Interpretation of the crystal structures of transition metal compounds and complexes
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Date
30/11/2020Author
Reeves, Matthew George
Metadata
Abstract
The Cambridge Structural Database (CSD) contains over half a million structures
containing transition metal compounds. The wealth of data available from these
structures is enormous and the potential knowledge and insight that be gained from
these structures is of great benefit to the field of inorganic and organometallic
chemistry.
Searching through these structures is facilitated by the CSD software Conquest,
which allows users to filter results to desired metals and ligand motifs. However,
some aspects are not currently possible through the Conquest GUI, while others,
such as oxidation state data, require the value to be explicitly mentioned by the
author in the assigned chemical name. The introduction of the CSD Python
Application Programming Interface (API) has allowed users to interpret, retrieve, and
manipulate data in new ways, and now presents an avenue to introduce new data to
CSD entries and user structures alike.
A highly reliable automated workflow for oxidation-state assignment in transitionmetal co-ordination complexes has been developed with CSD Python API scripts.
These scripts implement the bond-valence sum (BVS) method as well complementary
techniques. The strengths and limitations of these methods are discussed and the
application of confidence banding for improved assignment confidence is explored. In
total, four complementary techniques have been implemented in this study. The
resulting workflow overcomes the limitations of the BVS approach, widening the
applicability of an automated procedure to more CSD entries. Assignments are
successful for 99% of the cases where a high consensus between different
methodologies is observed.
Further exploiting the capabilities of the CSD Python API, and specifically the
integration with the Mercury software, a program has been developed for the direct
execution of PIXEL-CLP calculations from the Mercury interface. The PIXEL method
is a semi-empirical procedure for the calculation of intermolecular interaction and
lattice energies based on undistorted ab initio molecular electron densities. Following
initial set up of a crystallographic model, the ”MrPIXEL” software package assigns
atom types and writes necessary input files, submits the required electron density calculation either locally or to a remote server, downloads the results and submits
the PIXEL calculation itself. Full lattice energy calculations can be performed for
structures with up to two molecules in the crystallographic asymmetric unit, for more
complex cases molecule-molecule energies are calculated only.
Finally, the MrPIXEL software has been used to determine lattice and interaction
energies for structures of spin-crossover (SCO) complexes in the CSD. The results
of which have been studied in order to determine their influence and role in the
abruptness of spin-state transitions for the Fe(PM-L)2(NCS)2 family of SCO
complexes. The change in interaction energies between spin-states is found to
correlate with the abruptness of transition, with more abrupt transitions being
associated with much larger changes in interaction energies between spin-states. The
interaction energies, along with the changes in energies, are visually displayed in
Mercury using a new method developed for producing energy frameworks, similar to
those used in CrystalExplorer.