Proton transfer in nucleobases is mediated by water

Journal of Physical Chemistry A

Volumn 117, Issue 31, 2013, Pages 6789-6797

  Khistyaev, Kirill ^a   Golan, Amir ^b   Bravaya, Ksenia B ^a   Orms, Natalie ^a   Krylov, Anna I ^a   Ahmed, Musahid ^b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADIABATIC PASSAGES; ELECTRONIC STRUCTURE CALCULATIONS; ENERGY CONSIDERATIONS; GROUND ELECTRONIC STATE; HYDROXYL RADICALS; POTENTIAL ENERGY PROFILES; REACTION COORDINATES; VACUUM ULTRAVIOLET SYNCHROTRON RADIATION;

ELECTRONIC STRUCTURE; IONIZATION OF LIQUIDS; MASS SPECTROMETRY; MOLECULAR ORBITALS; MOLECULES; POTENTIAL ENERGY;

PROTON TRANSFER;

EID: 84881470910     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp406029p     Document Type: Article

References (45)

1. Rosspeintner, A.; Lang, B.; Vauthey, E. Ultrafast Photochemistry in Liquids Annu. Rev. Phys. Chem. 2013, 64, 247
2. Tolbert, L. M.; Solntsev, K. M. Excited-State Proton Transfer: From Constrained Systems to "Super" Photoacids to Superfast Proton Transfer Acc. Chem. Res. 2002, 35, 19-27
3. Formosinho, S. J.; Arnaut, L. G. Excited-State Proton Transfer Reactions II. Intramolecular Reactions J. Photochem. Photobiol. 1992, 75, 21-48
4. van Thor, J. J. Photoreactions and Dynamics of the Green Fluorecent Protein Chem. Soc. Rev. 2009, 38, 2935-2950
5. Carroll, E. C.; Song, S.-H.; Kumauchi, M.; vanStokkum, I. H. M.; Jailaubekov, A.; Hoff, W. D.; Larsen, D. S. Subpicosecond Excited-State Proton Transfer Preceding Isomerization During the Photorecovery of Photoactive Yellow Protein J. Phys. Chem. Lett. 2010, 1, 2793-2799
6. Schultz, T.; Samoylova, E.; Radloff, W.; Hertel, I. V.; Sobolewski, A. L.; Domcke, W. Efficient Deactivation of a Model Base Pair via Excited-State Hydrogen Transfer Science 2004, 306, 1765-1768
7. Ghosh, A. K.; Schuster, G. B. Role of the Guanine N1 Imino Proton in the Migration and Reaction of Radical Cations in DNA Oligomers J. Am. Chem. Soc. 2006, 128, 4172-4173
8. Charkaborty, T., Ed. Charge Migration in DNA; Springer: Berlin Heidelberg, Germany, 2007.
9. Bravaya, K. B.; Kostko, O.; Ahmed, M.; Krylov, A. I. 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
10. Golan, A.; Bravaya, K. B.; Kudirka, R.; Leone, S. R.; Krylov, A. I.; Ahmed, M. Ionization of Dimethyluracil Dimers Leads to Facile Proton Transfer in the Absence of H-bonds Nat, Chem. 2012, 4, 323-329
11. Barnet, R. N.; Joseph, J.; Landman, U.; Schuster, G. B. Oxidative Thymine Mutation in DNA: Water-Wire-Mediated Proton-Coupled Electron Transfer J. Am. Chem. Soc. 2013, 135, 3904-3914
12. Ball, P. The Importance of Water. In Astrochemistry and Astrobiology: Physical Chemistry in Action; Smith, I.W. M.; Cockell, C. S.; Leach, S., Eds.; Springer: Berlin, Heidelberg, Germany, 2013; pp 169-210.
13. Voth, G. A. Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems Acc. Chem. Res. 2006, 39, 143-150
14. Agmon, N. The Grotthuss Mechanism Chem. Phys. Lett. 1995, 244, 456-462
15. Chandler, D.; Dellago, C.; Geissler, P. Wired-up Water Nat. Chem. 2012, 4, 245-247
16. Relph, R. A.; Guasco, T. L.; Elliott, B. M.; Kamrath, M. Z.; McCoy, A. B.; Steele, R. P.; Schofield, D. P.; Jordan, K. D.; Viggiano, A. A.; Ferguson, E. E.; Johnson, M. A. How the Shape of an H-bonded Network Controls Proton-Coupled Water Activation in HONO Formation Science 2010, 327, 308-312
17. Mohammed, O. F.; Pines, D.; Dreyer, J.; Pines, E.; Nibbering, E. T. J. Sequential Proton Transfer Through Water Bridges in Acid-Base Reactions Science 2005, 310, 83-86
18. Kwon, O.-H.; Lee, Y.-S.; Yoo, B. K.; Jang, D.-J. Excited-State Triple Proton Transfer of 7-hydroxyquinoline along a Hydrogen-Bonded Alcohol Chain: Vibrationally Assisted Proton Tunneling Angew. Chem., Int. Ed. Engl. 2006, 45, 415-419
19. Lim, H.; Jeong, H.; Park, S.-Y.; Lee, J. Y.; Jang, D.-J. Excited-State Proton-Relay Dynamics of 7-Hydroxyquinoline Controlled by Solvent Reorganization in Room Temperature Ionic Liquids Phys. Chem. Chem. Phys. 2012, 14, 218-224
20. Manca, C.; Tanner, C.; Leutwyler, S. Excited State Hydrogen Atom Transfer in Ammonia-Wire and Water-Wire Clusters Int. Rev. Phys. Chem. 2005, 24, 457-488
21. Sukhodub, L. F. Interactions and Hydration of Nucleic Acid Bases in a Vacuum. Experimental Study Chem. Rev. 1987, 87, 589-606
22. Kim, S. K.; Lee, W.; Herschbach, D. R. Cluster Beam Chemistry: Hydration of Nucleic Acid Bases; Ionization Potentials of Hydrated Adenine and Thymine J. Phys. Chem. 1996, 100, 7933-7937
23. Kim, N. J.; Kim, H. M.; Kim, S. K. Ionization-Induced Proton Transfer in Thymine-Ammonia van der Waals Clusters Int. J. Mass. Spectrom. 2007, 261, 32
24. + (n=3-11) Chem. Sci. 2011, 2, 868-876
25. Zadorozhnaya, A. A.; Krylov, A. I. Zooming into Pi-Stacked Manifolds of Nucleobases: Ionized States of Dimethylated Uracil Dimers J. Phys. Chem. A 2010, 114, 2001-2009
26. Belau, L.; Wilson, K. R.; Leone, S. R.; Ahmed, M. Vacuum-Ultravioled Photoionization Studies of the Microhydration of DNA Bases (Guanine, Cytosine, Adenine, and Thymine) J. Phys. Chem. A 2007, 111, 7562-7568
27. Golan, A.; Ahmed, M. Molecular Beam Mass Spectrometry with Tunable Vacuum Ultraviolet (VUV) Synchrotron Radiation J. Vis. Exp. 2012, 68, e50164
28. Kostko, O.; Bravaya, K. B.; Krylov, A. I.; Ahmed, M. Ionization of Cytosine Monomer and Dimer Studied by VUV Photoionization and Electronic Structure Calculations Phys. Chem. Chem. Phys. 2010, 12, 2860-2872
29. Khistyaev, K.; Bravaya, K. B.; Kamarchik, E.; Kostko, O.; Ahmed, M.; Krylov, A. I. The Effect of Microhydration on Ionization Energies of Thymine Faraday Discuss. 2011, 150, 313-330
30. Bravaya, K. B.; Kostko, O.; Dolgikh, S.; Landau, A.; Ahmed, M.; Krylov, A. I. 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
31. Golubeva, A. A.; Krylov, A. I. 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
32. Krylov, A. I.; Gill, P. M. W. Q-Chem: An Engine for Innovation WIREs Comput. Mol. Sci. 2013, 3, 317-326
33. Shao, Y.; Fusti-Molnar, L.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P. Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package Phys. Chem. Chem. Phys. 2006, 8, 3172-3191
34. Chai, J.-D.; Head-Gordon, M. Systematic Optimization of Long-Range Corrected Hybrid Density Functionals J. Chem. Phys. 2008, 128, 084106
35. Chai, J.-D.; Head-Gordon, M. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Interactions Phys. Chem. Chem. Phys. 2008, 10, 6615-6620
36. Krylov, A. I. Equation-of-Motion Coupled-Cluster Methods for Open-Shell and Electronically Excited Species: The Hitchhiker's Guide to Fock Space Annu. Rev. Phys. Chem. 2008, 59, 433-462
37. Pieniazek, P. A.; Arnstein, S. A.; Bradforth, S. E.; Krylov, A. I.; Sherrill, C. D. Benchmark Full Configuration Interaction and EOM-IP-CCSD Results for Prototypical Charge Transfer Systems: Noncovalent Ionized Dimers J. Chem. Phys. 2007, 127, 164110
38. Ghosh, D.; Isayev, O.; Slipchenko, L. V.; Krylov, A. I. The Effect of Solvation on Vertical Ionization Energy of Thymine: From Microhydration to Bulk J. Phys. Chem. A 2011, 115, 6028-6038
39. Pieniazek, P. A.; Sundstrom, E. J.; Bradforth, S. E.; Krylov, A. I. The Degree of Initial Hole Localization/Delocalization in Ionized Water Clusters J. Phys. Chem. A 2009, 113, 4423-4429
40. Springer, A.; Hagen, V.; Cherepanov, D. A.; Antonenko, Y. N.; Pohl, P. Protons Migrate along Interfacial Water without Significant Contributions from Jumps Between Ionizable Groups on the Membrane Surface Proc. Natl. Acad. Sci. 2011, 108, 14461-14466
41. Kwon, O.-H.; Mohammed, O. F. Water-Wire Catalysis in Photoinduced Acid-Base Reactions Phys. Chem. Chem. Phys. 2012, 14, 8974-8980
42. Matsuda, Y.; Yamada, A.; i.Hanaue, K.; Mikami, N.; Fujii, A. Catalytic Action of a Single Water Molecule in a Proton-Migration Reaction Angew. Chem., Int. Ed. Engl. 2010, 49, 4898-4901
43. Buszek, R. J.; Barker, J. R.; Francisco, J. S. Water Effect on the OH + HCl Reaction J. Phys. Chem. A 2012, 116, 4712-4719
44. Kofinger, J.; Hummer, G.; Dellago, C. Single-File Water in Nanopores Phys. Chem. Chem. Phys. 2011, 13, 15403-15417
45. Mishra, H.; Enami, S.; Nielsen, R. J.; Hoffmann, M. R.; Goddard, W. A.; Colussi, A. J. Anions Dramatically Enhance Proton Transfer through Aqueous Interfaces Proc. Natl. Acad. Sci. 2012, 109, 10228-10232