Oh you might have a very good point about it not being sufficient! I just
meant that there's reason to think it's at least partly there.
On Fri, Oct 19, 2018, 5:15 PM Chris Neale <candrewn.gmail.com> wrote:
> Good point. I didn't realize that was sufficient.
>
> On Fri, Oct 19, 2018 at 3:03 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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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> > > >
> > > >
> > > > --
> > > > --------------------------------------------------------------
> > > > Christina Bergonzo
> > > > Research Chemist
> > > > NIST/IBBR NRC Postdoctoral Researcher
> > > > --------------------------------------------------------------
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Received on Fri Oct 19 2018 - 14:30:05 PDT
