Search results for: density functional tight binding

Authors: M. A. Lahmer, K. Guergouri

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The ferromagnetic properties of carbon-doped ZnO (ZnO:CO) and hydrogenated carbon-doped ZnO (ZnO:CO+H) are investigated using the density functional tight binding (DFTB) method. Our results reveal that CO-doped ZnO is a ferromagnetic material with a magnetic moment of 1.3 μB per carbon atom. The presence of hydrogen in the material in the form of CO-H complex decreases the total magnetism of the material without suppressing ferromagnetism. However, the system in this case becomes quickly antiferromagnetic when the C-C separation distance was increased.

Keywords: ZnO, carbon, hydrogen, ferromagnetism, density functional tight binding

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Authors: U. L. Fulco, E. L. Albuquerque, José X. Lima Neto, L. R. Da Silva

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The binding of the nonsteroidal anti-inflammatory drug ibuprofen (IBU) to human serum albumin (HSA) is investigated using density functional theory (DFT) calculations within a fragmentation strategy. Crystallographic data for the IBU–HSA supramolecular complex shows that the ligand is confined to a large cavity at the subdomain IIIA and at the interface between the subdomains IIA and IIB, whose binding sites are FA3/FA4 and FA6, respectively. The interaction energy between the IBU molecule and each amino acid residue of these HSA binding pockets was calculated using the Molecular Fractionation with Conjugate Caps (MFCC) approach employing a dispersion corrected exchange–correlation functional. Our investigation shows that the total interaction energy of IBU bound to HSA at binding sites of the fatty acids FA3/FA4 (FA6) converges only for a pocket radius of at least 8.5 °A, mainly due to the action of residues Arg410, Lys414 and Ser489 (Lys351, Ser480 and Leu481) and residues in nonhydrophobic domains, namely Ile388, Phe395, Phe403, Leu407, Leu430, Val433, and Leu453 (Phe206, Ala210, Ala213, and Leu327), which is unusual. Our simulations are valuable for a better understanding of the binding mechanism of IBU to albumin and can lead to the rational design and the development of novel IBU-derived drugs with improved potency.

Keywords: ibuprofen, human serum albumin, density functional theory, binding energies

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Authors: Matineh Sadat Hosseini Gheidari, Vahid Reza Yazdanpanah

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In this paper, we used the empirical tight-binding method (ETBM) with sp3s* approximation and considering the first nearest neighbor with spin-orbit interactions in order to model superlattice structure (SLS) of (AlₓGa₁₋ₓAs)ₘ/(GaAs)ₙ grown on GaAs (100) substrate at 300K. In the next step, we investigated the behavior of the energy gap and wavelength of this superlattice in terms of different thicknesses of core materials and Al mole fractions. As a result of this survey, we found out that as the Al composition increases, the energy gap of this superlattice has an upward trend and ranges from 1.42-1.63 eV. Also, according to the wavelength range that we gained from this superlattice in different Al mole fractions and various thicknesses, we can find a suitable semiconductor for a special light-emitting diode (LED) application.

Keywords: energy gap, empirical tight-binding method, light-emitting diode, superlattice, wavelength

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Authors: A. Nusrath Unissa, Sameer Hassan, Luke Elizabeth Hanna

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Altered drug binding may be an important factor in isoniazid (INH) resistance, rather than major changes in the enzyme’s activity as a catalase or peroxidase (KatG). The identification of structural or functional defects in the mutant KatGs responsible for INH resistance remains as an area to be explored. In this connection, the differences in the binding affinity between wild-type (WT) and mutants of KatG were investigated, through the generation of three mutants of KatG, Ser315Thr [S315T], Ser315Asn [S315N], Ser315Arg [S315R] and a WT [S315]) with the help of software-MODELLER. The mutants were docked with INH using the software-GOLD. The affinity is lower for WT than mutant, suggesting the tight binding of INH with the mutant protein compared to WT type. These models provide the in silico evidence for the binding interaction of KatG with INH and implicate the basis for rationalization of INH resistance in naturally occurring KatG mutant strains of Mycobacterium tuberculosis.

Keywords: Mycobacterium tuberculosis, KatG, INH resistance, mutants, modelling, docking

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Authors: Ankit Kargeti, Ravikant Shrivastav, Tabish Rasheed

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The electronic structure calculation for the nanoclusters of AsSiTeB/SiAsBTe quaternary semiconductor alloy belonging to the III-V Group elements was performed. Motivation for this research work was to look for accurate electronic and geometric data of small nanoclusters of AsSiTeB/SiAsBTe in the gaseous form. The two clusters, one in the linear form and the other in the bent form, were studied under the framework of Density Functional Theory (DFT) using the B3LYP functional and LANL2DZ basis set with the software packaged Gaussian 16. We have discussed the Optimized Energy, Frontier Orbital Energy Gap in terms of HOMO-LUMO, Dipole Moment, Ionization Potential, Electron Affinity, Binding Energy, Embedding Energy, Density of States (DoS) spectrum for both structures. The important findings of the predicted nanostructures are that these structures have wide band gap energy, where linear structure has band gap energy (Eg) value is 2.375 eV and bent structure (Eg) value is 2.778 eV. Therefore, these structures can be utilized as wide band gap semiconductors. These structures have high electron affinity value of 4.259 eV for the linear structure and electron affinity value of 3.387 eV for the bent structure form. It shows that electron acceptor capability is high for both forms. The widely known application of these compounds is in the light emitting diodes due to their wide band gap nature.

Keywords: density functional theory, DFT, density functional theory, nanostructures, HOMO-LUMO, density of states

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Authors: Bo-Gaun Chen, Chiung-Hui Huang, Mei-Ching Chiang, Kuo-Hsing Lee, Chia-Chen Ho, Chin-Ping Huang, Chin-Heng Tien

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It is known that the natural dyeing of cloth results moderate color, but with poor color fastness. This study points out the correlation between the macroscopic color fastness of natural dye to the cotton fiber and the microscopic binding energy of dye molecule to the cellulose. With the additive metallic mordant, the new-formed coordination bond bridges the dye to the fiber surface and thus affects the color fastness as well as the color appearance. The density functional theory (DFT) calculation is therefore used to explore the most possible mechanism during the dyeing process. Finally, the experimental results reflect the strong effect of three different metal ions on the natural dyeing clothes.

Keywords: binding energy, color fastness, density functional theory (DFT), natural dyeing, metallic mordant

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Authors: Nilay K. Doshi

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A theoretical probe describing the excited energy states of the electron density surrounding a nanoparticle (NP) is presented. An electromagnetic (EM) wave interacts with a NP much smaller than the incident wavelength. The plasmon that oscillates locally around the NP comprises of excited conduction electrons. The system is based on the Jellium model of a cluster of metal atoms. Hohenberg-Kohn (HK) equations and the variational Kohn-Sham (SK) scheme have been used to obtain the NP electron density in the ground state. Furthermore, a time-dependent density functional (TDDFT) theory is used to treat the excited states in a density functional theory (DFT) framework. The non-interacting fermionic kinetic energy is shown to be a functional of the electron density. The time dependent potential is written as the sum of the nucleic potential and the incoming EM field. This view of the quantum oscillation of the electron density is a part of the localized surface plasmon resonance.

Keywords: electron density, energy, electromagnetic, DFT, TDDFT, plasmon, resonance

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Authors: Karolis Leonavičius, Dalius Kučiauskas, Dangiras Lukošius, Arnoldas Jasiūnas, Kostas Zdanys, Rokas Stanislovas, Emilis Gegevičius, Žana Kapustina, Juozas Nainys

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Screening throughput is a common bottleneck in many research areas, including functional genomics, drug discovery, and directed evolution. High-throughput screening techniques can be classified into two main categories: (i) affinity-based screening and (ii) functional screening. The first one relies on binding assays that provide information about the affinity of a test molecule for a target binding site. Binding assays are relatively easy to establish; however, they reveal no functional activity. In contrast, functional assays show an effect triggered by the interaction of a ligand at a target binding site. Functional assays might be based on a broad range of readouts, such as cell proliferation, reporter gene expression, downstream signaling, and other effects that are a consequence of ligand binding. Screening of large cell or gene libraries based on direct activity rather than binding affinity is now a preferred strategy in many areas of research as functional assays more closely resemble the context where entities of interest are anticipated to act. Droplet sorting is the basis of high-throughput functional biological screening, yet its applicability is limited due to the technical complexity of integrating high-performance droplet analysis and manipulation systems. As a solution, the Droplet Genomics Styx platform enables custom droplet sorting workflows, which are necessary for the development of early-stage or complex biological therapeutics or industrially important biocatalysts. The poster will focus on the technical design considerations of Styx in the context of its application spectra.

Keywords: functional screening, droplet microfluidics, droplet sorting, dielectrophoresis

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Authors: Choukri Lekbir, Mira Mokhtari

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Hydrogen-Materials interaction and mechanisms can be modeled at nano scale by quantum methods. In this work, the effect of hydrogen on the electronic properties of a cluster material model «nickel» has been studied by using of density functional theoretical (DFT) method. Two types of clusters are optimized: Nickel and hydrogen-nickel system. In the case of nickel clusters (n = 1-6) without presence of hydrogen, three types of electronic structures (neutral, cationic and anionic), have been optimized according to three basis sets calculations (B3LYP/LANL2DZ, PW91PW91/DGDZVP2, PBE/DGDZVP2). The comparison of binding energies and bond lengths of the three structures of nickel clusters (neutral, cationic and anionic) obtained by those basis sets, shows that the results of neutral and anionic nickel clusters are in good agreement with the experimental results. In the case of neutral and anionic nickel clusters, comparing energies and bond lengths obtained by the three bases, shows that the basis set PBE/DGDZVP2 is most suitable to experimental results. In the case of anionic nickel clusters (n = 1-6) with presence of hydrogen, the optimization of the hydrogen-nickel (anionic) structures by using of the basis set PBE/DGDZVP2, shows that the binding energies and bond lengths increase compared to those obtained in the case of anionic nickel clusters without the presence of hydrogen, that reveals the armor effect exerted by hydrogen on the electronic structure of nickel, which due to the storing of hydrogen energy within nickel clusters structures. The comparison between the bond lengths for both clusters shows the expansion effect of clusters geometry which due to hydrogen presence.

Keywords: binding energies, bond lengths, density functional theoretical, geometry optimization, hydrogen energy, nickel cluster

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Authors: Abayomi T. Ogunjimi, Gbenga Alebiowu

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Mechanical properties of paracetamol tablets containing Neem (Azadirachta indica) gum were compared with standard Acacia gum BP as binder. Two dimensionless binding quantities BEN and BEC were used in assessing the influence of binder type on two mechanical properties, Tensile Strength (TS) and Brittle Fracture Index (BFI). The two quantities were also used to assess the influence of relative density and binder concentration on TS and BFI as well as compare Binding Efficiencies (BE). The result shows that TS is dependent on relative density, binder type and binder concentration while BFI is dependent on the binder type and binder concentration; and that although, the inclusion of NMG in a paracetamol tablet formulation may not enhance the TS of the tablets produced, however it will decrease the tendency of the tablets to cap or laminate. This work concludes that BEN may be useful in quantitative assessment while BEC may be appropriate for qualitative assessment.

Keywords: binding efficiency, brittle fracture index, dimensionless binding, tensile strength

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Authors: W. Nootcharin, S. Sujittra, K. Mayuso, K. Kornphimol, M. Rawiwan

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Silver has distinct antibacterial properties and has been used as a component of commercial products with many applications. An increasing number of commercial products cause risks of silver effects for human and environment such as the symptoms of Argyria and the release of silver to the environment. Therefore, the detection of silver in the aquatic environment is important. The colorimetric chemosensor is designed by the basic of ligand interactions with a metal ion, leading to the change of signals for the naked-eyes which are very useful method to this application. Dithizone ligand is considered as one of the effective chelating reagents for metal ions due to its high selectivity and sensitivity of a photochromic reaction for silver as well as the linear backbone of dithizone affords the rotation of various isomeric forms. The present study is focused on the conformation and interaction of silver ion and silver nanoparticles (AgNPs) with dithizone using density functional theory (DFT). The interaction parameters were determined in term of binding energy of complexes and the geometry optimization, frequency of the structures and calculation of binding energies using density functional approaches B3LYP and the 6-31G(d,p) basis set. Moreover, the interaction of silver–dithizone complexes was supported by UV–Vis spectroscopy, FT-IR spectrum that was simulated by using B3LYP/6-31G(d,p) and 1H NMR spectra calculation using B3LYP/6-311+G(2d,p) method compared with the experimental data. The results showed the ion exchange interaction between hydrogen of dithizone and silver atom, with minimized binding energies of silver–dithizone interaction. However, the result of AgNPs in the form of complexes with dithizone. Moreover, the AgNPs-dithizone complexes were confirmed by using transmission electron microscope (TEM). Therefore, the results can be the useful information for determination of complex interaction using the analysis of computer simulations.

Keywords: silver nanoparticles, dithizone, DFT, NMR

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Authors: Morteza Keshavarz

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In this work, using density functional theory (DFT) thermodynamic stability and quantum molecular descriptors of cyclophoshphamide (an anticancer drug)-functionalized zigzag (8,0) CNT, armchair (4,4) CNT and nanocone complexes in water, for two attachment namely the sidewall and tip, is considered. Calculation of the total electronic energy (Et) and binding energy (Eb) of all complexes indicates that the most thermodynamic stability belongs to the sidewall-attachment of cyclophosphamide into functional nanocone. On the other hand, results from chemical hardness show that drug-functionalized zigzag (8,0) and armchair (4,4) complexes in the tip-attachment configuration possess the smallest and greatest chemical hardness, respectively. By computing the solvation energy, it is found that the solution of the drug and all complexes are spontaneous in water. Furthermore, chirality, type of nanovector (nanotube or nanocone), or attachment configuration have no effects on solvation energy of complexes.

Keywords: carbon nanotube, drug delivery, cyclophosphamide drug, density functional theory (DFT)

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Authors: S. Behnia, S. Fathizadeh, A. Akhshani

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In the recent decades, DNA has increasingly interested in the potential technological applications that not directly related to the coding for functional proteins that is the expressed in form of genetic information. One of the most interesting applications of DNA is related to the construction of nanostructures of high complexity, design of functional nanostructures in nanoelectronical devices, nanosensors and nanocercuits. In this field, DNA is of fundamental interest to the development of DNA-based molecular technologies, as it possesses ideal structural and molecular recognition properties for use in self-assembling nanodevices with a definite molecular architecture. Also, the robust, one-dimensional flexible structure of DNA can be used to design electronic devices, serving as a wire, transistor switch, or rectifier depending on its electronic properties. In order to understand the mechanism of the charge transport along DNA sequences, numerous studies have been carried out. In this regard, conductivity properties of DNA molecule could be investigated in a simple, but chemically specific approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. In SSH model, the non-diagonal matrix element dependence on intersite displacements is considered. In this approach, the coupling between the charge and lattice deformation is along the helix. This model is a tight-binding linear nanoscale chain established to describe conductivity phenomena in doped polyethylene. It is based on the assumption of a classical harmonic interaction between sites, which is linearly coupled to a tight-binding Hamiltonian. In this work, the Hamiltonian and corresponding motion equations are nonlinear and have high sensitivity to initial conditions. Then, we have tried to move toward the nonlinear dynamics and phase space analysis. Nonlinear dynamics and chaos theory, regardless of any approximation, could open new horizons to understand the conductivity mechanism in DNA. For a detailed study, we have tried to study the current flowing in DNA and investigated the characteristic I-V diagram. As a result, It is shown that there are the (quasi-) ohmic areas in I-V diagram. On the other hand, the regions with a negative differential resistance (NDR) are detectable in diagram.

Keywords: DNA conductivity, Landauer resistance, negative dierential resistance, Chaos theory, mean Lyapunov exponent

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Authors: Hui Li, Xiongqi Pang

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In recent years, tight oil has become a hot spot for unconventional oil and gas exploration and development in the world. Dongpu Depression is a typical hydrocarbon-rich basin in the southwest of Bohai Bay Basin, in which tight sandstone oil and gas have been discovered in deep reservoirs, most of which are buried more than 3500m. The distribution and development characteristics of deep tight sandstone reservoirs need to be studied. The main source rocks in study area are dark mudstone and shale of the middle and lower third sub-member of Shahejie Formation. Total Organic Carbon (TOC) content of source rock is between 0.08-11.54%, generally higher than 0.6% and the value of S1+S2 is between 0.04–72.93 mg/g, generally higher than 2 mg/g. It can be evaluated as middle to fine level overall. The kerogen type of organic matter is predominantly typeⅡ1 andⅡ2. Vitrinite reflectance (Ro) is mostly greater than 0.6% indicating that the source rock entered the hydrocarbon generation threshold. The physical property of reservoir was poor, the most reservoir has a porosity lower than 12% and a permeability of less than 1×10⁻³μm. The rocks in this area showed great heterogeneity, some areas developed desserts with high porosity and permeability. According to SEM, thin section image, inclusion test and so on, the reservoir was affected by compaction and cementation during early diagenesis stage (44-31Ma). The diagenesis caused the tight reservoir in Huzhuangji, Pucheng, Weicheng Area while the porosity in Machang, Qiaokou, Wenliu Area was still over 12%. In the process of middle diagenesis phase stage A (31-17Ma), the reservoir porosity in Machang, Pucheng, Huzhuangji Area increased due to dissolution; after that the oil generation window of source rock was achieved for the first phase hydrocarbon charging (31-23Ma), formed the conventional oil deposition in Machang, Qiaokou, Wenliu, Huzhuangji Area and unconventional tight reservoir in Pucheng, Weicheng Area. Then came to stage B of middle diagenesis phase (17-7Ma), in this stage, the porosity of reservoir continued to decrease after the dissolution and led to a situation that the reservoirs were generally compacted. And since then, the second hydrocarbon filling has been processing since 7Ma. Most of the pools charged and formed in this procedure are tight sandstone oil reservoir. In conclusion, tight sandstone oil was formed in two patterns in Dongpu Depression, which could be concluded as ‘density fist then accumulation’ pattern and ‘accumulation fist next density’ pattern.

Keywords: accumulation process, diagenesis, dongpu depression, tight sandstone oil

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Authors: Rasha Al-Saedi, Anthony Meijer

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The progress of new porous materials has increased rapidly over the past decade for use in applications such as catalysis, gas storage and removal of environmentally unfriendly species due to their high surface area and high thermal stability. In this work, a theoretical study of the zirconium-based metal organic framework (MOFs) were examined in order to determine their potential for gas adsorption of various guest molecules: CO2, N2, CH4 and H2. The zirconium cluster consists of an inner Zr6O4(OH)4 core in which the triangular faces of the Zr6- octahedron are alternatively capped by O and OH groups which bound to nine formate groups and three benzoate groups linkers. General formula is [Zr(μ-O)4(μ-OH)4(HCOO)9((phyO2C)3X))] where X= CH2OH, CH2NH2, CH2CONH2, n(NH2); (n = 1-3). Three types of adsorption sites on the Zr metal center have been studied, named according to capped chemical groups as the ‘−O site’; the H of (μ-OH) site removed and added to (μ-O) site, ‘–OH site’; (μ-OH) site removed, the ‘void site’ where H2O molecule removed; (μ-OH) from one site and H from other (μ-OH) site, in addition to no defect versions. A series of investigations have been performed aiming to address this important issue. First, density functional theory DFT-B3LYP method with 6-311G(d,p) basis set was employed using Gaussian 09 package in order to evaluate the gas adsorption performance of missing-linker defects in zirconium cluster. Next, study the gas adsorption behaviour on different functionalised zirconium clusters. Those functional groups as mentioned above include: amines, alcohol, amide, in comparison with non-substitution clusters. Then, dispersion-corrected density functional theory (DFT-D) calculations were performed to further understand the enhanced gas binding on zirconium clusters. Finally, study the water effect on CO2 and N2 adsorption. The small functionalized Zr clusters were found to result in good CO2 adsorption over N2, CH4, and H2 due to the quadrupole moment of CO2 while N2, CH4 and H2 weakly polar or non-polar. The adsorption efficiency was determined using the dispersion method where the adsorption binding improved as most of the interactions, for example, van der Waals interactions are missing with the conventional DFT method. The calculated gas binding strengths on the no defect site are higher than those on the −O site, −OH site and the void site, this difference is especially notable for CO2. It has been stated that the enhanced affinity of CO2 of no defect versions is most likely due to the electrostatic interactions between the negatively charged O of CO2 and the positively charged H of (μ-OH) metal site. The uptake of the gas molecule does not enhance in presence of water as the latter binds to Zr clusters more strongly than gas species which attributed to the competition on adsorption sites.

Keywords: density functional theory, gas adsorption, metal- organic frameworks, molecular simulation, porous materials, theoretical chemistry

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Authors: N. Lebga, Kh. Bouamama, K. Kassali

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We report first-principles calculation results on the structural and elastic properties of ZnS x Se1−x alloy for which we employed the virtual crystal approximation provided with the ABINIT program. The calculations done using density functional theory within the local density approximation and employing the virtual-crystal approximation, we made a comparative study between the numerical results obtained from ab-initio calculation using ABINIT or Wien2k within the Density Functional Theory framework with either Local Density Approximation or Generalized Gradient approximation and the pseudo-potential plane-wave method with the Hartwigzen Goedecker Hutter scheme potentials. It is found that the lattice parameter, the phase transition pressure, and the elastic constants (and their derivative with respect to the pressure) follow a quadratic law in x. The variation of the elastic constants is also numerically studied and the phase transformations are discussed in relation to the mechanical stability criteria.

Keywords: density functional theory, elastic properties, ZnS, ZnSe,

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Authors: H. Paredes Gutiérrez, S. T. Pérez-Merchancano

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Motivated by recent experimental and theoretical developments, we investigate the influence of embedded quantum dot (EQD) of different geometries (lens, ring and pyramidal) in a double barrier heterostructure (DBH). We work with a general theory of quantum transport that accounts the tight-binding model for the spin dependent resonant tunneling in a semiconductor nanostructure, and Rashba spin orbital to study the spin orbit coupling. In this context, we use the second quantization theory for Rashba effect and the standard Green functions method. We calculate the current density as a function of the voltage without and in the presence of quantum dots. In the second case, we considered the size and shape of the quantum dot, and in the two cases, we worked considering the spin polarization affected by external electric fields. We found that the EQD generates significant changes in current when we consider different morphologies of EQD, as those described above. The first thing shown is that the current decreases significantly, such as the geometry of EQD is changed, prevailing the geometrical confinement. Likewise, we see that the current density decreases when the voltage is increased, showing that the quantum system studied here is more efficient when the morphology of the quantum dot changes.

Keywords: quantum semiconductors, nanostructures, quantum dots, spin polarization

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Authors: Han-Bin Kim, Sooim Shin, Moonsung Choi

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There is a growing interest in introducing a desired functional group on enzymes in the field of protein engineering. In here, various redox centers were newly created using histidine tag, which is widely used for protein purification, plus cobalt in one of cupredoxins, amicyanin. The coordination of Cobalt-His tag and reactivity of the Co²⁺ loaded His-tag also were characterized. 3xHis-tag, 6xHis-tag, and 9xHis-tag were introduced on amicyanin by site-directed mutagenesis, and then Co²⁺ was loaded on each His-tagged amicyanin. The spectral changes at 330 nm corresponding to cobalt binding on His-tag site indicated the binding ratio of 3xHis-tag, 6xHis-tag, and 9xHis-tag to cobalt as 1:1, 1:2, 1:3 respectively. Based on kinetic studies of binding cobalt to 3xHis-tag, 6xHis-tag, and 9xHis-tagged amicyanin, the nature of the sites was elucidated. In addition, internal electron transfer properties between Cu¹⁺ site and engineered site of amicyanin were determined. These results provide insight into improvement of metal coordination and alternation of the redox properties of metal as a new catalytic site on proteins.

Keywords: amicyanin, cobalt, histidine, protein engineering

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Authors: Hamza Rekab Djabri, Salah Daoud

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The present paper deals with the computational of structural and electronic properties of ThC and ThN compounds using density functional theory within generalized-gradient (GGA) apraximation and local density approximation (LDA). We employ the full potential linear muffin-tin orbitals (FP-LMTO) as implemented in the Lmtart code. We have used to examine structure parameter in eight different structures such as in NaCl (B1), CsCl (B2), ZB (B3), NiAs (B8), PbO (B10), Wurtzite (B4) , HCP (A3) βSn (A5) structures . The equilibrium lattice parameter, bulk modulus, and its pressure derivative were presented for all calculated phases. The calculated ground state properties are in good agreement with available experimental and theoretical results.

Keywords: DFT, GGA, LDA, properties structurales, ThC, ThN

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Authors: Shittu Akinpelu, Issac Popoola

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The compound NbRhGe has been predicted to be a semiconductor with excellent mechanical properties. It is an indirect band gap material. The potential of NbRhGe for non-volatile data storage via element addition is being studied using the Density Functional Theory (DFT). Preliminary results on the electronic and magnetic properties are suggestive for their application in spintronic.

Keywords: half-metals, Heusler compound, semiconductor, spintronic

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Authors: Saqib Ali, Man-Qun Wang

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The Japanese pine sawyer, Monochamus alternatus Hope (Coleoptera: Cerambycidae), is a major pest of pines and it is also the key vector of the exotic pinewood nematode in China. In the present study, we cloned, expressed, and purified a chemosensory protein (CSP) in M. alternatus. We surveyed its expression in various developmental stages of male and female adult tissues and determined its binding affinities for different pine volatiles using a competitive binding fluorescence assay. A CSP known as CSP5 in M. alternatus was obtained from an antennal cDNA library and expressed in Escherichia coli. Quantitative reverse transcription polymerase chain reaction results indicated that the CSP5 gene was mainly expressed in male and female antennae. Competitive binding assays were performed to test the binding affinity of recombinant CSP5 to 13 odour molecules of pine volatiles. The results showed that CSP5 showed very strong binding abilities to myrcene, (+)-β-pinene, and (−)-isolongifolene, whereas the volatiles 2-methoxy-4-vinylphenol, p-cymene, and (+)-limonene oxide have relatively weak binding affinity at pH 5.0. Three volatiles myrcene, (+)-β-pinene, and (−)-isolongifolene may play crucial roles in CSP5 binding with ligands, but this needs further study for confirmation. The sensitivity of insect to host plant volatiles can effectively be used to control and monitor the population through mass trapping as part of integrated pest management programs.

Keywords: olfactory-specific protein, volatiles, competitive binding assay, expression characteristics, qPCR

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Authors: Yingqian Chen, Sergei Manzhos

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Organic electrodes are a way to achieve high rate (high power) and environment-friendly batteries. We present a computational density functional theory study of Li and Na storage in tetracyanoethylene based molecular and crystalline materials. Up to five Li and Na atoms can be stored on TCNE chemisorbed on doped graphene (corresponding to ~1000 mAh/gTCNE), with binding energies stronger than cohesive energies of the Li and Na metals by 1-2 eV. TCNE has been experimentally shown to form a crystalline material with Li with stoichiometry Li-TCNE. We confirm this computationally and also predict that a similar crystal based of Na-TCNE is also stable. These crystalline materials have well defined channels for facile Li or Na ion insertion and diffusion. Specifically, Li and Na binding energies in Li-TCNE and Na-TCNE crystals are about 1.5 eV and stronger than the cohesive energy of Li and Na, respectively. TCNE immobilized on conducting graphene-based substrates and Li/Na-TCNE crystals could therefore become efficient anode materials for organic Li and Na ion batteries, with which it should also be possible to avoid reduction of common battery electrolytes.

Keywords: organic ion batteries, tetracyanoethylene, cohesive energies, electrolytes

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Authors: Sonam Kumari

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Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, possesses a remarkable feature of entering into and emerging from a persistent state. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes.Mtb has seven such proteins (WhiB1 to WhiB7).WhiB proteins are transcriptional regulators; their conserved C-terminal HTH motif is involved in DNA binding. They regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical Analysis of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: tuberculosis, WhiB proteins, mycobacterium tuberculosis, nucleic acid binding

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Authors: Fatemeh Safdari, Amirnaser Shamkhali, Gholamabbas Parsafar

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Carbon nanostructures are of great importance in academic research and industry, which can be mentioned to chemical sensors, catalytic processes, pharmaceutical and environmental issues. Common point in all of these applications is the occurrence of adsorption of molecules on these structures. Important carbon nanostructures in this case are mainly nanotubes and graphene. To modify pure graphene, recently, many experimental and theoretical studies have carried out to investigate of metal adsorption on graphene. In this work, the adsorption of CO molecules on pure graphene and on metal adatom on graphene surface has been simulated based on density functional theory (DFT). All calculations were performed by PBE functional and Troullier-Martins pseudopotentials. Density of states (DOS) for graphene-CO, graphen and CO around the Fermi energy has been moved and very small mixing occured which implies the physisorption of CO on the bare graphen surface. While, the results have showed that CO adsorption on transition-metal adatom on graphene surface is chemisorption.

Keywords: adsorption, density functional theory, graphene, metal adatom

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Authors: Setareh Shekarsaraei, Marjan Moridi, Nasser L. Hadipour

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In this study, nuclear magnetic resonance spectroscopy and nuclear quadrupole resonance spectroscopy parameters of 14N (Nitrogen in imidazole ring) in N–H…O hydrogen bonding for Histidine hydrochloride monohydrate were calculated via density functional theory. We considered a five-molecule model system of Histidine hydrochloride monohydrate. Also, we examined the trends of environmental effect on hydrogen bonds as well as cooperativity. The functional used in this research is M06-2X which is a good functional and the obtained results have shown good agreement with experimental data. This functional was applied to calculate the NMR and NQR parameters. Some correlations among NBO parameters, NMR, and NQR parameters have been studied which have shown the existence of strong correlations among them. Furthermore, the geometry optimization has been performed using M062X/6-31++G(d,p) method. In addition, in order to study cooperativity and changes in structural parameters, along with increase in cluster size, natural bond orbitals have been employed.

Keywords: hydrogen bonding, density functional theory (DFT), natural bond orbitals (NBO), cooperativity effect

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Authors: Rohit Singh Dangi, Ravi Kant Pal, Monica Sundd

Abstract:

Acyl-CoA binding protein (ACBP) is a housekeeping protein which functions as an intracellular carrier of acyl-CoA esters. Given the fact that the amastigote stage (blood stage) of Leishmania depends largely on fatty acids as the energy source, of which a large part is derived from its host, these proteins might have an important role in its survival. In Leishmania major, genome sequencing suggests the presence of six ACBPs, whose function remains largely unknown. For functional and structural characterization, one of the ACBP genes was cloned, and the protein was expressed and purified heterologously. Acyl-CoA ester binding and stoichiometry were analyzed by isothermal titration calorimetry and Dynamic light scattering. Our results shed light on high affinity of ACBP towards longer acyl-CoA esters, such as myristoyl-CoA to arachidonoyl-CoA with single binding site. To understand the binding mechanism & dynamics, Nuclear magnetic resonance assignments of this protein are being done. The protein's crystal structure was determined at 1.5Å resolution and revealed a classical topology for ACBP, containing four alpha-helical bundles. In the binding pocket, the loop between the first and the second helix (16 – 26AA) is four residues longer from other extensively studied ACBPs (PfACBP) and it curls upwards towards the pantothenate moiety of CoA to provide a large tunnel space for long acyl chain insertion.

Keywords: acyl-coa binding protein (ACBP), acyl-coa esters, crystal structure, isothermal titration, calorimetry, Leishmania

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Authors: S. Ghammamy, M. Mirzaabdollahiha

Abstract:

Quantum mechanical calculations of energies, geometries, and vibrational wavenumbers of fluorous 1,3-dion compounds are carried out using density functional theory (DFT/B3LYP) method with LANL2DZ basis sets. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecules. The thermodynamic functions of fluorous 1,3-dion compounds have been performed at B3LYP/LANL2DZ basis sets. The theoretical spectrograms for F NMR spectra of fluorous 1,3-dion compounds have also been constructed. The F NMR nuclear shieldings of fluoride ligands in fluorous 1,3-dion compounds have been studied quantum chemical.

Keywords: density function theory, natural bond orbital, HOMO, LOMO, fluorous

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Authors: Said Belaaouad

Abstract:

This study aimed to explore the quantitative structure-activity relationship (QSAR) of 1,2,4-Triazine-3(2H)-one derivative as a potential anticancer agent against breast cancer. The electronic descriptors were obtained using the Density Functional Theory (DFT) method, and a multiple linear regression techniques was employed to construct the QSAR model. The model exhibited favorable statistical parameters, including R2=0.849, R2adj=0.656, MSE=0.056, R2test=0.710, and Q2cv=0.542, indicating its reliability. Among the descriptors analyzed, absolute electronegativity (χ), total energy (TE), number of hydrogen bond donors (NHD), water solubility (LogS), and shape coefficient (I) were identified as influential factors. Furthermore, leveraging the validated QSAR model, new derivatives of 1,2,4-Triazine-3(2H)-one were designed, and their activity and pharmacokinetic properties were estimated. Subsequently, molecular docking (MD) and molecular dynamics (MD) simulations were employed to assess the binding affinity of the designed molecules. The Tubulin colchicine binding site, which plays a crucial role in cancer treatment, was chosen as the target protein. Through the simulation trajectory spanning 100 ns, the binding affinity was calculated using the MMPBSA script. As a result, fourteen novel Tubulin-colchicine inhibitors with promising pharmacokinetic characteristics were identified. Overall, this study provides valuable insights into the QSAR of 1,2,4-Triazine-3(2H)-one derivative as potential anticancer agent, along with the design of new compounds and their assessment through molecular docking and dynamics simulations targeting the Tubulin-colchicine binding site.

Keywords: QSAR, molecular docking, ADMET, 1, 2, 4-triazin-3(2H)-ones, breast cancer, anticancer, molecular dynamic simulations, MMPBSA calculation

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Authors: A. Kellou, L. Rouaiguia, L. Rabahi

Abstract:

In the present work, the atomic hydrogen absorption trend in the GdNi5 and GdNi4Cu rare earth compounds within the hexagonal CaCu5 type of crystal structure (space group P6/mmm) is investigated. The density functional theory (DFT) combined with the generalized gradient approximation (GGA) is used to study the site preference of atomic hydrogen at 0K. The octahedral and tetrahedral interstitial sites are considered. The formation energies and structural properties are determined in order to evaluate hydrogen effects on the stability of the studied compounds. The energetic diagram of hydrogen storage is established and compared in GdNi5 and GdNi4Cu. The magnetic properties of the selected compounds are determined using spin polarized calculations. The obtained results are discussed with and without hydrogen addition taking into account available theoretical and experimental results.

Keywords: density functional theory, hydrogen storage, rare earth compounds, structural and magnetic properties

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Authors: Y. Ruchi, A. Prerna, S. Deepshikha

Abstract:

Amyotrophic lateral sclerosis (ALS), also known as “Lou Gehrig’s disease”. It is a neurodegenerative disease associated with degeneration of motor neurons in the cerebral cortex, brain stem, and spinal cord characterized by distal muscle weakness, atrophy, normal sensation, pyramidal signs and progressive muscular paralysis reflecting. ALS2 is a juvenile autosomal recessive disorder, slowly progressive, that maps to chromosome 2q33 and is associated with mutations in the alsin gene, a putative GTPase regulator. In this paper we have done homology modeling of alsin2 protein using multiple templates (3KCI_A, 4LIM_A, 402W_A, 4D9S_A, and 4DNV_A) designed using the Prime program in Schrödinger software. Further modeled structure is used to identify effective binding sites on the basis of structural and physical properties using sitemap program in Schrödinger software, structural and function analysis is done by using Prosite and ExPASy server that gives insight into conserved domains and motifs that can be used for protein classification. This paper summarizes the structural, functional and binding site property of alsin2 protein. These binding sites can be potential drug target sites and can be used for docking studies.

Keywords: ALS, binding site, homology modeling, neuronal degeneration

Procedia PDF Downloads 360