This is a historical thing that goes back a long way to a previous system and
is almost definitely wrong.
Here are a couple papers arguing that nitro groups are certainly polar:
Crystal structures: http://scripts.iucr.org/cgi-bin/paper?S0108768197010239
Gas phase: http://www.sciencedirect.com/science/article/pii/S0040402001991616
-greg
P.s. I love citing papers from before I was born!
> On 21 Oct 2013, at 14:04, "Stiefl, Nikolaus" <nikolaus.sti...@novartis.com>
> wrote:
>
> Hmm – good question … I don't have that as lumped hydrohphobe. When you look
> at experimental values then you get e.g.:
> Exp
> predACD predChemAxon
> Benzene: 2.13
> 2.22 1.97
> Nitrobenzene 1.85
> 1.95 1.91
>
> So I would agree on the argument. My experience from X-rays is that the major
> interaction I have seen so far was H-acceptor with water or backbone.
>
> For the more complete fdef file – yes that's still on.
> Ciao
> Nik
>
>
> From: JP <jeanpaul.ebe...@inhibox.com>
> Date: Monday, October 21, 2013 11:17 AM
> To: "rdkit-discuss@lists.sourceforge.net Discuss"
> <rdkit-discuss@lists.sourceforge.net>
> Subject: [Rdkit-discuss] Chemistry 101 question...
>
>
> yo RDKitters,
>
> A quick question about some chemistry found in the RDKit from a computer
> scientist.
>
> Why is the nitro ("Nitro2") group in DATA/BaseFeatures.fdef and
> Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef specified as
> LumpedHydrophobe?
>
> # nitro groups in the RD code are always: *-[N+](=O)[O-]
> DefineFeature Nitro2 [N;D3;+](=O)[O-]
> Family LumpedHydrophobe
> Weights 1.0,1.0,1.0
> EndFeature
>
> Why is this a hydrophobe (it looks polar to me)? Or is this one of the too
> many corner cases?
>
> Also a related question, I seem to recall that at the UGM (over a delicious
> sandwich) there was talk of having a more complete fdef file out-of-the-box -
> is this still on?
>
> Many Thanks Folks,
> JP
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