Skip to main content
SpringerLink
Log in

IRMPD Action Spectroscopy of Alkali Metal Cation–Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation

  • Research Article
  • Published:
Journal of The American Society for Mass Spectrometry

Abstract

The gas-phase structures of alkali metal cation-cytosine complexes generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra of five alkali metal cation–cytosine complexes exhibit both similar and distinctive spectral features over the range of ~1000–1900 cm-1. The IRMPD spectra of the Li+(cytosine), Na+(cytosine), and K+(cytosine) complexes are relatively simple but exhibit changes in the shape and shifts in the positions of several bands that correlate with the size of the alkali metal cation. The IRMPD spectra of the Rb+(cytosine) and Cs+(cytosine) complexes are much richer as distinctive new IR bands are observed, and the positions of several bands continue to shift in relation to the size of the metal cation. The measured IRMPD spectra are compared to linear IR spectra of stable low-energy tautomeric conformations calculated at the B3LYP/def2-TZVPPD level of theory to identify the conformations accessed in the experiments. These comparisons suggest that the evolution in the features in the IRMPD action spectra with the size of the metal cation, and the appearance of new bands for the larger metal cations, are the result of the variations in the intensities at which these complexes can be generated and the strength of the alkali metal cation-cytosine binding interaction, not the presence of multiple tautomeric conformations. Only a single tautomeric conformation is accessed for all five alkali metal cation–cytosine complexes, where the alkali metal cation binds to the O2 and N3 atoms of the canonical amino-oxo tautomer of cytosine, M+(C1).

ᇵ

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6

Similar content being viewed by others

References

  1. Crick, F.: Central dogma of molecular biology. Nature 227, 561–563 (1970)

    Article  CAS  Google Scholar 

  2. Clarke, M.J.: Electrochemistry, synthesis, and spectra of pentaammineruthenium(III) complexes of cytidine, adenosine, and related ligands. J. Am. Chem. Soc. 100, 5068–5075 (1978)

    Article  CAS  Google Scholar 

  3. Lippert, B., Schöllhorn, H., Thewalt, U.: Metal-stabilized rare tautomers of nucleobases. 1. Iminooxo form of cytosine: formation through metal migration and estimation of the geometry of the free tautomer. J. Am. Chem. Soc 108, 6616–6621 (1986)

    Article  CAS  Google Scholar 

  4. Pichierri, F., Holthenrich, D., Zangrando, E., Lippert, B., Randaccio, L.: Metal-stabilized rare tautomers of nucleobases 5. Iminooxo tautomer of cytosine coordinated to Pt(II) with metal and nucleobase in syn and anti orientations. J. Biol. Inorg. Chem. 1, 439–445 (1996)

    Article  CAS  Google Scholar 

  5. Müller, J., Zangrando, E., Pahlke, N., Freisinger, E., Randaccio, L., Lippert, B.: Affinity of the iminooxo tautomer anion of 1-methylcytosine in trans-[Pt(NH3)2(1-MeC-N4)2]2+ for heterometals. Chem. Eur. J. 4, 397–405 (1998)

    Article  Google Scholar 

  6. Zamora, F., Kunsman, M., Sabat, M., Lippert, B.: Metal-stabilized rare tautomers of nucleobases. 6. Imino tautomer of adenine in a mixed-nucleobase complex of mercury(II). Inorg. Chem. 36, 1583–1587 (1997)

    Article  CAS  Google Scholar 

  7. Arpalahti, J., Klika, K.D.: Platination of the exocyclic amino group of the adenine nucleobase by Pt(II) migration. Eur. J. Inorg. Chem. 8, 1199–1201 (1999)

    Article  Google Scholar 

  8. Day, E.F., Crawford, C.A., Folting, K., Dunbar, K.R., Christon, G.: New metal-binding mode for adenine: A bidentate (N6, N7) bridging mode in the complex [Mo2(O2CCHF2)2(9-EtAH)2(MeCN)2](BF4)2•2MeCN. J. Am. Chem. Soc. 116, 9339–9340 (1994)

    Article  CAS  Google Scholar 

  9. Velders, A.H., van der Geest, B., Kooijman, H., Spek, A.L., Haasnoot, J.G., Reedijk, J.: Ruthenium(III) coordination to the exocyclic nitrogen of 9-methyladenine and stabilisation of the rare imine tautomer by intramolecular hydrogen bonding. Eur. J. Inorg. Chem. 369−372 (2001)

  10. Nei, Y.-W., Akinyemi, T.E., Kaczan, C.M., Steill, J.D., Berden, G., Oomens, J., Rodgers, M.T.: Infrared multiple photon dissociation action spectroscopy of sodiated uracil and thiouracils: Effects of thioketo-substitution on gas-phase conformation. Int. J. Mass Spectrom. 308, 191–202 (2011)

    Google Scholar 

  11. Yang, Z., Rodgers, M.T.: Tautomerization in the formation and collision-induced dissociation of alkali metal cation-cytosine complexes. Phys. Chem. Chem. Phys. 14, 4517–4526 (2012)

    Google Scholar 

  12. Watson, J.D., Crick, F.: Genetical implications of the structure of deoxyribonucleic acid. Nature 171, 964–967 (1953)

    Article  CAS  Google Scholar 

  13. Topal, M.D., Fresco, J.R.: Complementary base pairing and the origin of substitution mutations. Nature 263, 285–289 (1976)

    Article  CAS  Google Scholar 

  14. Šponer, J.: J., Hobza, P.: Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study. J. Am. Chem. Soc. 116, 709–714 (1994)

    Article  Google Scholar 

  15. Šponer, J., Hobza, P.: Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study. J. Phys. Chem. 98, 3161–3164 (1994)

    Google Scholar 

  16. Hall, R.J., Burton, N.A., Hillier, I.H., Young, P.E.: Tautomeric equilibria in 2-hydroxypyridine and in cytosine. An assessment of density functional methods, including gradient corrections. Chem. Phys. Lett. 220, 129–132 (1994)

    Google Scholar 

  17. Sobolewski, A.L., Adamowicz, L.: Theoretical investigations of proton transfer reactions in a hydrogen bonded complex of cytosine with water. J. Chem. Phys. 102, 5708–5718 (1995)

    Article  CAS  Google Scholar 

  18. Florián, J., Leszczyński, J., Johnson, B.G.: On the intermolecular vibrational modes of the guanine⋯cytosine, adenine–thymine and formamide–formamide H-bonded dimers. J. Mol. Struct. 349, 421–426 (1995)

    Article  Google Scholar 

  19. Fülscher, M.P., Roos, B.O.: Theoretical study of the electronic spectrum of cytosine. J. Am. Chem. Soc. 117, 2089–2095 (1995)

    Article  Google Scholar 

  20. Hobza, P., Šponer, J., Polásšek, M.: H-bonded and stacked DNA base pairs: Cytosine dimer. An ab initio second-order Moeller-Plesset study. J. Am. Chem. Soc. 117, 792–798 (1995)

    Article  CAS  Google Scholar 

  21. Colominas, C., Luque, F.J., Orozco, M.: Tautomerism and protonation of guanine and cytosine. Implications in the formation of hydrogen-bonded complexes. J. Am. Chem. Soc. 118, 6811–6821 (1996)

    Article  CAS  Google Scholar 

  22. Florián, J., Baumruk, V., Leszczyński, J.: IR and Raman spectra, tautomerism, and scaled quantum mechanical force fields of protonated cytosine. J. Phys. Chem. 100, 5578–5589 (1996)

    Article  Google Scholar 

  23. Kwiatkowski, J.S., Leszczyński, J.: Molecular structure and vibrational IR spectra of cytosine and its thio and seleno analogues by density functional theory and conventional ab initio calculations. J. Phys. Chem. 100, 941–953 (1996)

    Article  CAS  Google Scholar 

  24. Fogarasi, G.: High-level electron correlation calculations on some tautomers of cytosine. J. Mol. Struct. 413, 271–278 (1997)

    Article  Google Scholar 

  25. Kobayashi, R.: A CCSD(T) study of the relative stabilities of cytosine tautomers. J. Phys. Chem. A 102, 10813–10817 (1998)

    Article  CAS  Google Scholar 

  26. 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 105, 4735–4741 (2001)

    Article  CAS  Google Scholar 

  27. Russo, N., Toscano, M., Grand, A.: Bond energies and attachment sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase. J. Am. Chem. Soc. 123, 10272–10279 (2001)

    Article  CAS  Google Scholar 

  28. Fogarasi, G.: Relative stabilities of three low-energy tautomers of cytosine: A coupled cluster electron correlation study. J. Phys. Chem. A 106, 1381–1390 (2002)

    Google Scholar 

  29. Trygubenko, S.A., Bogdan, T.V., Rueda, M., Orozco, M., Luque, F.J., Šponer, J., Slavíček, P., 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 1. Cytosine. Phys. Chem. Chem. Phys. 4, 4192–4203 (2002)

    Google Scholar 

  30. Yang, Z., Rodgers, M.T.: Theoretical studies of the unimolecular and bimolecular tautomerization of cytosine. Phys. Chem. Chem. Phys 6, 2749–2757 (2004)

    Google Scholar 

  31. Mazzuca, D., Marino, T., Russo, N., Toscano, M.: A theoretical study on tautomerization processes of dehydrated and monohydrated cytosine. THEOCHEM. 811, 161–167 (2007)

    Article  CAS  Google Scholar 

  32. Szczesniak, M., Szczepaniak, K., Kwiatkowski, J.S., Kubulat, K., Person, W.B.: Matrix isolation infrared studies of nucleic acid constituents. 5. Experimental matrix-isolation and theoretical ab initio SCF molecular orbital studies of the infrared spectra of cytosine monomers. J. Am. Chem. Soc. 110, 8319–8330 (1988)

    Article  CAS  Google Scholar 

  33. Brown, R.D., Godfrey, P.D., McNaughton, D., Pierlot, A.P.: Tautomers of cytosine by microwave spectroscopy. J. Am. Chem. Soc. 111, 2308–2310 (1989)

    Article  CAS  Google Scholar 

  34. Monajjemi, M., Ghiasi, R., Sadjadi, M.A.S.: Metal-stabilized rare tautomers: N4 metalated cytosine (M = Li+, Na+, K+, Rb+ and Cs+), theoretical views. Appl. Organometal. Chem. 17, 635–640 (2003)

    Article  CAS  Google Scholar 

  35. Lippert, B., Gupta. D.: Promotion of rare nucleobase tautomers by metal binding. Dalton Trans. 4619−4634 (2009)

  36. Winter, M.: WebElements Periodic Table of the Elements | Cesium | biological information, WebElements (2012)

  37. Valle, J.J., Eyler, J.R., Oomens, J., Moore, D.T., van der Meer, A.F.G., von Helden, G., Meijer, G., Hendrickson, C.L., Marshall, A.G., Blakney, G.T.: Free electron laser-Fourier transform ion cyclotron resonance mass spectrometry facility for obtaining infrared multiphoton dissociation spectra of gaseous ions. Rev. Sci. Instrum. 76, 023103–7 (2005)

    Google Scholar 

  38. Polfer, N.C., Oomens, J., Moore, D.T., von Helden, G., Meijer, G., Dunbar, R.C.: Infrared spectroscopy of phenylalanine Ag(I) and Zn(II) complexes in the gas phase. J. Am. Chem. Soc. 128, 517–525 (2006)

    Article  CAS  Google Scholar 

  39. Polfer, N.C., Oomens, J.: Reaction products in mass spectrometry elucidated with infrared spectroscopy. Phys. Chem. Chem. Phys 9, 3804–3817 (2007)

    Google Scholar 

  40. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery Jr., J.A., Vreven, T., Kudin, K.N., Burant, J.C., Millam, J.M., Iyengar, S.S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G.A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J.E., Hratchian, H.P., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Ayala, P.Y., Morokuma, K., Voth, G.A., Salvador, P., Dannenberg, J.J., Zakrzewski, V.G., Dapprich, S., Daniels, A.D., Strain, M.C., Farkas, O., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Ortiz, J.V., Cui, Q., Baboul, A.G., Clifford, S., Cioslowski, J., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Gonzalez, C., Pople, J.A.: Gaussian 03, Revision C.02. Gaussian, Inc, Wallingford (2004)

    Google Scholar 

  41. Foresman, J.B., Frisch, Æ.:Exploring Chemistry with Electronic Structures Methods, 2nd ed.; Gaussian: Pittsburg, 1996, p. 64.

  42. Pople, J.A., Scott, A.P., Wong, M.W., Radom, L.: Scaling Factors for Obtaining Fundamental Vibrational Frequencies and Zero-Point Energies from HF/6-31G* and MP2/6-31G* Harmonic Frequencies. Isr. J. Chem. Soc. 33, 345–350 (1993)

    CAS  Google Scholar 

  43. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery Jr., J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J.: Gaussian 09, Revision A.1. Gaussian, Inc, Wallingford (2009)

    Google Scholar 

  44. Weigend, F., Ahlrichs, R.: Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys 7, 3297–3305 (2005)

    Google Scholar 

  45. Leininger, T., Nicklass, A., Kuechle, W., Stoll, H., Dolg, M., Bergner, A.: The accuracy of the pseudopotential approximation: Non-frozen-core effects for spectroscopic constants of alkali fluorides XF (X = K, Rb, Cs). Chem. Phys. Lett. 255, 274–280 (1996)

    Article  CAS  Google Scholar 

  46. Feller, D.: The role of databases in support of computational chemistry calculations. J. Comp. Chem. 17, 1571–1586 (1996)

    CAS  Google Scholar 

  47. Schuchardt, K.L., Didier, B.T., Elsethagen, T., Sun, L., Gurumoorthi, V., Chase, J., Li, J., Windus, T.L.: Basis set exchange: A community database for computational sciences. J. Chem. Inf. Model. 47, 1045–1052 (2007)

    Google Scholar 

  48. Armentrout, P.B., Chen, Y., Rodgers, M.T.: Metal cation dependence of interactions with amino acids: Bond energies of Cs+ to Gly, Pro, Ser, Thr, and Cys. J. Phys. Chem. A 116, 3989–3999 (2012)

    Google Scholar 

  49. McLean, A.D., Chandler, G.S.: Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, z = 11–18. J. Chem. Phys. 72, 5639–5648 (1980)

    Article  CAS  Google Scholar 

  50. Hay, P.J., Wadt, W.R.: Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. J. Chem. Phys. 82, 299–310 (1985)

    Google Scholar 

  51. Glendening, E.D., Feller, D., Thompson, M.A.: An ab initio investigation of the structure and alkali metal cation selectivity of 18-crown-6. J. Am. Chem. Soc. 116, 10657–10669 (1994)

    Article  CAS  Google Scholar 

  52. Rodgers, M.T., Armentrout, P.B.: A critical evaluation of the experimental and theoretical determination of lithium cation affinities. Int. J. Mass Spectrom. 267, 167–182 (2007)

    Article  CAS  Google Scholar 

  53. Armentrout, P.B., Austin, C.A., Rodgers, M.T.: Alkali metal cation interactions with 12-crown-4 in the gas phase: Revisited. Int. J. Mass Spectrom. 330/332, 16–26 (2012)

    Google Scholar 

  54. Wilson, R.G., Brewer, G.R.: Ion Beams with Applications to Ion Implantation. Wiley, New York (1973)

    Google Scholar 

  55. Salpin, J.-Y., Guillaumount, S., Tortajada, J., MacAleese, L., Lemaire, J., Maitre, P.: Infrared spectra of protonated uracil, thymine and cytosine. Chem. Phys. Chem. 8, 2235–2244 (2007)

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors acknowledge financial support for this work by the National Science Foundation, grants OISE-0730072 and CHE-0911191. The authors also like to thank WSU C&IT for computer time. This work is part of the research program of FOM, which is financially supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). The skillful assistance of the FELIX staff is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA

    Bo Yang, R. R. Wu & M. T. Rodgers

  2. Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA

    N. C. Polfer

  3. Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands

    G. Berden & J. Oomens

  4. van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands

    J. Oomens

Authors
  1. Bo Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. R. Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. N. C. Polfer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. G. Berden
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. Oomens
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. T. Rodgers
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. T. Rodgers.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 1090 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yang, B., Wu, R.R., Polfer, N.C. et al. IRMPD Action Spectroscopy of Alkali Metal Cation–Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation. J. Am. Soc. Mass Spectrom. 24, 1523–1533 (2013). https://doi.org/10.1007/s13361-013-0689-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13361-013-0689-7

Key words

Search

Navigation