Sharif Digital Repository

The structure and autoionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation (LDA) and generalized gradient approximation (GGA) for the exchange-correlation energy functional. Depending on the lipid headgroup, strongly enhanced ionization is observed, leading to the dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally  

Micro/nano gyroscopes which can measure angular rate or angle are types of merging gyroscope technology with MEMS/NEMS technology. They have extensively used in many fields of engineering, such as automotive, aerospace, robotics and consumer electronics. There are many studies of a variety of gyroscopes with various drive and detect methods and different resonator structures in last years. In case of electrostatically actuated and detected beam micro/nano-gyroscopes, DC voltages are applied in driving and sensing directions and AC voltage is utilized in driving direction in order to excite drive oscillation. The intermolecular surface forces are especially significant when the gyroscopes are... 

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... 

This chapter is dedicated to the surface properties of mixed protein/surfactant adsorption layers, formed by two different experimental approaches, i.e. by sequential and simultaneous adsorption, respectively. A special modification of a drop profile analysis tensiometer, consisting of a coaxial double capillary, provides a unique protocol for studies of mixed surface layers formed by sequential adsorption of the individual components in addition to the traditional simultaneous adsorption from their mixed solution. A CFD simulation allowed to optimize the drop exchange process performed with the special double capillary arrangement. The experiments show that properties of sequentially formed... 

Etheno-damaged DNA adducts such as 3,N4- ethenocytosine, N 2,3-ethenoguanine, and 1,N2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gasphase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare... 

The relative stabilities and noncovalent interactions of the six low-lying energy tautomers of cytosine nucleobase with some biological anions (such as F-, Cl-, and CN-) have been investigated in gas phase by density functional theory (DFT) method in conjunction with 6-311++G (d,p) atomic basis set. Furthermore, to systematically investigate all possible tautomerisms from cytosine induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase and in a continuum solvent using DFT calculation. We carried out geometrical optimizations with the integral equation formalism of polarizable continuum (IEF-PCM) model to account for the solvent effect, and the... 

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... 

The reaction pathway (including the transition state) of ethylene addition to permanganate (MnO4-) in the presence of ethylene glycol (EG) has been qualitatively and quantitatively studied by means of B3LYP/6-311++G* theoretical analysis. Interestingly, by cluster formation of the EG with permanganate, oxidation reaction becomes thermodynamically and kinetically more favorable. The influences of electron-withdrawing as well as electron-donating substituents were also explored. Results of the quantum theory of atoms in molecules and natural bond orbital analyses revealed that [3 + 2] addition reaction of alkenes in the presence of EG as hydrogen bonding donor to MnO4- becomes more exothermic.... 

By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA  

Reduced graphene oxide (RGO) was used to improve the hydrogen sensing properties of Pd and Pt-decorated TiO2 nanoparticles by facile production routes. The TiO2 nanoparticles were synthesized by sol-gel method and coupled on GO sheets via a photoreduction process. The Pd or Pt nanoparticles were decorated on the TiO2/RGO hybrid structures by chemical reduction. X-ray photoelectron spectroscopy demonstrated that GO reduction is done by the TiO2 nanoparticles and Ti-C bonds are formed between the TiO2 and the RGO sheets as well. Gas sensing was studied with different concentrations of hydrogen ranging from 100 to 10,000 ppm at various temperatures. High sensitivity (92%) and fast response time... 

In this study the extrudate swell of polymer solutions is estimated using the microstructure of polymer molecules. When a flexible polymer chain goes through a narrow die shear stress exerting on the chain will cause the polymer chain to be stretched along the flow direction. After emerging from die all external stresses vanish immediately and the chains tend to recover their previous state due to elastic recovery. This phenomenon will results in a gradual increase in extrudate diameter and this is used as the key idea for estimating swell ratio. A Giesekus based conformational model was used in order to predict polymer chains microstructure everywhere in the domain. The resulting PDE set... 

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... 

The optimum convolution of dual short pulse for producing the maximum wakefield and the highest dissociation probability of CH4 has been investigated. By using three fundamental shapes of pulses though four different arrangements, the generated wake are considered in plasma. It is found that when the first and second pulses were rectangular-triangular and sinusoidal pulse shapes, respectively, the resultant wakefield amplitude is the highest. This effect opens up a new novel way by pulse shaping mechanism in the photo dissociation dynamics of molecules and controlling of chemical reactions in the desired channels by short pulse intense lasers for reducing the computation time of genetic... 

The optimized minimum-energy geometries of different macrocyclic amines and their protonated structures were determined by using ab initio and density functional theory (DFT) calculations. All the gas phase optimizations and energy calculations were performed at the DFT/B3LYP/6-311++G(d,p) level of theory. The HF/6-31 + G(d,p) level was used for all single point calculations in the solution phase. Geometry optimizations indicate that the most stable structures are stabilized by intramolecular hydrogen bonds. The proton affinity (PA) of macrocyclic amines is controlled by the strength of intramolecular hydrogen bonds of macrocyclic amines. These hydrogen bonds strongly influence the basicity... 

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... 

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 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... 

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 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  

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...