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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]

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 normal H‐bonds in the conjugate base of cyclic glucose. In the conjugate base of glucose, the O–H···O bonds are categorized as mostly electrostatic and strong, whereas multiple interactions including C–H···O, C–H···H–C (dihydrogen bonding), C–H···C–H, and C=O···H are categorized as weak H‐bonds. The NBO results confirm that the O–H···O intramolecular H‐bonds should be the strongest among all H‐bonds existing within glucose. [ABSTRACT FROM AUTHOR]

In this article, we report the computational examination of the impact of hydrogen bonding (HB) on the stereoselectivity of a series of Diels–Alder (DA) reactions. Four different types of diene/dienophile couples were studied including (a) cyclopenta-2,4-dien-1-ol and heteroatom-substituted cyclopentenes, (b) substituted cyclopentadienes and N-protonated 2,5-dihydro-1H-pyrrole, (c) furan and N-protonated 5-azabicyclo[2.1.1]hex-2-ene, and (d) N-protonated cyclopenta-2,4-dien-1-amine and α,β-unsaturated carbonyl compounds. These systems were designed such that the HB can only exist in the exo reaction pathway. The optimized structures of the transition states (TSs) and products, along with the Gibbs free energies of activation and reaction were calculated in the gas phase and dichloromethane by B3LYP/6-31G++(d,p) method. It was found that the exo adduct is the most kinetically and thermodynamically favored product for all of the DA reactions mentioned above. Moreover, the role of the HB in stabilizing the exo stereoisomer (and the corresponding TS) was much more pronounced for the reactions involving cationic species (cases b–d). In the end, a hypothetical synthetic method was proposed for obtaining exo-2-alkylbicyclo[2.2.1]heptanes. Our findings suggest that the HB can be employed as an effective interaction to control the stereoselectivity of DA reactions. [ABSTRACT FROM AUTHOR]

Ionic liquids, which are widely known as room temperature molten salts, have been the subject of much scientific debate for more than a decade. These compounds can be used as green solvents or even as additives in many reactions. Due to their noticeable conductivity, which is a function of the interaction energies existing between the ion pairs in ionic liquids, the synthesis and introduction of new families of these chemicals are of importance. The target of this paper is to design new carboxylate-based ionic liquids containing OH and CF3 groups. Our results indicate that the properties of these ILs are highly affected by the presence of OH and CF3 groups, in which OH stabilizes the negative charge of the anion via intramolecular hydrogen bonds and CF3 stabilizes it through the electron withdrawing effect. These groups decrease the binding energy between the anion and cation of the carboxylate-based ionic liquids and thus affect their physical properties such as melting point and density as well as their chemical properties. All calculations in this study were performed in the gas phase at the B3LYP/6-311++G(d,p) level. [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]

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]

Polyols were used as model ligands for Mg2+, Ca2+, and Zn2+ complexes to study the role of the hydrogen bond network on the metal binding affinity and modulation of successive pKa values using density functional theory. The results confirm that the acidity of polyols dramatically increases upon metal complexation in the order Zn2+ ＞ Mg2+ ＞ Ca2+. For example, the three H-site positions in the hydroxyl groups of the heptaol, bound to Zn2+, are 11.2, 29.9, and 30.9 pKa units (in methanol) more acidic than those of pure heptaol. This acidity enhancement leads to making polyols as good ligands toward complexation. For instance, the formation constants of the heptaol in the presence of Zn2+, Mg2+, and Ca2+ in methanol were 5.67 × 1071, 6.46 × 1066, and 1.26 × 1053 times lower than those in its third deprotonation state, respectively. The natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and reduced density gradient (RDG) analyses show that the intramolecular hydrogen bond network and increment of carbon chain length lead to the enhancement of metal binding affinity. These findings can be used for the manipulation of ligands and metal cations in designing metalloproteins. [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]

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]

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]

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]

The reaction pathway (including the transition state) of ethylene addition to permanganate (MnOi) in the presence of ethylene glycol (EG) has been qualitatively and quantitatively studied by means of B3LYP/6-311++G** theoretical analysis. Interestingly, by cluster formation of the EG with permanganate, oxidation reaction becomes thermody-namically and kinetically more favorable. The influences of electron-withdrawing as well as electron-donating substituents were also explored. Results of the quantum theory of atoms in molecules and natural bond orbital analyses revealed that [3 + 2] addition reaction of alkenes in the presence of EG as hydrogen bonding donor to MnOi becomes more exothermic. Natural resonance theory (NRT) is used to calculate natural bond order and bond polarity. The NRT result indicates that the polarity of Mn-0 bond is affected by EG coordinated to Mn04-. Moreover, the conceptual DFT descriptors such as chemical potential (μ), hardness (η) and electrophilicity index (ω) show that hydrogen bonding to permanganate can affect the addition of Mn04- to double bond in a satisfactory way. We also carried out geometrical optimizations with the polarizable continuum model to account for the solvent effect, and the results were compared with those in the gas phase. [ABSTRACT FROM AUTHOR]

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 of heteroatoms in macrocycles. The highest PA value among the studied macrocyclic amines was found to be 264.9 kcal mol−1 for structure 7. This is comparable with PA of proton sponges such as 1,8-bis(dimethylamino)naphthalene. The solution phase calculations were carried out in the dimethyl sulfoxide solution as a commonly used solvent in organic reactions. Natural bond orbital analysis was performed to calculate the charge transfers and the second-order interaction energies ( E(2)) between the donor and acceptor. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of hydrogen bonds. QTAIM studies showed that the intramolecular hydrogen bonds in these structures are electrostatic (closed-shell) interactions as well as partially covalent and partially electrostatic in nature. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our goal is to gather data to help elucidate the structure and electronic properties of boron analogues of uracil. Density functional theory calculations were performed using a nonlocal hybrid B3LYP and 6-311++G (d,p) atomic basis set. The result of calculation revealed that the canonical 'keto' form is the most stable tautomeric form of uracil nucleobase and its boronated analogues in the gas phase at density functional theory and second-order Møller-Plesset levels. Hyperconjugation stabilization factors that affect the stability of generated radicals and anions in these molecules were investigated by natural bond orbital analysis. Furthermore, quantum theory of atoms in molecules analysis was performed to extract the bond critical point properties of various base pairs. The electron density can be considered as a good description of the strength of the different types of hydrogen bonding. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The interactions between five amino acid based anions([AA]−(AA = Gly, Phe, His, Try, and Tyr)) and N7,N9-dimethylguaniniumcation ([dMG]+) have been investigated by the hybrid densityfunctional theory method B3LYP together with the basis set 6-311++G(d,p).The calculated interaction energy was found to decrease in magnitudewith increasing side-chain length in the amino acid anion. The interactionbetween the [dMG]+cation and [AA]−anionin the most stable configurations of ion pairs is a hydrogen bondinginteraction. These hydrogen bonds (H bonds) were analyzed by the quantumtheory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities inbond critical points of hydrogen bonds and interaction energy as wellas vibrational frequencies in the most stable configurations of ionpairs have been checked. [ABSTRACT FROM AUTHOR]

Bridgehead C-H bond dissociation enthalpies of 105.7 ± 2.0, 102.9 ± 1.7, and 102.4 7plusmn; 1.9 kcal mol-1 for bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, and adamantane, respectively, were determined in the gas phase by making use of a thermodynamic cycle (i.e., BDE(R-H) = ΔHºacid(H-X) - IE(H) + EA(X)). These results are in good accord with high-level G3 theory calculations and the experimental values along with G3 predictions for bicyclo[1.1.1]pentane, bicyclo[2.2.1]hexane, bicyclo[3.1.1]heptane, and bicyclo[4.2.1]nonane the gas found to correlate with the flexibility of the ring system. Rare examples of alkyl anions in the gas phase are also provided. [ABSTRACT FROM AUTHOR]

Abstract: Abstraction of hydrogen atom from DNA and RNA subunits leads to formation of a neutral radical. The formation of these radicals can lead to harmful structural alternations and formation of multiple lesions in helixes of DNA and RNA. In the present work, we explore theoretically energetic and structural properties of the possible radicals formed via hydrogen atom 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. Two types of free radicals may be found by hydrogen abstraction of sugar part of cytosine nucleosides: carbon centered radicals and the oxygen centered radicals. The computation revealed 0–22.6kcal/mol energy disparity in these radical. Radical-centered carbon increases the extent of bonding with its adjacent atoms. This tendency should be important in predicting the reactivity of sugar-based radicals. The hydrogen abstracted sugar radicals of cytosine nucleosides have following stability sequence: raC2 ′> raC1 ′> raC3 ′> raC4 ′> raC5 ′> raO5 ′> raO2 ′> raO3 ′ for cytidine and radC1 ′> radC2 ′> radC4 ′> radC3 ′> radC5 ′> radO5 ′> radO3 ′ for deoxycytidine. Furthermore, to take into account the effect of solvent environment on the stability order of radicals integral equation formalism of the polarized continuum model (IEF-PCM) was employed to model aqueous solution. The role of CH⋯O and HO⋯H intramolecular hydrogen bonds in stability of radicals investigated based on results of topological properties of AIM theory. Moreover, variations of significant structural parameters such as puckering amplitudes and phase angles of sugar parts of cytosine nucleosides after radical formation are also found. These finding have several biological implications and may explain the possible degrees of damage to the DNA double strand. [Copyright &y& Elsevier]

Hydrogen bonds are the dominant motif for organizing the three-dimensional structures of biomolecules such as carbohydrates, nucleic acids, and proteins, and serve as templates for proton transfer reactions. Computations, gas-phase acidity measurements, and pKa determinations in dimethyl sulfoxide on a series of polyols indicate that multiple hydrogen bonds to a single charged center lead to greatly enhanced acidities. A new class of Brønsted acids, consequently, is proposed. [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]

B3LYP/aug-cc-pVDZ computations were carried out on polyamines with up to seven amino groups. The gas-phase proton affinities of these compounds are 219.6 (1-BuNH2), 238.6 (H2NCH2CH2CH2CH2NH2), 252.8 [(H2NCH2CH2CH2)2CHNH2], 261.3 [(H2NCH2CH2CH2)3CNH2 (1)], and 288.5 kcal mol-1 [(H2NCH2CH2CH(NH2)CH2CH2)3CNH2]. These results indicate that the tetraamine is near the top of the basicity scale and the heptaamine is more basic than any neutral organic compound which has been measured to date. A gas-phase equilibrium acidity determination between 1 and DBU also was carried out, and PA(1) = 256.2 ± 2.1 kcal mol-1 was obtained. This demonstrates that multiple intramolecular hydrogen bonds can greatly increase basicities, and represents a new motif for designing super bases. [ABSTRACT FROM AUTHOR]

Both C-H bond dissociation energies for cyclobutene were measured in the gas phase (BDE = 91.2 ± 2.3 (allyl) and 112.5 ± 2.5 (vinyl) kcal mol-1) via a thermodynamic cycle by carrying out proton affinity and electron-binding energy measurements on 1- and 3-cyclobutenyl anions. The results were compared to those for an acyclic model compound, cis-2-butene, and provide the needed information to experimentally establish the heat of formation of cyclobutadiene. Chemically accurate G3 and W1 calculations also were carried out on cycloalkanes, cycloalkenes, and selected reference compounds. It appears that commonly cited bond energies for cyclopropane, cyclobutane, and cyclohexane are 3 to 4 kcal mol-1 too small and their π bond strengths, as given by BDE1 - BDE2, are in error by up to 8 kcal mol-1. [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]

Natural and synthetic anion receptors are extensively employed, but the structures of their bound complexes are difficult to determine in the liquid phase. Infrared spectroscopy is used in this work to characterize the solution structures of bound anion receptors for the first time, and surprisingly only two of three hydroxyl groups of the neutral aliphatic triols are found to directly interact with Cl-. The binding constants of these triols with zero to three CF3 groups were measured in a polar environment, and ...(Cl-) = 1.1 x 106 M-1 for the tris(trifluoromethyl) derivative. This is a remarkably large value, and high selectivity with respect to interfering anions such as, Br-, NO3- and NCS- is also displayed. The effects of the third "noninteracting" hydroxyl groups on the structures and binding constants were also explored, and surprisingly they are as large or larger than the OH substituents that hydrogen bond to Cl-. That is, a remote hydroxyl group can play a larger role in binding than two OH substituents that directly interact with an anionic center. [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]

The pK, of an acyclic aliphatic heptaol ((HOCH2CH2CH(OH)CH2)3COH) was measured in DMSO, and its gas-phase acidity is reported as well. This tertiary alcohol was found to be 1O~ times more acidic than tert.butyl alcohol in DMSO and an order of magnitude more acidic than acetic acid (i.e., plC2 = 11.4 vs 12.3). This can be attributed to a 21.9 kcal mol' stabilization of the charged oxygen center in the conjugate base by three hydrogen bonds and another 6.3 kcal mol-1 stabilization resulting from an additional three hydrogen bonds between the uncharged I primary and secondary hydroxyl groups. Charge delocalization by both the first and second solvation shells may be used to facilitate enzymatic reactions. Acidity constants of a series of polyols were also computed, and the combination of hydrogen-bonding and electron-withdrawing substituents was found to afford acids that are predicted to be extremely acidic in DMSO (i.e., pK2< 0). These hydrogen bond enhanced acids represent an attractive class of Bronsted acid catalysts. [ABSTRACT FROM AUTHOR]

Abstract: Histidine as a natural amino acid is found to be biologically important and is known to function as a nucleophile or enzyme co-factor, or in proton transfer process. The properties of gaseous aromatic amino acid histidine depend on the structural forms it may take in gas-phase. Ab initio method has been used to characterize the gas-phase conformer/tautomers of histidine. Wide range of possible structures for histidine was surveyed at the MM level, and then the geometries of the unique conformers were refined at the B3LYP/6-311++G (d,p) levels. At this theoretical level, 25 conformers were located for both tautomers of histidine i.e., His [NπH] and His [NτH]. The MM level provides a poor description of the relative energies. Calculations at the B3LYP/6-311++G (d,p) level represent a significant improvement. Ab initio dipole moments are reported for all the conformers/tautomers. The results are compared to previous studies of amino acids and are analyzed in terms of intramolecular hydrogen-bonding interactions and Newman projections. In addition, we calculated the infrared frequencies and intensities of the most stable structures in order to assist in the assignment of hydrogen-bonding. Furthermore, Ramachandran backbone potential energy surfaces (PES) of 25 conformers of His [NπH] and His [NτH] tautomers of histidine were considered. The stationary points characterizing the potential energy profile of the various conformers/tautomers of histidine were investigated by the same density functional theory B3LYP/6-311++G (d,p). Minima and transition states characterizing the energetic paths for the interconversion of various structures of histidine were explored in detail. [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]

Understanding the nature of the interaction between metalnanoparticlesand biomolecules has been important in the development and designof sensors. In this paper, structural, electronic, and bonding propertiesof the neutral and anionic forms of glutathione tripeptide (GSH) complexeswith a Au3cluster were studied using the DFT-B3LYP with6-31**-LANL2DZ mixed basis set. Binding of glutathione with thegold cluster is governed by two different kinds of interactions: Au–X(X = N, O, and S) anchoring bond and Au···H–Xnonconventional hydrogen bonding. The influence of the intramolecularhydrogen bonding of glutathione on the interaction of this peptidewith the gold cluster has been investigated. To gain insight on therole of intramolecular hydrogen bonding on Au–GSH interaction,we compared interaction energies of Au–GSH complexes with thoseof cystein and glycine components. Our results demonstrated that,in spite of the ability of cystein to form highly stable metal–sulfideinteraction, complexation behavior of glutathione is governed by itsintramolecular backbone hydrogen bonding. The quantum theory of atomin molecule (QTAIM) and natural bond orbital analysis (NBO) have alsobeen applied to interpret the nature of interactions in Au–GSHcomplexes. Finally, conformational flexibility of glutathione duringcomplexation with the Au3cluster was investigated by meansof monitoring Ramachandran angles. [ABSTRACT FROM AUTHOR]