Formation Of Hydrogen-bonded Dimers Research Articles

Synthesis, XRD structural analysis and theoretical studies of a potential inhibitor against rheumatoid arthritis (RA).

This work focused on analyzing the properties of N-(5-nitrothiazol-2-yl)furan-2-carboxamide (C8H5N3O4S, NTFC) as a possible inhibitor of the rheumatoid arthritis process. The synthesis of NTFC was carried out and good-quality crystals were obtained and studied by NMR (1H and 13C), DEPT 135, UV-Vis, IR, MS and single-crystal X-ray diffraction. The structure of NTFC consists of two rings, thiazole and furan, and a central C-N-C(=O)-C segment, which appears to be planar. This central amide segment forms angles of 2.61 (10) and 7.97 (11)° with the planes of the thiazole and furan rings, respectively. The crystal structure of NTFC exhibits N-H...N, N-H...O and C-H...O hydrogen bonds, and C-H...π and π-π interactions that facilitate self-assembly and the formation of hydrogen-bonded dimers, which implies the appearance of R22(8) graph-set motifs in this interaction. The stability of the dimeric unit is complemented by the formation of strong intramolecular C-S...O interactions of chalcogen character, with an S...O distance of 2.6040 (18) Å. Hirshfeld surface (HS) analysis revealed that O...H/H...O interactions were dominant, accounting for 36.8% of the total HS, and that N-H...N interactions were fundamental to the formation of the dimeric structure. The molecular electrostatic potential (MEP) map showed a maximum energy of 46.73 kcal mol-1 and a minimum of -36.06 kcal mol-1. The interaction energies of molecular pairs around NTFC are highest for those interactions linked by N-H hydrogen bonds. The properties of the NTFC ligand as a potential inhibitor of the DHODH (dihydroorotate dehydrogenase) enzyme were evaluated by molecular docking, showing coupling energies very close to those obtained with the control drug for rheumatoid arthritis, i.e. leflunomide.

Volumetric studies of solvation of carboxylic acids in aqueous, carbon tetrachloride, methanolic and methanolic-urea binary solutions at 298.15 K

Abstract Experimental measurements of density property at 298.15 K for aqueous, carbon tetrachloride, methanolic, and 3.0004 mol·kg−1 urea in methanol as solvent systems for binary solutions of carboxylic acids (propionic acid, n-butyric acid, n-valeric acid and n-caproic acid) are reported. The data of density are used to obtain apparent molar volume of acids at the finite concentrations of solute (Vϕ) which were appropriately extrapolated to infinitely dilute concentration of acid to obtain the limiting apparent molar volumes (Vϕ0). The calculations of volume changes due to dimerization equilibria (in carbon tetrachloride and aqueous solutions) are made and used to study the volume changes due to dimerization of acid molecules. The results of Vϕ in methanol-urea solvent system are explained on the basis of channel-like structure-formation for the species (urea and acid molecules) in solution phase. The negative volume changes observed in case of aqueous solutions are explained on the basis of hydrophobic hydration while the same in carbon tetrachloride solutions occurring with positive volume changes are interpreted in terms of hydrogen-bonded dimer formation equilibria. The Vϕ variation with acid concentrations has been explained on the basis of solute-solvent interactions foe studied acids in methanol while in aqueous solutions, the same has been attributed to ionization (limiting concentration range), hydrogen bonding and hydrophobic interactions.

Nanostructures from Self‐Assembling Triazine Tertiary Amine N‐Oxide Amphiphiles

A new set of amphiphilic tertiary amine N-oxides has been prepared and their self-assembly properties observed in aqueous solution by tensiometry, dynamic and static light scattering. X-ray crystallographic analysis of parent amines and sulfoxide congeners indicates the formation of hydrogen-bonded dimers as the primary assembly unit for formation of vesicles in preference to the compact micelles typical of lauryl dimethylamine N-oxide (LDAO). 6-Benzyloxy-N,N'-bis(5-diethylaminopentylamine oxide)[1,3,5]triazine-2,4-diamine forms a 1 μm vesicle observed to entrap fluorescein. The [1,3,5]triazine core thus allows variation of the new self-assembled structures from nano- to micrometre length scales.

Chiral solvating properties of ( S)-1-benzyl-6-methylpiperazine-2,5-dione

In CDCl 3 solution, enantiopure ( S)-1-benzyl-6-methylpiperazine-2,5-dione ( S)- 1a formed diastereomeric C O⋯ H–N hydrogen-bonded associates with racemic ( RS, Z)-1-benzyl-3-[(dimethylamino)methylidene]piperazine-2,5-diones 2a and 2b, ( RS)- tert-butyl pyroglutamate ( RS)- 2c and ( RS)- N-benzoylalanine methyl ester ( RS)- 2d. This resulted in splitting (doubling) of the characteristic signals in the 1H NMR and 13C spectra of racemic compounds 2a– d in the presence of 1 equiv of ( S)- 1a. The formation of hydrogen-bonded dimers in CDCl 3 solution was studied by 1H NMR, 13C NMR and 2D NMR and confirmed by the intermolecular NOE observed between the hydrogen-bonded amide protons from each of the monomeric units, ( S)- 1a and 2a– c. On the other hand, a slightly different binding mode was proposed for association of ( S)- 1a with alaninamide ( RS)- 2d. Enantiomer compositions of known (weighed) mixtures of both enantiomers of tert-butyl pyroglutamate 2c were re-determined by 1H NMR in the presence of ( S)- 1a in CDCl 3. The experimental values were in good agreement with the theoretical values, thus indicating the potential applicability of ( S)- 1a and related diketopiperazines as chiral solvating agents in NMR spectroscopy.

Tailor-made naphthyridines: Self-assembling multiple hydrogen-bonded supramolecular architectures from dimer to helix

Stepwise changes of functional oxo and amino groups in 1,8-naphthyridines to modify the supramolecular architecture have been carried out. The first example of a naphthyridine helix has been found and its structure established by X-ray crystallography. The design is based on hydroxy and amido tautomeric naphthyridines which crystallize in dimers or catemers, one of them attaining helicity. The most stable tautomer present in all the compounds discussed in this paper, as well as the formation of hydrogen-bonded dimers or catemers, was established by X-ray crystallography and rationalized with theoretical calculations.

Ozonolysis of oleic acid particles: evidence for a surface reaction and secondary reactions involving Criegee intermediates

The heterogeneous reactions of ozone with monodisperse oleic acid and methyl oleate particles were studied by monitoring the loss of the condensed-phase species using an aerosol chemical ionization mass spectrometer (Aerosol CIMS). The reaction of ozone with oleic acid was determined to occur at the surface of the particles despite previous assumptions that it reacts in the bulk. The ozonolysis of methyl oleate particles, on the other hand, was found to be limited by the diffusion of ozone and does react in the bulk. The difference in reaction mechanisms is attributed to the larger degree of order in oleic acid known to result from the formation of hydrogen-bonded dimers. The reactive uptake coefficients, gamma, calculated from the rate of loss of the particle species are gamma = (1.38 +/- 0.06) x 10(-3) for oleic acid and gamma = (1.23 +/- 0.10) x 10(-3) for methyl oleate. However, it is found that secondary reactions between Criegee intermediates and the carboxylic acid moiety in oleic acid are responsible for 36% (+/-4%) of its observed loss. Hence, the rate of loss of ozone cannot be equated to the rate of loss of oleic acid. Accounting for this additional reaction the uptake coefficient for ozone on oleic acid particles is calculated to be gamma = (8.8 +/- 0.5) x 10(-4). The magnitude of these secondary reactions quantitatively reconciles discrepancies between previous coated flow tube and particle-based studies, and it illustrates the need to include additional loss mechanisms when calculating uptake coefficients from the rates of loss of particle species. Implications of reactions with Criegee intermediates in atmospheric particles are discussed.

Hydrogen bond patterns in aromatic and aliphatic dioximes

Despite their established hydrogen bonding capability, oxime functional groups (–C(R′)NOH) have received far less attention in supramolecular chemistry than their carboxyl and amide counterparts. Here we report a series of dioximes (R′H, CH3, NH2) for which hydrogen bonding patterns have been examined in the solid state to establish the reliability of hydrogen-bonded synthons available for use in supramolecular syntheses using oximes. In all cases, network structures were formed, most frequently propagated through oxime–oxime O–H⋯N hydrogen-bonded dimer formation [R22(6) graph set] and less often using C(3) chain or R44(12) ring arrangements. Even in the systems where R′ = NH2, robust and dominant oxime–oxime hydrogen bonding prevails, with amino groups playing a supporting role in network construction primarily via weaker N–H⋯O hydrogen bonds. The compounds studied are aromatic dioximes 1,3-C6H4(C(R′)NOH)21–3 and 1,4-C6H4(C(R′)NOH)24–6 (R′ = H, CH3, NH2), and aliphatic dioximes fumaramide dioxime 7 (R′ = NH2) and succinamide dioxime 8 (R′ = NH2).

2,2'-Bipyridine-5-sulfonic acid

The title compound, C 10 H 8 N 2 O 3 S, exists as a zwitterion, 6-(2-pyridinio)pyridine-3-sulfonate, following deprotonation of the sulfonic acid group and protonation of the N atom of the unsubstituted pyridyl ring. The orientation of this N-H bond facilitates the formation of hydrogen-bonded dimers via two N-H...O hydrogen bonds.

Raman study of vibrational dephasing in hydrogen-bonded binary and ternary complexes of C 6H 5Cl and methanol

The shifts and linewidth changes of three vibrational modes of C 6H 5Cl were studied in hydrogen-bonded binary mixtures C 6H 5Cl+CH 3OH at various mole fractions of C 6H 5Cl, C=0.05, 0.1, 0.2, 0.3, 0.5, 0.7 and 0.9. The study reveals that the phenomena of motional narrowing and diffusion play simultaneous roles in the dephasing of the ring breathing and trigonal bending modes at ∼1000 and ∼1024 cm −1, respectively. Minima at C=0.7 and 0.2 in the Γ L versus C plot are explained by the formation of hydrogen-bonded dimer, C 6H 5Cl⋯HOCH 3, and trimer, C 6H 5Cl⋯(HOCH 3) 2, complexes. The dephasing of a third mode at ∼700 cm −1 is explained using the indirect dephasing model of Fischer–Laubereau.

Theoretical studies of liquids by computer simulations: the methanol-pyridine mixture

The Monte Carlo method was used to calculate thermodynamic properties and radial distribution functions for methanol-pyridine mixtures as a function of composition. All calculations were performed in the isothermal and isobaric ensemble at T = 298.15 K and p = 1.0 atm. The optimized potentials for liquid simulations (OPLS) force field was used for pyridine and methanol molecules. In the OPLS force field the methanol molecule is represented by a three-site model, as the methyl group is considered as a united atom site. Two potential models were used for pyridine: a six-site one with carbon and hydrogen atoms represented by united atom sites, and an eleven-site model with all atoms explicitly included. The partial charges used in the eleven-site model for pyridine are derived from ab initio 6–31G∗ wavefunctions. The results obtained for the average configurational energy of the methanol-pyridine system as a function of the mole fraction are in good agreement with experimental data. The partitioning of the total configurational energy shows comparatively weak interaction between methanol and pyridine molecules. The values obtained for the methanol-pyridine interaction energy are slightly more negative when the hydrogen atoms of pyridine are considered explicitly. The radial distribution functions calculated for methanol-pyridine correlation show characteristic features indicating the formation of hydrogen-bonded dimers. The position and amplitude of the peaks observed on these distribution functions depend on the particular model used to represent the pyridine molecules. The coordination numbers obtained for methanol-methanol interaction in the pure liquid and in the equimolar methanol-pyridine mixture are very similar, indicating a small influence of pyridine in the association of methanol molecules. Molecular graphics representation confirms the association of methanol molecules through hydrogen bonding in the bulk of the methanol-pyridine mixture.

Dimerization behavior of substituted dibenzo-14-crown-4 alcohols studied by NMR spectroscopy

Abstract Dibenzo-14-crown-4 alcohols are shown to aggregate in chloroform by the formation of hydrogen-bonded dimers. Structural variations between crown ether alcohols significantly affect the degree of dimerization. This self-association is of relevance for understanding the complexation and extractive properties of these and related macrocycles.