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Silver- and gold-mediated nucleobase bonding

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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

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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.

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Correspondence to Paulo H. Acioli.

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This paper belongs to Topical Collection QUITEL 2013

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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

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Keywords

  • Nucleobase–noble metal interactions
  • Density functional theory calculations