Interpretation of the crystal structures of transition metal compounds and complexes
Reeves, Matthew George
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.