The role of hydrogen bonding in supercooled methanol

The role of hydrogen bonding on the microscopic properties of supercooled methanol has been analyzed by means of molecular dynamics simulations. Thermodynamic, structural, and dynamical properties have been investigated in supercooled methanol. The results have been compared with those of an ideal methanol-like system whose molecules have the same dipole moment as the methanol but lack sites for hydrogen bonding. Upon cooling the methanol samples, translational relaxation times increase more rapidly than reorientational ones. This effect is much more important when hydrogen bonds are suppressed. Suppression of hydrogen bonds also results in lower critical temperatures for diffusion and for several characteristic relaxation time constants. The anisotropy of individual dynamics and the existence of dynamical heterogeneities have also been investigated.     

Spectroscopic studies of intermolecular hydrogen bonding and proton transfer complexes of chromotropic acid with some amines in methanol

The proton transfer reactions between chromotropic acid (CTA) and some amines including benzylamine (BA), triethylamine (TEA), pyrrolidine (PY) and 1,8-bis(dimethylamino) naphthalene (DMAN) have been investigated spectrophotometrically in methanol. A long wavelength band at 365 nm has been recorded due to the proton transfer (PT) complex formation. The proton transfer equilibrium constants K_PT were estimated utilizing the minimum–maximum absorbances method. It has been found that K_PT were not depend on the amine pKa values, but strongly depend on the formed structures of the PT complexes. Job^’s method of continuous variations and photometric titrations were applied to identify the compositions of the formed PT complexes where 1:1 complexes (proton donor: proton acceptor) were produced. Due to the rapidity and simplicity of the proton transfer reactions and the stability of the formed complexes, a rapid and accurate spectrophotometric method for the determination of CTA was proposed for the first time.     

Intra- vs. intermolecular hydrogen bonding: dimers of alpha-hydroxyesters with methanol

Intermolecular hydrogen bonding competes with an intramolecular hydrogen bond when methanol binds to an alpha-hydroxyester. Disruption of the intramolecular OH...O=C contact in favour of a cooperative OH...OH...O=C sequence is evidenced by FTIR spectroscopy for the addition of methanol to the esters methyl glycolate, methyl lactate and methyl alpha-hydroxyisobutyrate in seeded supersonic jet expansions. Comparison of the OH stretching modes with quantum-chemical harmonic frequency calculations and 18O labelling of methanol unambiguously prove the insertion of methanol into the intramolecular hydrogen bond. This is in marked contrast to UV/IR hole burning studies of the homologous system methyl lactate: (+/-)-2-naphthyl-1-ethanol, where only addition complexes were found and the intramolecular hydrogen bond was conserved. This switch in hydrogen bond pattern from aliphatic to aromatic heterodimers is thought to reflect not only a kinetic propensity but also a thermodynamic preference for addition complexes when dispersion forces become more important in aromatic systems.     

Structure and hydrogen bonding in polyhydrated complexes of guanine

Abstract Molecular structure of complexes of guanine with 12, 13, 16, and 17 water molecules were calculated using B3LYP/6-311G(d,p) level of theory. Interaction with water results in some deformation of geometrical parameters of guanine, which can be described as contribution of zwitter-ionic resonant form into the structure of DNA base. Saturation of water binding sites within guanine creates possibilities for the formation of the N···H–O hydrogen bond where the nitrogen atom of amino group acts as proton acceptor. The NBO analysis of guanine–water interactions reveals that hydrogen bonds involving the N(3) and N(7) atoms of guanine represent a case of mixed N···H–O/π···H–O hydrogen bonds where contribution of π-system into total energy of interaction varies from 3% to 41%. This contribution significantly depends on orientation of the hydrogen atom of water molecule with respect to plane of purine bicycle and influence of neighboring water molecules. Graphical Abstract      

The role of hydrogen bonding in water-metal interactions

The hydrogen bond interaction between water molecules adsorbed on a Pd <111> surface, a nucleator of two dimensional ordered water arrays at low temperatures, is studied using density functional theory calculations. The role of the exchange and correlation density functional in the characterization of both the hydrogen bond and the water-metal interaction is analyzed in detail. The effect of non local correlations using the van der Waals density functional proposed by Dion et al. [M. Dion, H. Rydberg, E. Schr?der, D. C. Langreth and B. I. Lundqvist, Phys. Rev. Lett., 2004, 92, 246401] is also studied. We conclude that the choice of this potential is critical in determining the cohesive energy of water-metal complexes. We show that the interaction between water molecules and the metal surface is as sensitive to the density functional choice as hydrogen bonds between water molecules are. The reason for this is that the two interactions are very similar in nature. We make a detailed analogy between the water-water bond in the water dimer and the water-Pd bond at the Pd <111> surface. Our results show a strong similarity between these two interactions and based on this we describe the water-Pd bond as a hydrogen bond type interaction. These results demonstrate the need to obtain an accurate and reliable representation of the hydrogen bond interaction in density functional theory.     

Calculating the Gibbs energy of hydrogen bonding for proton acceptors with a solvent in methanol solutions

We propose a method for calculating the Gibbs energies of hydrogen bonding of solutes with associated solvents via the thermodynamic analysis of experimental values of solvation Gibbs energies. The method is applied to solutions of different proton acceptors in methanol. It is shown that the contribution of hydrogen bonding processes to the solvation Gibbs energy in methanol is in most cases very different in magnitude from the formation Gibbs energy of equimolar complexes of the solute and methanol. We demonstrate the need to include the contributions from solvophobic effects in investigating intermolecular interactions in associated solvents by means of thermodynamic data.     

Deciphering the role of hydrogen bonding in enhancing pDNA-polycation interactions

There is considerable interest in the binding and condensation of DNA with polycations to form polyplexes because of their possible application to cellular nucleic acid delivery. This work focuses on studying the binding of plasmid DNA (pDNA) with a series of poly(glycoamidoamine)s (PGAAs) that have previously been shown to deliver pDNA in vitro in an efficient and nontoxic manner. Herein, we examine the PGAA-pDNA binding energetics, binding-linked protonation, and electrostatic contribution to the free energy with isothermal titration calorimetry (ITC). The size and charge of the polyplexes at various ITC injection points were then investigated by light scattering and zeta-potential measurements to provide comprehensive insight into the formation of these polyplexes. An analysis of the calorimetric data revealed a three-step process consisting of two different endothermic contributions followed by the condensation/aggregation of polyplexes. The strength of binding and the point of charge neutralization were found to be dependent upon the hydroxyl stereochemistry of the carbohydrate moiety within each polymer repeat unit. Circular dichroism spectra reveal that the PGAAs induce pDNA secondary structure changes upon binding, which suggest a direct interaction between the polymers and the DNA base pairs. Infrared spectroscopy experiments confirmed both base pair and phosphate group interactions and, more specifically, showed that the stronger-binding PGAAs had more pronounced interactions at both sites. Thus, we conclude that the mechanism of poly(glycoamidoamine)-pDNA binding is most likely a combination of electrostatics and hydrogen bonding in which long-range Coulombic forces initiate the attraction and hydroxyl groups in the carbohydrate comonomer, depending on their stereochemistry, further enhance the association through hydrogen bonding to the DNA base pairs.     

Structure and some reactions of coriose

Coriose was obtained in a higher yield from the root of Coriaria japonica. The structure, -altro-3-heptulose (I) was determined by the sodium borohydride reduction which yielded volemitol (II) and -glycero- -altro-hepitol (IV). Other reactions in agreement with this structure (I) were also carried out: The oxidative degradation of coriose in cold alkali produced a pentanolactone syrup which was reduced to ribose, while the degradation at elevated temperature gave a hexanolactone syrup which yielded ribose on treatment with ferric acetate-hydrogen peroxide. The rearrangement of coriose in alkali at room temperature to 2-heptuloses was investigated. Lead tetraacetate oxidation of coriose produced -glyceraldehyde and -glyceric acid.     

An NMR study of hydrogen bonding in some azo dyestuffs

The ¹H, ¹³C, and ¹⁵N NMR data reported for compounds 1–4 show that in DMSO solutions all of them exist in the azo form only and do not participate in the azo–hydrazoimine equilibrium. The NMR data for compounds 1 and 2 show the presence of a weak hydrogen bond for the non-protonated forms, between N10 and the 2-NHCH₃ proton. All compounds have also been studied in TFA solutions in which they are protonated. The site of protonation of 1, 2 and 3 is determined to be at N10 in TFA solutions. These results are supported by some ab initio GIAO-CHF molecular orbital calculations.     

Kinetics and mechanism of the reactions of uracil with hydrogen peroxide in aqueous solutions

The kinetics of the reactions of 5-hydroxy-6-methyluracil and 6-methyluracil with hydrogen peroxide in aqueous solutions has been investigated. The reactions proceed via two competitive mechanisms, namely, free-radical and nonradical ones. The iron ions present in water as impurities make possible the free-radical mechanism.     

Specific photodynamics in thymine clusters: the role of hydrogen bonding

A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.     

Asymmetric Diels-Alder reactions with hydrogen bonding heterogeneous catalysts and mechanistic studies on the reversal of enantioselectivity

Chiral bis(oxazoline) complexes of Cu(II), Zn(II) and Mg(II) have been immobilized on silica support via hydrogen-bonding interactions. Up to 93% ee is obtained in the Diels-Alder reaction between 3-((E)-2-butenoyl)-1,3-oxazolin-2-one and cyclopentadiene at room temperature with the heterogeneous bis(oxazoline) complexes, and the catalysts can be recycled without losing enantioselectivity. Experimental and theoretical studies show that the reversal of the absolute product configuration upon immobilization of the PhBOX-Cu(II) catalyst is triggered by the anion dissociation from Cu(II) onto the surface of the support.     

Structure and property of the hydrogen bonding complex between triazines and water

The study of the intermolecular interactions that drive the solvation of six-membered nitrogenated aromatic rings is of particular importance since they are known to constitute key building blocks of pro- teins and nucleotides[1―5]. The investigation of the 1:1 adduct of these molecules with water will be the first step in the understanding of such interactions. These molecules possess two different proton-acceptor sites: the ring π cloud and the lone pairs of electrons on the nitrogen atoms…     

Distortion of the decavanadate polyhedron and the role of hydrogen bonding in dimethylammonium decavanadate

The dimethylammonium decavanadate, [Me₂NH₂]₆[V₁₀O₂₈] · H₂O was synthesized and its crystal structure determined by X-ray diffraction. I.r. and n.i.r. spectra were also recorded. The results, compared to the reported crystal structures of decavanadates, indicate that the deformations of isolated polyhedra and their crystal lattice packing are closely related to the anion interactions both with cations and/or water (or solvent) molecules. The i.r. spectra of the relatively strongly distorted (but unprotonated) decavanadate anion are very similar to the spectrum of protonated [Me₃CNH₃]₄[H₂V₁₀O₂₈] [1], with a different distribution of hydrogen bonds. Thus the i.r. spectra of the decavanadate salts provide no evidence for protonation. In each case, the analysis of a particular decavanadate spectrum by advanced quantum chemistry calculations is needed. The near i.r. spectra of [Me₂NH₂]₆[V₁₀O₂₈] · H₂O can be helpful in gaining a better understanding of decavanadate salts structures. These results are important because of the role of decavanadate in catalysis.     

The role of hydrogen bonds in Baeyer-Villiger reactions

Various Baeyer-Villiger (B-V) oxidation reactions were examined by density functional theory calculations. Proton movements in transition states (TSs) of the two key steps, the nucleophilic addition of a peroxyacid molecule to a ketone (TS1) and the migration-cleavage of O-O (TS3), were discussed. A new TS of a hydrogen-bond rearrangement in the Criegee intermediate (TS2) was found. The hydrogen-bond directionality requires a trimer of the peroxyacid molecules at the nucleophilic addition of a peroxyacid molecule to a ketone TS (TS1). At the migration-cleavage of O-O TS (TS3), also three peroxyacid molecules are needed. Elementary processes of the B-V reaction were determined by the use of the (acetone and (H-CO-OOH)n, n=3) system. The geometries of the nucleophilic addition of a peroxyacid molecule to a ketone TS (TS1) and the migration-cleavage of O-O TS (TS3) in the trimer (n=3) participating are nearly insensitive to the substituent on the peroxyacid. The directionality is satisfied in those geometries. The migration-cleavage of O-O TS (TS3) was found to be rate-determining in reactions, [Me2C=O+(H-CO-OOH)3], [Me2C=O+(F3C-CO-OOH)3], and [Me2C=O+(MCPBA)3]. In contrast, the nucleophilic addition of a peroxyacid molecule to a ketone (TS1) is rate-determining in the reaction, [Ph(Me)C=O+(H-CO-OOH)3].