Hydrogen-bonding Characteristics Research Articles

How strong are H-bonds at the fully hydroxylated silica surfaces? Insights from the B3LYP electron density topological analysis

The calculation through the supermolecular approach of the hydrogen bond strength EHB between silanol groups at the surface of an ample class of silica-based materials is hindered by the intrinsic difficulty to define the “H-bond free” reference system. We propose, for the first time, to evaluate EHB by adopting the literature empirical correlation relating the Bader local electronic kinetic energy density Gb computed at the H⋅⋅⋅O bond critical point with EHB. Remarkably, EHB for the hydroxylated surfaces of quartz polymorphs correlates with surface formation energy, showing that the surface EHB is responsible of the surface stability. A number of correlations between hydrogen bond features are established, with that between EHB and the enhanced infrared intensity associated to surface hydrogen bond formation, obeying the literature formula semi-quantitatively. The present results are quite general and can be extended to other inorganic surfaces where hydrogen bonds between surface sites are the dominant features.

Potential mesogens based on pyridine derivatives: The geometric structure, conformational properties and characteristics of intermolecular hydrogen bonds

Conformational properties of the main part (excluding OC3H7 radicals) of the p-n-propyloxybenzoic (A1) and p-n-propyloxycinnamic (A2) acids molecules (relating to mesomorphic compounds) as well as p-n-propyloxybenzoic acid pyridine ester (B1) and p-n-propyloxyphenylazopyridine (B2) molecules (relating to non-mesomorphic compounds) were studied by DFT(B3LYP)/cc-pVTZ method. It was shown that the main parts of A1 and A2 acids are rigid. The barrier to internal rotation of pyridine fragment in the B1 and B2 molecules depends on the nature of the bridging group. It was determined that all studied A1⋯B1, A2⋯B1 and A2⋯B2 complexes are characterized by a strong hydrogen bond. The binding energy of complexes (≈14 kcal/mol, with BSSE corrections, DFT(B97D)/6-311++G**) exceeds the energy per hydrogen bond in the corresponding acid dimers (≈10 kcal/mol). The structural non-rigidity of A⋯B complexes is mainly caused by possibility of OC3H7 radicals internal rotation and A and B molecules rotation about the (H)O⋯N line. The characteristics of intermolecular hydrogen bonds were determined by NBO-analysis. The obtained results indicate that examined complexes correspond to the basic requirements to mesogen molecular forms. The thermodynamic functions of the gas-phase complexation reactions (idealized model of the complexes formation in the condensed state) were calculated. Preliminary studies of mesogen–non-mesogen A1⋯B2 system by differential scanning calorimetry and polarizing optical microscopy, showed that it has mesomorphic properties.

A prevalent intraresidue hydrogen bond stabilizes proteins.

Current limitations in de novo protein structure prediction and design suggest an incomplete understanding of the interactions that govern protein folding. Here we demonstrate that previously unappreciated hydrogen bonds occur within proteins between the amide proton and carbonyl oxygen of the same residue. Quantum calculations, infrared spectroscopy, and nuclear magnetic resonance spectroscopy show that these interactions share hallmark features of canonical hydrogen bonds. Biophysical analyses demonstrate that selective attenuation or enhancement of these C5 hydrogen bonds affects the stability of synthetic β-sheets. These interactions are common, affecting approximately 5% of all residues and 94% of proteins, and their cumulative impact provides several kcal/mol of conformational stability to a typical protein. C5 hydrogen bonds stabilize, especially, the flat β-sheets of the amyloid state, which is linked with Alzheimer’s disease and other neurodegenerative disorders. Inclusion of these interactions in computational force fields would improve models of protein folding, function, and dysfunction.

Multi-centred hydrogen bonds between water and perchlorate anion

ABSTRACTResults of classical molecular dynamics simulations are presented for the re-orientational dynamics of water hydrogen bonded to perchlorate anion. Different mechanisms of bond formation are presented. Due to its regular tetrahedron geometry the perchlorate anion can make classical as well as bifurcated and trifurcated hydrogen bonds. The angular variation of water in the first solvation shell of perchlorate suggests the transitional character of multi-centred hydrogen bonds. As a result water molecules can slide around the anion.

Sensing Activity of a New Generation of Thiourea-based Receptors; A Theoretical Study on the Anion Sensing

A theoretical density functional theory (DFT) study was performed on a series of the neutral N-phenylthiourea substituents (p-OC2H5, p-CH3, m-CH3, H, p-Cl, p-Br, m-Cl, and p-NO2) as the sensor of acetate and fluoride anions. The hydrogen bond character was analyzed as a scale of the sensing activity. It was confirmed that hydrogen bond between the p-NO2 derivatives of N-phenylthiourea and fluoride anion is stronger than acetate in CH3CN as a solvent. Therefore, N-(p-nitrophenyl) thiourea acts as a better chemical sensor in fluoride detection. For the investigation of the N-H bond properties, donor-acceptor interaction energy through the natural bond orbital analysis was obtained. Topology analysis by estimation of the kinetic and potential energy densities of the hydrogen bonds was done. Finally, some correlations between the quantum chemistry descriptors and sensing characters of the studied compounds were obtained and analyzed.

Time-dependent density functional theory study on the excited-state hydrogen-bonding characteristics of polyaniline in aqueous environment

A theoretical study was carried out to study the excited-state of hydrogen-bonding characteristics of polyaniline (PANI) in aqueous environment. The hydrogen-bonded PANI-H2O complexes were studied using first-principles calculations based on density functional theory (DFT). The electronic excitation energies and the corresponding oscillator strengths of the low-lying electronically excited states for hydrogen-bonded complexes were calculated by time-dependent density functional theory (TDDFT). The ground-state geometric structures were optimized, and it is observed that the intermolecular hydrogen bonds CN⋯HO and NH⋯OH were formed in PANI-H2O complexes. The formed hydrogen bonds influenced the bond lengths, the charge distribution, as well as the spectral characters of the groups involved. It was concluded that all the hydrogen-bonded PANI-H2O complexes were primarily excited to the S1 states with the largest oscillator strength. In addition, the orbital transition from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) involved intramolecular charge redistribution resulting to increase the electron density of the quinonoid rings.

Hydrogen-bonding characteristics and unique ring-opening polymerization behavior ofOrtho-methylol functional benzoxazine

Monofunctional benzoxazine with ortho-methylol functionality has been synthesized and highly purified. The chemical structure of the synthesized monomer has been confirmed by 1H and 13C nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FT-IR) and elemental analysis. One-dimensional (1D) 1H NMR is used with respect to varied concentration of benzoxazines to study the specific nature of hydrogen bonding in both ortho-methylol functional benzoxazine and its para counterpart. The polymerization behavior of benzoxazine monomer has been also studied by in situ FT-IR and differential scanning calorimetry, experimentally supporting the polymerization mechanism of ortho-methylol functional benzoxazine we proposed before. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3635–3642

Activity coefficients at infinite dilution for organic solutes dissolved in two 1,2,3-tris(diethylamino)cyclopenylium based room temperature ionic liquids

Infinite dilution activity coefficients and gas-to-liquid partition coefficients have been determined for at least 45 different organic solutes of varying polarity and hydrogen-bonding character dissolved in anhydrous 1,2,3-tris(diethylamino)cyclopropenylium dicyanamide, ([TDC]+[DCA]−), and 1,2,3-tris(diethylamino)cyclopropenylium bis(trifluoromethylsulfonyl)imide, ([TDC]+[Tf2N]−). The measured infinite dilution activity coefficients were used to calculation selectivity values for various practical separation problems. Computations showed ([TDC]+[DCA]−) should afford better performance in hexane/benzene and hexane/pyridine separation problems than sulfolane and N-methyl-2-pyrrolidone. Abraham model correlations were derived for predicting solute transfer into both ([TDC]+[DCA]−) and ([TDC]+[Tf2N]−) from water and from the gas phase. The derived correlations describe the observed solute transfer partition coefficients to within 0.13 (or fewer) log units.

Hydrogen bond lifetimes in supercritical methanol–water mixtures via MD simulation

ABSTRACTDynamical features of hydrogen bonds in methanol–water mixtures have been analysed in terms of lifetime in the wide range of conditions, including supercritical states, using a molecular dynamics simulation with flexible potential models. Hydrogen bond characteristics in methanol–water mixtures were investigated by considering the combination of molecular species and donor–acceptor of hydrogen-bonded molecules. The hydrogen bond lifetimes mainly depend on temperature, and those in supercritical condition were about 1/10th of that at ambient condition. Focusing on the composition dependence of the hydrogen bond lifetime, the unique behaviour of that resulting from hydration structure was observed. Moreover, the molecular combination, which showed the largest hydrogen bond lifetime, was different for ambient and high temperature and high pressure conditions. The relationship between hydrogen bond lifetime and molar volume was also calculated to discuss the hydrogen bond lifetime in terms of the collision frequency of molecules and the intermolecular distance.

Abraham model linear free energy relationships as a means of extending solubility studies to include the estimation of solute solubilities in additional organic solvents

Abraham model solute descriptors are calculated for 5-nitro-8-hydroxyquinoline, 2-methyl-6-nitroaniline, and terephthaldialdehyde using experimental solubility data taken from papers published in This Journal in 2016. The calculated solute descriptors are then used to predict the solubility of the three fore-mentioned solutes in 29 different organic solvents of varying polarity and hydrogen-bonding character.

Different acid-base behaviour of a pyrazole and an isoxazole with organic acids: crystal and molecular structures of the salt 3-(4-fluorophenyl)-1H-pyrazolium 2,4,6-trinitrophenolate and of the cocrystal 4-amino-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzenesulfonamide-3,5-dinitrobenzoic acid (1/1).

Pyrazole and isoxazole rings differ only in the notional replacement of a potential hydrogen-bond-donor NH unit in pyrazole by a potential hydrogen-bond-acceptor O atom in isoxazole. It is thus of interest to compare the hydrogen-bonding characteristics of these rings. (4-Fluorophenyl)pyrazole undergoes protonation in the presence of 2,4,6-trinitrophenol to yield the salt 3-(4-fluorophenyl)-1H-pyrazolium 2,4,6-trinitrophenolate, C9H8FN2(+)·C6H2N3O7(-), (I), whereas there is no proton transfer between 4-amino-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzenesulfonamide and 3,5-dinitrobenzoic acid, whose reaction gives the 1:1 cocrystal, C11H13N3O3S·C7H4N2O6, (II). The bond lengths in salt (I) provide evidence for aromatic-type delocalization in the pyrazolium ring and for extensive delocalization of the negative charge into the ring of the trinitrophenolate anion. The O atoms of one of the nitro groups in the trinitrophenolate anion are disordered over two sets of atomic sites having occupancies of 0.571 (6) and 0.429 (6), but all of the other substituents on the carbocyclic rings are fully ordered. The ions in salt (I) are linked by an extensive series of N-H...O hydrogen bonds to form a three-dimensional framework structure, and in cocrystal (II), the molecular components are linked by a combination of O-H...N and N-H...O hydrogen bonds to form complex bilayers. Comparisons are made with some related compounds.

Infinite dilution activity coefficients of solutes dissolved in anhydrous alkyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide ionic liquids containing functionalized- and nonfunctionalized-alkyl chains

Infinite dilution activity coefficients and gas-to-liquid partition coefficients have been determined for at least 42 different organic solutes of varying polarity and hydrogen-bonding character dissolved in anhydrous ionic liquids comprising propyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, hexyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, 2-hydroxyethyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, cyanomethyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, and N,N,N′,N′-tetramethyl-N,N′-diisopropyl-1,9-nonanediaminium di[bis(trifluoromethylsulfonyl)imide]. The measured gas-to-liquid partition coefficient data were converted to water-to-liquid partition coefficients using standard thermodynamic relationships. Abraham model predictive correlations were developed from both sets of partition coefficients. The derived correlations describe the observed partitioning behavior to within 0.14 (or fewer) log units.

Catalytic Synthesis of Secondary Amine-Containing Polymers: Variable Hydrogen Bonding for Tunable Rheological Properties

A synthetic protocol using atom-economic, catalytic hydroaminoalkylation and ring-opening metathesis polymerization (ROMP) has been developed for the versatile synthesis of a new class of aryl-substituted secondary amine-containing polymers. This catalytic route minimizes waste generation and avoids protection/deprotection protocols, postpolymerization modification, and byproduct formation. Different amines can be readily incorporated to access variable hydrogen-bonding characteristics. Thermal and melt rheological characterization has shown the profound effect of hydrogen bonding on the bulk properties of these amine-containing norbornene polymers.

Crystal structure of [Bi(N-ethylthiourea)4(ClO4)2]ClO4

The structure of the bismuth(III) complex with N-ethylthiourea (Ettu) has been determined for the first time. We found that the crystal structure of [Bi(Ettu)4(ClO4)2]ClO4 is built of distorted octahedral cations [Bi(Ettu–S)4(ClO4)2]ClO4]+ and anions ClO 4 - . The deviation of one of the two independent Ettu molecules from the plane structure is explained by the mutual repulsion of the ligands and the formation features of hydrogen bonds. The C2H5(Ettu) group is in the cis position relative to the thiocarbonyl group.

NCI concept as a powerful tool to investigate the origin of Diels–Alder reaction accelerating inside the self-assembled softball nanoreactor

Thermodynamic and kinetic aspects of the Diels–Alder reaction between p–benzoquinone (1) and cyclohexadiene (2) have been investigated inside the softball nanoreactor, theoretically. The softball nanoreactor has remarkable effects on the possibility and facility of the inside reaction. Wall atoms effects of the nanoreactor on the reaction have been investigated by the evaluation of the non-covalent interactions (NCI) analysis. In addition, the hydrogen bond character of the bonds between the monomers of the nanoreactor, as a driving force for the nanoreactor construction, has been studied by topological analysis of the nanoreactor, electron localization function and localized orbital locator criteria. Two kinds of the hydrogen bond have been confirmed between the monomers of the nanoreactor by using the 2D and 3D NCI plots. NBO analysis has been applied for justification of these hydrogen bond formation. Finally, it has been concluded that the molecular nanoreactor accelerates Diels–Alder reaction through the van der Waals interactions with the reactants and transition states.

Extraction of Polysaccharides from Japanese Cedar Using Phosphonate-Derived Polar Ionic Liquids Having Functional Groups

Abstract Extraction of polysaccharides from Japanese cedar using ionic liquids has been demonstrated. To this aim, eleven types of phosphonate ionic liquids have been synthesized, their properties investigated, and applied to biomass processing. All ionic liquids prepared display strong hydrogen-bonding characteristics of Kamlet–Taft parameters (β > 1.1) which enabled the effective extraction of polysaccharides from Japanese cedar. In particular, 15 wt % of polysaccharides was extracted from Japanese cedar powder using 1-(3-methoxypropyl)-3-methylimidazolium ethyl ethylphosphonate. Since the ionic liquid is easily prepared using conventional reagents and might be applicable to large-scale reactions, it is expected that practical polysaccharide extraction using the ionic liquid might be possible from a wide variety of biomass resources.

Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms.

In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.

IR and Vibrational Circular Dichroism Spectroscopy of Matrine- and Artemisinin-Type Herbal Products: Stereochemical Characterization and Solvent Effects.

Five Chinese herbal medicines--matrine, oxymatrine, sophoridine, artemisinin, and dihydroartemisinin--were investigated using vibrational circular dichroism (VCD) experiments and density functional theory calculations to extract their stereochemical information. The three matrine-type alkaloids are available from the dry roots of Sophora flavescens and have long been used in various traditional Chinese herbal medicines to combat diseases such as cancer and cardiac arrhythmia. Artemisinin and the related dihydroartemisinin, discovered in 1979 by Professor Youyou Tu, a 2015 Nobel laureate in medicine, are effective drugs for the treatment of malaria. The VCD measurements were carried out in CDCl3 and DMSO-d6, two solvents with different dielectric constants and hydrogen-bonding characteristics. A "clusters-in-a-liquid" approach was used to model both explicit and implicit solvent effects. The studies show that effectively accounting for solvent effects is critical to using IR and VCD spectroscopy to provide unique spectroscopic features to differentiate the potential stereoisomers of these Chinese herbal medicines.

Molecular insights into water vapor absorption by aqueous lithium bromide and lithium bromide/sodium formate solutions

Aqueous lithium bromide (LiBr) solutions are commonly-employed as liquid desiccants, largely due to their low water vapor pressure at concentrations suitable for applications such as absorption refrigeration. However, LiBr-based desiccants have drawbacks such as corrosivity, crystallization at high concentrations, and high energy inputs to regenerate the absorbent. It was recently shown that adding formate salts (e.g., NaCOOH) into the LiBr+H2O mixture could mitigate disadvantages while maintaining most advantages, but these experimental findings were unable to elucidate the driving forces at the molecular level. Detailed knowledge of the molecular interactions that underpin absorption phenomenon in both traditional and newly developed ternary working fluids (e.g., LiBr+NaCOOH+H2O) is still incomplete. The present molecular modeling study of water vapor absorption by LiBr and LiBr+NaCOOH investigated the water vapor absorption kinetics, enabling the analysis of ionic clustering and hydrogen-bonding characteristics. Molecular simulations of LiBr+H2O compositions demonstrated that increasing the LiBr concentration enhances the absorption rate while decreasing the liquid–vapor interfacial thickness of the LiBr+H2O layer. The most interesting finding was the strong interaction between Li+ and COOH− which may enable the ternary mixture to accommodate more water molecules as a result of Li+–COOH− clustering compared to compositions containing only LiBr and H2O. Despite an increase in water vapor absorption capacity it was found that adding NaCOOH decreased the water vapor absorption rate. Elucidating the molecular origin that affects the performance of liquid desiccants upon addition of formate salts is a first step toward the rational design of new working fluids for liquid desiccant-related applications.

Far-Infrared Signatures of Hydrogen Bonding in Phenol Derivatives.

One of the most direct ways to study the intrinsic properties of the hydrogen-bond interaction is by gas-phase far-infrared (far-IR) spectroscopy because the modes involving hydrogen-bond deformation are excited in this spectral region; however, the far-IR regime is often ignored in molecular structure identification due to the absence of strong far-IR light sources and difficulty in assigning the observed modes by quantum chemical calculations. Far-IR/UV ion-dip spectroscopy using the free electron laser FELIX was applied to directly probe the intramolecular hydrogen-bond interaction in a family of phenol derivatives. Three vibrational modes have been identified, which are expected to be diagnostic for the hydrogen-bond strength: hydrogen-bond stretching and hydrogen-bond-donating and -accepting OH torsion vibrations. Their position is evaluated with respect to the hydrogen bond strength, that is, the length of the hydrogen-bonded OH length. This shows that the hydrogen bond stretching frequency is diagnostic for the size of the ring that is closed by the hydrogen bond, while the strength of the hydrogen bond can be determined from the hydrogen-bond-donating OH torsion frequency. The combination of these two normal modes allows the direct probing of intramolecular hydrogen-bond characteristics using conformation-selective far-IR vibrational spectroscopy.