Search for: molecular-conformation
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    Dynamic stereochemistry of erigeroside by measurement of 1H-1H and 13C-1H coupling constants

    , Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 70, Issue 2 , 2008 , Pages 350-357 ; 13861425 (ISSN) Tafazzoli, M ; Ghiasi, M ; Moridi, M ; Sharif University of Technology
    Erigeroside was extracted from Satureja khuzistanica Jamzad (Marzeh Khuzistani in Persian, family of lamiaceae), and 1H, 13C, 13C{1H}, 1H-1H COSY, HMQC and J-HMBC were obtained to identify this compound and determine a complete set of J-coupling constants (1JC-H, 2JC-H, 3JC-H and 3JH-H) values within the exocyclic hydroxymethyl group (CH2OH) and anomeric center. In parallel, density functional theory (DFT) using B3LYP functional and split-valance 6-311++G** basis set has been used to optimized the structures and conformers of erigeroside. In all calculations solvent effects were considered using a polarized continuum (overlapping spheres) model (PCM). The dependencies of 1J, 2J and 3J... 

    Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach

    , Article Solid State Nuclear Magnetic Resonance ; Volume 51-52 , 2013 , Pages 31-36 ; 09262040 (ISSN) Shaghaghi, H ; Ebrahimi, H. P ; Bahrami Panah, N ; Tafazzoli, M ; Sharif University of Technology
    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... 

    Mechanisms and kinetics of Thiotepa and tepa hydrolysis: DFT study

    , Article Journal of Molecular Modeling ; Volume 18, Issue 8 , 2012 , Pages 3563-3576 ; 16102940 (ISSN) Torabifard, H ; Fattahi, A ; Sharif University of Technology
    Springer  2012
    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 structure, magnetism and EPR spectra of a (μ-thiophenolato)(μ-pyrazolato-N,N′) double bridged dicopper(II) complex

    , Article Dalton Transactions ; Volume 44, Issue 5 , Dec , 2015 , Pages 2431-2438 ; 14779226 (ISSN) Khadir, N ; Boghaei, D. M ; Assoud, A ; Nascimento, O. R ; Nicotina, A ; Ghivelder, L ; Calvo, R ; Sharif University of Technology
    Royal Society of Chemistry  2015
    A new binuclear copper(ii) complex, namely [Cu2L(pz)(DMSO)], where L = 2,6-bis[(2-phenoxy)iminomethyl]-4-methylthiophenolate(3-) and pz = pyrazolate ligand, has been synthesized by a one-pot synthesis involving copper(ii) acetate monohydrate, the S-protected ligand precursor 2-(N,N-dimethylthiocarbamato)-5-methylisophthalaldehyde di-2′-hydroxy anil, (I), and pyrazole, in which a metal-promoted S-deprotection reaction occurs during the formation of the complex. This was characterized by routine physicochemical studies, single crystal X-ray diffraction and electron paramagnetic resonance (EPR) techniques. The structure analysis reveals that there are copper centres in two different... 

    Dynamic stereochemistry of rutin (vitamin P) in solution: Theoretical approaches and experimental validation

    , Article Carbohydrate Research ; Volume 345, Issue 12 , 2010 , Pages 1760-1766 ; 00086215 (ISSN) Ghiasi, M ; Taheri, S ; Tafazzoli, M ; Sharif University of Technology
    The 3D structure of vitamin P, an important bioflavonoid, has been studied in solution by 2D NMR spectroscopy and QM calculations. Rutin, vitamin P, was extracted from Salvia macrosiphon and identified by 1H, 13C, 1H-1H COSY, HMQC, and HMBC spectroscopy. In parallel, density functional theory (DFT) using B3LYP functional and split-valance 6-311G basis set has been used to optimize the structures and conformers of rutin. Also experimental and theoretical methods have been used to correlate the dependencies of 1J, 2J, and 3J involving 1H and 13C on the C5″-C6″ (ω), C6″-O6″ (θ), and C1‴-O6″ () torsion angles in the glycosidic moiety. New Karplus equations are proposed to assist in the... 

    Magnetic resonance tensors in uracil: calculation of 13C, 15N, 17O NMR chemical shifts, 17O and 14N electric field gradients and measurement of 13C and 15N chemical shifts

    , Article Solid State Nuclear Magnetic Resonance ; Volume 37, Issue 1-2 , 2010 , Pages 13-20 ; 09262040 (ISSN) Amini, S. K ; Shaghaghi, H ; Bain, A. D ; Chabok, A ; Tafazzoli, M ; Sharif University of Technology
    The experimental 13C NMR chemical shift components of uracil in the solid state are reported for the first time (to our knowledge), as well as newer data for the 15N nuclei. These experimental values are supported by extensive calculated data of the 13C, 15N and 17O chemical shielding and 17O and 14N electric field gradient (EFG) tensors. In the crystal, uracil forms a number of strong and weak hydrogen bonds, and the effect of these on the 13C and 15N chemical shift tensors is studied. This powerful combination of the structural methods and theoretical calculations gives a very detailed view of the strong and weak hydrogen bond formation by this molecule. Good calculated results for the... 

    Study of molecular conformation and activity-related properties of lipase immobilized onto core-shell structured polyacrylic acid-coated magnetic silica nanocomposite particles

    , Article Langmuir ; Volume 32, Issue 13 , 2016 , Pages 3242-3252 ; 07437463 (ISSN) Esmaeilnejad Ahranjani, P ; Kazemeini, M ; Singh, G ; Arpanaei, A ; Sharif University of Technology
    American Chemical Society 
    A facile approach for the preparation of core-shell structured poly(acrylic acid) (PAA)-coated Fe3O4 cluster@SiO2 nanocomposite particles as the support materials for the lipase immobilization is reported. Low- or high-molecular-weight (1800 and 100 000, respectively) PAA molecules were covalently attached onto the surface of amine-functionalized magnetic silica nanoacomposite particles. The successful preparation of particles were verified by scanning transmission electron microscopy (STEM), X-ray diffraction (XRD), vibrating sample magnetometer (VSM), thermogravimetric analysis (TGA), zeta potential measurement, and Fourier-transform infrared (FTIR) techniques. Once lipase is covalently... 

    Enhanced electron collection efficiency in dye-sensitized solar cells based on nanostructured TiO2 hollow fibers

    , Article Nano Letters ; Volume 10, Issue 5 , April , 2010 , Pages 1632-1638 ; 15306984 (ISSN) Ghadiri, E ; Taghavinia, N ; Zakeeruddin, S. M ; Grätzel, M ; Moser, J. E ; Sharif University of Technology
    Nanostructured TiO2 hollow fibers have been prepared using natural cellulose fibers as a template. This cheap and easily processed material was used to produce highly porous photoanodes incorporated in dye-sensitized solar cells and exhibited remarkably enhanced electron transport properties compared to mesoscopic films made of spherical nanoparticles. Photoinjected electron lifetime, in particular, was multiplied by 3-4 in the fiber morphology, while the electron transport rate within the fibrous photoanaode was doubled. A nearly quantitative absorbed photon-to-electrical current conversion yield exceeding 95% was achieved upon excitation at 550 nm and a photovoltaic power conversion... 

    The two-step thermochemical growth of ZnS:Mn nanocrystals and a study of luminescence evolution

    , Article Nanotechnology ; Volume 20, Issue 9 , 2009 ; 09574484 (ISSN) Hajisalem, G ; Marandi, M ; Taghavinia, N ; Houshiar, M ; Sharif University of Technology
    In this work we report a new thermochemical method for the synthesis of ZnS:Mn nanocrystals. Zn(NO3)2 and Na2S 2O3 were used as the precursors and Mn(NO 3)2 was the source of impurity. Thioglycerol (TG,C 3H8O2S) was also used as the capping agent and the catalyst of the reaction. Na2S2O3 is a heat sensitive material which releases S species upon heating. Consequently, the reaction proceeds in temperatures higher than room temperature. The reaction was done in two steps. In the first step, the precursors were heated at 96 °C for an hour without TG. In the second step, TG was injected to the solution and the heating process was continued for longer heating durations. A fast growth occurred in... 

    Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

    , Article Journal of Molecular Graphics and Modelling ; Volume 87 , 2019 , Pages 257-267 ; 10933263 (ISSN) Ebrahim Habibi, M. B ; Ghobeh, M ; Aghakhani Mahyari, F ; Rafii Tabar, H ; Sasanpour, P ; Sharif University of Technology
    Elsevier Inc  2019
    Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the...