Determination of oxidation states based on single-crystal diffraction experiments
Final Report Abstract
In the project "Determination of oxidation states from single crystal diffraction" modern algorithms for the calculation of elastic resonance scattering factors have been implemented. They will be tested against experimental diffraction data. First results show that the approximation of only dipole excitations during resonant scattering is insufficient and that the Taylor series should not be truncated after the first element. This approximation introduces significant systematic errors in the scattering factors, which interfere with the accurate determination of oxidation states from current diffraction models. To compensate this a fundamental mathematical and physical model was required, which had to be developed in close collaboration with mathematicians to revise the existing models and methods. The possibility of least squares refinement of the classically used resonant scattering factors has been introduced in the widely used software Olex2. This refinement was performed on a systematic series of diffraction data of Molybdenum atoms in several structurally related compounds at different wavelengths of X-rays. The observation of the difference in position and properties of the absorption edge could be correlated with chemical properties and resonance scattering factors reliably refined from the diffraction experiments. The refinement using the NoSpherA2 software within Olex2 has been extended to include the ability to refine structural models using a set of Slater function based scattering factors, either for the nuclear electrons or for the full atomic density. This is particularly important for the heavier elements of the periodic table, as it allows both a more accurate description of their scattering behavior and a separation of the scattering contributions of the core and valence electrons within the framework of quantum-mechanically derived wave functions using effective core potentials. In addition, a prototype for the use of density fitting coefficients has been implemented. This proves that it is not only possible, but also performs comparably to other established partitioning schemes such as Becke or Hirshfeld. To tackle larger structures, a method for decomposing a structure of logical building blocks into smaller subprocesses has been implemented in NoSpherA2. This allows a linear scaling of the computational time with the system size, for example when refining protein structures or co-crystals. The design allows refinement of a complex structure with a selection of methods appropriate for individual parts of the problem at hand.
Publications
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Dispersion refinements in the range of absorption edges. Acta Crystallographica Section A Foundations and Advances, 77(a2), C1268-C1268.
Meurer, Florian; Kleemiss, Florian; Dolomanov, Oleg V.; Vukovic, Vedran; Puschmann, Horst; Peyerimhoff, Norbert; Hennig, Christoph & Bodensteiner, Michael
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The benefit and challenges of non-spherical refinements – NoSpherA2. Acta Crystallographica Section A Foundations and Advances, 77(a2), C906-C906.
Kleemiss, Florian; Grabowsky, Simon; Dolomanov, Oleg V.; Puschmann, Horst & Bodensteiner, Michael
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NoSpherA2 – from inorganic to protein crystallography. Acta Crystallographica Section A Foundations and Advances, 78(a2), e590-e590.
Kleemiss, F.; Dolomanov, O.; Puschmann, H. & Bodensteiner, M.
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Refinement of anomalous dispersion correction parameters in single-crystal structure determinations. IUCrJ, 9(5), 604-609.
Meurer, Florian; Dolomanov, Oleg V.; Hennig, Christoph; Peyerimhoff, Norbert; Kleemiss, Florian; Puschmann, Horst & Bodensteiner, Michael
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Refinement of anomalous dispersion parameters. Acta Crystallographica Section A Foundations and Advances, 78(a2), e209-e210.
Meurer, F.; Dolomanov, O.V.; Hennig, C.; Peyerimhoff, N.; Kleemiss, F.; Puschmann, H. & Bodensteiner, M.
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Tackling anomalous X-ray scattering via Waller's dispersion formula. Acta Crystallographica Section A Foundations and Advances, 78(a2), e131-e131.
Peyerimhoff, N.; Kleemiss, F.; Bodensteiner, M. & Meurer, F.
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Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off. Journal of Applied Crystallography, 56(1), 116-127.
Jha, Kunal Kumar; Kleemiss, Florian; Chodkiewicz, Michał Leszek & Dominiak, Paulina Maria
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The effects of experimentally obtained electron correlation and polarization on electron densities and exchange-correlation potentials. The Journal of Chemical Physics, 158(12).
Hupf, Emanuel; Kleemiss, Florian; Borrmann, Tobias; Pal, Rumpa; Krzeszczakowska, Joanna M.; Woińska, Magdalena; Jayatilaka, Dylan; Genoni, Alessandro & Grabowsky, Simon
