Construct and study large (M12L24) cages with unsymmetrical ligands
DOI for publication: 10.1039/d2sc03856k
Installation:
Clone the repo and use enrivonment.yml and Anaconda or Miniconda to install the Python 3.9 environment including RDKIT and XTB from conda-forge.
CREST must be installed by the user (version 2.11.2 was used). In env_set.py, I set environment variables, including directories for output. E.g. the working directory for me is /data/atarzia/projects/big_unsymm.
Usage:
build_ligand.py:
build ligand precusor for cage construction -- includes optimisation. Generates ligands lowest energy conformer
build_metal_precusor.py:
will build the cis-protected Pd precursor for subsystems -- includes optimisation. Not used in the manuscript.
build_cage.py:
will build 4 cage symmetries -- includes optimisation
build_subsystems.py:
will build triangles, squares and 6-mem rings from metal precursor and ligand -- includes optimisation. Not used in the manuscript.
utilities.py:
defines utilities for construction
optimisation.py:
defines optimisation sequences.
topologies.py:
contains the new topology graph for the ring and updated M12L24
The metal complex topology was not used in this work.
analyse_cages.py:
for all desired systems:
* calculates total energies
* calculates metal-atom order parameter
* calculates ligand strain energy
analyse_subsystems.py and analyse_manual_subsytems.py:
for all desired systems: Not used in the manuscript.
* calculates total energies
* calculates metal-atom order parameter
* calculates ligand strain energy
plotting.py:
Utilities for plotting.
spinner.py:
Utilities for using SpinDry to orient building blocks.
Not used in the manuscript.
m24_optimising.py:
Script for running the optimisation of Pd24L48 systems from XYZ file.