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For the first time, the mechanism of Fischer esterification between acetic acid and ethanol over silica-functionalized propylsulfonic acid (silica-propyl-SO 3 H) catalyst was explored by means of computational modeling techniques. For this purpose, 6-edge-atom cage-like cluster comprising Si–O–Si sequences has been selected to represent the surface of the catalyst. The results indicate that the reaction goes through concerted transition states. In all optimized structures no proton (H + ) transfer occurs from catalyst to the substrates and the role of the catalyst is via the activation of the substrates through the formation of strong hydrogen bonds (H-bonds). Furthermore, the energetic diagram demonstrates that the activation energies of forward (esterification) and reverse (ester hydrolysis) reactions only differ by 0.3 kcal/mol. The quantum theory of atoms in molecules (QTAIM) analysis was performed to investigate the nature of H-bonds. Another mechanism in which the catalyst has been acted as the Brønsted acid/base was also provided for this reaction. [ABSTRACT FROM AUTHOR]

Computational investigations on the gas phase S N 2 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. S N 2 reactions of 2-fluoroethanol. In path( i ), β-hydroxyl group participates in hydrogen bonding (H-bonding) with fluoride ion as leaving group in transition state. However, in path( ii ), transition state includes H-bonding between hydroxyl group and nucleophile X − . Results indicate that in comparison with the absence of β-OH substituent i.e. reactions of fluoroethane, the activation barrier decreases in path( i ), but increases in path( ii ). The progress of each pathway depends on H-bonding character of nucleophile and leaving group. In addition, for X - = Cl - we compared β-OH group effect in the gas phase with its effect in dimethyl sulfoxide (DMSO). [ABSTRACT FROM AUTHOR]

Highlights: [•] Increasing methylene groups in aryl amines results in higher cation–π interactions. [•] There is good correlation between proton affinities and Hammett’s parameters. [•] Hydrogen atom of ammonium group is responsible for making cation–π interactions. [ABSTRACT FROM AUTHOR]

Highlights: [•] Good correlation exists between experimental and computed pK a values. [•] The average error was found to be less than 1.6pK a unit. [•] In the series of analogous structures, the PA values decrease as the number of phenyl groups increases. [ABSTRACT FROM AUTHOR]

Highlights: [•] Kinetic data indicate that trimidox is more active radical scavenger than other investigated compounds. [•] The most favorable mechanism for studied compounds is hydrogen atom transfer (HAT). [•] The results indicate that compounds with adjacent hydroxyl group on phenyl ring are most efficient hydrogen-donor systems. [•] The computational values are in accordance with experimental findings. [ABSTRACT FROM AUTHOR]

Abstract: 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 (CH3B(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. Natural Bond Orbital (NBO) analysis was examined as indicator for the variations observed in the calculated pK a. Natural resonance theory (NRT) was used to calculate the natural bond order and predict bond polarity. The NRT results indicate that the O–H bonds in all studied compounds have an electrovalency character. The results revealed that difference in acid strength is more relevant to the type of substituent. The electron withdrawing substituent will increase the acidic strength. However, the electron releasing substituent will have a reverse effect and decrease the acidic strength. There are good agreement between theoretical values and experimental results for this series of compounds, the average error was found to be less than 1.2 pK a unit. [Copyright &y& Elsevier]

Abstract: The noncovalent interactions between cytosine nucleobase with some biological anions such as F−, Cl−, CN−, , and OH− and cytosine nucleosides (i.e., cytidine and deoxycytidine molecules) with F−, Cl−, CN− anions have been demonstrated by DFT study. The molecular geometries, energy properties, H-bonding patterns, dipole moments and charge distribution of these complexes were investigated with the B3LYP method in conjunction with the 6-311++G(d,p) basis set. It has been found that anions can interact with cytosine nucleobase forming hydrogen bonds. In general, these interactions occur via N–H, O–H and C–H substituents of cytosine, cytidine and deoxycytidine. The presence of anions near these molecules strongly affects the electron distribution in the base structure. From this study, a greater understanding of hydrogen bonding interactions involving DNA and RNA molecules will be obtained. These interactions could provide insight to an unrecognized control element in biological processes, providing new and intriguing opportunities of exploring the electrostatic effects on biological processes. [Copyright &y& Elsevier]

Abstract: The coordination geometries, electronic features, absolute metal ion affinities, geometrical multiplicity and binding strength for the complexes formed by Mg2+, Ca2+, Zn2+ and Cu+ with cytidine and deoxycytidine have been determined theoretically employing the hybrid B3LYP exchange-correlation functional and using 6-311++G(d,p) orbital basis sets. Our study shows that the most stable coordination modes of cytosine nucleosides with these cations are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with three oxygen atoms: one from the carbonyl oxygen of cytosine moiety and two from the sugar unit (i.e., O5′ and O4′). The influences of metal cationization on the strength of the N-glycosidic bond, the values of the phase angle of pseudorotation P in the sugar unit and sugar ring conformation have been studied. In all cases, the N1; bond distance changes upon introducing positive charge in the nucleosides. [Copyright &y& Elsevier]

Abstract: Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1–C1′ bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids. [Copyright &y& Elsevier]

Abstract: We have compared the gas phase thermochemical properties of aspartame (artificial sweetener) and α- and β-glucose. These parameters include metal ion affinities with Li+-, Na+-, K+-, Mg+2-, Ca+2-, Fe+2-, Zn+2-ions, and chloride ion affinity by using DFT calculations. For example, for aspartame, the affinity values for the above described metal ions are, respectively, 86.5, 63.2, 44.2, 255.4, 178.4, 235.4, and 300.4, and for β-glucose are 65.2, 47.3 32.9, 212.9, 140.2, 190.1, and 250.0kcalmol−1, respectively. The study shows differences between the intrinsic chemistry of aspartame and glucose. [Copyright &y& Elsevier]

• Acidity enhancement of bioorganic compounds. • Hydrogen bonding effects on acidity of bioorganic molecules. • Stability of the conjugate base via H-bond network. 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 (H 2 O). Polarized continuum model was applied to calculate p K a 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 p K a units in solution phase for a typical metabolite of barbiturate due to the effect of intramolecular hydrogen bonds. Also, linear correlation between gas phase acidity (ΔG acid) and solution phase (p K a) was obtained and can be used for p K a prediction of metabolites in solution phase. [ABSTRACT FROM AUTHOR]

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 values of D-GlcN and GlcNAc sugars and the atomic numbers of Li, Na, and K. The calculated acidity values for GlcNAc at C 2 –NH and C 6 –HO 6 sites are 331 and 333 kcal mol−1, respectively. Whereas the calculated acidity values for D-GlcN at C 2 –NH and C 6 –HO 6 sites are 365 and 372 kcal mol−1, respectively. The AIM and NBO analyses indicate the presence of intramolecular H-bonds in GlcNAc sugar in both its neutral form and conjugate base; whereas D-GlcN indicates intramolecular H-bonds in only its conjugate base. Image 1 • Hydrogen bonding effect on Acidity of d -Glucosamine and N-Acetyl- d -Glucosamine. • Metal Ion Affinity of d -Glucosamine and N-Acetyl- d -Glucosamine. • D-Glucosamine and N-acetyl-D-glucosamine as ideal cation exchangers models. [ABSTRACT FROM AUTHOR]

Highlights: [•] The interaction energy decreases with the increase of side-chain length in anion. [•] The interactions are electrostatic in the nature. [•] The side-chain length has an important effect on the contribution of E elect term. [•] The H-bond interactions between cation and anion are noncovalent interaction. [Copyright &y& Elsevier]