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Partially Coherent Charge Transport in DNA

Partially Coherent Charge Transport in DNA. YiJing Yan Hong Kong University of Science and Technology. Collaborators: Prof. XinQi LI (Inst. Semiconductor, BeiJing) Dr. Houyu ZHANG (INFM Center S3, Italy) Mr. Ping HAN Acknowledgment: RGC-HK, NNSF-China.

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Partially Coherent Charge Transport in DNA

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  1. Partially Coherent Charge Transport in DNA YiJing Yan Hong Kong University of Science and Technology Collaborators: Prof. XinQi LI (Inst. Semiconductor, BeiJing) Dr. Houyu ZHANG (INFM Center S3, Italy) Mr. Ping HAN Acknowledgment:RGC-HK, NNSF-China ADMOL, 23 – 27 Feb. 2004, Dresden, Germany

  2. General Introduction • Motivation: bio-function & molecular device • Characteristics of nano-size: Partially coherent tunneling -Failure of (incoherence) Ohm’s law - Failure of (coherent) superexchange tunneling

  3. Electron Transfer Rate vs. Conduction Established correspondence (in formulation) ET rate constant  Electric conductance Chemical yield  Electric current Donor/Acceptor  Electrodes (chem. potential)DmDA  eV (applied voltage) See reviews,Nitzan, Ann. Rev. Phys. Chem. 52 (2001) 681; Yan & Zhang, J. Theo. & Comput. Chem. 1 (2002) 225

  4. GG… GAcceptor g1 g2 gn k1 kn-1 kn Experimental Observations acceptor (J.K.Barton; B.Giese; G.B.Schuster; P.F.Babara) G•+ATCTTGAGTGGG C TAGAACTCACCC donor Side reactions: deprotonation ofG+ w/ surrounding H2O Hole charge trapper

  5. The Ohm’s Law: Exact Results GG… GAcceptor g1 g2 gn k1 kn-1 kn I0 Ij-1 I1 Ij In G Acceptor k1 kj-1 kj kn Jj 1 j-1 j n J1 Jn Jj-1 Yan/Li/Zhang, JCP (01) 114:8248 ET rate constant  Electric conductance Chemical yield  Electric current

  6. Effect of Finite Incoherence:Partially Coherent Tunneling via Büttiker’s scattering matrix(Phenomenological model) f = 0, h = 0 Teff(e)/Teff(0) Degree of incoherence

  7. PCT via Quantum Chemistry Based Green’s Function • Key theoretical quantity: Teff(E) (Electron Transmission Function) • Quan. Chem. study of LR-CT in DNA W(E,m) = f(E) - f(E+m) f(E):Fermi function

  8. D- B1 - - BN- A Transmission Function • Effective DBA Hamiltonian (to be elaborated more) reservoirs self-energy: -Im SjDj • Green’s function: • Local transmission function via Geff(E) • Reflection function: Rj  1 – S’ Tjk  Tjj

  9. aD a´A b1 b´1 Formulating the TotalTeff(E) lTotal transmission coefficient: Teff = |a´A|2/|aD|2 J´A/JD lCurrent counting lBoundary condition: Jj (in) = Jj (out) Zhang et al. JCP (02) 117:4578; D’Amato/Pastawski, PRB (90) 41:7411

  10. Total Transmission Function • Total LR-ET transmission coefficient, via simple current counting with the boundary condition of Jj (in) = Jj (out), where j D or A, is coherent incoherent

  11. 5´ 3´ • HF/6-31G* level • Individual base energies • Coupling between different bases in DNA • A semiempirical level • Base-H2O coupling for complex self-energy SS(E) G C T A G+ C 3´ 5´ Quantum Chemistry Determination keff

  12. Coupling Between Base Pairs

  13. s V a g g Evaluation of Self-Energy spectral density Self-energyin semi-infinite chain A semiempirical approach to Ss(E) for DNA in H2O

  14. H2O’s IP a=13.51 eV H2O-H2O coupling g=0.34 eV Semiempirical Approach to Base-Water Couplings Dj(E): same FWHM and area of those in semi-rigid chain model

  15. keff Heff(E) Transmission Function

  16. About the Time Scale of 5 ps The calculated transfer rate for the 5’-GTGGG-3’ DNA duplex in water is found to be keff=0.2ps-1 [coincides w/ Barton and Zewail and co-workers PNAS 96 (1999) 6014] JCP 117 (02) 4578; JTCC 1 (02) 225

  17. Chemical Yield / 0.2ps -1 Hopping over G-bases

  18. PCT Through AT-bases Coherent (AT)n-tunneling is valid only for n =1 and 2

  19. Summary • Systematically established theories/models of long-range electron transfer/transport (LR-ET) -- ET rate  electric conduction -- PCT via scattering matrix -- PCT via Green’s function • Small fraction of incoherence can dramatically alter/enhance LR-ET behaviors • Quantum chemistry determination of mechanism for LR-ET in DNA in H2O

  20. Thanks !

  21. PCT Through AT-bases

  22. Electric Conductivity Theory vs. Experiment on Single DNA Molecule Li & Yan, APL (01) 79:2190

  23. Participation of Interstrand Transfer Pathways

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