1. Optical Methods to Identify Nanotube-DNA hybrids
Slava V. Rotkin, Stacy E. Snyder, Alexey Tsukanov#
Lehigh University,
# Moscow State University
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

2. ss-DNA is known to form a helical hybrid with a NT
Can we still think about DNA-NT material as "pristine nanotubes"?
DNA backbone is charged (about one electron per 7Å)
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

3. DNA NT complex: Modeling scheme
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NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

4. SWNT DNA Modeling (2) Poisson simulation cell
Charged phosphate groups of a nucleotide with a thymine base
Supercell of DNA-SWNT
hybrid
Integral # of wraps in integral # of UCs of bare tube;
How do the partial charges on DNA atoms affect the electronic structure of the SWNT?
Unit cell of bare (10,10) nanotube
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

5. Computational Scheme (1)
Self-consistent solution for the charge density of semiconductor [7,0] zigzag NT under DNA wrap perturbation
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

6. Modulation of the Density of States
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NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

7. DOS: Analytical Treatmentb) c)
(a) Pristine NT; (b) NT with z-type perturbation; (c) NT with a-type perturbation
details are in Europhys. Letters 77, (2007); Proc. of SPIE 6328, 63280D (2006).
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

8. Optical transitions: Symmetry breaking
Optical transitions in a metallic zigzag nanotube in circular light polarization change with the modulating field of the perturbation k E
Density of States, a.u.
DNA- NT hybrid
Energy, eV 10 20 30 40 -3 -2 -1 1 2 3
Pristine NT 3 2 1 k E
Energy, eV -1 -2 -3 10 20 30 40
Density of States, a.u.
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

9. Optics results (1): Band edge effects
Absorption spectra of a DNA-zigzag metallic SWNT hybrid in perpendicular polarization
[9,0] NT; λ0=1Å, u0=6eV, Eg=0.33eV, 2D1=3.08eV,
2D2=3.76eV, Γrad=0.0029eV
Puller, Rotkin, EuroPhys. Lett., 2007; Rotkin, Puller, Proc. of SPIE, 2006.
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

10. DNA NT Optics _____________
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

11. Optics results (2): Cross-absorption
Absorption in the SWNT : band-to-band optical transitions.
Absorption onset.
E, eV x 100
Abs.
wavevector
E, eV
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

12. Optics results (2): Cross-absorption
Absorption in the DNA - SWNT hybrids.
Strength of the potential : Optical modulation
Abs.
E, eV
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

13. Optics results (2): Cross-absorption
Absorption in the DNA - SWNT hybrids.
Detailed structure of the modulation
E, eV x 100
Abs.
wavevector
E, eV
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

14. Optics results (2): Cross-absorption
Absorption in the DNA - SWNT hybrids.
E, eV x 100
Abs.
wavevector
E, eV
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

15. Optics results (2): Line appearing
Absorption (a.u.)
[7,0] SWNT semiconductor
18x18 subbands
Unperturbed SWNT 25 50 75
100
125
150
Dm=+1
Dm=-1
ssDNA-Wrapped SWNT
3.5
2.5
1.5
0.8
1.8
2.8
1 >>> 2
2 >>> 1
1 >>> 1
Eg= E11=1.43 eV
Egpert = 1.33 eV
Re excitons—this is 1-e- theory; Electric field is perp. to the tube; e- and hole have diff ang mom; trans suppressed?? 1 2 3 4 5
Energy (eV)
For the helical perturbation, we expect optical selection rules to change. For example, we obtain an increase in 1>>>1 transitions in perpendicular polarization that are prohibited for the pristine nanotube.
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

16. Optics results (3): Circular Dichroism
[7,0] SWNT
Dm=+1
Dm=-1
Eg= E11=1.43 eV
Egpert = 1.33 eV
Unperturbed SWNT
ssDNA-Wrapped SWNT: +1
ssDNA-Wrapped SWNT: -1
Re excitons—this is 1-e- theory; Electric field is perp. to the tube; e- and hole have diff ang mom; trans suppressed??
Different optical selection rules for transitions in two circular polarizations result in CD, absent for the pristine nanotube.
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

17. Tight Binding Scheme (R)
Self-consistent solution for the charge density of semiconductor [7,0] zigzag NT under DNA wrap perturbation
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

18. Tight Binding Scheme (R)
Self-consistent solution for the charge density of semiconductor [7,0] zigzag NT under DNA wrap perturbation
Polarization interaction:
for [7,0] NT and {6:1 | 4e} wrap the cohesion energy due to the NT pi-e-system polarization de ~ 0.47 eV/b.p.
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

19. DNA-NT hybrids: Environmental Models
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NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

20. MC/MD Scheme
Monte-Carlo modeling of the water molecules inside the NT: a test example for adjusting the energy functional and a benchmark for larger scale simulations
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

21. Langevin Dipole Scheme
As a fast-check simulation approach (as compared to more expensive self-consistent Monte-Carlo and MD modeling) we use Langevin model to compute the water dipole :
Water dipoles align along the local electric field, which leads to the screening of this field. Temperature effect is to randomize (destroy) the dipole orientation.
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

22. Langevin Dipole Scheme (R)
In the Langevin model the water dipole depends on the local field
One correction to the local field was calculated by Onsager
Depolarization field also changes the local field
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

23. Langevin Dipole Scheme (R)1 2 3 4 5
-12
-10 -6 -4
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

24. Water Polarization: Analytical Lump Model
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NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

25. Langevin Dipole Scheme (R)
In the Langevin model the water dipole depends on the local field
One correction to the local field was calculated by Onsager
Depolarization field also changes the local field
= (Total field of the dipoles - Total surface charge field) = (1/2 - 1) = -1/2
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

26. Binding Energy in Langevin Water
Analytical solution of the Langevin model gives us effective screening:
NT screening, CQ/Cg, compensates the water shell polarization, hws
NT screening factor is the ratio of quantum to classical capacitance of the NT, CQ/Cg
Water screening factor (for e ~ 80) is larger, thus, it drops from the result
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

27. Binding Energy in Langevin Water
Estimate for the polarization component of the binding energy:
NT charge screening screening factor is the ratio CQ/Cg
External potential screening factor is ~ e/2
As a result of the compensation of the water screening and the NT screening, the binding energy is close to bare value
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

28. Water Polarization: Numerical Modeling
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NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

29. MC/MD Scheme
Monte-Carlo modeling of the polarization of the water molecules near the NT-DNA complex requires developing a new energy functional :
in addition to the standard terms (water-water Coulomb and vdW interactions + water-NT and water-DNA interactions) we include
self-consistent solution for the potential due to charge density of the (delocalized) valence electrons of the NT
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

30. MC + Tight Binding Scheme
Self-consistent solution for the charge density of NT under DNA wrap perturbation within the polar electrolyte solution
Key quantity : Water screening TB MC
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

31. Conclusions
We developed a numerical method for modeling the symmetry lowering in the DNA-NT hybrids
The helical symmetry breaking results in appearing of intrinsically forbidden optical lines in the perpendicular polarization
We propose this method to determine the wrap
We developed a numerical method and analytical lump model for taking into account the polarization of the water (any polar medium) around a NT (DNA-NT complex)
In frame of the model, we obtained a self-consistent screening factor which determines, for example, polarization component of the binding energy
For very strong screening by the medium, its depolarization factors drops off the final result. This suggests replacement of the screened Coulomb kernel by the bare one for the NT-NT interactions
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"

32. Acknowledgements Prof. Anand Jagota (LU) Dr. Ming Zheng (DuPont)
Dr. Vadim I. Puller (formerly at Lehigh)
Mr. S. Manohar
Mr. K. Khripin
Lehigh University
Feigl Scholarship Fund
Army Research Laboratory/Department of Defense
NASA-GFSC Mid-Atlantic Partnership Agreement
National Science Foundation
Center for Optical Technologies
Center for Advanced Materials and Nanotechnology
NIRT-IV, DuPont, 8/15/ Slava V Rotkin, "SWNT hybrids optics"