Skip to main content
SpringerLink
Log in
Book cover

Radiation Induced Molecular Phenomena in Nucleic Acids pp 265–299Cite as

Ultrafast Radiationless Decay in Nucleic Acids: Insights From Nonadiabatic Ab Initio Molecular Dynamics

  • Chapter

Part of the book series: Challenges and Advances In Computational Chemistry and Physics ((COCH,volume 5))

Abstract

Characterizing the photophysical properties of nucleic acid bases and base pairs presents a major challenge to theoretical modelling. In this Chapter, we focus on the contributions of nonadiabatic ab initio molecular dynamics (na-AIMD) simulations towards unravelling the dynamical mechanisms governing the radiationless decay of DNA and RNA building blocks. The na-AIMD method employed here is based entirely on plane-wave density functional theory and couples nonadiabatically the Kohn-Sham electronic ground state to the restricted open-shell Kohn-Sham first excited singlet state by means of a surface hopping scheme. This approach has been applied to a variety of different nucleobases and tautomers thereof. Gas phase calculations on canonical tautomers serve as a reference to study both substitution and solvation effects. The na-AIMD simulations of nonradiative decay in aqueous solution allow direct comparison with the gas phase results as the same computational setup can be used in both cases. Solute and solvent are both treated explicitly on an equal footing

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Hutter J et al. (2007) Car–Parrinello Molecular Dynamics: An Ab Initio Electronic Structure and Molecular Dynamics Program, see www.cpmd.org.

    Google Scholar 

  2. Abo-Riziq A, Grace L, Nir E, Kabelac M, Hobza P, de Vries MS (2005) Proc Natl Acad Sci USA 102:20.

    Article  CAS  Google Scholar 

  3. Becke AD (1988) {Phys Rev} A 38:3098.

    Article  CAS  Google Scholar 

  4. Bell RL, Taveras DL, Truong TN, Simons J (1997) Int J Quantum Chem 63:861.

    Article  CAS  Google Scholar 

  5. Canuel C, Mons M, Piuzzi F, Tardivel B, Dimicoli I, Elhanine M (2005) J Chem Phys 122:074,316.

    Article  Google Scholar 

  6. Car R, Parrinello M (1985) Phys Rev Lett 55:2471.

    Article  CAS  Google Scholar 

  7. Chargaff E (1950) Experientia 6:201.

    Article  Google Scholar 

  8. Chargaff E (1970) Experientia 26:810.

    Article  CAS  Google Scholar 

  9. Chargaff E (1971) Science 172:637.

    Article  CAS  Google Scholar 

  10. Chen H, Li S (2006) J Phys Chem A 110:12360.

    Article  CAS  Google Scholar 

  11. Chin W, Mons M, Dimicoli I, Tardivel B, Elhanine M (2002) Eur Phys J D 20:347.

    Article  CAS  Google Scholar 

  12. Cohen B, Hare PM, Kohler B (2003) J Am Chem Soc 125:13594.

    Article  CAS  Google Scholar 

  13. Cohen B, Crespo-Hernández CE, Kohler B (2004) Faraday Discuss 127:137.

    Article  CAS  Google Scholar 

  14. Crespo-Hernández CE, Cohen B, Hare PM, Kohler B (2004) Chem Rev 104:1977.

    Article  Google Scholar 

  15. Doltsinis NL (2002) In: Grotendorst J, Marx D, Muramatsu A (eds) Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, NIC, FZ Jülich, www.fz-juelich.de/ nic-series/volume10/doltsinis.pdf.

    Google Scholar 

  16. Doltsinis NL (2004) Mol Phys 102:499.

    Article  CAS  Google Scholar 

  17. Doltsinis NL (2004) Faraday Discuss 127:231.

    Google Scholar 

  18. Doltsinis NL (2006) In: Grotendorst J, Blügel S, Marx D (eds) Computational Nanoscience: Do it Yourself!, NIC, FZ Jülich, www.fz-juelich.de/nic-series/volume31/doltsinis1.pdf.

    Google Scholar 

  19. Doltsinis NL (2006) In: Grotendorst J, Blügel S, Marx D (eds) Computational Nanoscience: Do it Yourself!, NIC, FZ Jülich, www.fz-juelich.de/nic-series/volume31/doltsinis2.pdf.

    Google Scholar 

  20. Doltsinis NL, Fink K (2005) J Chem Phys 122:087101.

    Article  Google Scholar 

  21. Doltsinis NL, Marx D (2002) Phys Rev Lett 88:166402.

    Google Scholar 

  22. Doltsinis NL, Marx D (2002) J Theor Comput Chem 1:319–349.

    Google Scholar 

  23. Doltsinis NL, Sprik M (2003) Phys Chem Chem Phys 5:2612.

    Article  CAS  Google Scholar 

  24. Domcke W, Sobolewski AL (2003) Science 302:1693.

    Article  CAS  Google Scholar 

  25. Domcke W, Yarkony DR, Köppel H (2004) Conical Intersections: Electronic Structure, Dynamics and Spectroscopy, World Scientific, Singapore.

    Google Scholar 

  26. Frank I, Hutter J, Marx D, Parrinello M (1998) J Chem Phys 108:4060.

    Article  CAS  Google Scholar 

  27. Grimm S, Nonnenberg C, Frank I (2003) J Chem Phys 119:11574.

    Google Scholar 

  28. Grimm S, Nonnenberg C, Frank I (2003) J Chem Phys 119:11585.

    Google Scholar 

  29. Groenhof G, Schäfer LV, Boggio-Pasqua M, Goette M, Grubmüller H, Robb MA (2007) J Am Chem Soc 129:6812.

    Article  CAS  Google Scholar 

  30. Gustavsson T, Bányász A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R (2006) J Am Chem Soc 128:607.

    Article  CAS  Google Scholar 

  31. Ha TK, Keller HJ, Gunde R, Gunthard HH (1999) J Phys Chem A 103:6612.

    Article  CAS  Google Scholar 

  32. Hanus M, Ryjáček F, Kabeláč M, Kubar T, Bogdan TV, Trygubenko SA, Hobza P (2003) J Am Chem Soc 125:1257678.

    Article  Google Scholar 

  33. Häupl T, Windolph C, Jochum T, Brede O, Hermann R (1997) Chem Phys Lett 280:280520.

    Article  Google Scholar 

  34. He Y, Wu C, Kong W (2004) J Phys Chem A 108:943.

    Article  CAS  Google Scholar 

  35. Hutter M, Clark T (1996) J Am Chem Soc 118:7574.

    Article  CAS  Google Scholar 

  36. Ismail N, Blancafort L, Olivucci M, Kohler B, Robb MA (2002) J Am Chem Soc 124:6818.

    Article  CAS  Google Scholar 

  37. Kang H, Lee KT, Jung B, Ko YJ, Kim SK (2002) J Am Chem Soc 124:12958.

    Article  CAS  Google Scholar 

  38. Kang H, Jung B, Kim SK (2003) J Chem Phys 118:6717.

    Article  CAS  Google Scholar 

  39. Kim NJ, Jeong G, Kim YS, Sung J, Kim SK (2000) J Chem Phys 113:10051.

    Article  CAS  Google Scholar 

  40. Kistler KA, Matsika S (2007) J Phys Chem A 111:2650.

    Article  CAS  Google Scholar 

  41. Langer H 2006 Dissertation, Ruhr-Universität Bochum.

    Google Scholar 

  42. Langer H, Doltsinis NL In preparation.

    Google Scholar 

  43. Langer H, Doltsinis NL (2003) J Chem Phys 118:5400.

    Google Scholar 

  44. Langer H, Doltsinis NL (2003) Phys Chem Chem Phys 5:516.

    Google Scholar 

  45. Langer H, Doltsinis NL (2004) Phys Chem Chem Phys 6:2742.

    Article  CAS  Google Scholar 

  46. Langer H, Doltsinis NL, Marx D (2004) In: Wolf D, Münster G, Kremer M (eds) NIC Symposium 2004, NIC, FZ Jülich, for downloads see {\tt http://www.fz-juelich.de/ nic-series/volume20/doltsinis.pdf}.

    Google Scholar 

  47. Langer H, Doltsinis NL, Marx D (2005) Chemphyschem 6:61734.

    Article  Google Scholar 

  48. Lee C, Yang W, Parr RC (1988) Phys Rev B 37:785.

    Article  CAS  Google Scholar 

  49. Liang W, Li H, Hu X, Han S (2004) J Phys Chem A 108:10219.

    Article  CAS  Google Scholar 

  50. Lorentzon J, Fülscher MP, Roos BO (1995) J Am Chem Soc 117:9265.

    Article  CAS  Google Scholar 

  51. Lührs DC, Viallon J, Fischer I (2001) Phys Chem Chem Phys 3:1827.

    Article  Google Scholar 

  52. Malone RJ, Miller AM, Kohler B (2003) Photochem Photobiol 77:158.

    Article  CAS  Google Scholar 

  53. Marian CM (2007) J Phys Chem A 111:1545.

    Article  CAS  Google Scholar 

  54. Marian CM, Schneider F, Kleinschmidt M, Tatchen J (2002) Eur Phys J D 20:357.

    Article  CAS  Google Scholar 

  55. Markwick PRL, Doltsinis NL (2007) J Chem Phys 126:175102.

    Article  Google Scholar 

  56. Markwick PRL, Doltsinis NL, Schlitter J (2007) J Chem Phys 126:045104.

    Article  Google Scholar 

  57. Marx D, Hutter J (2000) In: Grotendorst J (ed) Modern Methods and Algorithms of Quantum Chemistry, NIC, Jülich, www.theochem.rub.de/go/cprev.html.

    Google Scholar 

  58. Matsika S (2004) J Phys Chem A 108:7584.

    Article  CAS  Google Scholar 

  59. Mennucci B, Toniolo A, Tomasi J (2001) J Phys Chem A 105:7126.

    Article  CAS  Google Scholar 

  60. Merchán M, Serrano-Andrés L (2003) J Am Chem Soc 125:8108.

    Article  Google Scholar 

  61. Mons M, Dimicoli I, Piuzzi F, Tardivel B, Elhanine M (2002) J Phys Chem A 106:5088.

    Article  CAS  Google Scholar 

  62. Mons M, Piuzzi F, Dimicoli I, Gorb L, Leszczynski J (2006) J Phys Chem A 110:10921.

    Article  CAS  Google Scholar 

  63. Müller U, Stock G (1997) J Chem Phys 107:6230.

    Article  Google Scholar 

  64. Nieber H, Doltsinis NL (2008) Chem Phys In press.

    Google Scholar 

  65. Nir E, Grace L, Brauer B, de Vries MS (1999) J Am Chem Soc 121:4896.

    Article  CAS  Google Scholar 

  66. Nir E, Kleinermanns K, de Vries MS (2000) Nature 408:949.

    Article  CAS  Google Scholar 

  67. Nir E, Janzen C, Imhof P, Kleinermanns K, de Vries MS (2001) J Chem Phys 115:4604.

    Article  CAS  Google Scholar 

  68. Nir E, Kleinermanns K, Grace L, de Vries MS (2001) J Phys Chem A 105:5106.

    Article  CAS  Google Scholar 

  69. Nir E, Müller M, Grace LI, de Vries MS (2002) Chem Phys Lett 355:59.

    Article  CAS  Google Scholar 

  70. Onidas D, Markovitsi D, Marguet S, Sharonov A, Gustavsson T (2002) J Phys Chem B 106:11367.

    Article  CAS  Google Scholar 

  71. Pal SK, Peon J, Zewail AH (2002) Chem Phys Lett 363:363.

    Article  Google Scholar 

  72. Peon J, Zewail AH (2001) Chem Phys Lett 348:255.

    Article  CAS  Google Scholar 

  73. Percourt JML, Peon J, Kohler B (2001) J Am Chem Soc 123:10370.

    Article  Google Scholar 

  74. Perun S, Sobolewski AL, Domcke W (2005) Chem Phys 313:107.

    Article  CAS  Google Scholar 

  75. Perun S, Sobolewski AL, Domcke W (2006) J Phys Chem A 110:13238.

    Article  CAS  Google Scholar 

  76. Perun S, Sobolewski AL, Domcke W (2006) J Phys Chem A 110:9031.

    Article  CAS  Google Scholar 

  77. Piuzzi F, Mons M, Dimicoli I, Tardivel B, Zhao Q (2001) Chem Phys 270:205.

    Article  CAS  Google Scholar 

  78. Plützer C, Nir E, de Vries MS, Kleinermanns K (2001) Phys Chem Chem Phys 3:5466.

    Article  Google Scholar 

  79. Schultz T, Samoylova E, Radloff W, Hertel IA, Sobolewski AL, Domcke W (2004) Science 306:1765.

    Article  CAS  Google Scholar 

  80. Shukla MK, Leszczynski J (2005) J Phys Chem A 109:7775.

    Article  CAS  Google Scholar 

  81. Shukla MK, Leszczynski J (2005) J Phys Chem B 109:17333.

    Google Scholar 

  82. Shukla MK, Mishra SK, Kumar A, Mishra PC (2000) J Comput Chem 21:826.

    Article  CAS  Google Scholar 

  83. Sobolewski AL, Domcke W (1999) J Phys Chem A 103:4494.

    Article  CAS  Google Scholar 

  84. Sobolewski AL, Domcke W (2002) Eur Phys J D 20:369.

    Article  CAS  Google Scholar 

  85. Sobolewski AL, Domcke W (2004) Phys Chem Chem Phys 6:2763.

    Article  CAS  Google Scholar 

  86. Sobolewski AL, Domcke W, Dedonder-Lardeux C, Jouvet C (2002) Phys Chem Chem Phys 4:1093.

    Article  CAS  Google Scholar 

  87. Sobolewski AL, Domcke W, Hättig C (2005) Proc Natl Acad Sci USA 102:17903.

    Article  CAS  Google Scholar 

  88. Sprik M (1998) Faraday Discuss 110:437–445.

    Article  CAS  Google Scholar 

  89. Sprik M (2000) Chem Phys 258:139.

    Article  CAS  Google Scholar 

  90. Strickler SJ, Berg RA (1962) J Chem Phys 37:814.

    Article  CAS  Google Scholar 

  91. Tanner C, Manca C, Leutwyler S (2003) Science 302:1736.

    Article  CAS  Google Scholar 

  92. Tomić K, Tatchen J, Marian CM (2005) J Phys Chem A 109:8410.

    Article  Google Scholar 

  93. Troullier N, Martins JL (1991) Phys Rev B 43:1993.

    Article  CAS  Google Scholar 

  94. Tully JC (1990) J Chem Phys 93:1061.

    Article  CAS  Google Scholar 

  95. Tully JC (1998) In: Berne BJ, Ciccotti G, Coker DF (eds) Classical and Quantum Dynamics in Condensed Phase Simulations, World Scientific, Singapore.

    Google Scholar 

  96. Tully JC (1998) In: Thompson DL (ed) Modern Methods for Multidimensional Dynamics Computations in Chemistry, World Scientific, Singapore.

    Google Scholar 

  97. Tully JC, Preston RK (1971) J Chem Phys 55:562.

    Article  CAS  Google Scholar 

  98. Ullrich S, Schultz T, Zgierski MZ, Stolow A (2004) Phys Chem Chem Phys 6:2796.

    Article  CAS  Google Scholar 

  99. Černý J, Špirko V, Mons M, Hobza P, Nachtigallová D (2006) Phys Chem Chem Phys 8:3059.

    Article  Google Scholar 

  100. Watson JD, Crick FHC (1953) Nature 171:737.

    Article  CAS  Google Scholar 

  101. Zewail AH (2000) Angew Chem Int Ed 39:2586–2631.

    Article  CAS  Google Scholar 

  102. Zgierski MZ, Patchkovskii S, Fujiwara T, Lim EC (2005) J Phys Chem A 109:9384.

    Article  CAS  Google Scholar 

  103. Zgierski MZ, Patchkovskii S, Lim EC (2005) J Chem Phys 123:081101.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany

    Nikos L. Doltsinis, Harald Nieber & Holger Langer

  2. Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom

    Nikos L. Doltsinis & Harald Nieber

  3. Unite de Bioinformatique Structurale, Institut Pasteur, 25–28 rue du Dr. Roux, CNRS URA 2185, 75015 Paris, France

    Phineus R. L. Markwick

Authors
  1. Nikos L. Doltsinis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Phineus R. L. Markwick
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Harald Nieber
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Holger Langer
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Chemistry, Jackson State University, 1325 J. R. Lynch Street, Jackson, MS 39217, USA

    Manoj K. Shukla  & Jerzy Leszczynski  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Doltsinis, N.L., Markwick, P.R., Nieber, H., Langer, H. (2008). Ultrafast Radiationless Decay in Nucleic Acids: Insights From Nonadiabatic Ab Initio Molecular Dynamics. In: Shukla, M.K., Leszczynski, J. (eds) Radiation Induced Molecular Phenomena in Nucleic Acids. Challenges and Advances In Computational Chemistry and Physics, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8184-2_10

Download citation

Publish with us

Policies and ethics

Search

Navigation