Geometry identification notebook comments

[schatzsc]

@cm-beilstein

Since the notebook does not appear to allow comments I have moved them here:

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 320 to 321 in 5b5bd93

	" elif num_neighbors == 1:\n",
	" return \"1-bond\", metal_atom\n",

Instead of 1-bond the correct term for this coordination mode is terminal

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 326 to 328 in 5b5bd93

	" if np.isclose(angle, 180, atol=10): \n",
	" return \"linear\", metal_atom\n",
	" else:\n",

A molecule is linear only when the angle is exactly 180°. One needs to discuss with our colleagues from CCDC about what the average inaccurancy of bond angles in the CSD is - but a tolerance of atol=10 is clearly too high

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 349 to 350 in 5b5bd93

	" if all(np.isclose(a, 120, atol=15) for a in angles): \n",
	" return \"trigonal planar\", metal_atom\n",

The requirement for a trigonal-planar structure is NOT that the three angles are all 120° but that the three ligand atoms and the metal are all in one plane (+/- a bit of tolerance). For example, all atoms planar and angles of 110°, 130° and 120° would also be trigonal-planar (and even more extreme distorted cases as angles of 90°, 100° and 170°).

The only special case is where all four atoms of MX3 are in one plane that is not trigonal-planar is when two angles are exactly 90° and the third one is extactly 180° which is "T-shaped"

All other 3-coordinated structures which are not T-shaped and not trigonal-planar are trigonal-pyramidal (and not unknown), therefore

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 352 to 353 in 5b5bd93

	" elif (np.isclose(avg_angle, 107, atol=5) or np.isclose(avg_angle, 109.5, atol=5)) and not is_planar:\n",
	" return \"trigonal pyramid\", metal_atom # Highly likely given the angle range\n",

is too narrow a definition as trigonal-planar cannot be identified from the L-M-L' angle but only from the fact that the metal atom is not in the same plane as the three ligands and

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 360 to 361 in 5b5bd93

	" # print(f\"Angles: {[f'{a:.2f}' for a in angles]} degrees\")\n",
	" return \"3-unknown\", metal_atom\n",

is simply incorrect.

[schatzsc]

@cm-beilstein

The same also applies to coodination number 4:

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 372 to 373 in 5b5bd93

	" elif any(np.isclose(a, 180, atol=10) for a in angles) and any(np.isclose(a, 90, atol=10) for a in angles):\n",
	" return \"square planar\", metal_atom\n",

A molecule ML4 is square-planar when the metal atom and all four ligands are in one plane. There is no restriction on the angles. For example, all five atoms in a plane and L-M-L' angles of 70°, 80°, 100°, and 110° would still be square-planar.

See-saw (polyhedral symbol SS-4) requires one angle L1-M-L2 of exactly 180° and the L1-M-L3 and L1-M-L4 angles of exactly 90° (which will also make L2-M-L3 and L2-M-L4 90° per the first requirement). L3-M-L4 does NOT have to be 120°.

Square-pyramidal is all four ligand atoms in one plane and the metal atom out of that plane. Again, no restrictions on the L-M-L' angles.

Everything that is not SP-4, SPY-4, or SS-4 is tetrahedral - thus

InChI/INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/geometry_identify_v1.ipynb

Lines 370 to 371 in 5b5bd93

	" if all(np.isclose(a, 109.5, atol=10) for a in angles): \n",
	" return \"tetrahedral\", metal_atom\n",

is incorrect since there is no requirement for the angles to be strictly 109.5°, only that the four ligands are not in one plane and there is no single angle of 180°

[schatzsc]

@cm-beilstein

And this continues with coordination number five:

Pentagonal-planar is all ML5 structures where the metal and the five ligand atoms are in one plane - no restrictions on the L-M-L' angles.

Square-pyramid only requires that four out of five ligand atoms are in one plane and the 5th ligand at 90° to all the other four. Metal position does not matter, can be in the "base plane" or above/below. Also no restrictions on the angles. "Base plane angles" of 80°, 110°, 120°, and 50° would still be square-pyramid.

Trigonal-pyramidal requires one L1-M-L2 angle of exactly 180° and the other L-M-L1 and L-M-L2 angles at 90°. "Central plane angles" do not need to be 120° but can be anything that sums up to 360°

Beyond these geometries, the is a continuum between SPY-5 and TBPY-5 which is hard to capture and usually described by the "tau parameter" tau = 0 is SPY-5 and tau = 1 is TBPY-5 but there can be anything inbetween - there are even examples of compounds with tau values of like 0.48 or 0.53

[schatzsc]

Finally, for octahedral geometry, there is no requirement for the angles to be strictly 3 x 180° and 3 x4 x 90° but that there are eight trigonal "outer" faces while trigonal-prismatic has two trigonal and three rectangular faces.