AMBER Archive (2007)

Subject: Re: AMBER: Pi-pi interactions

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Mon May 21 2007 - 10:34:37 CDT

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_at_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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