The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate)

2011 ◽  
Vol 67 (6) ◽  
pp. 552-559 ◽  
Author(s):  
Mihaela-Diana Şerb ◽  
Ruimin Wang ◽  
Martin Meven ◽  
Ulli Englert
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Electron Density ◽  
Organic Salt ◽  
X Ray Diffraction ◽  
Covalent Character ◽  
X Ray

N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H...O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interact via conventional N—H...O and nonclassical C—H...O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of the X—H...O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H...O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.

Charge-density analysis in polymorphs of urea–barbituric acid co-crystals

2011 ◽  
Vol 67 (2) ◽  
pp. 144-154 ◽  
Author(s):  
Marlena Gryl ◽  
Anna Krawczuk-Pantula ◽  
Katarzyna Stadnicka
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Charge Density ◽  
Barbituric Acid ◽  
Van Der Waals Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Analysis ◽  
Resolution Single

High-resolution single-crystal X-ray diffraction measurements at 100 K were performed for the two polymorphs of urea–barbituric acid co-crystals: (I) P21/c and (II) Cc. Experimental and theoretical charge density and its properties were analysed for (I) and (II) in order to confirm the previous observation that in the polymorphs studied the barbituric acid molecules adopt different mesomeric forms, leading to different hydrogen-bond systems. Koch and Popelier criteria were applied to distinguish between hydrogen bonds and van der Waals interactions in the structures presented.

Hirshfeld atom refinement for modelling strong hydrogen bonds

2014 ◽  
Vol 70 (5) ◽  
pp. 483-498 ◽  
Author(s):  
Magdalena Woińska ◽  
Dylan Jayatilaka ◽  
Mark A. Spackman ◽  
Alison J. Edwards ◽  
Paulina M. Dominiak ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Atom ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Electron Density ◽  
Diffraction Experiment ◽  
Neutron Diffraction Experiment ◽  
X Ray ◽  
Atom Model

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples ofZ′ > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O—H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment,e.g.the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

N—H...O and C—H...F hydrogen bonds in the incommensurately modulated crystal structure of adamantan-1-ammonium 4-fluorobenzoate

2014 ◽  
Vol 70 (4) ◽  
pp. 652-659 ◽  
Author(s):  
Andreas Schönleber ◽  
Sander van Smaalen ◽  
Hans-Christoph Weiss ◽  
Andreas J. Kesel
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Diffraction Data ◽  
Low Temperatures ◽  
Atomic Displacement ◽  
Organic Salt ◽  
X Ray Diffraction ◽  
X Ray ◽  
Molecular Cations ◽  
Atomic Displacement Parameters

At low temperatures the organic salt adamantan-1-ammonium 4-fluorobenzoate, C10H18N+·C7H4FO2−, possesses an incommensurately modulated crystal structure. The effect of the modulation on the atomic arrangement and intermolecular interactions is studied by analysing single-crystal X-ray diffraction data within the (3 + 1)-dimensional superspace approach and superspace groupP21/n(α0γ)00. The modulation strongly affects the position of the atoms as well as their atomic displacement parameters. Nevertheless, the molecular cations and anions are built by rigid moieties, which vary their orientation with respect to each other as a function of the phase of the modulationt. Cations and anions are connected into slabs by dense N—H...O and C—H...F hydrogen-bonded networks, which are characterized by being rather rigid and which show only a little variation as a function of the phase of the modulationt.

The crystal structure of deuterated trans-Tetraamminedinitronickel(II) at 4.2 K by neutron diffraction

1981 ◽  
Vol 34 (5) ◽  
pp. 993 ◽  
Author(s):  
BN Figgis ◽  
PA Reynolds ◽  
GA Williams ◽  
N Lehner
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Rigid Body ◽  
Large Amplitude ◽  
Translational Motion ◽  
Axial Direction ◽  
Full Matrix ◽  
X Ray

The crystal structure of deuterated trans-tetraamminedinitronickel(II), Ni(ND3)4(NO2)2, has been determined by single-crystal neutron diffraction methods at 4·2 K. Crystals are monoclinic, C2/m, a 1058(l), b 672(1), c 586.3(3) pm, β 114.82(5)�, Z = 2. Diffractometry has provided Bragg intensities for 219 independent reflections; and the structure has been refined by full-matrix least-squares methods to R(F2) 0·070 and χ2 3·8. There are slight differences in the molecular geometries determined by neutron diffraction and earlier X-ray determinations of Ni(NH3)4(NO2)2 at 295 and 130 K. Small, but significant, decreases are evident in all non-hydrogen bond lengths on decrease in temperature from 295 to 4·2 K, up to a maximum of 2·0(4) pm for the Ni-NH3/ND3 bond. The magnitudes of these decreases are correlated with the force constants of the bonds. The intermolecular geometry and thermal parameters show that in the ab plane there is a network of relatively strong, linear N-D···O hydrogen bonds. In the c* direction there is a slightly bent, longer, N-D(1)···O bond which is weaker. This causes a large amplitude of rigid-body translational motion in the c* direction, together with high thermal motion of D(1) in the b axial direction.

Investigation of Residual Strains of the Second Kind in Plastically Deformed Metallic Materials

1994 ◽  
Vol 376 ◽  
Author(s):  
M. Vrána ◽  
P. Klimanek ◽  
T. Kschidock ◽  
P. Lukáš ◽  
P. Mikula
Keyword(s):  
High Resolution ◽  
Neutron Diffraction ◽  
Stacking Faults ◽  
Metallic Materials ◽  
Line Broadening ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Diffractometer ◽  
Residual Strains ◽  
Good Agreement

ABSTRACTInvestigation of strongly distorted crystal structures caused by dislocations, stacking-faults etc. in both plastically deformed f.c.c. and b.c.c. metallic materials was performed by the analysis of the neutron diffraction line broadening. Measurements were realized by means of the high resolution triple-axis neutron diffractometer equipped by bent Si perfect crystals as monochromator and analyzer at the NPI Řež. The substructure parameters obtained in this manner are in good agreement with the results of X-ray diffraction analysis.

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.

Insight into the Electron Density Distribution in an O,N-Heterocyclic Stannylene by High-Resolution X-ray Diffraction Analysis

2019 ◽  
Vol 2019 (6) ◽  
pp. 875-884 ◽  
Author(s):  
Maxim G. Chegerev ◽  
Alexandr V. Piskunov ◽  
Kseniya V. Tsys ◽  
Andrey G. Starikov ◽  
Klaus Jurkschat ◽  
...  
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Diffraction Analysis ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Insight Into

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

scholarly journals Synthesis and Complexation Properties of 2-Hydroxy-5-methoxyphenylphosphonic Acid (H3L1). Crystal Structure of the [Cu(H2L1)2(Н2О)2] Complex

2021 ◽  
Vol 91 (11) ◽  
pp. 2176-2186
Author(s):  
G. S. Tsebrikova ◽  
Yu. I. Rogacheva ◽  
I. S. Ivanova ◽  
A. B. Ilyukhin ◽  
V. P. Soloviev ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Methoxy Group ◽  
Protonation Constants ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Oxygen Atoms

Abstract 2-Hydroxy-5-methoxyphenylphosphonic acid (H3L1) and the complex [Cu(H2L1)2(H2O)2] were synthesized and characterized by IR spectroscopy, thermogravimetry, and X-ray diffraction analysis. The polyhedron of the copper atom is an axially elongated square bipyramid with oxygen atoms of phenolic and of monodeprotonated phosphonic groups at the base and oxygen atoms of water molecules at the vertices. The protonation constants of the H3L1 acid and the stability constants of its Cu2+ complexes in water were determined by potentiometric titration. The protonation constants of the acid in water are significantly influenced by the intramolecular hydrogen bond and the methoxy group. The H3L1 acid forms complexes CuL‒ and CuL24‒ with Cu2+ in water.

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