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What roles do boron substitutions play in structural, tautomeric, base pairing and electronic properties of uracil? NBO & AIM analysis
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 9 , 2012 , Pages 787-796 ; 08943230 (ISSN) ; Abedin, A ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
Wiley
2012
Abstract
The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our...
Methane molecule over the defected and rippled graphene sheet
, Article Solid State Communications ; Volume 152, Issue 15 , August , 2012 , Pages 1493-1496 ; 00381098 (ISSN) ; Neek Amal, M ; Sharif University of Technology
Elsevier
2012
Abstract
Adsorption of a methane molecule (CH 4) onto a defected and rippled graphene sheet is studied using ab initio and molecular mechanics calculations. The optimal adsorption position and orientation of this molecule on the graphene surface (motivated by the recent realization of graphene sensors to detect individual gas molecules) is determined and the adsorption energies are calculated. In light of the density of states, we used the SIESTA code. It is found that (i) classical force field yields adsorption energy comparable with experimental result and ab initio calculation; (ii) the periodic nature of the van der Waals potential energy stored between methane and perfect sheet is altered due to...
Mixed protein-surfactant adsorption layers formed in a sequential and simultaneous way at water-air and water-oil interfaces
, Article Soft Matter ; Volume 8, Issue 22 , 2012 , Pages 6057-6065 ; 1744683X (ISSN) ; Kotsmar, C ; Ferri, J. K ; Javadi, A ; Karbaschi, M ; Krägel, J ; Wüstneck, R ; Miller, R ; Sharif University of Technology
2012
Abstract
Mixed protein-surfactant adsorption layers can be built up in two different ways. The classical way is when all components adsorb simultaneously from a mixed solution. Alternatively, the components adsorb one after another, i.e. in a sequential way. In the present work, the formation of such surface layers has been studied with the random coil protein β-casein in the presence of added anionic surfactant SDS and compared for two different interfaces: the water-air (W-A) and water-hexane (W-H) interfaces. The used experimental technique is a drop profile analysis tensiometer PAT-1 specially equipped with a coaxial double capillary for drop volume exchange during the experiments. The results...
Ionic liquid based on α-amino acid anion and N7,N9-dimethylguaninium cation ([dMG][AA]): Theoretical study on the structure and electronic properties
, Article Journal of Physical Chemistry A ; Volume 116, Issue 22 , April , 2012 , Pages 5436-5444 ; 10895639 (ISSN) ; Fattahi, A ; Bayat, A ; Sharif University of Technology
2012
Abstract
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...
Dithiocarbamic acids and thiols as nucleophiles in the Bargellini reaction
, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 551-554 ; 10263098 (ISSN) ; Saidi, M. R ; Sharif University of Technology
2012
Abstract
Dithiocarbamic acids and thiols are employed in the Bargellini reaction to generate useful intermediates for the synthesis of organic molecules. This is the first time that dithiocarbamic acids are used as nucleophile in this reaction
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...
Influence of quantum effect on deviation from linear isotherm regularity
, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 555-560 ; 10263098 (ISSN) ; Parsafar, G. A ; Sharif University of Technology
2012
Abstract
A general regularity was found based on an effective pair potential of Lennard-Jones LJ (12, 6), for both dense, nonmetallic and nonionic fluids and solids according to which (Z-1) v2 linearly varies with respect to ρ2 for each isotherm, and this equation of state (EoS I) is known as LIR. However, despite the fact that Ne is a simple spherical species, unexpectedly, its solid and liquid phases both show a significant deviation from EoS I. In this work, we have investigated the accuracy of the EoS I for other systems, including quantum light molecules, such as D 2, H 2 and He, in both fluid and solid states at different temperatures. Like Ne, we have noticed that these systems do not well...
Molecular structure and character of bonding of mono and divalent metal cations (Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and cu +) with guanosine: AIM and NBO analysis
, Article Structural Chemistry ; Volume 23, Issue 3 , June , 2012 , Pages 613-626 ; 10400400 (ISSN) ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
2012
Abstract
The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and Cu + cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 20-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA....
Influence of the water molecules (n 5 1-6) on the interaction between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue
, Article Structural Chemistry ; Volume 23, Issue 3 , 2012 , Pages 857-865 ; 10400400 (ISSN) ; Nasiri, M ; Fattahi, A ; Vafaeezadeh, M ; Sharif University of Technology
2012
Abstract
Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the...
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...
Hydration strongly affects the molecular and electronic structure of membrane phospholipids
, Article Journal of Chemical Physics ; Volume 136, Issue 11 , 2012 ; 00219606 (ISSN) ; Partovi Azar, P ; Jadidi, T ; Nafari, N ; Maass, P ; Tabar, M. R. R ; Bonn, M ; Bakker, H. J ; Sharif University of Technology
Abstract
We investigate the structure and electronic properties of phosphatidylcholine (PC) under different degrees of hydration at the single-molecule and monolayer type level by linear scaling ab initio calculations. Upon hydration, the phospholipid undergoes drastic long-range conformational rearrangements which lead to a sickle-like ground-state shape. The structural unit of the tilted gel-phase PC appears to be a water-bridged PC dimer. We find that hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids and consequently guides the interactions of the lipids with other molecules and the communication between cells
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...
Theoretical study of borazine: cation-π (Be 2+, Mg 2+, and Ca 2+) interaction
, Article Structural Chemistry ; 2012 , Pages 1-7 ; 10400400 (ISSN) ; Sharif University of Technology
2012
Abstract
The geometries of the complexes of Be 2+, Mg 2+, and Ca 2+ metal cations with borazine ring were studied. The complexes were optimized at the B3LYP level and the 6-311++G(d,p) basis set. Then, the interaction energies corrected by basis set super position error were calculated in the same level. The results show that interaction energy is strongly dependent on the charge-to-size ratio of the cation. Therefore, Be 2+ cation has the most interaction energy value with respect to Mg 2+ and Ca 2+ metal cations. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to...
Interaction of cations with 2′-deoxythymidine nucleoside and analysis of the nature and strength of cation bonds
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 2 , JAN , 2012 , Pages 153-161 ; 08943230 (ISSN) ; Fattahi, A ; Jamshidi, Z ; Sharif University of Technology
2012
Abstract
Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the 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 the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate...
Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2'-deoxythymidine with different anions
, Article Structural Chemistry ; Volume 23, Issue 1 , July , 2012 , Pages 17-28 ; 10400400 (ISSN) ; Fattahi, A ; Sharif University of Technology
2012
Abstract
Hydrogen bonding interactions between thymine nucleobase and 2'-deoxythymidine nucleoside (dT) with some biological anions such as F - (fluoride), Cl - (chloride), OH - (hydroxide), and NO 3 - (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory...
Charge transport properties in nanocomposite photoanodes of DSSCs: Crucial role of electronic structure
, Article EPJ Applied Physics ; Volume 57, Issue 2 , February , 2012 ; 12860042 (ISSN) ; Taghavinia, N ; Iraji Zad, A ; Marandi, M ; Tajabadi, F ; Sharif University of Technology
Abstract
TiO 2 nanorods, TiO 2 nanorod/TiO 2 nanoparticle and TiO 2 nanorod/ZnO nanoparticle composite structures were integrated as photoanodes in backside illuminated dye-sensitized solar cells (DSSCs). Incorporation of TiO 2 nanoparticles into the bare nanorods increased the dye loading and improved the short-circuit current density (J sc) from 2.22 mA/cm 2 to 3.57 mA/cm 2. ZnO nanoparticles electrochemically grown into the TiO 2 nanorod layer could increase the surface area. Nevertheless, this considerably reduced the J sc to 0.57 mA/cm 2 and consequently cell efficiency. Electrochemical impedance spectroscopy (EIS) results showed that ZnO incorporated samples have better effective diffusion...
Tunneling properties of nonplanar molecules in a gas medium
, Article Physical Review A - Atomic, Molecular, and Optical Physics ; Volume 84, Issue 6 , 2011 ; 10502947 (ISSN) ; Bassi, A ; Sharif University of Technology
Abstract
We propose a simple, general, and accurate formula for analyzing the tunneling between classical configurations of a nonplanar molecule in a gas medium, as a function of the thermodynamic parameters of the gas. We apply it to two interesting cases: (i) the shift to zero frequency of the inversion line of ammonia, upon an increase in the pressure of the gas; and (ii) the destruction of the coherent tunneling of D 2S 2 molecules in a He gas. In both cases, we compare our analysis with previous theoretical and experimental results
Developing cross drag expressions for nanotube bundles using molecular dynamics
, Article ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM 2011, 19 June 2011 through 22 June 2011 ; Volume 2 , June , 2011 , Pages 259-263 ; 9780791844649 (ISBN) ; Khaledi Alidusti, R ; Abbaspour, M ; Abbasi, H. R ; Sabouri, M ; Schneider, G. E ; Sharif University of Technology
2011
Abstract
The nonequilibrium molecular dynamics (NEMD) simulations are performed to calculation the cross drag over a nanotube located in a uniform liquid argon flow. As is known, the behavior of fluid flows in nano-scale sizes is very different from that in microscopic and macroscopic sizes. In this work, our concern is on the flow of argon molecules over a nanotube which occurs in nanoscale sizes. We calculate the cross drag enforced the nanotube at Re<10. In this regard, we use the molecular dynamics and simulate the flow of argon molecules over (6,0), (8,0) and (10,0) nanotubes. The simulations are performed at different velocities and the cross drag coefficient is computed at different Reynolds...
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...
Study of cut-off radius and temperature effects on water molecular behavior using molecular dynamics method
, Article ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM 2011, 19 June 2011 through 22 June 2011, Edmonton, AB ; Volume 2 , 2011 , Pages 277-282 ; 9780791844649 (ISBN) ; Khaledi-Alidusti, R ; Abbaspour, M ; Abbasi, H. R ; Schneider, G ; Sharif University of Technology
2011
Abstract
Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25...