Using invariom modelling to distinguish correct and incorrect central atoms in `duplicate structures' with neighbouring 3<i>d</i>elements

Wandtke, Claudia M.; Weil, Mat­thias; Dittrich, Birger

doi:10.1107/s2052520617010745

Cited by 16 publications

(9 citation statements)

References 97 publications

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“…Moreover, the integration of TAAM methodology with Olex2, which is available for structure refinement to the crystallography community, makes TAAM a reliable and user-friendly tool to be applied in the last steps of refinement during routine X-ray structure determination of organic molecule crystals. Application of TAAM to polymer network structures, disordered compounds (Bąk et al, 2009;Dittrich et al, 2016), organic fragments in organometallic complexes (Wandtke et al, 2017) or molecular biology (Jelsch et al, 1998;Malinska & Dauter, 2016) seems to be possible and it will be investigated in future works. General applicability of TAAM from a databank for metal atoms and inorganic structures is currently not possible with the existing atom-typing algorithm and multipolar model parametrization used to build the databank, and requires further feasibility studies.…”

Section: Discussionmentioning

confidence: 99%

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Jha

Gruza

Kumar

et al. 2020

Acta Crystallogr Sect B

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Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min 0.83 Å ) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

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Section: Discussionmentioning

confidence: 99%

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Jha

Gruza

Kumar

et al. 2020

Acta Crystallogr Sect B

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“…These authors also suggest difference electron-density plots relying on measurements above and below the absorption edge to visualize the effect of anomalous dispersion. In a later article, the same group reports on the opportunity to distinguish between neighbouring elements employing their different anomalous dispersion parameters even with laboratory sources in noncentrosymmetric space groups (Wandtke et al, 2017). However, it should be pointed out that this also applies to centrosymmetric structures, as we show herein using the example of Mo(CO) 6 , which crystallizes in the centrosymmetric space group Pnma.…”

Section: Resultsmentioning

confidence: 80%

Refinement of anomalous dispersion correction parameters in single-crystal structure determinations

Meurer¹,

Dolomanov²,

Hennig³

et al. 2022

IUCrJ

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Correcting for anomalous dispersion is part of any refinement of an X-ray diffraction crystal structure determination. The procedure takes the inelastic scattering in the diffraction experiment into account. This X-ray absorption effect is specific to each chemical compound and is particularly sensitive to radiation energies in the region of the absorption edges of the elements in the compound. Therefore, the widely used tabulated values for these corrections can only be approximations as they are based on calculations for isolated atoms. Features of the unique spatial and electronic environment that are directly related to the anomalous dispersion are ignored, although these can be observed spectroscopically. This significantly affects the fit between the crystallographic model and the measured intensities when the excitation wavelength in an X-ray diffraction experiment is close to an element's absorption edge. Herein, we report on synchrotron multi-wavelength single-crystal X-ray diffraction, as well as X-ray absorption spectroscopy experiments which we performed on the molecular compound Mo(CO)6 at energies around the molybdenum K edge. The dispersive (f′) and absorptive (f′′) terms of the anomalous dispersion can be refined as independent parameters in the full-matrix least-squares refinement. This procedure has been implemented as a new feature in the well-established OLEX2 software suite. These refined parameters are in good agreement with the independently recorded X-ray absorption spectrum. The resulting crystallographic models show significant improvement compared to those employing tabulated values.

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“…This experimental-theoretical approach makes it possible to obtain the ED distribution on the basis of data of routine XRD studies and theoretical calculations. The improved method based on the determination of the molecular invariom was applied for the organometallic compounds [10][11][12]. The use of this method provides an information about the topology of the ED in molecules with good accuracy [13,14].…”

Section: Introductionmentioning

confidence: 99%

Application of the Molecular Invariom Model for the Study of Interactions Involving Fluorine Atoms in the {$${\text{Yb}}_{{\text{2}}}^{{{\text{II}}}}$$(μ2-OCH(CF3)2)3(μ3-OCH(CF3)2)2YbIII(OCH(CF3)2)2(THF)(Et2O)} Complex

et al. 2021

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The electron density distributions obtained by the quantum-chemical (density functional theory) calculations and molecular invariom model in the trimeric ytterbium complex with the hexafluoroisopropoxide ligands {$${\text{Yb}}_{{\text{2}}}^{{{\text{II}}}}$$(μ2-OR)3(μ3-OR)2YbIII(OR)2(THF)(Et2O)} (I) (where R is CH(CF3)2, and THF is tetrahydrofuran) are compared. The main topological characteristics of the electron density at the critical points (3, –1) corresponding to the interactions of the ytterbium atoms in the coordination sphere obtained using two studied approaches demonstrate excellent agreement. The maximum divergence between the density functional calculations and molecular invariom model is observed for the intramolecular interactions involving the fluorine atoms (F···F, F···H, and F···O) in the structure of complex I. Geometry optimization leads to a higher number of these interactions in the complex. The energy corresponding to these interactions also increases. However, the main topological characteristics for the F···X interactions (X = F, H, O), which can be localized in the framework of both methods, remain within the transferability index range. An analysis of the deformation electron density shows that the Fδ–···Fδ– interactions are determined by the correspondence of the region of electron density concentration on one of the fluorine atoms to the region of electron density depletion on the second fluorine atom regardless of the method of measuring the electron density distribution.

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Using invariom modelling to distinguish correct and incorrect central atoms in `duplicate structures' with neighbouring 3delements

Cited by 16 publications

References 97 publications

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Refinement of anomalous dispersion correction parameters in single-crystal structure determinations

Application of the Molecular Invariom Model for the Study of Interactions Involving Fluorine Atoms in the {$${\text{Yb}}_{{\text{2}}}^{{{\text{II}}}}$$(μ2-OCH(CF3)2)3(μ3-OCH(CF3)2)2YbIII(OCH(CF3)2)2(THF)(Et2O)} Complex

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