Re: [Rdkit-discuss] para-stereochemistry
I always refer back to this graphic in Alberto Gobbi's "Handling of Tautomerism and Stereochemistry in Compound Registration" paper: https://pubs.acs.org/doi/10.1021/ci200330x [image: image.png] @Greg Landrum , I would interpret "para stereochemistry" as #3 in the above image. And "dependent stereochemistry" as #2 in the above plot since the stereochemistry depends on the stereochemistry of other centers. Alberto's paper defines the above as: 1. steroegenic atom/chiral: typical right/left; R/S 2. pseudo-chiral (referencing an IUPAC paper and the gold book); note, the same thing can happen with cis/trans double bond stereo, not depicted above 3. symmetric stereogenic centers 4. stereogenic bond: typical cis/trans; E/Z 5. atropisomers TLDR: english is so imprecise, show me the SMILES. :-) -Brian On Thu, May 27, 2021 at 5:32 AM Greg Landrum wrote: > > I first heard the term "para stereochemistry" from Salome Rieder (a PhD > student at the ETH Zurich), who pointed me to this paper as a source for > term: > https://pubs.acs.org/doi/pdf/10.1021/ci00016a003 > > I tend to call this "dependent stereochemistry" since I think it's clear, > but that's definitely something I just made up. :-) > > -greg > > > On Wed, May 26, 2021 at 10:54 PM Jean-Marc Nuzillard < > jm.nuzill...@univ-reims.fr> wrote: > >> Dear Paolo, >> >> According to https://goldbook.iupac.org/terms/view/P04921 >> your interpretation is certainly the correct one. >> I still have to find how this r/s assignment is determined. >> >> Many thanks again, >> >> Jean-Marc >> >> >> Le 26/05/2021 à 22:40, Paolo Tosco a écrit : >> > Dear Jean-Marc, >> > >> > I believe it indicates what the IUPAC Gold Book refers to as >> pseudoasymmetry. >> > Let’s see if others agree with my interpretation. >> > >> > Cheers, >> > P. >> > >> >> On 26 May 2021, at 22:28, Jean-Marc Nuzillard < >> jm.nuzill...@univ-reims.fr> wrote: >> >> >> >> I believed I sent a message with the same title a few minutes ago, >> but apparently something went wrong. >> >> >> >> Reading the RDKit book about function FindMolChiralCenters(), >> >> I saw that it provides a better handling of para-stereochemisry. >> >> This concept is not familiar to me. >> >> Google did not help and sent me back to the RDKit Book. >> >> So, what is para-stereochemistry? >> >> >> >> Best regards, >> >> >> >> Jean-Marc >> >> >> >> -- >> >> 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 66 >> >> http://www.univ-reims.fr/icmr >> >> http://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 >> >> >> -- >> 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 66 >> http://www.univ-reims.fr/icmr >> http://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 >> > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] para-stereochemistry
I first heard the term "para stereochemistry" from Salome Rieder (a PhD student at the ETH Zurich), who pointed me to this paper as a source for term: https://pubs.acs.org/doi/pdf/10.1021/ci00016a003 I tend to call this "dependent stereochemistry" since I think it's clear, but that's definitely something I just made up. :-) -greg On Wed, May 26, 2021 at 10:54 PM Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > Dear Paolo, > > According to https://goldbook.iupac.org/terms/view/P04921 > your interpretation is certainly the correct one. > I still have to find how this r/s assignment is determined. > > Many thanks again, > > Jean-Marc > > > Le 26/05/2021 à 22:40, Paolo Tosco a écrit : > > Dear Jean-Marc, > > > > I believe it indicates what the IUPAC Gold Book refers to as > pseudoasymmetry. > > Let’s see if others agree with my interpretation. > > > > Cheers, > > P. > > > >> On 26 May 2021, at 22:28, Jean-Marc Nuzillard < > jm.nuzill...@univ-reims.fr> wrote: > >> > >> I believed I sent a message with the same title a few minutes ago, but > apparently something went wrong. > >> > >> Reading the RDKit book about function FindMolChiralCenters(), > >> I saw that it provides a better handling of para-stereochemisry. > >> This concept is not familiar to me. > >> Google did not help and sent me back to the RDKit Book. > >> So, what is para-stereochemistry? > >> > >> Best regards, > >> > >> Jean-Marc > >> > >> -- > >> 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 66 > >> http://www.univ-reims.fr/icmr > >> http://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 > > > -- > 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 66 > http://www.univ-reims.fr/icmr > http://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 > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] para-stereochemistry
Dear Paolo, According to https://goldbook.iupac.org/terms/view/P04921 your interpretation is certainly the correct one. I still have to find how this r/s assignment is determined. Many thanks again, Jean-Marc Le 26/05/2021 à 22:40, Paolo Tosco a écrit : Dear Jean-Marc, I believe it indicates what the IUPAC Gold Book refers to as pseudoasymmetry. Let’s see if others agree with my interpretation. Cheers, P. On 26 May 2021, at 22:28, Jean-Marc Nuzillard wrote: I believed I sent a message with the same title a few minutes ago, but apparently something went wrong. Reading the RDKit book about function FindMolChiralCenters(), I saw that it provides a better handling of para-stereochemisry. This concept is not familiar to me. Google did not help and sent me back to the RDKit Book. So, what is para-stereochemistry? Best regards, Jean-Marc -- 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 66 http://www.univ-reims.fr/icmr http://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 -- 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 66 http://www.univ-reims.fr/icmr http://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
Re: [Rdkit-discuss] para-stereochemistry
Dear Jean-Marc, I believe it indicates what the IUPAC Gold Book refers to as pseudoasymmetry. Let’s see if others agree with my interpretation. Cheers, P. > On 26 May 2021, at 22:28, Jean-Marc Nuzillard > wrote: > > I believed I sent a message with the same title a few minutes ago, but > apparently something went wrong. > > Reading the RDKit book about function FindMolChiralCenters(), > I saw that it provides a better handling of para-stereochemisry. > This concept is not familiar to me. > Google did not help and sent me back to the RDKit Book. > So, what is para-stereochemistry? > > Best regards, > > Jean-Marc > > -- > 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 66 > http://www.univ-reims.fr/icmr > http://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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] para-stereochemistry
I believed I sent a message with the same title a few minutes ago, but apparently something went wrong. Reading the RDKit book about function FindMolChiralCenters(), I saw that it provides a better handling of para-stereochemisry. This concept is not familiar to me. Google did not help and sent me back to the RDKit Book. So, what is para-stereochemistry? Best regards, Jean-Marc -- 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 66 http://www.univ-reims.fr/icmr http://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
[Rdkit-discuss] para-stereochemistry
Dear all, the RDKit Book mentions, about function FindPotentialStereo(), the improved handling of "para-stereochemistry". Google sends me back to the the RDKit book when I search for this keyword. So, what is para-stereochemistry? Best regards, Jean-Marc -- 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 66 http://www.univ-reims.fr/icmr http://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