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

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Long-Range Charge Transfer in DNA II

Part of the book series: Topics in Current Chemistry ((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.

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Abbreviations

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

z A :

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)

z G :

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

k da :

Rate constant for charge transfer between donor and acceptor

V da :

Effective coupling between donor and acceptor states

H da :

Matrix element of Hamiltonian between diabatic donor and acceptor states

S da :

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

μ 12 :

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

References

  1. Bixon M, Jortner J (eds) (1999) Electron transfer from isolated molecules to biomolecules. Adv Chem Phys, vols 106 and 107

    Google Scholar 

  2. Jortner J, Ratner M (eds) (1997) Molecular electronics. Blackwell, Oxford

    Google Scholar 

  3. Cornil J, Beljonne D, Calbert JP, Bredas JL (2001) Adv Mater 13:17

    Google Scholar 

  4. Niemeyer C (2001) Angew Chem Int Ed 40:4128

    Google Scholar 

  5. Hall DB, Holmin RE, Barton JK (1996) Nature 382:731

    Google Scholar 

  6. Nunez ME, Barton JK (2000) Curr Opin Chem Biol 4:199

    Google Scholar 

  7. Schuster GB (2000) Acc Chem Res 33:253

    Google Scholar 

  8. Giese B (2001) Acc Chem Res 33:631

    Google Scholar 

  9. Lewis FD, Letsinger RL, Wasielewski MR (2001) Acc Chem Res 34:159

    Google Scholar 

  10. Bixon M, Jortner J (2001) J Am Chem Soc 123:12556

    Google Scholar 

  11. Ratner MA (1999) Nature 397:480

    Google Scholar 

  12. Berlin YA, Burin AL, Ratner MA (2001) J Am Chem Soc 123:260

    Google Scholar 

  13. Berlin YA, Grozema FC, Siebbeles LDA (2000) J Am Chem Soc 122:10903

    Google Scholar 

  14. Voityuk AA, Jortner J, Bixon M, Rösch N (2001) J Chem Phys 114:5614

    Google Scholar 

  15. Kurnikov IV, Tong GSM, Madrid M, Beratan DN (2002) J Phys Chem B 106:7

    Google Scholar 

  16. Tong GSM, Kurnikov IV, Beratan DN (2002) J Phys Chem B 106:2381

    Google Scholar 

  17. Olofsson J, Larsson S (2001) J Phys Chem B 105:10398

    Google Scholar 

  18. Meggers E, Michel-Beyerle ME, Giese B (1998) J Am Chem Soc 120:12950

    Google Scholar 

  19. Giese B, Wessely S, Spormann M, Lindemann U, Meggers E, Michel-Beyerle ME (1999) Angew Chem Int Ed 38:996

    Google Scholar 

  20. Bixon M, Giese B, Wessely S, Langenbacher T, Michel-Beyerle ME, Jortner J (1999) Proc Natl Acad Sci USA 96:11713

    Google Scholar 

  21. Bixon M, Jortner J (1999) Adv Chem Phys 106:35

    Google Scholar 

  22. Jortner J, Bixon M, Langenbacher T, Michel-Beyerle ME (1998) Proc Natl Acad Sci USA 95:12759

    Google Scholar 

  23. Bixon M, Jortner J (2000) J Phys Chem B 104:3906

    Google Scholar 

  24. Berlin YA, Burin AL, Ratner M (2000) J Phys Chem A 104:443

    Google Scholar 

  25. Marcus RA (1964) Annu Rev Phys Chem 15:155

    Google Scholar 

  26. Marcus RA, Sutin N (1985) Biochem Biophys Acta 811:265

    Google Scholar 

  27. Newton MD (1991) Chem Rev 91:767

    Google Scholar 

  28. Newton MD (1999) Adv Chem Phys 106:303

    Google Scholar 

  29. Mirkin CA, Ratner MA (1992) Annu Rev Phys Chem 43:719

    Google Scholar 

  30. Cheatham TE, Kollman PA (2000) Annu Rev Phys Chem 51:435

    Google Scholar 

  31. Voityuk AA, Siriwong K, Rösch N (2001) Phys Chem Chem Phys 3:5421

    Google Scholar 

  32. Troisi A, Orlandi G (2002) J Phys Chem B 106:2093

    Google Scholar 

  33. Grozema FC, Siebbeles LDA, Berlin YA, Ratner MA (2002) Chem Phys Chem 3:536

    Google Scholar 

  34. Fink HW, Schönenberger C (1999) Nature 398:407

    Google Scholar 

  35. Porath D, Bezryadin A, de Vries S, Dekker C (2000) Nature 403:635

    Google Scholar 

  36. Sanz JF, Malrieu JP (1993) J Phys Chem 97:99

    Google Scholar 

  37. Pacher T, Cederbaum LS, Köppel H (1993) Adv Chem Phys 84:293

    Google Scholar 

  38. Domcke W, Woywood C, Stengle M (1994) Chem Phys Lett 226:257

    Google Scholar 

  39. Cave RJ, Newton MD (1997) J Chem Phys 106:9213

    Google Scholar 

  40. Cave RJ, Newton MD (1996) Chem Phys Lett 249:15

    Google Scholar 

  41. Voityuk AA, Rösch N (2002) J Chem Phys 117:5607

    Google Scholar 

  42. Marcus RA, Sutin N (1985) Biochim Biophys Acta 811:265

    Google Scholar 

  43. Katz DJ, Stuchebrukhov AA (1997) J Chem Phys 106:5658

    Google Scholar 

  44. Daizadeh I, Gehlen JN, Stuchebrukhov AA (1998) J Chem Phys 109:4960

    Google Scholar 

  45. Ivashin N, Källebring B, Larsson S, Hansson Ö (1998) J Phys Chem B 102:5017

    Google Scholar 

  46. Voityuk AA, Rösch N, Bixon M, Jortner J (2000) J Phys Chem B 104:9740

    Google Scholar 

  47. Rust M, Lappe J, Cave RJ (2002) J Phys Chem A 106:3920

    Google Scholar 

  48. Matyushov DV, Voth GA (2000) J Phys Chem A 104:6470

    Google Scholar 

  49. Creutz C, Newton MD, Sutin N (1994) J Photochem Photobiol A Chem 82:47

    Google Scholar 

  50. Voityuk AA, Rösch N (2002) J Phys Chem B 106:3013

    Google Scholar 

  51. Voityuk AA, Jortner J, Bixon M, Rösch N (2000) Chem Phys Lett 324:430

    Google Scholar 

  52. Larsson S (1981) J Am Chem Soc 103:4034

    Google Scholar 

  53. Löwdin PO (1963) J Mol Spectrosc 10:12

    Google Scholar 

  54. Ratner MA (1990) J Phys Chem 94:4877

    Google Scholar 

  55. Skourtis SS, Beratan DN (1999) Adv Chem Phys 106:377

    Google Scholar 

  56. Priyadarshy S, Risser SM, Beratan DN (1996) J Phys Chem 100:17678

    Google Scholar 

  57. Steenken S, Jovanovich SV (1997) J Am Chem Soc 119:617

    Google Scholar 

  58. Rodrigues-Monge L, Larsson S (1996) J Phys Chem 100:6298

    Google Scholar 

  59. Hunter CA, Lu XJ (1997) J Mol Biol 265:603

    Google Scholar 

  60. Lu XJ, El Hassan MA, Hunter CA (1997) J Mol Biol 273:681

    Google Scholar 

  61. Clowney L, Jain SC, Srinivasan AR, Westbrook J, Olson WK, Berman HW (1996) J Am Chem Soc 118:509

    Google Scholar 

  62. Bloomfield VA, Crothers DM, Tinoco I (1999) Nucleic acids: structures, properties, and functions, University Science Books, Sausalito

    Google Scholar 

  63. Kelley SO, Barton JK (1998) Chem Biol 5:413

    Google Scholar 

  64. Baik MH, Silverman JS, Yang IV, Ropp PA, Szalai VA, Yang W, Thorp HH (2001) J Phys Chem B 105:6437

    Google Scholar 

  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. 58

    Google Scholar 

  66. Ridley JE, Zerner MC (1973) Theor Chim Acta 32:134

    Google Scholar 

  67. Dewar MJS, Thiel W (1977) J Am Chem Soc 99:4899

    Google Scholar 

  68. Dewar MJS, Zoebish EG, Healy EF, Stewart JJP (1985) J Am Chem Soc 107:3902

    Google Scholar 

  69. Stewart JJP (1989) J Comput Chem 10:209

    Google Scholar 

  70. Thiel W, Voityuk AA (1996) J Phys Chem 100:616

    Google Scholar 

  71. Voityuk AA, Zerner MC, Rösch N (1999) J Phys Chem A 103:4553

    Google Scholar 

  72. Voityuk AA, Rösch N (unpublished results)

    Google Scholar 

  73. Jortner J, Bixon M, Voityuk AA, Rösch N (2002) J Phys Chem A 106:7599

    Google Scholar 

  74. Rak J, Voityuk AA, Marquez A, Rösch N (2002) J Phys Chem A 106:7919

    Google Scholar 

  75. Dapprich S, Frenking G (1995) J Phys Chem 99:9352

    Google Scholar 

  76. Bagus PS, Hermann K, Bauschlicher CW (1984) J Chem Phys 80:4378

    Google Scholar 

  77. Nakatani K, Dohno C, Saito I (2000) J Am Chem Soc 122:5893

    Google Scholar 

  78. Lewis FD, Calgutcar R, Wu Y, Liu X, Hayes RT, Miller SE, Wasielewski MR (2000) J Am Chem Soc 122:2889

    Google Scholar 

  79. Lewis FD, Wu Y, Liu X, Hayes RT, Letsinger RL, Greenfield SR, Miller SE, Wasielewski MR (2000) J Am Chem Soc 122:12346

    Google Scholar 

  80. Tavernier HL, Fayer MD (2000) J Phys Chem B 104:11541

    Google Scholar 

  81. Siriwong K, Voityuk AA, Newton MD, Rösch N (2003) J Phys Chem B 107:2595

    Google Scholar 

  82. Davis WB, Hess S, Naydenova I, Haselsberger R, Ogrodnik A, Newton MD, Michel-Beyerle ME (2002) J Am Chem Soc 124:2422

    Google Scholar 

  83. Steenken S (1997) Biol Chem 378:1293

    Google Scholar 

  84. Carra C, Iordanova N, Hammes-Schiffer S (2002) 106:8415

    Google Scholar 

  85. Ladik J, Ye YJ (2002) Int J Quantum Chem 90:838

    Google Scholar 

  86. Hjort S, Stafström S (2001) Phys Rev Lett 87:228101

    Google Scholar 

  87. Endres RG, Cox DL, Singh RRP, Pati SK (2002) Phys Rev Lett 88:16601

    Google Scholar 

  88. Liao JL, Voth GA (2002) J Chem Phys 116:9174

    Google Scholar 

  89. Shafirovich VY, Dourandin A, Luneva NP, Geacintov NE (1997) J Phys Chem B 101:5863

    Google Scholar 

  90. Schwögler A, Burgdorf LT, Carell T (2000) Angew Chem Int Ed 39:3918

    Google Scholar 

  91. Lewis FD, Liu X, Miller SE, Hayes RT, Wasielewski MR (2002) J Am Chem Soc 124:11280

    Google Scholar 

  92. Voityuk AA, Michel-Beyerle ME, Rösch N (2001) Chem Phys Lett 342:231

    Google Scholar 

  93. Cai Z, Li X, Sevilla MD (2002) J Phys Chem B 106:2755

    Google Scholar 

  94. Al-Jihan I, Smets J, Adamowicz L (2000) J Phys Chem A 104:2994

    Google Scholar 

  95. Russo N, Toscano M, Grand A (2000) J Comput Chem 14:1243

    Google Scholar 

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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.

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  1. Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747, Garching, Germany

    Notker Rösch & Alexander A. Voityuk

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  1. Notker Rösch
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Correspondence to Notker Rösch .

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G.B. Schuster

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Rösch, N., Voityuk, A.A. Quantum Chemical Calculation of Donor–Acceptor Coupling for Charge Transfer in DNA. In: Schuster, G. (eds) Long-Range Charge Transfer in DNA II. Topics in Current Chemistry, vol 237. Springer, Berlin, Heidelberg. https://doi.org/10.1007/b94472

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  • DOI: https://doi.org/10.1007/b94472

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20131-1

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