Hi James, I know that my opinion might sound extreme but I had this discussion many times (mostly regarding tautomerism which is, however, similar in some way). The problem is, you can look at a chemical structure in many different ways - two scenarios are:
1. What can I perceive from a chemical structure if all I have is the pure connection table and nothing else (and maybe millions of them) 2. What can I find about a particular structure if a I can run fully fledged quantum-mechanical calculations, do an extensive literature search, and/or have carefully measured experimental data and conditions (rarely in the millions :-)) So, if I deal with something like implementing RDKit, things are probably always quite close to scenario 1, hence my suggestion to disregard stereochemistry on these type of N atoms (you need a lot of information from scenario 2 to even decide whether there is stereochemistry or not). The ideal solution, of course, would be to offer three different modes for stereo perception: "disregard", "keep", "perceive" from 3D (I am not sure if Greg likes that :-)). If these three modes would be available I still would suggest to set the default to "disregard" for 3-coordinated N because the other two modes require that you know what you are doing and/or have full trust in your data - otherwise you probably do more harm than good. Best, Markus On Fri, Aug 21, 2015 at 3:10 PM, James Davidson <j.david...@vernalis.com> wrote: > Hi Greg (and Markus, Peter, et al.), > > > > Personal opinion – my vote would be to always keep the chiral information at > 3-valent nitrogen centres… > > As Peter pointed-out, there are bridgehead examples (most of which, I guess, > will have additional carbon chiral centres – and offer diastereomeric > considerations). > > There are also, I believe, some nice oxaziridine examples where the > oxaziridine N is the only chiral centre present (interpreted from abstract > here: http://dx.doi.org/10.1039/C39850000998): > > > > 3,3-dimethyl (2S)-2-tert-butyloxaziridine-3,3-dicarboxylate > > COC(=O)C1(O[N@]1C(C)(C)C)C(=O)OC > > > > and many other examples of diastereomeric oxaziridines – where the N is a > chiral centre – eg see http://dx.doi.org/10.1016/j.tetasy.2008.09.016 > > > > > > Kind regards > > > > James > > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or postmas...@vernalis.com. Email is not a > secure method of communication and the Company cannot accept responsibility > for the accuracy or completeness of this message or any attachment(s). > Please check this email for virus infection for which the Company accepts no > responsibility. If verification of this email is sought then please request > a hard copy. Unless otherwise stated, any views or opinions presented are > solely those of the author and do not represent those of the Company. > > The Vernalis Group of Companies > 100 Berkshire Place > Wharfedale Road > Winnersh, Berkshire > RG41 5RD, England > Tel: +44 (0)118 938 0000 > > To access trading company registration and address details, please go to the > Vernalis website at www.vernalis.com and click on the "Company address and > registration details" link at the bottom of the page.. > ______________________________________________________________________ > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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
