Sharif Digital Repository

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... 

Thermodynamic micellization model is known as an appropriate approach for prediction of asphaltene precipitation. However, the reliability (i.e. accuracy) of this model for whole range of pressure or injected gas mole percent must be checked. In practice, the accuracy can be improved by using a suitable characterization method. In this research, a computer code for implementing the thermodynamic micellization model has been developed. Having used this program, we make the prediction of asphaltene precipitation by using data reported in the literature as well as the experimental data obtained from high pressure, high temperature asphaltene precipitation experiments under gas injection... 

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... 

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... 

In this article, the interaction of an arbitrary number of quantum dots behaving as artificial molecules with different energy levels and a multi-mode electromagnetic field is studied. We make the assumption that each quantum dot can be represented as an atom with zero kinetic energy, and that all excitonic effects except dipole-dipole interactions may be. disregarded. We use the. Jaynes-Cummings-Paul model with applications to quantum systems based on a time-dependent Hamiltonian and entangled states. We obtain a system of equations describing the interaction, and present a method to solve the equations analytically for a single mode fi,eld within the Rotating-Wave Approximation. As an... 

In this paper, the atomic-scale interactions between metallic tips and samples in noncontact atomic force microscopy (NC-AFM) are studied using molecular dynamics simulations. The effects of the tip and sample materials, the surface plane direction and the lateral position of the tip with respect to the sample, on the interaction force and the dissipated energy, are investigated. The simulations conducted demonstrate that, generally, we can classify the possible outcomes for the dynamics due to the tip-surface interactions into four major categories. The first category includes all cases in which there are no considerable instabilities in tip-surface interactions, leading to negligible... 

Ab initio quantum chemical calculations at the density functional theory (DFT) level were performed on eight pyridine derivative molecules as corrosion inhibitors for iron in an acidic solution. In this regard, the geometry of the molecules were optimized using the B3LYP/6-31G method first, and then interactions of these optimized structures with the iron atom were explored using the B3LYP/LANL1MB method. Two modes of adsorption were considered, i.e., planar adsorption (P) via the pyridine ring and vertical adsorption (V) through a nitrogen atom. The interaction energy was minimized through the variation of the inhibitor molecule-iron atom distance. These minimum energy values, along with... 

The behaviour of solvatochromic absorbance probes (4-nitroaniline, 4-nitroanisole, and Reichardt's dye) within binary mixtures of polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether (Triton X-100 or TX-100)/organic solvents (2-propanol, hexanol, butyl acetate, THF, toluene, and p-xylene) was extensively explored by using solvatochromism and the quantum theory of atoms in molecules (QTAIM). To be more precise, the polarity parameters, ET N, and Kamlet-Taft parameters, such as the hydrogen bond donor ability (HBD) (α), hydrogen bond acceptor ability (HBA) (β), and dipolarity/polarizability (π∗), have been investigated in selected mixtures at 298 K. All binary mixtures exhibit complex... 

In this study, the structural and electronic properties of a carbohydrate-based (6-amino-6-deoxy hexopyranose [ADHP]) ionic liquid were explored. The interactions among 3 anions (BF4 ¯, PF6 ¯, and ClO4 ¯) and ADHP as cation were investigated at B3LYP/6-311++G(d,p) level. Based on the calculated interaction energy, it was found that PF6 ¯ anion has the highest interaction energy with ADHP. It was found that the hydrogen bonds play an important role in the interaction of ion pairs. The nature of hydrogen bonds in the optimized ion pars was analyzed by using natural bond orbital analysis and the quantum theory of atoms in molecules. The linear relationship between electron density at the bond... 

CoMo/reduced graphene oxide (rGO) catalyst was synthesized for the oxidative desulfurization process (ODS) of dibenzothiophene (DBT) in n-decane. Parameters including total metal (Co and Mo) loading, Co/Mo and CA (citric Acid)/Mo molar ratios were investigated toward achieving optimum conditions. The catalysts were characterized by the XRD, ICP, FTIR, Raman Spectroscopy, BET-BJH, NH3-TPD, XPS, and TEM methods. The product sulfur content was measured by the ICP-OES while the product was evaluated using FTIR and 1H NMR analyses. All experimental stages were designed using Design-Expert software. High BET area, acidity, uniform particle size, and Co-promoter played key roles in this... 

The solubility of sulfur dioxide (SO2) and carbon dioxide (CO2) at P = 1 bar in a series of imidazolium-based room-temperature ionic liquids (RTILs) is calculated by Monte Carlo simulation in NPT ensemble using the OPLS-UA force field and Widom particle insertion method. The studied ILs were 1-butyl-3-methylimidazolium ([bmim]+) tetrafluoroborate ([BF4]-), [bmim]+ hexafluorophosphate ([PF 6]-), [bmim]+ bromide ([Br]-), [bmim]+ nitrate ([NO3]-), [bmim]+ bis-(trifluoromethyl) sulfonylimide ([Tf2N]-), and 1-ethyl-3-methylimidazolium tetrafluoroborate ([emim][BF4]). To validate the simulations, the liquid density of studied ILs and the solubility of CO2 in [bmim][PF6] was compared with... 

Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly... 

Gold nanoparticles are widely used as high efficient photon-thermal energy converters in a broad range of applications. This paper presents a theoretical investigation on using the optothermal properties of gold nanoparticle arrays to generate nanoscale molten and rubbery regions on the surface of an amorphous polymeric film. Nanoparticles are assumed to be embedded in a transparent silica layer and illuminated with a 7.5 ns pulsed laser at 532 nm. Simulation results are presented for systems with single gold nanoparticles, dimers and chains. Both electromagnetic and thermal interaction between nanoparticles are found to be important factors in determining the result of surface processing.... 

Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn2+ chelating domain, derived from rapeseed meal, merge with a... 

Nanodiamond particles, basically those produced by detonation method, are acquiring progressive attraction in different fields such as material, biomedical, and environmental engineering. Aqueous environments are usually dealt with at different stages of preparation, preservation, and application of these particles. The aim of this article is to perform a systematic first-principles density functional theory analysis on the interaction of C35 ultrasmall octahedral nanodiamond and its full homogeneous carboxylated and aminated forms, with water derived specie, namely, neutral, protonated, and deprotonated water and (H2O)20 water cluster. The effect of solvent media on the interactions has... 

The interaction potential energy and heat of sublimation of nanoparticles of HMX crystal polymorphs are studied by using molecular dynamics methods with a previously developed force field [Bedrov, et al., J. Comput.-Aided Mol. Des. 8 (2001) 77]. Molecular dynamics simulations of nanoparticles with 10, 20, 30, 40, 50, 60, 70, 80, 90, and 100 molecules of HMX are carried out at 300 K. The intermolecular, intramolecular and total interaction energies per mole for the nanoparticles are calculated at 300 K. Then, we have calculated sublimation enthalpy of HMX crystal polymorphs with different sizes. For the all sizes, the β-HMX is found to be the most stable phase, due to having the least total... 

Finesmigration is a noticeable problem in petroleum-production engineering. Plugging of throats in porous media occurs because of detachment of fine particles from sand surfaces. Thus, the study of interactions between fines and pore surfaces and the investigation of governing forces are important factors to consider when describing the mechanism of the fines-release process. The main types of these forces are electric double-layer repulsion (DLR) and London-van der Waals attraction (LVA). It may be possible to alter these forces with nanoparticles (NPs) as surface coatings. In comparison with repulsion forces, NPs increase the effect of attraction forces. In this paper, we present new... 

In this study, the local composition based models such as the Wilson, the nonrandom two-liquid (NRTL), and the Wilson-NRF have been applied in correlation and estimation of density, viscosity, and surface tension of biodiesels. The thermodynamic models have been used in correlating the thermophysical properties for 215 experimental data points. These models have the interaction energy between each pair that is considered as adjustable parameters. To decrease the number of these adjustable parameters, it is assumed that the biodiesels are composed of two hypothetical components. The average absolute deviation (AADs) of the correlated density of biodiesels for the Wilson, the NRTL, and the...