A scheme estimating the energy of intramolecular hydrogen bonds in diols

The relative energies of conformers of 1,2-ethanediol, 1,3-propanediol, and 1,4-butanediol are split into a sum of five different terms including the intramolecular OH?O interaction. This scheme allows to estimate the energy of the O-H?O intramolecular hydrogen bond of the tGG′g and gGG′g conformers of 1,3-propanediol, the g′GG′Gt and g′GG′Gg conformers of 1,4-butanediol, and the energy of the non-bonded O-H?O interaction in the g′Gt, g′Gg and g′Gg′ conformers of 1,2-ethanediol. This scheme provides pure hydrogen bond energies without assuming the geometry and/or electronic features to be constant between the conformation having a IHB and a reference conformation. The fitted energies show a perfect linear correlation with the corresponding r(H?O)⁻¹ values. QTAIM atomic electron population and energies of the donor hydrogen calculated along the H-O-C-C internal rotation are found to be linearly correlated. These linear correlations display small changes at the BCP formation in 1,3-propanediol.     

Quantum-chemical study,IR spectra,and intramolecular hydrogen bonds in dimeric 5- and 6-methyluracils

Comparative analysis of the geometry, atomic charges, force constants, and IR spectra of crystals of isomeric 5- and 6-methyluracils was performed by quantum-chemical methods. Dimeric and trimeric associates of C-methyluracil molecules and their dimers with adenine were calculated in order to estimate the energies of intramolecular hydrogen bonds. Thymine in DNA is impossible to replace by 6-methyluracillargely by steric reasons.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 12, 2004, pp. 2038–2047.Original Russian Text Copyright © 2004 by Naumov, Tafipolskii, Reznik.This revised version was published online in April 2005 with a corrected cover date.     

Possibility of intramolecular hydrogen bonds in 8-methoxypsoralene

Variants of the formation of weak intramolecular hydrogen bonds of C-H…O type in 8-methox-ypsoralene (8-MOP) were considered. Quantum-chemical calculations showed the possibility of an intramolecular hydrogen bond between the protons of the methoxy group and both (furan and pyrone) neighboring oxygen atoms of the psoralene system. The energy gain of this binding was detected by DFT, but not found by the Hartree-Fock method. The bond with pyrone oxygen is energetically more favorable, though the difference in energy between the two types of minima found on PES was small. This interaction had earlier been recorded for linear 8-substituted furocoumarins other than 8-MOP. The conclusion was drawn that the calculated energy barriers on the PES of methoxy group rotation were small enough (2.5 kcal/mol in the Hartree-Fock method, 1.1 kcal/mol in PBE, and 0.9 kcal/mol in B3LYP) to state that the methoxy group rotates freely, creating a steric hindrance for two close-lying oxygens of the psoralene structure, which are not involved in lone electron pair-π system interactions.     

Acidities in cyclohexanediols enhanced by intramolecular hydrogen bonds

Equilibrium gas-phase acidities of the six isomeric cyclohexanediols were measured in a Fourier transform ion cyclotron resonance mass spectrometer. Although all six cyclohexanediols have the same functional groups and similar structures, the acidities vary over 11 kcal/mol. This large difference is due mostly to the balance between hydrogen bonding and geometric strain. To understand the origins of the acidity differences in more detail, the conformations and energetics of the cyclohexanediols were studied using density functional theory, which gave good agreement with the experimental acidities. Finally, methanol-methoxide and methanol-methanol interactions were used as a model for the hydrogen bonding.     

Charge-assisted intramolecular hydrogen bonds in disubstituted cyclohexane derivatives

In this paper, the N(+)-H···N, N(+)-H···O, and O-H···O(-) charge-assisted intramolecular hydrogen bonds (CAHBs) are investigated using different theoretical approaches. Monocharged cyclohexyldiamines (CHDA), aminocyclohexanols (ACHO), and cyclohexanediols (CHDO) are used as model compounds. Geometry optimizations at the MP2/aug-cc-pVDZ level are used to find the equilibrium structures for all possible H-bonded conformers. CAHBs are characterized geometrically and spectroscopically, and their energy is evaluated by means of homodesmic reactions. By comparison with the neutral forms, the presence of the charge is found to have a deep influence on the geometric and energetic H-bond parameters. In addition, these parameters are strongly dependent on the type of the groups involved as well as on their relative position in the cyclohexyl ring. For the systems under study, the H-bond energies vary from -23 to -113 kJ mol(-1), being classified from moderate to strong H-bonds. These H-bonds are also characterized by the application of the NBO and AIM theories. NBO analysis reveals that the energy corresponding to the charge transfer between the lone-pairs of the electron donor group and the antibonding orbitals of the acceptor group represents an important contribution in the H-bond stabilization. From the application of the AIM theory it is possible to see that these H-bonds possess some covalence which varies according to the type and relative position of the intervenient groups.     

Estimates of the energy of intramolecular hydrogen bonds

A method for the estimation of the energy of intramolecular hydrogen bonds in conjugated systems existing in a variety of conformations is presented. The method is applied to determine the intramolecular hydrogen bond energy in 3-aminopropenal and 3-aminopropenthial. According to the proposed estimation scheme, the intramolecular H-bond energies are found to be of the order of 5-7 kcal/mol. These results are compared with those obtained by using other estimation schemes as well as with the recent results by other authors. Also, the H-bond energies in dimers and trimers of the two molecules are calculated and compared with the corresponding data for internally hydrogen-bonded monomers. This comparison shows that the bond equalization effect is primarily due to proton donor-proton acceptor proximity. In comparison with intermolecular hydrogen bonds, the rigidity of the chelate skeleton enhances this proximity effect. The same effect can be seen in systems with intermolecular hydrogen bonds, although its magnitude is diminished because of the absence of additional forces which pull the proton donor and proton acceptor groups toward each other. No specific resonance-assisted origin of the intramolecular hydrogen bond energy seems to be needed to elucidate the energetics of these bonds.     

Kinetics of hydrogen isotope exchange in molecules with strong intramolecular hydrogen bonds

Rate constants and activation energies of hydrogen exchange in solution between methanol and molecules with intramolecular H-bonds have been measured. It has been established that the rate-determining step is the dissociation of this bond.

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The nature and energy characteristics of intramolecular hydrogen bonds in crystals

The review concerns the results of systematic X-ray diffraction studies of the electron density distribution in the crystals of compounds with strong intramolecular hydrogen bonds N-H...O, O-H...O, O-H...N, and N-H...S. The advantages of the topological analysis of the electron density distribution function in the analysis of the nature and estimation of the H-bond energies directly from experimental data are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–14, January, 2006.     

Estimating the energy of intramolecular hydrogen bonds in chitosan oligomers

The effect the number of chitosan monomer units CTS_n (n = 1–5), the protonation of chitosan dimers, and the interaction between CTS_n (n = 1–3) and acetate ions have on the energy of intramolecular hydrogen bonds is investigated by means of QTAIM analysis and solving the vibrational problem within the cluster-continuum model. It is established that the number of H-bonds in CTS_n is 2n ? 1 and the total energy of H-bonds grows by ~20 kJ/mol. It is concluded that the hydrogen bonds between CTS and acetate ions play a major role in the stabilization of polyelectrolyte complexes in dilute acetic acid solutions of CTS.     

Conformational isomerism of chlorophenylthioureas and intramolecular N---H … Cl hydrogen bonds: IR spectra of N---H stretching vibrations

The vN---H regions of the IR spectra of thioureas with chlorophenyl (ClPh) groups and those with halophenyl groups were measured in dilute CCl₄ solution. The observed vN---H bands were classified into eight groups according to the wavenumbers and the two substituent groups. The suggested conformational states and the formation of intramolecular N---H … Cl hydrogen bonds in these compounds were discussed in comparison with those of the urea analogs. It was found that these thiourea derivatives are more stable in the cis form than the urea analogs and that thioureas with o-ClPh groups form fewer intramolecular N---H … Cl hydrogen bonds than do the urea analogs.     

A Schiff-base porphyrin complex with double intramolecular hydrogen bonds

We have designed a porphyrin with a Schiff-base substituent as a model to study intramolecular hydrogen-bonding. The corresponding complex [Zn(SATPP)(CH₃OH)] has been synthesized and characterized by X-ray crystallography, ¹H NMR, and UV-Vis spectroscopy. The structure shows that there are three phenyl groups and one salicylideneaminophenyl group at the meso positions of the porphyrin, and the phenol oxygen is involved in double hydrogen bonds, one within the salicylideneaminophenyl and the other between coordinated methanol and phenol oxygen. ¹H NMR spectra suggest that the binding of methanol to zinc is an equilibrium process in solution and the equilibrium constant has been determined by UV-Vis measurements. The intramolecular hydrogen bond stabilizes the structure, and the binding affinity increases 10 times over the corresponding TPP (TPP, dianion of meso-5,10,15,20-tetraphenylporphyrin).     

Structural and energetic consequences of the formation of intramolecular hydrogen bonds

Formation of intramolecular hydrogen bonds leads to structural modifications in the whole molecule, which are discussed on the basis of B3LYP/6-31G(d,p) calculations. The energy and the structure of various hydrogen-bonded and open conformers are considered for two groups of ortho-substituted phenols–N-dimethylaminomethylphenols (Mannich bases) and N-methylbenzylideneamines (Schiff bases). The energy of intramolecular hydrogen bond formation in Mannich bases was corrected for non-bonded interactions within the molecules, based on a thermodynamic cycle. Structural data were used to estimate the fraction of the ortho-quinoid (keto) form in particular tautomers. It is shown that proton transfer in Schiff bases leads to an increase of this fraction to about 40%, while opening of the hydrogen bond in the proton transferred form increases the keto fraction to 70%.     

Characterization of intramolecular hydrogen bonds by atomic charges and charge fluxes

The electronic charge redistribution and the infrared intensities of the two types of intramolecular hydrogen bonds, O-H···O and O-H···π, of o-hydroxy- and o-ethynylphenol, respectively, together with a set of related intermolecular hydrogen bond complexes are described in terms of atomic charges and charge fluxes derived from atomic polar tensors calculated at the B3LYP/cc-pVTZ level of theory. The polarizable continuum model shows that both the atomic charges and charge fluxes are strongly dependent on solvent. It is shown that their values for the OH bond in an intramolecular hydrogen bond are not much different from those for the "free" OH bond, but the changes are toward the values found for an intermolecular hydrogen bond. The intermolecular hydrogen bond is characterized not only by the decreased atomic charge but also by the enlarged charge flux term of the same sign producing thus an enormous increase in IR intensity. The overall behavior of the charges and fluxes of the hydrogen atom in OH and ≡CH bonds agree well with the observed spectroscopic characteristics of inter- and intramolecular hydrogen bonding. The main reason for the differences between the two types of the hydrogen bond lies in the molecular structure because favorable linear proton donor-acceptor arrangement is not possible to achieve within a small molecule. The calculated intensities (in vacuo and in polarizable continuum) are only in qualitative agreement with the measured data.     

Naphthalene diols: a new class of antioxidants intramolecular hydrogen bonding in catechols,naphthalene diols,and their aryloxyl radicals

1,8-Naphthalenediol, 5, and its 4-methoxy derivative, 6, were found to be potent H-atom transfer (HAT) compounds on the basis of their rate constants for H-atom transfer to the 2,2-di(4-t-octylphenyl)-1-picrylhydrazyl radical (DOPPH*), k(ArOH/DOPPH)*, or as antioxidants during inhibited styrene autoxidation, k(ArOH/ROO)*, initiated with AIBN. The rate constants showed that 5 and 6 are more active HAT compounds than the ortho-diols, catechol, 1, 2,3-naphthalenediol, 2, and 3,5-di-tert-butylcatechol, 3. Compound 6 has almost twice the antioxidant activity, k(ArOH/ROO)* = 6.0 x 10(6) M(-)(1) s(-1), of that of the vitamin E model compound, 2,2,5,7,8-pentamethyl-6-chromanol, 4. Calculations of the O-H bond dissociation enthalpies compared to those of phenols, (deltaBDEs), of 1-6 predict a HAT order of reactivity of 2 < 1 < 3 approximately 4 < 5 < 6 in general agreement with kinetic results. Calculations on the diols show that intramolecular H-bonding stabilizes the radicals formed on H-atom transfer more than it does the parent diols, and this effect contributes to the increased HAT activity of 5 and 6 compared to the activities of the catechols. For example, the increased stabilization due to the intramolecular H-bond of 5 radical over 5 parent of 8.6 kcal/mol was about double that of 2 radical over 2 parent of 4.6 kcal/mol. Linear free energy plots of log k(ArOH/DOPPH)* and log k(ArOH/ROO)* versus deltaBDEs for compounds 1-6 along with available literature values for nonsterically hindered monophenols placed the compounds on common scales. The derived Evans-Polanyi constants from the plots for the two reactions, alpha(DOPPH)* = 0.48 > alpha(ROO)* = 0.32, gave the expected order, since the ROO* reaction is more exothermic than the DOPPH* reaction. Compound 6 is sufficiently reactive to react directly with oxygen, and it lies off the log k(ArOH/ROO)* versus deltaBDE plot.     

Cooperativity in intramolecular bifurcated hydrogen bonds: an ab initio study

Molecular orbital and density functional theory calculations are performed on some di- and tetrasubstituted derivatives of anthraquinone, dihydrophenazine, and acridone to investigate cooperativity in a pair of bifurcated hydrogen bonds occurring in the same molecule. The various structures were selected as convenient model systems for three-center hydrogen bonding of both H...A...H and A...H...A types. In the former type, the C=O moieties in anthraquinone and acridone act as bifurcated hydrogen bond acceptors, and substituted OH groups act as hydrogen bond donors. In the latter type, the N-H moieties in dihydrophenazine, acridones act as bifurcated hydrogen bond donors, and the carbonyl oxygens of substituted CHO groups act as hydrogen bond acceptors. Different indicators of cooperativity reveal that two intramolecular bifurcated hydrogen bonds simultaneously present in the same molecule significantly reinforce each other.