scholarly journals Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Biosensors ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 59
Author(s):  
Hikmet Hakan Gürel ◽  
Bahadır Salmankurt
Keyword(s):  
Density Functional ◽  
2D Materials ◽  
High Surface ◽  
Experimental Studies ◽  
Interaction Mechanism ◽  
Volume Ratio ◽  
First Principle ◽  
Functional Theory ◽  
Silicon And Germanium ◽  
Insight Into

Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases’ sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green’s function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.

scholarly journals Mo-doped boron nitride monolayer as a promising single-atom electrocatalyst for CO2 conversion

2019 ◽  
Vol 10 ◽  
pp. 540-548 ◽  
Author(s):  
Qianyi Cui ◽  
Gangqiang Qin ◽  
Weihua Wang ◽  
Lixiang Sun ◽  
Aijun Du ◽  
...  
Keyword(s):  
Boron Nitride ◽  
Density Functional ◽  
Experimental Studies ◽  
Catalytic Performance ◽  
Reduction Reaction ◽  
Single Atom ◽  
Ambient Conditions ◽  
Functional Theory ◽  
Earth Abundant ◽  
Insight Into

The design of new, efficient catalysts for the conversion of CO2 to useful fuels under mild conditions is urgent in order to reduce greenhouse gas emissions and alleviate the energy crisis. In this work, a series of transition metals (TMs), including Sc to Zn, Mo, Ru, Rh, Pd and Ag, supported on a boron nitride (BN) monolayer with boron vacancies, were investigated as electrocatalysts for the CO2 reduction reaction (CRR) using comprehensive density functional theory (DFT) calculations. The results demonstrate that a single-Mo-atom-doped boron nitride (Mo-doped BN) monolayer possesses excellent performance for converting CO2 to CH4 with a relatively low limiting potential of −0.45 V, which is lower than most catalysts for the selective production of CH4 as found in both theoretical and experimental studies. In addition, the formation of OCHO on the Mo-doped BN monolayer in the early hydrogenation steps is found to be spontaneous, which is distinct from the conventional catalysts. Mo, as a non-noble element, presents excellent catalytic performance with coordination to the BN monolayer, and is thus a promising transition metal for catalyzing CRR. This work not only provides insight into the mechanism of CRR on the single-atom catalyst (Mo-doped BN monolayer) at the atomic level, but also offers guidance in the search for appropriate earth-abundant TMs as electrochemical catalysts for the efficient conversion of CO2 to useful fuels under ambient conditions.

Molecular Investigations of the Newly Synthesized Azomethines as Antioxidants: Theoretical and Experimental Studies

2019 ◽  
Vol 19 (6) ◽  
pp. 419-433 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Liudmila Filippovich ◽  
Evgenij Dikusar ◽  
Anhelina Pazniak ◽  
...  
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Experimental Studies ◽  
Antioxidant Property ◽  
Nbo Analysis ◽  
Antioxidant Potential ◽  
Functional Theory ◽  
Homo And Lumo ◽  
Intramolecular Hydrogen ◽  
Activity Mechanism

: In this study, the antioxidant property of new synthesized azomethins has been investigated as theoretical and experimental. Methods and Results: Density functional theory (DFT) was employed to investigate the Bond Dissociation Enthalpy (BDE), Mulliken Charges, NBO analysis, Ionization Potential (IP), Electron Affinities (EA), HOMO and LUMO energies, Hardness (η), Softness (S), Electronegativity (µ), Electrophilic Index (ω), Electron Donating Power (ω-), Electron Accepting Power (ω+) and Energy Gap (Eg) in order to deduce scavenging action of the two new synthesized azomethines (FD-1 and FD-2). Spin density calculations and NBO analysis were also carried out to understand the antioxidant activity mechanism. Comparison of BDE of FD-1 and FD-2 indicate the weal antioxidant potential of these structures. Conclusion: FD-1 and FD-2 have very high antioxidant potential due to the planarity and formation of intramolecular hydrogen bonds.

scholarly journals Ab Initio Study of Ferroelectric Critical Size of SnTe Low-Dimensional Nanostructures

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 732 ◽  
Author(s):  
Takahiro Shimada ◽  
Koichiro Minaguro ◽  
Tao Xu ◽  
Jie Wang ◽  
Takayuki Kitamura
Keyword(s):  
Density Functional ◽  
Critical Size ◽  
Density Functional Theory Calculations ◽  
Cell Width ◽  
Functional Theory ◽  
Unit Cells ◽  
Principle Density Functional Theory ◽  
Low Dimensional ◽  
Insight Into ◽  
Ferroelectric Perovskite

Beyond a ferroelectric critical thickness of several nanometers existed in conventional ferroelectric perovskite oxides, ferroelectricity in ultimately thin dimensions was recently discovered in SnTe monolayers. This discovery suggests the possibility that SnTe can sustain ferroelectricity during further low-dimensional miniaturization. Here, we investigate a ferroelectric critical size of low-dimensional SnTe nanostructures such as nanoribbons (1D) and nanoflakes (0D) using first-principle density-functional theory calculations. We demonstrate that the smallest (one-unit-cell width) SnTe nanoribbon can sustain ferroelectricity and there is no ferroelectric critical size in the SnTe nanoribbons. On the other hand, the SnTe nanoflakes form a vortex of polarization and lose their toroidal ferroelectricity below the surface area of 4 × 4 unit cells (about 25 Å on one side). We also reveal the atomic and electronic mechanism of the absence or presence of critical size in SnTe low-dimensional nanostructures. Our result provides an insight into intrinsic ferroelectric critical size for low-dimensional chalcogenide layered materials.

First principle simulation on oxidation mechanism of diethyl ether by nitrogen dioxide

2015 ◽  
Vol 14 (03) ◽  
pp. 1550020 ◽  
Author(s):  
Yuan Yuan ◽  
Wei Hu ◽  
Xuhui Chi ◽  
Cuihua Li ◽  
Dayong Gui ◽  
...  
Keyword(s):  
Diethyl Ether ◽  
Energy Barrier ◽  
Density Functional ◽  
Oxidation Process ◽  
Oxidation Mechanism ◽  
High Energy ◽  
First Principle ◽  
Functional Theory ◽  
The Third ◽  
High Energy Barrier

The oxidation mechanism of diethyl ethers by NO2was carried out using density functional theory (DFT) at the B3LYP/6-31+G (d, p) level. The oxidation process of ether follows four steps. First, the diethyl ether reacts with NO2to produce HNO2and diethyl ether radical with an energy barrier of 20.62 kcal ⋅ mol-1. Then, the diethyl ether radical formed in the first step directly combines with NO2to form CH3CH ( ONO ) OCH2CH3. In the third step, the CH3CH ( ONO ) OCH2CH3was further decomposed into the CH3CH2ONO and CH3CHO with a moderately high energy barrier of 32.87 kcal ⋅ mol-1. Finally, the CH3CH2ONO continues to react with NO2to yield CH3CHO , HNO2and NO with an energy barrier of 28.13 kcal ⋅ mol-1. The calculated oxidation mechanism agrees well with Nishiguchi and Okamoto's experiment and proposal.

A density functional theory insight into the structure and reactivity of diphenyltin(IV) derivative of glycylphenylalanine

2016 ◽  
Vol 39 (3-4) ◽  
Author(s):  
Sandeep Pokharia ◽  
Rachana Joshi ◽  
Mamta Pokharia ◽  
Swatantra Kumar Yadav ◽  
Hirdyesh Mishra
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Functional Theory ◽  
Insight Into

AbstractThe quantum-chemical calculations based on density functional theory (DFT) have been performed on the diphenyltin(IV) derivative of glycyl-phenylalanine (H

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