Stacking interaction of cytosine with carbon nanotubes: MP2, DFT and Raman spectroscopy study

Stepanian, S. G.; Karachevtsev, Maksym V.; Glamazda, A. Yu.; Karachevtsev, V. A.; Adamowicz, Ludwik

doi:10.1016/j.cplett.2008.05.035

Cited by 56 publications

(49 citation statements)

References 35 publications

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“…Our ab initio calculation of the stacking energy of cytosine and a semiconducting nanotube 0.79 nm in diameter gives an energy close to 14.9 kcal mol À1 . [43] The energy of p-p stacking between adenine and the SWNT surface is close to this value. The energy of adenine adsorption onto a metallic nanotube is not yet known.…”

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confidence: 65%

Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Karachevtsev¹,

Gladchenko²,

Karachevtsev³

et al. 2008

ChemPhysChem

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Adsorption of poly(rA) on a single-walled carbon nanotube surface in aqueous suspension and the subsequent hybridization of this polymer with free poly(rU) is studied. A comparison of the temperature dependence of the absorbance of free poly(rA) and poly(rA) adsorbed on the nanotube surface [poly(rA)(NT)] at nu(max)= 38,500 cm(-1) shows that the thermostability of the adsorbed polymer is higher. Molecular dynamics simulations demonstrate that more than half of the adenines are not stacked on the tube surface and some of them undergo self-stacking. After addition of a complementary poly(rU) to the poly(rA)(NT) suspension, a double-stranded polymer is formed as confirmed by the characteristic S-like form of its melting curve. However, the melting temperature of this polymer is lower than that of the free poly(rA)poly(rU) duplex. This result indicates that poly(rU) hybridization with poly(rA)(NT) occurs with defects along the whole length of the polymer because of pi-pi stacking between nitrogen bases and the nanotube surface, which hinders the usual hybridization process. Computer modeling demonstrates different possible structures of hybridized polymers on the nanotube surface.

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confidence: 65%

Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Karachevtsev¹,

Gladchenko²,

Karachevtsev³

et al. 2008

ChemPhysChem

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“…Concerning the density functional we faced certain restrictions with respect to CPU time and the implementation of periodic boundary conditions. This prohibits, for example, using new density functionals like MPWB1K [24][25][26]. Our calculations were performed with the PW91 [27] density functional which, while not including dispersion energy contributions, can efficiently be applied to large periodic systems.…”

Section: Methodsmentioning

confidence: 99%

Gas sensing properties of platinum derivatives of single-walled carbon nanotubes: A DFT analysis

Pannopard

Khongpracha

Probst

et al. 2009

Journal of Molecular Graphics and Modelling

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“…22 It must be noted, that generalised knowledge of the π•••π interactions origins, quantitative predictions of geometries and energies are not available yet, however, recently a lot of theoretical calculations have been made in this field, associated with both real and model systems. 21,23,24,25,26,27 The model systems, that are extensively analysed, are those ones containing small aromatic molecules like pyridine and benzene, arranged in selected arbitrary geometries. 23,28,29,30,31,32 They are good examples of systems in which π•••π interactions are present and they are easy to explore with the quantum chemistry methods.…”

Section: Introductionmentioning

confidence: 99%

Can Stacking Interactions Exist Beyond the Commonly Accepted Limits?

Kruszyński

Sierański

2016

Crystal Growth & Design

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Systematic study of π-π interactions of structurally characterised compounds containing parallel benzene and/or pyridine rings was carried out. The gathered geometrical parameters were analysed in statistical terms. The quantum mechanical calculations were made for the above mentioned ring systems in different arrangements and the calculated interaction energy values were referred to the statistical data. The maximum bonding energy of the studied systems is about 3 kcal/mol. The ring rotation about the vertical axis has almost no influence on the system binding energy. In the specific ring arrangements, the stacking interactions can be bonding even for ring centroids distances larger than 6 Å. The results prove that the appliance of the generally accepted geometrical criteria of stacking interactions leads to the omission of the multiple bonding intermolecular interactions during the interpreting of the reactivity, self assembly as well as the properties of the supramolecular compounds. AbstractSystematic study of π-π interactions of structurally characterised compounds containing parallel benzene and/or pyridine rings was carried out. The gathered geometrical parameters were analysed in statistical terms. The quantum mechanical calculations were made for the above mentioned ring systems in different arrangements and the calculated interaction energy values were referred to the statistical data. The maximum bonding energy of the studied systems is about 3 kcal/mol. The ring rotation about the vertical axis has almost no influence on the system binding energy. In the specific ring arrangements, the stacking interactions can be bonding even for ring centroids distances larger than 6 Å. The results prove that the appliance of the generally accepted geometrical criteria of stacking interactions leads to the omission of the multiple bonding intermolecular interactions during the interpreting of the reactivity, self assembly as well as the properties of the supramolecular compounds.

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Stacking interaction of cytosine with carbon nanotubes: MP2, DFT and Raman spectroscopy study

Cited by 56 publications

References 35 publications

Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Gas sensing properties of platinum derivatives of single-walled carbon nanotubes: A DFT analysis

Can Stacking Interactions Exist Beyond the Commonly Accepted Limits?

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