An intramolecular ionic hydrogen bond stabilizes a cis amide bond rotamer of a ring-opened rapamycin-degradation product

Rapamycin (1), a macrolide immunosuppressant, undergoes degradation into ring-opened acid products 2 and 3 under physiologically relevant conditions. The unsaturated product (3) was isolated and studied in this work. Unlike 1, which has its amide primarily in a trans conformation in solution, 3 has both cis and trans conformations in approximately a 1:1 ratio in dimethyl sulfoxide (DMSO). The amount of cis rotamer was increased dramatically in the presence of an organic base such as triethylamine. The detailed NMR results indicate that the cis rotamer is stabilized through an intramolecular ionic hydrogen bond of the carboxylate anion with the tertiary alcohol as part of a nine-membered ring system. This hydrogen bond was characterized further in organic media and the trans-cis rotamer equilibria were used to estimate the relative bond strengths in several solvents. The additional stabilization arising from this ionic hydrogen bond in the cis rotamer was determined to be 1.4 kcal mol(-1) in DMSO-d6, 2.0 kcal mol(-1) in CD3CN and 1.1 kcal mol(-1) in CD3OD.     

Low-barrier hydrogen bond between phosphate and the amide group in phosphopeptide

As the conversion between the monoionic (1) and diionic (2) form of the phosphate occurs, the phosphorylated peptides or proteins can not only cause the formation of a hydrogen bond between the phosphate group and the amide group but also change the strength of the hydrogen bond to form low-barrier hydrogen bonds (LBHBs). This reversible protonation of the phosphate group, which changes both the electrostatic properties of the phosphate group and the strength of the hydrogen bond, provides a possible mechanism in regulating protein function.     

Two-dimensional model of intramolecular hydrogen bond

One- and two-dimensional vibrational problems were solved to determine the states of H and D in the intramolecular hydrogen bond of malonic dialdehyde. Within the one-dimensional approach the model potential (barrier height 51 kJ/mol) satisfied with the IR and microwave spectroscopy data. For the two-dimensional problem an approach to evaluation of eigenvalues with high accuracy based on the Ritz method was developed. Within the two-dimensional approximation the barrier height was taken to be 57 kJ/mol. An introduction of the second dimension was found to give rise to the vibrational non-adiabatic effects.     

Manipulation of an intramolecular NH...O hydrogen bond by photoswitching between stable E/Z isomers of the cinnamate framework

Novel carboxylic acid derivatives were synthesized, which allowed switching of the intramolecular distance between amide group and carboxylic oxygen atoms using E to Z photoisomerization of the cinnamate framework. An intramolecular NH...O hydrogen bond was formed in the Z carboxylate compound not only in solution but also in the solid state. The pK(a) value of the carboxylic acid was lowered as a consequence of the E/Z photoisomerization.     

The intramolecular hydrogen bond in 2-hydroxy-benzamides

The two crystal structures of 5-chloro-2-hydroxy-benzamide and 2-hydroxy-N,N-diethyl-benzamide were determined by X-ray diffraction at 100 K. The intramolecular and intermolecular hydrogen bonds were found in these structurally similar 2-hydroxy-benzamides. Analysis of the hydrogen bonding was carried out on the basis of X-ray data, infrared spectra, and DFT calculations. Disruption of the intramolecular hydrogen bonding in the solid state by a steric effect is shown. Conformational analysis and potential energy calculations as functions of the turning angle around the C_aryl–C_alkyl bond were conducted. The values obtained for the HOMA index indicate mutual compensation of the amide and hydroxyl groups (due to the high degree aromaticity of the phenyl ring).     

Photoinduced intramolecular electron transfer between fluorescein and carbazole

Several dyads consisting of a fluoreseein covalently linked with a carhazole at site 2 or site 6 have been synthesized and characterized.Studies of absorption spectra,emission spectra and fluorescence lifetime quern hing Indicate that the ground-state interaction between fluorescein and carhazole in dyads is negligible and the intramolecular electron transfer (ET) reactions are mainly of dynamic process.Moreover,the efficiency and raie conslam of lectron transfer reactions in ZFO4 (carbazole linked at site 2'of fluorescein) are larg er than those in 4FOZ (carbazole linked at site 6 of fluorescein) 0 74; KET 11×108S-1),because the mutual orientation of donor and acceptor in ZFO4 is nearly face-to-face,which is more favorable to the process than the shoulder-to-shoulder mutual orientation in 4FOZ.Estimations are also formed of the free energy change of the photomduced electron transfer and the back reactions in the dyads.     

Photoinduced intermolecular and intramolecular actions between eosin and porphyrin

Two dyads of eosin and porphyrin linked with a semi-rigid (-CH2phCH2-) or flexible (-(CH2)4-) bridge and their reference model compounds were synthesized and characterized The intermoleccular interaction and intramolecular photoinduced singlet energy transfer and electron transfer were studied by their absorp tion spectra,fluorescence emission,excitation spectra and fluorescence lifetime The model compounds,ethyl ester of eosm (EoEt) and porphyrin (PorEt),could form complexes in the ground state.When the eosin moieties in dyads were excited,they could transfer some singlet energy to the porphyrins; in the meantime,they could also ndsce electron transfer between two chromophores.Exciting the porphyrin moieties in dyads could induce electron transfer from eosin moieties to porphyrin moieties.The efficiencies (EnT,ET) and rate constants (kEnT,kET) were related to the polarity of solvents and mutual orientation of the two chromophores in dyads.     

Investigating the effect of hydrogen bonding environments in amide cleavage reactions at zinc(II) complexes with intramolecular amide oxygen co-ordination

Amide oxygen co-ordination to a zinc(II) ion around a hydrogen bonding microenvironment is a common structural/functional feature of metalloproteases. We report two strategies to position hydrogen bonding groups in the proximity of a zinc(II)-bound amide oxygen, and we investigate their effect on the stability of the amide group. Polydentate tripodal ligands (6-R1-2-pyridylmethyl)-R2 (R1= NHCOtBu, R2= N(CH2-py-6-X)2 X = H L1, X = NH2, H L2, X = NH2 L3) form [(L)Zn]2+ cations (L =L1, 1; L2, 2; L3, 3) with intramolecular amide oxygen co-ordination (1-3), and intramolecular N-H...O=C(amide) hydrogen bonding (2, 3) rigidly fixed by the ligand framework. 1-3 undergo cleavage of the tert-butyl amide upon addition of Me4NOH.5H2O (1 equiv.) in methanol at 50(1) degrees C. Under these conditions the half-life, t(1/2), of the amide bond is 0.4 h for 1, 9 h for 2 and 320 h for 3. Mononuclear zinc(II) complexes of (6-NHCOtBu-2-pyridylmethyl)-R2(R2= N(CH2CH2)2S) L4 and chelating N2 ligands without hydrogen bonding groups (1,10-phenanthroline L5, 2-(aminomethyl)pyridine L6) as control compounds, and with an amino hydrogen bonding group (6-amino-2-(aminomethyl)pyridine L7) have been synthesised. Amide cleavage is in this case faster at the zinc(II) complex with the amino hydrogen bonding group. Thus, hydrogen bonding environments can both accelerate and slow down amide bond cleavage reactions at zinc(II) sites. Importantly, the magnitude of the effect exerted by the hydrogen bonding environments was found to be significant; 800-fold rate difference. This result highlights the importance of hydrogen bonding environments around metal centres in amide cleavage reactions, which may be relevant to the chemistry of natural metalloproteases and applicable to the design of more efficient artificial protein cleaving agents.     

New liquid-crystalline compounds with an intramolecular hydrogen bond

Abstract

New liquid-crystalline compounds with an intramolecular hydrogen bond are presented. They are derived from 2-methylalkanoic acid and resorcinol. The spontaneous polarization of the new compounds is larger than that of the analogues without the hydrogen bond. This paper details the method of synthesis and their physical properties.     

New liquid-crystalline compounds with an intramolecular hydrogen bond

New liquid-crystalline compounds with an intramolecular hydrogen bond are presented. They are derived from 2-methylalkanoic acid and resorcinol. The spontaneous polarization of the new compounds is larger than that of the analogues without the hydrogen bond. This paper details the method of synthesis and their physical properties.     

Molecular structure of dipivaloylmethane and the intramolecular hydrogen bond problem

Molecular structure of dipivaloylmethane was investigated by X-ray electron diffraction at 24°C. The C_2v and C_s geometrical models involving an intramolecular hydrogen bond are considered. The C_2v model with enol hydrogen lying symmetrically relative to the oxygen atoms has several advantages over the classical model of the enol tautomer. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 58-66, January–February, 2000     

Influence of intramolecular hydrogen bond strength on OH-stretching overtones

Vapor-phase OH-stretching overtone spectra of 1,3-propanediol and 1,4-butanediol were recorded and compared to the spectra of ethylene glycol to investigate the effect of increased intramolecular hydrogen bond strength on OH-stretching overtone transitions. The spectra were recorded with laser photoacoustic spectroscopy in the second and third OH-stretching overtone regions. The room-temperature spectra of each molecule are dominated by two conformers that show intramolecular hydrogen bonding. Anharmonic oscillator local-mode calculations of the OH-stretching transitions have been performed to aid assignment of the different conformers in the spectra and to illustrate the effect of the intramolecular hydrogen bonding. The hydrogen bond strength increases in the order ethylene glycol, 1,3-propanediol, and 1,4-butanediol. The overtone transitions of the hydrogen-bonded hydroxyl groups are more difficult to observe with increasing intramolecular hydrogen bond strength. We suggest that the bandwidth of these transitions increases with increasing hydrogen bond strength and with increasing overtone and furthermore that these changes are in part responsible for the lack of observed overtone spectra for complexes.     

The effect of intramolecular interactions on hydrogen bond acidity

DFT calculations on a range of molecules containing intramolecular hydrogen bonds are reported, with a view to establishing how intramolecular hydrogen bonding affects their intermolecular interactions. It is shown that properties such as the energy of the intramolecular H-bond are unrelated to the ability to form external H-bonds. Conversely, several properties of complexes with a reference base correlate well with an experimental scale of H-bond acidity, and accurate predictive models are determined. A more detailed study, using electrostatic and overlap properties of complexes with a reference base, is used to predict the location, as well as strength, of hydrogen bond acidity. The effects of intramolecular hydrogen bonding on acidity can be seen not just on O-H and N-H, where acidity is greatly reduced, but also on certain C-H groups, which in some cases become the primary source of acidity.     

Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.     

The intramolecular hydrogen bond in ortho-hydroxy acetophenones

The crystal structures of two ortho-hydroxy ketones (5-chloro-2-hydroxyacetophenone (I K) and 3,5-dichloro-2-hydroxyacetophenone (II K)) have been determined with X-ray diffraction at 100 K. A comparison of steric effects on properties of pseudoaromatic hydrogen bonds in ortho-hydroxy acetophenone and ortho-hydroxy ketimines have been carried out with the application of crystallographic data.

Nuclear quadrupole resonance (NQR) spectra have been measured and interpreted.