Skip to main content
SpringerLink
Log in

Silver- and gold-mediated nucleobase bonding

Journal of Molecular Modeling volume 20, Article number: 2391 (2014) Cite this article

Abstract

We report the results of a density functional theory investigation of the bonding of nucleobases mediated by silver and gold atoms in the gas phase. Our calculations use the Becke exchange and Perdew–Wang correlation functional (BPW91) combined with the Stuttgart effective core potentials to represent the valence electrons of gold, silver, and platinum, and the all-electron DGTZVP basis set for C, H, N, and O. This combination was chosen based on tests on the metal atoms and tautomers of adenine, cytosine, and guanine. To establish a benchmark to understand the metal-mediated bonding, we calculated the binding energy of each of the base pairs in their canonical forms. Our calculations show rather strong bonds between the Watson–Crick base pairs when compared with typical values for N–H–N and N–H–O hydrogen bonds. The neutral metal atoms tend to bond near the nitrogen atoms. The effect of the metal atoms on the bonding of nucleobases differs depending on whether or not the metal atoms bond to one of the hydrogen-bonding sites. When the silver or gold atoms bond to a non-hydrogen-bonding site, the effect is a slight enhancement of the cytosine–guanine bonding, but there is almost no effect on the adenine–thymine pairing. The metal atoms can block one of the hydrogen-bonding sites, thus preventing the normal cytosine–guanine and adenine–thymine pairings. We also find that both silver and gold can bond to consecutive guanines in a similar fashion to platinum, albeit with a significantly lower binding energy.

We report the results of a density functional theory investigation of the bonding of nucleobases mediated by silver and gold atoms in the gas phase. Our calculations use the Becke exchange and Perdew–Wang correlation functional (BPW91) combined with the Stuttgart effective core potentials to represent the valence electrons of gold, silver, and platinum, and the all-electron DGTZVP basis set for C, H, N, and O. This combination was chosen based on tests on the metal atoms and on tautomers of adenine, cytosine, and guanine. To establish a benchmark to understand the metal-mediated bonding, we calculated the binding energy of each of the base pairs in their canonical forms. Our calculations show rather strong bonds between the Watson–Crick base pairs when compared with typical values for N–H–N and N–H–O hydrogen bonds. The neutral metal atoms tend to bond near the nitrogen atoms. The effect of the metal atoms on the bonding of nucleobases differs depending on whether or not the metal atoms bond to one of the hydrogen-bonding sites. When the silver or gold atoms bond to a non-hydrogen-bonding site, the effect is a slight enhancement of the cytosine–guanine bonding, but there is almost no effect on the adenine–thymine pairing. The metal atoms can block one of the hydrogen-bonding sites, thus preventing the normal cytosine–guanine and adenine–thymine pairings. We also find that both silver and gold can bond to consecutive guanines in a similar fashion to platinum, albeit with a significantly lower binding energy. Stable gas-phase structures are shown in the figure: a guanine–Ag–guanine, b guanine–Au–guanine, and c guanine–Pt–guanine complexes

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7a–b
Fig. 8a–b
Fig. 9a–b
Fig. 10
Fig. 11
Fig. 12
Fig. 13a–c

References

  1. Lippert B (1999) Impact of cisplatin on the recent development of Pt coordination chemistry: a case study. Coord Chem Rev 182:263–295

    Article  Google Scholar 

  2. Lippert B (2000) Multiplicity of metal ion binding patterns to nucleobases. Coord Chem Rev 200–202:487–516

  3. Kryacko ES, Remacle F (2005) Complexes of DNA bases and Watson–Crick base pairs with small neutral gold clusters. J Phys Chem B 109:22746–22757

  4. Lu G, Wei F, Jiang H et al (2009) DFT study on the intermolecular interactions between Au n (n = 2–4) and thymine. J Mol Struc THEOCHEM 915:98–104

  5. Martinez A (2009) Do anionic gold clusters modify conventional hydrogen bonds? The interaction of anionic Au n (n = 2–4) with adenine–uracil base pair. J Phys Chem A 113:1134–1140

  6. Shukla MK, Dubey M, Zakar E et al (2009) DFT investigation of the interaction of gold nanoclusters with nucleic acid base guanine and Watson–Crick guanine–cytosine base pair. J Phys Chem C 113:3960–3966

  7. Sponer J, Burda JV, Sabat M et al (1998) Interaction between the guanine–cytosine Watson–Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. J Phys Chem A 102:5951–5857

  8. Burda JV, Sponer J, Leszczynski J et al (1997) Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): nonempirical ab initio calculations on structures, energies, and nonadditivity of the interaction. J Phys Chem B 101:9670–9677

  9. Schreiber M, González L (2007) Structure and bonding of Ag(I)–DNA base complexes and Ag(I)–adenine–cytosine mispairs: an ab initio study. J Comp Chem 28:2299–2308

  10. Yang B, Wau RR, Polfer NC et al (2013) IRMPD action spectroscopy of alkali metal cations-sytosine complexes: effects of alkali metal cation size on gas phase conformations. J Am Soc Mass Spec 24:1523–1533

  11. Berdakin M, Steinmetz V, Maitre P et al (2014) Gas phase structure of metal mediated (cytosine)2Ag+ mimics the hemiprotonated (cytosine)2H+ dimer in i-motif folding. J Phys Chem A 118:3804–3809

  12. Vrkic AK, Taverner T, James PF et al (2004) Gas phase ion chemistry of charged silver(I) adenine ions via multistage mass spectrometry experiments and DFT calculations. Dalton Trans 2004:197–208

  13. Soto-Verdugo V, Metiu H, Gwinn E (2010) The properties of small Ag clusters bound to DNA bases. J Chem Phys 132:195102

  14. Preuss M, Schmidt WG, Bechstedt F (2005) Coulombic amino group–metal bonding: adsorption of adenine on Cu(110). Phys Rev Lett 94:236102–236105

  15. Rauls E, Blankenburg S, Schmidt WG (2008) DFT calculations of adenine adsorption on coin metal (110) surfaces. Surf Sci 602:2170–2174

    Article  CAS  Google Scholar 

  16. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38(6):3098–3100

    Article  CAS  Google Scholar 

  17. Perdew JP, Wang Y (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys Rev B 45:13244–13249

    Article  Google Scholar 

  18. Frisch MJ et al (2004) Gaussian 03. Gaussian, Inc., Wallingford

  19. Andrae D, Haussermann U, Dolg M et al (1990) Energy-adjusted ab initio pseudopotentials for the second and third row transition elements. Theor Chim Acta 77:123–141

    Article  CAS  Google Scholar 

  20. Godbout N, Salahub DR, Andzelm J, Wimmer E (1992) Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation. Can J Chem 70(2):560–57

  21. Sosa C, Andzelm J, Elkin BC, Wimmer E, Dobbs KD, Dixon DA (1992) J Phys Chem 96(16):6630–6636

  22. Acioli PH, Burkland S, Srinivas S (2012) Exploration of the potential energy surface of the seven atom silver cluster and the carbon monoxide ligand. Eur Phys J D 66:215–222

  23. Singh RM, Ortiz JV, Mishra MK (2010) Tautomeric forms of adenine: vertical ionization energies and Dyson orbitals. Int J Quant Chem 110:1901–1915

  24. Hanus M, Ryjacek F, Kabelac M et al (2004) 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 108:2087–2097

  25. Trygubenko SA, Bogdan TV, Rueda M et al (2002) 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 Phys 4:4192–4203

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

  27. Fogarasi G (2002) Relative stabilities of three low-energy tautomers of cytosine: a coupled cluster electron correlation study. J Phys Chem A106:1381–1390

  28. Marian CM (2007) The guanine tautomer puzzle: quantum chemical investigation of ground and excited states. J Phys Chem A 111(8):1545–1553

  29. Hanus M, Ryjacek KM, Kubar T et al (2003) Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in microhydrated environment and in aqueous solution. Guanine: surprising stabilization of rare tautomers in aqueous solution. J Am Chem Soc 125:7678–7688

  30. Rejnek J, Hanus M, Kabelac M et al (2005) 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 Phys 7:2006–2017

  31. Civcir PU (2000) A theoretical study of tautomerism of cytosine, thymine, uracil and their 1-methyl analogues in the gas and aqueous phases using AM1 and PM3. J Mol Struc THEOCHEM 532:157–169

  32. Wu Z, Ono A, Kainosho M et al (2001) H…N hydrogen bond lengths in double stranded DNA from internucleotide dipolar couplings. J Biomol NMR 19:361–365

  33. Kimura-Suda H, Petrovykh DY, Tarlov MJ (2003) Base dependent competitive adsorption of single-stranded DNA on gold. J Am Chem Soc 125:9014–9015

  34. Estarella C, Frontera A, Quiñonero AI et al (2009) Energetic vs synergetic stability: a theoretical study. J Phys Chem A 113:3266–3273

  35. Carloni P, Sprik M, Andreoni W (2000) Key steps of the cisplatin–DNA interaction: density functional theory-based molecular dynamics simulations. J Phys Chem B 104(4):823–835

  36. Senthilnathan D, Vaideeswaran S, Venuvanalingam P et al (2011) Antitumor activity of bent metallocenes: electronic structure analysis using DFT computations. J Mol Mod 17:465–475

  37. Chval Z, Kabelac M, Burda JV (2013) Mechanism of the cis-[Pt(1R,2R‑DACH)(H2O) 2] 2+ intrastrand binding to the double-stranded (pGpG)·(CpC) dinucleotide in aqueous solution: a computational DFT study. Inorg Chem 52:5801–5813

  38. Chiavarino B, Crestoni ME, Fornarini S et al (2013) Interaction of cisplatin with adenine and guanine: a combined IRMPD, MS/MS and theoretical study. J Am Chem Soc 135:1445–1455

Download references

Acknowledgments

We acknowledge the financial support provided by an Extramural Associate Research Development Award (EARDA) Type G11 grant (5G11HD049644-03) from the National Institutes of Health and administered by Northeastern Illinois University, Chicago, IL, USA.

Author information

Authors and Affiliations

  1. Department of Physics and Astronomy, Northeastern Illinois University, 5500 N. Saint Louis Avenue, Chicago, IL, 60625, USA

    Paulo H. Acioli & Sudha Srinivas

Authors
  1. Paulo H. Acioli
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sudha Srinivas
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paulo H. Acioli.

Additional information

This paper belongs to Topical Collection QUITEL 2013

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Acioli, P.H., Srinivas, S. Silver- and gold-mediated nucleobase bonding. J Mol Model 20, 2391 (2014). https://doi.org/10.1007/s00894-014-2391-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-014-2391-5

Keywords

search

Navigation