AMBER Archive (2007)

Subject: Re: AMBER: Pi-pi interactions

From: Roberto Veiga (roberto.sapiens_at_gmail.com)
Date: Tue May 22 2007 - 04:27:22 CDT

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_at_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_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
> > > > -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber_at_scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu