Sharif Digital Repository

The noncovalent interactions between cytosine nucleobase with some biological anions such as F-, Cl-, CN-, NO3-, SO42 - and OH- and cytosine nucleosides (i.e., cytidine and deoxycytidine molecules) with F-, Cl-, CN- anions have been demonstrated by DFT study. The molecular geometries, energy properties, H-bonding patterns, dipole moments and charge distribution of these complexes were investigated with the B3LYP method in conjunction with the 6-311++G(d,p) basis set. It has been found that anions can interact with cytosine nucleobase forming hydrogen bonds. In general, these interactions occur via N-H, O-H and C-H substituents of cytosine, cytidine and deoxycytidine. The presence of anions... 

The potential of carbon-based nanosheet membranes with functionalized pores is great as water treatment membranes. Using the molecular dynamic simulation technique, the dimethyl sulfoxide (DMSO) separation from the water/DMSO binary solution is investigated, and the functionalized graphene nanosheets are used as a membrane. This membrane was functionalized by –F (fluorine) and –H (hydrogen) functional groups. For the separation of DMSO, external hydrostatic pressures up to 100 MPa were applied to the considered systems. The separation mechanism was based on molecular size. Multiple analyses were done to study the capability of considered membranes for the separation of DMSO molecules from... 

As a direct consequence of power systems restructuring on one hand and unprecedented renewable energy utilization on the other, the uncertainties of power systems are getting more and more attention. This fact intensifies the difficulty of decision making in the power system context; therefore, the uncertainty analysis of the system performance seems necessary. Generally, uncertainties in any engineering system study can be represented probabilistically or possibilistically. When sufficient historical data of the system variables is not available, a probability density function (PDF) might not be defined, they must be represented in another manner i.e. using possibilistic theory. When some... 

The binding of Mg 2+, Ca 2+, Zn 2+ and Cu + metal cations to 2′-deoxyguanosine has been analyzed, using the hybrid B3LYP, Density Functional Theory (DFT) method and 6311++G(d,p) orbital basis sets. Coordination geometries, absolute metal ion affinities, and free energies for the most stable complexes formed by Mg 2+, Ca 2+, Zn 2+ and Cu + with the nucleoside, 2′-deoxyguanosine, have been determined. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles and angle of Pseudorotation (P) have been studied. With respect to the results, it has been found that metal binding significantly changes the values of the phase angle of Pseudorotation... 

We have investigated the pathways of stability for NHCs derived from azole, di-azole, n-tetrazole, and ab-tetrazole (1a, 2a, 3a, and 4a, respectively), at the M06/6-311++G** level of theory. Optimization and vibrational frequency calculations of ground states (GS) and transition states (TS) are performed to identify Gibbs free energies and nature of stationary points, respectively. Two possible pathways of stability for 1a-4a are compared and contrasted which entail dimerization through hydrogen bonding (HB) and covalent bonding (CB). The CB pathway comprises head to head (HH) and head to tail (HT) dimerizations. Plausible reaction profiles are illustrated for 1a-4a along with the mechanism... 

In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),... 

In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),... 

Density functional theory generalized gradient approximation has been used to calculate the electronic and structural properties of BaFe2As2 compound up to 56 GPa by using Quantum Espresso code. Structural properties like bulk modulus, Fe-As bond length, and As-Fe-As bond angles have been investigated by pressure especially near the tetragonal to collapsed tetragonal (T-cT) structural phase transition. This study shows considerable changes of these parameters in the cT phase, which happens near our calculated critical pressure, Pc = 24 ± 2 GPa. Electronic band structure and its orbital-resolved, total and partial density of states and Fermi surfaces have been... 

We have studied the pressure-induced structural, magnetic and electronic properties of AeFe 2 As 2 (Ae = Ba, Sr, Ca) compounds in the framework of density functional theory within the GGA-PBE method. The effects of chemical pressure generated by Sr and Ca substitutions in BaFe 2 As 2 have been investigated. We have found a magnetic transition at the same primitive unit cell volume, around 81 Å 3 for the (Ba⧹Ca)Fe 2 As 2 compounds, which predicts a magnetic transition pressure of 12 GPa for SrFe 2 As 2 . The structural parameters of FeAs 4 tetrahedra are obtained after ionic relaxation and compared with the existing experimental results. The change of these internal parameters is ascribed to... 

The electron transport characteristics of a 1,10-dimethylene-1,10-dicarba-closo-decaborane (10-vertex carborane) single molecular conductor is investigated via the density functional-based non-equilibrium Green's function (DFT-NEGF) method. We consider three configurations for the molecular wire sandwiched between two Au(1 0 0) electrodes: the hollow site, top site and bridge site positions. Our results show that the energetically favorable hollow site configuration has a higher current intensity than the other configurations. The projection of the density of states (PDOS) and the transmission coefficients T(E) of the two-probe system at zero bias are analyzed, and it suggests that the... 

Metal-organic frameworks (MOFs) are a new class of porous crystalline materials being used as photocatalysts for efficient pollutant removal and environmental remediation. In this study, the TMU-32 MOF was synthesized as an effective photocatalyst for the photodegradation of tetracycline (TC) with 96% efficiency in 60 min under visible light. The high photocatalytic activity of the TMU-32 MOF is mainly due to its large specific surface area, which is beneficial for promoting both the adsorption of TC and the separation of the photoinduced charges. Moreover, its desired crystallinity makes it a semiconductor with an appropriate band gap energy. Next, a composite of the TMU-32 MOF with Fe3O4... 

Metal-organic frameworks (MOFs) are a new class of porous crystalline materials being used as photocatalysts for efficient pollutant removal and environmental remediation. In this study, the TMU-32 MOF was synthesized as an effective photocatalyst for the photodegradation of tetracycline (TC) with 96% efficiency in 60 min under visible light. The high photocatalytic activity of the TMU-32 MOF is mainly due to its large specific surface area, which is beneficial for promoting both the adsorption of TC and the separation of the photoinduced charges. Moreover, its desired crystallinity makes it a semiconductor with an appropriate band gap energy. Next, a composite of the TMU-32 MOF with Fe3O4...