Interaction of Nucleobases with Wrinkled Graphene Surface: Dispersion Corrected DFT and AFM Studies

Panigrahi, Suvasini; Bhattacharya, Anuradha; Banerjee, S.; Bhattacharyya, Dhananjay

doi:10.1021/jp207588s

Cited by 88 publications

(84 citation statements)

References 43 publications

(70 reference statements)

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“…[10] Van der Waals density functional (vdW-DF)[17–19] for adenine on graphene also yields a too low binding (16.4 kcal/mol), 1 [13] as compared to the result of Antony and Grimme (19.7kcal/mol[10]). The binding energies from the wB97XD/6-31G(d,p) with 8×8-ring graphene sheet[16] agree very well within 0.1–1.4 kcal/mol with those of Antony et al,[10] yet the relative strength for T and C are switched (G>A>C>T, 22.5>20.3>18.9 and 18.4 kcal/mol). Varghese et al carried out an experimental investigation into the binding of DNA nucleobases with graphene using isothermal titration calorimetry (ITC).…”

Section: Introductionmentioning

confidence: 59%

“…[9–16] Using B97-D, B2PLYP-D and SCS-MP2 methods, Antony et al extensively investigated the adsorption of the DNA nucleobases on a variety of graphene clusters from 24 to 150 carbon atoms. [10] The interaction sequence after basis set superposition error correction (BSSE) at B2PLYP-D/TVZ(2df,2pd)//B97-D/TZV(d,p) level for DNA bases on C 54 H 18 is, G (23.9 kcal/mol)>A (19.7 )>T(18.5)>C(18.2 ), and they suggested the proper size of nano graphene with at least about 50 carbon atoms.…”

Section: Introductionmentioning

confidence: 99%

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Insight into the interaction between DNA bases and defective graphenes: Covalent or non-covalent

Meher

Eustache

et al. 2014

Journal of Molecular Graphics and Modelling

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Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C72H24, C71H24, and C70H24 for pristine, mono- and divacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G>A>T>C on the pristine and di-vacant graphene and G>T>A>C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene.

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Section: Introductionmentioning

confidence: 59%

Section: Introductionmentioning

confidence: 99%

Insight into the interaction between DNA bases and defective graphenes: Covalent or non-covalent

Meher

Eustache

et al. 2014

Journal of Molecular Graphics and Modelling

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“…Strong NH···π interactions are responsible for the stabilization of such geometries. 33 One would have missed these minima if one had started from just the stacked initial geometry, and hence a study of the orientation dependence as performed here is necessary. Further, in some of the complexes (C−DBA-12, C−DBA-18, T−DBA-18, etc.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Stability of Nucleobases and Base Pairs Adsorbed on Graphyne and Graphdiyne

Shekar

Swathi

2014

J. Phys. Chem. C

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A theoretical understanding of the structure and energetics of the interaction of nucleobases (NBs) and amino acids with extended carbon-based network structures is crucial for understanding phenomena occurring at the nanobio interface. Herein, we investigate the adsorption of NBs and base pairs (BPs) on the new network materials in the carbon family, graphyne (GY), and graphdiyne (GDY) using dispersioncorrected density functional theory (ωB97XD functional) with a basis set of triple-ζ quality. Systematic investigations on the orientation dependence of the interaction of each of the NBs with a series of model compounds along with their superstructures reveal that the binding strengths of NBs on GY and GDY follow the order G > A > C > T > U, while those of BPs follow the order GC > AT > AU. The NBs and the BPs are found to adsorb at distances of ∼3 Å from the GY and GDY sheets, and the adsorption strengths are higher for GY than GDY. The small decrease in the hydrogen bond energies of the BPs subsequent to adsorption suggests that GY and GDY can serve as promising templates for the self-assembly of DNA and RNA. Our first-principles studies on how the NBs interact with GY and GDY can serve as a first and significant step toward the aim of understanding the interactions of DNA and RNA with GY and GDY as well as designing biomolecular devices based on GY and GDY. We believe that our findings will motivate several studies toward understanding the interface of biology and the nanoworld.

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“…[1][2][3][4][5][6][7][8] . A comprehensive analysis of the properties of these systems could be very useful for designing highly biocompatible materials and specific biosensors [9][10][11][12][13][14] .…”

Section: Introductionmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

100

113

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Computational spectroscopy techniques have become in the last years effective means to analyze and assign infrared (IR) spectra for molecular systems of increasing dimensions and in different environments. However, transition from compilations of harmonic data to full anharmonic simulations of spectra is still under way. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed to a quantitative reproduction of the spectra of nucleic acid bases complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work, we have chosen two popular and inexpensive approaches to model dispersion interaction, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

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Interaction of Nucleobases with Wrinkled Graphene Surface: Dispersion Corrected DFT and AFM Studies

Cited by 88 publications

References 43 publications

Insight into the interaction between DNA bases and defective graphenes: Covalent or non-covalent

Insight into the interaction between DNA bases and defective graphenes: Covalent or non-covalent

Stability of Nucleobases and Base Pairs Adsorbed on Graphyne and Graphdiyne

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

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