Late nights and ailing computers aren’t conducive to the best of work. So, when I posted about the clean chemical structure I obtained using ChemDraw I was genuinely excited about the quality of clean-up that was produced. However I slept on it and reminded myself to check that the output InChI was equivalent to the input InchI as my experience with structure cleaning is that it can swap stereocenters.

So, I returned to that particular problem and looked specifically at the InChI string fed to ChemDraw to convert and then converted the resulting strcture to an InChI in Chemdraw. So, to clarify, this was all done inside the package:

Here’s the stereo layer of the input structure:


and the stereo layer of the output InChI


This is the name of the structure generated by converting the original InChI to a structure and generating the name using nomenclature software: (4R,5E)-4-{[(1E,2S)-2-{[(E)-{2-[(1S)-1-amino-2-methylbutyl]-4,5-dihydro-1,3-thiazol-5-yl}(hydroxy)methylidene]amino}-1-hydroxy-4-methylpentylidene]amino}-5-{[(1E,2S)-1-{[(1E,3S,4E,6R,7E,9S,10E,12R,13E,15S,16E,18R,19E,21S)-18-(3-aminopropyl)-12-benzyl-15-(butan-2-yl)-6-(carboxymethyl)-2,5,8,11,14,17,20-heptahydroxy-3-(2-hydroxy-2-iminoethyl)-9-(1H-imidazol-5-ylmethyl)-1,4,7,10,13,16,19-heptaazacyclopentacosa-1,4,7,10,13,16,19-heptaen-21-yl]imino}-1-hydroxy-3-methylpentan-2-yl]imino}-5-hydroxypentanoic acid

This is the name of the structure generated by naming the structure produced by ChemDraw resulting from reversing the original InChI

(4R,5Z)-4-{[(1Z,2S)-2-{[(Z)-{(5R)-2-[(1S,2R)-1-amino-2-methylbutyl]-4,5-dihydro-1,3-thiazol-5-yl}(hydroxy)methylidene]amino}-1-hydroxy-4-methylpentylidene]amino}-5-{[(1Z,2S,3R)-1-{[(1Z,3S,4Z,6R,7Z,9S,10E,12R,13Z,15S,16Z,18R,19Z,21S)-18-(3-aminopropyl)-12-benzyl-15-[(2R)-butan-2-yl]-6-(carboxymethyl)-2,5,8,11,14,17,20-heptahydroxy-3-(2-hydroxy-2-iminoethyl)-9-(1H-imidazol-5-ylmethyl)-1,4,7,10,13,16,19-heptaazacyclopentacosa-1,4,7,10,13,16,19-heptaen-21-yl]imino}-1-hydroxy-3-methylpentan-2-yl]imino}-5-hydroxypentanoic acidCheck out and compare the names…look at the difference in stereocenters. Maybe there is someting I am not doing correctly and causing this effect. I am presently communicating with Cambridgesoft on this point to see if there is some setting I am missing that retains stereochemistry. This is exactly the issue I see with InChI reversals and CLEANING in other applications unfortunately. I will report back when I determine what the optimal settings are to stop such issues, if indeed they can be prevented.


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