Four bases score a run: Ab initio calculations quantify a cooperative effect of H-bonding and π-stacking on the ionization energy of adenine in the AATT tetramer

Journal of Physical Chemistry Letters

Volumn 3, Issue 18, 2012, Pages 2726-2732

  Bravaya, Ksenia B ^a   Epifanovsky, Evgeny ^a,b,c   Krylov, Anna I ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

General Theory; Molecular Structure; Quantum Chemistry

Indexed keywords

AB INITIO CALCULATIONS; ADENINE-THYMINE; BENCHMARK CALCULATIONS; COOPERATIVE EFFECTS; DELOCALIZATIONS; DOUBLE SUBSTITUTION; EQUATION OF MOTION COUPLED CLUSTERS; FUNCTIONALS; GENERAL THEORY; H-BONDING; IONIZED STATE; POINT CHARGE; STACKING INTERACTION; TETRAMERS; VERTICAL IONIZATION ENERGY; X-RAY STRUCTURE;

MOLECULAR MODELING; MOLECULAR STRUCTURE; MONOMERS; OLIGOMERS; QUANTUM CHEMISTRY;

IONIZATION;

EID: 84866630893     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz3011139     Document Type: Article

References (68)

1. Oka, S.; Ohno, M.; Tsuchimoto, D.; Sakumi, K.; Furuichi, M.; Nakabeppu, Y. Two Distinct Pathways of Cell Death Triggered by Oxidative Damage to Nuclear and Mitochondrial DNAs EMBO J. 2008, 27, 421-432
2. Cadet, J.; Douiki, T.; Ravanat, J.-L. Oxidatively Generated Damage to the Guanine Moiety of DNA: Mechanistic Aspects and Formations in Cells Acc. Chem. Res. 2008, 41, 1075-1083
3. Núñez, M.; Hall, D.; Barton, J. Long-Range Oxidative Damage to DNA: Effects of Distance and Sequence Chem. Biol. 1999, 6, 85-97
4. Seeman, N. C. Nanomaterials Based on DNA Annu. Rev. Biochem. 2010, 79, 65-87
5. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patters Nature 2006, 440, 297-302
6. Eley, D. D.; Spivey, D. I. Semiconductivity of Organic Substances. Part 9. Nucleic Acid in the Dry State Trans. Faraday Soc. 1962, 58, 411-415
7. Taniguchi, M.; Kawai, T. DNA Electronics Physica E 2006, 33, 1-12
8. Genereux, J. C.; Barton, J. K. DNA Charges Ahead Nat. Chem. 2009, 1, 106-107
9. Bravaya, K.; Kostko, O.; Dolgikh, S.; Landau, A.; Ahmed, M.; Krylov, A. Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra J. Phys. Chem. A 2010, 114, 12305-12317
10. Trofimov, A.; Schirmer, J.; Kobychev, V.; Potts, A.; Holland, D.; Karlsson, L. Photoelectron Spectra of the Nucleobases Cytosine, Thymine and Adenine J. Phys. B 2006, 39, 305-329
11. Satzger, H.; Townsend, D.; Stolow, A. Reassignment of the Low Lying Cationic States in Gas Phase Adenine and 9-methyl Adenine Chem. Phys. Lett. 2006, 430, 144-148
12. Zaytseva, I. L.; Trofimov, A. B.; Schirmer, J.; Plekan, O.; Feyer, V.; Richter, R.; Coreno, M.; Prince, K. C. Theoretical and Experimental Study of Valence-Shell Ionization Spectra of Guanine J. Phys. Chem. A 2009, 113, 15142-15149
13. Dolgounitcheva, O.; Zakrzewski, V.; Ortiz, J. Ionization Energies and Dyson Orbitals of Thymine and Other Methylated Uracils J. Phys. Chem. A 2002, 106, 8411-8416
14. Dolgounitcheva, O.; Zakrzewski, V.; Ortiz, J. Electron Propagator Calculations on Uracil and Adenine Ionization Energies Int. J. Quantum Chem. 2000, 80, 831-835
15. Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V. Electron Propagator Theory of Guanine and its Cations: Tautomerism and Photoelectron Spectra J. Am. Chem. Soc. 2000, 122, 12304-12309
16. Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V. Ionization Energies and Dyson Orbitals of Cytosine and 1-Methylcytosine J. Phys. Chem. A 2003, 107, 822-828
17. Roca-Sanjuán, D.; Rubio, M.; Merchán, M.; Serrano-Andrés, L. Ab Initio Determination of the Ionization Potentials of DNA and RNA Nucleobases J. Chem. Phys. 2006, 125, 084302
18. Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V. Vertical Ionization Energies of Adenine and 9-Methyl Adenine J. Phys. Chem. A 2009, 113, 14630-14635
19. Zhang, L.; Pan, Y.; Qi, F. Theoretical Studies on Photoionization of Guanine Tautomers and Interconversion of Guanine Radicals J. Theor. Comput. Chem. 2009, 8, 1103-1115
20. Golan, A.; Bravaya, K.; Kudirka, R.; Leone, S.; Krylov, A.; Ahmed, M. Ionization of Dimethyluracil Dimers Leads to Facile Proton Transfer in the Absence of H-Bonds Nat. Chem. 2012, 4, 323-329
21. Bravaya, K.; Kostko, O.; Ahmed, M.; Krylov, A. The Effect of π-Stacking, H-Bonding, And Electrostatic Interactions on the Ionization Energies of Nucleic Acid Bases: Adenine-Adenine, Thymine-Thymine and Adenine-Thymine Dimers Phys. Chem. Chem. Phys. 2010, 12, 2292-2307
22. Kostko, O.; Bravaya, K.; Krylov, A.; Ahmed, M. Ionization of Cytosine Monomer and Dimer Studied by VUV Photoionization and Electronic Structure Calculations Phys. Chem. Chem. Phys. 2010, 12, 2860-2872
23. Khistyaev, K.; Bravaya, K.; Kamarchik, E.; Ahmed, O. K. M.; Krylov, A. The Effect of Microhydration on Ionization Energies of Thymine Faraday Discuss. 2011, 150, 313-330
24. Zadorozhnaya, A.; Krylov, A. Zooming into π-Stacked Manifolds of Nucleobases: Ionized States of Dimethylated Uracil Dimers J. Phys. Chem. A 2010, 114, 2001-2009
25. Golubeva, A.; Krylov, A. The Effect of π-stacking and H-bonding on Ionization Energies of a Nucleobase: Uracil Dimer Cation Phys. Chem. Chem. Phys. 2009, 11, 1303-1311
26. Zadorozhnaya, A.; Krylov, A. Ionization-Induced Structural Changes in Uracil Dimers and Their Spectroscopic Signatures J. Chem. Theory Comput. 2010, 6, 705-717
27. Mantz, Y.; Gervasio, F.; Laino, T.; Parrinello, M. Charge Localization in Stacked Radical Cation DNA Base Pairs And the Benzene Dimer Studied by Self-Interaction Corrected Density-Functional Theory J. Phys. Chem. A 2007, 111, 105-112
28. Paukku, Y.; Hill, G. Theoretical Determination of One-Electron Redox Potentials for DNA Bases, Base Pairs, and Stacks J. Phys. Chem. A 2011, 115, 4804-4810
29. Kim, N. S.; LeBreton, P. R. UV Photoelectron and Ab initio Quantum Mechanical Evaluation of Nucleotide Ionization Potentials in Water-Counterion Environments: π Polarization Effects on DNA Alkylation by Carcinogenic Methylating Agents J. Am. Chem. Soc. 1996, 118, 3694-3707
30. Crespo-Hernández, C.; Close, D.; Gorb, L.; Leszczynski, J. Determination of Redox Potentials for the Watson-Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues J. Phys. Chem. B 2007, 111, 5386-5395
31. Close, D. M.; Ohman, K. T. Ionization Energies of the Nucleotides J. Phys. Chem. A 2008, 112, 11207-11212
32. Slavíček, P.; Winter, B.; Faubel, M.; Bradforth, S.; Jungwirth, P. Ionization Energies of Aqueous Nucleic Acids: Photoelectron Spectroscopy of Pyrimidine Nucleosides and Ab initio Calculations J. Am. Chem. Soc. 2009, 131, 6460-6467
33. Pluhařová, E.; Jungwirth, P.; Bradforth, S. E.; Slaviček, P. Ionization of Purine Tautomers in Nucleobases, Nucleosides, and Nucleotides: From the Gas Phase to the Aqueous Environment J. Phys. Chem. B 2011, 115, 1294
34. Kumar, A.; Sevilla, M. Density Functional Theory Studies of the Extent of Hole Delocalization in One-Electron Oxidized Adenine and Guanine Base Stacks J. Phys. Chem. B 2011, 115, 4990-5000
35. Bally, T.; Sastry, G. Incorrect Dissociation Behavior of Radical Ions in Density Functional Calculations J. Phys. Chem. A 1997, 101, 7923-7925
36. Polo, V.; Kraka, E.; Cremer, D. Electron Correlation and the Self-Interaction Error of Density Functional Theory Mol. Phys. 2002, 100, 1771-1790
37. Zhang, Y.; Yang, W. A Challenge for Density Functionals: Self-Interaction Error Increases for Systems with a Noninteger Number of Electrons J. Chem. Phys. 1998, 109, 2604-2608
38. Lundber, M.; Siegbahn, P. Quantifying the Effects of the Self-Interaction Error in DFT: When do the Delocalized States Appear? J. Chem. Phys. 2005, 122, 224103
39. Dreuw, A.; Head-Gordon, M. Single-Reference Ab Initio Methods for the Calculation of Excited States of Large Molecules Chem. Rev. 2005, 105, 4009-4037
40. Dreuw, A.; Head-Gordon, M. Comment on: 'Failure of Time-Dependent Density Functional Methods for Excitations in Spatially Separated Systems' by Wolfgang Hieringer and Andreas Gorling Chem. Phys. Lett. 2006, 426, 231-233
41. Slipchenko, L.; Krylov, A. Efficient Strategies for Accurate Calculations of Electronic Excitation and Ionization Energies: Theory and Application to the Dehydro-meta-xylylene Anion J. Phys. Chem. A 2006, 110, 291-298
42. Vanovschi, V.; Krylov, A.; Wenthold, P. Structure, Vibrational Frequencies, Ionization Energies, and Photoelectron Spectrum of the Para-benzyne Radical Anion Theor. Chim. Acta 2008, 120, 45-58
43. Félix, M.; Voityuk, A. DFT Performance for the Hole Transfer Parameters in DNA π-stacks Int. J. Quantum Chem. 2011, 111, 191201
44. Iikura, H.; Tsuneda, T.; Yanai, T.; Hirao, K. A Long-Range Correction Scheme for Generalized-Gradient-Approximation Exchange Functionals J. Chem. Phys. 2001, 115, 3540
45. Rohrdanz, M.; Martins, K.; Herbert, J. A Long-Range-Corrected Density Functional That Performs Well for Both Ground-State Properties and Time-Dependent Density Functional Theory Excitation Energies, Including Charge-Transfer Excited States J. Chem. Phys. 2009, 130, 054112
46. Baer, R.; Livshits, E.; Salzner, U. Tuned Range-Separated Hybrids in Density Functional Theory Annu. Rev. Phys. Chem. 2010, 61, 85-109
47. Chai, J.; Head-Gordon, M. Systematic Optimization of Long-Range Corrected Hybrid Density Functionals J. Chem. Phys. 2008, 128, 084106
48. Baer, R.; Neuhauser, D. Density Functional Theory With Correct Long-Range Asymptotic Behavior Phys. Rev. Lett. 2005, 94, 043002
49. Conwell, E.; Rakhmanova, S. Polarons in DNA Proc. Nat. Acad. Sci. U.S.A. 2000, 97, 4556
50. Gutiérrez, R.; Mandal, S.; Cuniberti, G. Dissipative Effects in the Electronic Transport through DNA Molecular Wires Phys. Rev. B 2005, 71, 235116
51. Roche, S. Sequence Dependent DNA-Mediated Conduction Phys. Rev. Lett. 2003, 91, 108101
52. Valeev, E.; Coropceanu, V.; da Silva Filho, D.; Salman, S.; Brédas, J.-L. Effect of Electronic Polarization on Chrage-Transport Parameters in Molecular Organic Semiconductors J. Am. Chem. Soc. 2006, 128, 9882-9886
53. Zhang, J.; Valeev, E. Hybrid One-Electron/Many-Electron Methods for Ionized States of Molecular Clusters Phys. Chem. Chem. Phys. 2012, 14, 7863-7871
54. Pal, S.; Rittby, M.; Bartlett, R.; Sinha, D.; Mukherjee, D. Multireference Coupled-Cluster Methods Using an Incomplete Model Space - Application to Ionization-Potentials and Excitation-Energies of Formaldehyde Chem. Phys. Lett. 1987, 137, 273-278
55. Stanton, J.; Gauss, J. Analytic Energy Derivatives for Ionized States Described by the Equation-of-Motion Coupled Cluster Method J. Chem. Phys. 1994, 101, 8938-8944
56. Kamiya, M.; Hirata, S. Higher-Order Equation-of-Motion Coupled-Cluster Methods for Ionization Processes J. Chem. Phys. 2006, 125, 074111-074125
57. Pieniazek, P.; Arnstein, S.; Bradforth, S.; Krylov, A.; Sherrill, C. Benchmark Full Configuration Interaction and EOM-IP-CCSD Results for Prototypical Charge Transfer Systems: Noncovalent Ionized Dimers J. Chem. Phys. 2007, 127, 164110
58. Pieniazek, P.; Bradforth, S.; Krylov, A. Charge Localization and Jahn-Teller Distortions in the Benzene Dimer Cation J. Chem. Phys. 2008, 129, 074104
59. Pieniazek, P.; Krylov, A.; Bradforth, S. Electronic Structure of the Benzene Dimer Cation J. Chem. Phys. 2007, 127, 044317
60. Pieniazek, P.; VandeVondele, J.; Jungwirth, P.; Krylov, A.; Bradforth, S. Electronic Structure of the Water Dimer Cation J. Phys. Chem. A 2008, 112, 6159-6170
61. Pieniazek, P.; Sundstrom, E.; Bradforth, S.; Krylov, A. The Degree of Initial Hole Localization/Delocalization in Ionized Water Clusters J. Phys. Chem. A 2009, 113, 4423-4429
62. Kamarchik, E.; Kostko, O.; Bowman, J.; Ahmed, M.; Krylov, A. Spectroscopic Signatures of Proton Transfer Dynamics in the Water Dimer Cation J. Chem. Phys. 2010, 132, 194311
63. Ghosh, D.; Isayev, O.; Slipchenko, L.; Krylov, A. The Effect of Solvation on Vertical Ionization Energy of Thymine: From Microhydration to Bulk J. Phys. Chem. A 2011, 115, 6028-6038
64. Ghosh, D.; Roy, A.; Seidel, R.; Winter, B.; Bradforth, S.; Krylov, A. A First-Principle Protocol for Calculating Ionization Energies and Redox Potentials of Solvated Molecules and Ions: Theory and Application to Aqueous Phenol and Phenolate J. Phys. Chem. B 2012, 116, 72697280
65. Golubeva, A.; Pieniazek, P.; Krylov, A. A New Electronic Structure Method for Doublet States: Configuration Interaction in the Space of Ionized 1h and 2h1p Determinants J. Chem. Phys. 2009, 130, 124113
66. Narayana, N.; Weiss, M. Crystallographic Analysis of a Sex-Specific Enhancer Element: Sequence-Dependent DNA Structure, Hydration, and Dynamics J. Mol. Biol. 2009, 385, 469-490
67. Chai, J.; Head-Gordon, M. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Interactions Phys. Chem. Chem. Phys. 2008, 10, 6615-6620
68. Truhlar, D. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals Theor. Chim. Acta 2008, 120, 215241