Short Report about My Activity in Dresden

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DNA-wrapped Carbon Nanotubes
Andrey Enyashin Institute of Physical Chemistry,
TU Dresden, Germany enyashin_at_theory.chm.tu-dresden
.de enyashin_at_ihim.uran.ru
SLONANO2007, Ljubljana
11. October 2007
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Known hybrides of carbon nanotubes (CNT) and
deoxyribonucleic acids (DNA)
Supramolecular conjugates of CNT and DNA D.
Nepal et al., 2005
SWCNTs wrapped by DNA M. Zheng et al., 2003
MWCNT covered by DNA Z. Guo et al., 1998
Self-assembled SWNTs with DNA as linkers Y. Li
et al., 2006
Covalently linked DNACNT adducts S.E. Baker et
al., 2002
polyA-DNA inside of SWNTs T. Okada et al., 2006
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Possible Applications Noncovalent bonding of
DNA and CNT gives possibilities for- dispersion
of the SWNT bundles in a hydrofilic solventunder
mild conditions- non-destructive purification of
SWNTs - radius separation and/or high-resolution
length sorting of SWNT (for instance, using
chromatographical methods)without any chemical
modification of CNTs and followingwith
preservation of the CNT walls and the CNT
properties
Chromatogram of size-exclusion column (SEC)
length separation of DNA-CNT complexes and AFM
images of three representative fractions of
SEC X. Huang et al., 2005
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Possible Applications The non-covalent
associates of DNA and CNTs can be useful- at
stabilizing of an interface, that forms between
two immiscible liquids (emulsions), by producing
of the liquid crystals - in analytical chemistry
and biochemistry for creation of nanoscale
chemical sensors on various gases and devices for
express-recognition of a DNA sequence and
hybridization
An emulsion of toluene in water stabilized by the
ssDNA-wrapped SWCNTs E.K. Hobbie et al., 2005
First water-based nematic phase of
unfunctionalied and freely dispesed CNTs S.
Badaire et al., 2005
A scheme of experimental device to recognize the
odors (electronic nose or tongue) C. Staii et
al., 2005
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Topic of work - developing of the atomic
models of the DNA-wrapped SWNTs (in next,
CNT_at_DNA complexes)- quantum-chemical simulation
of the stability and electronic properties of
these complexes based on homopolymeric DNAs
Method used All quantum-chemical calculations
of the stability and electronic structure were
performed using the density-functional based
tight-binding (DFTB) method with full geometry
optimization including dispersion interactions in
framework of UFF method 1 D. Porezag, T.
Frauenheim, T. Köhler, G. Seifert, R. Kashner,
Phys. Rev. B 51 (1995) 12947. 2 G. Seifert, D.
Porezag, T. Frauenheim, Int. J. Quantum Chem. 58
(1996) 185.3 A.M. Koster, G. Geudtner, A.
Goursot, T. Heine, A. Vela, D.R. Salahub, DeMon
Package, 2002 NRC Canada.
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Basis for construction of the models of CNT_at_DNA
complexes DNA
Double stranded polyGC-DNA
Nucleobasic residues linked to sugar
phosphatepurine bases adenine, guanine,
pyrimidine bases thymine, cytosine
The schematic structure of a deoxyribose nucleic
acid double-stranded DNA J.D.Watson,
F.H.C.Crick, 1953
Single stranded polyG-DNA
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Basis for construction of the models of CNT_at_DNA
complexes SWCNT
A structure of a graphite monolayer and possible
variants of its cutting to roll a unit cell of
a (n,m) CNT M.S. Dresselhaus et al., 1992
Three kinds of CNTs concerning interrelation of n
and m indexes
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Basis for construction of the models of CNT_at_DNA
complexes
In the case of single-stranded DNA one can take
for
where lC-N denotes the length of a C-N bond
linking a base with phosphosugar backbone (about
1.5 Å)
where x, y are integer numbers, the numbers of
unit cells of CNT and DNA within a unit cell of
CNT_at_DNA complex
These simple estimations show, for example, that
a unit cell of a complex of (5,5) nanotube with a
single DNA chain can be constructed using 16 unit
cells of CNT and 1 unit cell of DNA composed by
12 nucleotides
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Basis for construction of the models of CNT_at_DNA
complexes
These simple estimations show, for example, that
a unit cell of a complex of (5,5) nanotube with a
single DNA chain can be constructed using 16 unit
cells of CNT and 1 unit cell of DNA composed by
12 nucleotides
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Formation of the CNT_at_DNA complexes
DFTB based energetical model for association of
DNA and CNT

• Let us consider as a model reaction of a CNT_at_DNA
  complex formation next reaction cycle
• - we neglect an influence of medium
• we consider only one kind of DNA deformation
  radial distortion of a chain

single CNT
CNT_at_DNA complex
a CNT bundle
DE energy of formation from CNT bundles and
ss-DNA Ecoh cohesion energy of CNT within their
bundles Estrain strain energy of distorted
ss-DNA molecule Eads adsorption energy of DNA
nucleobases on graphite surface
nondistorted ss-DNA molecule
distorted ss-DNA molecule
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Formation of the CNT_at_DNA complexes
Cohesion Energy of CNTs within Bundles
An array of three (5,5) CNTs
Two examples of SWCNT rope M. Monthioux et al.,
2001
A hexagonal crystal of (5,5) CNTs
J. Tersoff et al., 1994
A cubic crystal of (12,0) CNTs
An example of DWCNT rope M. Endo et al., 2005
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Formation of the CNT_at_DNA complexes
Cohesion Energy of CNTs within Bundles
Dependence of the CNT cohesion energy on the
radii of nanotubes (RCNT) for different CNT
packings
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Formation of the CNT_at_DNA complexes
Strain Energy of distorted ss-DNA Molecules
1
2
3
4
Images of nondistorted ss-polyC-DNA molecule of
RDNA 7.2 Å (1) with nucleobases stacked and
distorted one with nucleobases nonstacked and
RDNA equal to 7.2 Å, 10.8 Å and 14.4 Å (2,3,4)
respectively
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Formation of the CNT_at_DNA complexes
Strain Energy of distorted ss-DNA Molecules
Dependence of the strain energy of ss-DNA
molecules on the radii (RDNA) for the case of
radial deformation
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Formation of the CNT_at_DNA complexes
Adsorption Energy of DNA Nucleotides on Graphite
Surface
Energies of adsorption ofadenosinmonophosphate
(A), guanosinmonophosphate (G),cytidinmonophospha
te (C) thymidinmonophosphate (T) on graphite
surface, eV/base
Adenosinmonophosphate on a graphite surface
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Formation of the CNT_at_DNA complexes
Energetical model for association of DNA and CNT
Energy of formation DE of the CNT_at_DNA complexes
from a SWCNT bundle and ss-DNA depending on type
of homo-DNA and radius of CNT. On the left a CNT
bundle is considered as hexagonal crystal of
CNTs, on the right as a 3-membered rope
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Formation of the CNT_at_DNA complexes
Energetical model for association of DNA and CNT
N number of chains, L distance between two
neighboring chains
For (5,5)CNT_at_NpolyG-DNA at L 10 Å
DEtot /N
-0.1704 eV/Å
-0.1491 eV/Å
-0.1588 eV/Å
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Formation of the CNT_at_DNA complexes
Energetical model for association of DNA and CNT
Energy of formation DE of the CNT_at_DNA complexes
from a SWCNT bundle and N chains of ss-DNA
depending on type of homo-DNA and radius of CNT.
On the left a CNT bundle is considered as
hexagonal crystal of CNTs, on the right as a
3-membered rope
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Formation of the CNT_at_DNA complexes
Direct DFTB calculations
Energy of formation DE of the CNT_at_DNA complexes
from a SWCNT bundle and 1 chain of
poly-ss-DNA. CNT bundles are considered as
hexagonal crystals of CNTs1
Energy of formation DE of the CNT_at_polyC-DNA
complexes from a SWCNT bundle and 1 chain of
ss-DNA. Solid line the data obtained using
energetical model
1 Metallic nanotubes are marked red
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Electronic Properties of the CNT_at_DNA complexes
Densities of States
nondistorted polyC-DNA
strained polyC-DNA
(7,3)CNT_at_polyC-DNA
free (7,3)CNT
?E 0.27 eV/Å QCNT -0.01e
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Electronic Properties of the CNT_at_DNA complexes
Densities of States
free (5,5)CNT
(5,5)CNT_at_polyC-DNA
?E 0.27 eV/Å QCNT -0.01e
free (9,0)CNT
(9,0)CNT_at_polyC-DNA
?E 0.28 eV/Å QCNT -0.01e
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Electronic Properties of the CNT_at_DNA complexes
Densities of States
free (8,2)CNT
(8,2)CNT_at_polyC-DNA
?E -0.17 eV/Å QCNT -0.37e
free (7,4)CNT
(7,4)CNT_at_polyA-DNA
?E 0.19 eV/Å QCNT -0.11e
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Electronic Properties of the CNT_at_DNA complexes
Charge Transfer
Charge transfer from DNA to CNT within the
CNT_at_DNA complexes1
Equipotential surfaces 0.4 e/Å (yellow) and -0.4
e/Å (blue) of electrostatic field for
(5,5)_at_polyC-DNA, (8,2)_at_polyC-DNA and
(8,2)_at_2polyC-DNA (from left to right).
1 Metallic nanotubes are marked red 2 The value
of QCNT is given also for (8,2)CNT_at_2polyC-DNA
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Electronic Properties of the CNT_at_DNA complexes
Charge Transfer
Charge transfer from DNA to CNT within the
CNT_at_DNA complexes1
1 Metallic nanotubes are marked red 2 The value
of QCNT is given also for (8,2)CNT_at_2polyC-DNA
The charge of a (8,2) CNT fragment wrapped by DNA
fragment composed of 12 nucleotides in dependence
on the number of cytodinmonophosphates among them
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Conclusions 1. Atomic models of the CNT_at_DNA
complexes were constructed.2. Energetic
considerations using DFTB(UFF) method show, that
- wrapping of a single chain of ss-DNA does not
give an essential gain in energy of the CNT_at_DNA
formation from CNT bundles and nondistorted
ss-DNA must be more chains adsorbed -
homo-ss-DNA based on the pyrimidine nucleotydes
are more effective for wrapping of CNTs, but in
spite of purine ones are less sensitive.
Probably, for extraction of CNTs in a solution
and their separation hetero-ss-DNAs composed of
both kinds of nucleotydes have to be used. 3.
Direct calculations of formation energy of
CNT_at_DNA using DFTB method show, that in the case
of the chiral metallic CNTs the model above
mentioned is not valid. Their CNT_at_DNA complexes
have less values of formation energy.4.
Densities of states (DOS) of CNT_at_DNA complexes
based on polyC-DNA and chiral metallic CNTs
cannot be presented like a superposition of DOSs
of free components. They have metallic-like
spectra with Fermi level composed by 2pO-states
of the cytosine rests, what is accompanied by
charge transfer from polyC-DNA to CNT.
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Aknowledgments
I am grateful to Dr. Gemming and Prof.
Seifertfor helpful discussions!
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Aknowledgments
Thank You for Your attention!