MOLECULAR DYNAMIC MODELLING OF TRANSPORT THROUGH
CHEMICALLY MODIFIED SYNTHETIC NANOTUBULES
Lajos HÖFLER
Department of Inorganic and Analytical Chemistry
Budapest University of Technology and Economics
H–1111 Budapest
Supervisor: Róbert E Gyurcsányi
In the recent years application of chemically modified synthetic
nanotubules/nanopores for biomolecular recognition is a new and promising
research area [1]. The pore diameter of the nanotubules is in the order of
magnitude of macromolecules therefore selective binding of biological origin
macromolecules to the inner wall of nanotubules results in a significant
modulation of rate of molecule/ion transport. The effectiveness of the transport
modulation depends among others on the size, geometry and number of the
nanopores as well as on the surface modification.
The theoretical interpretation of transport through chemically modified
synthetic nanotubules has not been worked out yet. Therefore we have used
molecular dynamics to support and explain our experimental results regarding
the bioanalytical use of the chemically modified nanopores [2]. With this
theoretical method we could study the behavior of relatively large (20 nm)
systems at relatively long time scales (50 ns).
We have used a coarse grained model to extend the simulation space
and time [3] (a grain consists of 4-5 atoms, H atoms are not included). Four main
types according of grains are distinguished based on their polarizability and
further 4 subtypes according to the ability of the grain to form H bonds. Quantum
chemical calculations have been used to create the coarse grained
representation of molecules.
Protein and DNA assays performed with synthetic nanotubules by our
group have shown that the predominant mechanisms affecting the transport of
ions through nanopores are based on steric and electrostatic hindrance. Steric
hindrance occurs when a small molecular weight receptor immobilized into the
nanotubule forms a complex with a large molecular weight ligand (protein)
(biotin-avidin system) sterically blocking the transport of molecules/ions.
Electrostatic hindrance can be observed when ionic molecules (DNA) are bound
to uncharged analogues immobilized into the nanopores.
The molecular dynamic calculations were carried out using the
GROMACS software package, while separate software was developed to
generate the initial coordinates and properties of the simulated nanopore system.
.
Initial model of a DNA modified nanopore (surface coverage: 1.6 10-11 mol/cm2)
The ion transport through nanopores modified with different ionic
molecules (different surface coverage values) was simulated. We have
determined the number of ions that got into the single negatively charged 2mercaptoethanesulfonic acid modified nanopores at different surface coverage
values, demonstrating that at increasing surface coverage the electrostatic
repulsion (exclusion) effect is enhanced. The same effect was observed in the
case of DNA strands bearing multiple negative charges and correlated with
experimental results.
References:
[1] Kohli, P; Harrell, CC; Cao, ZH; Gasparac, R; Tan, WH; Martin, CR
Science 2004, 984-986
[2] Gyurcsanyi, R E; Vigassy, T; Pretsch, E Chem Commun 2003, 25602561.
[3] Marrink, SJ; de Vries, AH; Mark, AE J. Phys. Chem. B 108 2004,
750-760