Optical Methods to Identify Nanotube-DNA hybrids

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Optical Identification of Helical ss-DNA Wrapping on the Nanotube

Presentation transcript:

Optical Methods to Identify Nanotube-DNA hybrids Slava V. Rotkin, Stacy E. Snyder, Alexey Tsukanov# Lehigh University, # Moscow State University NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

DNA NT complex: Modeling scheme _____________ NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Computational Scheme (1) Self-consistent solution for the charge density of semiconductor [7,0] zigzag NT under DNA wrap perturbation NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Modulation of the Density of States _____________ NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

DOS: Analytical Treatment b) c) (a) Pristine NT; (b) NT with z-type perturbation; (c) NT with a-type perturbation details are in Europhys. Letters 77, 27006 (2007); Proc. of SPIE 6328, 63280D (2006). NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

DNA NT Optics _____________ NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Optics results (2): Cross-absorption Absorption in the DNA - SWNT hybrids. Strength of the potential : Optical modulation Abs. E, eV NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Optics results (2): Cross-absorption Absorption in the DNA - SWNT hybrids. E, eV x 100 Abs. wavevector E, eV NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Tight Binding Scheme (R) Self-consistent solution for the charge density of semiconductor [7,0] zigzag NT under DNA wrap perturbation NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

DNA-NT hybrids: Environmental Models _____________ NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Langevin Dipole Scheme (R) 1 2 3 4 5 -12 -10 -6 -4 NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Water Polarization: Analytical Lump Model _____________ NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

Water Polarization: Numerical Modeling _____________ NIRT-IV, DuPont, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"

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, 8/15/07 Slava V Rotkin, "SWNT hybrids optics"