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Dinuclear Metal-Mediated Guanine–Uracil Base Pairs: Theoretical Studies of GUM22+ (M = Cu, Ag, and Au) Ions

  • Guo-Jin CaoEmail author
  • Hai-Li Hou
Original Paper
  • 31 Downloads

Abstract

Dinuclear metal-mediated hetero base pairs with the d10–d10 closed-shell interactions have significant stability. It is interesting to identify whether coinage metal-mediated Wobble base pairs are also stable. Geometric and electronic structures of the lowest-lying isomers of GUM22+ (G = guanine, U = uracil, M = Cu, Ag, and Au) cluster ions were investigated with density functional theory. In the lowest-lying isomers of these dinuclear metal-mediated base pairs, the 2-oxo-4-hydroxy-trans-N1H isomer of uracil is derived from the canonical tautomer of uracil by the hydrogen atom transfer. M22+ cations remain as an unbroken unit and interact with the G···U ligand through two sets of closely linear N···M···O units, while the reciprocal hydrogen bonds between the Wobble base pair (G–U) are entirely substituted by the M–N or M–O interactions in these complexes. The atoms in molecules and EDA–NOCV calculations really reveal that the σ interactions in GUM22+ cations are the paramount term of ΔEOrb. The obtained instantaneous interaction energies ΔEint and bond dissociation energies of the metal–ligand interactions give the trend of the bond strength as Cu > Au > Ag.

Keywords

Dinuclear metal-mediated base pairs Metal–ligand interactions Density functional theory Geometric and electronic structures Coinage metal–nucleobase clusters 

Notes

Acknowledgements

This work was supported by the Natural Science Foundation of China (Grant No. 21501114), the Natural Science Foundation of Shanxi Province (Grant No. 2015021048), and the Open Fund of Beijing National Laboratory for Molecular Sciences (Grant No. BNLMS20150051).

Supplementary material

10876_2019_1503_MOESM1_ESM.docx (2 mb)
Supplementary material 1 (DOCX 2090 kb)

References

  1. 1.
    G. H. Clever, C. Kaul, and T. Carell (2007). Angew. Chem. Int. Ed. 46, 6226–6236.CrossRefGoogle Scholar
  2. 2.
    K. Tanaka and M. Shionoya (2007). Coord. Chem. Rev. 251, 2732–2742.CrossRefGoogle Scholar
  3. 3.
    W. He, R. M. Franzini, and C. Achim (2008). Inorg. Chem. 55, 545–612.Google Scholar
  4. 4.
    J. Müller (2008). Eur. J. Inorg. Chem. 2008, 3749–3763.CrossRefGoogle Scholar
  5. 5.
    R. Mas-Ballesté, O. Castillo, P. J. Sanz Miguel, D. Olea, J. Gómez-Herrero, and F. Zamora (2009). Eur. J. Inorg. Chem. 2009, 2885–2896.CrossRefGoogle Scholar
  6. 6.
    J. Liu, Z. Cao, and Y. Lu (2009). Chem. Rev. 109, 1948–1998.CrossRefGoogle Scholar
  7. 7.
    G. H. Clever and M. Shionoya (2010). Coord. Chem. Rev. 254, 2391–2402.CrossRefGoogle Scholar
  8. 8.
    A. Ono, H. Torigoe, Y. Tanaka, and I. Okamoto (2011). Chem. Soc. Rev. 40, 5855–5866.CrossRefGoogle Scholar
  9. 9.
    Y. Takezawa and M. Shionoya (2012). Acc. Chem. Res. 45, 2066–2076.CrossRefGoogle Scholar
  10. 10.
    S. Mandal, M. Hebenbrock, and J. Müller (2016). Angew. Chem. Int. Ed. 55, 15520–15523.CrossRefGoogle Scholar
  11. 11.
    S. Mandal and J. Müller (2017). Curr. Opin. Chem. Biol. 37, 71–79.CrossRefGoogle Scholar
  12. 12.
    S. Taherpour, O. Golubev, and T. Lönnberg (2016). Inorg. Chim. Acta. 452, 43–49.CrossRefGoogle Scholar
  13. 13.
    A. Ono and H. Togashi (2004). Angew. Chem. Int. Ed. 43, 4300–4302.CrossRefGoogle Scholar
  14. 14.
    T. Ehrenschwender, W. Schmucker, C. Wellner, T. Augenstein, P. Carl, J. Harmer, F. Breher, and H. A. Wagenknecht (2013). Chem. Eur. J. 19, 12547–12552.CrossRefGoogle Scholar
  15. 15.
    E. Toomey, J. Xu, S. Vecchioni, L. Rothschild, S. Wind, and G. E. Fernandes (2016). J. Phys. Chem. C 120, 7804–7809.CrossRefGoogle Scholar
  16. 16.
    K. S. Park, C. Jung, and H. G. Park (2010). Angew. Chem. Int. Ed. 49, 9757–9760.CrossRefGoogle Scholar
  17. 17.
    T. Carell (2011). Nature 469, 45–46.CrossRefGoogle Scholar
  18. 18.
    J. Liu and Y. Lu (2007). Angew. Chem. 119, 7731–7734.CrossRefGoogle Scholar
  19. 19.
    X. Liu, C.-H. Lu, and I. Willner (2014). Acc. Chem. Res. 47, 1673–1680.CrossRefGoogle Scholar
  20. 20.
    A. Rioz-Martínez and G. Roelfes (2015). Curr. Opin. Chem. Biol. 25, 80–87.CrossRefGoogle Scholar
  21. 21.
    D. A. Megger, C. F. Guerra, J. Hoffmann, B. Brutschy, F. M. Bickelhaupt, and J. Müller (2011). Chem. Eur. J. 17, 6533–6544.CrossRefGoogle Scholar
  22. 22.
    M. Su, M. Tomás-Gamasa, and T. Carell (2015). Chem. Sci. 6, 632–638.CrossRefGoogle Scholar
  23. 23.
    H. Mei, S. A. Ingale, and F. Seela (2014). Chem. Eur. J. 20, 16248–16257.CrossRefGoogle Scholar
  24. 24.
    H. Mei, H. Yang, I. Röhl, and F. Seela (2014). ChemPlusChem 79, 914–918.CrossRefGoogle Scholar
  25. 25.
    H. Yang, H. Mei, and F. Seela (2015). Chem. Eur. J. 21, 10207–10219.CrossRefGoogle Scholar
  26. 26.
    I. Sinha, C. F. Guerra, and J. Müller (2015). Angew. Chem. Int. Ed. 54, 3603–3606.CrossRefGoogle Scholar
  27. 27.
    S. Mandal, A. Hepp, and J. Müller (2015). Dalton Trans. 44, 3540–3543.CrossRefGoogle Scholar
  28. 28.
    S. Mandal, M. Hebenbrock, and J. Müller (2018). Inorg. Chim. Acta. 472, 229–233.CrossRefGoogle Scholar
  29. 29.
    J. Kondo, T. Sugawara, H. Saneyoshi, and A. Ono (2017). Chem. Commun. 53, 11747–11750.CrossRefGoogle Scholar
  30. 30.
    S. Mandal, M. Hebenbrock, and J. Müller (2017). Chem. Eur. J. 23, 5962–5965.CrossRefGoogle Scholar
  31. 31.
    J. M. Méndez-Arriaga, C. R. Maldonado, J. A. Dobado, and M. A. Galindo (2018). Chem. Eur. J. 24, 1–8.CrossRefGoogle Scholar
  32. 32.
    J. V. Burda, J. Špřoner, J. Leszczynski, and P. Hobza (1997). J. Phys. Chem. B 101, 9670–9677.CrossRefGoogle Scholar
  33. 33.
    E. S. Kryachko and F. Remacle (2005). J. Phys. Chem. B 109, 22746–22757.CrossRefGoogle Scholar
  34. 34.
    A. Kumar, P. C. Mishra, and S. Suhai (2006). J. Phys. Chem. A 110, 7719–7727.CrossRefGoogle Scholar
  35. 35.
    P. J. Mohan, A. Datta, S. S. Mallajosyula, and S. K. Pati (2006). J. Phys. Chem. B 110, 18661–18664.CrossRefGoogle Scholar
  36. 36.
    N. Vyas and A. K. Ojha (2012). Comput. Theor. Chem. 984, 93–101.CrossRefGoogle Scholar
  37. 37.
    E. S. Kryachko and F. Remacle (2005). Nano Lett. 5, 735–739.CrossRefGoogle Scholar
  38. 38.
    G.-J. Cao, H.-G. Xu, R.-Z. Li, and W. Zheng (2012). J. Chem. Phys. 136, 014305.CrossRefGoogle Scholar
  39. 39.
    G.-J. Cao, H.-G. Xu, W.-J. Zheng, and J. Li (2014). Phys. Chem. Chem. Phys. 16, 2835–2928.Google Scholar
  40. 40.
    P. Wang, H.-G. Xu, G.-J. Cao, W.-J. Zhang, X.-L. Xu, and W.-J. Zheng (2017). J. Phys. Chem. A 121, 8973–8981.CrossRefGoogle Scholar
  41. 41.
    J. Valdespino-Saenz and A. Martínez (2008). J. Phys. Chem. A 112, 2408–2414.CrossRefGoogle Scholar
  42. 42.
    G.-J. Cao, H.-G. Xu, X.-L. Xu, P. Wang, and W.-J. Zheng (2016). Int. J. Mass Spectrom. 407, 118–125.CrossRefGoogle Scholar
  43. 43.
    M. V. Vázquez and A. Martínez (2008). J. Phys. Chem. A 112, 1033–1039.CrossRefGoogle Scholar
  44. 44.
    N. Russo, M. Toscano, and A. Grand (2003). J. Mass Spectrom. 38, 265–270.CrossRefGoogle Scholar
  45. 45.
    L. A. Espinosa Leal and O. Lopez-Acevedo (2015). Nanotechnol. Rev. 4, 173–191.CrossRefGoogle Scholar
  46. 46.
    S. J. Stohs and D. Bagchi (1995). Free Radic. Biol. Med. 18, 321–336.CrossRefGoogle Scholar
  47. 47.
    K. Yamamoto and S. Kawanishi (1989). J. Biol. Chem. 264, 15435–15440.Google Scholar
  48. 48.
    J. L. Sagripanti and K. H. Kraeme (1989). J. Biol. Chem. 264, 1729–1734.Google Scholar
  49. 49.
    V. I. Danilov, V. M. Anisimov, N. Kurita, and D. Hovorun (2005). Chem. Phys. Lett. 412, 285–293.CrossRefGoogle Scholar
  50. 50.
    J. Šponer, M. Sabat, J. V. Burda, J. Leszczynski, and P. Hobza (1999). J. Phys. Chem. B 103, 2528–2534.CrossRefGoogle Scholar
  51. 51.
    J. M. Weber, J. A. Kelley, W. H. Robertson, and M. A. Johnson (2001). J. Chem. Phys. 114, 2698–2706.CrossRefGoogle Scholar
  52. 52.
    M. D. Topal and J. R. Fresco (1976). Nature 263, 285–289.CrossRefGoogle Scholar
  53. 53.
    J. Florián and J. Leszczyński (1996). J. Am. Chem. Soc. 118, 3010–3017.CrossRefGoogle Scholar
  54. 54.
    G.-J. Cao (2017). Sci. Rep. 7, 14896.CrossRefGoogle Scholar
  55. 55.
    M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox Gaussian 09, Revision C. 01 (Gaussian, Inc., Wallingford, 2010).Google Scholar
  56. 56.
    A. D. Becke (1993). J. Chem. Phys. 98, 5648–5652.CrossRefGoogle Scholar
  57. 57.
    C. Lee, W. Yang, and R. G. Parr (1988). Phys. Rev. B 37, 785–789.CrossRefGoogle Scholar
  58. 58.
    D. Figgen, G. Rauhut, M. Dolg, and H. Stoll (2005). Chem. Phys. 311, 227–244.CrossRefGoogle Scholar
  59. 59.
    K. A. Peterson and C. Puzzarini (2005). Theor. Chem. Acc. 114, 283–296.CrossRefGoogle Scholar
  60. 60.
    J. P. Foster and F. Weinhold (1980). J. Am. Chem. Soc. 102, 7211–7218.CrossRefGoogle Scholar
  61. 61.
    R. F. W. Bader (1991). Chem. Rev. 91, 893–928.CrossRefGoogle Scholar
  62. 62.
    R. F. W. Bader (1998). J. Phys. Chem. A 102, 7314–7323.CrossRefGoogle Scholar
  63. 63.
    R. F. W. Bader, et al. Atoms in Molecules (Wiley, New York, 1990).Google Scholar
  64. 64.
    T. Lu and F. Chen (2012). J. Comput. Chem. 33, 580–592.CrossRefGoogle Scholar
  65. 65.
    A. D. Becke (1988). Phys. Rev. A 38, 3098–3100.CrossRefGoogle Scholar
  66. 66.
    J. P. Perdew and W. Yue (1986). Phys. Rev. B 33, 8800–8802.CrossRefGoogle Scholar
  67. 67.
    C. F. Guerra, J. G. Snijders, G. T. Velde, and E. J. Baerends (1998). Theor. Chem. Acc. 99, 391–403.Google Scholar
  68. 68.
    G. T. Velde, F. M. Bickelhaupt, E. J. Baerends, C. F. Guerra, S. J. A. V. Gisbergen, J. G. Snijders, and T. Ziegler (2001). J. Comput. Chem. 22, 931–967.CrossRefGoogle Scholar
  69. 69.
    See http://www.scm.com for ADF2013.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands. Accessed 01 July 2017.
  70. 70.
    E. V. Lenthe, A. Ehlers, and E. J. Baerends (1999). J. Chem. Phys. 110, 8943–8953.CrossRefGoogle Scholar
  71. 71.
    E. V. Lenthe and E. Jan Baerends (2000). J. Chem. Phys. 112, 8279–8292.CrossRefGoogle Scholar
  72. 72.
    G.-J. Cao (2018). J. Chem. Phys. 149, 144308.CrossRefGoogle Scholar
  73. 73.
    G.-J. Cao and W.-J. Zheng (2013). Acta Phys. Chim Sin. 29, 2135–2147.Google Scholar
  74. 74.
    P. Pyykkö (2004). Angew. Chem. Int. Ed. 43, 4412–4456.CrossRefGoogle Scholar
  75. 75.
    P. Pyykkö (2005). Inorg. Chim. Acta. 358, 4113–4130.CrossRefGoogle Scholar
  76. 76.
    P. Pyykko (2008). Chem. Soc. Rev. 37, 1967–1997.CrossRefGoogle Scholar
  77. 77.
    P. Pyykkö (1988). Chem. Rev. 88, 563–594.CrossRefGoogle Scholar
  78. 78.
    P. Pyykkö (1979). Acc. Chem. Res. 12, 276–281.CrossRefGoogle Scholar
  79. 79.
    P. Pyykkö (2002). Angew. Chem. Int. Ed. 41, 3573–3578.CrossRefGoogle Scholar
  80. 80.
    I. Mayer (1984). Int. J. Quantum Chem. 26, 151–154.CrossRefGoogle Scholar
  81. 81.
    I. Mayer (1985). Theor. Chim. Acta 67, 315–322.CrossRefGoogle Scholar
  82. 82.
    I. Mayer (1983). Chem. Phys. Lett. 97, 270–274.CrossRefGoogle Scholar
  83. 83.
    A. J. Bridgeman, G. Cavigliasso, L. R. Ireland, and J. Rothery (2001). J. Chem. Soc. Dalton Trans. (14), 2095–2108.  https://doi.org/10.1039/B102094N.
  84. 84.
    P. L. Ayers, R. J. Boyd, P. Bultinck, M. Caffarel, R. Carbó-Dorca, M. Causá, J. Cioslowski, J. Contreras-Garcia, D. L. Cooper, P. Coppens, C. Gatti, S. Grabowsky, P. Lazzeretti, P. Macchi, Á. Martín Pendás, P. L. A. Popelier, K. Ruedenberg, H. Rzepa, A. Savin, A. Sax, W. H. E. Schwarz, S. Shahbazian, B. Silvi, M. Solà, and V. Tsirelson (2015). Comput. Theor. Chem. 1053, 2–16.CrossRefGoogle Scholar
  85. 85.
    G.-J. Cao, W. H. Eugen Schwar, and J. Li (2015). Inorg. Chem. 54, 3695–3701.CrossRefGoogle Scholar
  86. 86.
    P. Jerabek, H. W. Roesky, G. Bertrand, and G. Frenking (2014). J. Am. Chem. Soc. 136, 17123–17135.CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Institute of Molecular ScienceShanxi UniversityTaiyuanChina

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