Orbitals: 3D Clean Up, Clean Up Structure

BRIEF DESCRIPTION:

There are three issues:
1. ANY structure with attached orbitals looses association with the corresponding attachment point during "Clean Up Structure" command.

1. If 3D Clean Up of the molecula leads to a non-planar structure, none of the attached orbitals follow associated atoms during 3D Clean Up step.

2. If atoms in the structure with some attached orbitals do not shift relative to each other during "3D Clean Up" command or, alternatively, if orbitals are added to the atoms AFTER "3D Clean Up", "Clean Up Structure" command doesn't affect location or 3D shape of the corresponding orbitals.

DISCUSSION:

ANY structure with attached orbitals looses association with the corresponding attachment point during "Clean Up Structure" command. For instance:

1. Using Chain Tool draw 5+ C-chain alkane vertically (VD-BetaV21-0027.png). Ad some p-orbitals to the carbon atoms.

2. Using Cyclohexane tool draw slightly tilted cyclohexane and add some p-orbitals as well (VD-BetaV21-0027.png).

3. Select one of the obtained structures and apply "Clean Up Structure" command. Observe, when the atoms of the molecula are shifted, attached p-orbitals remain on previous positions (VD-BetaV21-0028.png). Repeat for a second structure. Notice, p-orbitals don't loose association with the molecula [double click on any of the bond using selection tool (Marquee or Lasso) leads to the selection of the molecule with all attached p-orbitals] (Orbitals & Clean Up Structure.mp4).

Similar to "Clean Up Structure" command, if 3D Clean Up of the molecula leads to a non-planar structure, none of the attached orbitals follow associated atoms during 3D Clean Up step.

1. Draw (R)-bromochloroiodomethane molecule as shown at VD-BetaV21-0029.png.

2. Add Open s-orbital to the H-atom.

3. Select the structure. Apply "3D Clean Up" command.

4. Using "Structure Perspective", rotate the structure around X-axis for 90 degrees. Notice, Orbital didn't follow the H-atom during "3D Clean Up" transformation.

5. Observe a similar behaviour for (1R,2S)-1,2-dimethylcyclohexane or propylcyclohexane (Orbitals & 3D Clean Up.mp4).

If atoms in the structure with some attached orbitals do not shift relative to each other during "3D Clean Up" command or, alternatively, if orbitals are added to the atoms AFTER "3D Clean Up", "Clean Up Structure" command doesn't affect location or 3D shape of the corresponding orbitals. For instance:

1. Draw (R)-bromochloroiodomethane molecule as shown at VD-BetaV21-0029.png.

2. Select the molecule and perform "3D Clean Up" command.

3. Add Open s-orbital to the H-atom.

4. Using "Structure Perspective", rotate the structure around X-axis for 90 degrees. Notice, that shape of orbital is not retained as a circle (it's treated as a rotation o the flat circle).

5. Apply "Clean Up Structure" command and observe (Orbitals & 3D Clean Up with Clean Up Structure.mp4):
   - the orbital doesn't move;
   - the orbital doesn't follow associated H-atom;
   - the orbital remains oval, not circle.

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FILES:

VD-BetaV21-0027.png
VD-BetaV21-0028.png
Orbitals & Clean Up Structure.mp4
VD-BetaV21-0029.png

Orbitals & 3D Clean Up.mp4
Orbitals & 3D Clean Up with Clean Up Structure.mp4

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