Sharif Digital Repository

A five-coordinated Fe(III) complex with the distorted trigonal bipyramidal configuration was synthesized by reactions of FeCl36H2O and 2-(2′-hydroxyphenyl)oxazoline (Hphox) as a bidentate ON donor oxazoline ligand. Complex [Fe(phox)2Cl] was fully characterized, including by single-crystal X-ray structure analysis. DFT calculations were accompanied with experimental results in order to obtain a deeper insight into the electronic structure and vibrational normal modes of complex. Oxidation of sulfides to sulfoxides in one-step was conducted by this complex as catalyst using urea hydrogen peroxide (UHP) in mixture of CH2Cl 2/CH3OH (1:1) under air at room temperature. The results show that using... 

We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and... 

Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers,... 

Fully supramolecular dendrosomes (FSD) as bi-phase drug delivery systems are reported in this work. For preparation of FSD, amphiphilic linear-dendritic supramolecular systems (ALDSS) have been synthesized by host-guest interactions between hyperbranched polyglycerol having β-cyclodextrin core and bi-chain polycaprolactone (BPCL) with a fluorescine focal point. Self-assembly of ALDSS in aqueous solutions led to FSD. They were able to encapsulate paclitaxel with a high loading capacity. The dendrosome-based drug delivery systems were highly sensitive to pH and temperature. They were stable at 20-37. °C and pH7-8, but dissociated and released drug at temperatures lower than 20. °C or higher... 

We study the phase diagram of the anisotropic spin-1 Heisenberg chain with single ion anisotropy (D) using a ground-state fidelity approach. The ground-state fidelity and its corresponding susceptibility are calculated within the quantum renormalization group scheme where we obtained the renormalization of fidelity preventing calculation of the ground state. Using this approach, the phase boundaries between the antiferromagnetic Néel, Haldane and large-D phases are obtained for the whole phase diagram, which justifies the application of quantum renormalization group to trace the symmetry-protected topological phases. In addition, we present numerical exact diagonalization (Lanczos) results... 

A signaling pathway is a sequence of proteins and passenger molecules that transmits information from the cell surface to target molecules. Understanding signal transduction process requires detailed description of the involved pathways. Several methods and tools resolved this problem by incorporating genomic and proteomic data. However, the difficulty of obtaining prior knowledge of complex signaling networks limited the applicability of these tools. In this study, based on the simulation of signal flow in signaling network, we introduce a method for determining dominant pathways and signal response to stimulations. The model uses topology-weighted transit compartment approach and comprises... 

Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used... 

Symmetric T junctions have been used widely in microfluidics to generate equal-sized microdroplets, which are applicable in drug delivery systems. A newly proposed method for generating unequal-sized microdroplets at a T junction is investigated theoretically and experimentally. Asymmetric T junctions with branches of identical lengths and different cross sections are utilized for this aim. An equation for the critical breakup of droplets at asymmetric T junctions and one for determining the breakup point of droplets are developed. A good agreement was observed between the theories (present and previous) and the experiments  

Solid state 13C and 15N chemical shifts of uracil and imidazole have been calculated using a 2-layer ONIOM approach at 32 levels of theory. The effect of electron correlation between two layers has been investigated by choosing two different kinds of layer selection. Factorial design has been applied as a multivariate technique to analyze the effect of wave function and layer selection on solid state 13C and 15N chemical shifts calculations. PBEPBE/6-311+G(d,p) was recommended as an optimally selected level of theory for high layer in both models. It is illustrated that considering the electron correlation of two layers of ONIOM models is important factor to calculate solid state 15N... 

Response surface methodology was used to investigate the effects of operating parameters such as impeller speed, binder mass and granulation time on the average size of granules produced in a lab scale conical high shear granulator. Two quadratic models were proposed to express granule mean size as a function of impeller speed and binder mass as well as impeller speed and granulation time. It was found out that in the studied domain, the influence of each parameter on granule size differs from one another. While increasing binder mass at constant quantity of powder increased the average size linearly, increasing impeller speed changed the mean size in accordance with quadratic trend. The... 

A multicomponent lattice Boltzmann scheme is used to investigate the surface coating of substrates with two topographical features by a gravity-driven thin liquid film. The considered topographies are U- and V-shaped grooves and mounds. For the case of substrates with two grooves, our results indicate that for each of the grooves there is a critical width such that if the groove width is larger than the critical width, the groove can be coated successfully. The critical width of each groove depends on the capillary number, the contact angle, the geometry, and the depth of that groove. The second groove critical width depends on, in addition, the geometry and the depth of the first groove;... 

The lipid membranes of living cells form an integral part of biological systems, and the mechanical properties of these membranes play an important role in biophysical investigations. One interesting problem to be evaluated is the effect of protein insertion in one leaflet of a bilayer on the physical properties of lipid membrane. In the present study, an all atom (fine-grained) molecular dynamics simulation is used to investigate the binding of cytotoxin A3 (CTX A3), a cytotoxin from snake venom, to a phosphatidylcholine lipid bilayer. Then, a 5 ms coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment... 

To determine the outward permeability of retina-choroid-sclera (RCS) layer for different ophthalmic drugs and to develop correlations between drug physicochemical properties and RCS permeability. A finite volume model was developed to simulate pharmacokinetics in the eye following drug administration by intravitreal injection. The RCS permeability was determined for 32 compounds by best fitting the drug concentration-time profile obtained by simulation with previously reported experimental data. Multiple linear regression was then used to develop correlations between best fit RCS permeability and drugs physicochemical properties. The RCS drug permeabilities had values that ranged over 3 ×... 

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... 

Purpose. Drug release from nanosystems at the sites of either absorption or effect biophase is a major determinant of its biological action. Thus, in vitro drug release is of paramount importance in gaining insight for the systems performance in vivo. Methods. A novel in vitro in vivo correlation, IVIVC, model denoted as double reciprocal area method was presented and applied to 19 drugs from 55 nano formulations with total 336 data, gathered from literature. Results. The proposed model correlated the in vitro with in vivo parameters with overall error of 12.4 ± 3.9%. Also the trained version of the model predicted the test formulations with overall error of 15.8 ± 3.7% indicating the... 

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... 

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... 

Dinuclear cis-dioxomolybdenum(VI) complex [{MoO 2(Bz 2Benzenediyldtc)} 2] coordinated by a quadradentate dithiocarbamate (Bz 2Benzenediyldtc 2- = 1,4-benzenediylbis(benzyldithiocarbamate)(2-)) has been prepared and characterized by elemental analysis, 13C NMR, IR and UV-vis spectroscopy. The kinetics of the oxygen atom transfer between [{MoO 2(Bz 2Benzenediyldtc)} 2] and PPh 3 was studied spectrophotometrically in CH 2Cl 2 medium at 520 nm and four different temperatures, 288, 293, 298 and 303 K, respectively. The reaction follows second order kinetics with the rate constant k = 0.163(2) M -1 S -1 and its increasingly strong absorption at 520 nm clearly indicate the formation of a μ-oxo... 

Adsorption of human serum proteins (Albumin and total protein) onto high purity synthesis nano-hydroxyapatite (HA), Ca 10(PO 4) 6(OH) 2, has been studied in a wide temperature range by UV-visible spectrophotometer. Adsorption isotherm is basically important to describe how solutes interact with adsorbent, andiscriticalinoptimizing the use of adsorbent. Inthe present study, the experimental results werefitted tothe Langmuir, Freundlich, Temkin and Dubinin-Radushkevich (DR) models to obtain the characteristic parameters of each model and square of the correlation coefficients (R 2). According to the results, the DR isotherm model had the best agreement with the experimental data. The effect of... 

New chemical process design strategies utilizing computer-aided molecular design (CAMD) can provide significant improvements in process safety by designing chemicals with required target properties and the substitution of safer chemicals. An important aspect of this methodology concerns the prediction of properties given the molecular structure. This study utilizes one such emerging method for prediction of a hazardous property, flash point (FP), which is in the center of attention in safety studies. Using such a reliable data set comprising 1651 organic and inorganic chemicals, from 79 diverse material classes, and robust dynamic binary particle swarm optimization for the feature selection...