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1.  Purification, crystallization and preliminary X-ray crystallographic analysis of glycosyltransferase-1 from Bacillus cereus  
The purification, crystallization and preliminary X-ray crystallographic analysis of B. cereus glycosyltransferase-1 are reported.
Glycosyltransferases (GTs), which are distributed widely in various organisms, including bacteria, fungi, plants and animals, play a role in synthesizing biological compounds. Glycosyltransferase-1 from Bacillus cereus (BcGT-1), which is capable of transferring glucose to small molecules such as kaempferol and quercetin, has been identified as a member of the family 1 glycosyltransferases which utilize uridine diphosphate glucose (UDP-glucose) as the sugar donor. BcGT-1 (molecular mass 45.5 kDa) has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction of BcGT-1 crystals to 2.10 Å resolution, the crystal belonged to space group P1, with unit-cell parameters a = 54.56, b = 84.81, c = 100.12 Å, α = 78.36, β = 84.66, γ = 84.84°. Preliminary analysis indicates the presence of four BcGT-1 molecules in the asymmetric unit with a solvent content of 50.27%.
doi:10.1107/S2053230X14014629
PMCID: PMC4157424  PMID: 25195897
glycosyltransferase; Bacillus cereus
2.  Studies on the Red Sea Sponge Haliclona sp. for its Chemical and Cytotoxic Properties 
Pharmacognosy Magazine  2016;12(46):114-119.
Background:
A great number of novel compounds with rich chemical diversity and significant bioactivity have been reported from Red Sea sponges.
Objective:
To isolate, identify, and evaluate the cytotoxic activity of the chemical constituents of a sponge belonging to genus Haliclona collected from the Eastern coast of the Red Sea.
Materials and Methods:
The total ethanolic extract of the titled sponge was subjected to intensive chromatographic fractionation and purification guided by cytotoxic bioassay toward various cancer cell lines. The structures of the isolated compounds were elucidated using spectroscopic techniques including one-dimension and two-dimension nuclear magnetic resonance, mass spectrometry, ultraviolet, and infrared data, as well as comparison with the reported spectral data for the known compounds. X-ray single-crystal structure determination was performed to determine the absolute configuration of compound 4. The screening of antiproliferative activity of the compounds was carried on three tumor cell lines, namely the human cervical cancer (HeLa), human hepatocellular carcinoma (HepG2), and human medulloblastoma (Daoy) cells using MTT assay.
Results:
This investigation resulted in the isolation of a new indole alkaloid, 1-(1H-indol-3-yloxy) propan-2-ol (1), with the previously synthesized pyrrolidine alkaloid, (2R, 3S, 4R, 5R) pyrrolidine-(1-hydroxyethyl)-3,4-diol hydrochloride (4), isolated here from a natural source for the first time. In addition, six known compounds tetillapyrone (2), nortetillapyrone (3), 2-methyl maleimide-5-oxime (5), maleimide-5-oxime (6), 5-(hydroxymethyl) dihydrofuran-2 (3H)-one (7), and ergosta-5,24 (28)-dien-3-ol (8) were also identified. Most of the isolated compounds exhibited weak cytotoxic activity against HepG-2, Daoy, and HeLa cancer cell lines.
Conclusion:
This is the first report of the occurrence of the indole and pyrrolidine alkaloids, 1-(1H-indol-2-yloxy) propan-2-ol (1), and the - (1-hydroxyethyl)-3,4-diol hydrochloride (4), in the Red Sea Haliclona sp.
SUMMARY
From the Red Sea Haliclona sp. two alkaloids with indole and pyrrolidine nuclei, 1-(1H-indol-2-yloxy) propan-2-ol-(1) and pyrrolidine-(1-hydroxyethyl)-3,4-diol hydrochloride (4) were isolated and fully characterized; in addition to six known compounds (2, 3, 5-8)The absolute configuration and the three-dimension stereo-molecular structure of compound 4 were determined by X-ray crystallographyThe different extracts and isolated compounds showed weak cytotoxic activity against HepG-2, Daoy, and HeLa cancer cell lines.
doi:10.4103/0973-1296.177906
PMCID: PMC4809165  PMID: 27076747
5-(hydroxymethyl) dihydrofuran-2 (3H)-one; Haliclona sp.; indole alkaloid; maleimide-5-oxime; pyrrolidine alkaloid
3.  Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism 
Scientific Reports  2015;5:16441.
ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOTTM). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.
doi:10.1038/srep16441
PMCID: PMC4643347  PMID: 26563565
4.  Crystal structures of 3,5-bis­[(E)-3-hy­droxy­benzyl­idene]-1-methyl­piperidin-4-one and 3,5-bis­[(E)-2-chloro­benzyl­idene]-1-methyl­piperidin-4-one 
3,5-Bis[(E)-3-hy­droxy­benzyl­idene]-1-methyl­piperidin-4-one and the 2-chloro­benzyl­idene derivative are monocarbonyl analogues of curcumin, and the conformations of the two compounds are very similar. In the 3-hy­droxy­benzyl­idene compound, O—H⋯O, O—H⋯N and C—H⋯O hydrogen bonds link the mol­ecules, forming sheets lying parallel to the ac plane. In the crystal of the 2-chloro­benzyl­idene derivative, mol­ecules are linked via weak C—H⋯Cl hydrogen bonds, forming zigzag chains along the [204] direction.
The title compounds, C20H19NO3, (1), and C20H17Cl2NO, (2), are the 3-hy­droxy­benzyl­idene and 2-chloro­benzyl­idene derivatives, respectively, of curcumin [systematic name: (1E,6E)-1,7-bis­(4-hy­droxy-3-meth­oxy­phen­yl)-1,6-hepta­diene-3,5-dione]. The dihedral angles between the benzene rings in each compound are 21.07 (6)° for (1) and 13.4 (3)° for (2). In both compounds, the piperidinone rings adopt a sofa confirmation and the methyl group attached to the N atom is in an equatorial position. In the crystal of (1), two pairs of O—H⋯N and O—H⋯O hydrogen bonds link the mol­ecules, forming chains along [10-1]. The chains are linked via C—H⋯O hydrogen bonds, forming undulating sheets parallel to the ac plane. In the crystal of (2), mol­ecules are linked by weak C—H⋯Cl hydrogen bonds, forming chains along the [204] direction. The chains are linked along the a-axis direction by π–π inter­actions [inter-centroid distance = 3.779 (4) Å]. For compound (2), the crystal studied was a non-merohedral twin with the refined ratio of the twin components being 0.116 (6):0.886 (6).
doi:10.1107/S2056989015020976
PMCID: PMC4719820  PMID: 26870411
crystal structure; benzyl­idene; piperidinone; methyl­piperidin-4-one; hydrogen bonding
5.  Structural and spectral investigations of the recently synthesized chalcone (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one, a potential chemotherapeutic agent 
Background
Chalcones (1,3-diaryl-2-propen-1-ones, represent an important subgroup of the polyphenolic family, which have shown a wide spectrum of medical and industrial application. Due to their redundancy in plants and ease of preparation, this category of molecules has inspired considerable attention for potential therapeutic uses. They are also effective in vivo as anti-tumor promoting, cell proliferating inhibitors and chemo preventing agents.
Results
Synthesis and molecular structure investigation of (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one (3) is reported. The structure of the title compound 3 is confirmed by X-ray crystallography. The optimized molecular structure of the studied compound is calculated using DFT B3LYP/6-311G (d,p) method. The calculated geometric parameters are in good agreement with the experimental data obtained from our reported X-ay structure. The calculated IR fundamental bands were assigned and compared with the experimental data. The electronic spectra of the studied compound have been calculated using the time dependant density functional theory (TD-DFT). The longest wavelength band is due to H → L (79 %) electronic transition which belongs to π-π* excitation. The 1H- and 13C-NMR chemical shifts were calculated using gauge independent atomic orbitals (GIAO) method, which showed good correlations with the experimental data (R2 = 0.9911–0.9965). The natural bond orbital (NBO) calculations were performed to predict the natural atomic charges at different atomic sites. The molecular electrostatic potential (MEP) was used to visualize the charge distribution on the molecule. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb and may act as potential anti-diabetic compound.
Conclusions
(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one single crystal is grown and characterized by single crystal X-ray diffraction, FT-IR, UV–vis, DFT and optimized geometrical parameters are close to the experimental bond lengths and angles. Molecular stability was successfully analyzed using NBO and electron delocalization is confirmed by MEP. Prediction of Activity Spectra Analysis of the title compound, predicts anti-diabetic activity with probability to have an active value of 0.348.
Graphical Abstract(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one: a crystal structure and computational studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13065-015-0112-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13065-015-0112-5
PMCID: PMC4477317  PMID: 26106444
Aldol product; Chalcone; X-Ray; DFT compution; PAAS
6.  Structural and spectral investigations of the recently synthesized chalcone (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one, a potential chemotherapeutic agent 
Background
Chalcones (1,3-diaryl-2-propen-1-ones, represent an important subgroup of the polyphenolic family, which have shown a wide spectrum of medical and industrial application. Due to their redundancy in plants and ease of preparation, this category of molecules has inspired considerable attention for potential therapeutic uses. They are also effective in vivo as anti-tumor promoting, cell proliferating inhibitors and chemo preventing agents.
Results
Synthesis and molecular structure investigation of (E)-3-mesityl-1-(naphthalen-2-yl) prop-2-en-1-one (3) is reported. The structure of the title compound 3 is confirmed by X-ray crystallography. The optimized molecular structure of the studied compound is calculated using DFT B3LYP/6-311G (d,p) method. The calculated geometric parameters are in good agreement with the experimental data obtained from our reported X-ay structure. The calculated IR fundamental bands were assigned and compared with the experimental data. The electronic spectra of the studied compound have been calculated using the time dependant density functional theory (TD-DFT). The longest wavelength band is due to H → L (79 %) electronic transition which belongs to π-π* excitation. The 1H- and 13C-NMR chemical shifts were calculated using gauge independent atomic orbitals (GIAO) method, which showed good correlations with the experimental data (R2 = 0.9911–0.9965). The natural bond orbital (NBO) calculations were performed to predict the natural atomic charges at different atomic sites. The molecular electrostatic potential (MEP) was used to visualize the charge distribution on the molecule. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb and may act as potential anti-diabetic compound.
Conclusions
(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one single crystal is grown and characterized by single crystal X-ray diffraction, FT-IR, UV–vis, DFT and optimized geometrical parameters are close to the experimental bond lengths and angles. Molecular stability was successfully analyzed using NBO and electron delocalization is confirmed by MEP. Prediction of Activity Spectra Analysis of the title compound, predicts anti-diabetic activity with probability to have an active value of 0.348.
Graphical Abstract(E)-3-Mesityl-1-(naphthalen-2-yl) prop-2-en-1-one: a crystal structure and computational studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13065-015-0112-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13065-015-0112-5
PMCID: PMC4477317  PMID: 26106444
Aldol product; Chalcone; X-Ray; DFT compution; PAAS
7.  Crystal structure of tetra­aqua­bis(3,5-di­amino-4H-1,2,4-triazol-1-ium)cobalt(II) bis­[bis­(pyridine-2,6-di­carboxyl­ato)cobaltate(II)] dihydrate 
The asymmetric unit of the title compound, [Co(C2H6N5)2(H2O)4][Co(C7H3NO4)2]2·2H2O, features 1.5 CoII ions (one anionic complex and one half cationic complex) and one water mol­ecule. In the cationic complex, the CoII atom is located on an inversion centre and is coordinated by two triazolium cations and four water mol­ecules, adopting an octa­hedral geometry where the N atoms of the two triazolium cations occupy the axial positions and the O atoms of the four water mol­ecules the equatorial positions. The two triazole ligands are parallel offset (with a distance of 1.38 Å between their planes). In the anionic complex, the CoII ion is six-coordinated by two N and four O atoms of the two pyridine-2,6-di­carboxyl­ate anions, exhibiting a slightly distorted octa­hedral coordination geometry in which the mean plane of the two pyridine-2,6-di­carboxyl­ate anions are almost perpendicular to each other, making a dihedral angle of 85.87 (2)°. In the crystal, mol­ecules are linked into a three-dimensional network via C—H⋯O, C—H⋯N, O—H⋯O and N—H⋯O hydrogen bonds.
doi:10.1107/S2056989015010014
PMCID: PMC4459343  PMID: 26090171
crystal structure; pyridine-2,6-di­carboxyl­ate; triazolium; CoII complex; hydrogen bonding
8.  Crystal structure of (E)-2-hy­droxy-4′-meth­oxy­aza­stilbene 
The title compound has an E conformation with respect to the azomethine C=N bond and the aromatic rings are inclined to one another by 3.29 (4)°. In the crystal, mol­ecules are linked via C—H⋯O hydrogen bonds, forming zigzag chains along [10-1].
The title aza­stilbene derivative, C14H13NO2 {systematic name: (E)-2-[(4-meth­oxy­benzyl­idene)amino]­phenol}, is a product of the condensation reaction between 4-meth­oxy­benzaldehyde and 2-amino­phenol. The mol­ecule adopts an E conformation with respect to the azomethine C=N bond and is almost planar, the dihedral angle between the two substituted benzene rings being 3.29 (4)°. The meth­oxy group is coplanar with the benzene ring to which it is attached, the Cmeth­yl—O—C—C torsion angle being −1.14 (12)°. There is an intra­molecular O—H⋯N hydrogen bond generating an S(5) ring motif. In the crystal, mol­ecules are linked via C—H⋯O hydrogen bonds, forming zigzag chains along [10-1]. The chains are linked via C—H⋯π inter­actions, forming a three-dimensional structure.
doi:10.1107/S2056989015008348
PMCID: PMC4459367  PMID: 26090124
crystal structure; aza­stilbene; anti­bacterial; anti-oxidant; hydrogen bonding
9.  Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition 
Structures of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase from zebrafish and its complexes are reported.
10-Formyltetrahydrofolate dehydrogenase (FDH), which is composed of a small N-terminal domain (Nt-FDH) and a large C-terminal domain, is an abundant folate enzyme in the liver and converts 10-formyltetrahydrofolate (10-FTHF) to tetrahydrofolate (THF) and CO2. Nt-FDH alone possesses a hydrolase activity, which converts 10-FTHF to THF and formate in the presence of β-mercaptoethanol. To elucidate the catalytic mechanism of Nt-FDH, crystal structures of apo-form zNt-FDH from zebrafish and its complexes with the substrate analogue 10-formyl-5,8-dideazafolate (10-FDDF) and with the products THF and formate have been determined. The structures reveal that the conformations of three loops (residues 86–90, 135–143 and 200–203) are altered upon ligand (10-FDDF or THF) binding in the active site. The orientations and geometries of key residues, including Phe89, His106, Arg114, Asp142 and Tyr200, are adjusted for substrate binding and product release during catalysis. Among them, Tyr200 is especially crucial for product release. An additional potential THF binding site is identified in the cavity between two zNt-FDH molecules, which might contribute to the properties of product inhibition and THF storage reported for FDH. Together with mutagenesis studies and activity assays, the structures of zNt-FDH and its complexes provide a coherent picture of the active site and a potential THF binding site of zNt-FDH along with the substrate and product specificity, lending new insights into the molecular mechanism underlying the enzymatic properties of Nt-FDH.
doi:10.1107/S1399004715002928
PMCID: PMC4388273  PMID: 25849409
10-formyltetrahydrofolate dehydrogenase; zebrafish
10.  Synthesis, Spectral Characterization and Crystals Structure of some Arsane Derivatives of Gold (I) Complexes: A Comparative Density Functional Theory Study 
PLoS ONE  2015;10(3):e0119620.
A series of complexes of the type LAuCl where L = tris(p-tolylarsane), tris(m-tolylarsane), bis(diphenylarsano)ethane, and tris(naphthyl)arsane have been synthesized. All of the new complexes, 1-4, have been fully characterized by means of 1H NMR and 13C NMR spectroscopy and single crystal X-ray crystallography. The structures of complexes 1-4 have been determined from X-ray diffraction data. The linear molecules have an average bond distance between gold-arsenic and gold-chlorine of 2.3390Å and 2.2846Å, respectively. Aurophilic interaction was prominent in complex 1 and 3, whereas complex 2 and 4 do not show any such interaction. The intermolecular gold interaction bond length was affected by the electronegativity of the molecule. The computed values calculated at DFT level using B3LYP function are in good agreement with the experimental results.
doi:10.1371/journal.pone.0119620
PMCID: PMC4370652  PMID: 25798915
11.  Synthesis, Structural and Antioxidant Studies of Some Novel N-Ethyl Phthalimide Esters 
PLoS ONE  2015;10(3):e0119440.
A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity.
doi:10.1371/journal.pone.0119440
PMCID: PMC4351070  PMID: 25742494
12.  Crystal structure of 3-[(4-benzyl­piperazin-1-yl)meth­yl]-5-(thio­phen-2-yl)-2,3-di­hydro-1,3,4-oxa­diazole-2-thione 
The title 1,3,4-oxa­diazole-2-thione derivative, C18H20N4OS2, crystallized with two independent mol­ecules (A and B) in the asymmetric unit. The 2-thienyl rings in both mol­ecules are rotationally disordered over two orientations by approximately 180° about the single C—C bond that connects it to the oxa­diazole thione ring; the ratios of site occupancies for the major and minor components were fixed in the structure refinement at 0.8:0.2 and 0.9:0.1 in mol­ecules A and B, respectively. The 1,3,4-oxa­diazole-2-thione ring forms dihedral angles of 7.71 (16), 10.0 (11) and 77.50 (12)° (mol­ecule A), and 6.5 (3), 6.0 (9) and 55.30 (12)° (mol­ecule B) with the major and minor parts of the disordered thio­phene ring and the mean plane of the adjacent piperazine ring, respectively, resulting in approximately V-shaped conformations for the mol­ecules. The piperazine ring in both mol­ecules adopts a chair conformation. The terminal benzene ring is inclined towards the mean plane of the piperazine ring with N—C—C—C torsion angles of −58.2 (3) and −66.2 (3)° in mol­ecules A and B, respectively. In the crystal, no inter­molecular hydrogen bonds are observed. The crystal packing features short S⋯S contacts [3.4792 (9) Å] and π–π inter­actions [3.661 (3), 3.664 (11) and 3.5727 (10) Å], producing a three-dimensional network.
doi:10.1107/S2056989015002273
PMCID: PMC4350721  PMID: 25844234
crystal structure; 1,3,4-oxa­diazole; piperazin-1-yl; disorder; π–π inter­actions; S⋯S contacts
13.  Crystal structure of 3-(adamantan-1-yl)-4-(4-chloro­phen­yl)-1H-1,2,4-triazole-5(4H)-thione 
The title compound, C18H20ClN3S, is a functionalized triazoline-3-thione derivative. The benzene ring is almost perpendic­ular to the planar 1,2,4-triazole ring [maximum deviation = 0.007 (1) Å] with a dihedral angle of 89.61 (5)° between them and there is an adamantane substituent at the 3-position of the triazole­thione ring. In the crystal, N—H⋯S hydrogen-bonding inter­actions link the mol­ecules into chains extending along the c-axis direction. The crystal packing is further stabilized by weak C—H⋯π inter­actions that link adjacent chains into a two-dimensional structure in the bc plane. The crystal studied was an inversion twin with a 0.50 (3):0.50 (3) domain ratio.
doi:10.1107/S2056989015000596
PMCID: PMC4384613  PMID: 25878859
crystal structure; adamantane; 1,2,4-triazole; starting material; hydrogen bonding
14.  Crystal structure of 2-(1,3-dioxoindan-2-yl)iso­quinoline-1,3,4-trione 
In the title iso­quinoline-1,3,4-trione derivative, C18H9NO5, the five-membered ring of the indane fragment adopts an envelope conformation with the nitro­gen-substituted C atom being the flap. The planes of the indane benzene ring and the iso­quinoline-1,3,4-trione ring make a dihedral angle of 82.06 (6)°. In the crystal, mol­ecules are linked into chains extending along the bc plane via C—H⋯O hydrogen-bonding inter­actions, enclosing R 2 2(8) and R 2 2(10) loops. The chains are further connected by π–π stacking inter­ations, with centroid-to-centroid distances of 3.9050 (7) Å, forming layers parallel to the b axis.
doi:10.1107/S2056989014025997
PMCID: PMC4331915  PMID: 25705509
crystal structure; iso­quinoline-1,3,4-trione derivative; synthesis; hydrogen bonding; pharmacological properties
15.  Crystal structure of cyclo­hexyl­ammonium thio­cyanate 
In the title salt, C6H11NH3 +·SCN−, the cyclo­hexyl­ammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial inter­actions. In the crystal, the components are linked by N—H⋯N and N—H⋯S hydrogen-bonding inter­actions, resulting in a three-dimensional network.
doi:10.1107/S2056989014027297
PMCID: PMC4331923  PMID: 25705511
crystal structure; cyclo­hexyl­ammonium; distorted chair; hydrogen bonding
16.  Crystal structure of 2-(adamantan-1-yl)-5-(4-bromo­phen­yl)-1,3,4-oxa­diazole 
In the title mol­ecule, C18H19BrN2O, the benzene ring is inclined to the oxa­diazole ring by 10.44 (8)°. In the crystal, C—H⋯π inter­actions link the mol­ecules in a head-to-tail fashion, forming chains extending along the c-axis direction. The chains are further connected by π–π stacking inter­actions, with centroid–centroid distances of 3.6385 (7) Å, forming layers parallel to the bc plane.
doi:10.1107/S1600536814023861
PMCID: PMC4257436  PMID: 25553016
crystal structure; adamntane derivative; 1,3,4-oxa­diazole; C—H⋯π hydrogen bonds; π–π inter­actions
17.  Crystal structure of 6-chloro-5-iso­propyl­pyrimidine-2,4(1H,3H)-dione 
In the mol­ecule of the title compound, C7H9ClN2O2, the conformation is determined by intra­molecular C—H⋯O and C—H⋯Cl hydrogen bonds, which generate S(6) and S(5) ring motifs. The isopropyl group is almost perpendicular to the pyrimidine ring with torsion angles of −70.8 (3) and 56.0 (3)°. In the crystal, two inversion-related mol­ecules are linked via a pair of N—H⋯O hydrogen bonds into R 2 2(8) dimers; these dimers are connected into chains extending along the bc plane via an additional N—H⋯O hydrogen bond and weaker C—H⋯O hydrogen bonds. The crystal structure is further stabilized by a weak π–π inter­action [3.6465 (10) Å] between adjacent pyrimidine-dione rings arranged in a head-to-tail fashion, producing a three-dimensional network.
doi:10.1107/S1600536814021382
PMCID: PMC4257309  PMID: 25484791
crystal structure; pyrimidine-2,4-dione; hydrogen bonds; π–π inter­action
18.  Crystal structure of bis­{2-[(E)-(4-fluoro­benz­yl)imino­meth­yl]phenolato-κ2 N,O}nickel(II) 
In the square-planar [Ni(C14H11FNO)2] complex, weak C—H⋯F and C—H⋯π inter­actions play an important role in the mol­ecular self-assembly, resulting in the formation of 2D mol­ecular sheets which are stacked along the b axis.
The asymmetric unit of the title complex, [Ni(C14H11FNO)2], contains one-half of the mol­ecule with the NiII cation lying on an inversion centre coordinated by a bidentate Schiff base anion. The cationic NiII center is in a distorted square-planar coordination environment chelated by the imine N and phenolate O donor atoms of the two Schiff base ligands. The N and O donor atoms of the two ligands are mutually trans with Ni—N and Ni—O bond lengths of 1.9242 (10) and 1.8336 (9) Å, respectively. The fluoro­phenyl ring is almost orthogonal to the coordination plane and makes a dihedral angle of 82.98 (7)° with the phenolate ring. In the crystal, mol­ecules are linked into screw chains by weak C—H⋯F hydrogen bonds. Additional C—H⋯π contacts arrange the mol­ecules into sheets parallel to the ac plane.
doi:10.1107/S1600536814020546
PMCID: PMC4257226  PMID: 25484666
Crystal structure; Ni(II) complex; NO donors; Schiff base; anti­bacterial activity
19.  Crystal structure of bis­{2-[(E)-(4-meth­oxy­lbenz­yl)imino­meth­yl]phenolato-κ2 N,O 1}nickel(II) 
The NiII atom in the title compound shows a square-planar NiN2O2 coordination with the imine N and phenolate O atoms of the two Schiff base ligands. C—H⋯O and C—H⋯π interactions result in the formation of sheets of molecules parallel to the ac plane.
The asymmetric unit of the title compound, [Ni(C15H14NO2)2], comprises an NiII cation, lying on an inversion centre, and a Schiff base anion that acts as a bidentate ligand. The NiII cation is in a square-planar coordination environment binding to the imine N and phenolate O atoms of the two Schiff base ligands. The N- and O-donor atoms of the two ligands are mutually trans, with Ni—N and Ni—O bond lengths of 1.9191 (11) and 1.8407 (9) Å, respectively. The plane of the meth­oxy­benzene ring makes a dihedral angle of 84.92 (6)° with that of the phenolate ring. In the crystal, mol­ecules are linked into screw chains by weak C—H⋯O hydrogen bonds. Additional C—H⋯O hydrogen bonds, together with C—H⋯π contacts, arrange the mol­ecules into sheets parallel to the ac plane.
doi:10.1107/S160053681401650X
PMCID: PMC4158500  PMID: 25249867
crystal structure; nickel(II) complex; NO donors; Schiff base
20.  Bis{2-meth­oxy-6-[(E)-(4-methyl­benz­yl)imino­meth­yl]phenolato}palladium(II) chloro­form monosolvate 
In the title complex, [Pd(C16H16NO2)2]·CHCl3, the PdII cation lies on an inversion center. One Cl atom of the CHCl3 solvent mol­ecule lies on a twofold axis and the C—H group is disordered with equal occupancies about this axis with the other Cl atom in a general position with full occupancy. The PdII cation is four-coordinate and adopts a square-planar geometry via coordination of the imine N and phenolic O atoms of the two bidentate Schiff base anions. The N and O atoms of these ligands are mutually trans. The plane of the benzene ring makes a dihedral angle of 73.52 (10)° with that of the meth­oxy­phenolate ring. In the crystal, mol­ecules of the PdII complex are arranged into sheets parallel to the ac plane, and the chloro­form solvent mol­ecules are located in the inter­stitial areas between the complex mol­ecules. Weak inter­molecular C—H⋯O and C—H⋯π inter­actions stabilize the packing.
doi:10.1107/S1600536814015025
PMCID: PMC4158526  PMID: 25249876
crystal structure
21.  6-[(2-Methyl­phen­yl)sulfan­yl]-5-propyl­pyrimidine-2,4(1H,3H)-dione 
In the title pyrimidine-2,4-dione derivative, C14H16N2O2S, the dihedral angle between the six-membered rings is 77.81 (10)°. The mol­ecule is twisted about the Cp—S (p = pyrimidine) bond, with a C—S—C—N torsion angle of −59.01 (17)°. An intramolecular C—H⋯S hydrogen bond generates an S(5) ring motif. In the crystal, bifurcated acceptor N—H⋯O and C—H⋯O hydrogen bonds generate inversion-related dimers incorporating R 2 1(9) and R 2 2(8) loops. These dimers are connected into a chain extending along the a-axis direction by a second pair of inversion-related N—H⋯O hydrogen bonds, forming another R 2 2(8) loop. The crystal structure is further stabilized by weak inter­molecular C—H⋯π inter­actions, generating a three-dimensional network.
doi:10.1107/S1600536814013269
PMCID: PMC4120546  PMID: 25161558
22.  3-(Adamantan-1-yl)-4-benzyl-1H-1,2,4-triazole-5(4H)-thione 
The title compound, C19H23N3S, is a functionalized triazoline-3-thione derivative. The benzyl ring is almost normal to the planar 1,2,4-triazole ring (r.m.s. deviation = 0.007 Å) with a dihedral angle of 86.90 (7)°. In the crystal, molecules are linked by pairs of N—H⋯S hydrogen bonds, forming inversion dimers that enclose R 2 2(8) loops. The crystal packing is further stabilized by weak C—H⋯π inter­actions that link adjacent dimeric units into supra­molecular chains extending along the a-axis direction.
doi:10.1107/S1600536814013257
PMCID: PMC4120616  PMID: 25161557
23.  Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives 
Background
Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized.
Results
The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by 1HNMR, 13CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed.
Conclusions
Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation
, to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V), these heterosynthons are centrosymmetrically paired via N---H · · · O hydrogen bonds and each forms a complementary DADA [D = donor and A = acceptor] array of quadruple hydrogen bonds, with graph-set notation, and .
Electronic supplementary material
The online version of this article (doi: 10.1186/1752-153X-8-31) contains supplementary material, which is available to authorized users.
doi:10.1186/1752-153X-8-31
PMCID: PMC4032391  PMID: 24887234
24.  Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives 
Background
Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized.
Results
The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by 1HNMR, 13CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed.
Conclusions
Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation
R228
, to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V), these heterosynthons are centrosymmetrically paired via N---H · · · O hydrogen bonds and each forms a complementary DADA [D = donor and A = acceptor] array of quadruple hydrogen bonds, with graph-set notation R238, R228 and R238.
doi:10.1186/1752-153X-8-31
PMCID: PMC4032391  PMID: 24887234

Results 1-25 (1338)