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The Use of Enhanced Chemometric Methods in QSAR and Pattern Recognition Studies
, Ph.D. Dissertation Sharif University of Technology ; Jalali Heravi, Mehdi (Supervisor)
Abstract
Chemometrics is an interdisciplinary subject which has many applications among science and industrial process. Environmental chemist, Food chemist, biologist and so on depend on good analytical chemistry measurement and so need chemometrics to interpret their data. In this project, we have developed different chemometrics and machine learning methods for considering the quantitative structure-activity relationship between different drug-like molecules. Also some chemometrics techniques were applied for the pattern recognition of NIR data on human plasma for discriminating between healthy and infected HIV-1 patients. At first, Quantitative structure-activity relationship (QSAR) models for...
Emergence of molecular chirality due to chiral interactions in a biological environment
, Article Journal of Biological Physics ; Vol. 40, issue. 4 , Jul , 2014 , p. 369-386 ; Ghahramani, F. T ; Shafiee, A ; Sharif University of Technology
Abstract
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...
The oscillatory behavior, static and dynamic analyses of a micro/nano gyroscope considering geometric nonlinearities and intermolecular forces
, Article Acta Mechanica Sinica/Lixue Xuebao ; Volume 29, Issue 6 , 2013 , Pages 851-863 ; 05677718 (ISSN) ; Ahmadian, M. T ; Firoozbakhsh, K ; Sharif University of Technology
2013
Abstract
The nonlinear dynamic and static deflection of a micro/nano gyroscope under DC voltages and base rotation are investigated. The gyroscope undertakes two coupled bending motions along the drive and sense directions and subjected to electrostatic actuations and intermolecular forces. The nonlinear governing equations of motion for the system with the effect of electrostatic force, intermolecular tractions and base rotation are derived using extended Hamilton principle. Under constant voltage, the gyroscope finds the preformed shape. First, the deflection of the micro/nano gyroscope under electrostatic forces is obtained by static and dynamic analyses. Furthermore, the static and dynamic...
Hydrophobic nanocarriers embedded in a novel dual-responsive poly(N-isopropylacrylamide)/chitosan/(cyclodextrin) nanohydrogel
, Article Journal of Polymer Research ; Volume 20, Issue 10 , 2013 ; 1572-8935 (Online ISSN) ; Hemmatinejad, N ; Pourjavadi, A ; Sharif University of Technology
2013
Abstract
The incorporation of modified β-cyclodextrin (β-CD) into a poly(N-isopropylacrylamide) (PNIPAAm)/chitosan (PNCS) nanohydrogel was studied. β-CD was functionalized with acrylic groups, with different numbers of vinyl bonds added per β-CD molecule. The surfactant-free dispersion polymerization (SFDP) semi-batch method was used to synthesize the nanohydrogel. Increasing the number of vinyl groups per β-CDAC (β-CD acrylate) molecule induced the formation of smaller nanogels with diameters ranging from 142 to 68 nm. The cyclodextrin-modified dual-responsive nanogels obtained presented an LCST (lower critical solution temperature) in aqueous medium at around 31 C. The incorporation of β-CDAC into...
Glucose interaction with Au, Ag, and Cu clusters: Theoretical investigation
, Article International Journal of Quantum Chemistry ; Volume 113, Issue 8 , 2013 , Pages 1062-1070 ; 00207608 (ISSN) ; Farhangian, H ; Tehrani, Z. A ; Sharif University of Technology
2013
Abstract
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...
Interactions of coinage metal clusters with histidine and their effects on histidine acidity; Theoretical investigation
, Article Organic and Biomolecular Chemistry ; Volume 10, Issue 47 , Oct , 2012 , Pages 9373-9382 ; 14770520 (ISSN) ; Jamshidi, Z ; Tehrani, Z. A ; Fattahi, A ; Sharif University of Technology
2012
Abstract
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...
Analysis of impedance stabilization of natural and metallic DNA molecules
, Article 2012 19th Iranian Conference of Biomedical Engineering, ICBME 2012 ; 2012 , Pages 139-142 ; 9781467331302 (ISBN) ; Khakestar, A. S ; Hejazi, M. S ; Fardmanesh, M ; Sharif University of Technology
2012
Abstract
In this work, we used λ-DNA to produce metallic DNA samples and we investigated the stabilization time of their impedances. This is in order to show that the DNA molecules can possibly be utilized as a frame for assembling the nanocircuits and as an electronic element as well, in nanoelectric devices. It has been shown that metallic DNA has lower stabilization time than natural DNA. As expected, it is shown that making the bundled DNA oriented, impacts their impedance stabilization. In order to find the characteristic impedance of the DNA molecules under direct current, we designed and made patterned electrodes to make electrical connections between the DNAs and the used current source. The...
Sol-gel-based molecularly imprinted xerogel for capillary microextraction
, Article Analytical and Bioanalytical Chemistry ; Volume 404, Issue 5 , September , 2012 , Pages 1597-1602 ; 16182642 (ISSN) ; Piri-Moghadam, H ; Sharif University of Technology
Springer
2012
Abstract
A novel molecularly imprinted xerogel (MIX) based on organically modified silica (ORMOSIL) was successfully prepared for on-line capillary microextraction (CME) coupled with high-performance liquid chromatography (HPLC). The sol-gel-based xerogel was prepared using only one precursor and exhibited extensive selectivity towards triazines along with significant thermal and chemical stability. Atrazine was selected as a model template molecule and 3-(trimethoxysilyl)propylmethacrylate (TMSPMA) as a precursor in which the propylmethacrylate moiety was responsible for van der Waals, dipole-dipole, and hydrogen-bond interactions with the template. This moiety plays a key role in creation of...
Spectrophotometric determination of glutathione and cysteine based on aggregation of colloidal gold nanoparticles
, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 958-963 ; 10263098 (ISSN) ; Seyedhosseini, E ; Robatjazi, H ; Sharif University of Technology
2012
Abstract
We report herein the development of a highly sensitive colorimetric method for the determination of cysteine and glutathione, based on aggregation of the citrate capped gold nanoparticles (Au NPs). This was exploited from high affinity of low-molecular-weight aminothiols towards the Au NPs surface, which could induce displacement of the citrate shell by the thiolate shell of target molecules, resulting in aggregation of the NPs through intermolecular electrostatic interaction or hydrogen-bonding. As a result of aggregation, which can be affected by the ionic strength, pH and concentration of Au NPs, the plasmon band at around 521 nm decreases gradually, along with formation of a new red...
Interactions of glutathione tripeptide with gold cluster: Influence of intramolecular hydrogen bond on complexation behavior
, Article Journal of Physical Chemistry A ; Volume 116, Issue 17 , 2012 , Pages 4338-4347 ; 10895639 (ISSN) ; Jamshidi, Z ; Javan, M. J ; Fattahi, A ; Sharif University of Technology
2012
Abstract
Understanding the nature of the interaction between metal nanoparticles and biomolecules has been important in the development and design of sensors. In this paper, structural, electronic, and bonding properties of the neutral and anionic forms of glutathione tripeptide (GSH) complexes with a Au 3 cluster were studied using the DFT-B3LYP with 6-31+G**-LANL2DZ mixed basis set. Binding of glutathione with the gold cluster is governed by two different kinds of interactions: Auâ€"X (X = N, O, and S) anchoring bond and Au··•·•H-X nonconventional hydrogen bonding. The influence of the intramolecular hydrogen bonding of glutathione on the interaction of this peptide with the gold cluster has been...
Adsorption and solar light activity of transition-metal doped TiO 2 nanoparticles as semiconductor photocatalyst
, Article Journal of Materials Science: Materials in Electronics ; Volume 23, Issue 3 , 2012 , Pages 659-667 ; 09574522 (ISSN) ; Simchi, A ; Jafari, T ; Sharif University of Technology
Abstract
There is an eminent interest to improve the photoactivity of TiO 2 nanostructures via doping with midband gap donors or acceptors to achieve a high solar absorption. In the present work, Cr- and V-doped TiO 2 nanoparticles were prepared via a facile chemical vapor synthesis method. The effect of the transition metals (TM) on the solar light activity of the semiconductor nanoparticles as photocatalyst was examined by degradation of methylene blue and acid red 27. Induced coupled plasma and X-ray photoelectron spectroscopy analyses indicated high efficiency of the doping process in the hot wall reactor without surface covering of the TiO 2 nanoparticles by the dopants. Diffuse reflectance...
On the binding of Mg 2+, Ca 2+, Zn 2+ and Cu + metal cations to 2 ′ -deoxyguanosine: Changes on sugar puckering and strength of the N-glycosidic bond
, Article Scientia Iranica ; Volume 18, Issue 6 , December , 2011 , Pages 1343-1352 ; 10263098 (ISSN) ; Fattahi, A ; Sharif University of Technology
2011
Abstract
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...
Contribution of nonlocal interactions to DNA elasticity
, Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
2011
Abstract
A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA
Vesicle deformations by clusters of transmembrane proteins
, Article Journal of Chemical Physics ; Volume 134, Issue 8 , 2011 ; 00219606 (ISSN) ; Jalali, M. A ; Sharif University of Technology
2011
Abstract
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters change the shapes of their host vesicles. The effects of depletion force and vesiculation on protein clustering are also investigated. By increasing the protein concentration, clusters are fragmented to smaller bundles, which are then redistributed to form more symmetric structures corresponding to lower bending energies. Big clusters and highly aspherical vesicles cannot be formed when the fraction of protein to lipid molecules is large
Extreme bendability of DNA double helix due to bending asymmetry
, Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) ; Eslami Mossallam, B ; Naderi, S ; Ejtehadi, M. R ; Sharif University of Technology
American Institute of Physics Inc
2015
Abstract
Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule...
Morphology transition control of polyaniline from nanotubes to nanospheres in a soft template method
, Article Polymer International ; Volume 64, Issue 1 , June , 2015 , Pages 88-95 ; 09598103 (ISSN) ; Ghorbani, M ; Shojaei, A ; Sharif University of Technology
John Wiley and Sons Ltd
2015
Abstract
A soft template route is reported for the fabrication of polyaniline nanospheres via the oxidative polymerization of aniline in the presence of β-naphthalenesulfonic acid (β-NSA) as both surfactqant and dopant, and ammonium persulfate as oxidant at 2-5°C. Control over the morphology and size of the nanoparticles was achieved by changing the reaction medium via addition of an organic cosolvent (i.e. ethanol or ethylene glycol) and by controlling the concentrations of aniline and β-NSA and the molar ratio of β-NSA to aniline. By this means the size of the β-NSA-aniline micelles and the way that aniline monomer interacts with the micelles were controlled. In fact the lower dielectric constant...
Amine-functionalized magnetic nanocomposite particles for efficient immobilization of lipase: effects of functional molecule size on properties of the immobilized lipase
, Article RSC Advances ; Volume 5, Issue 42 , Apr , 2015 , Pages 33313-33327 ; 20462069 (ISSN) ; Kazemeini, M ; Singh, G ; Arpanaei, A ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
A cost-effective design of reusable enzyme-functionalized particles with better catalytic activity is of great scientific interest due to their applications in a wide range of catalytic reactions in several industrial processes. In this work, a systematic approach for preparing amine-functionalized magnetic nanocomposite particles through the surface modification of core/shell type Fe3 O4 cluster@SiO2 particles by the small molecules of 3-(2-aminoethyl)aminopropyltrimethoxysilane (AAS) or the large molecules of polyethyleneimine (PEI) with two different molecular weights, as the support materials for enzyme immobilization, has been demonstrated. The functional...
Meta hybrid density functional theory study of adsorption of imidazolium and ammonium based ionic liquids on graphene sheet
, Article Journal of Physical Chemistry C ; Volume 119, Issue 13 , March , 2015 , Pages 7095-7108 ; 19327447 (ISSN) ; Jamshidi, Z ; Bayat, A ; Kamath, G ; Sharif University of Technology
American Chemical Society
2015
Abstract
In this study, two types of ionic liquids (ILs) based on 1 butyl 3 methylimidazolium [Bmim]+ and butyltrimethylammonium [Btma]+ cations, paired to tetrafluoroborate [BF4], hexafluorophosphate [PF6], dicyanamide [DCA], and bis(trifluoromethylsilfonyl)imide [Tf2N] anions, were chosen as adsorbates to investigate the influence of cation and anion type on the adsorption of ILs on the graphene surface. The adsorption process on the graphene surface (circumcoronene) was studied using M06 2X/cc pVDZ level of theory. Empirical dispersion correction (D3) was also added to the M06 2X functional to investigate the effects of dispersion on the binding energy values. The graphene···IL configurations,...
Comparative studies of some heterocyclic compounds as corrosion inhibitors of copper in phosphoric acid media
, Article Chemical Engineering Communications ; Volume 197, Issue 10 , 2010 , Pages 1303-1314 ; 00986445 (ISSN) ; Arshadi, M. R ; Biglar, M ; Sharif University of Technology
2010
Abstract
Corrosion inhibition properties of some heterocyclic compounds (3-mercapto 1,2,4 triazole, benzotriazole, thiophene, and tetra hydro-thiophene) in Cu/H3PO4 medium were investigated theoretically and experimentally via cluster/polarized continuum and gravimetric approaches. Second-order Møller-Plesset perturbation and density functional theories were applied, and the electronic chemical potential, molecular softness, and extent of charge transfer were determined for inhibitor molecules at the metal/solution interface. Good correlations were observed for both theories between the calculated quantities and experimental data. To reveal the quality of metal-inhibitor interactions, comprehensive...
Adsorption of proteins at the solution/air interface influenced by added nonionic surfactants at very low concentrations for both components. 3. dilational surface rheology
, Article Journal of Physical Chemistry B ; Volume 119, Issue 9 , January , 2015 , Pages 3768-3775 ; 15206106 (ISSN) ; Aksenenko, E. V ; Lylyk, S. V ; Lotfi, M ; Miller, R ; Sharif University of Technology
Abstract
The influence of the addition of the nonionic surfactants C12 DMPO, C14 DMPO, C10 OH, and C10 EO5 at concentrations between 10-5 and 10-1 mmol/L to solutions of β-casein (BCS) and β-lactoglobulin (BLG) at a fixed concentration of 10-5 mmol/L on the dilational surface rheology is studied. A maximum in the viscoelasticity modulus |E| occurs at very low surfactant concentrations (10-4 to 10-3 mmol/L) for mixtures of BCS with C12 DMPO and C14 DMPO and for mixtures of BLG with C10 EO5 , while for mixture of BCS with C10 EO5 the value of |E| only slightly increased. The |E| values...