Spectroscopic study of hydrogen bonding in the enol form of β-diketones—II. Symmetry of the hydrogen bond

The effects of proton potential on the i.r. and Raman spectra of β-diketones are discussed. The spectroscopic behaviour of the asymmetric hydrogen bond stretching mode and of the out-of-plane hydrogen bond bending modes indicates a relatively high barrier double minimum potential.From the observed O…O distances and these predicted from the spectroscopic results for intermolecular H-bonds, a bent hydrogen bond was concluded. The spectroscopic data show a great change in the internal modes of β-diketones upon deuteration. This was attributed to the lengthening of the O…O distance which is a known characteristic of a double minimum potential.     

Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding

Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.     

IR spectroscopic study of the hydrogen bond network in the water–3-amino-1-propanol system and its comparison with the spatial network of hydrogen bonds in the water–monoethanolamine system

IR spectroscopy was used to explore the water–3-amino-1-propanol (3AP) system in the range of 400–4000 cm^-1. Based on the stretching vibrations of OH, NH₂ and CH groups and skeletal bending vibrations of 3AP it was concluded that mixed spatial networks are formed in the water–3AP system that predominate at medium 3AP concentrations. The obtained results are similar to the IR spectroscopic data for the water–monoethanolamine system, viz., the networks of both amino alcohols are incorporated into the spatial     

Hydrogen bond CH…O in a methanolic solution of hydrogen chloride

The existence of a hydrogen bond in which a methyl group of the (MeOH)₂H⁺ ion acts as a proton donor is examined. The fundamental vibration frequencies of this ion were calculated for different numbers and strengths of CH…O bonds. The atomic charges in neutral ((MeOH) _n ,n=1–4) and protonated ((MeOH) _m H⁺,m=2–6) associates of methanol molecules were also calculated. The experimentally observed decrease in the v(CH) vibration frequencies of the (MeOH)₂H⁺ ion to 2890 cm⁻¹ and 2760 cm⁻¹ is attributable to the fact that each methyl group of the ion is involved in formation of two CH…O bonds with strength of −12.5 kJ mol⁻¹. The proton-donating ability of the CH bond depends on the charge on its H atom; however, it does not correlate with the dipole moment of this bond. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 306–312, February, 1999.     

Spectroscopic study of hydrogen bonding in the enol form of β-diketones—I. Vibrational assignment and strength of the bond

The i.r. and Raman spectra of the trans-enol form of some β-diketones and their deuterated analogues in α position are examined in the 4000-50cm⁻¹ range and an approximate assignment is given for the fundamental vibrations. The ν_as(OH) and ν(CO) values suggest that the intramolecular H-bond strength increases in the order: hexafluoroacetylacetone < trifluoroacetylacetone < acetylacetone < α - Cl - acetylacetone < benzoylacetone < dibenzoylmethane < tetraacetylethane.The observed relative Raman intensities of the ν(CC) and ν(CC) bands also support this feature. The spectroscopic results show a great change in the internal modes of the β-diketones upon deuteration; this behaviour indicates a greater localization of the π-electron system of the chelate ring and a weakening of the H-bond on deuteration. The ν_s(OH) vibration seems to be involved in one of the in-plane ring deformational modes.     

1,1-Diamino-2-nitroethylenes as excellent hydrogen bond donor organocatalysts in the Michael addition of carbon-based nucleophiles to β-nitrostyrenes

A new class of hydrogen bond donor catalysts based on the 1,1-diamino-2-nitroethylene scaffold has been introduced for the activation of trans-β-nitrostyrenes toward reactions with a range of carbon-based nucleophiles, affording the corresponding adducts in excellent yields. Importantly, this new set of organocatalysts is easily prepared from commercially available starting materials in mild reaction conditions.     

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.     

A new insight on hydrogen bond donor property of bridged B–H–B protons in the interaction of diborane with some hydrogen bond acceptor molecules

Structural Chemistry - Ab initio calculations at the MP2/6-311++G(d,p) computational level were used to analyze the interactions between a molecule of B2H6 with some small molecules which often...     

The reactivity of tert-butoxyl radicals in reactions of hydrogen abstraction and β-elimination

The transition states of competing reactions of abstraction of the H atom from hydrocarbon molecules by tert-butoxyl radical and its -elimination were studied by the semiempirical quantum-chemical AM1 method. The calculated activation enthalpy and entropy of these reactions correlate with the experimental values. A correlation between the reactivity in homolytic hydrogen abstraction and the parameters of the chemical structure of the reactants was found.     

Synthesis and crystal structure of β-hexanitrohexaazaisowurtzitane

A polycyclic caged compound with high strain—hexanitrohexaazaisowurtzitane (HNIW)—has been synthesized via a three-step reaction: condensation, hydrogenolysis debenzylation and nitrolysis, starting with benzylamine and glyoxal. HNIW is the most powerful high energy density compound (HEDC) ever tested. β-HNIW possesses a caged structure consisting of two five-membered rings and one six-membered ring with a nitro group attached to each of the six bridging nitrogens. The nitro group lies basically within a plane. The lengths of C—C bonds of β-HNIW range from 0. 156 nm to 0.159 nm, 0.002–0.005 nm longer than the sp³ C-C bond. The β-HNIW’s crystal belongs to orthorhombic system and space groupPca2₁ with parameters:a = 0.9670 (2),b = 1.1616 (2),c = 1.3032 (3) nm;V = 1.4638(5) nm³,Z = 4; D_c = 1.989 g/cm³ and D_m = 1.982 g/cm³. Project supported by the Advanced Research Funds (12060451867) from the Commission of Science and Technology for National Defence.     

Synthesis and crystal structure of β-hexanitrohexaazaisowurtzitane

A polycyclic caged compound with high strain——hexanitrohexaazaisowurtzitane (HNIW)——has been synthesized via a three-step reaction: condensation, hydrogenolysis debenzylation and nitrolysis, starting with benzylmine and glyoxal. HNIW is the most powerful high energy density compound (HEDC) ever tested. β-HNIW possesses a caged structure consisting of two five-membered rings and one six-membered ring with a nitro group attached to each of the six bridging nitrogens. The nitro group lies basically within a plane. The lengths of C--C bonds of β-HNIW range from 0.156 nm to 0.159 nm, 0.002--0.005 nm longer than the sp~3 C-C bond. The β-HNIW's crystal belongs to orthorhombic system and space group Pca2_1 with parameters: a=0.9670 (2), b=1.1616 (2), c=1.3032 (3) nm; V=1.4638(5) nm~3, Z=4; D_c=1.989 g/cm~3 and D_m=1.982 g/cm~3.     

Function of the hydrogen bond in the conversion of α- to β-Mo8O264− ions: Formation and structure of tetra(tributylhydrogenammonium) β-octamolybdate

Complex β-(Bu₃NH)₄Mo₈O₂₆ has been transformed from α-(Bu₄N)₄Mo₈O₂₆ in the presence of o-mercaptophenol (H₂mp) and CuCl₂ in MeOH, and structurally characterized. It can be considered as a dimer [(Bu₃NH)₂Mo₄O₁₃]₂ with a center of symmetry. Each molybdenum atom is in a severely distorted octahedral environment. Two types of H bond between the cations and the anions have been found in the complex: N–H⋯O and C–H⋯O, which may play important roles in the α→β transformation.     

Intramolecular hydrogen bond energy and cooperative interactions in α-, β-, and γ-cyclodextrin conformers

Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs). Further, the structure and stability of different conformers of α-, β-, and γ-CDs are explained based on the energetics and cooperative contribution to the strength of these H-bonds. The estimated O-H···O H-bond energies in the various CD conformers are found to vary widely from 1.1 to 8.3 kcal mol(-1). The calculated energy contributions to cooperativity toward the H-bond strengths fall in the range of 0.25-2.75 kcal mol(-1).     

O?O bond homolysis in hydrogen peroxide

O O bond homolysis in hydrogen peroxide (H₂O₂) has been studied using theoretical methods of four conceptually different types: hybrid DFT (B3LYP, M06‐2X), double‐hybrid DFT (B2‐PLYP), coupled‐cluster (CCSD(T)), and multiconfigurational (CASPT2). In addition, the effects of basis set size have also been analyzed. For all of these methods, the O O bond homolysis in hydrogen peroxide has been found to proceed through hydrogen bonded radical pair complexes. Reaction barriers for collapse of the radical pairs to hydrogen peroxide are minute, leading to an overall very flat potential energy surface. However, hydrogen bonding energies in the radical pair complex expressed as the energy difference to two separate hydroxyl radicals are sizeable and exceed 10 kJ/mol for all theoretical methods considered in this study. © 2017 Wiley Periodicals, Inc.     

Liquid crystal polymorphism of boron difluoride β-diketonates

Boron difluoride 2-alkyl-β-diketonates possessing liquid crystal polymorphism and luminescence properties were first obtained. Influence of the ligand structure on the liquid crystal properties of the boron difluoride complexes was demonstrated.     

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.     

N-Cα bond cleavage of the peptide backbone via hydrogen abstraction

The specific cleavage of N-C_α bonds on the peptide backbone to form the so-called ‘c’ and ‘z + 2’ products, which can be used for the rapid determination of protein amino-acid sequences, has been examined to clarify the mechanism(s) that occur during hydrogen abstraction induced by bombardment with 337-nm laser photons in matrix-assisted laser desorption/ionization (MALDI) method. Intramolecular hydrogen abstraction, which results from the hydrogen(s) on the C_α or C_β carbon, did not occur with a deuterium-labeled dodecapeptide. To confirm a proposition that intermolecular hydrogen abstraction occurs between the peptide and the MALDI matrix, a deuterium dodecapeptide embedded in a deuterium 2,5-dihydroxybenzoic acid matrix at a molar ratio of 1:7000 was analyzed. The resulting deuterium c product ions suggested that c ions form via intermolecular hydrogen abstraction, although the results obtained did not deny any other possibilities such as intramolecular transfer of labile hydrogen. A mechanism for the N-C_α bond cleavage has been proposed that the formation of hypervalent radical species and subsequent prompt bond cleavages occur. The proposed mechanism successfully rationalizes the formation of both the z + 2 and the c product ions.     

Solid–solvent molecular interactions observed in crystal structures of β-chitin complexes

Three β-chitin structures [anhydrous, di-hydrate, mono-ethylenediamine (EDA)] recently determined by synchrotron X-ray and neutron fiber diffraction were reviewed from the viewpoint of molecular interactions. Both water and EDA molecules interact with the chitin chains through multiple hydrogen bonds. When water complexes with chitin, the hydrogen bonding pattern rearranges with the replacement of an intrachain chitin hydrogen bond by a stronger hydrogen bond between chitin and water, with an associated reduction in the degrees of freedom; the water oxygen is a much stronger acceptor than the O5 ring atom. The behavior of hydrogen exchange by deuterium supports this interpretation. EDA-molecules change the conformation of hydroxymethyl group from gg to gt, accompanied by changes in hydrogen bonds due to the strong accepting ability of the EDA nitrogen atoms. Some important interactions are in common with experimental crystallographic results of cellulosic crystals and of molecular dynamics studies. These new insights into solid–solvent interactions are valuable in understanding molecular interactions in other polysaccharides-solvents system in solution or on surface.     

Host–guest system of Vitamin B10 in β-cyclodextrin: characterization of the interaction in solution and in solid state

Conventional drugs are usually formulated for the immediate release of the medicinal substances and for obtaining the desired therapeutic effect. The aim of this paper was to investigate the possible interactions between Vitamin B10 and β-cyclodextrin (β-CD), to determine the physical-chemical characteristics and the interactions present in the corresponding inclusion compound. The so-obtained compounds were characterized by X-ray diffraction, DSC and FTIR spectroscopy. ¹H NMR and UV–vis spectroscopic methods were employed to study the inclusion process in aqueous solution. The X-ray powder diffraction patterns demonstrate the inclusion compound formation, especially for the lyophilized product where the amorphous phase dominates. The existence of the inclusion compounds obtained by different methods was confirmed by comparing with DSC and FTIR data of the pure compounds and the (1:1) Vitamin B10:β-CD physical mixture (pm). ¹H NMR measurements on aqueous solutions of Vitamin B10 and β-CD in D₂O allowed us to establish the corresponding Vitamin B10’s and cyclodextrin’s protons implied in the complexation process. 2D NMR spectroscopy established the geometry of the inclusion complex. ¹H NMR, UV–Vis and fluorescence data were used to obtain the stoichiometry and the stability constant of the complex.