Crystal structure oftrans-N,N′-bis(3,5-di-tert-butyl-2-hydroxyphenyl)oxamide methanol monosolvate

The here crystallized oxamide was previously characterized as an unsolvated species [Jímenez-Pérezet al.(2000).J. Organomet. Chem.614–615, 283–293], and is now reported with methanol as a solvent of crystallization, C30H44N2O4·CH3OH, in a different space group. The introduction of the solvent influences neither the molecular symmetry of the oxamide, which remains centrosymmetric, nor the molecular conformation. However, the unsolvated molecule crystallized as an ordered system, while many parts of the solvated crystal are disordered. The hydroxy group in the oxamide is disordered over two chemically equivalent positions, with occupancies 0.696 (4):0.304 (4); onetert-butyl group is disordered by rotation about the C—C bond, and was modelled with three sites for each methyl group, each one with occupancy 1/3. Finally, the methanol solvent, which lies on a twofold axis, is disordered by symmetry. The disorder affecting hydroxy groups and the solvent of crystallization allows the formation of numerous supramolecular motifs using four hydrogen bonds, with N—H and O—H groups as donors and the oxamide and methanol molecule as acceptors.

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Threefold helical assembly via hydroxy hydrogen bonds: the 2:1 co-crystal of bicyclo[3.3.0]octane-endo-3,endo-7-diol and bicyclo[3.3.0]octane-endo-3,exo-7-diol

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989021001730 ◽

2021 ◽

Vol 77 (3) ◽

pp. 270-276

Author(s):

Isa Y. H. Chan ◽

Mohan M. Bhadbhade ◽

Roger Bishop

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Hydroxy Group ◽

Network Structure ◽

General Position ◽

Three Dimensional ◽

Screw Axis ◽

Hydroxy Groups

Reduction of bicyclo[3.3.0]octane-3,7-dione yields a mixture of the endo-3,endo-7-diol and endo-3, exo-7-diol (C8H14O2) isomers (5 and 6). These form (5)2·(6) co-crystals in the monoclinic P21/n space group (with Z = 6, Z′ = 1.5) rather than undergoing separation by means of fractional recrystallization or column chromatography. The molecule of 5 occupies a general position, whereas the molecule of 6 is disordered over two orientations across a centre of symmetry with occupancies of 0.463 (2) and 0.037 (2). Individual diol hydroxy groups associate around a pseudo-threefold screw axis by means of hydrogen bonding. The second hydroxy group of each diol behaves in a similar manner, generating a three-dimensional hydrogen-bonded network structure. This hydrogen-bond connectivity is identical to that present in three known helical tubuland diol–hydroquinone co-crystals, and the new crystal structure is even more similar to two homologous aliphatic diol co-crystals.

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Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2+

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x20007256 ◽

2020 ◽

Vol 76 (6) ◽

pp. 271-277

Author(s):

Hideaki Unno ◽

Shuhei Higuchi ◽

Shuichiro Goda ◽

Tomomitsu Hatakeyama

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Water Molecule ◽

Binding Affinity ◽

Hydroxy Group ◽

Carbohydrate Recognition ◽

Independent Manner ◽

Saxidomus Purpuratus ◽

Hydroxy Groups ◽

Complex Crystal

The C-type lectins SPL-1 and SPL-2 from the bivalve Saxidomus purpuratus are composed of A and B chains and of two B chains, respectively. They bind specific carbohydrates containing acetamido groups, such as N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc), in a Ca2+-independent manner. Unlike ordinary C-type lectins, which require Ca2+ ions for carbohydrate recognition, these lectins recognize specific carbohydrates mainly through interactions with the acetamido group without Ca2+ ions, even though Ca2+ enhances the binding affinity of these lectins, especially SPL-1. In the present study, the crystal structure of the SPL-1–GlcNAc complex in the presence of Ca2+ revealed that the binding of SPL-1 to GlcNAc is stabilized by hydrogen bonds to the water molecule(s) coordinating Ca2+, whereas in ordinary C-type lectins Ca2+ directly forms coordinate bonds to the hydroxy groups of carbohydrates. These differences may also allow SPL-1 and SPL-2 to recognize both GlcNAc and GalNAc, which have different orientations of the 4-hydroxy group.

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Synthesis, crystal structure and molecular conformation of (±)-1-oxoferruginol and (±)-shonanol

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1524/zkri.219.10.659.50814 ◽

2004 ◽

Vol 219 (10) ◽

Author(s):

Swastik Mondal ◽

Monika Mukherjee ◽

Arnab Roy ◽

Debabrata Mukherjee

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Diffraction Data ◽

Molecular Conformation ◽

Membered Ring ◽

Methyl Groups ◽

Single Bond ◽

X Ray Diffraction ◽

X Ray ◽

Chemical Structures

Abstract(±)-1-oxoferruginol and (±)-shonanol, two potential intermediates in the synthesis of tricyclic diterpenoid ferruginol, have been prepared and crystal structures of the compounds have been investigated using single-crystal X-ray diffraction data. The methyl groups of the isopropyl moiety in (±)-shonanol are disordered over two positions with occupation factors 0.65(1) and 0.35(1), respectively. Although the chemical structures of two compounds are very similar, a C—C single bond in the terminal six-membered ring of (±)-1-oxoferruginol is replaced by a C=C bond in (±)-shonanol, the quantitative isostructurality index calculations indicate that the structures are not isostructural. Intermolecular O—H…O hydrogen bonds between pairs of molecules in the compounds related by center of inversion lead to characteristic dimers forming R

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Crystal structure of β-D,L-fructose

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015016503 ◽

2015 ◽

Vol 71 (10) ◽

pp. o719-o720 ◽

Cited By ~ 2

Author(s):

Tomohiko Ishii ◽

Tatsuya Senoo ◽

Akihide Yoshihara ◽

Kazuhiro Fukada ◽

Genta Sakane

Keyword(s):

Crystal Structure ◽

Aqueous Solution ◽

Hydrogen Bonds ◽

Title Compound ◽

Three Dimensional ◽

Equimolar Mixture ◽

Compound C ◽

Dimensional Network ◽

Hydroxy Groups

The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of D- and L-fructose (1,3,4,5,6-pentahydroxyhexan-2-one,arabino-hexulose or levulose), and it was confirmed that D-fructose (or L-fructose) formed β-pyranose with a2C5(or5C2) conformation. In the crystal, two O—H...O hydrogen bonds between the hydroxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral molecules into a column along theaaxis. The columns are linked by other O—H...O hydrogen bonds between D- and L-fructose molecules, forming a three-dimensional network.

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Crystal structure ofcatena-poly[[[bis(pyridine-4-carbothioamide-κN1)cadmium]-di-μ-thiocyanato-κ2N:S;κ2S:N] methanol disolvate]

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989016002632 ◽

2016 ◽

Vol 72 (3) ◽

pp. 370-373 ◽

Cited By ~ 3

Author(s):

Tristan Neumann ◽

Inke Jess ◽

Christian Näther

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Title Compound ◽

Methanol Molecule ◽

Donor Group ◽

Asymmetric Unit ◽

Thiocyanate Anion ◽

Anionic Ligands ◽

Hydrogen Bonded

The asymmetric unit of the polymeric title compound, {[Cd(NCS)2(C6H6N2S)]·2CH3OH}n, consists of one cadmium(II) cation that is located on a centre of inversion as well as one thiocyanate anion, one pyridine-4-carbothioamide ligand and one methanol molecule in general positions. The CdIIcations are octahedrally coordinated by the pyridine N atom of two pyridine-4-carbothioamide ligands and by the S and N atoms of four thiocyanate anions and are linked into chains along [010] by pairs of anionic ligands. These chains are further linked into layers extending along (201) by intermolecular N—H...O and O—H...S hydrogen bonds. One of the amino H atoms of the pyridine-4-carbothioamide ligand is hydrogen-bonded to the O atom of a methanol molecule, and a symmetry-related methanol molecule is the donor group to the S atom of another pyridine-4-carbothioamide ligand whereby each of the pyridine-4-carbothioamide ligands forms two pairs of centrosymmetric N—H...S and O—H...S hydrogen bonds. The methanol molecules are equally disordered over two orientations.

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Crystal structure of racemic [(1R,2S,3R,4S,6S)-2,6-bis(furan-2-yl)-4-hydroxy-4-(thiophen-2-yl)cyclohexane-1,3-diyl]bis(thiophen-2-ylmethanone)

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989016009452 ◽

2016 ◽

Vol 72 (7) ◽

pp. 976-979 ◽

Cited By ~ 3

Author(s):

Ísmail Çelik ◽

Cem Cüneyt Ersanlı ◽

Mehmet Akkurt ◽

Hayrettin Gezegen ◽

Rahmi Köseoğlu

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Hydroxy Group ◽

Title Compound ◽

Furan Ring ◽

Chair Conformation ◽

Cyclohexane Ring ◽

Π Interactions ◽

Compound C

In the title compound, C28H22O5S3, the central cyclohexane ring adopts a chair conformation. The atoms of the furan ring attached to the 6-position of the central cyclohexane ring are disordered over two sets of sites with occupancies of 0.832 (5) and 0.168 (5). The hydroxy group is disordered over two positions (at the 4- and 6-positions of the cyclohexane ring) in the ratio 0.832 (5):0.168 (5). In the crystal, molecules are linked by C—H...O hydrogen bonds and C—H...π interactions, forming layers parallel to (100).

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Crystal structure of (2S/2R,3S/3R)-3-hydroxy-2-phenylchroman-4-one

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015001346 ◽

2015 ◽

Vol 71 (2) ◽

pp. o131-o132 ◽

Cited By ~ 1

Author(s):

Roumaissa Belguedj ◽

Sofiane Bouacida ◽

Hocine Merazig ◽

Aissa Chibani ◽

Abdelmalek Bouraiou

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Hydroxy Group ◽

Phenyl Ring ◽

Minor Component ◽

Chair Conformation ◽

Ring System ◽

Dihedral Angles ◽

Graph Set ◽

Title Molecule

In the title molecule, C15H12O3, the C atoms bearing the hydroxy group and the phenyl ring are disordered over two sets of sites with refined occupancies of 0.573 (7) and 0.427 (7). There is also disorder of the phenyl ring but the hydroxy group was refined as ordered. The dihedral angles between the benzene ring of the chromane ring system and the phenyl ring are 89.7 (2)° for the major component of disorder and 72.1 (3)° for the minor component. Both disorder components of the the dihydropyran ring are in a half-chair conformation. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers with anR22(10) graph-set motif. Weak C—H...π interactions link these dimers into ladders along [001].

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Crystal Structure of a Cationic Bile Salt Derivative ([3,5,7,12]-3-(2-naphthyloylamino)-7,12-dihydroxycholan-24-triethylammonium iodide)

Crystals ◽

10.3390/cryst9030135 ◽

2019 ◽

Vol 9 (3) ◽

pp. 135

Author(s):

Francisco Meijide ◽

María Pilar Vázquez-Tato ◽

Julio Seijas ◽

Santiago de Frutos ◽

Juan V. Trillo Novo ◽

...

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Quaternary Ammonium ◽

Electrostatic Interactions ◽

Amide Bond ◽

Orthorhombic Space Group ◽

Steroid Nucleus ◽

Quaternary Ammonium Group ◽

Group A ◽

Hydroxy Groups

The crystal structure of the iodide salt of a quaternary ammonium derivative of cholic acid having a naphthalene group attached to the 3rd position of the steroid nucleus through an amide bond ([3,5,7,12]-3-(2-naphthyloylamino)-7,12-dihydroxycholan-24-triethylammonium iodide) has been resolved. The compound crystallizes in the P212121 orthorhombic space group (a/Å = 10.9458(3); b/Å = 12.1625(3); c/Å = 28.4706(7)). The lateral chain adopts a fully extended tttt conformation because the quaternary ammonium group cannot participate in the formation of hydrogen bonds. The iodide ion is involved in the formation of hydrogen bonds as well as the amide group and the two steroid hydroxy groups. Hirshfeld surface analysis confirms that these contacts, as well as the electrostatic interactions, stabilize the structure. The helixes around the 21 screw axis are right-handed ones.

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Synthesis and crystal structures of two purpurin derivatives: 1,4-dihydroxy-2-propoxyanthraquinone and 2-butoxy-1,4-dihydroxyanthraquinone

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989017014724 ◽

2017 ◽

Vol 73 (11) ◽

pp. 1687-1691 ◽

Cited By ~ 1

Author(s):

Eric Bosch ◽

Emily N. McClain

Keyword(s):

Carbon Atom ◽

Hydrogen Bonds ◽

Sodium Hydride ◽

Maximum Deviation ◽

Independent Molecule ◽

Asymmetric Unit ◽

Terminal Carbon Atom ◽

Butyl Group ◽

Independent Molecules ◽

Hydroxy Groups

The title compounds were obtained by deprotonation of 1,2,4-trihydroxyanthraquinone (purpurin) using sodium hydride followed by reaction with either 1-bromopropane or 1-bromobutane. 1,4-Dihydroxy-2-propoxyanthraquinone crystallizes as a 1:1 solvate from acetonitrile, C17H14O5·CH3CN. The anthraquinone core of the molecule is essentially planar and both hydroxy groups participate in intramolecular O—H...O (carbonyl) hydrogen bonds. The propyl chain is angled slightly above the plane of the anthraquinone moiety with a maximum deviation of 0.247 (2) Å above the plane for the terminal carbon atom. In contrast, 2-butoxy-1,4-dihydroxyanthraquinone, C18H16O5, crystallizes from nitromethane with two independent molecules in the asymmetric unit. The anthraquinone core of each independent molecule is essentially planar and both hydroxy groups on both molecules participate in intramolecular O—H...O(carbonyl) hydrogen bonds. The butyl chain in one molecule is also angled slightly above the plane of the anthraquinone moiety, with a maximum deviation of 0.833 (5) Å above the plane for the terminal carbon atom. In contrast, the butyl group on the second molecule is twisted out of the plane of the anthraquinone core with a torsion angle of 65.1 (3)°, resulting in a maximum deviation of 1.631 (5) Å above the plane for the terminal carbon atom.

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Crystal structure of 7-{[bis(pyridin-2-ylmethyl)amino]methyl}-5-chloroquinolin-8-ol

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015022410 ◽

2015 ◽

Vol 71 (12) ◽

pp. 1545-1547

Author(s):

Koji Kubono ◽

Kimiko Kado ◽

Yukiyasu Kashiwagi ◽

Keita Tani ◽

Kunihiko Yokoi

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Hydrogen Bonds ◽

Hydroxy Group ◽

Title Compound ◽

Dihedral Angles ◽

Π Interactions ◽

Compound C ◽

Centroid Distance ◽

Ring Motif

In the title compound, C22H19ClN4O, the quinolinol moiety is almost planar [r.m.s. deviation = 0.012 Å]. There is an intramolecular O—H...N hydrogen bond involving the hydroxy group and a pyridine N atom forming anS(9) ring motif. The dihedral angles between the planes of the quinolinol moiety and the pyridine rings are 44.15 (9) and 36.85 (9)°. In the crystal, molecules are linkedviaC—H...O hydrogen bonds forming inversion dimers with anR44(10) ring motif. The dimers are linked by C—H...N hydrogen bonds, forming ribbons along [01-1]. The ribbons are linked by C—H...π and π–π interactions [inter-centroid distance = 3.7109 (11) Å], forming layers parallel to (01-1).

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