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Quantum Chemical Calculation of Donor–Acceptor Coupling for Charge Transfer in DNA

  • Notker Rösch
  • Alexander A. Voityuk
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 237)

Abstract

The electronic coupling V da is the parameter which determines most strongly how the charge-transfer rate between donor and acceptor depends on the distance between the sites and the mutual orientation of donor and acceptor moieties. We discuss quantum chemical procedures to estimate electronic coupling matrix elements of hole transfer in DNA. The two-state model was shown to be quite reliable when applied to the coupling between neighboring Watson–Crick pairs. However, one has to be careful when employing the two-state model to estimate V da in systems where donor and acceptor are separated by a bridge of base pairs. We considered the gross features of base-pair specificity, directional asymmetry, and conformation sensitivity of the couplings. Matrix elements between base pairs are found to be extremely sensitive to conformational changes of DNA. This strongly suggests that a combined QM/MD approach should be best suited for estimating V da within DNA fragments.

Comparison of the effective couplings mediated by π-stack bridges TBT and ABA (B=A, zA, G, T, C) demonstrate that the efficiency of charge transfer is considerably affected by the nature of B; in turn, the effect of B strongly depends on the neighboring pairs. Especially large effects are due to the variation of the oxidation potential of guanine and adenine (B=G, A). Chemical modification of these species or changes of their environment strongly influence the efficiency of charge transfer.

We conclude with a discussion of several open questions and problems concerning the calculation of electronic couplings in DNA-related systems.

Keywords

Electronic coupling Charge transfer DNA Quantum chemical calculations 

Abbreviations and Symbols

A, C, G, T

Nucleobases adenine, cytosine, guanine, and thymine, respectively. In DNA duplexes A, C, G, T stand for the corresponding Watson–Crick pairs, e.g., G in the duplex GGG corresponds to the (GC) Watson–Crick pair

zA

7-Deazaadenine

AM1

Austin Model 1

AO

Atomic orbital

au

Atomic units

B3LYP

Hybrid Becke-3-parameter exchange and Lee–Yang–Parr correlation approximation

CNDO

Complete neglect of differential overlap

CSOV

Constrained space orbital variation (analysis)

CT

Charge transfer

DC

Divide-and-conquer (strategy)

DFT

Density functional theory

EA

Electron affinity

ET

Electron transfer

FC

Thermally weighted Franck–Condon factor

FCD

Fragment charge difference (method)

zG

7-Deazaguanine

GMH

Generalized Mulliken–Hush (method)

HF

Hartree–Fock (method)

HOMO

Highest occupied molecular orbital

INDO

Intermediate neglect of differential overlap (method)

IP

Ionization potential

MD

Molecular dynamics

MNDO

Modified neglect of differential overlap (method)

MNDO/d

MNDO method, parameterization with d orbitals

MO

Molecular orbital

NDDO

Neglect of diatomic differential overlap (method)

NDDO-G

Special parameterization of the NDDO method

NDDO-HT

Parameterization of the NDDO method for hole transfer in DNA

PM3

Parameterized Model 3

QM/MD

Hybrid quantum mechanics/molecular dynamics (method)

SCF

Self-consistent field (method)

SFCD

Simplified fragment charge difference (method)

WCP

Watson–Crick pair

a

Acceptor

b

Bridge

d

Donor

kda

Rate constant for charge transfer between donor and acceptor

Vda

Effective coupling between donor and acceptor states

Hda

Matrix element of Hamiltonian between diabatic donor and acceptor states

Sda

Overlap integrals between donor and acceptor states

Δ

Energy gap between adiabatic states

μ1, μ2

Dipole moments of the ground state and the first excited states, respectively

μ12

Transition dipole moment

β, βel

Decay parameter of the rate constant, decay parameter due to electronic contributions, respectively

λ, λi, λs

Reorganization energy, internal and solvent contributions, respectively

6–31G*

Gaussian basis set of so-called double-zeta quality for valence orbitals, augmented by polarization d-functions (*) on all atoms except hydrogen; used here to generate reference values of hole coupling matrix elements

6–311++G**

Very flexible Gaussian basis set of triple-zeta quality for valence orbitals, augmented by two sets of diffuse exponents (++) on all atoms (except hydrogen) and polarization functions on all atoms; other symbols for basis sets are to be read accordingly

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Notes

Acknowledgements

We thank M. Bixon, J. Jortner, A. Marquez, M.E. Michel-Beyerle, M.D. Newton, J. Rak, and K. Siriwong for stimulating discussions and various contributions to the work described here. Our research was supported by Deutsche Forschungsgemeinschaft (SFB 377), Volkswagen Foundation, and Fonds der Chemischen Industrie.

References

  1. 1.
    Bixon M, Jortner J (eds) (1999) Electron transfer from isolated molecules to biomolecules. Adv Chem Phys, vols 106 and 107Google Scholar
  2. 2.
    Jortner J, Ratner M (eds) (1997) Molecular electronics. Blackwell, OxfordGoogle Scholar
  3. 3.
    Cornil J, Beljonne D, Calbert JP, Bredas JL (2001) Adv Mater 13:17Google Scholar
  4. 4.
    Niemeyer C (2001) Angew Chem Int Ed 40:4128Google Scholar
  5. 5.
    Hall DB, Holmin RE, Barton JK (1996) Nature 382:731Google Scholar
  6. 6.
    Nunez ME, Barton JK (2000) Curr Opin Chem Biol 4:199Google Scholar
  7. 7.
    Schuster GB (2000) Acc Chem Res 33:253Google Scholar
  8. 8.
    Giese B (2001) Acc Chem Res 33:631Google Scholar
  9. 9.
    Lewis FD, Letsinger RL, Wasielewski MR (2001) Acc Chem Res 34:159Google Scholar
  10. 10.
    Bixon M, Jortner J (2001) J Am Chem Soc 123:12556Google Scholar
  11. 11.
    Ratner MA (1999) Nature 397:480Google Scholar
  12. 12.
    Berlin YA, Burin AL, Ratner MA (2001) J Am Chem Soc 123:260Google Scholar
  13. 13.
    Berlin YA, Grozema FC, Siebbeles LDA (2000) J Am Chem Soc 122:10903Google Scholar
  14. 14.
    Voityuk AA, Jortner J, Bixon M, Rösch N (2001) J Chem Phys 114:5614Google Scholar
  15. 15.
    Kurnikov IV, Tong GSM, Madrid M, Beratan DN (2002) J Phys Chem B 106:7Google Scholar
  16. 16.
    Tong GSM, Kurnikov IV, Beratan DN (2002) J Phys Chem B 106:2381Google Scholar
  17. 17.
    Olofsson J, Larsson S (2001) J Phys Chem B 105:10398Google Scholar
  18. 18.
    Meggers E, Michel-Beyerle ME, Giese B (1998) J Am Chem Soc 120:12950Google Scholar
  19. 19.
    Giese B, Wessely S, Spormann M, Lindemann U, Meggers E, Michel-Beyerle ME (1999) Angew Chem Int Ed 38:996Google Scholar
  20. 20.
    Bixon M, Giese B, Wessely S, Langenbacher T, Michel-Beyerle ME, Jortner J (1999) Proc Natl Acad Sci USA 96:11713Google Scholar
  21. 21.
    Bixon M, Jortner J (1999) Adv Chem Phys 106:35Google Scholar
  22. 22.
    Jortner J, Bixon M, Langenbacher T, Michel-Beyerle ME (1998) Proc Natl Acad Sci USA 95:12759Google Scholar
  23. 23.
    Bixon M, Jortner J (2000) J Phys Chem B 104:3906Google Scholar
  24. 24.
    Berlin YA, Burin AL, Ratner M (2000) J Phys Chem A 104:443Google Scholar
  25. 25.
    Marcus RA (1964) Annu Rev Phys Chem 15:155Google Scholar
  26. 26.
    Marcus RA, Sutin N (1985) Biochem Biophys Acta 811:265Google Scholar
  27. 27.
    Newton MD (1991) Chem Rev 91:767Google Scholar
  28. 28.
    Newton MD (1999) Adv Chem Phys 106:303Google Scholar
  29. 29.
    Mirkin CA, Ratner MA (1992) Annu Rev Phys Chem 43:719Google Scholar
  30. 30.
    Cheatham TE, Kollman PA (2000) Annu Rev Phys Chem 51:435Google Scholar
  31. 31.
    Voityuk AA, Siriwong K, Rösch N (2001) Phys Chem Chem Phys 3:5421Google Scholar
  32. 32.
    Troisi A, Orlandi G (2002) J Phys Chem B 106:2093Google Scholar
  33. 33.
    Grozema FC, Siebbeles LDA, Berlin YA, Ratner MA (2002) Chem Phys Chem 3:536Google Scholar
  34. 34.
    Fink HW, Schönenberger C (1999) Nature 398:407Google Scholar
  35. 35.
    Porath D, Bezryadin A, de Vries S, Dekker C (2000) Nature 403:635Google Scholar
  36. 36.
    Sanz JF, Malrieu JP (1993) J Phys Chem 97:99Google Scholar
  37. 37.
    Pacher T, Cederbaum LS, Köppel H (1993) Adv Chem Phys 84:293Google Scholar
  38. 38.
    Domcke W, Woywood C, Stengle M (1994) Chem Phys Lett 226:257Google Scholar
  39. 39.
    Cave RJ, Newton MD (1997) J Chem Phys 106:9213Google Scholar
  40. 40.
    Cave RJ, Newton MD (1996) Chem Phys Lett 249:15Google Scholar
  41. 41.
    Voityuk AA, Rösch N (2002) J Chem Phys 117:5607Google Scholar
  42. 42.
    Marcus RA, Sutin N (1985) Biochim Biophys Acta 811:265Google Scholar
  43. 43.
    Katz DJ, Stuchebrukhov AA (1997) J Chem Phys 106:5658Google Scholar
  44. 44.
    Daizadeh I, Gehlen JN, Stuchebrukhov AA (1998) J Chem Phys 109:4960Google Scholar
  45. 45.
    Ivashin N, Källebring B, Larsson S, Hansson Ö (1998) J Phys Chem B 102:5017Google Scholar
  46. 46.
    Voityuk AA, Rösch N, Bixon M, Jortner J (2000) J Phys Chem B 104:9740Google Scholar
  47. 47.
    Rust M, Lappe J, Cave RJ (2002) J Phys Chem A 106:3920Google Scholar
  48. 48.
    Matyushov DV, Voth GA (2000) J Phys Chem A 104:6470Google Scholar
  49. 49.
    Creutz C, Newton MD, Sutin N (1994) J Photochem Photobiol A Chem 82:47Google Scholar
  50. 50.
    Voityuk AA, Rösch N (2002) J Phys Chem B 106:3013Google Scholar
  51. 51.
    Voityuk AA, Jortner J, Bixon M, Rösch N (2000) Chem Phys Lett 324:430Google Scholar
  52. 52.
    Larsson S (1981) J Am Chem Soc 103:4034Google Scholar
  53. 53.
    Löwdin PO (1963) J Mol Spectrosc 10:12Google Scholar
  54. 54.
    Ratner MA (1990) J Phys Chem 94:4877Google Scholar
  55. 55.
    Skourtis SS, Beratan DN (1999) Adv Chem Phys 106:377Google Scholar
  56. 56.
    Priyadarshy S, Risser SM, Beratan DN (1996) J Phys Chem 100:17678Google Scholar
  57. 57.
    Steenken S, Jovanovich SV (1997) J Am Chem Soc 119:617Google Scholar
  58. 58.
    Rodrigues-Monge L, Larsson S (1996) J Phys Chem 100:6298Google Scholar
  59. 59.
    Hunter CA, Lu XJ (1997) J Mol Biol 265:603Google Scholar
  60. 60.
    Lu XJ, El Hassan MA, Hunter CA (1997) J Mol Biol 273:681Google Scholar
  61. 61.
    Clowney L, Jain SC, Srinivasan AR, Westbrook J, Olson WK, Berman HW (1996) J Am Chem Soc 118:509Google Scholar
  62. 62.
    Bloomfield VA, Crothers DM, Tinoco I (1999) Nucleic acids: structures, properties, and functions, University Science Books, SausalitoGoogle Scholar
  63. 63.
    Kelley SO, Barton JK (1998) Chem Biol 5:413Google Scholar
  64. 64.
    Baik MH, Silverman JS, Yang IV, Ropp PA, Szalai VA, Yang W, Thorp HH (2001) J Phys Chem B 105:6437Google Scholar
  65. 65.
    To illustrate the weak effect of electron correlation on the electronic coupling for hole transfer, we mention HF and CASPT2 results for an ethylene dimer at an intermolecular distance of 3.5 Å, 0.571 eV, and 0.555 eV, respectively; cf. Ref. 58Google Scholar
  66. 66.
    Ridley JE, Zerner MC (1973) Theor Chim Acta 32:134Google Scholar
  67. 67.
    Dewar MJS, Thiel W (1977) J Am Chem Soc 99:4899Google Scholar
  68. 68.
    Dewar MJS, Zoebish EG, Healy EF, Stewart JJP (1985) J Am Chem Soc 107:3902Google Scholar
  69. 69.
    Stewart JJP (1989) J Comput Chem 10:209Google Scholar
  70. 70.
    Thiel W, Voityuk AA (1996) J Phys Chem 100:616Google Scholar
  71. 71.
    Voityuk AA, Zerner MC, Rösch N (1999) J Phys Chem A 103:4553Google Scholar
  72. 72.
    Voityuk AA, Rösch N (unpublished results)Google Scholar
  73. 73.
    Jortner J, Bixon M, Voityuk AA, Rösch N (2002) J Phys Chem A 106:7599Google Scholar
  74. 74.
    Rak J, Voityuk AA, Marquez A, Rösch N (2002) J Phys Chem A 106:7919Google Scholar
  75. 75.
    Dapprich S, Frenking G (1995) J Phys Chem 99:9352Google Scholar
  76. 76.
    Bagus PS, Hermann K, Bauschlicher CW (1984) J Chem Phys 80:4378Google Scholar
  77. 77.
    Nakatani K, Dohno C, Saito I (2000) J Am Chem Soc 122:5893Google Scholar
  78. 78.
    Lewis FD, Calgutcar R, Wu Y, Liu X, Hayes RT, Miller SE, Wasielewski MR (2000) J Am Chem Soc 122:2889Google Scholar
  79. 79.
    Lewis FD, Wu Y, Liu X, Hayes RT, Letsinger RL, Greenfield SR, Miller SE, Wasielewski MR (2000) J Am Chem Soc 122:12346Google Scholar
  80. 80.
    Tavernier HL, Fayer MD (2000) J Phys Chem B 104:11541Google Scholar
  81. 81.
    Siriwong K, Voityuk AA, Newton MD, Rösch N (2003) J Phys Chem B 107:2595Google Scholar
  82. 82.
    Davis WB, Hess S, Naydenova I, Haselsberger R, Ogrodnik A, Newton MD, Michel-Beyerle ME (2002) J Am Chem Soc 124:2422Google Scholar
  83. 83.
    Steenken S (1997) Biol Chem 378:1293Google Scholar
  84. 84.
    Carra C, Iordanova N, Hammes-Schiffer S (2002) 106:8415Google Scholar
  85. 85.
    Ladik J, Ye YJ (2002) Int J Quantum Chem 90:838Google Scholar
  86. 86.
    Hjort S, Stafström S (2001) Phys Rev Lett 87:228101Google Scholar
  87. 87.
    Endres RG, Cox DL, Singh RRP, Pati SK (2002) Phys Rev Lett 88:16601Google Scholar
  88. 88.
    Liao JL, Voth GA (2002) J Chem Phys 116:9174Google Scholar
  89. 89.
    Shafirovich VY, Dourandin A, Luneva NP, Geacintov NE (1997) J Phys Chem B 101:5863Google Scholar
  90. 90.
    Schwögler A, Burgdorf LT, Carell T (2000) Angew Chem Int Ed 39:3918Google Scholar
  91. 91.
    Lewis FD, Liu X, Miller SE, Hayes RT, Wasielewski MR (2002) J Am Chem Soc 124:11280Google Scholar
  92. 92.
    Voityuk AA, Michel-Beyerle ME, Rösch N (2001) Chem Phys Lett 342:231Google Scholar
  93. 93.
    Cai Z, Li X, Sevilla MD (2002) J Phys Chem B 106:2755Google Scholar
  94. 94.
    Al-Jihan I, Smets J, Adamowicz L (2000) J Phys Chem A 104:2994Google Scholar
  95. 95.
    Russo N, Toscano M, Grand A (2000) J Comput Chem 14:1243Google Scholar

Authors and Affiliations

  1. 1.Institut für Physikalische und Theoretische ChemieTechnische Universität MünchenGarchingGermany

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