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.     

Effect of solvent on the cis-trans conformational equilibrium of a proline imide bond of short model peptides in solution.

Proton NMR spectra of proline-containing short peptides with N-terminal sequences of N-acetyl-prolyl- (Ac-Pro-) N-tert-butoxycarbonyl-phenylalanyl-prolyl- (Boc-Phe-Pro-) and N-tert-butoxycarbonyl-leucyl-prolyl- (Boc-Leu-Pro-) were measured in mixed solvents of hexadeuterodimethylsulfoxide and deuterochloroform (CDCl3). Population ratios of cis and trans conformers with respect to the proline imide bond and chemical shifts of NH protons were obtained as a function of a CDCl3 fraction of solvent. With increasing fraction of CDCl3, the trans percentages of the Ac-Pro-imide bonds increased. On the other hand, those of Boc-Phe-Pro- decreased, and those of Boc-Leu-Pro- exhibited middle tendency. From the solvent-dependent variation of the chemical shifts of the NH protons, intramolecular hydrogen bonds that stabilize the trans form of Ac-Pro- and the cis form of Boc-Phe-Pro- were discussed. For the Ac-Pro- peptides, only the trans forms are found to the compatible with 7-, 10-, and 13-membered hydrogen-bonded rings that would be similar to the ordinary secondary structures, gamma- and beta-turns and alpha-helix, respectively. For the cis form of Boc-Phe-Pro-R (R = O-methyl or glycyl-O-ethyl), the hydrogen-bonded structure is found to be similar to the type-VIa beta-turn. On the other hand, for Boc-Phe-Pro-Pro-Leu-Gly-NH2, it has been suggested that two different hydrogen bonds, which are different from that of the type-VIa beta-turn, support each other and cooperatively stabilize the cis form.     

Substituent effects on the isomerization of hydrazone switches driven by the intramolecular hydrogen bond

In this work, the substituent effects on hydrogen bonding in one kind of hydrazone-based switch are revealed. The E/Z isomerization ratios of these hydrazones and their intramolecular hydrogen bond strengths in the Z form were evaluated using NMR technique. Linear correlations between these parameters and Hammett empirical values for substituent effects are explored as well.     

Preorganization-enhanced halogen bonding via intramolecular hydrogen bonding: a theoretical study

Structural Chemistry - Cationic and neutral halogen bonding (XB) donors use two types (I and II) of intramolecular hydrogen bonding (HB) to preorganize structures and increase the efficiency of...     

Dipole moment,isomerization, and intramolecular hydrogen bond in some benzene derivatives (computations)

The dipole moment vectors of some benzene monoderivatives are calculated to test the method used in an attempt to explain the dipole moments of o-, m- and p-substituted phenols (X-C₆H₄-OH; X = -OH, -F, -NO₂, -CHO, -COOH, -CH₃). The vectors seem to include contributions from a mixture of planar conformers whose populations obey a Boltzmann-type distribution. The calculated intramolecular interaction moment is proposed as a simple criterion indicating the strength of the intramolecular hydrogen bond in o-phenols.     

Localized orbital studies of hydrogen bonding: III. The intramolecular hydrogen bond in 4-methylimino 2-pentanone

Geometry optimizations using the INDO molecular orbital method are carried out on the three possible isomeric forms of 4-methylimino- 2-pentanone. It is found that the molecule strongly prefers a structure containing a hydrogen-bonded chelate ring. Of the two possible isomers containing an intramolecular hydrogen bond, only the structure with the chelated proton closer to the oxygen corresponds to an energy minimum, although the energy surface connecting these two isomers is very flat. The results are interpreted using experimental and calculated NMR properties and energy localized molecular orbitais.     

High pressure FTIR study of intramolecular hydrogen bonding and conformation of a small peptide in solution

Effect of pressure on conformational equilibria of a small peptide N-acetyl-l-Pro-l-Leu-Gly-NH₂ in a chloroform solution has been studied by FTIR spectroscopy. Absorption in the NH stretching region was measured at pressures in the 1–1080 bar range and at 296 K, and decomposed into component bands by least-squares fitting. Intensity ratios of bands which were assigned to a hydrogen-bond-free conformer and intramolecularly hydrogen-bonded conformers with 10- and 13-membered hydrogen bonded rings, respectively, were examined as a function of pressure. It was found that the conformer with the 13-membered ring has definitely smaller partial molar volume than the other two conformers which have nearly the same volume with each other. On the basis of a simple dielectric model, we have shown that the conformer with the 13-membered hydrogen-bonded ring has a considerably large dipole moment which is consistent with the α-helical structure suggested by the previous variable-temperature FTIR study.     

Inter- and intramolecular hydrogen bonding in phenol derivatives: a model system for poly-L-tyrosine

The ultrafast dynamics of solutions of phenol and two phenol derivatives--hydroquinone (1,4-benzenediol) and pyrocatechol (1,2-benzenediol)--have been studied with Optically Heterodyne-Detected Optical Kerr-Effect (OHD-OKE) spectroscopy. The solvents, methanol and acetonitrile, were selected to provide strong and weak solvent-solute hydrogen-bonding interactions, respectively, while pyrocatechol features an intramolecular hydrogen bond. Together these provide a series of model systems for polypeptides such as polytyrosine, which facilitate the direct study of inter- and intramolecular hydrogen bonding. A broad contribution to the Raman spectral density of the methanol solutions at frequencies between 150 and 300 cm(-1) has been observed that is absent in acetonitrile. This contribution has been assigned to solvent-solute hydrogen-bond stretching vibrations. The OHD-OKE response of poly-L-tyrosine has been measured and was found to contain a similar contribution. Density functional theory geometry optimizations and normal mode calculations have been performed using the B3LYP hybrid functional and 6-311++G** basis set. These have yielded a complete assignment of the low-frequency Raman and far-infrared spectra of pyrocatechol for the first time, which has provided information on the nature of the intramolecular hydrogen bond of pyrocatechol.     

一个新的七元环吡咯-吡啶氢键分子激发态分子内质子转移的理论研究

运用含时密度泛函理论(TD-DFT)方法和以环己烷为溶剂的可极化连续模型(PCM),研究了2-[2-(1 H-pyrrol-2-yl)-cyclopent-1-enyl]-pyridine(7-HB)发生激发态分子内质子转移(ESIPT)的反应机制.结果表明,7-HB分子被光激发到Franck-Condon区域后,在第一光学亮态(S_1)上会发生一个超快的从Normal(N)式到Tautomer(T)式的质子转移反应,其反应的能垒仅有0.05eV.此外,在相同计算水平下,还研究了7-HB分子的吸收和发射光谱,所得结果与实验数据吻合得很好.     

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.     

Synthesis of linear and cyclic aromatic peptides with fixed conformation owing to intramolecular hydrogen bonding by condensation polymerization method

Chain-growth condensation polymerization of 3-(4-octyloxybenzylamino)benzoic acid esters bearing an alkoxy group on the benzene ring was investigated for the synthesis of polyamides having a specific conformation owing to intramolecular hydrogen bonding of CONH?OR. The 4-octyloxybenzyl group on the nitrogen of the amide linkage was easily removed with trifluoroacetic acid after polymerization to afford the desired polyamides, which had lower solubility than expected. Furthermore, we found that a cyclic triamide was selectively obtained by slow addition of the base to a solution of the monomer.     

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.     

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     

Proton tunnelling in the intramolecular hydrogen bond of 9-Hydroxyphenalenone

Inelastic neutron scattering spectra of the 9-hydroxyphenalenone and ring deuterated analogue reveal an intense band at 91 cm⁻¹ with all characteristics anticipated for a tunnelling the transition of a (quasi)symmetric double minimum potential for proton transfer along the intramolecular hydrogen bond. This frequency is compared to those previously reported for similar systems.