Boron cages in MOF
Miroslav Pospíšil, Jorge Javier Garcia Jimenez
1Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, Prague 2, 12116, Czechia
miroslav.pospisil@matyz.cuni.cz
Crystallographic techniques are powerful tools for determining the structure and spatial arrangement of atoms and molecules in crystalline materials. However, not all molecules form well-ordered crystals. In cases where high precision methods such as X-ray or electron diffraction do not provide sufficient structural detail, force field based molecular dynamic simulations can offer valuable insights into the positions and behavior of individual molecules within Metal-Organic Frameworks (MOF) .
Applying molecular dynamics to MOF structures containing boron-18 clusters and cyclohexane molecules can significantly accelerate the process of crystal structure determination. This approach allows for a more detailed understanding of anchoring sites and intermolecular interactions within the frameworks.
The first phase of calculations focuses on the preparation of MOFs and their detailed characterization, particularly in terms of crystallinity and number of defects (expressed as the ligand-to-metal ratio). The study begins with the well-established prototypical Fujita MOF [(ZnI2)3(tpt)2],[1] where tpt denotes 2,4,6-tris(4-pyridyl)-1,3,5- triazine. This MOF serves as a host structure for the adsorption of non-polar molecules such as cyclohexane and boron clusters.
Using this model system with stable boron 18 cages, we will investigate the potential and limitations of combining molecular dynamics simulations with single crystal X-ray diffraction to improve the precision of structural determination.
Figure 1. Z-view of MOF structure with boron (B18) cages and cyclohexane molecules from quench molecular dynamics in NVT ensemble, T = 298 K, timestep 1 fs, Nose thermostat.
1. Y. Inokuma, et al. Nature, 495, (2013), 461-466. doi.org/10.1038/nature11990
This study was supported by the Grant Agency of the Czech Republic No. 25-16442S.