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Influence of cation-heteroatom (Li+, Na+, and K +) interaction on the structural and thermochemical properties of 2′-deoxythymidine nucleoside: Qtaim and NBO analyzes
, Article Journal of Theoretical and Computational Chemistry ; Volume 12, Issue 2 , December , 2013 ; 02196336 (ISSN) ; Fattahi, A ; Sharif University of Technology
2013
Abstract
Density functional theory (DFT) method and B3LYP/6-311++G(d,p) basis set were used to determine coordination geometries, binding strength, and metal ion affinity (MIA) for interaction of 2′-deoxythymidine (dT) with alkali metal cations including Li+, Na+, and K+. Calculations demonstrated that the interaction of dT with these cations is tri-coordinated η (O2, O4′, O5′). Among these cations, Li + cation exhibited the most tendency for interaction with 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 base unit with respect to sugar ring and the acidity of O5′H, O3′H, and N3H groups in 2′-dT...
Synthesis and Study on Complexation of Naphthalene Azacrown Macrocycle Ligands with [60] Fullerene and Metal Cations Like Cu2+
, Ph.D. Dissertation Sharif University of Technology ; Ghanbari, Bahram (Supervisor)
Abstract
In the present research, two series of N2O2- and N4O2-naphthadiaza-crown macrocyclic ligands with different macroring size, 15-21 memberd (L1-L7) were synthesized using direct method. The products were characterized by applying 1H and 13C NMR, IR spectroscopy, mass spectrometry and elemental analysis and in some cases by X-ray crystallography. Firstly, to study on emission properties of naphthadiaza-crown macrocyclic ligands as a fluorophore, we employed different amines as fluorescence quencher. It was observed that the quenching effects of 3o aliphatic amines like triethylamine were more pronounce than other group of amines. Also, the quenching constants for interactions of macrocyclic...
Study of Cationic Impregnation Method on Zeolite Catalyst for Upgrading of Methanol to Gasoline (MTG)Process
, Ph.D. Dissertation Sharif University of Technology ; Ghanbari, Bahram (Supervisor)
Abstract
In the present research, the conversion of methanol to hydrocarbons was studied over a new series of mesoporous low-silica HZSM-5 (Si/Al=11) catalysts impregnated with cations such as Fe, Zn, Mo and Cr. A systematic study on the effect of stepwise modification of the catalysts for the conversion of methanol to gasoline (MTG) was undertaken in a fixed-bed tubular reactor under ambient pressure at 375 °C, feeding with weight hourly space velocity (WHSV) of 2 h−1. The catalysts were prepared in the absence and presence of cationic promoted factors, in both alkaline and neutral aqueous solutions. The final catalysts characterized by using Fourier-transform infrared, X-ray diffraction, X-ray...
DFT study of the interaction of cytidine and 2′-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond
, Article Carbohydrate Research ; Volume 344, Issue 6 , 2009 , Pages 771-778 ; 00086215 (ISSN) ; Fattahi, A. R ; Pourjavadi, A ; Sharif University of Technology
2009
Abstract
Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were...
Theoritical Investigation of Metallic Cations and Gas Adsorption on Surface of Carbon Nanostructures
, Ph.D. Dissertation Sharif University of Technology ; Tafazoli, Mohsen (Supervisor) ; Shamkhali, Amir Nasser (Supervisor)
Abstract
Carbon nanostructures are of great importance in scientific and industrial research. Two case of the important two-dimensional carbon nanostructures are graphitic carbon nitride (g-C3N4) and graphene. In the first part of this work, adsorption of important heavy metal cations including Hg+2, Ag+, Cr+3, Pb+2, Cu+2, Ni+2, Cd+2, Tl+, Sb+3, Zn+2 and As+3 on the surface of (g-C3N4) was investigated by density functional theory (DFT). The main purpose of this theoretical study is to evaluate the ability of g-C3N4 to adsorb pollutant cations. The most prominent result of this work was the ability of g-C3N4 for effective adsorption of As+3 and Sb+3 ions from aqeous solutions. Also, another...
Influence of metal complexation on acidity of cytosine nucleosides: Part I, Li +, Na + and K + cation
, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 535-545 ; 10263098 (ISSN) ; Fattahi, A ; Pourjavadi, A ; Sharif University of Technology
2012
Abstract
Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M +-L (where L represents cytosine nucleosides and M + is an alkali metal ion, including Li +, Na + and K +) complexes have been investigated theoretically, employing B3LY P6-311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been...
Alkali metal cation incorporation in conductive TiO2 nanoflakes with improved photoelectrochemical h2 generation
, Article ChemElectroChem ; Volume 7, Issue 7 , March , 2020 , Pages 1699-1706 ; Mohajernia, S ; Hejazi, S ; Mehdipour, H ; Naseri, N ; Moradlou, O ; Liu, N ; Moshfegh, A. Z ; Schmuki, P ; Sharif University of Technology
Wiley-VCH Verlag
2020
Abstract
In this research, we investigate the effect of alkali metal cations including Li, Na and Cs in hydrothermal solution on the morphology, stability, and photoactivity of nanostructured TiO2 nanoflakes as a photoanode. The TiO2 nanoflakes are formed through hydrothermal treatment of Ti foil in 1.0 M LiOH, NaOH or CsOH at 100 °C for 3 h. By subsequent thermal reduction of the structure in an optimized Ar/H2 environment, conductive TiO2 nanoflakes were formed. The reduction treatment remarkably improves the photocurrent density of the TiO2 nanoflakes and has the highest impact on the sample treated in the NaOH alkali solution. For the nanoflakes produced in NaOH alkali solution, the bandgap is...
Comparison of acidity and metal ion affinity of D-Glucosamine and N-acetyl-D-glucosamine, a DFT study
, Article Journal of Molecular Graphics and Modelling ; Volume 98 , April , 2020 ; Fattahi, A ; Sharif University of Technology
Elsevier Inc
2020
Abstract
The derivatives of glucose such as glucosamine (β-D-GlcN) and N-acetyl-D-β-glucosamine (GlcNAc) are significant in several biological systems. D-GlcN has been used widely to treat osteoarthritis in humans and animal models as well as GlcNAc has been proposed as a treatment for autoimmune diseases. The DFT/B3LYP/6–311++G (d,p) method as well as QTAIM and NBO analyses were used to the acidity values of D-GlcN and GlcNAc sugars and their complexes with alkali ions in the gas phase. The Li+, Na+ and K+ prefer bi-dentate chelate in these complexes. The computed results indicate that metal ion affinity (MIA) in GlcNAc is higher than that in D-GlcN. There are direct correlations between the MIA...
DFT study of the interaction of thymine with Cu+ and Zn 2+
, Article Scientia Iranica ; Volume 16, Issue 2 C , 2009 , Pages 75-80 ; 10263098 (ISSN) ; Fattahi, A ; Sharif University of Technology
2009
Abstract
Interaction of the DNA thymine base with Cu+ and Zn3+ was studied to explore: a) The metal binding energy (MIA) of thymine with Cu+ and Zn2+ and b) The possible correlation between charge transfer and MIAs. The gas-phase Cu+ and Zn2+ affinities of thymine, as well as the Mulliken charges, on the complexed metal cations were both determined at the same computational level, including the density functional level and employing the hybrid B3LYP exchange correlation potential in connection with the 6-311++G (d,p) basis set. All the molecular complexes were obtained by interaction between the most stable tautomer of thymine and two transition mono and divalent (Cu+, Zn2+) metal ions. To probe all...