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Using density functional theory, polyols were used as model ligands for Cu+/Cu2+ complexes to study the role of the hydrogen bond network on the metal binding affinity. In addition to the gas phase studies, the calculations were performed in 1‐decanol and DMSO solvents. The Cu2+ complexes were the most stable complexes with the highest bond dissociation energies (BDE). The presence of three H‐bonds in the first shell increased BDE values up to 17.99 and 57.07 kcal/mol for Cu+ and Cu2+ complexes in the gas phase, respectively, whereas the presence of another three H‐bonds in the second shell increased BDE values up to 7.27 and 24.35 kcal/mol for Cu+ and Cu2+ complexes in the gas phase, respectively. Therefore, this H‐bond network caused, for example, a more stable Cu+ complex with a formation constant of 1.4 × 1017 times. The natural bond orbital (NBO), atoms in molecules (AIM), and reduced density gradient (RDG) analyses showed that the intramolecular hydrogen bond network led to the enhancement of metal‐binding affinity. [ABSTRACT FROM AUTHOR]

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]

In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: ON˙ and ON˙O) and their precursors (ONH and ONOH, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (HO˙ and HOO˙) and their precursors (HOH and HOOH, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD), critical point (CP) eigenvalues (atoms in molecules [AIM] analysis), and natural bond orbital (NBO) analysis including natural population analysis (NPA) and change of charge transfer energy (ΔECT). Our results show that in the presence of Au3 NC, BDEs of the NH and OH bonds increase in both ONHAu3 (1) and ONOHAu3 (2) compared with their free forms (ONH and ONOH, respectively). In other words, the tendency to dissociate these bonds and form their corresponding RNS (1′ and 2′) decreases in the presence of gold. This is exactly the opposite of what is observed for the OH bonds in HOHAu3 (3), HOOHAu3 (4), and their corresponding ROS (3′ and 4′). Therefore, we can conclude that gold shows a different behavior in the face of RNS compared with ROS where it is a better scavenger of ROS than RNS. [ABSTRACT FROM AUTHOR]

Abstract: In this study, the structural and electronic properties of a carbohydrate‐based (6‐amino‐6‐deoxy hexopyranose [ADHP]) ionic liquid were explored. The interactions among 3 anions (BF4¯, PF6¯, and ClO4¯) and ADHP as cation were investigated at B3LYP/6‐311++G(d,p) level. Based on the calculated interaction energy, it was found that PF6¯ anion has the highest interaction energy with ADHP. It was found that the hydrogen bonds play an important role in the interaction of ion pairs. The nature of hydrogen bonds in the optimized ion pars was analyzed by using natural bond orbital analysis and the quantum theory of atoms in molecules. The linear relationship between electron density at the bond critical points of hydrogen bonds and the interaction energy values was checked. [ABSTRACT FROM AUTHOR]

Abstract: Anticancer character of gold cluster has been indicated through its free radical scavenging properties. This is in contrast to its free radical promoting ability suggested by other workers. Here, we address this controversy by probing the stabilizing effects of Au3 cluster on RO• vs its impacts on RO–H bond dissociation enthalpy, at B3LYP/ LACVP+* level (R═H, methyl, ethyl, n‐propyl, i‐propyl, n‐butyl, t‐butyl, and phenyl). In the presence of Au3 cluster, bond dissociation enthalpy of O–H bond and the spin density at the RO• oxygen are reduced dramatically. These are clear evidences for both the Au3 facilitation of the RO–H bond breakage and its scavenging of RO• radical. Since O–Au anchoring bond is responsible for the interaction of Au3 cluster and ROH (or RO•), its nature was interpreted by means of the quantum theory of atoms in molecules and the natural bond orbital. The results indicate that O–Au bond is stronger and has more covalent character in RO•–Au3 than in ROH–Au3. The interaction of Au3 cluster with RO• is 1.5 to 3 times more than that with ROH. As a result, gold cluster scavenging property appears more prominent than its free radical initiation activity. [ABSTRACT FROM AUTHOR]

Abstract: The free radical activity of lespedezacoumestan was investigated toward hydroxyl (˙OH) radical in polar and nonpolar media using density functional theory. Four reaction mechanisms including radical adduct formation, hydrogen atom transfer, sequential single electron‐proton transfer (SET‐PT), and sequential proton loss electron transfer were considered. The rate constants and branching ratio for all possible sites of reaction were calculated and reported for the first time. According to the obtained results, lespedezacoumestan reacts faster with ˙OH radical in aqueous solution than in nonpolar media. Also, lespedezacoumestan is an excellent ˙OH radical scavenger regardless of the environment polarity. [ABSTRACT FROM AUTHOR]

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]

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]

Silica gelâ€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 1â€ethylâ€3â€methylimidazoliumâ€based IL with various anions (Clâˆ', Brâˆ', HSO4âˆ', NO3âˆ', BF4âˆ', and PF6âˆ') and the surface of the silica gel were studied using density functional theory. Hence, a hydroxylated cageâ€like cluster of silica gel, Si4O6(OH), was selected to mimic the surface. The values of Î'Einteraction show that ILs with halogen counter ions have stronger interactions than that of the IL with BF4âˆ' and PF6âˆ' counter ions. We also carried out stirringâ€'filtration method for some prepared samples of IL@silica to experimentally explore the leaching phenomena. The results show good agreement with computational achievements. Copyright © 2013 John Wiley & Sons, Ltd. [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]

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 electron density ρ( r) as well as its Laplacian $$ \nabla^{2} $$ ρ( r) at the hydrogen bond critical point predicted by QTAIM is strongly correlated with hydrogen bond structural parameter and the second-order perturbation energies in NBO scheme. Our results show that most of hydrogen bonds in normal Watson-Crick and non-natural base pairs must be considered as electrostatic interactions. Results of calculations revealed that energetic values of hydrogen bonds in T- A base pair are more than those in ac T- ac A base pair, while values of hydrogen bonds in C- G base pair and ac C- ac G base pair are almost the same. These results confirmed stability order of stabilization energies of these base pairs. [ABSTRACT FROM AUTHOR]

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 , and . Calculations demonstrated that the interaction of dT with these cations is tri-coordinated η (O2, O4′, O5′). Among these cations, 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 nucleoside. Natural bond orbital (NBO) analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of interactions. It was shown that in these complexes, (dT-, dT-, and dT-), the bonds are an electrostatic (closed-shell) interaction in the nature. [ABSTRACT FROM AUTHOR]

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 results were compared with those in the gas phase. The result of calculation revealed that anions bind mostly in a bidentate manner via hydrogen bond, and stabilization energies of these complexes are larger than those in the case when anions bind in a monodentate manner. The quantum theory of atoms in molecules (QTAIM), natural bonding orbital (NBO) and energy decomposition analysis (EDA) have also been applied to understand the nature of hydrogen bond interactions in these complexes. NBO analysis reveals that the interaction patterns between the anions and the tautomers are σ-type interaction between lone pairs and $$ \sigma_{{_{{{\text{N}}--{\text{H}}}} }}^{*} $$, $$ \sigma_{{_{{{\text{O}}--{\text{H}}}} }}^{*} $$ and $$ \sigma_{{_{{{\text{H}}--{\text{F}}}} }}^{*} $$ antibonding orbitals. Also, according to these theories, the interactions are found to be partially electrostatic and partially covalent. EDA results identify that these bonds have less than 35% covalent character and more than 65% electrostatic, and the covalent character increases in different anions in the order F > CN > Cl. On the other hand, orbital interaction energies of complexes of F anion are more than those of Cl and CN complexes. The lower orbital interaction energies in complexes of Cl and CNanions imply less charge transfer and stronger ionic bond character. Furthermore, relationship between the orbital interaction energy ( E) with hydrogen bonding energy ( E) and the electron density (ρ( r)) with hydrogen bonding energy of F, Cl and CN complexes have also been investigated. [ABSTRACT FROM AUTHOR]

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]

• 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]

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]

Like-chargeion pairing is commonly observed in protein structuresand plays a significant role in biochemical processes. Density functionalcalculations combined with the conductor-like polarizable continuummodel were employed to study the formation possibilities of doublycharged noncovalently linked complexes of a series of model compoundsand amino acids in the gas phase and in solution. Hydrogen bond interactionswere found to offset the Coulombic repulsion such that cation–cationclusters are minima on the potential energy surfaces and neither counterionsnor solvent molecules are needed to hold them together. In the gasphase the dissociation energies are exothermic, and the separationbarriers span from 1.7 to 15.6 kcal mol–1. Liquid-phasecomputations indicate that the separation enthalpies of the cation–cationcomplexes become endothermic in water and nonpolar solvents with dielectricconstants of ≥7 (i.e., the value for THF). These results revealthat electrostatically defying noncovalent complexes of like-chargedions can overcome their Coulombic repulsion even in low-polarity environments. [ABSTRACT FROM AUTHOR]