Molecular conformation of sodium heparan sulphate in the condensed phase

H F Elloway; E D T Atkins

doi:10.1042/bj1610495

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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On cellulose spatial organization and interactions as unraveled by diffraction and spectroscopic methods throughout the 20th century

Pure and Applied Chemistry ◽

10.1515/pac-2021-0306 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Adriana Šturcová

Keyword(s):

Hydrogen Bonds ◽

Spatial Organization ◽

Molecular Conformation ◽

Hydrophobic Interactions ◽

X Ray Diffraction ◽

X Ray ◽

Sum Frequency ◽

Polarized Infrared Spectroscopy ◽

Cellulose Crystal Structure

Abstract This contribution attempts to describe the path towards determination of cellulose crystal structure down to atomic coordinates, towards the determination of its molecular conformation, as well as towards the details of the intricate pattern of hydrogen bonds and their dynamics. This path started at the beginning of the 20th century with X-ray diffraction, continued with electron diffraction, infrared and Raman spectroscopy, and significant knowledge was gained by methods of NMR spectroscopy. Towards the end of the 20th century and at the beginning of the 21st century, X-ray diffraction in conjunction with neutron diffraction provided the position of hydrogens, which led to detailed description of the geometry of hydrogen bonding network in cellulose. Quantum chemical and molecular dynamics calculations, polarized infrared spectroscopy and sum frequency generation vibrational spectroscopy were used to identify the origins of the vibrational modes in cellulose and to describe their extensive coupling mediated by hydrogen bonds. The role of amphiphilic character of cellulose macromolecule (and consequent hydrophobic interactions) in cellulose properties and behavior has been gaining more recognition in the 21st century.

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Acemetacin cocrystals and salts: structure solution from powder X-ray data and form selection of the piperazine salt

IUCrJ ◽

10.1107/s2052252514004229 ◽

2014 ◽

Vol 1 (2) ◽

pp. 136-150 ◽

Cited By ~ 37

Author(s):

Palash Sanphui ◽

Geetha Bolla ◽

Ashwini Nangia ◽

Vladimir Chernyshev

Keyword(s):

Hydrogen Bonds ◽

Dissolution Rate ◽

Aqueous Medium ◽

Acid Amide ◽

Three Dimensional ◽

X Ray Diffraction ◽

Reference Drug ◽

X Ray ◽

Time Period ◽

Solid Form

Acemetacin (ACM) is a non-steroidal anti-inflammatory drug (NSAID), which causes reduced gastric damage compared with indomethacin. However, acemetacin has a tendency to form a less soluble hydrate in the aqueous medium. We noted difficulties in the preparation of cocrystals and salts of acemetacin by mechanochemical methods, because this drug tends to form a hydrate during any kind of solution-based processing. With the objective to discover a solid form of acemetacin that is stable in the aqueous medium, binary adducts were prepared by the melt method to avoid hydration. The coformers/salt formers reported are pyridine carboxamides [nicotinamide (NAM), isonicotinamide (INA), and picolinamide (PAM)], caprolactam (CPR),p-aminobenzoic acid (PABA), and piperazine (PPZ). The structures of an ACM–INA cocrystal and a binary adduct ACM–PABA were solved using single-crystal X-ray diffraction. Other ACM cocrystals, ACM–PAM and ACM–CPR, and the piperazine salt ACM–PPZ were solved from high-resolution powder X-ray diffraction data. The ACM–INA cocrystal is sustained by the acid...pyridine heterosynthon and N—H...O catemer hydrogen bonds involving the amide group. The acid...amide heterosynthon is present in the ACM–PAM cocrystal, while ACM–CPR contains carboxamide dimers of caprolactam along with acid–carbonyl (ACM) hydrogen bonds. The cocrystals ACM–INA, ACM–PAM and ACM–CPR are three-dimensional isostructural. The carboxyl...carboxyl synthon in ACM–PABA posed difficulty in assigning the position of the H atom, which may indicate proton disorder. In terms of stability, the salts were found to be relatively stable in pH 7 buffer medium over 24 h, but the cocrystals dissociated to give ACM hydrate during the same time period. The ACM–PPZ salt and ACM–nicotinamide cocrystal dissolve five times faster than the stable hydrate form, whereas the ACM–PABA adduct has 2.5 times faster dissolution rate. The pharmaceutically acceptable piperazine salt of acemetacin exhibits superior stability, faster dissolution rate and is able to overcome the hydration tendency of the reference drug.

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Crystal structure of 3-benzyl-2-[(E)-2-(furan-2-yl)ethenyl]-2,3-dihydroquinazolin-4(1H)-one and 3-benzyl-2-[(E)-2-(thiophen-2-yl)ethenyl]-2,3-dihydroquinazolin-4(1H)-one from synchrotron X-ray diffraction

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989017017479 ◽

2018 ◽

Vol 74 (1) ◽

pp. 10-14

Author(s):

Flavien A. A. Toze ◽

Vladimir P. Zaytsev ◽

Lala V. Chervyakova ◽

Elisaveta A. Kvyatkovskaya ◽

Pavel V. Dorovatovskii ◽

...

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Axial Position ◽

Isatoic Anhydride ◽

X Ray Diffraction ◽

X Ray ◽

Bond Angles ◽

Pyramidal Geometry ◽

Three Component Reaction ◽

Racemic Crystals

The chiral title compounds, C21H18N2O2, (I), and C21H18N2OS, (II) – products of the three-component reaction between benzylamine, isatoic anhydride and furyl- or thienyl-acrolein – are isostructural and form isomorphous racemic crystals. The tetrahydropyrimidine ring in (I) and (II) adopts a sofa conformation. The amino N atom has a trigonal–pyramidal geometry [sum of the bond angles is 347.0° for both (I) and (II)], whereas the amido N atom is flat [sum of the bond angles is 359.3° for both (I) and (II)]. The furyl- and thienylethenyl substituents in (I) and (II) are planar and the conformation about the bridging C=C bond isE. These bulky fragments occupy the axial position at the quaternary C atom of the tetrahydropyrimidine ring, apparently, due to steric reasons. In the crystals, molecules of (I) and (II) form hydrogen-bonded helicoidal chains propagating along [010] by strong intermolecular N—H...O hydrogen bonds.

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Crystal and molecular structure of diorganoammonium oxalatotrimethylstannate, [R2NH2][Me3Sn(C2O4)] (R=i-Bu, cyclohexyl)

Main Group Metal Chemistry ◽

10.1515/mgmc-2011-0018 ◽

2011 ◽

Vol 34 (5-6) ◽

pp. 127-130 ◽

Cited By ~ 3

Author(s):

Yaya Sow ◽

Libasse Diop ◽

Kieran C. Molloy ◽

Gabrielle Kociok-Köhn

Keyword(s):

Molecular Structure ◽

Hydrogen Bonds ◽

Diffraction Study ◽

Crystal And Molecular Structure ◽

X Ray Diffraction ◽

X Ray ◽

Trigonal Bipyramidal ◽

Trans Complex ◽

A Chain ◽

Distorted Trigonal Bipyramidal

Abstract The title compounds [R2NH2][C2O4SnMe3](R=i-Bu, Cy), in which tin atoms adopt a distorted trigonal bipyramidal configuration, have been prepared and submitted to an X-ray diffraction study. These compounds have been obtained from the reaction of (Cy2NH2)2C2O4·H2O or (i-Bu2NH2)2C2O4 with SnMe3Cl. In both [R2NH2][C2O4SnMe3] compounds, the trans complex has an almost regular trigonal bipyramidal geometry around the tin atom. The SnMe3 residues are connected as a chain with bridging oxalate anions in a trans-SnC3O2 framework, the oxygen atoms being in axial positions. The cations connect linear adjacent chains through NH…O hydrogen bonds giving layered structures.

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Salts of purine alkaloids caffeine and theobromine with 2,6-dihydroxybenzoic acid as coformer: structural, theoretical, thermal and spectroscopic studies

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229621010883 ◽

2021 ◽

Vol 77 (11) ◽

Author(s):

Mateusz Gołdyn ◽

Anna Komasa ◽

Mateusz Pawlaczyk ◽

Aneta Lewandowska ◽

Elżbieta Bartoszak-Adamska

Keyword(s):

Hydrogen Bonds ◽

Water Solubility ◽

Theoretical Calculations ◽

Spectroscopic Studies ◽

X Ray Diffraction ◽

Dihydroxybenzoic Acid ◽

Scanning Calorimetry ◽

X Ray ◽

Purine Alkaloids ◽

Vis Spectroscopy

The study of various forms of pharmaceutical substances with specific physicochemical properties suitable for putting them on the market is one of the elements of research in the pharmaceutical industry. A large proportion of active pharmaceutical ingredients (APIs) occur in the salt form. The use of an acidic coformer with a given structure and a suitable pK a value towards purine alkaloids containing a basic imidazole N atom can lead to salt formation. In this work, 2,6-dihydroxybenzoic acid (26DHBA) was used for cocrystallization of theobromine (TBR) and caffeine (CAF). Two novel salts, namely, theobrominium 2,6-dihydroxybenzoate, C7H9N4O2 +·C7H5O4 − (I), and caffeinium 2,6-dihydroxybenzoate, C8H11N4O2 +·C7H5O4 − (II), were synthesized. Both salts were obtained independently by slow evaporation from solution, by neat grinding and also by microwave-assisted slurry cocrystallization. Powder X-ray diffraction measurements proved the formation of the new substances. Single-crystal X-ray diffraction studies confirmed proton transfer between the given alkaloid and 26DHBA, and the formation of N—H...O hydrogen bonds in both I and II. Unlike the caffeine cations in II, the theobromine cations in I are paired by noncovalent N—H...O=C interactions and a cyclic array is observed. As expected, the two hydroxy groups in the 26DHBA anion in both salts are involved in two intramolecular O—H...O hydrogen bonds. C—H...O and π–π interactions further stabilize the crystal structures of both compounds. Steady-state UV–Vis spectroscopy showed changes in the water solubility of xanthines after ionizable complex formation. The obtained salts I and II were also characterized by theoretical calculations, Fourier-transform IR spectroscopy (FT–IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and elemental analysis.

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Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

Letters in Organic Chemistry ◽

10.2174/1570178619666211231105233 ◽

2021 ◽

Vol 19 ◽

Author(s):

Kikuko Iida ◽

Toyokazu Muto ◽

Miyuki Kobayashi ◽

Hiroaki Iitsuka ◽

Kun Li ◽

...

Keyword(s):

Hydrogen Bonds ◽

Title Compound ◽

Molecular Conformation ◽

Weak Interactions ◽

Carbonyl Oxygen ◽

Hirshfeld Surface ◽

Molecular Surface ◽

Hydrogen Atoms ◽

X Ray ◽

Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

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Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229621013607 ◽

2022 ◽

Vol 78 (2) ◽

Author(s):

Sehrish Akram ◽

Arshad Mehmood ◽

Sajida Noureen ◽

Maqsood Ahmed

Keyword(s):

Hydrogen Bonds ◽

Glutamic Acid ◽

Single Crystal ◽

Diffraction Data ◽

Density Functional ◽

Quantitative Estimation ◽

Topological Analysis ◽

Pyroglutamic Acid ◽

X Ray Diffraction ◽

X Ray

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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Silver(I)-Saccharinato Complexes with 2-(Aminomethyl)pyridine and 2-(2-Aminoethyl)pyridine Ligands: [Ag(sac)(ampy)] and [Ag2(sac)2(μ-aepy)2]

Zeitschrift für Naturforschung B ◽

10.1515/znb-2005-0912 ◽

2005 ◽

Vol 60 (9) ◽

pp. 978-983 ◽

Cited By ~ 22

Author(s):

Sevim Hamamci ◽

Veysel T. Yilmaz ◽

William T. A. Harrison

Keyword(s):

Thermal Analysis ◽

Hydrogen Bonds ◽

Monoclinic Space Group ◽

Stacking Interactions ◽

Coordination Geometry ◽

X Ray Diffraction ◽

Triclinic Space Group ◽

Space Group ◽

X Ray ◽

Pyridine Ligands

Two new saccharinato-silver(I) (sac) complexes, [Ag(sac)(ampy)] (1), and [Ag2(sac)2(μ-aepy)2] (2), [ampy = 2-(aminomethyl)pyridine, aepy = 2-(2-aminoethyl)pyridine], have been prepared and characterized by elemental analysis, IR spectroscopy, thermal analysis and single crystal X-ray diffraction. Complexes 1 and 2 crystallize in the monoclinic space group P21/c and triclinic space group P1̄, respectively. The silver(I) ions in both complexes 1 and 2 exhibit a distorted T-shaped AgN3 coordination geometry. 1 consists of individual molecules connected into chains by N-H···O hydrogen bonds. There are two crystallographically distinct dimers in the unit cell of 2 and in each dimer, the aepy ligands act as a bridge between two silver(I) centers, resulting in short argentophilic contacts [Ag1···Ag1 = 3.0199(4) Å and Ag2···Ag2 = 2.9894(4) Å ]. Symmetry equivalent dimers of 2 are connected by N-H···O hydrogen bonds into chains, which are further linked by aromatic π(py)···π(py) stacking interactions into sheets.

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Evolution structurale de la nacrite en fonction de la nature des molécules organiques intercalees

Journal of Applied Crystallography ◽

10.1107/s0021889800011730 ◽

2000 ◽

Vol 33 (6) ◽

pp. 1351-1359 ◽

Cited By ~ 11

Author(s):

A. Ben Haj Amara ◽

H. Ben Rhaiem ◽

A. Plançon

Keyword(s):

Ir Spectroscopy ◽

Hydrogen Bonds ◽

Dimethyl Sulfoxide ◽

Organic Molecules ◽

Interlayer Space ◽

X Ray Diffraction ◽

X Ray ◽

Intercalated Compounds ◽

Xrd Study ◽

Intercalation Process

Nacrite has been intercalated with two polar organic molecules: dimethyl sulfoxide (DMSO) andN-methylacetamide (NMA). The homogeneous nacrite complexes have been studied by X-ray diffraction (XRD) and infrared (IR) spectroscopy. The XRD study is based on a comparison between experimental and calculated patterns. The structures of the intercalated compounds have been determined, including the mutual positions of the layers after intercalation and the positions of the intercalated molecules in the interlayer space. It has been shown that the intercalation process causes not only a swelling of the interlayer space but also a shift in the mutual in-plane positions of the layers. This shift depends on the nature of the intercalated molecules and is related to their shape and the hydrogen bonds which are established with the surrounding surfaces. For a given molecule, the intercalation process is the same for the different polytypes of the kaolinite family. These XRD results are consistent with those of IR spectroscopy.

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