Browsing by Author "Grabowsky, S"

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    Accurate H-atom parameters for the two polymorphs of L-histi­dine at 5, 105 and 295 K
    (International Union of Crystallography, 2021-10-01) Novelli, G; McMonagle, CJ; Kleemiss, F; Probert, MR; Puschmann, H; Grabowsky, S; Maynard-Casely, HE; McIntyre, GJ; Parsons, S
    The crystal structure of the monoclinic polymorph of the primary amino acid L-histi­dine has been determined for the first time by single-crystal neutron diffraction, while that of the orthorhombic polymorph has been reinvestigated with an untwinned crystal, improving the experimental precision and accuracy. For each polymorph, neutron diffraction data were collected at 5, 105 and 295 K. Single-crystal X-ray diffraction experiments were also performed at the same temperatures. The two polymorphs, whose crystal packing is interpreted by intermolecular interaction energies calculated using the Pixel method, show differences in the energy and geometry of the hydrogen bond formed along the c direction. Taking advantage of the X-ray diffraction data collected at 5 K, the precision and accuracy of the new Hirshfeld atom refinement method im­ple­mented in NoSpherA2 were probed choosing various settings of the functionals and basis sets, together with the use of explicit clusters of molecules and enhanced rigid-body restraints for H atoms. Equivalent atomic coordinates and aniso­tropic displacement parameters were com­pared and found to agree well with those obtained from the corresponding neutron structural models.© International Union of Crystallography
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    Fast and accurate quantum crystallography: from small to large, from light to heavy
    (American Chemical Society, 2019-10-21) Malaspina, LA; Wieduwilt, EK; Bergmann, J; Kleemiss, F; Meyer, B; Ruiz-López, MF; Pal, R; Hupf, E; Beckmann, J; Piltz, RO; Edwards, AJ; Grabowsky, S; Genoni, A
    The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects. © 2019 American Chemical Society
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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
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    Nickel and palladium complexes of a PP(O)P pincer ligand based upon a peri-substituted acenaphthyl scaffold and a secondary phosphine oxide
    (American Chemical Society, 2022-05-24) Duvinage, D; Puylaert, P; Wieduwilt, EK; Malaspina, LA; Edwards, AJ; Lork, E; Mebs, S; Hupf, E; Grabowsky, S; Beckmann, J
    A PP(O)P pincer ligand based upon a peri-substituted acenaphthyl (Ace) scaffold and a secondary phosphine oxide, (5-Ph2P-Ace-6-)2P(O)H, was prepared and fully characterized including a neutron diffraction study. The reaction with [Ni(H2O)6]Cl2and PdCl2produced ionic metal(II) complexes [κ3-P,P',P''((5-Ph2P-Ace-6-)2P(OH))MCl]Cl, which upon addition of Et3N gave rise to zwitterionic metal(II) complexes κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))MCl (M = Ni, Pd). The reaction with Ni(COD)2(COD = cyclooctadiene) provided the η3-cyclooctenyl Ni(II) complex κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))Ni(η3-C8H13). A detailed complementary bonding analysis of the P-H, P-O, and P-M interactions was carried out (M = Ni, Pd). © 2022 American Chemical Society.
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    On the temperature dependence of H-Uiso in the riding hydrogen model
    (Acta Crystallographica, 2014-07) Lübben, J; Volkmann, C; Grabowsky, S; Edwards, AJ; Morgenroth, W; Fabbiani, FPA; Sheldrick, GM; Dittrich, B
    The temperature dependence of H-Uiso in N-acetyl-L-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found. © International Union of Crystallography