This is out of my scope, condensed phase simulations
could be tricky. I would expect, though I am not sure,
that common polarization and many body effects can be important.
To be honest, we do not have a solid estimate so far
for many body effects in aromatic clusters, I have done
some calcs for base stack systems but only at the MP2 level,
which considers only the first order nonadditivities, thus
HF many body corrections. To get dispersion nonadditivity CCSD(T)
would be needed.
With pair additive force field the missing many body effects
can often be taken into account by some effective factors, constants,
etc.
Jiri
[ Charset ISO-8859-1 unsupported, converting... ]
> Hmmm... I was thinking about another thing. If I use benzene (or
> toluene) as a solvent in my MD simulation, at 300 K, maybe I don't
> need anyway to care about pi-pi interactions between the solvent
> molecules. I confess I don't have much idea about the geometry of
> benzene liquid, I have to look for. But, once again, thank you very
> much for the useful references.
>
> Regards,
>
> Roberto
>
> 2007/5/21, Jiri Sponer <sponer.ncbr.chemi.muni.cz>:
> > Dear Roberto,
> >
> > I am not completely sure with the benzene dimer % accuracy due to
> > the limited set of atom centered point charges and its
> > weak binding. And I do
> > not remember whether a rigorous scan AMBER vs. QM has been done.
> > You would need to compare with the available reference data
> > for the benzene dimer.
> >
> > Original data by Hobza from nineties -
> >
> > Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures: T-shaped and parallel-displaced
> > Author(s): Hobza P, Selzle HL, Schlag EW
> > ource: JOURNAL OF PHYSICAL CHEMISTRY 100 (48): 18790-18794 NOV 28 1996
> >
> > show the nature of interactions.
> >
> > These were several times recalculated recently (chemistry unchanged,
> > numbers differ somewhat).
> >
> > Origin of attraction and directionality of the x/x interaction: Model chemistry calculations of benzene dimer interaction
> > Author(s): Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K
> > Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 124 (1): 104-112 JAN 9 2002
> >
> > Estimates of the ab initio limit for pi-pi interactions: The benzene dimer
> > Author(s): Sinnokrot MO, Valeev EF, Sherrill CD
> > Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 124 (36): 10887-10893 SEP 11 2002
> >
> > Benzene dimer is different from bases as it is
> > dominated, besides dispersion forces, by quadrupole - quadrupole
> > electrostatics (thus T-shaped and parallel displaced structures
> > are competing). There, however, appears to be no fundamental
> > difference in the nature of the forces. The parallel displaced
> > and T-shape structures can be explained by "classical"
> > electrostatics with no need for specific pi-pi terms.
> >
> > Note that for any rigorous comparisons you would need a number
> > of points on PES, and take into consideration polarization effects
> > when rationalizing the differences.
> >
> > Intercalators were done, too, very good outcome for amber,
> > except of polarizition effects with +1 and +2 systems.
> >
> > Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study
> > Author(s): Reha D, Kabelac M, Ryjacek F, Sponer J, Sponer JE, Elstner M, Suhai S, Hobza P
> > Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 124 (13): 3366-3376 APR 3 2002
> >
> > see also
> > The nature of intermolecular interactions between aromatic amino acid residues
> > Author(s): Gervasio FL, Chelli R, Procacci P, Schettino V
> > Source: PROTEINS-STRUCTURE FUNCTION AND GENETICS 48 (1): 117-125 JUL 1 2002
> >
> >
> > Best wishes, Jiri
> >
> >
> > [ Charset ISO-8859-1 unsupported, converting... ]
> > > Dear Jiri:
> > >
> > > thank you very much. I'm gonna get all the references you recommended.
> > > Right now I'm thinking of the simplest case: two benzene rings
> > > interacting with each other.
> > >
> > > []s,
> > >
> > > Roberto
> > >
> > > 2007/5/21, Jiri Sponer <sponer.ncbr.chemi.muni.cz>:
> > > > Aromatic base stacking and similar interactions are very
> > > > well described by ESP charges + reasonable vdW term.
> > > >
> > > > Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
> > > > Author(s): Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M, Hobza P
> > > > Source: CHEMISTRY-A EUROPEAN JOURNAL 12 (10): 2854-2865 MAR 20 2006
> > > >
> > > > Potential energy surface of the cytosine dimer: MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field
> > > > Author(s): Jurecka P, Sponer J, Hobza P
> > > > Source: JOURNAL OF PHYSICAL CHEMISTRY B 108 (17): 5466-5471 APR 29 2004
> > > >
> > > > etc .. etc..
> > > >
> > > > The original reference with the above statement is:
> > > >
> > > > Nature of nucleic acid-base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs
> > > > Author(s): Sponer J, Leszczynski J, Hobza P
> > > > Source: JOURNAL OF PHYSICAL CHEMISTRY 100 (13): 5590-5596 MAR 28 1996
> > > >
> > > > Pi charges were (without much effect) tested in:
> > > >
> > > > Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
> > > > Author(s): Sponer J, Leszczynski J, Hobza P
> > > > Source: JOURNAL OF COMPUTATIONAL CHEMISTRY 17 (7): 841-850 MAY 1996
> > > >
> > > > Jiri Sponer
> > > >
> > > >
> > > >
> > > >
> > > > [ Charset ISO-8859-1 unsupported, converting... ]
> > > > > Dear all:
> > > > >
> > > > > are the Amber force fields suitable to this kind of interaction (pi-pi)?
> > > > >
> > > > > []s,
> > > > >
> > > > > Roberto
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Received on Wed May 23 2007 - 06:07:36 PDT
