Sharif Digital Repository

Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the... 

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd  

The microscopic features of binary solvent systems formed by molecular solvents (methanol, ethanol, 2-methylpropan-2-ol, water, pyridine, acetonitrile, 1-propanol, 2-propanol, dimethylformamide) and the ionic liquid ([bmim]BF 4) as cosolvent were used to select mixed solvents with particular characteristics. Molecular-microscopic solvent parameters corresponding to these binary mixtures were utilised to study the kinetics of the nucleophilic substitution reaction between 2-chloro-3,5-dinitropyridine and aniline to investigate and compare the effects of the solvents on a model chemical reaction. For these mixtures, the solvation behaviour is dominated by both the dipolarity/ polarisability... 

The concentration and temperature behaviors of the self-diffusion coefficient were analyzed in glycerol-water and methanol-water solutions using Diffusion-Ordered Spectroscopy (DOSY) experiment. Our results indicate that the self-diffusion coefficient dips with increasing concentration and decreasing temperature. The concentration behavior shows that there is hydrogen bond interaction between water and alcohol, which declines the self-diffusion coefficients of both in the aqueous binary mixtures. The self-diffusion activation energies were estimated 13.6, 29.4, and 32.8 (kJ/mol) for methanol and 24.8, 25.5, and 27.6 (kJ/mol) for water in the methanol-water solutions with 0.03, 0.10, and 0.20... 

Nowadays, environmental hazards caused by plastic wastes are a major concern in academia and industry. Utilization of biodegradable polymers derived from renewable sources for replacing common petroleum-based plastics is a potential solution for reducing the problem. In this regard, starch has become one of the most promising alternatives to non-biodegradable polymers for depleting plastic waste thanks to its low expense, abundance, renewability and biodegradability. However, the main drawbacks of starch are its poor processability, weak mechanical properties and severe hydrophilicity. In this work, thermoplastic starch (TPS) samples have been prepared using glycerol and sorbitol as... 

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd  

Detection of pentaerythritol tetranitrate (PETN) as an explosive has been of great interest because of public safety and military concerns. Here, we have presented a simple, selective and sensitive colorimetric method for direct detection of PETN. The gold nanoparticles (AuNPs) were first exposed to arginine which has primary amines in its structure. Electron deficient –NH2 groups from arginine could strongly interact with –NO2 groups of PETN as electron donors. Hydrogen bonding happens between the –NO2 group of PETN and –NH2 group of arginine molecules. Therefore, selective aggregation of AuNPs happened because of the donor-acceptor and hydrogen bonding interactions. Due to the aggregation,... 

The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned... 

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... 

A novel colorimetric nanosensor is reported for the selective and sensitive determination of cysteine using magnetic-sulfur, nitrogen graphene quantum dots (Fe3O4/S, N-GQDs), and gold nanoparticles (Au NPs). Thus, S, N-GQDs was firstly immobilized on Fe3O4 nanoparticles through its magnetization in the presence of Fe3+ in the alkali solution. The prepared Fe3O4/S, N-GQDs were dispersed in cysteine solution resulting in its quick adsorption on the surface of the Fe3O4/S, N-GQDs through hydrogen bonding interaction. Then, Au NPs solution was added to this mixture that after a short time, the color of Au NPs changed from red to blue, the intensity of surface plasmon resonance peak of Au NPs at... 

A novel colorimetric nanosensor is reported for the selective and sensitive determination of cysteine using magnetic-sulfur, nitrogen graphene quantum dots (Fe3O4/S, N-GQDs), and gold nanoparticles (Au NPs). Thus, S, N-GQDs was firstly immobilized on Fe3O4 nanoparticles through its magnetization in the presence of Fe3+ in the alkali solution. The prepared Fe3O4/S, N-GQDs were dispersed in cysteine solution resulting in its quick adsorption on the surface of the Fe3O4/S, N-GQDs through hydrogen bonding interaction. Then, Au NPs solution was added to this mixture that after a short time, the color of Au NPs changed from red to blue, the intensity of surface plasmon resonance peak of Au NPs at... 

In this survey, a reliable and applicable Y–Y shaped micro–channel in a microfluidic device was designed and manufactured. A number of micro–scaled hedges were precisely fabricated inside the micro–channel to facilitate the immobilization of synthesized core–shell Fe3O4@SiO2 magnetic nanoparticles (MNPs), functionalized by triethoxyphenylsilane (TEPS) by sol-gel technique. Both sample and reagents were introduced into the microfluidic device by a syringe pump to perform the extraction and desorption steps. The functionalized MNPs were characterized by transmission electron microscopy, X-ray diffraction spectroscopy and Fourier transform infrared spectroscopy. By adopting the strategy of...