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.

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.

scholarly journals Engineering short, strong hydrogen bonds in urea di-carboxylic acid complexes

CrystEngComm ◽  
2014 ◽  
Vol 16 (35) ◽  
pp. 8177-8184 ◽  
Author(s):  
Andrew O. F. Jones ◽  
Charlotte K. Leech ◽  
Garry J. McIntyre ◽  
Chick C. Wilson ◽  
Lynne H. Thomas
Keyword(s):  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Structural Changes ◽  
Acid Amide ◽  
Molecular Complexes ◽  
Temperature Dependent ◽  
X Ray ◽  
Methyl Substitution

The persistence of the acid⋯amide heterodimer and the effect of methyl substitution on the short strong O–H⋯O hydrogen bond is investigated in urea and methylurea di-carboxylic acid molecular complexes. Temperature dependent structural changes are also reported utilising X-ray and neutron diffraction in tandem.

Neutron diffraction experiment with the Y116S variant of transthyretin using iBIX at J-PARC: application of a new integration method

2020 ◽  
Vol 76 (11) ◽  
pp. 1050-1056
Author(s):  
Katsuhiro Kusaka ◽  
Takeshi Yokoyama ◽  
Taro Yamada ◽  
Naomine Yano ◽  
Ichiro Tanaka ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Amyloid Fibrils ◽  
Integration Method ◽  
Proton Accelerator ◽  
Diffraction Experiment ◽  
Wild Type ◽  
Neutron Diffraction Experiment ◽  
X Ray ◽  
Attr Amyloidosis

Transthyretin (TTR) is one of more than 30 amyloidogenic proteins, and the amyloid fibrils found in patients afflicted with ATTR amyloidosis are composed of this protein. Wild-type TTR amyloids accumulate in the heart in senile systemic amyloidosis (SSA). ATTR amyloidosis occurs at a much younger age than SSA, and the affected individuals carry a TTR mutant. The naturally occurring amyloidogenic Y116S TTR variant forms more amyloid fibrils than wild-type TTR. Thus, the Y116S mutation reduces the stability of the TTR structure. A neutron diffraction experiment on Y116S TTR was performed to elucidate the mechanism of the changes in structural stability between Y116S variant and wild-type TTR through structural comparison. Large crystals of the Y116S variant were grown under optimal crystallization conditions, and a single 2.4 mm3 crystal was ultimately obtained. This crystal was subjected to time-of-flight (TOF) neutron diffraction using the IBARAKI biological crystal diffractometer (iBIX) at the Japan Proton Accelerator Research Complex, Tokai, Japan (J-PARC). A full data set for neutron structure analysis was obtained in 14 days at an operational accelerator power of 500 kW. A new integration method was developed and showed improved data statistics; the new method was applied to the reduction of the TOF diffraction data from the Y116S variant. Data reduction was completed and the integrated intensities of the Bragg reflections were obtained at 1.9 Å resolution for structure refinement. Moreover, X-ray diffraction data at 1.4 Å resolution were obtained for joint neutron–X-ray refinement.

SHADEweb server for estimation of hydrogen anisotropic displacement parameters

2006 ◽  
Vol 39 (5) ◽  
pp. 757-758 ◽  
Author(s):  
Anders Østergaard Madsen
Keyword(s):  
Hydrogen Atom ◽  
Neutron Diffraction ◽  
Electron Density ◽  
Atomic Motion ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Reference Models ◽  
Anisotropic Displacement Parameters ◽  
Advanced Applications

TheSHADEweb server estimates anisotropic displacement parameters for hydrogen atoms by combining a rigid-body analysis of the non-hydrogen-atom anisotropic displacement parameters (ADPs) with a contribution from internal atomic motion. The contributions from internal mean square displacements are based on a previously compiled database derived from analysis of neutron diffraction experiments. The estimated hydrogen-atom ADPs can be used as fixed parameters in advanced applications of high-resolution X-ray diffraction, such as electron density studies using multipole modelling. The resulting electron density models have been shown to be in excellent agreement with reference models based on atomic motion derived from neutron diffraction experiments.

Microscopic structure of low temperature liquid ammonia: A neutron diffraction experiment

1995 ◽  
Vol 102 (19) ◽  
pp. 7650-7655 ◽  
Author(s):  
M. A. Ricci ◽  
M. Nardone ◽  
F. P. Ricci ◽  
C. Andreani ◽  
A. K. Soper
Keyword(s):  
Low Temperature ◽  
Neutron Diffraction ◽  
Liquid Ammonia ◽  
Microscopic Structure ◽  
Diffraction Experiment ◽  
Neutron Diffraction Experiment ◽  
Temperature Liquid

scholarly journals On hydrogen bonding in 1,6-anhydro-β-D-glucopyranose (levoglucosan): X-ray and neutron diffraction and DFT study

2006 ◽  
Vol 62 (5) ◽  
pp. 912-918 ◽  
Author(s):  
Ľubomír Smrčok ◽  
Mariana Sládkovičová ◽  
Vratislav Langer ◽  
Chick C. Wilson ◽  
Miroslav Koóš
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Dft Calculations ◽  
Diffraction Data ◽  
Neutron Diffraction Study ◽  
Single Crystal Diffraction ◽  
X Ray

The geometry of hydrogen bonds in 1,6-anhydro-β-D-glucopyranose (levoglucosan) is accurately determined by refinement of time-of-flight neutron single-crystal diffraction data. Molecules of levoglucosan are held together by a hydrogen-bond array formed by a combination of strong O—H...O and supporting weaker C—H...O bonds. These are fully and accurately detailed by the neutron diffraction study. The strong hydrogen bonds link molecules in finite chains, with hydroxyl O atoms acting as both donors and acceptors of hydroxyl H atoms. A comparison of molecular and solid-state DFT calculations predicts red shifts of O—H and associated blue shifts of C—H stretching frequencies due to the formation of hydrogen bonds in this system.

Polysulfonylamine, CXLII [1]. Ein supramolekulares Monomer-Dimer-Paar: Starke und schwache Wasserstoffbrücken in den Kristallstrukturen von Pyridinium-dimesylamid und 4,4´-Bipyridindiium-bis(dimesylamid) / Polysulfonylamines, CXLII [1]. A Supramolecular Monomer-Dimer Pair: Strong and Weak Hydrogen Bonding in the Crystal Structures of Pyridinium Dimesylamide and 4,4´-Bipyridinediium Bis(dimesylamide)

2001 ◽  
Vol 56 (10) ◽  
pp. 1041-1051 ◽  
Author(s):  
Oliver Moers ◽  
Ilona Lange ◽  
Karna Wijaya ◽  
Armand Blaschette ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Strong Hydrogen Bond ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Normalized Parameters ◽  
Hydrogen Bonding Networks

In order to study packing arrangements and hydrogen bonding networks, low-temperature X-ray structures were determined for pyH+(MeSO2)2N- (M, orthorhombic, space group P212121, Z′ = 1) and 4,4′-bipyH22+ ·(MeSO2)2N- (D, monoclinic, C2/c, Z′ = 0.5). The structures consist of ionic formula entities assembled by N+-H···N- hydrogen bonds; the dication in D displays crystallographic C2 symmetry and has its two pyridyl moieties twisted by 43.9°. According to the packing architectures, D represents a supramolecular dimer of the monomeric congener M. In particular, the (MeSO2)2N- ions of the M structure are associated via short C(sp3) - H···O contacts to form a diamondoid network, whereas in D a topologically congruent framework is constructed from weakly hydrogen-bonded [(MeSO2)N-]2 nodes. Hexagonal channels in the anion substructures each include two adjacent stacks of monomeric pyH+ or “dimeric” 4,4-bipyH22+ cations that are linked to the channel walls by the strong hydrogen bond(s) and a set of short Car-H···O contacts. All C - H···O taken into consideration have normalized parameters d(H···O) ≤ 270 pm and θ(C - H···O) ≥ 115°.

Neutron diffraction of a complex of 1,8-bis(dimethylamino)naphthalene with 1,2-dichloromaleic acid

1996 ◽  
Vol 52 (4) ◽  
pp. 691-696 ◽  
Author(s):  
K. Wozniak ◽  
C. C. Wilson ◽  
K. S. Knight ◽  
W. Jones ◽  
E. Grech
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Strong Correlation ◽  
Equivalent Temperature ◽  
Neutron Data ◽  
Crystalline Complex ◽  
X Ray ◽  
Temperature Factors ◽  
Atom Temperature

A neutron study of the crystalline complex of 1,8-bis(dimethylamino)naphthalene (DMAN) with 1,2-dichloromaleic acid (ClMH2) has been carried out at 100 K using the Laue time-of-flight technique. The moieties are planar. The neutron data indicate that both [N—H...N]+ and [O—H...O]− hydrogen bonds in the complex are asymmetric. There are significant differences between the neutron and X-ray temperature factors, C—H, N—H and O—H bond lengths. There is a strong correlation between the neutron and X-ray temperature factors for non-H atoms and no correlation for H-atom temperature factors. According to the neutron data the involvement of a given H atom in a weak C—H...O hydrogen bond can be correlated with the ratio of equivalent temperature factors of the H and non-H atoms to which they are attached.

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