Literature DB >> 25176996

Hirshfeld atom refinement for modelling strong hydrogen bonds.

Magdalena Woińska1, Dylan Jayatilaka2, Mark A Spackman2, Alison J Edwards3, Paulina M Dominiak1, Krzysztof Woźniak1, Eiji Nishibori4, Kunihisa Sugimoto5, Simon Grabowsky2.   

Abstract

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 of Z' > 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.

Entities:  

Keywords:  Hirshfeld atom refinement; aspherical scattering factors; electron density; hydrogen bonds; hydrogen maleate; structure refinement

Year:  2014        PMID: 25176996     DOI: 10.1107/S2053273314012443

Source DB:  PubMed          Journal:  Acta Crystallogr A Found Adv        ISSN: 2053-2733            Impact factor:   2.290


  12 in total

1.  On the temperature dependence of H-U(iso) in the riding hydrogen model.

Authors:  Jens Lübben; Christian Volkmann; Simon Grabowsky; Alison Edwards; Wolfgang Morgenroth; Francesca P A Fabbiani; George M Sheldrick; Birger Dittrich
Journal:  Acta Crystallogr A Found Adv       Date:  2014-05-28       Impact factor: 2.290

2.  Hydrogen atoms can be located accurately and precisely by x-ray crystallography.

Authors:  Magdalena Woińska; Simon Grabowsky; Paulina M Dominiak; Krzysztof Woźniak; Dylan Jayatilaka
Journal:  Sci Adv       Date:  2016-05-27       Impact factor: 14.136

3.  Quantum crystallographic charge density of urea.

Authors:  Michael E Wall
Journal:  IUCrJ       Date:  2016-06-08       Impact factor: 4.769

4.  Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2.

Authors:  Malte Fugel; Dylan Jayatilaka; Emanuel Hupf; Jacob Overgaard; Venkatesha R Hathwar; Piero Macchi; Michael J Turner; Judith A K Howard; Oleg V Dolomanov; Horst Puschmann; Bo B Iversen; Hans-Beat Bürgi; Simon Grabowsky
Journal:  IUCrJ       Date:  2018-01-01       Impact factor: 4.769

5.  Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks.

Authors:  Birger Dittrich; Jens Lübben; Stefan Mebs; Armin Wagner; Peter Luger; Ralf Flaig
Journal:  Chemistry       Date:  2017-03-15       Impact factor: 5.236

Review 6.  Quantum crystallography.

Authors:  Simon Grabowsky; Alessandro Genoni; Hans-Beat Bürgi
Journal:  Chem Sci       Date:  2017-03-27       Impact factor: 9.825

7.  Energetics of interactions in the solid state of 2-hydroxy-8-X-quinoline derivatives (X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements.

Authors:  Magdalena Woinska; Monika Wanat; Przemyslaw Taciak; Tomasz Pawinski; Wladek Minor; Krzysztof Wozniak
Journal:  IUCrJ       Date:  2019-07-15       Impact factor: 4.769

8.  The advanced treatment of hydrogen bonding in quantum crystallography.

Authors:  Lorraine A Malaspina; Alessandro Genoni; Dylan Jayatilaka; Michael J Turner; Kunihisa Sugimoto; Eiji Nishibori; Simon Grabowsky
Journal:  J Appl Crystallogr       Date:  2021-04-16       Impact factor: 3.304

9.  Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program.

Authors:  Jens Lübben; Luc J Bourhis; Birger Dittrich
Journal:  J Appl Crystallogr       Date:  2015-11-10       Impact factor: 3.304

10.  fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins.

Authors:  Justin Bergmann; Max Davidson; Esko Oksanen; Ulf Ryde; Dylan Jayatilaka
Journal:  IUCrJ       Date:  2020-01-17       Impact factor: 4.769

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