This is the continuation of the previous reply, to elaborate on "the stripped structure can always be represented using wedged bonds".
One potential problem is that a bond is required to be wedged from both ends. But this should not happen. For an atom to be chiral, it needs to be attached to at least 3 other atoms. If it is attached to 3 atoms, its chirality can be specified by using a wedge on any one of the three bonds. Hence there should always be enough possibilities to avoid the potential problem. I could be wrong. I can't proof it. But this is what it feels like to me, especially if no atom is bonded to more than 4 other atoms. Ling Chan <lingtrek...@gmail.com> 於 2021年3月9日週二 上午11:32寫道： > 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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