Structure and bonding of Ag(I)–DNA base complexes and Ag(I)–adenine–cytosine mispairs: An ab Initio study

Schreiber, Marko; González, Leticia

doi:10.1002/jcc.20743

Cited by 33 publications

(29 citation statements)

References 64 publications

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“…From the same authors [98], the interaction with the cationic silver atom shows the order C (65.9 kcal/mol) > U (43.9 kcal/mol) and the discrepancy respect our calculations is, on average, only 3.4 kcal/mol. Most accurate calculations [99] using a MP2/cc-pVTZ/MWB level of theory shows a binding energy for the cationic Ag-adenine of 53.1 kcal/mol; this value compares very well with our result of 57.99 kcal/mol. For the Ag-cytosine cation, the same authors reports a value of 61.9 kcal/mol, we obtained a binding energy of 68.50 kcal/mol.…”

Section: Cationic Nucleobasessupporting

confidence: 86%

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On the interaction between gold and silver metal atoms and DNA/RNA nucleobases – a comprehensive computational study of ground state properties

Leal

Lopez-Acevedo

2015

Nanotechnology Reviews

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On the interaction between gold and silver metal atoms and DNA/RNA nucleobasesa comprehensive computational study of ground state properties Abstract: The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an exhaustive study of the ground state electronic properties of DNA/RNA nucleobases interacting with gold and silver atoms at three charge states: neutral, cationic, and anionic. We describe the nature of the stability and electronic properties in each hybrid metallic structure. In addition to the metal interacting with the five isolated nucleobases, we included their respective DNA-WC base pairs and one case with the protonated sugarphosphate backbone. As a general trend, we discerned that the energetic ordering of isomers follows simple electrostatic rules as expected from previous studies. Also, we found that although the metal localizes almost all of the extra charge in the anionic system, a donation of charge is shared almost equally in the cationic system. Furthermore, the frontier orbitals of the cationic system tend to have more effects from the pairing and inclusion of the backbone than the anionic system. Finally, the electronic gap varies greatly among all of the considered structures and could be further used as a fingerprint when searching DNA-metal hybrid structures. -Acevedo: DNA/RNA nucleobases interacting with gold and silver atoms 191 University, Finland. Her research interest focuses on the quantum modeling of hybrid soft-nano systems and the development of computational methods for multi-scale simulations. She obtained her Bachelor's and Master's degrees in physics from the University of Strasbourg, France. In 2006, she obtained a PhD in theoretical physics working on quantum algorithmics from the University of Cergy-Pontoise, France. Her postdoctoral experience includes stays at

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Section: Cationic Nucleobasessupporting

confidence: 86%

“…The available results only consider the lowest energetic tautomers [69,99]. Therefore, our results in energetics and stabilization can not be directly compared.…”

Section: A(n1)-t(o4) > A(n1)-t(o2) > A(n6)-t(o4) > A(n3) > A(n7)mentioning

confidence: 84%

On the interaction between gold and silver metal atoms and DNA/RNA nucleobases – a comprehensive computational study of ground state properties

Leal

Lopez-Acevedo

2015

Nanotechnology Reviews

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“…47, 48 We have not tested whether the much weaker binding of neutral Ag clusters can also cause such tautomerization, because doing this in a meaningful way would require inclusion of solvent effects, and thus is beyond the scope of the current work. 47, 48 We have not tested whether the much weaker binding of neutral Ag clusters can also cause such tautomerization, because doing this in a meaningful way would require inclusion of solvent effects, and thus is beyond the scope of the current work.…”

Section: A Ground Statementioning

confidence: 99%

The properties of small Ag clusters bound to DNA bases

Soto-Verdugo

Metiu

Gwinn

2010

The Journal of Chemical Physics

113

140

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We study the binding of neutral silver clusters, Ag(n) (n=1-6), to the DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T) and the absorption spectra of the silver cluster-base complexes. Using density functional theory (DFT), we find that the clusters prefer to bind to the doubly bonded ring nitrogens and that binding to T is generally much weaker than to C, G, and A. Ag(3) and Ag(4) make the stronger bonds. Bader charge analysis indicates a mild electron transfer from the base to the clusters for all bases, except T. The donor bases (C, G, and A) bind to the sites on the cluster where the lowest unoccupied molecular orbital has a pronounced protrusion. The site where cluster binds to the base is controlled by the shape of the higher occupied states of the base. Time-dependent DFT calculations show that different base-cluster isomers may have very different absorption spectra. In particular, we find new excitations in base-cluster molecules, at energies well below those of the isolated components, and with strengths that depend strongly on the orientations of planar clusters with respect to the base planes. Our results suggest that geometric constraints on binding, imposed by designed DNA structures, may be a feasible route to engineering the selection of specific cluster-base assemblies.

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“…To explain the complexity of various tautomeric forms of purine bases by energetic stabilities and hydrogen bonding interactions, quantum chemical calculations have been introduced. [6].…”

Section: Introductionmentioning

confidence: 95%