Sharif Digital Repository

We show that a metal-organic framework (MOF) sustained by a nanosized Ag12 cuboctahedral node can be applied to selectively extract traces of lead(II) ion from environmental water samples. The MOF was characterized by thermogravimetric and differential thermal analysis, scanning electron microscopy, FTIR, and X-ray diffraction. The effects of pH value, flow rates, of type, concentration and volume of the eluent, of break-through volume and potentially interfering ions on the separation and determination of lead were evaluated. Following desorption with EDTA, Pb(II) was quantified by FAAS. The use of the MOF results in excellent analytical figures of merit including an analytical range from 2... 

The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical... 

Etheno-damaged DNA adducts such as 3,N4- ethenocytosine, N 2,3-ethenoguanine, and 1,N2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gasphase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare... 

The relative stabilities and noncovalent interactions of the six low-lying energy tautomers of cytosine nucleobase with some biological anions (such as F-, Cl-, and CN-) have been investigated in gas phase by density functional theory (DFT) method in conjunction with 6-311++G (d,p) atomic basis set. Furthermore, to systematically investigate all possible tautomerisms from cytosine induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase and in a continuum solvent using DFT calculation. We carried out geometrical optimizations with the integral equation formalism of polarizable continuum (IEF-PCM) model to account for the solvent effect, and the... 

The cation radicals of DNA constituents generated by the ionizing radiation initiate the alteration of the bases, which is one main type of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break, and it is important to identify the cation radical formation at particular atomic site in these molecules so that the major pathway for the nucleic acid damage may be trapped. In the present study, we explored theoretically energetic, structural, and electronic properties of the possible radicals formed via proton atom abstraction at various sites of sugar part of deoxycytidine cation radical by employing density functional theory at... 

Density functional theory is used in a spin-polarized plane wave pseudopotential implementation to investigate molecular oxygen adsorption and dissociation on graphite and nickel-doped graphite surfaces. Molecular oxygen physisorbs on graphite surface retaining its magnetic property. The calculated adsorption energy is consistent with the experimental value of 0.1eV. It is found that substituting a carbon atom of the graphite surface by a single doping nickel atom (2.8% content) makes the surface active for oxygen chemisorption. It is found that the molecular oxygen never adsorbs on doping nickel atom while it adsorbs and dissociates spontaneously into atomic oxygens on the carbon atoms... 

A new, simple, fast and reliable solid-phase extraction method has been developed for separation/preconcentration of trace amounts of Pb(II) using dithizone/sodium dodecyl sulfate-immobilized on alumina-coated magnetite nanoparticles, and its determination by flame atomic absorption spectrometry (FAAS) and graphite furnace atomic absorption spectrometry (GFAAS) after eluting with 4.0 mol L -1 HNO 3. Optimal experimental conditions including pH, sample volume, eluent concentration and volume, and co-existing ions have been studied and established. Under the optimal experimental conditions, the preconcentration factor, detection limit, linear range and relative standard deviation of Pb(II)... 

The geometries of the complexes of Be 2+, Mg 2+, and Ca 2+ metal cations with borazine ring were studied. The complexes were optimized at the B3LYP level and the 6-311++G(d,p) basis set. Then, the interaction energies corrected by basis set super position error were calculated in the same level. The results show that interaction energy is strongly dependent on the charge-to-size ratio of the cation. Therefore, Be 2+ cation has the most interaction energy value with respect to Mg 2+ and Ca 2+ metal cations. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to... 

Abstraction of hydrogen atom from DNA and RNA subunits leads to formation of a neutral radical. The formation of these radicals can lead to harmful structural alternations and formation of multiple lesions in helixes of DNA and RNA. In the present work, we explore theoretically energetic and structural properties of the possible radicals formed via hydrogen atom abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. Two types of free radicals may be found by hydrogen abstraction of sugar part of cytosine nucleosides: carbon centered radicals and the oxygen centered radicals. The computation... 

Growth of thin layers of compound semiconductors such as GaAs and Al x Ga1-x As was obtained by Liquid Phase Epitaxy (LPE) at 838-828 ° C in thickness range of 0.1-4.3 μm which was estimated by Scanning Electron Microscopy (SEM). By Secondary Ion Mass Spectroscopy (SIMS) measurements, type of impurity atoms and their density and uniformity with respect to thickness were measured. In this way we are sure that variation of impurity atoms such as Si, Te, Sn and Ge indicates that epilayers were formed uniformly and it demonstrated that the LPE growth was a suitable way to obtain a good quality of epitaxy layers. Amount of composition parameter x in the compound semiconductor AlxGa1-xAs was... 

The adsorption and dissociation of H2O2 on small PdxM3-x (M=Pt, Cu; x = 1-3) clusters is investigated using the B3PW91 hybrid density functional method. Natural bond orbitals are analysed to obtain partial charges on atoms, dipole moments, bond orders, and hybrid orbitals of the PdxM3-x-H2O2 systems. The calculated adsorption energies are in the range of -0.32 to -2.12 eV. Generally, H2O2 adsorbs on top positions through one of its oxygen atoms and only in a few cases reacts with the cluster through both oxygen and hydrogen sides. In the latter case the cluster sites which are negatively charged interact with the hydrogen atoms. Interestingly, on the triplet Pd2Pt cluster, H2O2 dissociates... 

Small high-quality Au/p-Si Schottky barrier diodes (SBDs) with extremely low reverse leakage current using wet lithography were produced. Their effective barrier heights (BHs) and ideality factors from currentvoltage (IV) characteristics were measured by a conducting probe atomic force microscope (C-AFM). In spite of identical preparation of the diodes there was a diode-to-diode variation in ideality factor and barrier height parameters. By extrapolating the plots the built-in potential of the Au/p-Si contact was obtained as Vbi=0.5425 V and the barrier height value (ΦB(C-V)) was calculated to be ΦB(C-V)=0.7145 V for Au/p-Si for a typical 100 μm diode diameters. In the present work the... 

Small high-quality Au/P-Si Schottky barrier diodes (SBDs) with an extremely low reverse leakage current using wet lithography were produced. Their effective barrier heights (BHs) and ideality factors from current-voltage (I -V) characteristics were measured by a conducting probe atomic force microscope (C-AFM). In spite of the identical preparation of the diodes there was a diode-to-diode variation in ideality factor and barrier height parameters. By extrapolating the plots the built in potential of the Au /p-Si contact was obtained as Vbi D 0:5425 V and the barrier height value φB(C-V) was calculated to be φB(C-V) D 0:7145 V for Au/p-Si. It is found that for the diodes with diameters... 

This letter adopts an atomistic modeling approach to study free vibrational characteristics of C60, C70, and C80 fullerenes. In this regard, we use the molecular structural mechanics consisting of equivalent structural beams to calculate the nonzero natural frequencies. The simulation results indicate that the first natural frequency of the fullerene is in the order terahertz and decreases nonlinearly with respect to the number of the carbon atoms  

The behavior of an electrified liquid jet breakup and modes of disintegration were investigated at different flow rates and voltages. The current phenomenology belongs to a new injector introduced recently by Morad et al. (2016). This injector has proven to highly extend the stability and flow rate of electrospray particularly in the Taylor cone-jet mode. The experimental investigation was performed using a high-power light-emitting diode (LED) illumination as the light source. The light source was developed to operate in the pulsing condition when synchronized with a digital camera and was particularly designed to function properly in the presence of high electromagnetic interference (EMI).... 

In this paper, a fast algorithm for overcomplete sparse decomposition, called SL0, is proposed. The algorithm is essentially a method for obtaining sparse solutions of underdetermined systems of linear equations, and its applications include underdetermined sparse component analysis (SCA), atomic decomposition on overcomplete dictionaries, compressed sensing, and decoding real field codes. Contrary to previous methods, which usually solve this problem by minimizing the ℓ1 norm using linear programming (LP) techniques, our algorithm tries to directly minimize the ℓ0 norm. It is experimentally shown that the proposed algorithm is about two to three orders of magnitude faster than the... 

α-Fe with low carbon content is a base material which is commonly used in manufacturing of Reactor Pressure Vessel (RPV) of commercial nuclear power plants. Carbon is generally diffused to α-Fe matrix to improve some of its mechanical properties. The presence of carbon may alter the irradiation response of the steel. In the current study, using molecular dynamics simulations, we have investigated the influence of carbon (∼in either dispersed form or carbon-rich region as chain) in the primary damage states of α-Fe low carbon steels. It is found that carbons in dispersed form have no significant effect on the self-interstitial atoms (SIAs) in α-Fe. While, carbon-rich (C-rich as... 

In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the... 

Argon is often considered as an innocent probe that can be attached and detached to study the structure of a particular species without perturbing the species too much. We have investigated whether this assumption also holds for small copper cationic clusters and demonstrated that small but significant charge transfer from argon to metal changes the remaining binding positions, leading in general, to weaker binding of other argon atoms. The exception is binding to just one copper ion, where the binding of the first argon facilitates the binding of the second. © 2020 American Chemical Society  

The production of high-purity aluminum nanoparticles (Al-NPs) is challenging due to the highly reactive nature of Al metals. Electromagnetic levitation gas condensation (ELGC) is a promising method to produce high-purity metallic particles as it avoids the interaction between molten metal and refractory-lined, which guarantees the removal of impurities such as oxygen (O). In this research, high-purity Al-NPs were successfully fabricated via ELGC process and fully characterized. The effects of power input and gas flow rate on particle size and distribution were analyzed using field emission scanning electron microscopy (FESEM), energy dispersive spectroscopy (EDS), and dynamic light...