Data for "Sterics and Hydrogen Bonding Control Stereochemistry and Self-Sorting in BINOL-Based Assemblies"

Written and performed by Andrew Tarzia. Please contact me with any issues about this work: [e-mail]

Previously uploaded in 10.5281/zenodo.8432296 and https://github.com/andrewtarzia/citable_data

scripts:

latex_table.py - writes a latex table with relative structure energies from a .csv file with structure energies in au.

strain_energy.py - extracts ligands from structures defined in 'cage_dir' (most of the process is hard coded). For each extracted ligand, the script will find its lowest energy conformer in 'low_c_dir' and calculate the strain energy, which is output to a json file for each structure.

strain_energy_dft.py - same as strain_energy.py, however the ligand energies are read in from low_e_dft_spe.csv (pre calculated at DFT level).

directories:

./ : main directory contains:

python scripts

these use an outdated code base: https://github.com/andrewtarzia/atools - if you have issues, contact me

initial structures "name".xyz

.csv files with extracted structure energies

low_e_dft_spe.csv - energies of free and extracted ligands at DFT level, used by strain_energy_dft.py to calculate strain energies.

spe1_energies.csv - energies of all structures after xtb optimisation at def2-svp level

spe2_energies.csv - energies of all structures after DFT (def2-svp) optimisation at def2-tzvp level

xtb_energies.csv - energies of all structures after xtb optimisation at GFN2-xTB level 

extracted ligand structures (NA is number of atoms in ligand):

"name"_xtb_sgNA....mol -> from the xtb optimised structure

"name"_xtb_dft_sgNA....mol -> from the xtb optimised structure

./xtb1_opts : contains input and output structures for GFN2-xTB optimisations

./orca_spe1 : contains input and output SPE calculations of xtb optimised structures at Def2-SVP level

./orca_opt : contains input and output structures of DFT optimisation of xtb optimised structures at Def2-SVP level 

./orca_spe2 : contains input and output SPE calculations of DFT optimised structures at Def2-TZVP level

./low_e_bb_confs : contains input and output of lowest energy conformer search of free ligands (binolA, binolB, longC, longD; names match those in the paper)

cr_*/ directories contain input and output of CREST conformer searches -- produces "name"_opt.mol/.xyz in

./low_e_bb_confs

dft_opt/ directory contains input and output of DFT optimisation of lowest energy conformers from CREST -- produces "name"_dopt.mol/.xyz in ./low_e_bb_confs

./low_dft_spe : contains input and output SPE calculations of DFT optimised lowest energy conformers of ligand structures (binolA, binolB, longC, longD) and extracted ligand structures at Def2-TZVP level