scholarly journals Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds?

2019 ◽  
Vol 28 (11) ◽  
pp. 1966-1972
Author(s):  
Jimin Wang
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Photoactive Yellow Protein ◽  
X Ray ◽  
Low Barrier Hydrogen Bonds

The protonation of the ethylenediphosphinetetraacetate anion and the crystal structure of the bis (hydrogen bromide) of ethylenediphosphinetetraacetic acid

1981 ◽  
Vol 46 (12) ◽  
pp. 3063-3073 ◽  
Author(s):  
Jana Podlahová ◽  
Bohumil Kratochvíl ◽  
Vratislav Langer ◽  
Josef Šilha ◽  
Jaroslav Podlaha
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Free Acid ◽  
Hydrogen Bromide ◽  
Carboxyl Groups ◽  
Spectroscopic Methods ◽  
X Ray ◽  
Partial Formation

The equilibria and mechanism of addition of protons to the ethylenediphosphinetetraacetate anion (L4-) were studied in solution by the UV, IR, 1H and 31P NMR spectroscopic methods. A total of six protons can be bonded to the anion. They are added stepwise, first with partial formation of zwitterions containing P-H bonds, which then dissociate with formation of the free acid, H4L, where all four protons are bonded in carboxyl groups. The formation of zwitterions is strongly dependent on the concentration. In the final stage, the acid bonds two additional protons to form the bis-phosphonium cation, H6L2+. A number of isostructural salts containing this cation, H4L.2 HX (X = Cl, Br, I), have been prepared. The X-ray crystal structure determination of the bromide confirmed the expected arrangement. The bromide crystals are monoclinic, a = 578.2, b = 1 425.0, c = 1 046.7 pm, β = 103.07° with a space group of P21/c, Z = 2. The final R factor was 0.059 based on 1 109 observed reflections. The structure consists of H6L2+ cations containing protons bonded to phosphorus atoms (P-H distance 134 pm) and of bromide anions, located in gaps which are also sufficiently large for I- anions in the isostructural iodide. The interbonding of phosphonium cations proceeds through hydrogen bonds, C-OH...O=C, in which the O...O distance is 275.3 pm.

Crystal structure of oxybutynin hydrochloride hemihydrate, C22H32NO3Cl(H2O)0.5

2019 ◽  
Vol 34 (1) ◽  
pp. 50-58
Author(s):  
James A. Kaduk ◽  
Nicholas C. Boaz ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Layered Crystal ◽  
Powder Diffraction File ◽  
X Ray ◽  
Layered Crystal Structure ◽  
Oxybutynin Hydrochloride

The crystal structure of oxybutynin hydrochloride hemihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Oxybutynin hydrochloride hemihydrate crystallizes in space group I2/a (#15) with a = 14.57266(8), b = 8.18550(6), c = 37.16842(26) Å, β = 91.8708(4)°, V = 4421.25(7) Å3, and Z = 8. The compound exhibits X-ray-induced photoreduction of the triple bond. Prominent in the layered crystal structure is the N–H⋅⋅⋅Cl hydrogen bond between the cation and anion, as well as O–H⋅⋅⋅Cl hydrogen bonds from the water molecule and hydroxyl group of the oxybutynin cation. C–H⋅⋅⋅Cl hydrogen bonds also contribute to the crystal energy, and help determine the conformation of the cation. The powder pattern is included in the Powder Diffraction File™ as entry 00-068-1305.

scholarly journals Powder study of 3-azabicyclo[3.3.1]nonane-2,4-dione form 2

2006 ◽  
Vol 62 (7) ◽  
pp. o3046-o3048 ◽  
Author(s):  
Ashley T Hulme ◽  
Philippe Fernandes ◽  
Alastair Florence ◽  
Andrea Johnston ◽  
Kenneth Shankland
Keyword(s):  
Crystal Structure ◽  
Simulated Annealing ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Title Compound ◽  
Variable Temperature ◽  
Polycrystalline Sample ◽  
Asymmetric Unit ◽  
X Ray ◽  
Compound C

A polycrystalline sample of a new polymorph of the title compound, C8H11NO2, was produced during a variable-temperature X-ray powder diffraction study. The crystal structure was solved at 1.67 Å resolution by simulated annealing from laboratory powder data collected at 250 K. Subsequent Rietveld refinement yielded an R wp of 0.070 to 1.54 Å resolution. The structure contains two molecules in the asymmetric unit, which form a C 2 2(8) chain motif via N—H...O hydrogen bonds.

scholarly journals 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

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.

3,3′-N,N′-Bis(amino)-2,2′-bipyridine — An unusually methylation-resistant amine

2011 ◽  
Vol 89 (8) ◽  
pp. 971-977
Author(s):  
Danielle M. Chisholm ◽  
Robert McDonald ◽  
J. Scott McIndoe
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Complex Mixtures ◽  
Amino Groups ◽  
Intramolecular Hydrogen Bonds ◽  
X Ray ◽  
Intramolecular Hydrogen

Methylation of aromatic amino groups is usually straightforward, but the formation of two intramolecular hydrogen bonds in 3,3′-N,N′-bis(amino)-2,2′-bipyridine and (or) the potential for ring methylation prevents the clean tetramethylation of this molecule. Numerous attempts to make 3,3′-N,N′-bis(dimethylamino)-2,2′-bipyridine produced only complex mixtures of variously methylated products, and the only isolated molecule was 3,3′-N,N′-bis(methylamino)-2,2′-bipyridine, for which an X-ray crystal structure was obtained.

Systhesis, Characterization and Spectroscopic Properties of (2E,6E)-2,6-Bis(2,3,4-tri-methoxy-benzylidene)cyclohexanone

2011 ◽  
Vol 396-398 ◽  
pp. 2338-2341
Author(s):  
Xing Chuan Wei ◽  
Zhi Li Liu ◽  
Kun Zhang ◽  
Zhi Yun Du ◽  
Xi Zheng
Keyword(s):  
Crystal Structure ◽  
Acetic Acid ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Spectroscopic Properties ◽  
Spectral Studies ◽  
Double Bonds ◽  
X Ray ◽  
Π Interactions ◽  
X Ray Crystallography

In this paper, (2E,6E)-2,6-Bis(2,3,4-tri-methoxy -benzylidene)cyclohexanone (omitted as tmbcho) (1) was obtained by the reaction of acetic acid, tetrahydrofuran, cyclohexanone and 2,3,4-tri-methoxy-benzaldehyde. Three non-classic hydrogen bonds were observed in the compound. X-ray crystallography shows that the crystal structure is stabilized by intermolecular C-H•••π interactions and it contains plenty of conjugated double bonds. The title compound was characterized by UV-vis and fluorescent spectral studies.

Boron Chelates and Boron-Metal Chelates, X [1]. 3-(2-Hydroxyphenyl)-2,2-diphenyl-1-oxa-3-azonia-2-borata-naphthalene-methanol (1/1): Synthesis, Spectroscopic Investigations and Crystal Structure

1982 ◽  
Vol 37 (11) ◽  
pp. 1450-1455 ◽  
Author(s):  
Rudolf Allmann ◽  
Eberhard Hohaus ◽  
Stanislaw Olejnik
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structure Analysis ◽  
Title Compound ◽  
Chelate Ring ◽  
Boron Chelates ◽  
X Ray ◽  
Membered Chelate Ring ◽  
Compound C ◽  
Overall Ratio

The title compound, C25H20BNO2 · CH3OH, was examined by UV, IR, 1H, and 13C NMK spectroscopy as well as by thermogravimetry and X-ray structure analysis (Pbnb, a = 8.815, b = 17.309, c=28.992 Å, R= 5.5%). These investigations show the six-membered chelate ring (chelate A) to exist as formulated in [2] and not as a five-membered chelate ring B. One methanol molecule connects two chelate molecules by hydrogen bonds, resulting in an overall ratio of chelate to methanol of 1 : 1.

Structure of ammonium hydrogen succinate above and below the phase transition around 170K

1996 ◽  
Vol 52 (2) ◽  
pp. 323-327 ◽  
Author(s):  
A. Hirano ◽  
Y. Kubozono ◽  
H. Maeda ◽  
H. Ishida ◽  
S. Kashino
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Order Phase Transition ◽  
Space Group ◽  
X Ray ◽  
Ammonium Hydrogen ◽  
Significant Change ◽  
Short Hydrogen Bonds ◽  
Second Order Phase Transition

For crystals of ammonium hydrogen succinate it is known that the space group is P{\bar 1} with Z = 2 at 293 K and the second-order phase transition occurs around 170 K. X-ray crystal structure analyses above and below 170 K have been carried out in order to study the change in mode of short hydrogen bonds between the hydrogen succinate ions. The space group was determined to be P{\bar 1} at 150 and 190 K by structure analysis. No ordering of the H-atom positions in the short hydrogen bonds occurs by the phase transition. The hydrogen bonds show a decrease in the O...O distances with a decrease in temperature from 290 to 190 K, but no significant change in the geometries between 190 and 150 K. Disorder of the NH4 + ion is not observed at 297, 190 and 150 K. Significant change through the phase transition is found only in the geometry of one of the N—H...O hydrogen bonds between ammonium and hydrogen succinate ions.

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

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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