Reactivity and Aromaticity of Nucleobases are Sensitive Toward External Electric Field

Dutta, Biswa Jyoti; Bhattacharyya, Pradip

doi:10.1021/jp5047535

Cited by 28 publications

(19 citation statements)

References 87 publications

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“…The hybrid B3LYP functional was implemented in combination with the all‐electron def2‐SVP basis sets; the auxiliary def2/J basis sets were adopted for the resolution‐of‐identity procedure in the ORCA program . The B3LYP method was adopted on the basis of its wide application to analyze the aromatic character of nucleic acid bases . Taking into account that nucleobases are mainly stabilized by long‐range interactions onto intrinsic graphene, dispersion corrections for the SCF energies and gradients were included through the DFT‐D3 procedure, including also the Becke–Johnson damping function to avoid repulsive interatomic forces at short distances; basis set superposition errors were corrected by the geometrical counterpoise correction (gCP) .…”

Section: Computational Detailssupporting

confidence: 92%

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

Cortés‐Arriagada

Ortega

2018

Int J of Quantum Chemistry

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In the last years, experimental/theoretical studies have shown that graphene has a strong affinity toward nucleobases, serving as a promising nanomaterial for self-assembly, sensing, and/or sequencing of DNA/RNA constituents. Then, a complete picture of the properties of the nucleobase-graphene systems is required for its use in technological applications. This work describes a detailed quantum chemical analysis of the aromaticity of adsorbed nucleobases on graphene, comparing between aromaticity indexes based on magnetic, geometry, electron density, and electron delocalization properties of graphene-nucleobase systems. Contrary to the stated by magnetic-based aromaticity criteria (such as nucleus-independent chemical shifts), it is proved that the aromatic character of nucleobases is not increased/decreased upon binding on graphene. Therefore, magnetic aromaticity criteria are not recommended to analyze aromaticity in related systems, unless a fragmented scheme be adopted. Finally, these results are expected to expand the knowledge about the understanding of biomolecules-graphene interactions.

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Section: Computational Detailssupporting

confidence: 92%

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

Cortés‐Arriagada

Ortega

2018

Int J of Quantum Chemistry

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“…49 Aer energy minimization and 4 ns equilibration in the NPT ensemble, the systems were additionally equilibrated for 1 ns in the canonical (NVT) ensemble at 310 K. The volume of the simulation box was found to converge during the equilibration period (see Fig. 77,78 As our simulation box size in the x-direction is $100Å, the strength of the external eld applied along the x-direction ranged from about 9.7 Â 10 À5 to 4.4 Â 10 À4 a.u ( Table 1). Following this, a uniform electric eld of strength E x was applied in the direction parallel to the SWCNT axis (i.e.…”

Section: Adaptive Biasing Force (Abf) Free Energy Calculationsmentioning

confidence: 99%

Aβ self-association and adsorption on a hydrophobic nanosurface: competitive effects and the detection of small oligomers via electrical response

Jana

Sengupta

2015

Soft Matter

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Treatment of Alzheimer's disease (AD) is impeded by the lack of effective early diagnostic methods. Small, soluble Aβ globulomers play a major role in AD neurotoxicity, and detecting their presence in aqueous fluids could lead to suitable sensors. We evaluate the adsorption behavior of small Aβ oligomers on the surface of a single walled carbon nanotube of high curvature. While the intrinsic self-assembly propensity of Aβ is markedly hindered by adsorption, the oligomeric units show high degrees of surface immobilization. Immobilized complexes are capable of oligomeric growth, but with a shifted monomer-oligomer equilibrium compared to the free states. In the presence of an ionic solution and suitable external electric fields, magnitudes of the current blockades are found to be sensitive to the oligomeric number of the adsorbed complex. However, this sensitivity gradually diminishes with increasing oligomeric size. The results provide a proof-of-concept basis for further investigations in the design of sensors for detecting the toxic small oligomers of Aβ.

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“…6 Ionization potentials (IPs) and electron affinities (EAs) are the important intrinsic properties of NABs allowing a deep understanding of the specific mechanisms, such as various radiation-induced phenomena of genetic materials, 7,8 the charge-transfer process along the DNA strand, 9 and the reactivity and aromaticity of NABs in an external electric field. 10 The reliable experimental determination of IPs and EAs of NABs is relatively limited due to the various base pairing and stacking models, 11,12 complicated surrounding environment and tautomerization in the gas phase. 13 The uncertainties in experimental determination of EAs are within a broad range from negative to positive values, extending up to several electron volts (eVs).…”

Section: Introductionmentioning

confidence: 99%

Applicability of optimal functional tuning in density functional calculations of ionization potentials and electron affinities of adenine–thymine nucleobase pairs and clusters

Sun

Zhang

Sun

2015

Phys. Chem. Chem. Phys.

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The intrinsic properties of DNA and RNA nucleic acid bases (NABs) such as ionization potentials (IPs) and electron affinities (EAs) are crucial to reveal various biochemical mechanisms. Successful application of density functional theory (DFT) using nonempirically tuned long-range corrected (LC) functionals for calculation of vertical ionization potentials (VIPs) and electron affinities (VEAs) of various adenine-thymine (AT) nucleobase pairs and clusters is demonstrated. We employ a tuning method by applying an asymptotically correct exchange-correlation potential adjusted to give frontier orbital energies (-εHOMO and -εLUMO) representing IPs and EAs and assess the quality of prediction which is comparable to high-level EOM-IP-CCSD/CCSD methods. The delocalization error calculated using different DFT functionals is quantified by calculations using fractional electron numbers. The cooperative effect of H-bonding and π-stacking on the IPs of AT clusters, as well as the reactivity parameters (global hardness and electrophilicity), is quantitatively characterized using the tuned LC functionals. The present work aims at providing a reliable and efficient theoretical tool for the prediction of the related electron donor and acceptor abilities of the NAB systems.

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Reactivity and Aromaticity of Nucleobases are Sensitive Toward External Electric Field

Cited by 28 publications

References 87 publications

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

Aβ self-association and adsorption on a hydrophobic nanosurface: competitive effects and the detection of small oligomers via electrical response

Applicability of optimal functional tuning in density functional calculations of ionization potentials and electron affinities of adenine–thymine nucleobase pairs and clusters

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