Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

2016-04-30 Thread Konrad Koehler
Hi Greg, Thanks for your response. Peter is exactly right. There is wide spread agreement that the pi electrons of aromatic nitrogen atoms are not hydrogen bond acceptors. I do not have any experimental data off the top of my head to prove this. However from first principles, it is clear th

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

2016-04-30 Thread Greg Landrum
Hi Konrad, You (and Peter later in the thread) make valid points about whether or not particular functional groups are donors or acceptors. There are certainly interesting discussions to be had about that - particularly when those discussions are backed up by an analysis of experimental data - but

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

2016-04-30 Thread Peter S. Shenkin
Speaking from the peanut gallery, that seems to me to be a rather important point, at least as far as pyrrole NH is concerned. I assume there is widespread agreement that these are not acceptors. I think thiophene S is usually regarded as a receptor, albeit a weak one, but F is highly debatable. S

[Rdkit-discuss] Gobbi hydrogen bond acceptor definition

2016-04-30 Thread Konrad Koehler
Hi All, The following is a relatively minor point, but IMHO, the Gobbi hydrogen bond acceptor definition probably should be modified so that only aromatic nitrogen atoms with two and not three non-hydrogen attachments are considered as acceptors. For example, the aromatic nitrogen atom pyridin