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... 

In this study, drastic influence of the intramolecular cation-π interaction on the basicity of selected amines has been considered. The optimized minimum energy geometries of different studied amines and their protonated structures were determined by using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. Geometry optimizations indicate that the most stable structures of protonated amines are stabilized by intramolecular cation-π interaction. The proton affinity (PA) of selected amines is controlled by the strength of intramolecular cation-π interaction of ammonium with aromatic ring. These cation-π interactions strongly influence the basicity of amines. Natural bond orbital (NBO)... 

Silica gel-confined ionic liquid (IL) is a class of heterogeneous catalysts with broad catalytic applications. Leaching of the IL from the surface of the support is the major drawback of these catalysts, which reduce the catalyst efficiency during the chemical reactions. To investigate the effect of the hydrogen bonding on the leaching phenomena, the interaction between the 1-ethyl-3-methylimidazolium-based IL with various anions (Cl-, Br-, HSO4 -, NO3 -, BF 4 -, and PF6 -) and the surface of the silica gel were studied using density functional theory. Hence, a hydroxylated cage-like cluster of silica gel, Si4O6(OH), was selected to mimic the surface. The values of ÎEinteraction show that... 

A novel mesoporous silica-functionalized dual Brønsted acidic species has been introduced as an efficient catalyst for solvent-free esterification of fatty acids with ethanol. The structure of the catalyst has been characterized by FT-IR spectroscopy, thermal gravimetric analysis (TGA), TEM and N2 adsorption-desorption. TGA of catalyst 1 showed no weight loss before 200 °C, indicating a high degree of hydrophobicity of the surface of the mesoporous silica. TEM images and nitrogen adsorption-desorption showed no noticeable changes to the structure of the catalyst before and after acid treatment. pH metric analysis was performed for the catalyst to determine the loading of the acidic sites.... 

The pKa value for protonated forms of different benzo-substituted quinuclidines in aqueous solution has been calculated using DFT methods (MP2//B3LYP, B3LYP and M06-2X) and 6-311++G(d,p) basis set and are compared with corresponding experimental values. The results were obtained from different theoretical methods so close to the corresponding experimental values but the best agreement were achieved with B3LYP/6-311+G(d,p) level of theory. The average error was found to be less than 1.6pKa unit. Relative pKa values were computed for each protonated benzo-substituted quinuclidine using quinuclidine as a reference. Solvation was included in the calculations in all used different methods using... 

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... 

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... 

The free radical scavenging activity of a series of hydroxybenzohydroxamic acid derivatives have been studied in gas phase, water and benzene environments, using the density functional theory. Different mechanisms of reactions have been considered: single electron transfer (SET), hydrogen atom transfer (HAT). Rate constants were determined to know if the radical scavenging activity of these compounds proceeds via an H-atom or an electron-transfer mechanism. Calculations showed that the presence of the adjacent hydroxyl groups on phenyl ring increases the radical stability through intramolecular hydrogen bonds. The calculated bond dissociation enthalpy (BDE) values for hydroxyl groups on... 

In the present density functional theory study, we have compared intrinsic properties of non-natural nucleobases (acA, acG, acC, and acT nucleobases) such as proton affinities, gas phase acidities, tautomerization, and hydrogen-bonding properties with those in normal Watson-Crick nucleobases (A, G, C, T nucleobases). The hydrogen-bonding interactions in non-natural and Watson-Crick base pairs were studied at B3LYP/6-311++G (d,p) level regarding their geometries, energies, and topological features of the electron density. The quantum theory of atoms-in-molecule (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in base pairs. The... 

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

In this study, ionic liquids formed between 1-ethyl-3-methylimidazolium cation ([emim]+) and alkyltrifluoroborate ([RBF3]-, R = n-CmH2m+1 (m = 1-5)) anions have been investigated theoretically. The interactions between the cation and anions have also been calculated at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory. The calculated interaction energies were found to decrease in magnitude with the increase of side-chain length in anions. The results of energy decomposition analysis (EDA) show that the interaction of these anions with [emim]+ cation is electrostatic in the nature and the side chain length in the anions has an important effect on the contribution of ΔEelect term. The... 

Density functional theory (DFT) method and B3LYP/6-311++G(d,p) basis set were used to determine coordination geometries, binding strength, and metal ion affinity (MIA) for interaction of 2′-deoxythymidine (dT) with alkali metal cations including Li+, Na+, and K+. Calculations demonstrated that the interaction of dT with these cations is tri-coordinated η (O2, O4′, O5′). Among these cations, Li + cation exhibited the most tendency for interaction with 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 base unit with respect to sugar ring and the acidity of O5′H, O3′H, and N3H groups in 2′-dT... 

Thiotepa (N,N′,N″-triethylenethiophosphoramide) and its major metabolite (Tepa) as trifunctional alkylating agents has recently been used in cancer therapy. In vivo and vitro studies show the possible pathways of alkylation of DNA by Thiotepa and Tepa. Two pathways are suggested, but the main pathway of mechanism remains unclear. In pathway 1, forming cross-links with DNA molecules can be carried out via two different mechanisms. In first mechanism, these agents undergo the ring opening reaction which is initiated by protonating aziridine, which then becomes the main target of nucleophilic attack by the N7-Guanine of DNA. The second probable mechanism is ring opening of aziridyl group by... 

In this study, the drastic influence of the boron atom on the acidity of alcohol has been considered. The calculated ΔHacid (320.9-338.1 kcal/mol) and pKa range of boron containing alcohol (-0.1-9.4) indicate that the boronation of alcohol leads to considerable enhancement of its acidity. For instance, we have obtained the ΔHacid values 338.1, 335.2 kcal/mol and the pKa values 4.12, 2.81 for BH 2CH2OH, BF2CH2OH alcohols, respectively, which are much smaller than that of CH3OH (with ΔHacid = 374.9 kcal/mol and pKa = 15). The increase in the acidity of boronated alcohol can be related to the stabilization of alkoxy ion due to overlap of unoccupied orbital of boron atom with the electron pairs... 

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... 

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... 

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... 

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.... 

With the specific target of calculating the pK a values of boronic acids (RB(OH) 2) in aqueous solution we inquired the solute-solvent interactions of these acids and their corresponding conjugate base. Relative pK a values were computed for each boronic acid using methylboronic acid (CH 3B(OH) 2) as a reference. All gas phase computations were performed at (MP2/6-311++G(d,p)//B3LYP/6-31+G(d)) level of theory. Solvation was included in the calculations using the polarized continuum model (PCM) at the HF/6-31G(d,p) level. The geometry optimization of studied structures was performed with DFT computation and the optimized structures were used to carry out Natural Bond Orbital (NBO) analysis....