Quantum mechanical studies of the photophysics of DNA and RNA Bases

Challenges and Advances in Computational Chemistry and Physics

Volumn 7, Issue , 2009, Pages 285-339

  Kistler, Kurt A ^a   Matsika, Spiridoula ^a  

^a Temple University   (United States)

Author keywords

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

Indexed keywords

EID: 77951965512     PISSN: 25424491     EISSN: 25424483     Source Type: Book Series    
DOI: 10.1007/978-1-4020-9956-4_11     Document Type: Chapter

References (264)

1. Kraemer KH (1997) Sunlight and skin cancer: another link revealed. Proc Natl Acad Sci USA 94:11
2. Mukhtar H, Elmets CA (1996) Photocarcinogenesis: mechanisms, models and human health implications. Photochem Photobiol 63:355
3. Cadet J, Vigny P (1990) In: Morrison H (ed.) Bioorganic photochemistry. John Wiley, New York, pp. 1–272
4. Daniels M (1976) In: Wang SY (ed.) Photochemistry and Photobiology of Nucleic Acids, vol 1. Academic Press, New York, p 23
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 1289
6. Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Ultrafast excited-state dynamics in nucleic acids. Chem Rev 104:1977
7. Born M, Oppenheimer R (1927) Zur Quantentheorie der Molekeln. Ann Phys 84:457
8. Landau LD (1932) Z. Sowjetunion U.R.S.S. 2:46
9. Zener C (1932) Non-adiabatic crossing of energy levels. Proc Roy Soc A137:696
10. Domcke W, Yarkony DR, Köppel H (2004) Conical intersections. World Scientific, Singapore,
11. Rice OK (1929) Phys Rev 33:748
12. Dantus M, Zewail A (2004) Introduction: femtochemistry. Chem Rev 104:1717
13. von Neumann J, Wigner EP (1929) On the behaviour of eigenvalues in adiabatic processes. Physik Z 30:467
14. Teller E (1937) The crossing of potential surfaces. J Phys Chem 41:109
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 99:5251
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 223:269
17. Yarkony DR (1998) Conical intersections: diabolical and often misunderstood. Acc Chem Res 31:511
18. Yarkony DR (1996) Diabolical conical intersections. Rev Mod Phys 68:985
19. Yarkony DR (1996) Current issues in nonadiabatic chemistry. J Phys Chem 100:18612
20. Yarkony DR (2001) Conical intersections: the new conventional wisdom. J Phys Chem A 105:6277
21. Bernardi F, Olivucci M, Robb MA (1990) Predicting forbidden and allowed cycloaddition reactions: potential surface topology and its rationalization. Acc Chem Res 23:405
22. Bernardi F, Olivucci M, Robb MA (1996) Potential energy surface crossings in organic photochemistry. Chem Soc Rev 25:321
23. Barckholtz TA, Miller TA (1998) Quantitative insights about molecules exhibiting jahn-teller and related effects. Int Rev Phys Chem 17:435
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 87–146
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 83–124
26. Klessinger M, Michl J (1995) Excited states and photochemistry of organic molecules. VCH Publishers, Inc., New York
27. Michl J, Bonaĉić Koutecký V (1990) Electronic aspects of organic photochemistry. Wiley Inter-science, New York
28. +2 protonated shiff base: an ab initio minimal model for retinal photoisomerization. J Am Chem Soc 119:6891
29. Kobayashi T, Saito T, Ohtani H (2001) Real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization. Nature 414:531
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 97:9379
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 105:9857
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 127:179
33. Toniolo A, Olsen S, Manohar L, Martinez TJ (2004) Conical intersection dynamics in solution: the chromophore of green fluorescent protein. Faraday Discuss 127:149
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 126:5452
35. Worth GA, Cederbaum LS (2001) Mediation of ultrafast transfer in biological systems by conical intersections. Chem Phys Lett 338:219
36. Atchity GJ, Xantheas SS, Ruedenberg K (1991) Potential energy surfaces near intersections. J Chem Phys 95:1862
37. Köppel H, Domcke W, Cederbaum LS (1984) Multimode molecular dynamics beyond the born-oppenheimer approximation. Adv Chem Phys 57:59
38. Domcke W, Stock G (1997) Theory of ultrafast nonadiabatic excited-state processes and their spectroscopic detection in real time. Adv Chem Phys 100:1–170
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 114:2601
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.
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 65–169
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 189–275
43. Roos BO, Taylor PR (1980) A complete active space SCF method (CASSCF) using a density-matrix formulated super-CI approach. Chem Phys 48:157
44. Roos BO (1987) The complete active space self consistent field method and its applications in electronic structure calculations. Adv Chem Phys 69:399
45. Shepard R (1987) Geometrical energy derivative evaluation with MRCI wave functions. Int J Quantum Chem 31:33
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 345
47. ∗ valence-and n−(3s, 3 p) rydberg states of formaldehyde. Mol Phys 100:1647
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.
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 3:664
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 120:7322
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 120:7330
52. Werner H-J, Knowles PJ (1988) An efficient internally contracted multiconfiguration reference CI method. J Chem Phys 89:5803
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 programs
54. Andersson K, Malmqvist PA, Roos BO, Sadlej AJ, Wolinski K (1990) Second-order perturbation-theory with a CASSCF reference function. J Phys Chem 94:5483
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 96:1218
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 28:222
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: Pri-gogine I Rice SA (eds) New methods in computational quantum mechanics, Vol. 93 of Advances in Chemical Physics, Wiley, New York, p 219
58. Nakano H (1993) Quasidegenerate perturbation theory with multiconfigurational self-consistent-field reference functions. J Chem Phys 99:7983
59. Finley J, Malmqvist PA, Roos BO, Serrano-Andrès L (1998) The multi-state CASPT2 method. Chem Phys Lett 288:299
60. Serrano-Andrès L, Merchán M, Lindh R (2005) Computation of conical intersections by using perturbation techniques. J Chem Phys 122:104107
61. Hirao K (1992) Multireference möller-plesset method. Chem Phys Lett 190:374
62. + with correlated wavefunctions. Phys Chem Chem Phys 1:967
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 14:1347
64. Nakano H (1993) Quasidegenerate perturbation theory with multiconfigurational self-consistent-field reference functions. J Chem Phys 99:7983–7992
65. Nakano H (1993) MCSCF reference quasidegenerate perturbation theory with EpsteinNesbet partitioning. Chem Phys Lett 207:372–378
66. Dreuw A, Head-Gordon M (2005) Single-reference ab initio methods for the calculation of excited states of large molecules. Chem Rev 105:4009–4037
67. Head-Gordon M, Oumi M, Maurice D (1999) Quasidegenerate second-order perturbation corrections to single-excitation configuration interaction. Mol Phys 96:593
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 448:132–137
69. 2 O. J Chem Phys 93:3345
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 98:7029
71. Krylov AI (2001) Size-consistent wave functions for bond-breaking: the equation-of-motion spin-flip model. Chem Phys Lett 338:375
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 39:83–91
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 68:2053
74. Christiansen O, Koch H, Jorgensen P (1995) The second-order approximate coupled cluster singles and doubles model CC2. Chem Phys Lett 243:409–418
75. Hättig C, Weigend F (2000) CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. J Chem Phys 113:5154
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 162:165–169
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 1–86
78. Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52:997
79. Levine BG, Ko C, Quenneville J, Martinez TJ (2006) Conical intersections and double excitations in time-dependent density functional theory. Mol Phys 104:1039
80. Grimme S, Waletzke M (1999) A combination of KohnSham density functional theory and multireference configuration interaction methods. J Chem Phys 111:5645–5655
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 171:675
82. Callis PR (1983) Electronic states and luminescence of nucleic acid systems. Ann Rev Phys Chem 34:329
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 122:9348
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 123:10370
85. Cohen B, Hare P, Kohler B (2003) Ultrafast excited-state dynamics of adenine and monomethy-lated adenines in solution: implications for the nonradiative decay mechanism. J Am Chem Soc 125:13594
86. Cohen B, Crespo-Hernandez CE, Kohler B (2004) Strickler-berg analysis of excited singlet state dynamis in DNA and RNA nucleosides. Faraday Discuss 127:137
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 348:255
88. Gustavsson T, Sharonov A, Markovitsi D (2002) Thymine, thymidine and thymidine 5’-monophosphate studied by femtosecond fluorescence upconversion spectroscopy. Chem Phys Lett 351:195
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 356:49
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 106:11367
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 380:173–180
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 128:607–619
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 110:12843–12847
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 429:551–557
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 147:538
96. Nir E, Kleinermanns K, Grace L, de Vries MS (2001) On the photochemistry of purine nucleobases. J Phys Chem A 105:5106
97. Nir E, Müller M, Grace LI, de Vries MS (2002) REMPI spectroscopy of cytosine Chem Phys Lett 355:59
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 5:4780
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 270:205
100. Lührs DC, Viallon J, Fischer I (2001) Excited state spectroscopy and dynamics of isolated adenine and 9-methyladenine. Phys Chem Chem Phys 3:1827
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 107:5145
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 108:943
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 124:12958
104. Kang H, Jung B, Kim SK (2003) Mechanism for ultrafast internal conversion of adenine, J Chem Phys 118:6717
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 113:10051
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 126:2262
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 6:2796
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: 10196–10201
109. Nir E, Grace LI, Brauer B, de Vries MS (1999) REMPI spectroscopy of jet-cooled guanine. J Am Chem Soc 121:4896–4897
110. 2 O clusters. Phys Chem Chem Phys 7:3015–3020
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 7:3015–3020
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 122:074316
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 110:10921–10924
114. ∗ states in the photoinduced processes of adenine, adenine dimer, and adeninewater complexes. J Chem Phys 122:224320
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 127:1782–1786
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 104:435–440
117. Schwalb NK, Temps F (2007) Ultrafast electronic relaxation in guanosine is promoted by hydrogen bonding with cytidine. J Am Chem Soc 129:9272
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 102:20–23
119. Crespo-Hernandez CE, Cohen B, Kohler B (2005) Base stacking controls excited-state dynamics in A-T DNA. Nature 436:1141–1144
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: E7
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 101:3589
122. Shukla MK, Leszczynski J (2002) Phototautomerism in uracil: a quantum chemical investigation. J Phys Chem A 106:8642
123. Shukla MK, Mishra PC (1999) A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil. Chem Phys 240:319
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 111:5482–5491
125. Lorentzon J, Fülscher MP, Roos BO (1995) Theoretical study of the electronic spectrum of uracil and thymine. J Am Chem Soc 117:9265
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 111:8500–8508
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 96:6992
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 109:9384–9387
129. Neiss C, Saalfrank P, Parac M, Grimme S (2003) Quantum chemical calculation of excited states of flavin-related molecules. J Phys Chem A 107:140
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 20:357
131. Shukla MK, Leszczynski J (2004) TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach. J Comput Chem 25:768–778
132. Clark LB, Peschel GG, Tinoco I Jr (1965) Vapor spectra and heats of vaporization of some purine and pyrimidine bases. J Phys Chem 69:3615
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 109:8410–8418
134. Fülscher MP, Roos BO (1995) Theoretical study of the electronic spectrum of cytosine. J Am Chem Soc 117:2089
135. Clark LB, Tinoco I Jr (1965) Correlations in the ultraviolet spectra of the purine and pyrimidine bases. J Am Chem Soc 87:11
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 90:6163–6170
137. Platt JR (1949) Classification of spectra of cata-condensed hydrocarbons. J Chem Phys 17:484
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 127:6257–6265
139. Marian CM (2005) A new pathway for the rapid decay of electronically excited adenine. J Chem Phys 122:104314
140. ∗ electronic singlet state. J Am Chem Soc 125:8108
141. Blancafort L (2006) Excited-state potential energy surface for the photophysics of adenine. J Am Chem Soc 128:210–219
142. Clark LB (1990) Electronic spectrum of the adenine chromophore. J Phys Chem 94:2873–2879
143. Fülscher MP, Serrano-Andres L, Roos BO (1997) A theoretical study of the electronic spectra of adenine and guanine. J Am Chem Soc 119:6168
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 111:8708–8716
145. Chen H, Li SH (2006) Ab initio study on deactivation pathways of excited 9H-guanine. J Chem Phys 124:154315
146. Clark LB (1977) Electronic spectra of crystalline 9-ethylguanine and guanine hydrochloride. J Am Chem Soc 99:3934
147. Matsika S (2004) Radiationless decay of excited states of uracil through conical intersections. J Phys Chem A 108:7584
148. Zgierski MZ, Fujiwara T, Kofron WG, Lim EC (2007) Highly effective quanching of the ultrafast radiationless decay of photoexcited pyrimidine bases by covalent modification: photophysics of 5,6-trimethylenecytosine and 5,6-trimethyleneuracil. Phys Chem Chem Phys 9: 3206–3209
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 128:16312–16322
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: 26471–26476
151. ∗ state. J Phys Chem B 110:18641
152. Perun S, Sobolewski AL, Domcke W (2006) Conical intersections in thymine. J Phys Chem A 110:13238
153. ∗ state switch. J Am Chem Soc 124:6818
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 108:10609
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 123:081101
156. Blancafort L (2007) Energetics of cytosine singlet excited-state decay paths – A difficult case for CASSCF and CASPT2. Photochem Photobiol 83:603–610
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 111:2650–2661
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 20:369
159. ∗ states: a new paradigm for nonradiative decay in aromatic biomolecules. J Phys Chem Chem Phys 4:1093–1100
160. Perun S, Sobolewski AL, Domcke W (2005) Photostability of 9h-adenine: mechanisms of the radiationless deactivation of the lowest excited singlet states. Chem Phys 313:107–112
161. ∗ state in 9H-adenine: a quantum chemical ab initio study. Phys Chem Chem Phys 9:2075–2084
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 6:1276
163. Serrano-Andrés L, Merchán M, Borin AC (2006) A three-state model for the photophysics of adenine. Chem Eur J 12:6559–6571
164. Serrano-Andrés L, Merchán M, Borin AC (2006) Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry. Proc Natl Acad Sci USA 103:8691–8696
165. Chen H, Li SH (2005) Theoretical study toward understanding ultrafast internal conversion of excited 9H-adenine. J Phys Chem A 109:8443–8446
166. Zgierski MZ, Patchkovskii S, Lim EC (2007) Biradical radiationless decay channel in adenine and its derivatives. Can J Chem 85:124
167. Langer H, Doltsinis NL (2003) Selected photostabilisation of guanine by methylation. Phys Chem Chem Phys 5:4516–4518
168. Langer H, Doltsinis NL (2003) Excited state tautomerism of the DNA base guanine: a restricted open-shell kohn-sham study. J Chem Phys 118:5400–5407
169. Langer H, Doltsinis NL (2004) Nonradiative decay of photoexcited methylated guanine. Phys Chem Chem Phys 6:2742–2748
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 110:12360–12362
171. Marian CM (2007) The guanine tautomer puzzle: quantum chemical investigation of ground and excited states. J Phys Chem A 111:1545–1553
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 440:145–149
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 90:76–81
174. Rappaport HP (1988) The 6-thioguanine/5-methyl-2-pyrimidinone base pair. Nucl Acids Res 16(15):7253–7267
175. Rappaport HP (1989) Artificial DNA base pair analogues
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 29:6508–6514
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 45:2457–2461
178. Barrio JR, Sattsangi PD, Gruber GA, Dammann LG, Leonard NJ (1976) Species responsible for 3,n4-ethenocytidine. J Am Chem Soc 98(23):7408–7414
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 107:8923–8931
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 83:611–624
181. Thompson KC, Miyake N (2005) Properties of a new fluorescent cytosine analogue, pyrrolocytosine. J Phys Chem B 109:6012–6019
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: 9145–9155
183. Jean JM, Hall KB (2002) 2-aminopurine electronic structure and fluorescence properties in DNA. Biochem 41:13152–13161
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 83:5434–5438
185. Rachofsky EL, Osman R, Ross JBA (2001) Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. Biochem 40:946–956
186. Wang Q, Raytchev M, Fiebig T (2007) Ultrafast energy delocalization and electron transfer dynamics in 2-aminopurine-containing trinucleotides. Photochem Photobiol 83:637–641
187. Seefeld KA, Plützer C, Löwenich D, Haber 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 7:3021–3026
188. Kodali G, Kistler KA, Matsika S, Stanley RJ (2007) 2-aminopurine excited state electronic structure measured by stark spectroscopy. J Phys Chem B 111:10615–10625
189. Häupl T, Windolph C, Jochum T, Brede O, Hermann R (1997) Picosecond fluorescence of nucleic acid bases. Chem Phys Lett 280:520–524
190. Rachofsky EL, Ross JBA, Krauss M, Osman R (1998) Spectroscopy of 2-aminopurine: an MCSCF study. Acta Phys Polon A 94:735–748
191. Rachofsky EL, Ross JBA, Krauss M, Osman R (2001) CASSCF investigation of electronic excited states of 2-aminopurine. J Phys Chem A 105:190–197
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: 2564–2577
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 102:526
194. Perun S, Sobolewski AL, Domke W (2006) Ab initio studies of the photophysics of 2-aminopurine. Mol Phys 104:1113–1121
195. Mamos P, Aerschot AAV, Weyns NJ, Hardewijn PA (1992) Straightforward c-8 alkylation of adenosine analogues with tetraalkyltin reagents. Tet Lett 33:2413–2416
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 ribonu-cleotide reductase, Tetrahedron 59:7315–7322
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 33:1031–1039
198. Kenfack CA, Burger A, Mély Y (2006) Excited-state propertes and transitions of fluorescent 8-vinyl adenosine in DNA. J Phys Chem A 110:26327–26336
199. Spencer RD, Weber G, Tolman GL, Barrio JR, Leonard NJ (1974) Species responsible for the fluorescence of 1:N6-ethenoadenosine. Eur J Biochem 45:425–429
200. Bersuker IB (1984) The jahn-teller effect and vibronic interactions in modern chemistry. Plenum Press, New York
201. +4. Chem Phys Lett 76:259
202. Keating SP, Mead CA (1985) Conical intersections in a system of four identical nuclei. J Chem Phys 82:5102
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 119:11562
204. Han S, Yarkony DR (2003) Nonadiabatic processes involving three electronic states. I. Branch cuts and linked pairs of conical intersections. J Chem Phys 119:5058
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 127:4560
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 110:618–630
207. Matsika S, Yarkony DR (2002) Accidental conical intersections of three states of the same symmetry. I. Location and relevance. J Chem Phys 117:6907
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 125:10672
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 125:12428
210. Matsika S (2005) Three-state conical intersections in nucleic acid bases. J Phys Chem A 109:7538
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 8:1385–1393
212. Zhang RB, Zeegers-Huyskens T, Ceulemans A, Nguyen MT (2005) Interaction of triplet uracil and thymine with water. Chem Phys 316:35
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 126:14320
214. ∗ states of uracil in water. Phys Chem Chem Phys 9:4907–4912
215. Shukla MK, Leszczynski J (2002) Interaction of water molecules with cytosine tautomers: An excited-state quantum chemical investigation. J Phys Chem A 106:11338
216. Blancafort L, Migani A (2007) Water effect on the excited-state decay paths of singlet excited cytosine. J Photochem Photobiol A 190:283–289
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 56:1355
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 21:826
219. Mennucci B, Toniolo A, Tomasi J (2001) Theoretical study of the photophysics of adenine in solution: tautomerism, deactivation mechanisms, and comparison with the 2-aminopurine fluorescent isomer. J Phys Chem A 105:4749
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 105:7126
221. ∗ excited-state geometry of guanine: a theoretical study. J Phys Chem B 109:17333–17339
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 109:7775–7780
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 129:2901–2909
224. Yoshikawa A, Matsika S (2008) Excited electronic states and photophysics of uracil-water complexes. Chem Phys 347:393–404
225. Mourik TV, Price SL, Clary DC (1999) Ab initio calculations on uracil-water. J Phys Chem A 103:1611
226. Crespo-Hernandez CE, Cohen B, Kohler B (2006) Molecular spectroscopy: complexity of excited-state dynamics in DNA-Reply. Nature 441:E8
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 109:16109–16118
228. Bittner ER (2007) Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices. J Photochem Photobiol A 190:328–334
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 104:4794–4797
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 128:11894–11905
231. Nir E, Kleinermanns K, de Vries MS (2000) On the photochemistry of purine nucleobases. Nature 408:949
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 20:309
233. Plützer C, Hünig I, Kleinermanns K, Nir E, de Vries MS (2003) On the photochemistry of purine nucleobases. Chem Phys Chem 4:838–842
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 306:1765
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 102:17903–17906
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 294:2763
237. Sobolewski AL, Domcke W (2004) Ab initio studies on the photophysics of the guanine-cytosine base pair. Phys Chem Chem Phys 6:2763
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: 9031–9038
239. Sobolewski AL, Domcke W (2007) Computational studies of the photophysics of hydrogen-bonded molecular systems. J Phys Chem A 111:11725–11735
240. Shukla MK, Leszczynski J (2002) A theoretical investigation of excited-state properties of the adenine–uracil base pair. J Phys Chem A 106:1011–1018
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 129:6812–6819
242. Markwick PRL, Doltsinis NL (2007) Ultrafast repair of irradiated DNA: nonadiabatic ab initio simulations of the guanine-cytosine photocycle. J Chem Phys 126:175102
243. Markwick PRL, Doltsinis NL, Schlitter J (2007) Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics. J Chem Phys 126:045104
244. Jean JM, Hall KB (2001) 2-aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc Natl Acad Sci USA 98:37–41
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 125:231102
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 104:9931–9936
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 110:7129–7138
248. Tinoco I (1960) Hypochromism in polynucleotides. J Am Chem Soc 82:4785–4790
249. Frenkel J (1931) On the transformation of light into heat in solids. II. Phys Rev 37:1276–1294
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 275:75–92
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: 13512–13522
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 6:1387–1392
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 9:5143–5148
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 111:9644–9650
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 129:14574–14575
256. Bittner ER (2006) Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA. J Chem Phys 125:094909
257. Czader A, Bittner ER (2008) Calculations of the exciton coupling elements between DNA bases using the transition density cube method. J Chem Phys 128:035101
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 315:625–629
259. Durbeej B, Eriksson LA (2002) Reaction mechanism of thymine dimer formation in DNA induced by UV light. Photochem Photobiol A 152:95–101
260. Zhang RB, Eriksson LA (2006) A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA. J Phys Chem B 110:7556–7562
261. Boggio-Pasqua M, Groenhof G, Schäfer LV, Brubmüller H, Robb MA (2007) Ultrafast deactivation channel for thymine dimerization. J Am Chem Soc 129:10996–10997
262. Blancafort L, Migani A (2007) Modeling thymine photodimerizations in DNA: mechanism and correlation diagrams. J Am Chem Soc 129:14540–14541
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 125:211101
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 106:4251