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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. [ABSTRACT FROM AUTHOR]

The unusual monosaccharaides such as deoxy‐hexose sugars, including methyl‐pentose and aldo‐pentose, are promising and important sugars in life science. However, little research on H‐bond interactions in these systems has been reported. The aldo‐pentose has a proton instead of the CH2OH group on C5; conversely, methyl‐pentose has a CH3 group on C5. The aim of the present study is to investigate the role and nature of intramolecular H‐bonds on acidity of CH3‐pentose sugars (L‐fucose and L‐rhamnose) and aldo‐pentose sugars (D‐xylose, L‐lyxose, D‐ribose, and L‐arabinose) using B3LYP/6‐311++G (d, p) level. The calculated acidity values (ΔHacid) of these Dexoy‐hexose were found to be from 343 to 369 kcal.mol−1, indicating they are stronger acid than ethanol and 2‐propanol with the acidity values of 378.3 and 375.1 kcal.mol−1, respectively. This is related to the stabilization of the conjugate bases of these sugar through intramolecular H‐bonds, which were analyzed in this study using atoms in molecules (AIM) and natural bonding orbital (NBO) methods. AIM and NBO analyses indicate the presence of one bifurcated intramolecular H‐bond in the conjugate bases of L‐lyxose and L‐arabinose and two bifurcated H‐bonds in conjugate base of D‐ribose, whereas the conjugate bases of L‐fucose, L‐rhamnose, and D‐xylose present one normal intramolecular H‐bond. According to the topological parameters and charge transfer data, existence of normal and bifurcated intramolecular H‐bonds could greatly increase acidity of deoxy‐hexose sugars. The H‐bond strength in the conjugate bases of aldo‐pentose sugars is higher than that in the conjugate bases of methyl‐pentose sugars including CH3 group on C5, making aldo‐pentose sugars stronger acid than methyl‐pentose sugars. [ABSTRACT FROM AUTHOR]

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of alkyl and polyolalkyl in the gas and solution (H2O, DMSO, and CH3CN) phase. Polarized continuum model was applied to calculate p Ka values of alkyl and polyolalkyl . A comparison between acidity of alkyl and polyolalkyl in the gas and solution phase indicates that the acidity strength of polyolalkyl enhances with the increase of the cooperativity effect of hydrogen bonds in polyolalkyl . Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of cooperativity effect on the acidity of polyolalkyl . Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

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 ΔHacidityvalues of these catalysts were investigated. DFT calculations revealed that a notable gap of ΔHacidityvalues exists between the structures considering lateral hydrogen bonding with the surface of the silicaHB structureand the structures with omitted surface interactions (non-HB structures). Natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses were carried out to obtain detailed information about the nature of the H–bonds. [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]

In this study, the drastic influence of the boron atom on the acidity of alcohol has been con-sidered. 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 BH2CH2OH, BF2CH2OH alcohols, respectively, which are much smaller than that of CH3OH (with ΔHacid = 374.9kcal/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 unoc-cupied orbital of boron atom with the electron pairs of negative oxygen. All gas phase computations were performed at MP2/6-311++G(d,p)//(B3LYP/6-31+G(d)) level. The primary results indicate that the presence of boron atom in an alcohol might make it as acidic as nitric acid. The geometry optimization of studied structures was performed with DFT computation and optimized structures were used to carry out natural bond orbital (NBO) analysis. NBO analysis revealed that the increase in the acidity of boron-containing alcohols is due to the charge transfer from the negative oxygen (in deprotonated structure) to the empty orbital of --BH2 and --BF2. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of bonds formed in the deprotonated structure. [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]

The radical cations of DNA constituents generated by the ionizing radiation initiate an alteration of the bases, which is one of the main types of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break. In this study, the gas-phase intrinsic chemical properties of the gaseous radical cations of cytosine and its base pair with guanine were examined by employing density functional theory (B3LYP) with the 6-311++G(d,p) basis set. Structures, geometries, adiabatic ionization energies, adiabatic electron affinities, charge distributions, molecular orbital analysis and proton-transfer process of these molecules were investigated. The influence of cation radical formation on acidities of multiple sites in cytosine molecule was investigated. Results of calculations revealed that cytosine radicals formed by deprotonation of cytosine cation radicals can exothermically abstract hydrogen atoms from thiol groups, phenol, and α-positions of amino acid. Furthermore, comparison of acidity value of N-H sites of cytosine cation radical with the known proton affinities (PA) of organic and biological molecules implied that cytosine cation radical can exothermically transfer onto basic sites of amino acids and peptides. [ABSTRACT FROM AUTHOR]

In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidine–M2+ (M2+ = Mg2+, Ca2+, Zn2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg2+, Ca2+, Zn2+ are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with oxygen and two nitrogen atoms: one from the terminal NH2 and one from the imidazole ring. All computations indicate that the metal ion affinity (MIA) decreases on going from Zn2+ to Mg2+ and Ca2+, for the considered amino acid. This indicates that histidine prefers to bind to the transition metal cation rather than alkali earth metals. The influence of theses cations on the acidity of histidine were also considered. As expected, upon metal complexation, proton dissociation of histidine becomes much more favorable, that is, its acidity becomes much less endothermic. [ABSTRACT FROM AUTHOR]

The gas-phase metal affinities of histidine Li+, Na+ and K+ ions have been determined theoretically employing the hybrid B3LYP exchange–correlation functional and using 6-311++G** basis sets. All computations indicate that the metal ion affinity decreases on going from Li+ to Na+ and K+ for the considered amino acid. Different types of M+ coordinations on several histidine conformers/tautomers were considered in detail. The optimized structures indicate that Li+ and Na+ prefer a tri-dentate coordination, bonding with a nitrogen atom of imidazole ring (Nτ), –NH2, and an oxygen atom of a carbonyl, while in the K+-histidine lowest-energy conformer, the cation appears to be bi-coordinated to both oxygen atoms of the zwitterionic form by the energy values not too far from that of tri-coordination. We also performed the DFT calculations for proton dissociation energy of histidine both in the presence and absence of alkali metal ions. Our results also reveal that the acidity of histidine dramatically increases upon metal ion complexation. [ABSTRACT FROM AUTHOR]

The effects of selected metal ions on the gas-phase acidity of weak organic acids have been explored using the DFT and Moller–Plesset Perturbation Theory (MP2) calculations. The three organic acids selected for this study were acetic acid (aliphatic), benzoic acid (aromatic), and glycine (amino acid). The acidities of these compounds are compared with the acidity of their Li+-, Na+-, and K+-complexed species. The results indicate that upon complexation with Li+, Na+, and K+ at 298 K, the gas-phase acidity of acetic acid, for example, varies from 345.3 to 218.8, 230.2, and 240.1 kcal/mol, respectively (i.e., its dissociation becomes much less endothermic). These values indicate that a weak organic acid can be converted to a super acid when it is complexed with an ionic metal. Copyright © 2007 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

• 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]

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 (H2O, 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 intramolecular hydrogen bonding effect on acidity. Quantum theory of atoms in molecules (QTAIM) was also used to study the nature of hydrogen bonds. QTAIM results showed that the intramolecular hydrogen bonds in these structures are electrostatic (closed‐shell) interactions in nature. In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy‐1,4‐benzoquinone derivatives are explored by using ab initio and density functional theory (DFT) calculations. It was found that remote hydrogen bonding could play a surprisingly role in increasing the acidity of hydroxy‐1,4‐benzoquinone. [ABSTRACT FROM AUTHOR]