Small Molecule Design within MultiMize
Bernd
Mayer*1, Ch. T. Klein1, A. Parusel1,
G. Marconi2 and G. Köhler1,3
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1Institute for Theoretical
Chemistry
University of Vienna, UZAII
Althanstrasse 14, A-1090 Vienna, Austria2Institute
for Photochemistry and High Energy Radiation
CNR Bologna
Via P. Gobetti 101, I-40129 Bologna, Italy
3Austrian Society for
Aerospace Medicine
Lustkandlgasse 52/3, A-1090 Vienna, Austria
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This is an abstract for
a poster to be presented at the
Fifth
Foresight Conference on Molecular Nanotechnology.
There will be a link from here to the full article when it is
available on the web.
MultiMize is a program package suitable for rational
design of small molecules and molecular ensembles. The basic idea
behind MultiMize is to combine various physico-chemical
parameters as potential energies, free energy contributions
arising from solvation and spectroscopic properties as e.g. the
rotatory power, in one single optimization procedure.
Structural and dynamical features of general host-guest
systems as well as of peptides and small proteins and of their
aggregates may be explored by MultiMize.
Potential energies are, depending on the type of system,
computed within a MM3-, GROMOS-, AMBER- or ECEPP-force field
based routine. Contributions from solvation are implemented by a
continuum solvent approximation using experimentally derived
atomic solvation parameters. The rotatory power is calculated
within the Tinoco expressions for the induced Circular Dichroism
adopting the polarizability approximation when computing
host-guest systems and the full equations for the natural
Circular Dichroism of peptides. The energetic contributions are
combined in a modified Metropolis criterion and the respective
acceptance probabilities are weighted by a term considering the
variance of computed and experimentally derived spectral
information. The optimization procedure itself is embedded either
in a Monte Carlo scheme or within a Genetic Algorithm.
We present two systems computed within MultiMize, i)
highly ordered molecular necklaces resembling a molecular wire
formed by poly-alkylene oxide multiply complexed by
Cyclodextrins, and ii) alanine-based, helical polypeptides
suitable as transmembrane channel elements.
References:
[1] Influence of Solvation on the Helix Formation of
Poly-Alanine Studied by Multiple Annealing Simulations. C.
Th. Klein, B. Mayer, G. Köhler and P. Wolschann; Theochem
J. Mol. Struct., 370, 33, 1996.
[2] Excited State Proton Transfer of 2-Naphthol
Inclusion Complexes with Cyclodextrins. H. -R. Park, B.
Mayer, P. Wolschann and G. Köhler. J. Phys. Chem.,
98, 6158, 1994.
[3] Higher Order C60 - Fullerene gamma - Cyclodextrin
Inclusion Complexes. G. Marconi, B. Mayer, Ch. T. Klein and
G. Koumlhler; Chem. Phys. Lett., 260, 589, 1996.
*Corresponding Address:
Bernd Mayer, Institute for Theoretical Chemistry, University of
Vienna, UZAII
Althanstrasse 14, A-1090 Vienna, Austria
phone: +43 1 31336 1578, fax: +43 1 31336 790
e-mail: [email protected]
Web: http://asterix.msp.univie.ac.at/local-link
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