Jmol-SwingJS icon indicating copy to clipboard operation
Jmol-SwingJS copied to clipboard

unwanted chirality in -SO3H groups

Open nbehrnd opened this issue 3 years ago • 0 comments

Jmol (14.32.39) possibly assigns sulfonic acids as chiral.

Related to an earlier post here, I observe Jmol assigns chirality for -SO3H when issuing the command

 print {thisModel}.find("SMILES");

though the displayed bond order suggests two S=O, i.e. two out of four substitutents as equal. Their bond length is pretty much similar (1.45 A), while the S-O are distinctly longer (1.61 A):

2022-03-22_Jmol_SO3H_chirality

To ease the comparison, the .sdf in question is attached below.

2022-03-22_examples_SO3H.sdf.zip

nbehrnd avatar Mar 22 '22 14:03 nbehrnd