I think that might be true if it were only vdw, but don't forget that these
atoms have partial charges and the rings have quadrupoles. The inner parts
of the ring are substantially negative compared to the outer edge atoms (eg
for a benzene or Phe). The indeed gives a favorable cation-pi interaction,
and will influence relative energies of T vs stacked geometries. Of course
the level of accuracy is open to debate, but the terms aren't completely
absent.
On Fri, Oct 19, 2018, 4:38 PM Chris Neale <candrewn.gmail.com> wrote:
> Should VDW not (incorrectly) favor in-register-parallel over
> parallel-displaced and T-shaped geometries for aromatic rings?
> http://www.jbc.org/content/273/25/15458.long
>
> And how does the Hamiltonian at all account for cation-pi?
>
> I do agree that other parts of the force field might lead to configurations
> that are stabilized by pi-based interactions in real life though not in
> simulation, and that disrupting the associated pi-based interaction may
> thereby have an experimental effect.
>
>
>
>
>
> On Fri, Oct 19, 2018 at 6:50 AM Christina Bergonzo <cbergonzo.gmail.com>
> wrote:
>
> > Hi,
> >
> > I wanted to give a more nuanced look at the pi-pi and cation-pi
> interaction
> > in MD force fields.
> >
> > While there is no explicit force field term for pi-pi or cation-pi
> > interactions, you can of course look for their effects, which are indeed
> > represented using MD - otherwise my DNA duplexes would be in trouble!
> > Force fields rely on van der Waals to pick up the effects of these
> > interactions, and generally they can capture those effects - of course,
> > this is modulated by the desired level of accuracy.
> >
> > You can take a look at these papers to get an understanding of the issue
> > w.r.t. QM:
> > https://www.ncbi.nlm.nih.gov/pubmed/22260616
> > https://link.springer.com/content/pdf/bbm%3A978-3-319-15382-7%2F1.pdf
> >
> > Here is an example where we measured base eversion pathways, noted a
> > cation-pi interaction, and experimental collaborators made the mutation
> to
> > disrupt it, causing catalytic activity of the protein with an (aromatic)
> > damaged DNA base to decrease, but leaving the activity of the
> > (non-aromatic) apurinic damage intact:
> > https://academic.oup.com/nar/article/44/2/683/2468125
> >
> > And here is an example of base stacking in RNA, where it is argued that
> > pi-pi stacking is overstabilized:
> > http://www.pnas.org/content/110/42/16820
> >
> >
> http://www.pnas.org/content/pnas/suppl/2013/09/11/1309392110.DCSupplemental/pnas.201309392SI.pdf
> >
> >
> > For analysis of these types of interactions, I would make sure to look at
> > not only the energies but also the distances and geometries of pi-pi or
> > cation-pi binding pairs.
> >
> > Hope this helps,
> > Christina
> >
> > On Thu, Oct 18, 2018 at 11:27 PM Chris Neale <candrewn.gmail.com> wrote:
> >
> > > Be careful... atomistic force fields typically don't have any pi
> electron
> > > effects in the Hamiltonian, so why would you analyze for them? In fact,
> > > most atomistic force fields do a pretty terrible job at pi-based
> effects
> > > like aromatic stacking. Same goes for cation-pi interactions.
> > >
> > > On Thu, Oct 18, 2018 at 8:08 PM Meng Wu <wumeng.shanghaitech.edu.cn>
> > > wrote:
> > >
> > > > Dear all,
> > > >
> > > > I have MD for my channel protein and substrate molecules and I
> have
> > > > used the "lie" command to calculate the EELEC and EVDW terms. Now I
> > want
> > > to
> > > > analysis like the pi-pi interactions or aromatic interactions between
> > the
> > > > substrates and protein & residue to residue in protein, could anybody
> > > give
> > > > me some suggestions? Thank you in advance!
> > > >
> > > > Best regards,
> > > > Meng Wu
> > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
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> > > >
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> > >
> >
> >
> > --
> > --------------------------------------------------------------
> > Christina Bergonzo
> > Research Chemist
> > NIST/IBBR NRC Postdoctoral Researcher
> > --------------------------------------------------------------
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 19 2018 - 14:30:03 PDT
