The hydrated Li+-adenine-thymine complex by IRMPD spectroscopy in the N-H/O-H stretching region

International Journal of Mass Spectrometry

Volumn 297, Issue 1-3, 2010, Pages 2-8

  Gillis, Elizabeth A L ^a   Fridgen, Travis D ^a  

^a MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

Author keywords

Adenine; Hydrated; IRMPD Spectroscopy; Lithium cation; Thymine

Indexed keywords

EID: 78049279272     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2010.04.005     Document Type: Article

References (79)

1. Saenger W. Principles of Nucleic Acid Structure 1984, Springer-Verlag, New York.
2. + binding to the DNA and RNA nucleobases. Bond energies and attachment sites from the dissociation of metal ion-bound heterodimers. J. Am. Chem. Soc. 1996, 118:11884-11892.
3. Dhar S.K. Metal ions in biological systems: studies of some biochemical and environmental problems. Advances in Experimental Medicine and Biology 1973, Plenum, New York.
4. Potaman V.N., Soyfer V.N. Divalent metal cations upon coordination to the N7 of purines differentially stabilize the PyPuPu DNA triplex due to unequal Hoogsteen-type hydrogen bond enhancement. J. Biomol. Struct. Dyn. 1994, 11:1035-1040.
5. McFail-Isom L., Sines C.C., Williams L.D. DNA structure: cations in charge?. Curr. Opin. Struct. Biol. 1999, 9:298-304.
6. Shui X., Sines C.C., McFail-Isom L., VanDerveer D., Williams L.D. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 1998, 37:16877-16887.
7. Blackburn G.M., Gait M.J. Nucleic Acids in Chemistry and Biology 1990, Oxford University Press, Oxford.
8. 2+ ions on the hydrogen bonds of the Watson-Crick base pairs. Biopolymer 1990, 29:757-769.
9. 2+). J. Phys. Chem. 1996, 100:7250-7255.
10. Franska M. Interactions of nucleobases with alkali earth metal cations. Eur. J. Mass Spectrom. 2007, 13:339-346.
11. +-uracil complexes by IRMPD spectroscopy in the N-H/O-H stretching region. J. Phys. Chem. A 2009, 113:824-832.
12. Guillaumont S., Tortajada J., Salpin J.-Y., Lamsabhi A.M. Experimental and computational study of the gas-phase interactions between lead(II) ions and two pyrimidic nucleobases: uracil and thymine. Int. J. Mass Spectrom. 2005, 243:279-293.
13. Hashemianzadeh S.M., Faraji S., Amin A.H., Ketabi S. Theoretical study of the interactions between isolated DNA bases and various groups IA and IIA metal ions by ab initio calculations. Monatsh. Chem./Chem. Monthly 2008, 139:89-100.
14. 2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study. J. Phys. Chem. B 2006, 110:14515-14523.
15. Koch K.J., Aggerholm T., Nanita S.C., Cooks R.G. Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization. J. Mass Spectrom. 2002, 37:676-686.
16. Martin R.B. Nucleoside sites for transition metal ion binding. Acc. Chem. Res. 1985, 18:32-38.
17. Monajjemi M., Ghiasi R., Passdar H., Mollaamin F., Ketabi S., Asaddian F., Chahkandi B., Karimkhani M. Theoretical study of alkali metals interactions with thymine tautomers: comparison and analysis. J. Mol. Des. 2003, 2:741-756.
18. Rajabi K., Gillis E.A.L., Fridgen T.D. Structures of hydrated alkali metal ion-bound adenine complexes by IRMPD spectroscopy in the N-H/O-H stretching region. J. Phys. Chem. A 2010, 114:3449-3456.
19. +) of nucleobases and modified nucleobases by electrospray ionization ion trap mass spectrometry. Rapid Commun. Mass Spectrom. 2004, 18:1686-1692.
20. Rodgers M.T., Armentrout P.B. Noncovalent interactions of nucleic acid bases (uracil, thymine, and adenine) with alkali metal ions. Threshold collision-induced dissociation and theoretical studies. J. Am. Chem. Soc. 2000, 122:8548-8558.
21. Rodgers M.T., Armentrout P.B. Influence of d orbital occupation on the binding of metal ions to adenine. J. Am. Chem. Soc. 2002, 124:2678-2691.
22. 2+) and the nucleic acid bases (T, U, C, A, G) in the gas phase. Inter. J. Quant. Chem. 2002, 90:903-909.
23. Russo N., Toscano M., Grand A. Lithium affinity for DNA and RNA nucleobases. The role of theoretical information in the elucidation of the mass spectrometry data. J. Phys. Chem. B 2001, 105:4735-4741.
24. Russo N., Toscano M., Grand A. Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase. J. Am. Chem. Soc. 2001, 123:10272-10279.
25. Zhu W., Luo X., Puah C.M., Tan X., Shen J., Gu J., Chen K., Jiang H. The multiplicity, strength, and nature of the interaction of nucleobases with alkaline and alkaline earth metal cations: a density functional theory investigation. J. Phys. Chem. A 2004, 108:4008-4018.
26. + association on the A-T and G-C pairs. J. Mol. Struct. (Theochem) 1985, 124:201-212.
27. Lee G.-Y. DFT studies of the lithium complexes of DNA bases. Bull. Korean Chem. Soc. 2002, 23:1023-1026.
28. Rodgers M.T., Armentrout P.B. A critical evaluation of the experimental and theoretical determination of lithium cation affinities. Int. J. Mass Spectrom. 2007, 267:167-182.
29. del Bene J.E. Molecular orbital study of the Li' complexes of the DNA bases. J. Phys. Chem. 1984, 88:5927-5931.
30. Brown R.D., Godfrey P.D., McNaughton D., Pierlot A.P. Microwave spectrum of the major gas-phase tautomer of thymine. J. Chem. Soc. Chem. Commun. 1989, 1:37-38.
31. Buda A., Sygula A. MNDO study of the tautomers of nucleic bases. Part I. Uracil, thymine and cytosine. Theochem 1983, 9:255-265.
32. Chen E.C.M., Herder C., Chen E.S. The experimental and theoretical gas phase acidities of adenine, guanine, cytosine, uracil, thymine and halouracils. J. Mol. Struct. 2006, 798:126-133.
33. Ha T.K., Gunthard H.H. Quantum chemical investigation of the structure and stability of all geometric isomers and conformers of all tautomeric forms of thymine. J. Am. Chem. Soc. 1993, 115:11939-11950.
34. Ha T.-K., Keller H.-J., Gunde R., Gunthard H.-H. Energy increment method based on quantum chemical results: a general recipe for approximative prediction of isomerization and tautomerization energies of pyrimidine and purine nucleic acid bases and related compounds. J. Phys. Chem. A 1999, 103:6612-6623.
35. Katritzky A.R., Karelson M. AM1 calculations of reaction field effects on the tautomeric equilibria of nucleic acid pyrimidine and purine bases and their 1-methyl analogs. J. Am. Chem. Soc. 1991, 113:1561-1566.
36. Piacenza M., Grimme S. Systematic quantum chemical study of DNA-base tautomers. J. Comput. Chem. 2004, 25:83-99.
37. Rejnek J., Hanus M., Kabeláč M., Ryjáček F., Hobza P. Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine. Phys. Chem. Chem. Phys. 2005, 7:2006-2017.
38. Salpin J.-Y., Guillaumont S., Tortajada J., MacAleese L., Lemaire J., Maitre P. Infrared spectra of protonated uracil, thymine and cytosine. ChemPhysChem 2007, 8:2235-2244.
39. Hanus M., Kabelač M., Rejnek J., Ryjáček F., Hobza P. Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment, and in aqueous solution. Part 3. Adenine. J. Phys. Chem. B 2004, 108:2087-2097.
40. Tureček F., Chen X. Protonated adenine: tautomers solvated clusters, and dissociation mechanisms. J. Am. Soc. Mass Spectrom. 2005, 16:1713-1726.
41. Sygula A., Buda A. MNDO study of the tautomers of nucleic bases. Part II. Adenine and guanine. J. Mol. Struct. 1983, 92:267-277.
42. Chen X., Syrstad E.A., Nguyen M.T., Gerbaux P., Tureček F. Distonic isomers and tautomers of the adenine cation radical in the gas phase and aqueous solution. J. Phys. Chem. A 2004, 108:9283-9293.
43. Casaes R.N., Paul J.B., McLaughlin R.P., Saykally R.J., van Mourik T. Infrared cavity ringdown spectroscopy of jet-cooled nucleotide base clusters and water complexes. J. Phys. Chem. A 2004, 108:10989-10996.
44. Sukhodub L.F. Interactions and hydration of nucleic acid bases in a vacuum. Experimental study. Chem. Rev. 1987, 87:589-606.
45. Del Bene J.E. Molecular orbital theory of the hydrogen bond. XXIX. Water-thymine complexes. J. Chem. Phys. 1982, 76:1058-1063.
46. Dolgounitcheva O., Zakrzewski V.G., Ortiz J.V. Anionic and neutral complexes of uracil and water. J. Phys. Chem. A 1999, 103:7912-7917.
47. Fogarasi G. Water-mediated tautomerization of cytosine to the rare imino form: an ab initio dynamics study. Chem. Phys. 2008, 349:204-209.
48. Fogarasi G., Szalay P.G. The interaction between cytosine tautomers and water: an MP2 and coupled cluster electron correlation study. Chem. Phys. Lett. 2002, 356:383-390.
49. Gadre S.R., Babu K., Rendell A.P. Electrostatics for exploring hydration patterns of molecules. 3. Uracil. J. Phys. Chem. A 2000, 104:8976-8982.
50. Gaigeot M.P., Kadri C., Ghomi M. Analysis of uracil hydration by means of vibrational spectroscopy and density functional calculations. J. Mol. Struct. 2001, 565-566:469-473.
51. Gu J., Leszczynski J. A DFT study of the water-assisted intramolecular proton transfer in the tautomers of Adenine. J. Phys. Chem. A 1999, 103:2744-2750.
52. Hunter K.C., Rutledge L.R., Wetmore S.D. The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia. J Phys. Chem. A 2005, 109:9554-9562.
53. Ilich P., Hemann C.F., Hille R. Molecular vibrations of solvated uracil. Ab initio reaction field calculations and experiment. J. Phys. Chem. B 1997, 101:10923-10938.
54. Jalbout A.F., Adamowicz L. Dipole-bound anions of adenine-water clusters. Ab initio study. J. Phys. Chem. A 2001, 105:1033-1038.
55. Kim N.J., Kim Y.S., Jeong G., Ahn T.K., Kim S.K. Hydration of DNA base cations in the gas phase. Int. J. Mass Spectrom. 2002, 219:11-21.
56. Kim S., Wheeler S.E., Schaefer H.F. Microsolvation effects on the electron capturing ability of thymine: thymine-water clusters. J. Chem. Phys. 2006, 124:204310-204318.
57. 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.
58. Kryachko E.S., Nguyen M.T., Zeegers-Huyskens T. Theoretical study of uracil tautomers. 2. Interaction with water. J. Phys. Chem. A 2001, 105:1934-1943.
59. 2O)n, n=2 to 4. Phys. Chem. Chem. Phys. 2001, 3:2886-2892.
60. van Mourik T., Benoit D.M., Price S.L., Clary D.C. Ab initio and diffusion Monte Carlo study of uracil-water, thymine-water, cytosine-water, and cytosine-(water)2. Phys. Chem. Chem. Phys. 2000, 2:1281-1290.
61. van Mourik T., Price S., Clary D. Diffusion Monte Carlo simulations on uracil-water using an anisotropic atom-atom potential model. Faraday Discuss 2001, 118:95-108.
62. van Mourik T., Price S.L., Clary D.C. Ab initio calculations on uracil-water. J. Phys. Chem. A 1999, 103:1611-1618.
63. Robertson E.G., Simons J.P. Getting into shape: conformational and supramolecular landscapes in small biomolecules and their hydrated clusters. Phys. Chem. Chem. Phys. 2001, 3:1-18.
64. Ohta Y., Tanaka H., Baba Y., Kagemoto A., Nishimoto K. Solvent effect on the hydrogen-bonding interaction between adenine and uracil. J. Phys. Chem. 1986, 90:4438-4442.
65. Kumar A., Mishra P.C., Suhai S. Adiabatic electron affinities of the polyhydrated adenine thymine base pair: a density functional study. J. Phys. Chem. A 2005, 109:3971-3979.
66. Neidle S. DNA-water interactions. Principles of Nucleic Acid Structure 2008, 132-203. Academic Press Elsevier, London.
67. Cerón-Carrasco J.P., Requena A., Michaux C., Perpète E.A., Jacquemin D. Effects of hydration on the proton transfer mechanism in the adenine-thymine base pair. J. Phys. Chem. A 2009, 113:7892-7898.
68. 2+): nonempirical ab initio calculations on structures, energies, and nonadditivity of the interaction. J. Phys. Chem. B 1997, 101:9670-9677.
69. Plützer C., Hünig I., Kleinermanns K., Nir E., Vries M.S.D. Pairing of isolated nucleobases: double resonance laser spectroscopy of adenine-thymine. Chem. Phys. Chem. 2003, 4:838-842.
70. Krishnan G.M., Kuhn O. Identifying adenine-thymine base pairing by anharmonic analysis of the hydrogen-bonded NH stretching vibrations. Chem. Phys. Lett. 2007, 435:132-135.
71. Eyler J.R. Infrared multiple photon dissociation spectroscopy of ions in Penning traps. Mass Spectrom. Rev. 2009, 28:448-467.
72. Fridgen T.D. Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes. Mass Spectrom. Rev. 2009, 28:586-607.
73. Polfer N.C., Oomens J. Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance. Mass Spectrom. Rev. 2009, 28:468-494.
74. Rajabi K., Easterling M.L., Fridgen T.D. Solvation of electrosprayed ions in the accumulation/collision hexapole of a hybrid Q-FTMS. J. Am. Soc. Mass Spectrom. 2009, 20:411-418.
75. Frisch M.J., Truks T., Schlegel G.W., Scuseria H.B., Robb G.E., Cheeseman M.A., Montgomery J.R., Vreven J.A., Kudin T., Burant K.N., Millam J.C., Iyengar J.M., Tomasi S.S., Barone J., Mennucci V., Cossi B., Scalmani M., Rega G., Petersson N., Nakatsuji G.A., Hada H., Ehara M., Toyota M., Fukuda K., Hasegawa R., Ishida J., Nakajima M., Honda T., Kitao Y., Nakai O., Klene H., Li M., Knox X., Hratchian J.E., Cross H.P., Bakken J.B., Adamo V., Jaramillo C., Gomperts J., Stratmann R., Yazyev R.E., Austin O., Cammi A.J., Pomelli R., Ochterski C., Ayala J.W., Morokuma P.Y., Voth K., Salvador G.A., Dannenberg P., Zakrzewski J.J., Dapprich V.G., Daniels S., Strain A.D., Farkas M.C., Malick O., Rabuck D.K., Raghavachari A.D., Foresman K., Ortiz J.B., Cui J.V., Baboul Q., Clifford A.G., Cioslowski S., Stefanov J., Liu B.B., Liashenko G., Piskorz A., Komaromi P., Martin I., Fox R.L., Keith D.J., Al-Laham T., Peng M.A., Nanayakkara C.Y., Challacombe A., Gill M., Johnson P.M.W., Chen B., Wong W., Gonzalez M.W., Pople J.A. Gaussian 03 2004, Gaussian, Inc., Wallingford, CT.
76. Dennington R., Keith T., Millam J., Eppinnett K., Hovell W.L., Gilliland R. GaussView 2003, Semichem, Inc., Shawnee Mission, KS.
77. Merrick J.P., Moran D., Radom L. An evaluation of harmonic vibrational frequency scale factors. J. Phys. Chem. A 2007, 111:11683-11700.
78. Rajabi K., Theel K., Gillis E.A.L., Beran G., Fridgen T.D. The structure of the protonated adenine dimer by infrared multiple photon dissociation spectroscopy and electronic structure calculations. J. Phys. Chem. A 2009, 113:8099-8107.
79. Zierkiewicz W., Komorowski L., Michalska D., Cerny J., Hobza P. The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine. J. Phys. Chem. B 2008, 112:16734-16740.