Skip to main content
SpringerLink
Log in
Book cover

Kinetics and Dynamics pp 213–245Cite as

Simulation of Charge Transfer in DNA

  • Chapter
  • First Online:

  • 1647 Accesses

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 12))

Abstract

The phenomenon of charge migration in DNA has attracted considerable interest of experimental as well as computational research in the last decade. It poses a huge challenge for simulation, due to the large system size and the long relevant time scales. Simple modeling frameworks may miss or overapproximate several important factors influencing the charge transfer in DNA, most prominently the dynamical and solvent effects. Therefore, modern approaches make use of multi-scale coarse-grained computational schemes, which have been developed in several labs recently. These techniques combine empirical force fields to capture the DNA dynamics and quantum-chemical methods to describe the actual charge transfer events. The performed simulations show that the dynamics and solvent effects play a major role in DNA charge transfer.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   259.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Notes

  1. 1.

    More precisely, this holds only if the diabatic states, i.e. HOMOs are orthogonal. If this is not the case, a correction should be introduced, as mentioned in Section 8.2.3.1.

  2. 2.

    In this second phase of an FO calculation, a different DFTB basis set is used. The standard DFTB basis set uses markedly compressed electron density, which leads to underestimated electronic couplings. Therefore, a re-optimized basis set featuring nearly uncompressed density is used in the second phase of FO, in order to provide couplings of good quality. See [55] for details.

  3. 3.

    Note the distance of stacked nucleobases in the A- or B-DNA structure of as little as 3.5 Å.

  4. 4.

    Alternatively, it would be possible to evaluate the CT parameters for a static DNA structure – for instance idealized B-DNA, an X-ray structure or an averaged structure from MD simulation.

  5. 5.

    Or on a group of nucleobases, if the hole can spread over them.

  6. 6.

    This phenomenon may be described as a polaron, which is accompanying the migrating hole.

References

  1. Schuster GB (ed) (2004) Long-range charge transfer in DNA I & II, Topics in Current Chemistry, vol 236 and 237. Springer, Heidelberg

    Google Scholar 

  2. Wagenknecht HA (ed) (2005) Charge transfer in DNA: from mechanism to application. Wiley, Weinheim

    Google Scholar 

  3. Hall DB, Holmlin E, Barton JK (1996) Nature 382:731–735

    Article  CAS  Google Scholar 

  4. Gasper SM, Schuster GB (1997) J Am Chem Soc 119:12762–12771

    Article  CAS  Google Scholar 

  5. Porath D, Bezryadin A, De Vries S, Dekker C (2000) Nature 403:635–638

    Article  CAS  Google Scholar 

  6. Xu B, Zhang P, Li X, Tao N (2004) Nano Lett 4:1105–1108

    Article  CAS  Google Scholar 

  7. van Zalinge H, Schiffrin DJ, Bates AD, Haiss W, Ulstrup J, Nichols RJ (2006) ChemPhysChem 7:94–98

    Article  Google Scholar 

  8. Boon EM, Livingston AL, Chmiel NH, David SS, Barton JK (2003) Proc Natl Acad Sci USA 100:12543–12547

    Article  CAS  Google Scholar 

  9. Holman MR, Ito T, Rokita SE (2007) J Am Chem Soc 129:6–7

    Article  CAS  Google Scholar 

  10. Paleček E (1996) Electroanalysis 8:7–14

    Article  Google Scholar 

  11. Kelley SO, Barton JK, Jackson NM, Hill MG (1997) Bioconjugate Chem 8:31–37

    Article  CAS  Google Scholar 

  12. Wong ELS, Gooding JJ (2006) Anal Chem 78:2138–2144

    Article  CAS  Google Scholar 

  13. Cuniberti G, Fagas G, Richter K (eds) (2005) Introducing molecular electronics, Lecture notes in physics, vol 680. Springer, Berlin

    Google Scholar 

  14. Joachim C, Ratner MA (2005) Proc Natl Acad Sci USA 102:8801–8808

    Article  CAS  Google Scholar 

  15. Slavíček P, Winter B, Faubel M, Bradforth SE, Jungwirth P (2009) J Am Chem Soc 131:6460–6467

    Article  Google Scholar 

  16. Orlov VM, Smirnov AN, Varshavsky YM (1976) Tetrahedron Lett 17:4377–4378

    Article  Google Scholar 

  17. Steenken S, Jovanovic SV (1997) J Am Chem Soc 119:617–618

    Article  CAS  Google Scholar 

  18. Saito I, Takayama M, Sugiyama H, Nakatani K (1995) J Am Chem Soc 117:6406–6407

    Article  CAS  Google Scholar 

  19. Lewis FD, Kalgutkar RS, Wu Y, Liu X, Liu J, Hayes RT, Miller SE, Wasielewski MR (2000) J Am Chem Soc 122:12346–12351

    Article  CAS  Google Scholar 

  20. Berlin YA, Burin AL, Ratner MA (2001) J Am Chem Soc 123:260–268

    Article  CAS  Google Scholar 

  21. Jortner J, Bixon M, Langenbacher T, Michel-Beyerle ME (1998) Proc Natl Acad Sci USA 95:12759–12765

    Article  CAS  Google Scholar 

  22. Bixon M, Jortner J (2001) J Am Chem Soc 123:12556–12567

    Article  CAS  Google Scholar 

  23. Murphy CJ, Arkin MR, Jenkins Y, Ghatlia ND, Bossmann SH, Turro NJ, Barton JK (1993) Science 262:1025–1029

    Article  CAS  Google Scholar 

  24. Núñez ME, Hall DB, Barton JK (1999) Chem Biol 6:85–97

    Article  Google Scholar 

  25. Wan C, Fiebig T, Schiemann O, Barton JK, Zewail AH (2000) Proc Natl Acad Sci USA 97:14052–14055

    Article  CAS  Google Scholar 

  26. Kelley SO, Barton JK (1999) Science 283:375–381

    Article  CAS  Google Scholar 

  27. Meggers E, Michel-Beyerle ME, Giese B (1998) J Am Chem Soc 120:12950–12955

    Article  CAS  Google Scholar 

  28. Giese B, Amaudrut J, Köhler AK, Spormann M, Wessely S (2001) Nature 412:318–320

    Article  CAS  Google Scholar 

  29. Lewis FD, Liu JQ, Zuo XB, Hayes RT, Wasielewski MR (2003) J Am Chem Soc 125:4850–4861

    Article  CAS  Google Scholar 

  30. Lewis FD, Zhu H, Daublain P, Fiebig T, Raytchev M, Wang Q, Shafirovich V (2006) J Am Chem Soc 128:791–800

    Article  CAS  Google Scholar 

  31. Henderson PT, Jones D, Hampikian G, Kan Y, Schuster GB (1999) Proc Natl Acad Sci USA 96:8353–8358

    Article  CAS  Google Scholar 

  32. Conwell EM, Rakhmanova SV (2000) Proc Natl Acad Sci USA 97:4556–4560

    Article  CAS  Google Scholar 

  33. Su WP, Schrieffer JR, Heeger AJ (1980) Phys Rev B 22:2099–2111

    Article  CAS  Google Scholar 

  34. Barnett RN, Cleveland CL, Joy A, Landman U, Schuster GB (2001) Science 294:567–571

    Article  CAS  Google Scholar 

  35. Williams TT, Odom DT, Barton JK (2000) J Am Chem Soc 122:9048–9049

    Article  CAS  Google Scholar 

  36. O’Neill MA, Barton JK (2004) J Am Chem Soc 126:11471–11483

    Article  Google Scholar 

  37. Conwell E (2005) Proc Natl Acad Sci USA 102:8795–8799

    Article  CAS  Google Scholar 

  38. Gervasio FL, Carolini P, Parrinello M (2002) Phys Rev Lett 89:108102

    Article  Google Scholar 

  39. Marcus RA (1956) J Chem Phys 24:966–978

    Article  CAS  Google Scholar 

  40. Marcus RA, Sutin N (1985) Biochim Biophys Acta 811:265–322

    Article  CAS  Google Scholar 

  41. Newton MD (1991) Chem Rev 91:767–792

    Article  CAS  Google Scholar 

  42. Priyadarshy S, Risser SM, Beratan DN (1996) J Phys Chem 100:17678–17682

    Article  CAS  Google Scholar 

  43. Lewis FD, Liu J, Weigel W, Rettig W, Kurnikov IV, Beratan DN (2002) Proc Natl Acad Sci USA 99:12536–12541

    Article  CAS  Google Scholar 

  44. Olofsson J, Larsson S (2001) J Phys Chem B 105:10398–10406

    Article  CAS  Google Scholar 

  45. Cramer T, Krapf S, Koslowski T (2004) J Phys Chem B 108:11812–11819

    Article  CAS  Google Scholar 

  46. Bixon M, Jortner J (2006) Chem Phys 326:252–258

    Article  CAS  Google Scholar 

  47. Jakobsson M, Stafström S (2008) J Chem Phys 129:125102

    Article  Google Scholar 

  48. Řeha D, Barford W, Harris S (2008) Phys Chem Chem Phys 10:5436–5444

    Article  Google Scholar 

  49. Voityuk AA, Jortner J, Bixon M, Rösch N (2000) Chem Phys Lett 324:430–434

    Article  CAS  Google Scholar 

  50. Rösch N, Voityuk AA (2004) Top Curr Chem 237:37–72

    Article  Google Scholar 

  51. Troisi A, Orlandi G (2001) Chem Phys Lett 344:509–518

    Article  CAS  Google Scholar 

  52. Endres RG, Cox DL, Singh RRP (2002) Electronic properties of DNA: structural and chemical influence on the quest for high conductance and charge transfer. arXiv:cond-mat/:0201404

    Google Scholar 

  53. Senthilkumar K, Grozema FC, Guerra CF, Bickelhaupt FM, Lewis FD, Berlin YA, Ratner MA, Siebbeles LDA (2005) J Am Chem Soc 127:14894–14903

    Article  CAS  Google Scholar 

  54. Voityuk AA, Rösch N, Bixon M, Jortner J (2000) J Phys Chem B 104:9740–9745

    Article  CAS  Google Scholar 

  55. Kubař T, Woiczikowski PB, Cuniberti G, Elstner M (2008) J Phys Chem B 112:7937–7947

    Article  Google Scholar 

  56. Loewdin PO (1950) J Chem Phys 18:365–375

    Article  Google Scholar 

  57. Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Phys Rev B 58:7260–7268

    Article  CAS  Google Scholar 

  58. Warshel A, Levitt M (1976) J Mol Biol 103:227–249

    Article  CAS  Google Scholar 

  59. Field MJ, Bash PA, Karplus M (1990) J Comput Chem 11:700–733

    Article  CAS  Google Scholar 

  60. Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M (2001) J Phys Chem B 105:569–585

    Article  CAS  Google Scholar 

  61. Elstner M (2006) Theor Chem Acc 116:316–325

    Article  CAS  Google Scholar 

  62. Troisi A, Orlandi G (2002) J Phys Chem B 106:2093–2101

    Article  CAS  Google Scholar 

  63. Voityuk AA, Siriwong K, Rösch N (2001) Phys Chem Chem Phys 3:5421–5425

    Article  CAS  Google Scholar 

  64. Troisi A, Ratner M, Zimmt M (2004) J Am Chem Soc 126:2215–2224

    Article  CAS  Google Scholar 

  65. Hatcher E, Balaeff A, Keinan S, Venkatramani R, Beratan DN (2008) J Am Chem Soc 130:11752–11761

    Article  CAS  Google Scholar 

  66. Balabin IA, Beratan DN, Skourtis SS (2008) Phys Rev Lett 101:158102

    Article  Google Scholar 

  67. Grozema FC, Tonzani S, Berlin YA, Schatz GC, Siebbeles LDA, Ratner MA (2008) J Am Chem Soc 130:5157–5166

    Article  CAS  Google Scholar 

  68. Voityuk AA, Siriwong K, Rösch N (2004) Angew Chem Int Ed 43:624–627

    Article  CAS  Google Scholar 

  69. Steinbrecher T, Koslowski T, Case DA (2008) J Phys Chem B 112:16935–16944

    Article  CAS  Google Scholar 

  70. Kubař T, Elstner M (2008) J Phys Chem B 112:8788–8798

    Article  Google Scholar 

  71. Grozema FC, Berlin YA, Siebbeles LDA (2000) J Am Chem Soc 122:10903–10909

    Article  CAS  Google Scholar 

  72. Kubař T, Kleinekathöfer U, Elstner M (2009) J Phys Chem B 113:13107–13117

    Article  Google Scholar 

  73. Tong GSM, Kurnikov IV, Beratan DN (2002) J Phys Chem B 106:2381–2392

    Article  CAS  Google Scholar 

  74. Woiczikowski PB, Kubař T, Gutiérrez R, Caetano RA, Cuniberti G, Elstner M (2009) J Chem Phys 130:215104

    Article  Google Scholar 

  75. Tavernier HL, Fayer MD (2000) J Phys Chem B 104:11541–11550

    Article  CAS  Google Scholar 

  76. LeBard DN, Lilichenko M, Matyushov DV, Berlin YA, Ratner MA (2003) J Phys Chem B 107:14509–14520

    Article  CAS  Google Scholar 

  77. Siriwong K, Voityuk AA, Newton MD, Rösch N (2003) J Phys Chem B 107:2595–2601

    Article  CAS  Google Scholar 

  78. Ando K (2001) J Chem Phys 115:5228–5237

    Article  CAS  Google Scholar 

  79. Vladimirov E, Ivanova A, Rösch N (2008) J Chem Phys 129:194515

    Article  Google Scholar 

  80. Kubař T, Elstner M (2009) J Phys Chem B 113:5653–5656

    Article  Google Scholar 

  81. Kurnikov IV, Tong GSM, Madrid M, Beratan DN (2002) J Phys Chem B 106:7–10

    Article  CAS  Google Scholar 

  82. Mantz YA, Gervasio FL, Laino T, Parrinello M (2007) Phys Rev Lett 99:058104

    Article  Google Scholar 

  83. Niehaus TA, Heringer D, Torralva B, Frauenheim T (2005) Eur Phys J D 35:467–477

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors are grateful to Ben Woiczikowski for his contribution to this research. The fruitful collaboration with Rafael Gutiérrez and Giovanni Cuniberti is acknowledged. This work was supported by the Deutsche Forschungsgemeinschaft, Project DFG-EL 206/5-2.

Author information

Authors and Affiliations

  1. Theoretical Chemical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany

    Tomáš Kubař & Marcus Elstner

Authors
  1. Tomáš Kubař
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marcus Elstner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tomáš Kubař .

Editor information

Editors and Affiliations

  1. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Piotr Paneth

  2. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Agnieszka Dybala-Defratyka

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Netherlands

About this chapter

Cite this chapter

Kubař, T., Elstner, M. (2010). Simulation of Charge Transfer in DNA. In: Paneth, P., Dybala-Defratyka, A. (eds) Kinetics and Dynamics. Challenges and Advances in Computational Chemistry and Physics, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3034-4_8

Download citation

Publish with us

Policies and ethics

Search

Navigation