Sharif Digital Repository

(Equation present) Density functional theory (DFT) was used to investigate the acidity of the various silica alkyl sulfonic acids. In this regard, cluster models with various alkyl spacer lengths were selected to mimic the surface of silica gel. The effects of distance from the surface and the role of hydrogen bond (H-bond) on the ΔHacidity values of these catalysts were investigated. DFT calculations revealed that a notable gap of ΔH acidity values exists between the structures considering lateral hydrogen bonding with the surface of the silica HB structure and the structures with omitted surface interactions (non-HB structures). Natural bonding orbital (NBO) and quantum theory of atoms in... 

A series of N2O2-donor naphthodiaza-crown macrocyclic ligands, L1-L5, were synthesized and characterized by IR, 1H and 13C NMR spectroscopy, mass spectrometry as well as microanalysis. Preliminary observations employing UV-vis spectrophotometry of L3 in ethanol revealed that triethylamine (TEA) has a significant blue-shift effect on the entire of the spectra. Then, the detection of aliphatic and aromatic amines by L3 were followed by monitoring of fluorescence quenching of the resulting adducts in terms of their binding with L1-L5. Both steady-state and time-resolved spectroscopic measurements in the... 

Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6–311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6–311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced... 

Ab initio, DFT, Monte Carlo statistical mechanics and atom in molecule methods have been applied to investigate the hydrogen bonding effect of protic solvents, apart from the bulk properties, on the reaction of cyclopentadiene and vinyl acetate. The results show that methanol accelerates the rate of the reaction more than water. DFT calculations demonstrate that the interaction of the carbonyl group oxygen atom with solvent molecules in transition state is stronger and more effective than the ether-type oxygen atom. Also, when the solvent molecule is near the oxygen of the carbonyl group the rate of reaction is larger than when it is near the ether-type oxygen. In addition, methanol... 

Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density Δ2 ρ(r) from Bader's atom in molecules theory. Charge transfer energies based on... 

Ab initio, DFT, Monte Carlo statistical mechanics and atom in molecule methods have been applied to investigate the hydrogen bonding effect of protic solvents, apart from the bulk properties, on the reaction of cyclopentadiene and vinyl acetate. The results show that methanol accelerates the rate of the reaction more than water. DFT calculations demonstrate that the interaction of the carbonyl group oxygen atom with solvent molecules in transition state is stronger and more effective than the ether-type oxygen atom. Also, when the solvent molecule is near the oxygen of the carbonyl group the rate of reaction is larger than when it is near the ether-type oxygen. In addition, methanol... 

B3LYP/aug-cc-pVDZ computations were carried out on polyamines with up to seven amino groups. The gas-phase proton affinities of these compounds are 219.6 (1-BuNH2), 238.6 (H2NCH2CH2CH 2CH2NH2), 252.8 [(H2NCH 2CH2CH2)2CHNH2], 261.3 [(H2NCH2CH2CH2) 3CNH 2 (1)], and 288.5 kcal mol-1 [(H2NCH 2CH2CH(NH2)CH2CH2) 3CNH2]. These results indicate that the tetraamine is near the top of the basicity scale and the heptaamine is more basic than any neutral organic compound which has been measured to date. A gas-phase equilibrium acidity determination between 1 and DBU also was carried out, and PA(1) = 256.2 ± 2.1 kcal mol-1 was obtained. This demonstrates that multiple intramolecular hydrogen bonds can... 

In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinone derivatives have been investigated ab initio by employing density functional theory (DFT) methods. The computational studies were performed for both gas and solution (H 2 O, DMSO, and MeCN solutions) phases. Our results indicated that remote hydrogen bonding could play an important role in increasing the acidity of hydroxy-1,4-benzoquinone. Noncovalent interaction reduced density gradient (NCI-RDG) methods were used to visualize the attractive and repulsive interactions in the studied acids and their conjugate bases. Natural bond orbital (NBO) analysis was performed to confirm... 

The chemical preparation and crystal structure for a 4,4′- azodi(phenylcyanamide) salt) in the solid state are reported. This compound crystallizes in the triclinic space group P with the following unit cell parameters: a = 9.759(3) Å, b = 11.237(4) Å, c = 11.919(4) Å, α = 95.54(3)°, β = 98.50(3)°, γ = 109.39(2)°, Z = 1 and V = 1204.4(7) Å3. The 4,4′-azodi(phenylcyanamide) dianion, azodicyd2-, is approximately planar, with the cyanamide groups (-N=C=N) in an anti conformation relative to each other and the azo group (-N=N-) adopting the more thermodynamically stable trans conformation. The crystal X-ray analysis shows that there are one azo molecule cation, two tetrabutylammonium cations and... 

Density functional theory method and B3LYP/6-31+G(d) level of theory were used to predict the acidity of barbiturates and their corresponding metabolites in the gas and solution phase (H2O). Polarized continuum model was applied to calculate pKa values of barbiturates and metabolites. A comparison between acidity of barbiturates and metabolites in the gas and solution phase indicates that the acidity strength of barbiturates enhances with the increase of intramolecular hydrogen bonds in metabolites. This acidity can increase to 9.47 kcal/mol in gas phase and 2.73 pKa units in solution phase for a typical metabolite of barbiturate due to the effect of intramolecular hydrogen bonds. Also,... 

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution (H2O, DMSO, and CH 3CN) phase. Polarized continuum model was applied to calculate pKa values of alkyl sulfonic acids and polyolalkyl sulfonic acids. A comparison between acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution phase indicates that the acidity strength of polyolalkyl sulfonic acids enhances with the increase of the cooperativity effect of intramolecular hydrogen bonds in polyolalkyl sulfonic acids. Natural bond orbital and quantum theory of atoms in molecules... 

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... 

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 reaction of 15-18 membered benzodiazacrown ethers with salicylaldehyde afforded n-membered O2N2-donor macrocyclic ligands mounted with 1,3-diazacyclohexane subrings (1-4) in high yields. The products were characterized by FT-IR, 1H, 13C NMR spectroscopy, elemental analyses, and single crystal X-ray studies. The solid state structures revealed strong intramolecular hydrogen bonding between the pendant phenolic group and the tertiary nitrogen of the corresponding macroring  

Betaine-based natural deep eutectic solvents (NADESs), a new class of green solvents, were immobilized into a porous polyvinylidene fluoride (PVDF) support and evaluated for the separation of CO2 from CO2/N2 and CO2/CH4 mixtures. Two types of NADESs were synthesized by mixing betaine (hydrogen bond acceptor-HBA) with malic acid and tartaric acid (hydrogen bond donors-HBD) respectively. FTIR and Raman spectroscopy were studied to confirm the synthesis and purity of the NADESs. The thermal strength of the NADESs was investigated using thermogravimetric analysis. The gas permeation results of the fabricated NADES-based-supported liquid membranes (NADES-SLMs) showed that the permeability of CO2... 

The second-order rate coefficients for aromatic nucleophilic substitution reaction between 1-chloro-2,4-dinitrobenzene and aniline have been measured in aqueous solutions of ethanol and methanol at 25°C. The plots of rate constants versus mole fraction of water show a maximum in all-aqueous solutions. The effect of four empirical solvent parameters including hydrogen bond donor acidity (α), dipolarity/polarizability (π*). normalized polarity (ETN), and solvophobicity (Sp) has been investigated. This investigation has been carried out by means of simple and multiple regression models A dual-parameter equation of log k2 versus Sp and α was obtained in all-aqueous solutions (n = 41, r = 0.962,... 

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... 

Computational investigations on the gas phase SN2 reactions of X ions (X-=OH-,F-,Cl-,Br-, and I-) with fluoroethane and 2-fluoroethanol (β-hydroxyl ethyl fluoride) were performed by using MPW1K, M06 and CCSD(T) methods with a range of basis sets including 66-311++G**, TZVP, aug-cc-pVDZ and SDD. To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis and Bader's quantum theory of atoms in molecules (QTAIM). In our calculations, we took into account two possible pathways for these reactions, i.e. SN2 reactions of 2-fluoroethanol. In path(i), β-hydroxyl group participates in hydrogen bonding...