Adsorption of thymine and uracil on 1 : 1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

Michalkova, A.; Robinson, Teri L.; Leszczyński, Jerzy

doi:10.1039/c1cp00008j

Cited by 56 publications

(64 citation statements)

References 114 publications

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“…Moreover, this finding agrees well with the results of other theoretical studies of adsorption of aromatic molecules (thymine (−34.3 vs −26.9 kcal mol −1 ), and uracil (−35.9 vs −28.2 kcal mol −1 , B3LYP)[43], benzene (−4.5 vs + 0.1 kcal mol −1 )[41,42]), and NACs (DNT, −19 vs −9 kcal mol −1[19] and −17.7 vs −6.5 kcal mol −1[15]) on the surfaces of kaolinite. This finding corresponds well with the stronger and more numerous adsorbate-surface H-bonds in K(o)-NCC than in K(t)-NCC.…”

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confidence: 91%

Theoretical study of adsorption of nitrogen-containing environmental contaminants on kaolinite surfaces

Scott

Burns²,

Hill

2014

J Mol Model

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The adsorption of nitrogen-containing compounds (NCCs) including 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazol-5-one (NTO) on kaolinite surfaces was investigated. The M06-2X and M06-2X-D3 density functionals were applied with the cluster approximation. Several different positions of NCCs relative to the adsorption sites of kaolinite were examined, including NCCs in perpendicular and parallel orientation toward both surface models of kaolinite. The binding between the target molecules and kaolinite surfaces was analyzed and bond energies were calculated applying the atoms in molecules (AIM) method. All NCCs were found to prefer a parallel orientation toward both kaolinite surfaces, and were bound more strongly to the octahedral than to the tetrahedral site. TNT exhibited the strongest interaction with the octahedral surface and DNAN with the tetrahedral surface of kaolinite. Hydrogen bonding was shown to be the dominant non-covalent interaction for NCCs interacting with the octahedral surface of kaolinite with a small stabilizing effect of dispersion interactions. In the case of adsorption on the tetrahedral surface, kaolonite-NCC binding was shown to be governed by the balance between hydrogen bonds and dispersion forces. The presence of water as a solvent leads to a significant decrease in the adsorption strength for all studied NCCs interacting with both kaolinite surfaces.

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confidence: 91%

Theoretical study of adsorption of nitrogen-containing environmental contaminants on kaolinite surfaces

Scott

Burns²,

Hill

2014

J Mol Model

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“…The most obvious one is that, in almost all cases, a spontaneous proton transfer to the base is observed, the transfer being more pronounced for Osub than for Tsub surfaces, due to the larger acidity of the Brønsted site in the former. The total interaction energy is driven by this favorable proton transfer, leading to stabilizing contacts with the surface via H-bonds which seem to play a relatively important role as observed in previous studies, 37,38 and by dispersion interaction with the surface. Surprisingly the feasibility of the proton transfer seems not to be driven by the proton affinity, but rather by the accessibility of the heteroatom.…”

Section: Discussionmentioning

confidence: 75%

Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite

Mignon

Sodupe

2012

Phys. Chem. Chem. Phys.

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In the present study, DFT periodic plane wave calculations, at the PBE-D level of theory, were carried out to investigate the interaction of DNA nucleobases with acidic montmorillonite. The surface model was considered in its octahedral (Osub) and tetrahedral (Tsub) substituted forms, known to have different acidic properties. The adsorption of adenine, guanine and cytosine was considered in both orthogonal and coplanar orientations with the surface, interacting with the proton via a given heteroatom. In almost all considered cases, adsorption involved the spontaneous proton transfer to the nucleobase, with a more pronounced character in the Osub structures. The binding energy is about 10 kcal mol(-1) larger for Osub than for Tsub complexes mainly due to the larger acidity in Osub surfaces and due to the better stabilization by H-bond contacts between the negatively charged surface and the protonated base. The binding energy of coplanar orientations of the base is observed to be as large as the orthogonal ones due to a balance between electrostatic and dispersion contributions. Finally the binding of guanine and adenine on the acidic surface amounts to 50 kcal mol(-1) while that of cytosine rises to 44 kcal mol(-1).

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“…The [(Al 3+ ) 6 (s-HO À ) 12 (i-HO À ) 6 (a-O 2À ) 6 ] 12À model with various termination strategies at the periphery and charge neutralization is a common model in the literature. 17 2D) parallel and perpendicular to the asymmetry of the cluster model, respectively. Furthermore, we employed 12 Na + and 8 Mg 2+ counter ions to neutralize the model's negative charge.…”

Section: Development Of the Cluster Modelmentioning

confidence: 98%

The positions of inner hydroxide groups and aluminium ions in exfoliated kaolinite as indicators of the external chemical environment

Taborosi

Kurdi

Szilágyi

2014

Phys. Chem. Chem. Phys.

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Kaolinite as a remarkable industrial raw material has notable structural features despite its simple chemical composition (Al2O3·2SiO2·2H2O). We report here a systematic development of a coordination chemical model for the [6Al-6(OH)] honeycomb-like unit of kaolinite's octahedral sheet, which was proposed to be the adsorption site for small molecules from earlier studies. The coordination environment of the Al(3+) ions was completed with outer sphere groups from both octahedral and tetrahedral sheets. Dangling bonds were terminated by additional Al(3+) and Si(4+) ions with hydroxide and oxide groups from the second coordination sphere versus simple protonation. A cage of Na(+) and Mg(2+) ions rendered the computational model to be charge neutral. In this exfoliated kaolinite model, the inner hydroxide groups and the adjacent Al(3+) ions have compositionally the most complete environments with respect to the crystal structure. Thus, their atomic positions were used as a benchmark for the level of theory dependence of the optimized structures. We evaluated the performance of a representative set of density functionals, basis sets, point-charges, identified pitfalls and caveats. Importantly, the structural changes during optimization of periodic and cluster models suggest pliability for the exfoliated kaolinite layers, which is influenced by the external chemical environment.

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Adsorption of thymine and uracil on 1 : 1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

Cited by 56 publications

References 114 publications

Theoretical study of adsorption of nitrogen-containing environmental contaminants on kaolinite surfaces

Theoretical study of adsorption of nitrogen-containing environmental contaminants on kaolinite surfaces

Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite

The positions of inner hydroxide groups and aluminium ions in exfoliated kaolinite as indicators of the external chemical environment

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