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…     

Synthesis of a fluorescein–porphyrin hybrid and its supramolecular self-assembly with amino-porphyrinatocopper(II) by hydrogen bonding

A fluorescein–porphyrin hybrid (Fl-PTPP) has been synthesized and characterized by UV/Vis, IR, ¹H NMR, ES-MS and elemental analysis. The supramolecular self-assembly of Fl-PTPP with the copper(II) complex of 5-(p-amino-phenyl)-10,15,20-triphenylporphyrin, (CuAPTPP), by hydoxyl-amino type hydrogen bonding was studied using vapor pressure osmometry (VPO) measurements, ES-MS, UV/Vis, ¹H NMR and fluorescence spectroscopic titration. The data indicate formation of a (Fl-PTPP)–CuAPTPP supramolecular complex. Fluorescence strengthening character was observed in a spectroscopic titration experiment for the Fl-PTPP/CuAPTPP system. The association constant of the supramolecular complex was calculated from the fluorescence titration data, and found to be less than that of a carboxyl–carboxyl type hydrogen-bonding system.     

Unique interactions between diborane and pi orbitals: blue- or red-shifted hydrogen bonding?

A new type of hydrogen-bonding interaction in the diborane (B 2H 6)...pi (benzene C 6H 6, 1,3-cyclopentadiene C 5H 6, and cyclobutadiene C 4H 4) system is identified with the natural bond orbital and atoms-in-molecules analyses based on ab initio calculations. In comparison with the symmetric and asymmetric stretching vibrational modes of the bridging hydrogen atoms in free B 2H 6, the frequencies of the symmetric mode are red-shifted for B 2H 6...C 6H 6 and B 2H 6...C 5H 6 but blue-shifted for B 2H 6...C 4H 4. The frequency blue shifts of the asymmetric mode are found for all three complexes; the most significant blue shift is 14.73 cm (-1) for the asymmetric mode in B 2H 6...C 4H 4. In these complexes, the electron-deficient three-center two-electron bond B-H 1-B facing the pi orbital is shortened, while the opposite B-H 2-B bond is elongated.     

Strong phenyl-perfluorophenyl π-π stacking and C-H?F-C hydrogen bonding interactions in the crystals of the corresponding aromatic aldimines

The X-ray diffraction analysis of two co-crystals, 1·2 (aldimines 1 and 2) and 3·4 (aldimines 3 and 4), reveals that there are strong phenyl-perfluorophenyl π-π stacking and intermolecular hydrogen bonding interactions. The new perfluoroaryl-aryl face-to-face interaction of the crystalline aldimines provides a design motif for a new class of self-assembling system.     

Phase equilibria of supercritical CO_2-ethanol-stearic acid ternary system and hydrogen bonding between ethanol and stearic acid

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Hydrogen bonding interactions between α-, β-glucose,and methacrylic acid

Intermolecular interactions between α-, β-glucose, and methacrylic acid (MAA) have been investigated. Twenty-two possible conformations have been optimized at the DFT(B3LYP) level of theory with the 6-31G(d) basis set. The geometrical parameters for the most stable configurations of hydrogen bonding sites in the optimized systems have been determined. The binding energies ΔE _bind have been calculated at the MP2/6-311++G(d,p) level of approximation taking into account the basis set superposition error (BSSE) and the zero-point vibrational energies corrections. Results indicate that the most stabilized complexes form hydrogen bonds either through carboxylic and hemiacetal oxygen atoms acting as proton acceptors. Both, α- and β-anomers are studied in the pyranose six-membered ring. In all complexes, the nuclear quadrupole coupling constants (χ) for ¹⁷O nuclei were obtained about 10.0 MHz, while for the ²H atoms they vary from ≈200.0 to ≈350.0 kHz.     

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol⁻¹. This value increases by ca. 1 kcal mol⁻¹ on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol⁻¹ depending on the structure of the β-diketone in question.     

New supramolecular liquid crystals induced by hydrogen bonding between pyridyl‐1,2,4‐oxadiazole derivatives and 2,5‐thiophene dicarboxylic acid

Supramolecular liquid crystalline complexes were obtained from binary mixtures of 3‐(4‐pyridyl)‐5‐(4‐n‐alkoxy)phenyl‐1,2,4‐oxadiazoles and 2,5‐thiophene dicarboxylic acid. Although the oxadiazole derivatives and the dicarboxylic acid are non‐mesomorphic, the H‐bonded complexes exhibit mesomorphism. Their liquid crystalline properties were investigated by differential scanning calorimetry and polarizing optical microscopy. The complexes exhibit enantiotropic nematic phases. A structural study involving AM1 semi‐empirical calculations is also described.     

Formation of 1-D ladder- and 2-D sheet-like networks due to stereospecific π–π stacking and hydrogen bonding between enantiomeric sulfur-bridged dinuclear complexes of penicillaminates

Reaction of trans(N)-[Co(D-pen)₂]^? (pen = penicillaminate) or trans(N)-[Co(L-pen)₂]^? with [MCl₂(L)] {M = Pd or Pt, L = 2,2′-bipyridine (bpy) or 1,10-phenanthroline (phen)} in the presence of tetrafluoroborate stereoselectively gave an optically active S-bridged dinuclear complex, [M(L){Co(D-pen)₂}]BF₄ · 2H₂O or [M(L){Co(L-pen)₂}]BF₄ · 2H₂O. The mixture of equimolar amounts of these enantiomers in H₂O crystallizes as [M(L){Co(D-pen)₂}]_0.5[M(L){Co(L-pen)₂}]_0.5BF₄ · 4H₂O (DLbpyM · 4H₂O, DLphenM-A · 4H₂O), in which the enantiomeric complex cations are included by the ratio of 1 : 1. In crystals of DLbpyM · 4H₂O and DLphenM-A · 4H₂O, [M(L){Co(D-pen)₂}]⁺ and [M(L){Co(L-pen)₂}]⁺ interact stereospecifically with each other through π-conjugated systems to form dimeric structures. Other racemic crystals with the same chemical compositions as DLphenM-A · 4H₂O, DLphenM-B · 4H₂O, were obtained from equimolar amounts of [M(phen){Co(D-pen)₂}]⁺ and [M(phen){Co(L-pen)₂}]⁺ in aqueous acetonitrile solution. In the crystals of DLphenM-B · 4H₂O, [M(phen){Co(D-pen)₂}]⁺ and [M(phen){Co(L-pen)₂}]⁺ are arranged alternately while overlapping phen planes, and the π electronic systems of phen interact with each other. Although stereospecific hydrogen bonds between the coordinated ?NH₂ and ?COO^? groups are formed in both DLphenM-A · 4H₂O and DLphenM-B · 4H₂O, their bonding modes differ noticeably from each other. As a result, DLphenM-A · 4H₂O builds up 1-D ladder-like networks due to the stereospecific π–π stackings and hydrogen bondings between enantiomers, while 2-D sheet-like networks are established for DLphenM-B · 4H₂O.     

Structures and IR/UV spectra of neutral and ionic phenol-Ar(n) cluster isomers (n ≤ 4): competition between hydrogen bonding and stacking

The structures, binding energies, and vibrational and electronic spectra of various isomers of neutral and ionic phenol-Ar(n) clusters with n ≤ 4, PhOH((+))-Ar(n), are characterized by quantum chemical calculations. The properties in the neutral and ionic ground electronic states (S(0), D(0)) are determined at the M06-2X/aug-cc-pVTZ level, whereas the S(1) excited state of the neutral species is investigated at the CC2/aug-cc-pVDZ level. The Ar complexation shifts calculated for the S(1) origin and the adiabatic ionisation potential, ΔS(1) and ΔIP, sensitively depend on the Ar positions and thus the sequence of filling the first Ar solvation shell. The calculated shifts confirm empirical additivity rules for ΔS(1) established recently from experimental spectra and enable thus a firm assignment of various S(1) origins to their respective isomers. A similar additivity model is newly developed for ΔIP using the M06-2X data. The isomer assignment is further confirmed by Franck-Condon simulations of the intermolecular vibrational structure of the S(1) ← S(0) transitions. In neutral PhOH-Ar(n), dispersion dominates the attraction and π-bonding is more stable than H-bonding. The solvation sequence of the most stable isomers is derived as (10), (11), (30), and (31) for n ≤ 4, where (km) denotes isomers with k and m Ar ligands binding above and below the aromatic plane, respectively. The π interaction is somewhat stronger in the S(1) state due to enhanced dispersion forces. Similarly, the H-bond strength increases in S(1) due to the enhanced acidity of the OH proton. In the PhOH(+)-Ar(n) cations, H-bonds are significantly stronger than π-bonds due to additional induction forces. Consequently, one favourable solvation sequence is derived as (H00), (H10), (H20), and (H30) for n ≤ 4, where (Hkm) denotes isomers with one H-bound ligand and k and m π-bonded Ar ligands above and below the aromatic plane, respectively. Another low-energy solvation motif for n = 2 is denoted (11)(H) and involves nonlinear bifurcated H-bonding to both equivalent Ar atoms in a C(2v) structure in which the OH group points toward the midpoint of an Ar(2) dimer in a T-shaped fashion. This dimer core can also be further solvated by π-bonded ligands leading to the solvation sequence (H00), (11)(H), (21)(H), and (22) for n ≤ 4. The implications of the ionisation-induced π → H switch in the preferred interaction motif on the isomerisation and fragmentation processes of PhOH((+))-Ar(n) are discussed in the light of the new structural and energetic cluster parameters.     

Syntheses and structures of nickel(II) and copper(II) complexes with biacetyl bis(benzoylhydrazone): one-dimensional self-assembly via π–π interaction and hydrogen bonding

Reactions of Ni(O₂CCH₃)₂·4H₂O and Cu(O₂CCH₃)₂·H₂O with biacetyl bis(benzoylhydrazone) (H₂babh) in alcoholic media afford mononuclear nickel(II) and copper(II) complexes of general formula [M(babh)]. The complexes have been characterized by microanalysis (C, H, N), magnetic susceptibility, and various spectroscopic measurements. X-ray structures of both complexes have been determined. The metal centre in [Ni(babh)] is in square-planar N₂O₂ environment provided by the tetradentate babh²⁻. On the other hand, [Cu(babh)] crystallizes as distorted square-pyramidal [Cu(babh)(CH₃OH)] from methanol. Here the tetradentate babh²⁻ constitutes the N₂O₂ square-base and the O-coordinating methanol occupies the apical site. In the crystal lattice, the molecules of [Ni(babh)] form a one-dimensional π-stacked structure. The [Cu(babh)(CH₃OH)] molecules also form a one-dimensional structure with alternating long and short Cu···Cu distances via intermolecular O–H···N hydrogen bonding and π–π interaction.     

UV spectroscopic study of the interaction betweenα-,β-, andγ-cyclodextrins and pyridine derivatives

Complex formation between-,- and-cyclodextrins and some pyridine derivatives (hydroxy,O- andN-methyl) have been investigated by UV spectroscopy. Inclusion processes do not exert any noticeable influence on the UV absorption spectra of most of the guests which do not give rise to tautomeric equilibria or which show a strong prevalence for one of the tautomeric forms. In contrast, the equilibrium between the lactim and the lactim forms of 3-hydroxypyridine (which are present in comparable amounts in aqueous solution) was shown to be markedly affected by the inclusion process with a preferential complexation of the latter tautomer.     

Are C-H groups significant hydrogen bonding sites in anion receptors? Benzene complexes with Cl-, NO3-, and ClO4-

Theoretical calculations,examination of crystallographic data, and experimental binding energies suggest that even in the absence of electron-withdrawing substituents, simple arenes such as benzene form hydrogen bonds with anions that can exceed 50% of the strength of those formed by O-H and N-H groups. Thus, when present in a receptor, even moderately acidic C-H groups can significantly enhance the anion binding affinity and they should be considered as additional binding sites within the host cavity.     

Analysis of binding interaction between (-)-epigallocatechin (EGC) and β-lactoglobulin by multi-spectroscopic method

The binding interaction between (−)-epigallocatechin (EGC) with bovine β-lactoglobulin (βLG) was investigated by fluorescence, circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy methods. The binding parameters were determined by Stern–Volmer equation and the thermodynamic parameters were calculated according to the van’t Hoff equation. The results suggested that βLG was bound by EGC, which resulted in change of native conformation of βLG. van der Waals interactions and hydrogen bonding probably played major roles in the binding process. Our study is helpful for further elucidation of binding interactions between catechins with milk proteins, which would contribute to the development of novel milk products.     

Competition between hydrogen bonding and dispersion interactions in the indole···pyridine dimer and (indole)2···pyridine trimer studied in a supersonic jet

Structures of the indole···pyridine dimer and (indole)2···pyridine trimer have been investigated in a supersonic jet using resonant two-photon ionization (R2PI) and IR-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. R2PI spectra of the dimer and the trimer recorded by electronic excitation of the indole moiety show that the red-shift in the band origin of the dimer with respect to the 0(0)(0) band of the monomer is larger compared to that of the trimer. The presence of only one conformer in the case of both the dimer and the trimer has been confirmed from IR-UV hole-burning spectroscopy. The structures of the dimer and the trimer have been determined from resonant ion dip infrared (RIDIR) spectra combined with ab initio as well as DFT/M05-2X and DFT/M06-2X calculations. It has been found that the dimer, observed in the experiment, has a V-shaped geometry stabilized by N–H···N and C–H···N hydrogen bonding interactions, as well as C–H···π and π···π dispersion interactions. The geometry of the trimer has been found to be a cyclic one stabilized by N–H···N, N–H···π, C–H···π, and C–H···N interactions. The most important finding of this current study is the observation of the mixed dimer and trimer, which are stabilized by hydrogen bonding as well as dispersion interactions.     

Stabilization of β-hairpin structures via inter-strand π-π and hydrogen bond interactions in α-, β-, γ-hybrid peptides

Synthesis and conformational studies of α-, β-, γ-hybrid peptides containing a pyrrole amino acid (Paa, 1) and a furan amino acid (Faa, 2), namely Boc-β-Phe-Faa-d-Pro-Gly-Paa-β-HGly-Faa-OMe (3) and Boc-Paa-β-Phe-Faa-d-Pro-Gly-Paa-β-HGly-Faa-OMe (4), were carried out and they adopt β-hairpin structures stabilized via inter-strand π-π and hydrogen bonding interactions.     

Stereoselective Synthesis of(Z)-α-Alkylidene-γ-Butyrolactones via Pd-Catalyzed CO Insertion and Cyclization

Four new (Z)-2-phenoxymethylene-α-pentanolide derivatives and four (Z)-2-phenoxymethyl-2-penten-γ-lactone derivatives were prepared via Pd-catalyzed carbon monoxide insertion and intramolecular cyclization. All compounds were characterized by IR, 1H NMR, 13C NMR, MS spectra and elemental analysis. The plausible mechanism of the reaction was discussed.     

(±)-3-(3-Oxo­cyclo­hexyl)­propionic acid: dual conformational selection and hydrogen bonding in an ɛ-keto acid

The asymmetric unit of the title compound, C₉H₁₄O₃, consists of two mol­ecules having conformations that differ by a rotation of 111.7 (5)° about the equatorial substituent bond, so that the side chains of the two species extend away from the ring in different directions. Each conformer forms centrosymmetric hydrogen-bonded acid-to-acid dimers with its own enantiomer [O⋯O = 2.681 (3) and 2.698 (4) Å]. There is an intermolecular C—H⋯O close contact involving the ketone group of one of the conformers.     

How Strong Is the Coordination Bond between a Histidine Tag and Ni - Nitrilotriacetate? An Experiment of Mechanochemistry on Single Molecules

Isolation of a His-tagged protein by means of a Ni - nitrilotriacetate-functionalized chromatographic matrix or biosensor was simulated in a single-molecule experiment, and the mechanochemistry-that is, the interplay between mechanical and chemical forces (shown schematically)-was studied with a scanning force microscope.