The effect of hydrogen bonds on the conformation of glycosphingolipids. Methylated and unmethylated cerebroside studied by X-ray single crystal analysis and model calculations

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

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Crystal structure of tris(pyridine)(salicylaldehyde semicarbazonato(2-))cobalt(III)-trichloropyridinecobaltate(II) at 293 and 120K

Journal of the Serbian Chemical Society ◽

10.2298/jsc0701063b ◽

2007 ◽

Vol 72 (1) ◽

pp. 63-71 ◽

Cited By ~ 4

Author(s):

Goran Bogdanovic ◽

Vukadin Leovac ◽

Ljiljana Vojinovic-Jesic ◽

Biré-Spasojevic De

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Single Crystal ◽

Intermolecular Interaction ◽

Complex Anion ◽

Octahedral Geometry ◽

Pyridine Ligand ◽

Similar Composition ◽

X Ray ◽

Preferential Position

The crystal structure of [CoIII(L)(py)3][CoIICl3(py)] (H2L=salicylaldehyde semicarbazone)was determined by X-ray analysis based on two single crystal X-ray experiments performed at 120 K and 293 K, respectively. It was found that the pyridine ligand of the complex anion is disordered over two positions. The preferential position of this pyridine found at120Kwas explained in terms of the C-H...Cl intermolecular interaction between the tetrahedral [CoII(py)Cl3]- anions. The mer-octahedral geometry of the cation in the presented crystal structure was compared with previously published structures of similar composition, [CoIII(L1)(py)3]+[CoIICl3(py)]-?EtOH and [CoIII(LI)(py)3]+I3-(H2LI = salicylaldehyde S-methylisothiosemicarbazone). Although the tetrahedral [CoIICl3(py)]- anions possess the same charge, they mutually form different intermolecular interactions which can be realized either by C-H...Cl hydrogen bonds or by ?-? interactions between the pyridine rings.

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Honeycomb molecular network based upon a hydrate of 4,6-dichlororesorcinol and the photoproduct rtct-tetrakis(pyridin-4-yl)cyclobutane

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229621000590 ◽

2021 ◽

Vol 77 (2) ◽

pp. 111-115

Author(s):

Carlos L. Santana ◽

Jessica D. Battle ◽

Daniel K. Unruh ◽

Ryan H. Groeneman

Keyword(s):

Hydrogen Bonds ◽

Water Molecule ◽

Single Crystal ◽

Organic Materials ◽

Molecular Network ◽

Molecular Solids ◽

X Ray ◽

Bridging Ligand ◽

Metal Organic ◽

Cyclobutane Ring

The formation of a self-interpenetrated honeycomb molecular network based upon 4,6-dichlororesorcinol (4,6-diCl res), a water molecule, and the photoproduct rtct-tetrakis(pyridin-4-yl)cyclobutane ( rtct -TPCB) is reported. Interestingly, only three of the four pyridine rings on the central cyclobutane ring are found to engage in O—H...N hydrogen bonds with either the 4,6-diCl res or an included water molecule, resulting in a three-connected net. Notably, the solid (4,6-diCl res)·( rtct -TPCB)·(H2O), C6H4Cl2O2·C24H20N4·H2O, contains channels that run along the crystallographic b axis, which are found to be interpenetrated. Although rtct -TPCB has been employed as a bridging ligand in the formation of numerous metal–organic materials, surprisingly neither the single-component X-ray structure nor any multi-component molecular solids based upon this stereoisomer have been reported previously. Lastly, the single-crystal X-ray structure of the photoproduct rtct -TPCB is also reported.

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1-[N-Methyl-N-(Phenyl)amino]-3- (4-Methylphenyl)Thiourea

Molbank ◽

10.3390/m1052 ◽

2019 ◽

Vol 2019 (1) ◽

pp. M1052 ◽

Cited By ~ 1

Author(s):

Chien Yeo ◽

Edward Tiekink

Keyword(s):

Hydrogen Bond ◽

Solid State ◽

Hydrogen Bonds ◽

Single Crystal ◽

Elemental Analysis ◽

Title Compound ◽

Molecular Conformation ◽

Phenyl Hydrazine ◽

X Ray ◽

X Ray Crystallography

The title compound, 1-[N-methyl-N-(phenyl)amino]-3-(4-methylphenyl)thiourea (1), was synthesized by the reaction of 1-methyl-1-phenyl hydrazine and 4-tolyl isothiocyanate, and was characterized by spectroscopy (1H and 13C{1H} NMR, IR, and UV), elemental analysis as well as by single crystal X-ray crystallography. In the solid state, the molecule exists as the thioamide tautomer and features an anti-disposition of the thioamide–N–H atoms; an intramolecular N–H⋯N hydrogen bond is noted. The molecular conformation resembles that of the letter L. In the molecular packing, thioamide-N1–H⋯S1(thione) hydrogen bonds lead to centrosymmetric eight-membered {⋯HNCS}2 synthons. The dimers are assembled into a supramolecular layer in the bc-plane by phenyl- and methyl-C–H⋯π(phenyl) interactions.

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Zum System Wasser—Fluorwasserstoff: Phasenverhalten und Kristallstruktur von 2 D2O• 3 DF, einer deuterierten Verbindung ohne protoniertes Analogon / Concerning the System Water—Hydrogen Fluoride: Phase Behaviour and Crystal Structure of 2 D2O· 3 DF, a Deuterated Compound Lacking the Protonated Analogue

Zeitschrift für Naturforschung B ◽

10.1515/znb-1989-1106 ◽

1989 ◽

Vol 44 (11) ◽

pp. 1359-1364 ◽

Cited By ~ 7

Author(s):

Wolfgang Poll ◽

Michaela Lohmeyer ◽

Dietrich Mootz

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Single Crystal ◽

Phase Behaviour ◽

X Ray ◽

Quasibinary System ◽

Molecular Adduct ◽

Oxonium Salt ◽

System Water ◽

Additional Phase

The melting diagram of the quasibinary system D2O— DF was determined by low-temperature DTA and X-ray powder diffraction. It was found to be largely similar to that of the corresponding non-deuterated system H2O—HF with the striking exception of an additional phase with a composition of its own, 2D2O· 3 DF, and stable between ca. —78 and —71°C. Its structure, determined from single-crystal MoKā diffractometer data at —150°C, is rhombohedral (space group R3c, Z = 6, a = 769.9, c = 1242.1 pm) and strongly related to that of NH, · 4 HF or NH4[F(HF)3] with also seven H (as to be compared to D) and five non-H (non-D) atoms per formula unit. But with the O atom involved in four hydrogen bonds, one O · · · O and three O · · · F. at distances of 273.9 and 259.5 pm, respectively, the compound appears to be a molecular adduct rather than an oxonium salt. The D atoms in the hydrogen bonds are distributed over two positions each. — The remaining intermediary phases of the deuterated system, i. e. D2O · DF, D2O· 2 DF and D2O · 4 DF, are isotypic to their protonated counterparts of known crystal structure. For D2O · DF and D2O-2 DF these results from powder patterns were confirmed by two more single-crystal studies. The ionic structures — D3OF and D3O[F(DF)], respectively — show no distinctive effect of the H/D substitution even on details of the interatomic geometries.

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Spectral, Thermal, Crystal Structure, Hirshfeld Surface Analyses and Biological Activities of New Hydrazinium Dipicolinato Copper(II) Tetrahydrate

Asian Journal of Chemistry ◽

10.14233/ajchem.2019.21958 ◽

2019 ◽

Vol 31 (8) ◽

pp. 1755-1761

Author(s):

K. Naresh ◽

B.N. Sivasankar

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Single Crystal ◽

Water Clusters ◽

Hirshfeld Surface ◽

Water Molecules ◽

X Ray ◽

Biological Studies ◽

Calf Thymus ◽

Hydrazinium Cation

A new copper complex of pyridine-2,6-dicarboxylate containing hydrazinium cation, formulated as (N2H5)2[Cu(PDC)2]·4H2O (PDC = pyridine-2,6-dicarboxylate) has been synthesized from copper(II) nitrate, hydrazine hydrate and pyridine-2,6-dicarboxylic acid as a single crystal and characterized by elemental analysis and spectroscopic (IR and UV-visible), thermal (TG/DTG), single crystal X-ray diffraction and biological studies. A six-coordinate complex with a distorted octahedral geometry around Cu(II) ion is proposed and confirmed by X-ray single crystal method. The structure reveals that two pyridine-2,6-dicarboxylate species acting as tridentate ligands and hydrazinium cation present as a counter ion along with non-coordinated four water molecules. The structural units of copper(II) is mutually held by the hydrogen bonds and π···π and C–O···π interactions. The copper(II) complex is connected to one another via O–H···O hydrogen bonds, forming water clusters, which plays an important role in the stabilization of the crystal structure. In the water clusters, the water molecules are trapped by the cooperative association of coordination interactions as well as hydrogen bonds. Both cation and anion interactions and crystal from various types of intermolecular contacts and their importance were explored using Hirshfeld surface analysis. This indicates that O···H/H···O interactions are the superior interactions conforming excessive H-bond in the molecular structure. The interaction of copper(II) complex with calf thymus DNA (CT-DNA) was investigated by electronic absorption spectroscopic technique. The electronic evidence strongly shows that the compound interacts with calf thymus through intercalation with a binding constant of Kb = 5.7 × 104 M–1.

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On the Origin of the Red Color of Aqueous-Solutions of 2,3-Dichloro-5,6-Dicyano-1,4-Benzoquinone (ddq). Crystal Structure of the Ammonium Salt of 2-Cyano-5,6-Dichloro-3-Hydroxy-1,4-Benzoquinone

Australian Journal of Chemistry ◽

10.1071/ch9870625 ◽

1987 ◽

Vol 40 (3) ◽

pp. 625 ◽

Cited By ~ 1

Author(s):

HD Becker ◽

BW Skelton ◽

AH White

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Aqueous Solutions ◽

Single Crystal ◽

Ammonium Salt ◽

Structure Determination ◽

Aqueous Ethanol ◽

X Ray ◽

Red Color ◽

Hydrolysis Of

Hydrolysis of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone in aqueous ethanol gives the deep-red coloured ammonium salt of a monocyano-dichloro-monohydroxy-benzoquinone which crystallizes in the tetragonal space group I41 /a, a 20.832(5), c 8.618(2) �, Z 16. Single-crystal X-ray structure determination (R 0.036 for 1185 'observed' reflections) show the presence of ammonium cations forming hydrogen bonds in the lattice alternatingly with the tautomeric anion of 2-cyano-5,6-dichloro-3-hydroxy-1,4-benzoquinone and 3-cyano-5,6-dichloro-4-hydroxy-1,2-benzoquinone.

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Notizen: Solid State Structure of N,N-Dibenzylhydroxylamine

Zeitschrift für Naturforschung B ◽

10.1515/znb-1995-0441 ◽

1995 ◽

Vol 50 (4) ◽

pp. 699-701 ◽

Cited By ~ 1

Author(s):

Norbert W. Mitzel ◽

Jürgen Riede ◽

Klaus Angermaier ◽

Hubert Schmidbaur

Keyword(s):

Solid State ◽

Hydrogen Bonds ◽

Single Crystal ◽

Unit Cell ◽

Monoclinic Space Group ◽

State Structure ◽

X Ray Diffraction ◽

Space Group ◽

Solid State Structure ◽

X Ray

The solid-state structure of N,N-dibenzylhydroxylamine (1) has been determined by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P 21/n with four formula units in the unit cell. N,N-dibenzylhydroxylamine dimerizes to give N2O2H2 sixmembered rings as a result of the formation of two hydrogen bonds O - H ··· N in the solid state.

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Preparation and Crystal Structure Er (III) Complex with 2-Formylbenzenesulfonic Sodium-3-Thiosemicarbazide

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.396-398.993 ◽

2011 ◽

Vol 396-398 ◽

pp. 993-996

Author(s):

Xi Shi Tai

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Single Crystal ◽

Layered Structure ◽

Ir Spectrum ◽

Two Dimensional ◽

Single Crystal Diffraction ◽

Element Analysis ◽

X Ray ◽

Complex Forms

A novel ligand containing sulfonic has been synthesized using 2-formylbenzenesulfonic sodium and 3-thiosemicarbazide as starting materials, and a Er (III) complex was synthesized. The ligand was characterized by element analysis and IR spectrum. The crystal structure of the Er (III) complex was determined by X-ray single crystal diffraction. The results showed that the compound was triclinic, with P-1, a = 1.0596(4) nm, b = 1.3700(5) nm, c = 1.8305(7) nm, V = 2.4726(16) nm3, Z=2, M r= 1244.42, De =1.671 g/cm3, T = 273(2) K, F (000) = 1270, R = 0.0517 and wR = 0.1124. The complex forms two-dimensional layered structure through hydrogen bonds and π-π stacking.

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The modulated structure of the calcium aluminate Ca6(AlO2)12·Bi2O3

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768110035792 ◽

2010 ◽

Vol 66 (6) ◽

pp. 585-593 ◽

Cited By ~ 2

Author(s):

O. Pérez ◽

S. Malo ◽

M. Hervieu

Keyword(s):

Single Crystal ◽

Calcium Aluminate ◽

Three Dimensional ◽

X Ray Diffraction ◽

Electron Pairs ◽

Modulated Structure ◽

X Ray ◽

Trigonal Bipyramidal ◽

Superspace Formalism ◽

Single Crystal Analysis

Bismuth calcium aluminate, Bi2Ca6Al12O27, has been prepared as a ceramic and a single crystal. Analysis of reciprocal space using both electron and X-ray diffraction show an R-centred hexagonal unit cell: a = b = 17.3892 (4), c = 6.986 (1) Å. Additional weak reflections are observed; they require the introduction of a modulation wavevector q = 0.0453 (2)c* for indexing. The modulated structure has been solved using the superspace formalism [superspace group X\overline{3}(00\gamma)0]. A framework of corner-sharing AlO4 tetrahedra forms corrugated sixfold rings and uncommon triple rings. The Ca2+ cations exhibit an eightfold coordination sphere; edge-sharing CaO8 polyhedra form intertwinned zigzagging rows along c creating a three-dimensional net. Bi atoms are located in large hexagonal tunnels parallel to c and form Bi2O3 pairs, which adopt a trigonal bipyramidal configuration. The 6s 2 lone-electron pairs (Lp) point along c, in the opposite direction to the three Bi—O strong bonds to form two BiO3Lp tetrahedra with a common base. Different orientations of the Bi2O3Lp2 pairs, rotated by 60° around c, are observed. Their stacking modes in each of the hexagonal tunnels are described. The sequence of the stacking varies along c in each of the tunnels.

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