scholarly journals Predicting Finite-Bias Tunneling Current Properties from Zero-Bias Features: The Frontier Orbital Bias Dependence at an Exemplar Case of DNA Nucleotides in a Nanogap

Nanomaterials ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3021
Author(s):  
Ivana Djurišić ◽  
Vladimir P. Jovanović ◽  
Miloš S. Dražić ◽  
Aleksandar Ž. Tomović ◽  
Radomir Zikic
Keyword(s):  
Transport Properties ◽  
Single Molecule ◽  
Density Functional ◽  
Tunneling Current ◽  
High Sensitivity ◽  
Orbital Energy ◽  
Frontier Orbital ◽  
Zero Bias ◽  
Electronic Tunneling ◽  
Tunneling Transport

The electrical current properties of single-molecule sensing devices based on electronic (tunneling) transport strongly depend on molecule frontier orbital energy, spatial distribution, and position with respect to the electrodes. Here, we present an analysis of the bias dependence of molecule frontier orbital properties at an exemplar case of DNA nucleotides in the gap between H-terminated (3, 3) carbon nanotube (CNT) electrodes and its relation to transversal current rectification. The electronic transport properties of this simple single-molecule device, whose characteristic is the absence of covalent bonding between electrodes and a molecule between them, were obtained using density functional theory and non-equilibrium Green’s functions. As in our previous studies, we could observe two distinct bias dependences of frontier orbital energies: the so-called strong and the weak pinning regimes. We established a procedure, from zero-bias and empty-gap characteristics, to estimate finite-bias electronic tunneling transport properties, i.e., whether the molecular junction would operate in the weak or strong pinning regime. We also discuss the use of the zero-bias approximation to calculate electric current properties at finite bias. The results from this work could have an impact on the design of new single-molecule applications that use tunneling current or rectification applicable in high-sensitivity sensors, protein, or DNA sequencing.

C60 as Electron Acceptor and Donor: A Comparative DFT Study of Li@C60 and F@C60

2018 ◽  
Vol 71 (12) ◽  
pp. 953 ◽  
Author(s):  
Ambrish Kumar Srivastava ◽  
Sarvesh Kumar Pandey ◽  
Anoop Kumar Pandey ◽  
Neeraj Misra
Keyword(s):  
Charge Transfer ◽  
Electron Acceptor ◽  
Density Functional ◽  
Energy Gap ◽  
Orbital Energy ◽  
Prototype System ◽  
Theory Approach ◽  
Frontier Orbital ◽  
Functional Theory ◽  
Fundamental Properties

Fullerene (C60) is a stable prototype system for a special class of nanomaterials. In this work, the smallest alkali metal (Li) and halogen (F) atoms were encapsulated in the C60 cage, and comparative quantum chemical calculations (QCCs) were performed on their various properties using a density functional theory approach. It was noted that the off-centre distance of Li is higher than that of F. The QCCs of the charge transfer to and from C60 were also analysed. Although charge transfer to and from the C60 cage takes place in both cases, Li@C60 becomes more polar than F@C60, suggesting a better electron-accepting nature of C60 than electron-donating behaviour. This fact is consistent with the natural bond orbital (NBO) charge on the trapped atoms and the dipole moment as well as the binding energy values of the encapsulated C60. Although the encapsulation of both atoms reduces the frontier orbital energy gap, the frontier orbital gap of Li@C60 is smaller than that of F@C60. More interestingly, the depression in the polarizability of Li@C60 is significantly large relative to that of F@C60. These findings also support the tendency of C60 to act as electron acceptor. This study provides some insights into the fundamental properties of C60 and should be helpful in designing new endofullerene complexes for a variety of applications.

scholarly journals Diboron- and Diaza-Doped Anthracenes and Phenanthrenes: Their Electronic Structures for Being Singlet Fission Chromophores

2020 ◽  
Author(s):  
Ekadashi Pradhan ◽  
Tao Zeng
Keyword(s):  
Excited States ◽  
Electronic Structures ◽  
Density Functional ◽  
Orbital Energy ◽  
Frontier Orbital ◽  
Singlet Fission ◽  
Functional Theory ◽  
Alternant Hydrocarbon ◽  
Mirror Relation ◽  
Frontier Orbital Energy

<p>We used quantum chemistry methods at the levels of mixed-reference spin-flipping time-dependent density functional theory and multireference perturbation theory to study diboron- and diaza-doped anthracenes and phenanthrenes. This class of structures recently surged as potential singlet fission chromophores. We studied electronic structures of their excited states and clarify the reasons why they satisfy or fail to satisfy the energy criteria for singlet fission chromophores. Many studied structures have their S<sub>1</sub> states not dominated by HOMO->LUMO excitation, so that they cannot be described using the conventional two sites model. This is attributed to frontier orbital energy shifts induced by the doping and different charge transfer energies in different one-electron singlet excitations, or in other words different polarizations of hole and/or particle orbitals in their S<sub>1</sub> and T<sub>1</sub> states. There is a mirror relation between the orbital energy shifts induced by diboron- and diaza-dopings, which, together with alternant hydrocarbon pairings of occupied and unoccupied orbitals, leads to more mirror relations between the excited states' electronic structures of the two types of doped structures. </p>

Enhancement of tunneling current in phosphorene tunnel field effect transistors by surface defects

2018 ◽  
Vol 20 (8) ◽  
pp. 5699-5707 ◽  
Author(s):  
Juan Lu ◽  
Zhi-Qiang Fan ◽  
Jian Gong ◽  
Jie-Zhi Chen ◽  
Huhe ManduLa ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Transport Properties ◽  
Field Effect ◽  
Density Functional ◽  
Surface Defects ◽  
Field Effect Transistors ◽  
Tunneling Current ◽  
Functional Theory ◽  
Non Equilibrium Green’S Function ◽  
Nitrogen Phosphorus

The effects of the staggered double vacancies, hydrogen (H), 3d transition metals, for example cobalt, and semiconductor covalent atoms, for example, germanium, nitrogen, phosphorus (P) and silicon adsorption on the transport properties of monolayer phosphorene were studied using density functional theory and non-equilibrium Green's function formalism.

scholarly journals Diboron- and Diaza-Doped Anthracenes and Phenanthrenes: Their Electronic Structures for Being Singlet Fission Chromophores

2020 ◽  
Author(s):  
Ekadashi Pradhan ◽  
Tao Zeng
Keyword(s):  
Excited States ◽  
Electronic Structures ◽  
Density Functional ◽  
Orbital Energy ◽  
Frontier Orbital ◽  
Singlet Fission ◽  
Functional Theory ◽  
Alternant Hydrocarbon ◽  
Mirror Relation ◽  
Frontier Orbital Energy

<p>We used quantum chemistry methods at the levels of mixed-reference spin-flipping time-dependent density functional theory and multireference perturbation theory to study diboron- and diaza-doped anthracenes and phenanthrenes. This class of structures recently surged as potential singlet fission chromophores. We studied electronic structures of their excited states and clarify the reasons why they satisfy or fail to satisfy the energy criteria for singlet fission chromophores. Many studied structures have their S<sub>1</sub> states not dominated by HOMO->LUMO excitation, so that they cannot be described using the conventional two sites model. This is attributed to frontier orbital energy shifts induced by the doping and different charge transfer energies in different one-electron singlet excitations, or in other words different polarizations of hole and/or particle orbitals in their S<sub>1</sub> and T<sub>1</sub> states. There is a mirror relation between the orbital energy shifts induced by diboron- and diaza-dopings, which, together with alternant hydrocarbon pairings of occupied and unoccupied orbitals, leads to more mirror relations between the excited states' electronic structures of the two types of doped structures. </p>

Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

2019 ◽  
Author(s):  
Jiajun Wang ◽  
Meng-Yin Li ◽  
Jie Yang ◽  
Ya-Qian Wang ◽  
Xue-Yuan Wu ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Genetic Diseases ◽  
High Sensitivity ◽  
Dna Lesions ◽  
Lesion Detection ◽  
The Novel ◽  
Structural Variations ◽  
Dna Lesion ◽  
Base Lesion

DNA lesion such as metholcytosine(<sup>m</sup>C), 8-OXO-guanine(<sup>O</sup>G), inosine(I) <i>etc</i> could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (<sup>m</sup>C, <sup>O</sup>G, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

On the Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory

2019 ◽  
Author(s):  
Brandon B. Bizzarro ◽  
Colin K. Egan ◽  
Francesco Paesani
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Molecular Orbital ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Orbital Energy ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Many Body ◽  
Functional Theory

<div> <div> <div> <p>Interaction energies of halide-water dimers, X<sup>-</sup>(H<sub>2</sub>O), and trimers, X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, with X = F, Cl, Br, and I, are investigated using various many-body models and exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models demonstrates the need to capture important short-range interactions in the regime of large inter-molecular orbital overlap, such as charge transfer and charge penetration. Failure to reproduce these effects can lead to large deviations relative to reference data calculated at the coupled cluster level of theory. Decompositions of interaction energies carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of XC functionals (from generalized gradient corrected (GGA) to hybrid and range-separated functionals), while significant variance is found for charge transfer energies predicted by different XC functionals. Since GGA and hybrid XC functionals predict the most and least attractive charge transfer energies, respectively, the large variance is likely due to the delocalization error. In this scenario, the hybrid XC functionals are then expected to provide the most accurate charge transfer energies. The sum of Pauli repulsion and dispersion energies are the most varied among the XC functionals, but it is found that a correspondence between the interaction energy and the ALMO EDA total frozen energy may be used to determine accurate estimates for these contributions. </p> </div> </div> </div>

Spectroscopic investigations and DFT studies of synthesized 4-acetamidophenyl 3,4,5-trimethoxybenzoate and 4-acetyl phenyl 3,4,5-trimethoxybenzoate a novel conjugate of gallic acid

2020 ◽  
Vol 17 ◽  
Author(s):  
Sangeeta Srivastava ◽  
Nadeem Ahmad Ansari ◽  
Sadaf Aleem
Keyword(s):  
Gallic Acid ◽  
Density Functional ◽  
Energy Gap ◽  
Basis Set ◽  
Major Constituent ◽  
Orbital Energy ◽  
Reactivity Descriptors ◽  
Homo And Lumo ◽  
Electrophilic Reactivity ◽  
Global And Local

: Gallic acid is abundantly found in amla (Phyllanthus emblica), a deciduous of the family phyllanthaceae. Gallic acid, the major constituent of the plant was methylated to 3,4,5 trimethoxy gallic acid, which then underwent steglich esterification first with paracetamol and then with 4-hydroxy acetophenone to yield 4-acetamidophenyl 3,4,5-trimethoxybenzoate and 4-acetyl phenyl 3,4,5-trimethoxybenzoate “respectively”. 1H NMR, 13C NMR, UV, FT-IR and mass spectroscopy were used to characterize the synthesized compounds. Density functional theory (B3YLP) using 6-31G (d,p) basis set have been used for quantum chemical calculations. AIM (Atom in molecule) approach depicted weak molecular interactions within the molecules whereas the reactive site and reactivity within the molecule were examined by global and local reactivity descriptors. The HOMO and LUMO energies and frontier orbital energy gap were calculated by time dependant DFT approach using IEFPCM model. Small value for HOMO–LUMO energy gap indicated that easier charge transfer occurs within compound 4. The nucleophilic and electrophilic reactivity were determined by MEP (molecular electrostatic potential) experiment. Polarizability, dipole moment, and first hyperpolarizability values were calculated to depict the NLO (nonlinear optical) property of both the synthesized compounds. The antimicrobial activity was also carried out and broad spectrum antibacterial activity against several strains of bacteria and certain unicellular fungi were exhibited by synthesized compound 3.

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