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[BUG] Elongated C-H bond after GAFF UFF optimization #5

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akalikadien opened this issue Jan 19, 2021 · 1 comment
Open

[BUG] Elongated C-H bond after GAFF UFF optimization #5

akalikadien opened this issue Jan 19, 2021 · 1 comment
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Describe the bug
After functionalization of a Co-porphyrin an elongated C-H bond appears that stretches between a phenyl ring. GFN2-xTB, GFN-FF, UFF and GAFF are not able to handle this. Convergence issues were observed with ~40 of the 280 functionalizations.

To Reproduce
Steps to reproduce the behavior:

  1. Take the co_por_C6H6-CH3_meta_1 skeleton
  2. add functionalization_list = [[40,36],[45,43],[39,34],[42,38],[41,37],[54,50],[58,57],[53,48],[56,52],[55,51],[68,64],[73,71],[67,62],[70,66],[69,65],[82,78],[86,85],[81,76],[84,80],[83,79],[2,6],[5,4],[13,12],[11,10],[27,26],[24,25],[16,17],[19,22]] to the skeleton .xyz file
  3. in functionalize_and_optimize_obabel.sh change the variables to the following input:
    STARTING_C_SUBSTITUENT = 1-octanol
    RANDOM_C_SUBSTITUENTS = C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol 1-octanol C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol 1-octanol C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol 1-octanol C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol NH2 CH3 CH3 NH2 NH2 CH3 CH3 NH2

Expected behavior
A symmetrically functionalized Co-porphyrin with normal bond lengths which GFN2-xTB can optimize further

Screenshots
image

MDL Molfile of structure shown in screenshot:

[[23, 22], [20, 21], [12, 13], [15, 18]]
 OpenBabel11262017193D

419430  0  0  1  0  0  0  0  0999 V2000
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    6.6270   -0.9402   -6.2848 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9235   -2.2870   -5.1593 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.4721   -3.2486   -5.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0749   -1.9314   -6.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
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419417  1  0  0  0  0
M  END
@akalikadien akalikadien added the bug Something isn't working label Jan 19, 2021
@akalikadien akalikadien self-assigned this Jan 19, 2021
@vsinha027
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This issue seems to be pertinent with an alkane chain penetrating a phenyl ring during placement. FF methods cannot solve this issue so far. A possible solution is to make use of contact maps via van der Waals radius. We can pre-examine the space in which the ligand would prospectively go. Then using vdW radii based envelopes check if there are overlaps with neighbors or any ring penetration. Normal overlaps with neighbors can be take care of by FFs but it would be good to have this noted anyway.

If ring penetration is detected, we can consider placing a shorter homologue of the ligand and iteratively elongate it.

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