/NiPyC_analogues

Primary LanguageJupyter Notebook

File structure:

  • analysis
  • data
  • depreciated
  • gcmc_simulation
  • mof_construction
  • structure_optimization
  • XRD

Data

The data directory contains input and output files for GCMC simulations.

NOTATION:

  • MOF_experimental.cif coresponds to the .cif file produced by experimentalists.
  • MOF_relax.cif corresponds to the .cif file generated by performing DFT relaxation using fixed-volume such that the cell parameters are the same as the experimental values.
  • MOF_vc-relax.cif corresponds to the .cif file generated by performing DFT relaxation and allowing the cell parameters to varry (i.e. vc = variable cell).

The directories NiPyC2_experimental, NiPyC2_relax, and NiPyC2_vc-relax are populated with 2x1x1 replicated and functionalized versions of their respective .cif files. The replication is done so that we can get a larger sampling to the randomized position of the functional group while not being so large that the DFT calculations take too long to converge.

Resources:

https://pubs.acs.org/doi/full/10.1021/jacs.6b10455 Ni(PyC)2 downloaded from here and the DMF solvent was deleted via cutting out lines of the .cif

https://pubs.acs.org/doi/full/10.1021/cg300274n SBMOF-1 downloaded from here, cg300274n_si_003.cif (14.66 kb), corresponding to the activated structure. (there are two, one activated, one not).