Search for: computational-chemistry
Exploring cellular interactions of liposomes using protein corona fingerprints and physicochemical properties, Article ACS Nano ; Volume 10, Issue 3 , 2016 , Pages 3723-3737 ; 19360851 (ISSN) ; Palchetti, S ; Pozzi, D ; Hormozi Nezhad, M. R ; Baldelli Bombelli, F ; Caracciolo, G ; Mahmoudi, M ; Sharif University of Technology
American Chemical Society
To control liposomes fate and transport upon contact with biofluids, it is essential to consider several parameters affecting the synthetic and biological identity of liposomes, as well as liposome-protein corona (PC) aspects. As a powerful tool in this data mining adventure, quantitative structure-activity relationship (QSAR) approach is used to correlate physicochemical properties of liposomes and their PC fingerprints to multiple quantified biological responses. In the present study, the relationship between cellular interactions of a set of structurally diverse liposomal formulations and their physicochemical and PC properties has been investigated via linear and nonlinear QSAR models....
M.Sc. Thesis Sharif University of Technology ; Ghanbari, Bahram
In this research, a new group of N2O2–azacrown macrocyclic ligands with different macroring size from 15 to 18 was synthesized using one-pot facile and high yield reaction. The products were characterized applying FT-IR, 1H and 13C NMR spectroscopies as well as elemental analysis. The single crystal structure of 18-membered macrocyclic ligand was also determined by x-ray crystallography. The crystallographic data showed such strong inter-molecular hydrogen bonding which excluded their nitrogen-donor groups, and initial investigation with UV-Vis spectroscopy shows no intraction with fullerene, despite of presence of these interacrtions in their parent macrocycles. The result of Job’s...
Synthesis of Five Membered Nitrogen Containing Heterocycles Including Pyrrole, Imidazole and Tetrazole in Aqueous Media, Ph.D. Dissertation Sharif University of Technology ; Mahmoudi Hashemi , Mohammad
This thesis contains four chapters. In first chapter the role of water in organic reactions as a ecofriendly solvent, computational chemistry and dynamic nuclear magnetic resonance were studied. In the second chapter synthesis of new 4-hydroxy pyrrole derivatives in water were reported. For the synthesis of these compounds arylglyoxal derivatives, 1,3-dicarbonyl compounds and ammonium acetate were used. The reaction conditions are very mild. The third chapter contains the synthesis of new (4 or 5)-Aryl-2-aryloeil-(1H)-imidazole compounds in aqueous media. We also investigated the tauto-isomerisation of isomeric imidazoles during this reaction using DNMR technique. In forth chapter a...
Design and Structural Study of Functionalized Nanoporous Catalysts Confined with Ionic Liquids and Their Applications in Some Organic Transformations, M.Sc. Thesis Sharif University of Technology ; Mahmoodi Hashemi, Mohammad
The current thesis deals with designing of functionalized nanoporous catalysts modified with organic groups and ionic liquids and their applications for some challenging organic reactions such as synthesis of adipic acid and fatty acid esterifications. In this condition the catalysts show enhanced activity since the hydrophobicity of the surface can tune by applying organic groups. In this regard, oxidation of cyclohexene was performed using hydrogen peroxide as oxidant in the present of tungstate based task–specific ionic liquids and silica–functionalized ammonium tungstate as green catalysts. The results indicate that adipic acid achieves in high yield with excellent selectivity....
Synthesis and Study of the Interaction of Aza-Crwon Macrocyclic Ligands with Carboxylate Side Arms with Cd Salts, M.Sc. Thesis Sharif University of Technology ; Ghanbari, Bahram
In the present study, the coordination chemistry of an amino acid azacrown macrocycle ligand bearing one carboxylic acid arm (MA1) was investigated by employing NMR spectroscopy, crystallography and computational chemistry. MA1 was synthetized by the reaction of chloroacetic acid with the parent azacrown macrocycle and its purity was confirmed with 13C and 1H NMR for the first time. A new MA1 homologue, MA3 was also successfully prepared and characterized with NMR, mass spectrometry, and elemental analysis. NMR studies showed that MA1 binds to cadmium via the carboxylate arm in solution. Crystallographic studies showed that MA1 formed a one-dimensional polymer with cadmium, wherein the...
The Study of Antioxidant Mechanism of some Flavonoids without and in Presence of Cyclodextrins: Theoretical Point of View, Ph.D. Dissertation Sharif University of Technology ; Tafazzoli, Mohsen ; Ghiasi, Mina
Antioxidants are compounds with anti-cancer, anti-bacterial, anti-viral, anti-aging and anti-allergic properties. In the present study, a quantum mechanical approach has been used to shed light on the presence effect of glycoside group on the antioxidant ability of chrysin as one of the most important consumable flavonoids and two glycoside derivatives, chrysin-6-C-fucopyranoside and chrysin-3-malonyl-6-C-fucopyranoside which has electron-withdrawing group (EWG) in its C3 of glycoside group. Density functional theory (DFT) using B3LYP and UB3LYP functional and split-valance 6-311++G ** basis set were used to optimize chrysin, its different derivatives, and their radicals. Analysis of...
Design of Methods for Synthesis and Immobilization of Nitrogen Ligands Such as Pyridine onto the Mesoporous Silica Nanoparticles and Design of Pharmaceutical Structures Based on Amino Acids and Carbohydrates to Inhibit Polymerase Η for the Treatment of Leukemia and their Applications In Resins and Ionic Liquids, Ph.D. Dissertation Sharif University of Technology ; Matloubi Moghaddam, Firouz ; Fattahi, Alireza
1- Mesoporous silica materials have been found to possess pore sizes ranging from 2 -10 nm alongside 2D-hexagonal and 3D-cubic structural features. The specific properties of nanoparticles of the mesoporous silica family, such as the collected size, porosity, morphology, and high chemical stability, make them among the best drug delivery systems and catalysts. Designing the catalysts with advanced structures that effectively locate the transition metals and create active centres onto the surfaces of mesoporous silica materials has attracted extraordinary attention. According to many studies, mesoporous silica materials without organic functional groups cannot be used as catalysts in chemical...
Article RSC Advances ; Volume 5, Issue 70 , 2015 , Pages 57030-57037 ; 20462069 (ISSN) ; Hormozi Nezhad, M. R ; Parastar, H ; Sharif University of Technology
Royal Society of Chemistry 2015
There are, to date, few general answers to fundamental questions related to the interactions of nanoparticles (NPs) with living cells. Studies reported in the literature have delivered only limited principles about the nano-bio interface and thus the biological behavior of NPs is yet far from being completely understood. Combining computational tools with experimental approaches in this regard helps to precisely probe the nano-bio interface and allows the development of predictive and descriptive relationships between the structure and the activity of nanomaterials. In the present contribution, a nano-quantitative structure-activity relationship (nano-QSAR) model has been statistically...
Numerical study of pollutant emissions in a Jet stirred reactor under elevated pressure Lean premixed conditions, Article Mathematical Problems in Engineering ; Volume 2016 , 2016 ; 1024123X (ISSN) ; Shakeri, A ; Sharif University of Technology
Hindawi Publishing Corporation 2016
Numerical study of pollutant emissions (NO and CO) in a Jet Stirred Reactor (JSR) combustor for methane oxidation under Elevated Pressure Lean Premixed (EPLP) conditions is presented. A Detailed Flow-field Simplified Chemistry (DFSC) method, a low computational cost method, is employed for predicting NO and CO concentrations. Reynolds Averaged Navier Stokes (RANS) equations with species transport equations are solved. Improved-coefficient five-step global mechanisms derived from a new evolutionary-based approach were taken as combustion kinetics. For modeling turbulent flow field, Reynolds Stress Model (RSM), and for turbulence chemistry interactions, finite rate-Eddy dissipation model are...
Article Combustion and Flame ; Volume 235 , 2022 ; 00102180 (ISSN) ; Salehi, M. M ; Sharif University of Technology
Elsevier Inc 2022
A novel functional form for approximating the conditional scalars in turbulent reacting flows is introduced based on the Bernstein polynomial. Multi-scalar measurement data of turbulent premixed and non-premixed flames are used to demonstrate that the new functional form provides an excellent reduced-order model for the conditional scalars. This model order reduction technique can be used to improve the accuracy, reduce the computational cost and enhance the spatial localization of the Conditional Source-term Estimation (CSE) model. CSE is a turbulence-chemistry interaction model similar to the Conditional Moment Closure (CMC) model, except that the conditional scalars are estimated from the...
Article Current Applied Physics ; Volume 15, Issue 11 , November , 2015 , Pages 1389-1396 ; 15671739 (ISSN) ; Afsharmanesh, B ; Akbari, E ; Sharif University of Technology
Predominance of nano-scale effects observed in material behavior at small scales requires implementation of new simulation methods which are not merely based on classical continuum mechanic. On the other hand, although the atomistic modeling methods are capable of modeling nano-scale effects, due to the computational cost, they are not suitable for dynamic analysis of nano-structures. In this research, we aim to develop a continuum-based model for nano-beam vibrations which is capable of predicting the results of molecular dynamics (MD) simulations with considerably lower computational effort. In this classical-based modeling, the surface and core regions are taken to have different...
First heterobimetallic AgI–CoIII coordination compound with both bridging and terminal –NO2 coordination modes: Synthesis, characterization, structural and computational studies of (PPh3)2AgI– (μ-κ2O,O′:κN-NO2)–COIII(DMGH)2(κN-NO2), Article Acta Crystallographica Section C: Structural Chemistry ; Volume 74, Issue 8 , 2018 , Pages 882-888 ; 20532296 (ISSN) ; Batmanghelich, S ; Raithby, P. R ; Sharif University of Technology
An unusual heterobimetallic bis(triphenylphosphane)(NO2)AgI–CoIII(dimethyl-glyoximate)(NO2) coordination compound with both bridging and terminal –NO2 (nitro) coordination modes has been isolated and characterized from the reaction of [CoCl(DMGH)2(PPh3)] (DMGH2 is dimethylglyoxime or N,N′-di-hydroxybutane-2,3-diimine) with excess AgNO2. In the title compound, namely bis(dimethylglyoximato-1κ2O,O′)(μ-nitro-1κN:2κ2O,O′)(nitro-1κN)bis(triphenyl-phosphane-2κP)cobalt(III)silver(I), [AgCo(C4H7N2O2)2(NO2)2(C18H15P)2], one of the ambidentate –NO2 ligands, in a bridging mode, chelates the AgI atom in an isobidentate κ2O,O′-manner and its N atom is coordinated to the CoIII atom. The other –NO2 ligand...
Analysis of mechanical and thermal properties of carbon and silicon nanomaterials using a coarse-grained molecular dynamics method, Article International Journal of Mechanical Sciences ; Volume 187 , December , 2020 ; Ali Madadi, A ; Bajalan, Z ; Nejat Pishkenari, H ; Sharif University of Technology
Elsevier Ltd 2020
The main concern in Molecular Dynamics (MD) simulations is the computational cost, and coarse-graining methods accelerate simulations by reducing the degrees of freedom in the system. Yet, the utilization of these methods should be carefully followed. In this paper, we presented an energy-based coarse-graining method for Tersoff and Stillinger-Weber potential functions. The presented coarse-graining method is based on the domain mapping and modification of potential function. The focus of this paper is on Carbon and Silicon materials; however, this method can be applied to model other materials for which Tersoff and Stillinger-Weber potentials are defined. This method has been validated by...
Atomistic study of the effect of crystallographic orientation on the twinning and detwinning behavior of NiTi shape memory alloys, Article Computational Materials Science ; Volume 203 , 2022 ; 09270256 (ISSN) ; Izadifar, M ; Dolado, J. S ; Ramazani, A ; Sadrnezhaad, S. K ; Sharif University of Technology
Elsevier B.V 2022
Understanding the effect of crystallographic orientation on the twinnin/detwinning mechanisms in NiTi shape memory alloys at an atomistic scale can help to control and tune the mechanical properties and failure behavior of such materials. In this work, we employed classical molecular dynamics (MD) and density functional theory (DFT) computational methods to better understand how twinning and detwinning occurs through a combination of slip, twin, and shuffle on 〈0 1 0〉, 〈1 1 0〉, and 〈1 1 1〉 crystallographic orientations under uniaxial tensile test. Elastic constants including Young's Modulus (E), Bulk modulus (B), Poisson's ratio (ν), and Shear Modulus (G) are obtained and computed for...
Chemometrics-assisted effect-directed analysis of crude and refined oil using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry, Article Environmental Science and Technology ; Vol. 48, issue. 5 , 2014 , pp. 3074-3083 ; ISSN: 0013936X ; Thomas, K. V ; Parastar, H ; Diez, S ; Tauler, R ; Bayona, J. M ; Sharif University of Technology
An effect-directed analysis (EDA) of fresh and artificially weathered (evaporated, photooxidized) samples of North Sea crude oil and residual heavy fuel oil is presented. Aliphatic, aromatic, and polar oil fractions were tested for the presence of aryl hydrocarbon receptor (AhR) agonist and androgen receptor (AR) antagonist, demonstrating for the first time the AR antagonist effects in the aromatic and, to a lesser extent, polar fractions. An extension of the typical EDA strategy to include an N-way partial least-squares (N-PLS) model capable of relating the comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) data set to the bioassay data...