[gmx-users] Double vs. Charged Single bonded Oxygen in GROMOS96.1

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 18:32:26 CET 2008

On Monday 27 October 2008 18:08, Justin A. Lemkul wrote:
> Peyman Yamin wrote:
> > Hi again dears,
> >
> > I should ask for another comment. I have a Phorphorus to which two Oxygen
> > atoms are bonded. One O is double bonded and the other has only a single
> > bond while being negatively charged. In the topology file I get from
> > prodrg both Os are denoted with OA (GROMOS96.1) atom type. both have the
> > same charge (-0.421) and mass (15.9994). I guess the charge is reasonable
> > for the double-bonded one, but not for the one with a single bond and a
> > free electron. How could I correct this?
> There is no true double or single bond.  Think resonance!

Impressive answer! But, well, I'm not sure about that resonance thing?

...C-O-P(+3)-O-C... So far it's OK! but P still has 3 fellow electrons to 
share. it does share two of them at once with another O. I understand till 
here. there is another O who wants to get 2 electrons shared, but only 
receives one: it needs more => so we call it a "negatively charges fellow 
oxygen", don't we?

Well I'm well aware of my chemistry knowledge fading away, but you'll tell me 
an OA will do well for both??

Thanks for the time, indeed,

> -Justin
> > Cheers,
> > Peyman

Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

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