯H-N). Computational studies suggest that the disorder model is slightly more stable, but the energy difference is very small.

Sodium [N,N′-ethylenebis(D-penicillaminato)]indate(III) tetrahydrate

The asymmetric unit of the title compound {systematic name: sodium [2-({2-[(1-carboxylato-2-methyl-2-sulfanidylpropyl)amino]ethyl}amino)-3-methyl-3-sulfanidylbutanoato-κ4 S,N,N′,S′]indate(III) tetrahydrate}, Na[In(C12H20N2O4S2)]·4H2O, contains four indate(III) complex anions {[In(D-ebp)]−; D-H4ebp = N,N′-ethyelenebis(D-penicillamine)], four sodium(I) cations and sixteen water molecules. The indate(III) anions and sodium cations are alternately connected through coordination bonds between Na+ ions and the carboxylate groups of the complex anions, forming an infinite sixfold right-handed helix along the c-axis direction. In the crystal, the helices are linked by O—H...O hydrogen bonds between water molecules bound to Na+ ions and carboxylate groups. The crystal studied was twinned via a twofold axis about [001].

Bis(4-hydroxy-N,N-di-n-propyltryptammonium) fumarate tetrahydrate

The title compound (systematic name: bis{[2-(4-hydroxy-1H-indol-3-yl)ethyl]bis(propan-2-yl)azanium} but-2-enedioate tetrahydrate), 2C16H25N2O+·C4H2O4 2−·4H2O, has a singly protonated DPT cation, one half of a fumarate dianion (completed by a crystallographic centre of symmetry) and two water molecules of crystallization in the asymmetric unit. A series of N—H...O and O—H...O hydrogen bonds form a three-dimensional network in the solid state.

Tetra-n-butyl-ammonium orotate monohydrate: knowledge-based comparison of the results of accurate and lower-resolution analyses and a non-routine disorder refinement.

The title hydrated mol-ecular salt (systematic name: tetra-n-butyl-ammonium 2,6-dioxo-1,2,3,6-tetra-hydro-pyrimidine-4-carboxyl-ate monohydrate), C16H36N+·C5H3N2O4 -·H2O, crystallizes with N-H⋯O and O-H⋯O hydrogen-bonded double-stranded anti-parallel ribbons consisting of the hydro-philic orotate monoanions and water mol-ecules, separated by the bulky hydro-phobic cations. The hydro-phobic and hydro-philic regions of the structure are joined by weaker non-classical C-H⋯O hydrogen bonds. An accurate structure analysis conducted at T = 100 K is compared to a lower-resolution less accurate determination using data measured at T = 295 K. The results of both analyses are evaluated using a knowledge-based approach, and it is found that the less accurate room-temperature structure analysis provides geometric data that are similar to those derived from the accurate low-temperature analysis, with both sets of results consistent with previously analyzed structures. A minor disorder of one methyl group in the cation at low temperature was found to be slightly more complex at room temperature; while still involving a minor fraction of the structure, the disorder at room temperature was found to require a non-routine treatment, which is described in detail.

1,1′,3,3′-Tetramesitylquinobis(imidazole)-2,2′-dithione

The solid-state structural analysis of the title compound [systematic name: 5,11-disulfanylidene-4,6,10,12-tetrakis(2,4,6-trimethylphenyl)-4,6,10,12-tetraazatricyclo[7.3.0.03,7]dodeca-1(9),3(7)-diene-2,8-dione], C44H44N4O2S2 [+solvent], reveals that the molecule crystallizes in a highly symmetric cubic space group so that one quarter of the molecule is crystallographically unique, the molecule lying on special positions (two mirror planes, two twofold axes and a center of inversion). The crystal structure exhibits large cavities of 193 Å3 accounting for 7.3% of the total unit-cell volume. These cavities contain residual density peaks but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent molecules to the scattering was removed using a solvent mask and is not included in the reported molecular weight. No classical hydrogen bonds are observed between the main molecules.

Characterization and Structural Analysis of Genkwanin, a Natural Product from Callicarpa americana

The natural compound Genkwanin (systematic name: 5-hydroxy-2-(4-hydroxyphenyl)-7-methoxychromen-4-one) C16H12O5 (1) is a non-glycosylated flavonoid isolated from Callicarpa americana. Microcrystals of Genkwanin were prepared by slow evaporation of a methanol solution under low temperature conditions. The structure of 1 was determined based on spectroscopic analyses, one-dimensional NMR, HRESIMS and was confirmed by single-crystal X-ray diffraction. The crystals grow as very thin needles with an extremely high aspect ratio and with the long axis (along the y-axis) corresponding to the very short unit cell b-axis. There are two independent molecules in the asymmetric unit with two different conformations and modes of packing in the crystal. One molecule has a higher degree on non-planarity than the other. The short stacking distance and separation between the molecules implies a high degree of co-planarity consistent with a conjugated system. The crystal structure is non-centrosymmetric but achiral.

Synthesis and redetermination of the crystal structure of salicyl-aldehyde N(4)-morpholino-thio-semi-carbazone.

The structure of the title compound (systematic name: N-{[(2-hy-droxy-phen-yl)methyl-idene]amino}-morpholine-4-carbo-thio-amide), C12H15N3O2S, was prev-iously determined (Koo et al., 1977 ▸) using multiple-film equi-inclination Weissenberg data, but has been redetermined with higher precision to explore its conformation and the hydrogen-bonding patterns and supra-molecular inter-actions. The mol-ecular structure shows intra-molecular O-H⋯N and C-H⋯S inter-actions. The configuration of the C=N bond is E. The mol-ecule is slightly twisted about the central N-N bond. The best planes through the phenyl ring and the morpholino ring make an angle of 43.44 (17)°. In the crystal, the mol-ecules are connected into chains by N-H⋯O and C-H⋯O hydrogen bonds, which combine to generate sheets lying parallel to (002). The most prominent contribution to the surface contacts are H⋯H contacts (51.6%), as concluded from a Hirshfeld surface analysis.

The synthesis and crystal structure of bis-[3,3-diethyl-1-(phenyl-imino-κN)thio-urea-κS]silver hexa-fluorido-phosphate.

The structure of the title complex, [Ag(C11H15N3S)2]PF6, has monoclinic (P21/c) symmetry, and the silver atom has a distorted square-planar geometry. The coordination complex crystallized from mixing silver hexa-fluorido-phosphate with a concentrated tetra-hydro-furan solution of N,N-di-ethyl-phenyl-azo-thio-formamide [ATF; systematic name: 3,3-diethyl-1-(phenyl-imino)-thio-urea] under ambient conditions. The resultant coordination complex exhibits a 2:1 ligand-to-metal ratio, with the silver(I) atom having a fourfold AgN2S2 coordination sphere, with a single PF6 counter-ion. In the crystal, however, one sulfur atom from an ATF ligand of a neighboring complex coordinates to the silver atom, with a bond distance of 2.9884 (14) Å. This creates a polymeric zigzag chain propagating along the c-axis direction. The chains are linked by C-H⋯F hydrogen bonds, forming slabs parallel to the ac plane.

Crystal structure and Hirshfeld surface analysis of lapachol acetate 80 years after its first synthesis.

Lapachol acetate [systematic name: 3-(3-methyl-but-2-en-yl)-1,4-dioxonaph-thalen-2-yl acetate], C17H16O4, was prepared using a modified high-yield procedure and its crystal structure is reported for the first time 80 years after its first synthesis. The full spectroscopic characterization of the mol-ecule is reported. The mol-ecular conformation shows little difference with other lapachol derivatives and lapachol itself. The packing is directed by inter-molecular π-π and C-H⋯O inter-actions, as described by Hirshfeld surface analysis. The former inter-actions make the largest contributions to the total packing energy in a ratio of 2:1 with respect to the latter.

The fumarate salts of the N-isopropyl-N-methyl derivatives of DMT and psilocin.

The solid-state structures of the salts of two substituted tryptamines, namely N-isopropyl-N-methyl-tryptaminium (MiPT) fumarate {systematic name: [2-(1H-indol-3-yl)eth-yl](meth-yl)propan-2-yl-aza-nium 3-carb-oxy-prop-2-enoate}, C14H21N2 +·C4H3O4 -, and 4-hy-droxy-N-isopropyl-N-methyl-tryptaminium (4-HO-MiPT) fumarate monohydrate {systematic name: [2-(4-hy-droxy-1H-indol-3-yl)eth-yl](meth-yl)propan-2-yl-aza-nium 3-carb-oxy-prop-2-enoate monohydrate}, C14H21N2O+·C4H3O4 -·H2O, are reported. Both salts possess a proton-ated tryptammonium cation and a 3-carb-oxy-acrylate (hydrogen fumarate) anion in the asymmetric unit; the 4-HO-MiPT structure also contains a water mol-ecule of crystallization. Both cations feature disorder of the side chain over two orientations, in a 0.630 (3):0.370 (3) ratio for MiPT and a 0.775 (5):0.225 (5) ratio for 4-HO-MiPT. In both extended structures, N-H⋯O and O-H⋯O hydrogen bonds generate infinite two-dimensional networks.

A tolbutamide–metformin salt based on antidiabetic drug combinations: synthesis, crystal structure analysis and pharmaceutical properties

A drug-drug anhydrous pharmaceutical salt containing tolbutamide {systematic name: 3-butyl-1-[(4-methylbenzene)sulfonyl]urea, TOL, C12H18N2O3S} and metformin (systematic name: 1-carbamimidamido-N,N-dimethylmethanimidamide, MET, C4H11N5) was created based on antidiabetic drug combinations to overcome the poor pharmaceutical properties of the parent drugs. Proton transfer and the proportion of the two components were confirmed by 1H NMR spectroscopy and single-crystal X-ray diffraction analysis. Comprehensive characterization of the new pharmaceutical salt crystal, 2-[(dimethylamino)(iminiumyl)methyl]guanidine (butylcarbamoyl)[(4-methylbenzene)sulfonyl]azanide, C4H12N5+·C12H17N2O3S-, was performed and showed enhancement of the pharmaceutical properties, such as lower hygroscopicity and greater accelerated stability than the parent drug MET, and higher solubility and dissolution rate than TOL. The property alterations were correlated with the crystal packing features and potential hydrogen-bonding sites through observed changes in the crystal structures.

A sulfur coordination polymer with wide bandgap semiconductivity formed from zinc(II) and 5-methylsulfanyl-1,3,4-thiadiazole-2-thione.

The sulfur coordination polymer catena-poly[zinc(II)-μ2-bis[5-(methylsulfanyl)-2-sulfanylidene-2,3-dihydro-1,3,4-thiadiazol-3-ido-κ2N3:S]], [Zn(C3H3N2S3)2]n or [Zn2MTT4]n, constructed from Zn2+ ions and 5-methylsulfanyl-1,3,4-thiadiazole-2-thione (HMTT), was synthesized successfully and structurally characterized. [Zn2MTT4]n crystallizes in the tetragonal space group I-4 (No. 82). Each MTT- ligand (systematic name: 5-methylsulfanyl-2-sulfanylidene-2,3-dihydro-1,3,4-thiadiazol-3-ide) coordinates to two different ZnII ions, one via the thione group and the other via a ring N atom, with one ZnII atom being in a tetrahedral ZnS4 and the other in a tetrahedral ZnN4 coordination environment. These tetrahedral ZnS4 and ZnN4 units are alternately linked by the organic ligands, forming a one-dimensional chain structure along the c axis. The one-dimensional chains are further linked via C-H...N and C-H...S hydrogen bonds to form a three-dimensional network adopting an ABAB-style arrangement that lies along both the a and b axes. The three-dimensional Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots confirm the major interactions as C-H...S hydrogen bonds with a total of 35.1%, while 7.4% are C-H...N hydrogen-bond interactions. [Zn2MTT4]n possesses high thermal and chemical stability and a linear temperature dependence of the bandgap from room temperature to 270 °C. Further investigation revealed that the bandgap changes sharply in ammonia, but only fluctuates slightly in other solvents, indicating its promising application as a selective sensor.

N-Tosyl-L-proline benzene hemisolvate: a rare example of a hydrogen-bonded carboxylic acid dimer with symmetrically disordered H atoms.

The carboxylic acid group is an example of a functional group which possess a good hydrogen-bond donor (-OH) and acceptor (C=O). For this reason, carboxylic acids have a tendency to self-assembly by the formation of hydrogen bonds between the donor and acceptor sites. We present here the crystal structure of N-tosyl-L-proline (TPOH) benzene hemisolvate {systematic name: (2S)-1-[(4-methylbenzene)sulfonyl]pyrrolidine-2-carboxylic acid benzene hemisolvate}, C12H15NO4S·0.5C6H6, (I), in which a cyclic R22(8) hydrogen-bonded carboxylic acid dimer with a strong O-(1/2H)...(1/2H)-O hydrogen bond is observed. The compound was characterized by single-crystal X-ray diffraction and NMR spectroscopy, and crystallizes in the space group I2 with half a benzene molecule and one TPOH molecule in the asymmetric unit. The H atom of the carboxyl OH group is disordered over a twofold axis. An analysis of the intermolecular interactions using the noncovalent interaction (NCI) index showed that the TPOH molecules form dimers due to the strong O-(1/2H)...(1/2H)-O hydrogen bond, while the packing of the benzene solvent molecules is governed by weak dispersive interactions. A search of the Cambridge Structural Database revealed that the disordered dimeric motif observed in (I) was found previously only in six crystal structures.

N-Decyltrimethylammonium bromide

The title compound, C13H30N+·Br− (systematic name: N,N,N-trimethyl-1-decanaminium bromide), forms crystals having a bilayer structure, comprised of layers of trimethylammonium cations and bromide anions separated by the inter-digitated n-decyl groups of the cation; close ammonium-methyl-C—H...Br contacts connect the ions. The n-decyl chain adopts a slightly distorted all-trans conformation. The n-decyl chain exhibits positional disorder with all atoms at half occupancy. The sample was a racemic twin.

Bis(2-methyllactato)borate tetrahydrate

The asymmetric unit of the title compound (systematic name: 3,3,8,8-tetramethyl-1,4,6,9-tetraoxa-λ4-boraspiro[4.4]nonane-2,7-dione tetrahydrate), C8H12BO6·4H2O, consists of half a bis(2-methyllactato)borate molecule and two water molecules of solvation. In the crystal, O—H...O hydrogen bonds link the components into a three-dimensional network.