Advertisement

Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases

  • Kurt A. Kistler
  • Spiridoula Matsika
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 7)

Abstract

This chapter reviews current computational studies of the photophysical behavior of DNA and RNA bases. The theoretical concepts and electronic structure methods appropriate for computational photophysical and photochemical studies are presented. The natural nucleobases have ultrashort excited state lifetimes and very low quantum yields for fluorescence. Quantum chemical calculations revealing radiationless decay pathways that quench fluorescence are discussed

Keywords

keywords Fluorescence quenching Nucleobase Photophysics Photochemistry Quantum Chemistry Computational Photochemistry Conical intersections Radiationless decay Ab initio 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Kraemer KH (1997) Sunlight and skin cancer: another link revealed. Proc Natl Acad Sci USA 94:11CrossRefGoogle Scholar
  2. 2.
    Mukhtar H, Elmets CA (1996) Photocarcinogenesis: mechanisms, models and human health implications. Photochem Photobiol 63:355CrossRefGoogle Scholar
  3. 3.
    Cadet J, Vigny P (1990) In: Morrison H (ed.) Bioorganic photochemistry. John Wiley, New York, pp. 1–272Google Scholar
  4. 4.
    Daniels M (1976) In: Wang SY (ed.) Photochemistry and Photobiology of Nucleic Acids, vol 1. Academic Press, New York, p 23Google Scholar
  5. 5.
    Ruzsicska BP, Lemaire DGE In: Horspool WM, Song P-S (eds.) CRC Handbook of Organic Photochemistry and Photobiology, CRC Press, Boca Raton, FL, p 1289Google Scholar
  6. 6.
    Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Ultrafast excited-state dynamics in nucleic acids. Chem Rev 104:1977CrossRefGoogle Scholar
  7. 7.
    Born M, Oppenheimer R (1927) Zur Quantentheorie der Molekeln. Ann Phys 84:457CrossRefGoogle Scholar
  8. 8.
    Landau LD (1932) Z. Sowjetunion U.R.S.S. 2:46Google Scholar
  9. 9.
    Zener C (1932) Non-adiabatic crossing of energy levels. Proc Roy Soc A137:696Google Scholar
  10. 10.
    Domcke W, Yarkony DR, Köppel H (2004) Conical intersections. World Scientific, Singapore,Google Scholar
  11. 11.
    Rice OK (1929) Phys Rev 33:748CrossRefGoogle Scholar
  12. 12.
    Dantus M, Zewail A (2004) Introduction: femtochemistry. Chem Rev 104:1717CrossRefGoogle Scholar
  13. 13.
    von Neumann J, Wigner EP (1929) On the behaviour of eigenvalues in adiabatic processes. Physik Z 30:467Google Scholar
  14. 14.
    Teller E (1937) The crossing of potential surfaces. J Phys Chem 41:109CrossRefGoogle Scholar
  15. 15.
    Manaa MR, Yarkony DR (1993) On the intersection of two potential energy surfaces of the same symmetry. Systematic characterization using a lagrange multiplier constrained procedure. J Chem Phys 99:5251CrossRefGoogle Scholar
  16. 16.
    Bearpark MJ, Robb MA, Schlegel HB (1994) A direct method for the location of the lowest energy point on a potential surface crossing. Chem Phys Lett 223:269CrossRefGoogle Scholar
  17. 17.
    Yarkony DR (1998) Conical intersections: diabolical and often misunderstood. Acc Chem Res 31:511CrossRefGoogle Scholar
  18. 18.
    Yarkony DR (1996) Diabolical conical intersections. Rev Mod Phys 68:985CrossRefGoogle Scholar
  19. 19.
    Yarkony DR (1996) Current issues in nonadiabatic chemistry. J Phys Chem 100:18612CrossRefGoogle Scholar
  20. 20.
    Yarkony DR (2001) Conical intersections: the new conventional wisdom. J Phys Chem A 105:6277CrossRefGoogle Scholar
  21. 21.
    Bernardi F, Olivucci M, Robb MA (1990) Predicting forbidden and allowed cycloaddition reactions: potential surface topology and its rationalization. Acc Chem Res 23:405CrossRefGoogle Scholar
  22. 22.
    Bernardi F, Olivucci M, Robb MA (1996) Potential energy surface crossings in organic photochemistry. Chem Soc Rev 25:321CrossRefGoogle Scholar
  23. 23.
    Barckholtz TA, Miller TA (1998) Quantitative insights about molecules exhibiting jahn-teller and related effects. Int Rev Phys Chem 17:435CrossRefGoogle Scholar
  24. 24.
    Robb MA, Garavelli M, Olivucci M, Bernardi F (2000) A computational strategy for organic photochemistry. In Lipkowitz KB Boyd DB (eds) Reviews in computational chemistry, vol. 15 Wiley-VCH, New York; pp 87–146CrossRefGoogle Scholar
  25. 25.
    Matsika S (2007) Conical intersections in molecular systems. In: Lipkowitz KB and Cundari TR (eds.) Reviews in computational chemistry, vol. 23, Wiley-VCH, New Jersey, pp 83–124CrossRefGoogle Scholar
  26. 26.
    Klessinger M, Michl J (1995) Excited states and photochemistry of organic molecules. VCH Publishers, Inc., New YorkGoogle Scholar
  27. 27.
    Michl J, Bonaĉić Koutecký V (1990) Electronic aspects of organic photochemistry. Wiley Interscience, New YorkGoogle Scholar
  28. 28.
    Garavelli M, Gelani P, Bernardi F, Robb MA, Olivucci M (1997) The C5H6NH+ 2 protonated shiff base: an ab initio minimal model for retinal photoisomerization. J Am Chem Soc 119:6891CrossRefGoogle Scholar
  29. 29.
    Kobayashi T, Saito T, Ohtani H (2001) Real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization. Nature 414:531CrossRefGoogle Scholar
  30. 30.
    Ben-Nun M, Molnar F, Schulten K, Martinez TJ (2000) The role of intersection topography in bond selectivity of cis-trans photoisomerization. Proc Natl Acad Sci USA 97:9379CrossRefGoogle Scholar
  31. 31.
    Warshel A, Chu ZT (2001) Nature of the surface crossing process in bacteriorhodopsin: computer simulations of the quantum dynamics of the primary photochemical event. J Phys Chem B 105:9857CrossRefGoogle Scholar
  32. 32.
    Migani A, Sinicropi A, Ferr N, Cembran A, Garavelli M, Olivucci M (2004) Structure of the intersection space associated with Z/E photoisomerization of retinal in rhodopsin proteins. Faraday discuss 127:179CrossRefGoogle Scholar
  33. 33.
    Toniolo A, Olsen S, Manohar L, Martinez TJ (2004) Conical intersection dynamics in solution: the chromophore of green fluorescent protein. Faraday Discuss 127:149CrossRefGoogle Scholar
  34. 34.
    Martin ME, Negri F, Olivucci M (2004) Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution. J Am Chem Soc 126:5452CrossRefGoogle Scholar
  35. 35.
    Worth GA, Cederbaum LS (2001) Mediation of ultrafast transfer in biological systems by conical intersections. Chem Phys Lett 338:219CrossRefGoogle Scholar
  36. 36.
    Atchity GJ, Xantheas SS, Ruedenberg K (1991) Potential energy surfaces near intersections. J Chem Phys 95:1862CrossRefGoogle Scholar
  37. 37.
    Köppel H, Domcke W, Cederbaum LS (1984) Multimode molecular dynamics beyond the born-oppenheimer approximation. Adv Chem Phys 57:59CrossRefGoogle Scholar
  38. 38.
    Domcke W, Stock G (1997) Theory of ultrafast nonadiabatic excited-state processes and their spectroscopic detection in real time. Adv Chem Phys 100:1–170CrossRefGoogle Scholar
  39. 39.
    Yarkony DR (2001) Nuclear dynamics near conical intersections in the adiabatic representation. I. The effects of local topography on interstate transition. J Chem Phys 114:2601CrossRefGoogle Scholar
  40. 40.
    Schlegel HB (1995) Geometry optimization on potential energy surfaces, in: Yarkony DR (ed) modern electronic structure theory part I World Scientifc, Singapore p 459–500, Advance Series in Physical Chemistry.Google Scholar
  41. 41.
    Bartlett RJ, Stanton JF (1994) Applications of post-hartree-fock methods: a tutorial. In: Lipkowitz KB Boyd DB (eds) Reviews in computational chemistry, vol. 5. Wiley-VCH, New York, pp 65–169CrossRefGoogle Scholar
  42. 42.
    Shavitt I (1977) The method of configuration interaction. In: Schaefer III HF (ed) Methods of Electronic Structure Theory, vol. 4 of Modern Theoretical Chemistry; Plenum Press, New York; pp 189–275Google Scholar
  43. 43.
    Roos BO, Taylor PR (1980) A complete active space SCF method (CASSCF) using a density-matrix formulated super-CI approach. Chem Phys 48:157CrossRefGoogle Scholar
  44. 44.
    Roos BO (1987) The complete active space self consistent field method and its applications in electronic structure calculations. Adv Chem Phys 69:399CrossRefGoogle Scholar
  45. 45.
    Shepard R (1987) Geometrical energy derivative evaluation with MRCI wave functions. Int J Quantum Chem 31:33CrossRefGoogle Scholar
  46. 46.
    Shepard R (1995) The analytic gradient method for configuration interaction wave functions. Yarkony DR (ed) In: Modern electronic structure theory part I, World Scientific, Singapore, p 345Google Scholar
  47. 47.
    Lischka H, Dallos M, Shepard R (2002) Analytic MRCI gradient for excited states: formalism and application to the nπ* valence- and n–(3s, 3p) rydberg states of formaldehyde. Mol Phys 100:1647CrossRefGoogle Scholar
  48. 48.
    Lengsfield BH, Yarkony DR (1992) Nonadiabatic interactions between potential energy surfaces: theory and applications. In Baer M, Ng CY (eds) State-selected and state-to-state ion-molecule reaction dynamics: part 2 theory, Vol. 82 of Advances in Chemical Physics, John Wiley and Sons, New York, p 1–71.Google Scholar
  49. 49.
    Lischka H, Shepard R, Pitzer RM, Shavitt I, Dallos M, Müller Th, Szalay PG, Seth M, Kedziora GS, Yabushita S, Zhang Z (2001) High-level multireference methods in the quantum-chemistry program system COLUMBUS: analytic MR-CISD and MR-AQCC gradients and MR-AQCC-LRT for excited states, GUGA spin-orbit CI and parallel CI density. Phys Chem Chem Phys 3:664CrossRefGoogle Scholar
  50. 50.
    Lischka H, Dallos M, Szalay PG, Yarkony DR, Shepard R (2004) Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. I. Formalism. J Chem Phys 120:7322CrossRefGoogle Scholar
  51. 51.
    Dallos M, Lischka H, Shepard R, Yarkony DR, Szalay PG (2004) Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. II. Minima on the crossing seam: formaldehyde and the photodimerization of ethylene. J Chem Phys 120:7330CrossRefGoogle Scholar
  52. 52.
    Werner H-J, Knowles PJ (1988) An efficient internally contracted multiconfiguration reference CI method. J Chem Phys 89:5803CrossRefGoogle Scholar
  53. 53.
    Werner HJ, Knowles PJ, Lindh R, Schütz M, Celani P, Korona T, Manby FR, Rauhut G, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Hampel C, Hetzer G, Lloyd AW, McNicholas SJ, Meyer W, Mura ME, Nicklass A, Palmieri P, Pitzer R, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T (2003) Molpro, version 2002.6, a package of ab initio programsGoogle Scholar
  54. 54.
    Andersson K, Malmqvist PA, Roos BO, Sadlej AJ, Wolinski K (1990) Second-order perturbation-theory with a CASSCF reference function. J Phys Chem 94:5483CrossRefGoogle Scholar
  55. 55.
    Anderson K, Malmqvist PA, Roos BO (1992) Second-order perturbation-theory with a complete active space self-consistent field reference function. J Chem Phys 96:1218CrossRefGoogle Scholar
  56. 56.
    Karlström G, Lindh R, Malmqvist P-Å, Roos B, Ryde U, Veryazov V, Widmark P-O, Cossi M, Schimmelpfennig B, Neogrady P, Seijo L (2003) Molcas: a program package for computational chemistry. Comput material sci 28:222CrossRefGoogle Scholar
  57. 57.
    Roos BO, Andersson K, Fulscher MP, Malmqvist PA, Serrano-Andrès L, Pierloot K, Merchán M (1996) Multiconfigurational perturbation theory: applications in electronic spectroscopy. In: Prigogine I Rice SA (eds) New methods in computational quantum mechanics, Vol. 93 of Advances in Chemical Physics, Wiley, New York, p 219Google Scholar
  58. 58.
    Nakano H (1993) Quasidegenerate perturbation theory with multiconfigurational self-consistent-field reference functions. J Chem Phys 99:7983CrossRefGoogle Scholar
  59. 59.
    Finley J, Malmqvist PA, Roos BO, Serrano-Andrès L (1998) The multi-state CASPT2 method. Chem Phys Lett 288:299CrossRefGoogle Scholar
  60. 60.
    Serrano-Andrès L, Merchán M, Lindh R (2005) Computation of conical intersections by using perturbation techniques. J Chem Phys 122:104107CrossRefGoogle Scholar
  61. 61.
    Hirao K (1992) Multireference möller-plesset method. Chem Phys Lett 190:374CrossRefGoogle Scholar
  62. 62.
    Glaesemann KR, Gordon MS, Nakano H (1999) A study of feCO+ with correlated wavefunctions. Phys Chem Chem Phys 1:967Google Scholar
  63. 63.
    Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) Computation of conical intersections by using perturbation techniques. J Comput Chem 14:1347CrossRefGoogle Scholar
  64. 64.
    Nakano H (1993) Quasidegenerate perturbation theory with multiconfigurational self-consistent-field reference functions. J Chem Phys 99:7983–7992CrossRefGoogle Scholar
  65. 65.
    Nakano H (1993) MCSCF reference quasidegenerate perturbation theory with EpsteinNesbet partitioning. Chem Phys Lett 207:372–378CrossRefGoogle Scholar
  66. 66.
    Dreuw A, Head-Gordon M (2005) Single-reference ab initio methods for the calculation of excited states of large molecules. Chem Rev 105:4009–4037CrossRefGoogle Scholar
  67. 67.
    Head-Gordon M, Oumi M, Maurice D (1999) Quasidegenerate second-order perturbation corrections to single-excitation configuration interaction. Mol Phys 96:593CrossRefGoogle Scholar
  68. 68.
    Laikov D, Matsika S (2007) Inclusion of second-order correlation effects for the ground and singly-excited states suitable for the study of conical intersections: the CIS(2) model. Chem Phys Lett 448:132–137CrossRefGoogle Scholar
  69. 69.
    Koch H, Jensen HJA, Jorgensen P, Helgaker T (1990) Excitation-energies from the coupled cluster singles and doubles linear response function (CCSDLR) – applications to be, CH+, CO, and H2O. J Chem Phys 93:3345CrossRefGoogle Scholar
  70. 70.
    Stanton JF, Bartlett RJ (1993) The equation of motion coupled-cluster method - a systematic biorthogonal approach to molecular-excitation energies, transition-probabilities, and excited-state properties. J Chem Phys 98:7029CrossRefGoogle Scholar
  71. 71.
    Krylov AI (2001) Size-consistent wave functions for bond-breaking: the equation-of-motion spin-flip model. Chem Phys Lett 338:375CrossRefGoogle Scholar
  72. 72.
    Krylov AI (2006) Spin-flip equation-of-motion coupled-cluster electronic structure method for a description of excited states, bond breaking, diradicals, and triradicals. Acc Chem Res 39:83–91CrossRefGoogle Scholar
  73. 73.
    Nakatsuji H, Hirao K (1978) Cluster expansion of the wavefunction. symmetry-adapted-cluster expansion, its variational determination, and extension of open-shell orbital theory. J Chem Phys 68:2053CrossRefGoogle Scholar
  74. 74.
    Christiansen O, Koch H, Jorgensen P (1995) The second-order approximate coupled cluster singles and doubles model CC2. Chem Phys Lett 243:409–418CrossRefGoogle Scholar
  75. 75.
    Hättig C, Weigend F (2000) CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. J Chem Phys 113:5154CrossRefGoogle Scholar
  76. 76.
    Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on workstation computers: The program system turbomole. Chem Phys Lett 162:165–169CrossRefGoogle Scholar
  77. 77.
    Bickelhaupt FM, Baerends EJ (2000) Kohn-sham density functional theory: predicting and understanding chemistry. In: Lipkowitz KB Boyd DB (eds) Reviews in computational chemistry, vol. 15. Wiley-VCH, New York, pp 1–86CrossRefGoogle Scholar
  78. 78.
    Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52:997CrossRefGoogle Scholar
  79. 79.
    Levine BG, Ko C, Quenneville J, Martinez TJ (2006) Conical intersections and double excitations in time-dependent density functional theory. Mol Phys 104:1039CrossRefGoogle Scholar
  80. 80.
    Grimme S, Waletzke M (1999) A combination of KohnSham density functional theory and multi-reference configuration interaction methods. J Chem Phys 111:5645–5655CrossRefGoogle Scholar
  81. 81.
    Daniels M, Hauswirth W (1971) Fluorescence of the purine and pyrimidine bases of the nucleic acids in neutral aqueous solution at 300 K. Science 171:675CrossRefGoogle Scholar
  82. 82.
    Callis PR (1983) Electronic states and luminescence of nucleic acid systems. Ann Rev Phys Chem 34:329CrossRefGoogle Scholar
  83. 83.
    Pecourt J-ML, Peon J, Kohler B (2000) Ultrafast internal conversion of electronically excited RNA and DNA nucleosides in water. J Am Chem Soc 122:9348CrossRefGoogle Scholar
  84. 84.
    Pecourt J-ML, Peon J, Kohler B (2001) DNA excited-state dynamics: ultrafast internal conversion and vibrational cooling in a series of nucleosides. J Am Chem Soc 123:10370CrossRefGoogle Scholar
  85. 85.
    Cohen B, Hare P, Kohler B (2003) Ultrafast excited-state dynamics of adenine and monomethylated adenines in solution: implications for the nonradiative decay mechanism. J Am Chem Soc 125:13594CrossRefGoogle Scholar
  86. 86.
    Cohen B, Crespo-Hernandez CE, Kohler B (2004) Strickler-berg analysis of excited singlet state dynamis in DNA and RNA nucleosides. Faraday Discuss 127:137CrossRefGoogle Scholar
  87. 87.
    Peon J, Zewail AH (2001) DNA/RNA nucleotides and nucleosides: direct measurement of excited-state lifetimes by femtosecond fluorescence up-conversion. Chem Phys Lett 348:255CrossRefGoogle Scholar
  88. 88.
    Gustavsson T, Sharonov A, Markovitsi D (2002) Thymine, thymidine and thymidine 5’-monophosphate studied by femtosecond fluorescence upconversion spectroscopy. Chem Phys Lett 351:195CrossRefGoogle Scholar
  89. 89.
    Gustavsson T, Sharonov A, Onidas D, Markovitsi D (2002) Adenine, deoxyadenosine and deoxyadenosine 5’-monophosphate studied by femtosecond fluorescence upconversion spectroscopy. Chem Phys Lett 356:49CrossRefGoogle Scholar
  90. 90.
    Onidas D, Markovitsi D, Marguet S, Sharonov A, Gustavsson T (2002) Fluorescence properties of DNA nucleosides and nucleotides: a refined steady-state and femtosecond investigation. J Phys Chem B 106:11367CrossRefGoogle Scholar
  91. 91.
    Sharonov A, Gustavsson T, Carré V, Renault E, Markovitsi D (2003) Cytosine excited state dynamics studied by femtosecond absorption and fluorescence spectroscopy. Chem Phys Lett 380:173–180CrossRefGoogle Scholar
  92. 92.
    Gustavsson T, Banyasz A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R (2006) Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives. J Am Chem Soc 128:607–619CrossRefGoogle Scholar
  93. 93.
    Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Barone V, Improta R (2006) Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water. J Phys Chem B 110:12843–12847CrossRefGoogle Scholar
  94. 94.
    Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Improta R (2006) Singlet excited-state dynamics of uracil and thymine derivatives: a femtosecond fluorescence upconversion study in acetonitrile. Chem Phys Lett 429:551–557CrossRefGoogle Scholar
  95. 95.
    Brady BB, Peteanu L, Levy DH (1988) The electronic spectra of the pyrimidine bases uracil and thymine in a supersonic molecular beam. Chem Phys Lett 147:538CrossRefGoogle Scholar
  96. 96.
    Nir E, Kleinermanns K, Grace L, de Vries MS (2001) On the photochemistry of purine nucleobases. J Phys Chem A 105:5106CrossRefGoogle Scholar
  97. 97.
    Nir E, Müller M, Grace LI, de Vries MS (2002) REMPI spectroscopy of cytosine Chem Phys Lett 355:59Google Scholar
  98. 98.
    Nir E, Kleinermanns IHK, de Vries MS (2003) The nucleobase cytosine and the cytosine dimer investigated by double resonance laser spectroscopy and ab initio calculations. Phys Chem Chem Phys 5:4780CrossRefGoogle Scholar
  99. 99.
    Piuzzi F, Mons M, Dimicoli I, Tardivel B, Zhao Q (2001) Ultraviolet spectroscopy and tautomerism of the DNA base quanine and its hydrate formed in a supersonic jet. Chem Phys 270:205CrossRefGoogle Scholar
  100. 100.
    Lührs DC, Viallon J, Fischer I (2001) Excited state spectroscopy and dynamics of isolated adenine and 9-methyladenine. Phys Chem Chem Phys 3:1827CrossRefGoogle Scholar
  101. 101.
    He Y, Wu C, Kong W (2003) Decay pathways of thymine and methyl-substituted uracil and thymine in the gas phase. J Phys Chem A 107:5145CrossRefGoogle Scholar
  102. 102.
    He Y, Wu C, Kong W (2004) Photophysics of methyl-substituted uracils and thymines and their water complexes in the gas phase. J Phys Chem A 108:943CrossRefGoogle Scholar
  103. 103.
    Kang H, Lee KT, Jung B, Ko YJ, Kim SK (2002) Intrinsic lifetimes of the excited state of DNA and RNA bases. J Am Chem Soc 124:12958CrossRefGoogle Scholar
  104. 104.
    Kang H, Jung B, Kim SK (2003) Mechanism for ultrafast internal conversion of adenine, J Chem Phys 118:6717CrossRefGoogle Scholar
  105. 105.
    Kim NJ, Jeong G, Kim YS, Sung J, Kim SK, Park YD (2000) Resonant two-photon ionization and laser induced fluorescence spectroscopy of jet-cooled adenine. J Chem Phys 113:10051CrossRefGoogle Scholar
  106. 106.
    Ullrich S, Schultz T, Zgierski MZ, Stolow A (2004) Direct observation of electronic relaxation dynamics in adenine via time-resolved photoelectron spectroscopy. J Am Chem Soc 126:2262CrossRefGoogle Scholar
  107. 107.
    Ullrich S, Schultz T, Zgierski MZ, Stolow A (2004) Electronic relaxation dynamics in DNA and RNA bases studied by time-resolved photoelectron spectroscopy. Phys Chem Chem Phys 6:2796CrossRefGoogle Scholar
  108. 108.
    Satzger H, Townsend D, Zgierski MZ, Patchkovskii S, Ullrich S, Stolow A (2006) Primary processes underlying the photostability of isolated DNA bases: adenine. Proc Natl Acad Sci USA 103:10196–10201CrossRefGoogle Scholar
  109. 109.
    Nir E, Grace LI, Brauer B, de Vries MS (1999) REMPI spectroscopy of jet-cooled guanine. J Am Chem Soc 121:4896–4897CrossRefGoogle Scholar
  110. 110.
    Crews B, Abo-Riziq A, Grace LI, Callahan M, Kabelác M, Hobza P, de Vries MS (2005) IR-UV double reonance spectroscopy of guanine-H2O clusters. Phys Chem Chem Phys 7:3015–3020CrossRefGoogle Scholar
  111. 111.
    Abo-Riziq A, Crews BO, Compagnon I, Oomens J, Meijer G, Helden GV, Kabelác M, Hobza P, de Vries MS (2005) The mid-IR spectra of 9-ehtyl guanine, guanosine, and 2-deoxyguanosine. Phys Chem Chem Phys 7:3015–3020Google Scholar
  112. 112.
    Canuel C, Mons M, Piuzzi F, Tardinel B, Dimicoli I, Elhanine M (2005) Excited states dynamics of DNA and RNA bases: characterization of a stepwise deactivation pathway in the gas phase. J Chem Phys 122:074316CrossRefGoogle Scholar
  113. 113.
    Mons M, Piuzzi F, Dimicoli I, Gorb L, Lesczynski J (2006) Near-UV resonant two-photon ionization spectroscopy of gas phase guanine: evidence for the observation of three rare tautomers. J Phys Chem A 110:10921–10924CrossRefGoogle Scholar
  114. 114.
    Ritze H-H, Lippert H, Samoylova E, Smith VR, Hertel IV, Radloff W, Schultz T (2005) Relevance of πσ* states in the photoinduced processes of adenine, adenine dimer, and adeninewater complexes. J Chem Phys 122:224320CrossRefGoogle Scholar
  115. 115.
    Samoylova E, Lippert H, Ullrich S, Hertel IV, Radloff W, Schultz T, (2005) Dynamics of photoinduced processes in adenine and thymine base pairs. J Am Chem Soc 127:1782–1786CrossRefGoogle Scholar
  116. 116.
    Hare PM, Crespo-Hernandez CE, Kohler B (2007) Internal conversion to the electronic ground state occurs via two distinct pathways for the pyrimidine bases in aqueous solution. Proc Natl Acad Sci USA 104:435–440CrossRefGoogle Scholar
  117. 117.
    Schwalb NK, Temps F (2007) Ultrafast electronic relaxation in guanosine is promoted by hydrogen bonding with cytidine. J Am Chem Soc 129:9272CrossRefGoogle Scholar
  118. 118.
    Abo-Riziq A, Grace L, Nir E, Kabelac M, Hobza P, de Vries MS (2005) Photochemical selectivity in guanine-cytosine base-pair structures. Proc Natl Acad Sci USA 102:20–23CrossRefGoogle Scholar
  119. 119.
    Crespo-Hernandez CE, Cohen B, Kohler B (2005) Base stacking controls excited-state dynamics in A-T DNA. Nature 436:1141–1144CrossRefGoogle Scholar
  120. 120.
    Markovitsi D, Talbot F, Gustavsson T, Onidas D, Lazzarotto E, Marguet S (2006) Molecular spectroscopy: complexity of excited state dynamics in DNA. Nature 442: E7CrossRefGoogle Scholar
  121. 121.
    Broo A, Holmén A (1997) Calculations and characterization of the electronic spectra of DNA bases based on ab initio MP2 geometries of different tautomeric forms. J Phys Chem A 101:3589CrossRefGoogle Scholar
  122. 122.
    Shukla MK, Leszczynski J (2002) Phototautomerism in uracil: a quantum chemical investigation. J Phys Chem A 106:8642CrossRefGoogle Scholar
  123. 123.
    Shukla MK, Mishra PC (1999) A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil. Chem Phys 240:319CrossRefGoogle Scholar
  124. 124.
    Fleig T, Knecht S, Hättig C (2007) Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level. J Phys Chem A 111:5482–5491CrossRefGoogle Scholar
  125. 125.
    Lorentzon J, Fülscher MP, Roos BO (1995) Theoretical study of the electronic spectrum of uracil and thymine. J Am Chem Soc 117:9265CrossRefGoogle Scholar
  126. 126.
    Hudock HR, Levine BG, Thompson AL, Satzger H, Townsend D, Gador N, Ullrich S, Stolow A, Martinez TJ (2007) Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine. J Phys Chem A 111:8500–8508CrossRefGoogle Scholar
  127. 127.
    Petke JD, Maggiora GM, Christoffersen RE (1992) Ab-initio configuration interaction and random phase approximation caclulations of the excited singlet and triplet states of uracil and cytosine. J Phys Chem 96:6992CrossRefGoogle Scholar
  128. 128.
    Zgierski MZ, Patchkovskii S, Fujiwara T, Lim EC (2005) On the origin of the ultrafast internal conversion of electronically excited pyrimidine bases. J Phys Chem A 109:9384–9387CrossRefGoogle Scholar
  129. 129.
    Neiss C, Saalfrank P, Parac M, Grimme S (2003) Quantum chemical calculation of excited states of flavin-related molecules. J Phys Chem A 107:140CrossRefGoogle Scholar
  130. 130.
    Marian CM, Schneidaer F, Kleinschmidt M, Tatchen J (2002) Electronic excitation and singlet-triplet coupling in uracil tatutomers and uracil-water complexes. Eur Phys J D 20:357CrossRefGoogle Scholar
  131. 131.
    Shukla MK, Leszczynski J (2004) TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach. J Comput Chem 25:768–778CrossRefGoogle Scholar
  132. 132.
    Clark LB, Peschel GG, Tinoco I Jr (1965) Vapor spectra and heats of vaporization of some purine and pyrimidine bases. J Phys Chem 69:3615CrossRefGoogle Scholar
  133. 133.
    Tomić K, Jörg T, Marian CM (2005) Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine. J Phys Chem A 109:8410–8418CrossRefGoogle Scholar
  134. 134.
    Fülscher MP, Roos BO (1995) Theoretical study of the electronic spectrum of cytosine. J Am Chem Soc 117:2089CrossRefGoogle Scholar
  135. 135.
    Clark LB, Tinoco I Jr (1965) Correlations in the ultraviolet spectra of the purine and pyrimidine bases. J Am Chem Soc 87:11CrossRefGoogle Scholar
  136. 136.
    Voelter W, Records R, Bunnenberg E, Djerassi C (1968) Magnetic circular dichroism studies. vi. investigation of some purines, pyrimidines, and nucleosides. J Am Chem Soc 90:6163–6170CrossRefGoogle Scholar
  137. 137.
    Platt JR (1949) Classification of spectra of cata-condensed hydrocarbons. J Chem Phys 17:484CrossRefGoogle Scholar
  138. 138.
    Perun S, Sobolewski AL, Domcke W (2005) Ab initio studies on the radiationless decay mechanisms of the lowest excited singlet states of 9H-adenine. J Am Chem Soc 127:6257–6265CrossRefGoogle Scholar
  139. 139.
    Marian CM (2005) A new pathway for the rapid decay of electronically excited adenine. J Chem Phys 122:104314CrossRefGoogle Scholar
  140. 140.
    Merchán M, Serrano-Andrés L (2003) Ultrafast internal conversion of excited cytosine via the lowest ππ* electronic singlet state. J Am Chem Soc 125:8108CrossRefGoogle Scholar
  141. 141.
    Blancafort L (2006) Excited-state potential energy surface for the photophysics of adenine. J Am Chem Soc 128:210–219CrossRefGoogle Scholar
  142. 142.
    Clark LB (1990) Electronic spectrum of the adenine chromophore. J Phys Chem 94:2873–2879CrossRefGoogle Scholar
  143. 143.
    Fülscher MP, Serrano-Andres L, Roos BO (1997) A theoretical study of the electronic spectra of adenine and guanine. J Am Chem Soc 119:6168CrossRefGoogle Scholar
  144. 144.
    Kistler KA, Matsika S (2007) Cytosine in context: a theoretical study of substituent effects on the excitation energies of 2-pyrimidinone derivatives. J Phys Chem A 111:8708–8716CrossRefGoogle Scholar
  145. 145.
    Chen H, Li SH (2006) Ab initio study on deactivation pathways of excited 9H-guanine. J Chem Phys 124:154315CrossRefGoogle Scholar
  146. 146.
    Clark LB (1977) Electronic spectra of crystalline 9-ethylguanine and guanine hydrochloride. J Am Chem Soc 99:3934CrossRefGoogle Scholar
  147. 147.
    Matsika S (2004) Radiationless decay of excited states of uracil through conical intersections. J Phys Chem A 108:7584CrossRefGoogle Scholar
  148. 148.
    Zgierski MZ, Fujiwara T, Kofron WG, Lim EC (2007) Highly effective quanching of theultrafast radiationless decay of photoexcited pyrimidine bases by covalent modification: photophysics of 5,6-trimethylenecytosine and 5,6-trimethyleneuracil. Phys Chem Chem Phys 9:3206–3209CrossRefGoogle Scholar
  149. 149.
    Santoro F, Barone V, Gustavsson T, Improta R (2006) Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: a computational study of 5-fluorouracil and uracil in acetonitrile and water. J Am Chem Soc 128:16312–16322CrossRefGoogle Scholar
  150. 150.
    Merchán M, Gonzalez-Luque R, Climent T, Serrano-Andrés L, Rodriuguez E, Reguero M, Pelaez D (2006) Unified model for the ultrafast decay of pyrimidine nucleobases. J Phys Chem B 110:26471–26476CrossRefGoogle Scholar
  151. 151.
    Hare PM, Crespo-Hernandez CE, Kohler B (2006) Solvent-dependent photophysics of1-cyclohexyluracil: ultrafast branching in the initial bright state leads nonradiatively to the electronic ground state and a long-lived 1 nπ* state. J Phys Chem B 110:18641CrossRefGoogle Scholar
  152. 152.
    Perun S, Sobolewski AL, Domcke W (2006) Conical intersections in thymine. J Phys Chem A 110:13238CrossRefGoogle Scholar
  153. 153.
    Ismail N, Blancafort L, Olivucci M, Kohler B, Robb MA (2002) Ultrafast decay of electronically excited singlet cytosine via ππ* to nπ* state switch. J Am Chem Soc 124:6818CrossRefGoogle Scholar
  154. 154.
    Blancafort L, Robb MA (2004) Key role of a threefold state crossing in the ultrafast decay of electronically excited cytosine. J Phys Chem A 108:10609CrossRefGoogle Scholar
  155. 155.
    Zgierski MZ, Patchkovskii S, Lim EC (2005) Ab initio study of a biradical radiationless decay channel of the lowest excited electronic state of cytosine and its derivatives. J Chem Phys 123:081101CrossRefGoogle Scholar
  156. 156.
    Blancafort L (2007) Energetics of cytosine singlet excited-state decay paths – A difficult case for CASSCF and CASPT2. Photochem Photobiol 83:603–610Google Scholar
  157. 157.
    Kistler KA, Matsika S (2007) Radiationless decay mechanism of cytosine: an ab initio study with comparisons to the fluorescent analogue 5-methyl-2-pyrimidinone. J Phys Chem A 111:2650–2661CrossRefGoogle Scholar
  158. 158.
    Sobolewski AL, Domcke W (2002) On the mechanism of nonradiative decay of DNA bases: ab initio and TDDFT results for the excited states of 9H-adenine. Eur Phys J D 20:369CrossRefGoogle Scholar
  159. 159.
    Sobolewski AL, Domcke W, Dedonder-Lardeux C, Jouvet C (2002) Excited-state hydrogen detachment and hydrogen transfer driven by repulsive (1)pi sigma* states: a new paradigm for nonradiative decay in aromatic biomolecules. J Phys Chem Chem Phys 4:1093–1100Google Scholar
  160. 160.
    Perun S, Sobolewski AL, Domcke W (2005) Photostability of 9 h-adenine: mechanisms of the radiationless deactivation of the lowest excited singlet states. Chem Phys 313:107–112CrossRefGoogle Scholar
  161. 161.
    Chung WC, Lan Z, Ohtsuki Y, Shimakura N, Domcke W, Fujimura Y (2007) Conical intersections involving the dissociative 1πσ* state in 9H-adenine: a quantum chemical ab initio study. Phys Chem Chem Phys 9:2075–2084CrossRefGoogle Scholar
  162. 162.
    Nielsen SB, Solling TI (2005) Are conical intersections responsible for the ultrafast processes of adenine, protonated adenine, and the corresponding nucleosides?. Chem Phys Chem 6:1276Google Scholar
  163. 163.
    Serrano-Andrés L, Merchán M, Borin AC (2006) A three-state model for the photophysics of adenine. Chem Eur J 12:6559–6571CrossRefGoogle Scholar
  164. 164.
    Serrano-Andrés L, Merchán M, Borin AC (2006) Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry. Proc Natl Acad Sci USA 103:8691–8696CrossRefGoogle Scholar
  165. 165.
    Chen H, Li SH (2005) Theoretical study toward understanding ultrafast internal conversion ofexcited 9H-adenine. J Phys Chem A 109:8443–8446CrossRefGoogle Scholar
  166. 166.
    Zgierski MZ, Patchkovskii S, Lim EC (2007) Biradical radiationless decay channel in adenine and its derivatives. Can J Chem 85:124CrossRefGoogle Scholar
  167. 167.
    Langer H, Doltsinis NL (2003) Selected photostabilisation of guanine by methylation. Phys Chem Chem Phys 5:4516–4518CrossRefGoogle Scholar
  168. 168.
    Langer H, Doltsinis NL (2003) Excited state tautomerism of the DNA base guanine: a restricted open-shell kohn-sham study. J Chem Phys 118:5400–5407CrossRefGoogle Scholar
  169. 169.
    Langer H, Doltsinis NL (2004) Nonradiative decay of photoexcited methylated guanine. Phys Chem Chem Phys 6:2742–2748CrossRefGoogle Scholar
  170. 170.
    Chen H, Li SH (2006) Theoretical study on the excitation energies of six tautomers of guanine: evidence for the assignment of the rare tautomers. J Phys Chem A 110:12360–12362CrossRefGoogle Scholar
  171. 171.
    Marian CM (2007) The guanine tautomer puzzle: quantum chemical investigation of ground and excited states. J Phys Chem A 111:1545–1553CrossRefGoogle Scholar
  172. 172.
    Zgierski MZ, Patchkovskii S, Fujiwarab T, Lim EC (2007) The role of out-of-plane deformations in subpicosecond internal conversion of photoexcited purine bases: absence of the ultrafast decay channel in propanodeoxyguanosine. Chem Phys Lett 440:145–149CrossRefGoogle Scholar
  173. 173.
    Laland SG, Serck-Hanssen G (1964) Synthesis of pyrimidin-2-one deoxyribosides and their ability to support the growth of the deoxyriboside-requiring organism lactobacillus acidophilus r26. Biochem J 90:76–81Google Scholar
  174. 174.
    Rappaport HP (1988) The 6-thioguanine/5-methyl-2-pyrimidinone base pair. Nucl Acids Res 16(15):7253–7267CrossRefGoogle Scholar
  175. 175.
    Rappaport HP (1989) Artificial DNA base pair analoguesGoogle Scholar
  176. 176.
    Wu P, Norland TM, Gildea B, McLaughlin LW (1990) Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base. Biochem 29:6508–6514CrossRefGoogle Scholar
  177. 177.
    Berry DA, Jung K-Y, Wise DS, Sercel AD, Pearson WH, Mackie H, Randolph JB, Somers RL (2004) Pyrrolo-dc and pyrrolo-c: fluorescent analogs of cytidine and 2’-deoxycytidine for the study of oligonucleotides. Tet Lett 45:2457–2461CrossRefGoogle Scholar
  178. 178.
    Barrio JR, Sattsangi PD, Gruber GA, Dammann LG, Leonard NJ (1976) Species responsible for 3,n4-ethenocytidine. J Am Chem Soc 98(23):7408–7414CrossRefGoogle Scholar
  179. 179.
    Major DT, Fisher B (2003) Theoretical study of the ph-dependent photophysics of n1,n6-ethenoadenine and n3,n4-ethenocytosine. J Phys Chem A 107:8923–8931CrossRefGoogle Scholar
  180. 180.
    Kistler KA, Matsika S (2007) The fluorescence mechanism of 5-methyl-2-pyrimidinone: an ab initio study of a fluorescent pyrimidine analog. Photoch Photob 83:611–624Google Scholar
  181. 181.
    Thompson KC, Miyake N (2005) Properties of a new fluorescent cytosine analogue, pyrrolocytosine. J Phys Chem B 109:6012–6019CrossRefGoogle Scholar
  182. 182.
    Hardman SJO, Thompson KC (2006) Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochem 45:9145–9155CrossRefGoogle Scholar
  183. 183.
    Jean JM, Hall KB (2002) 2-aminopurine electronic structure and fluorescence properties in DNA. Biochem 41:13152–13161CrossRefGoogle Scholar
  184. 184.
    Sowers LC, Fazakerley GV, Eritja R, Kaplan BE (1986) Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proc Natl Acad Sci USA 83:5434–5438CrossRefGoogle Scholar
  185. 185.
    Rachofsky EL, Osman R, Ross JBA (2001) Probing structure and dynamics of DNA with2-aminopurine: effects of local environment on fluorescence. Biochem 40:946–956CrossRefGoogle Scholar
  186. 186.
    Wang Q, Raytchev M, Fiebig T (2007) Ultrafast energy delocalization and electron transfer dynamics in 2-aminopurine-containing trinucleotides. Photochem Photobiol 83:637–641CrossRefGoogle Scholar
  187. 187.
    Seefeld KA, Plützer C, Löwenich D, H”aber T, Linder R, Kleinermanns K, Tatchen J, Marian CM (2005) Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory. Phys Chem Chem Phys 7:3021–3026CrossRefGoogle Scholar
  188. 188.
    Kodali G, Kistler KA, Matsika S, Stanley RJ (2007) 2-aminopurine excited state electronic structure measured by stark spectroscopy. J Phys Chem B 111:10615–10625CrossRefGoogle Scholar
  189. 189.
    Häupl T, Windolph C, Jochum T, Brede O, Hermann R (1997) Picosecond fluorescence of nucleic acid bases. Chem Phys Lett 280:520–524CrossRefGoogle Scholar
  190. 190.
    Rachofsky EL, Ross JBA, Krauss M, Osman R (1998) Spectroscopy of 2-aminopurine: an MCSCF study. Acta Phys Polon A 94:735–748Google Scholar
  191. 191.
    Rachofsky EL, Ross JBA, Krauss M, Osman R (2001) CASSCF investigation of electronic excited states of 2-aminopurine. J Phys Chem A 105:190–197CrossRefGoogle Scholar
  192. 192.
    Borin AC, Serrano-Andrés L, Ludwig V, Coutinho K, Canuto S (2006) Theoretical electronic spectra of 2-aminopurine in vapor and in water. Int J Quant Chem 106: 2564–2577CrossRefGoogle Scholar
  193. 193.
    Broo A (1998) A theoretical investigation of the physical reason for the very diffferent luminescence properties of the two isomers adenine and 2-aminopurine. J Phys Chem A 102:526CrossRefGoogle Scholar
  194. 194.
    Perun S, Sobolewski AL, Domke W (2006) Ab initio studies of the photophysics of 2-aminopurine. Mol Phys 104:1113–1121CrossRefGoogle Scholar
  195. 195.
    Mamos P, Aerschot AAV, Weyns NJ, Hardewijn PA (1992) Straightforward c-8 alkylation of adenosine analogues with tetraalkyltin reagents. Tet Lett 33:2413–2416CrossRefGoogle Scholar
  196. 196.
    Lang P, Gerez C, Tritsch D, Fontecave M, Biellmann J-F, Burger A (2003) Synthesis of 8-vinyladenosine 50-di- and 50-triphosphate: evaluation of the diphosphate compound on ribonucleotide reductase, Tetrahedron 59:7315–7322CrossRefGoogle Scholar
  197. 197.
    Gaied NB, Glasser N, Ramalanjaona N, Beltz H, Wolff P, Marquet R, Burger A, Mly Y (2005) 8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2’-deoxyribosyl-2-aminopurine with improved properties. Nucl Acids Res 33:1031–1039CrossRefGoogle Scholar
  198. 198.
    Kenfack CA, Burger A, Mély Y (2006) Excited-state propertes and transitions of fluorescent 8-vinyl adenosine in DNA. J Phys Chem A 110:26327–26336Google Scholar
  199. 199.
    Spencer RD, Weber G, Tolman GL, Barrio JR, Leonard NJ (1974) Species responsible for the fluorescence of 1:N6-ethenoadenosine. Eur J Biochem 45:425–429CrossRefGoogle Scholar
  200. 200.
    Bersuker IB (1984) The jahn-teller effect and vibronic interactions in modern chemistry. Plenum Press, New YorkGoogle Scholar
  201. 201.
    Katriel J, Davidson ER (1980) The non-crossing rule: triply degenerate ground-state geometries of CH+ 4. Chem Phys Lett 76:259CrossRefGoogle Scholar
  202. 202.
    Keating SP, Mead CA (1985) Conical intersections in a system of four identical nuclei. J Chem Phys 82:5102CrossRefGoogle Scholar
  203. 203.
    Han S, Yarkony DR (2003) Conical intersections of three states. Energies, derivative couplings, and the geometric phase effect in the neighborhood of degeneracy subspaces. Application to the allyl radical. J Chem Phys 119:11562Google Scholar
  204. 204.
    Han S, Yarkony DR (2003) Nonadiabatic processes involving three electronic states. I. Branch cuts and linked pairs of conical intersections. J Chem Phys 119:5058CrossRefGoogle Scholar
  205. 205.
    Coe JD, Martinez TJ (2005) Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer. J Am Chem Soc 127:4560CrossRefGoogle Scholar
  206. 206.
    Coe JD, Martinez TJ (2006) Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde. J Phys Chem A 110:618–630CrossRefGoogle Scholar
  207. 207.
    Matsika S, Yarkony DR (2002) Accidental conical intersections of three states of the same symmetry. I. Location and relevance. J Chem Phys 117:6907CrossRefGoogle Scholar
  208. 208.
    Matsika S, Yarkony DR (2003) Beyond two-state conical intersections. Three-state conical intersections in low symmetry molecules: The allyl radical. J Chem Soc 125:10672CrossRefGoogle Scholar
  209. 209.
    Matsika S, Yarkony DR (2003) Conical intersections of three electronic states affect the ground state of radical species with little Or no symmetry: pyrazolyl. J Am Chem Soc 125:12428CrossRefGoogle Scholar
  210. 210.
    Matsika S (2005) Three-state conical intersections in nucleic acid bases. J Phys Chem A 109:7538CrossRefGoogle Scholar
  211. 211.
    Zazza C, Amadei A, Sanna N, Grandi A, Chillemi G, Nola AD, D’Abramo M, Aschi M (2006) Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution. Phys Chem Chem Phys 8:1385–1393CrossRefGoogle Scholar
  212. 212.
    Zhang RB, Zeegers-Huyskens T, Ceulemans A, Nguyen MT (2005) Interaction of triplet uracil and thymine with water. Chem Phys 316:35CrossRefGoogle Scholar
  213. 213.
    Improta R, Barone V (2004) Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TDDFT quantum mechanical study. J Am Chem Soc 126:14320CrossRefGoogle Scholar
  214. 214.
    Ludwig V, Coutinho K, Canuto S (2007) A Monte Carlo-quantum mechanics study of the lowest n – π* and π – π* states of uracil in water. Phys Chem Chem Phys 9:4907–4912CrossRefGoogle Scholar
  215. 215.
    Shukla MK, Leszczynski J (2002) Interaction of water molecules with cytosine tautomers: An excited-state quantum chemical investigation. J Phys Chem A 106:11338CrossRefGoogle Scholar
  216. 216.
    Blancafort L, Migani A (2007) Water effect on the excited-state decay paths of singlet excited cytosine. J Photochem Photobiol A 190:283–289CrossRefGoogle Scholar
  217. 217.
    Mishra SK, Shukla MK, Mishra PC (2000) Electronic spectra of adenine and 2-aminopurine: an ab initio study of energy level diagrams of different tautomers in gas phase and aqueous solution. Spectrochim Acta A 56:1355CrossRefGoogle Scholar
  218. 218.
    Shukla MK, Mishra SK, Kumar A, Mishra PC (2000) An ab initio study of excited states of guanine in the gas phase and aqueous media: Electronic transitions and mechanism of spectral oscillations. J Comput Chem 21:826CrossRefGoogle Scholar
  219. 219.
    Mennucci B, Toniolo A, Tomasi J (2001) Theoretical study of the photophysics of adenine insolution: tautomerism, deactivation mechanisms, and comparison with the 2-aminopurine fluorescent isomer. J Phys Chem A 105:4749CrossRefGoogle Scholar
  220. 220.
    Mennucci B, Toniolo A, Tomasi J (2001) Theoretical study of guanine from gas phase to aqueous solution: role of tautomerism and its implications in absorption and emission spectra. J Phys Chem A 105:7126CrossRefGoogle Scholar
  221. 221.
    Shukla MK, Leszczynski J (2005) Effect of hydration on the lowest singlet ππ* excited-stategeometry of guanine: a theoretical study. J Phys Chem B 109:17333–17339CrossRefGoogle Scholar
  222. 222.
    Shukla MK, Leszczynski J (2005) Excited state proton transfer in guanine in the gas phase and in water solution: a theoretical study. J Phys Chem A 109:7775–7780CrossRefGoogle Scholar
  223. 223.
    Yamazaki S, Kato S (2007) Solvent effect on conical intersections in excited-state 9H-adenine: radiationless decay mechanism in polar solvent. J Am Chem Soc 129:2901–2909CrossRefGoogle Scholar
  224. 224.
    Yoshikawa A, Matsika S (2008) Excited electronic states and photophysics of uracil-water complexes. Chem Phys 347:393–404CrossRefGoogle Scholar
  225. 225.
    Mourik TV, Price SL, Clary DC (1999) Ab initio calculations on uracil-water. J Phys Chem A 103:1611CrossRefGoogle Scholar
  226. 226.
    Crespo-Hernandez CE, Cohen B, Kohler B (2006) Molecular spectroscopy: complexity of excited-state dynamics in DNA - Reply. Nature 441:E8CrossRefGoogle Scholar
  227. 227.
    Emanuele E, Zakrzewska K, Markovitsi D, Lavery R, Millie P (2005) Exciton states of dynamic dna double helices: alternating dcdg sequences. J Phys Chem B 109:16109–16118CrossRefGoogle Scholar
  228. 228.
    Bittner ER (2007) Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices. J Photochem Photobiol A 190:328–334CrossRefGoogle Scholar
  229. 229.
    Buchvarov I, Raytchev QWQM, Trifonov A, Fiebig T (2007) Electronic energy delocalization and dissipation in single- and double-stranded DNA. Proc Natl Acad Sci USA 104:4794–4797CrossRefGoogle Scholar
  230. 230.
    Kwok W-M, Ma C, Phillips DL (2006) Femtosecond time- and wavelength-resolved fluorescence and absorption spectroscopic study of the excited states of adenosine and an adenine oligomer. J Am Chem Soc 128:11894–11905CrossRefGoogle Scholar
  231. 231.
    Nir E, Kleinermanns K, de Vries MS (2000) On the photochemistry of purine nucleobases. Nature 408:949CrossRefGoogle Scholar
  232. 232.
    Weinkauf R, Schermann JP, de Vries MS, Kleinermanns K (2002) Molecular physics of building blocks of life under isolated or defined conditions. Eur Phys J D 20:309CrossRefGoogle Scholar
  233. 233.
    Plützer C, Hünig I, Kleinermanns K, Nir E, de Vries MS (2003) On the photochemistry of purine nucleobases. Chem Phys Chem 4:838–842Google Scholar
  234. 234.
    Schultz T, Samoylova E, Radloff W, Hertel IV, Sobolewski AL, Domcke W (2004) Efficient deactivation of a model base pair via excited-state hydrogen transfer. Science 306:1765CrossRefGoogle Scholar
  235. 235.
    Sobolewski AL, Domcke W, Hättig C (2005) Tautomeric selectivity of the excited-state lifetime of guanine/cytosine base pairs: The role of electron-driven proton-transfer processes. Proc Natl Acad Sci USA 102:17903–17906CrossRefGoogle Scholar
  236. 236.
    Sobolewski AL, Domcke W (2003) Ab initio study of the excited-state coupled electron-proton-transfer process in the 2-aminopyridine dimer. Chem Phys 294:2763CrossRefGoogle Scholar
  237. 237.
    Sobolewski AL, Domcke W (2004) Ab initio studies on the photophysics of the guanine-cytosine base pair. Phys Chem Chem Phys 6:2763CrossRefGoogle Scholar
  238. 238.
    Sobolewski AL, Domcke W (2006) Role of electron-driven proton-transfer processes in the excited-state deactivation adenine–thymine base pair. J Phys Chem A 110: 9031–9038CrossRefGoogle Scholar
  239. 239.
    Sobolewski AL, Domcke W (2007) Computational studies of the photophysics of hydrogen-bonded molecular systems. J Phys Chem A 111:11725–11735CrossRefGoogle Scholar
  240. 240.
    Shukla MK, Leszczynski J (2002) A theoretical investigation of excited-state properties of the adenine–uracil base pair. J Phys Chem A 106:1011–1018CrossRefGoogle Scholar
  241. 241.
    Groenhof G, Schafer LV, Boggio-Pasqua M, Goette M, Grubmuller H, Robb MA (2007) Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. J Am Chem Soc 129:6812–6819CrossRefGoogle Scholar
  242. 242.
    Markwick PRL, Doltsinis NL (2007) Ultrafast repair of irradiated DNA: nonadiabatic ab initio simulations of the guanine-cytosine photocycle. J Chem Phys 126:175102CrossRefGoogle Scholar
  243. 243.
    Markwick PRL, Doltsinis NL, Schlitter J (2007) Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics. J Chem Phys 126:045104CrossRefGoogle Scholar
  244. 244.
    Jean JM, Hall KB (2001) 2-aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc Natl Acad Sci USA 98:37–41CrossRefGoogle Scholar
  245. 245.
    Olaso-González G, Roca-Sanjuán D, Serrano-Andrés L, Merchán M (2006) Toward the understanding of DNA fluorescence: the singlet excimer of cytosine. J Chem Phys 125:231102CrossRefGoogle Scholar
  246. 246.
    Santoro F, Barone V, Improta R (2007) Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations. Proc Natl Acad Sci USA 104:9931–9936CrossRefGoogle Scholar
  247. 247.
    Varsano D, Di Felice R, Marques MAL, Rubio A (2006) A TDDFT study of the excited states of DNA bases and their assemblies. J Phys Chem B 110:7129–7138CrossRefGoogle Scholar
  248. 248.
    Tinoco I (1960) Hypochromism in polynucleotides. J Am Chem Soc 82:4785–4790CrossRefGoogle Scholar
  249. 249.
    Frenkel J (1931) On the transformation of light into heat in solids. II. Phys Rev 37:1276–1294CrossRefGoogle Scholar
  250. 250.
    Bouvier B, Gustavsson T, Markovitsi D, Millié P (2002) Dipolar coupling between electronic transitions of the DNA bases and its relevance to exciton states in double helices. Chem Phys 275:75–92CrossRefGoogle Scholar
  251. 251.
    Bouvier B, Dognon J-P, Lavery R, Markovitsi D, Millié P, Onidas D, Zakrzewska K (2003) Influence of conformational dynamics on the exciton states of DNA oligomers. J Phys Chem B 107:13512–13522CrossRefGoogle Scholar
  252. 252.
    Emanuele E, Markovitsi D, Milli P, Zakrzewska K (2005) UV spectra and excitation delocalization in DNA: influence of the spectral width. Chem Phys Chem 6:1387–1392Google Scholar
  253. 253.
    Onidas D, Gustavsson T, Lazzarotto E, Markovitsi D (2007) Fluorescence of the DNA double helices (dAdT)n·(dAdT)n studied by femtosecond spectroscopy. Phys Chem Chem Phys 9:5143–5148CrossRefGoogle Scholar
  254. 254.
    Onidas D, Gustavsson T, Lazzarotto E, Markovitsi D (2007) Fluorescence of the DNA double helix (dA)20·(dT)20 studied by femtosecond spectroscopy effect of the duplex size on the properties of the excited states. J Phys Chem B 111:9644–9650CrossRefGoogle Scholar
  255. 255.
    Miannay F-A, Bányász á, Gustavsson T, Markovitsi D (2007) Ultrafast excited-state deactivation and energy transfer in guanine-cytosine DNA double helices. J Am Chem Soc 129:14574–14575CrossRefGoogle Scholar
  256. 256.
    Bittner ER (2006) Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA. J Chem Phys 125:094909CrossRefGoogle Scholar
  257. 257.
    Czader A, Bittner ER (2008) Calculations of the exciton coupling elements between DNA bases using the transition density cube method. J Chem Phys 128:035101CrossRefGoogle Scholar
  258. 258.
    Schreier WJ, Schrader TE, Koller FO, Gilch P, Crespo-Hernandez CE, Swaminathan VN, Carell T, Zinth W, Kohler B (2007) Thymine dimerization in DNA is an ultrafast photoreaction. Science 315:625–629CrossRefGoogle Scholar
  259. 259.
    Durbeej B, Eriksson LA (2002) Reaction mechanism of thymine dimer formation in DNA induced by UV light. Photochem Photobiol A 152:95–101CrossRefGoogle Scholar
  260. 260.
    Zhang RB, Eriksson LA (2006) A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA. J Phys Chem B 110:7556–7562CrossRefGoogle Scholar
  261. 261.
    Boggio-Pasqua M, Groenhof G, Schäfer LV, Brubmüller H, Robb MA (2007) Ultrafast deactivation channel for thymine dimerization. J Am Chem Soc 129:10996–10997CrossRefGoogle Scholar
  262. 262.
    Blancafort L, Migani A (2007) Modeling thymine photodimerizations in DNA: mechanism and correlation diagrams. J Am Chem Soc 129:14540–14541CrossRefGoogle Scholar
  263. 263.
    Valiev M, Kowalski K (2006) Hybrid coupled cluster and molecular dynamics approach: Application to the excitation spectrum of cytosine in the native DNA environment. J Chem Phys 125:211101CrossRefGoogle Scholar
  264. 264.
    Salter LM, Chaban GM (2002) Theoretical study of gas phase tautomerization reaction for the ground and first excited electronic states of adenine. J Phys Chem A 106:4251CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Kurt A. Kistler
    • 1
  • Spiridoula Matsika
    • 1
  1. 1.Department of ChemistryTemple UniversityPhiladelphiaUSA

Personalised recommendations