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, 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... 

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... 

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... 

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)... 

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... 

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 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... 

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.... 

The cation radicals of DNA constituents generated by the ionizing radiation initiate the alteration of the bases, which is one main type of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break, and it is important to identify the cation radical formation at particular atomic site in these molecules so that the major pathway for the nucleic acid damage may be trapped. In the present study, we explored theoretically energetic, structural, and electronic properties of the possible radicals formed via proton atom abstraction at various sites of sugar part of deoxycytidine cation radical by employing density functional theory at... 

The geometries of the complexes of Be 2+, Mg 2+, and Ca 2+ metal cations with borazine ring were studied. The complexes were optimized at the B3LYP level and the 6-311++G(d,p) basis set. Then, the interaction energies corrected by basis set super position error were calculated in the same level. The results show that interaction energy is strongly dependent on the charge-to-size ratio of the cation. Therefore, Be 2+ cation has the most interaction energy value with respect to Mg 2+ and Ca 2+ metal cations. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to... 

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... 

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... 

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 B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and Cu + cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 20-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA.... 

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... 

Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M +-L (where L represents cytosine nucleosides and M + is an alkali metal ion, including Li +, Na + and K +) complexes have been investigated theoretically, employing B3LY P6-311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been...