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TurboCoord

TurboCoord is a suite of tools used to find empty spaces within coordination complexes. It is a very crude approach -- essentially a heuristic based algorithm to find the least sterically hindered spaces within the first coordination sphere.

Grid of generated structures

Features

  • Find sterically unhindered spaces within a coordination complex
  • Create a file to view all potential spaces with dummy atoms (using Avogadro, Molden, etc.)
  • Create all acceptable coordination complexes of a desired molecule - ligand pair and write to an .xyz file
    • I would like to thank Robert Shaw for making his xyz to numpy converter freely available at geomConvert
  • Automate TURBOMOLE dft jobs using yaml files (they're like easier to read JSON files)
    • This utility comes mostly from the turbomoleio package maintained by Matgenix SRL

Example of ridft run parameters for a Yb complex using the turbomoleio package

basis: def2-TZVPP
basis_atom: null
ecp_atom: {yb: ecp-28-mwb}
charge: null
coord_file: coord
desy: false
desy_eps: null
ex_all_states: null
ex_exopt: null
ex_frequency: null
ex_frequency_unit: null
ex_irrep_states: null
ex_method: null
ex_mp2: null
ex_multi: null
functional: tpss
gridsize: m4
ired: false
marij: true
maxcor: null
maxiter: null
method: dft
metric: null
mp2energy: false
usemo: null
ri: true
rijk: false
scfconv: 6
scfiterlimit: 400
sym: c1
sym_eps: null
title: ridft
turbobin: null
unpaired_electrons: null
use_f12: false
use_f12*: null
copymo: null