Browsing by Author "Sugimoto, K"

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    Hirshfeld atom refinement for modelling strong hydrogen bonds
    (International Union of Crystallography, 2014-01-01) Woinska, M; Jayatilaka, D; Spackman, MA; Edwards, AJ; Dominiak, DJ; Wozniak, PM; Nishibori, E; Sugimoto, K; Grabowsky, S
    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. © 2014, International Union of Crystallography.
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    Mapping the trajectory of proton transfer via experimental electron density
    (International Union of Crystallography (IUCr), 2017-12-01) Malaspina, LA; Sugimoto, K; Edwards, AJ; Grabowsky, S
    Hydrogen maleate (HM) salts offer the unique opportunity to follow a pseudo-reaction pathway of a proton transfer not only in theoretical simulations but also experimentally because the position of the hydrogen atom inside the strong and short intramolecular O-H···O hydrogen bond (low-barrier hydrogen bond is highly flexible dependent on the cation and/or crystalline environment (Figure 1). There is a great number of crystal structures of hydrogen maleate salts in the Cambridge Structural Database (CSD) (303 entries) which show that the O···O distance varies from 2.361 Å to 2.540 Å with a large variety of intermediate distances. Neutron diffraction studies establish that the O-H distances vary from 1.079 Å up to 1.215 Å. This means that snapshots along a pseudo-reaction pathway can be measured and, with the symmetric hydrogen bonds, even a model for a possible transition state is accessible. In this study nine different hydrogen maleate salts (4-aminopyridinium HM, 8-hydroxyquinolinium HM, barium bis-HM tetrahydrate, calcium bis-HM pentahydrate, potassium HM, lithium HM dihydrate, magnesium bis-HM hexahydrate, sodium HM trihydrate and L-phenylalaninium HM that span the whole range from perfectly symmetric to highly asymmetric intramolecular hydrogen bonds are presented. The trajectory of the proton transfer is mapped through experimental electron density (ED) studies using high-resolution low-temperature synchrotron X-ray diffraction, data measured at the beamline BL02B1 of SPring-8, Japan. For this aim, it is crucial to obtain the precise and accurate position and displacement parameters of the hydrogen atom in the low-barrier hydrogen bond. Therefore the position of the proton in all compounds presented is supported by low-temperature neutron diffraction, data measured at the beamline KOALA of the Bragg Institute of ANSTO, Australia. The response of the hydrogen atom in question to various properties, such as the experimentally derived electric field imposed by the crystallographic environment, will be discussed. © 2017 International Union of Crystallography