Research Article: Using invariom modelling to distinguish correct and incorrect central atoms in ‘duplicate structures’ with neighbouring 3d elements

Date Published: October 01, 2017

Publisher: International Union of Crystallography

Author(s): Claudia M. Wandtke, Matthias Weil, Jim Simpson, Birger Dittrich.


Aspherical atom refinement with conventional data sets is now possible for coordination compounds. As example structures, a number of pairs of published structures, where the element-type assignment of the metal was unclear, have been re-investigated. Identification of which structure is correct can be made from the deposited Bragg intensities alone.

Partial Text

Structure determination from single-crystal X-ray diffraction (XRD) has become a mature technique in recent decades (Spek, 2009 ▸). Thus, the number of crystal structures published each year has increased exponentially, as shown by the statistics of the Cambridge Structural Database (CSD; Groom et al., 2016 ▸), where most published structures are deposited. Very successful validation procedures concerning crystallographic information exist in the form of the automated checkCIF procedure (, which relies on the program PLATON (Spek, 2003 ▸, 2009 ▸). However, assessing the chemical/physical correctness of a crystal structure remains challenging and ultimately requires human judgement. While missing or misplaced H atoms and incorrectly assigned atom types, in general, can often be identified already by specific indicators deduced from a structural model by checkCIF, problematic atom-type assignments for metal atoms are not easily recognized. Even possible fraud can sometimes be detected from an analysis and comparison of reflection data (Harrison et al., 2010 ▸; Zhong et al., 2010 ▸; Liu et al., 2010 ▸; IUCr Editorial Office, 2011a ▸,b ▸, 2012a ▸,b ▸)1. Other useful tools for structure validation rely on deposited structures and a statistical analysis of bonding. Here, deviations from known ranges of bond lengths that exceed a statistically significant threshold can be identified, e.g. with the program Mogul (Bruno et al., 2004 ▸, 2011 ▸). A more general discussion of structure validation (from the viewpoint of macromolecular structure determination) has been given by Dauter et al. (2014) ▸.

Four of the 11 cases studied are discussed as examples here, while the other structures are discussed in a similar way in the supporting information and included in the overview at the end of this section.

Aspherical-atom refinement with conventional data sets is now possible for coordination compounds. New model compounds and those already present in the invariom database have been geometry-optimized using the Minnesota density functional M06, in combination with Ahlrichs’ def2TZVP all-electron basis set, increasing the range to include all elements up to bromine (krypton). This method/basis set combination has been used successfully for a series of compounds containing 3d transition metals and permits the treatment of all the elements present at the same level of theory. To highlight current progress, we have re-investigated a number of pairs of published structures, where the element-type assignment of the metal was unclear, and where duplicates were published based on the same sets of X-ray data or with different data sets but the same unit-cell parameters. We show that aspherical scattering factors permit identification of the correct structure without any further chemical or spectroscopic evidence using the originally deposited diffraction data. These data were usually of conventional resolution (d ≤ 0.84 Å) and measured at room temperature. An interesting aspect is that distinguishing the 3d metal atoms did not usually require the modelling of the asphericity of the metal atom itself.

References cited in the supporting information include: El Haouzi et al. (1996 ▸), Frisch et al. (2013 ▸), Hollemann et al. (2007 ▸), Hübschle et al. (2007 ▸), Kitajima et al. (1990 ▸), Müller et al. (2006 ▸) and Sheldrick et al. (2015a ▸).




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