Hello Jean-Marc, This is a very interesting question.
Given any molecule, consider its structure stripped of all H's. There is no reason why this stripped structure cannot be represented using wedged bonds etc. (Will continue on the next reply.) Hence potential problems can only arise when the added Hs themselves introduce new chirality / stereochemistry, or that the position of the added H itself is not uniquely defined by the stripped structure. One example I can think of is the secondary amine, if you only consider one state (say if the temperature is so low that it is locked in that geometry). But if there is a rule saying that "the implicit hydrogen is understood to lie in the plane of the paper", then everything will still be fine. Just that the drawings may look a bit strange, as attached. But for stereo bonds, perhaps there is no escape. You will need to draw the explicit hydrogen. See attached. But then how about the orientation of hydroxyl groups in general? They are usually neglected in chemical representations, aren't they?? Ling Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> 於 2021年3月9日週二 上午1:04寫道： > Sure, testosterone may be drawn as > > > > Jean-Marc > > > Le 08/03/2021 à 18:26, Rocco Moretti a écrit : > > On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> > wrote: > >> On 08/03/2021 13:55, Jean-Marc Nuzillard wrote: >> > >> > Is it always possible to represent an organic molecule in 2D with all >> necessary >> > configuration hints (bond wedges pointing to the front or to the back) >> > without introducing any explicit hydrogen atom? >> >> No. Testosterone. >> > > Is that "not possible" or simply "against convention"? One could certainly > imagine someone attempting to put the dashed and wedged designations on the > ring bonds, and leaving the hydrogens implicit. (Flagrantly ignoring how > much it would mess with steroid chemists' brains.) > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > -- > Jean-Marc Nuzillard > Directeur de Recherches au CNRS > > Institut de Chimie Moléculaire de Reims > CNRS UMR 7312 > Moulin de la Housse > CPCBAI, Bâtiment 18 > BP 1039 > 51687 REIMS Cedex 2 > France > > Tel : 03 26 91 82 10 > Fax : 03 26 91 31 > 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html > http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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