Sharif Digital Repository

Interactions of α-D-glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM-B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α-D-glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M.H-O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy... 

Transition metal lithium orthosilicates are of interest as cathode materials for lithium batteries. Density functional theory (DFT) calculations were performed to evaluate the structural and electrochemical properties of the different polymorphs of Li2MnSiO4. Our computational studies predict superior properties for the Pmn21 polymorph even after extraction of two Li per formula unit. We state that the shortcomings observed for Li2MnSiO4 as a cathode are caused by two mechanisms. Switching of the magnetic state occurs during the first cycles. The subsequent transition, under delithiated conditions, from the Pmn21 or Pmnb polymorphs to the electrochemically weakest P21/n polymorph is the... 

Thiotepa (N,N′,N″-triethylenethiophosphoramide) and its major metabolite (Tepa) as trifunctional alkylating agents has recently been used in cancer therapy. In vivo and vitro studies show the possible pathways of alkylation of DNA by Thiotepa and Tepa. Two pathways are suggested, but the main pathway of mechanism remains unclear. In pathway 1, forming cross-links with DNA molecules can be carried out via two different mechanisms. In first mechanism, these agents undergo the ring opening reaction which is initiated by protonating aziridine, which then becomes the main target of nucleophilic attack by the N7-Guanine of DNA. The second probable mechanism is ring opening of aziridyl group by... 

Electronic and phonon structures of the BaFe2As2 superconductor in the magnetic-orthorhombic phase have been investigated by the ab-initio density functional theory using the pseudopotential Quantum Espresso code. Density of state and electronic band structure for this phase has been studied, but phonon dispersion has been obtained only for the nonmagnetic-orthorhombic phase. Electronic band structure and density of states are in good agreement with other calculations in the literature. The electronic state near the Fermi energy are essentially made from Fe3d and As4p orbital that indicate in-plane conductivity in FeAs layers in this system. Comparing calculated phonon dispersions with... 

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M3 clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M3 clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H⋯M and O-H⋯M hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next... 

A new di-manganese complex with "back-to-back" 1,4-bis(2,2′:6,2′′-terpyridin-4′-yl) benzene ligation has been synthesized and characterised by a variety of techniques. The back-to-back ligation presents a novel new mononuclear manganese catalytic centre that functions as a heterogeneous catalysis for the evolution of oxygen in the presence of an exogenous oxidant. We discuss the synthesis and spectroscopic characterizations of this complex and propose a mechanism for oxygen evolution activity of the compound in the presence of oxone. The di-manganese complex also shows efficient and selective catalytic oxidation of sulfides in the presence of H2O2. Density functional theory calculations were... 

We analyze an experiment in which two distinct superconducting phases YBa2Cu3O7-δ (Y123) and Y 3Ba5Cu8O18-δ (Y358) coexisted. This experiment enabled us to characterize the recently introduced Y358 phase in contrast to the Y123 phase, thus to resolve some discrepancies reported in associated properties of Y358. Specifically, our experiment indicates the transition temperature Tmid C = 105 K and 94 K for Y358 and Y123, respectively, and that Y358 has five CuO2 planes and three CuO chains, with Pmm2 symmetry and lattice parameter (a, b, c) = (3.845, 3.894, 31.093) Å, in agreement with density functional theory predictions for this specific structure  

The optimized minimum-energy geometries of different macrocyclic amines and their protonated structures were determined by using ab initio and density functional theory (DFT) calculations. All the gas phase optimizations and energy calculations were performed at the DFT/B3LYP/6-311++G(d,p) level of theory. The HF/6-31 + G(d,p) level was used for all single point calculations in the solution phase. Geometry optimizations indicate that the most stable structures are stabilized by intramolecular hydrogen bonds. The proton affinity (PA) of macrocyclic amines is controlled by the strength of intramolecular hydrogen bonds of macrocyclic amines. These hydrogen bonds strongly influence the basicity... 

The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our... 

Ni II-(N,N′-bis(2,4-dihydroxyacetophenone)-2, 2-dimethylpropandiimine (Ni II{salnptn(4-OH) 2}) complex has been encapsulated within the supercage of zeolite-NaY by reacting Ni 2+-exchanged NaY with the flexible Schiff-base ligand that diffuses into the cavities. The encapsulated complex is characterized by EDX, scanning electron microscopy, powder X-ray diffraction, FT-IR, and cyclic voltammetry studies. Density functional calculation is being carried out on both the free nickel Schiff-base complex and that encapsulated in NaY zeolite to investigate changes in structural parameters, energies of the HOMO and LUMO, and absolute hardness and softness. Electrochemical properties of the NaY... 

N,N′,N″-triethylenethiophosphoramide (Thiotepa) and its oxo analogue (Tepa) as the major metabolite are trifunctional alkylating agents with a broad spectrum of antitumor activity. In vivo and vitro studies show alkylation of DNA by Thiotepa and Tepa can follow two pathways, but it remains unclear which pathway represents the precise mechanism of action. In pathway 1, these agents are capable of forming cross-links with DNA molecules via two different mechanisms. In the first mechanism, the ring opening reaction is initiated by protonating the aziridine, which then becomes the primary target of nucleophilic attack by the N7-Guanine. The second one is a direct nucleophilic ring opening of... 

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... 

The interactions between five amino acid based anions ([AA] - (AA = Gly, Phe, His, Try, and Tyr)) and N7,N9-dimethylguaninium cation ([dMG] +) have been investigated by the hybrid density functional theory method B3LYP together with the basis set 6-311++G(d,p). The calculated interaction energy was found to decrease in magnitude with increasing side-chain length in the amino acid anion. The interaction between the [dMG] + cation and [AA] - anion in the most stable configurations of ion pairs is a hydrogen bonding interaction. These hydrogen bonds (H bonds) were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations... 

Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the... 

A new manganese complex of the formula [Mn(tptz)(OH 2) 3](CF 3SO 3) 2·EtOH, (1, where tptz = (2,4,6-tris(2-pyridyl)-1,3,5-triazine) is presented, exhibiting an excellent catalytic activity and selectivity in oxidation of various sulfides to the corresponding sulfoxides with UHP (urea hydrogen peroxide) as oxidant under air at room temperature. A modified preparation procedure produces another new manganese complex of the formula [Mn(tptz)(CH 3COO)(OH 2) 2](CF 3SO 3)·3H 2O (2). X-ray structures of both Mn(II) complexes, properties (elemental analysis, electrochemistry, EPR, IR, Raman, and UV-Vis spectra), as well as DFT studies results are reported  

Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate... 

Hydrogen bonding interactions between thymine nucleobase and 2'-deoxythymidine nucleoside (dT) with some biological anions such as F - (fluoride), Cl - (chloride), OH - (hydroxide), and NO 3 - (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory... 

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... 

The low temperature thermoelectric properties of hydrogen-passivated graphene-based antidot lattices are theoretically investigated. Calculations are performed using density functional theory in conjunction with the Landauer formula to obtain the ballistic transport coefficients. Antidot lattices with hexagonal, triangular and rectangular antidot shapes are studied. Methods to reduce the thermal conductance and to increase the thermoelectric power factor of such structures are studied. Our results indicate that triangular antidot lattices have the smallest thermal conductance due to longer boundaries, the smallest distance between the neighboring antidots, and the armchair edges. This... 

A specific structure of doped graphene with substituted silicon impurity is introduced and ab initio density-functional approach is applied for the energy band structure calculation of the proposed structure. Using the band structure calculation for different silicon sites in the host graphene, the effect of silicon concentration and unit cell geometry on the bandgap of the proposed structure is also investigated. Chemically, silicon-doped graphene results in an energy gap as large as 2eV according to density-functional theory calculations. As the authors will show, in contrast to previous bandgap engineering methods, such structure has significant advantages including wide gap tuning...