Sharif Digital Repository

An efficient method for synthesis of 2-iminium-1,3-dithiolane as a new family of ionic liquids with reaction of dithiocarbamates with methyl triflouromethanesulfonate was described. Theoretical study on the synthesized ionic liquids was also performed by quantum chemistry calculation. Geometry optimization on the ion pairs was carried out with the B3LYP/6-311++G(d,p) level of theory. The interaction energies were calculated, and corrected by the basis set superposition error (BSSE) calculated by the counterpoise method. The results of natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses indicate that the interactions occur via hydrogen bonding between oxygen... 

(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... 

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... 

In this paper, we explore theoretically energetic and structural properties of the possible cations formed via hydride ion abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. In general, the hydride ion abstracted sugar cations of cytosine nucleosides have the following stability sequence: caH2′ > caH1′ > caH3′ > caH4′ > caH5′ for cytidine and caH1′ > caH4′ > caH3′ > caH5′ > caH2′ for deoxycytidine. Furthermore, the effect of solvent environment on the stability order of cations integral equation formalism of the polarized model (IEF-PCM) was employed to model aqueous solution. The... 

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... 

Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the 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 the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate... 

Hydrogen bonding interactions between thymine nucleobase and 2'-deoxythymidine nucleoside (dT) with some biological anions such as F - (fluoride), Cl - (chloride), OH - (hydroxide), and NO 3 - (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory... 

The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical... 

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 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... 

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... 

The derivatives of glucose such as glucosamine (β-D-GlcN) and N-acetyl-D-β-glucosamine (GlcNAc) are significant in several biological systems. D-GlcN has been used widely to treat osteoarthritis in humans and animal models as well as GlcNAc has been proposed as a treatment for autoimmune diseases. The DFT/B3LYP/6–311++G (d,p) method as well as QTAIM and NBO analyses were used to the acidity values of D-GlcN and GlcNAc sugars and their complexes with alkali ions in the gas phase. The Li+, Na+ and K+ prefer bi-dentate chelate in these complexes. The computed results indicate that metal ion affinity (MIA) in GlcNAc is higher than that in D-GlcN. There are direct correlations between the MIA... 

In this work, the intramolecular H-bonds in galactose were studied using DFT at the B3LYP/6–311++G (d,p) levels of theory, atoms in molecules (AIM), and natural bond orbital (NBO). AIM and NBO analysis revealed a cooperative network of trifurcated, bifurcated, and normal H-bonds for the conjugate bases of open galactse (O-Gal). While for the conjugate base of the cyclic form of galactose, we identified bifurcated and normal H-bonds, which may highlight a crucial feature of the biological activity of a whole class of natural sugars. The O-H…O bonds are categorized as mostly electrostatic, strong H-bonds and more favorable, whereas for multiple interactions involving C=O…H, C-H…O and C-H…H-C... 

We have studied the intramolecular H-bonds existing in cyclic and open forms of glucose using B3LYP/6-311++G(d,p) level, AIM, and NBO methods. The theoretical results indicated that based on acidity values, (ΔHacid), glucose in the open form is more acidic than cyclic form. The acidity values for open and cyclic glucose (332 and 338 kcal/mol) exhibit significantly lower values (i.e., stronger acid) than the reported acidity values for α-/ß-anomers of D-glucopyranose and simple alcohols. Because their conjugate bases are more stabilized through trifurcated and bifurcated intramolecular H-bonds. AIM analysis showed normal H-bonds in the conjugate bases of open glucose (O-Glc), bifurcated, and... 

The synthesis, characterization, structural and computational studies of Re(I) tricarbonyl bromo complexes bearing alkyl-substituted 1,4-diazabutadiene ligands, [Re(CO)3(1,4-DAB)Br], where 1,4-DAB = N,N-bis(2,4-dimethylbenzene)-1,4-diazabutadiene,2,4-Me 2DAB (1); N,N-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene,2,4-Me 2DABMe (2); N,N-bis(2,4,6-trimethylbenzene)-1,4-diazabutadiene,2,4,6-Me 3DAB (3); and N,N-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene,2,6-ipr 2DAB (4) are reported. The complexes were characterized by different spectroscopic methods such as FT-IR,1 H-NMR,13C-NMR, and elemental analyses and their solid-state structures were confirmed by X-ray diffraction. In each...