Molecular dynamics models and thermodynamic characteristics of hydrogen bonds in 1,2-ethanediol

A correlation between the lifetimes of hydrogen bonds and the thermodynamic characteristics of their formation and breaking, and the experimental relaxation times of dielectric spectra and the energy characteristics of relaxation processes, is observed via molecular dynamics (MD) simulation of the rearranging of the network structure of 1,2-ethanediol. The MD torsional frequency of the transition of gauche conformer tGg′ at 224.1 cm_?1 and the experimental frequency of the band maximum of torsional vibrations at 230 cm_?1 in the infrared spectrum correlate with the oscillation frequency of molecules at 240 cm_?1 inside clusters in the Dissado–Hill (DH) model. The MD and DH models indicate a predominantly parallel alignment of the electric dipole moments of conformers tGg′ in the three-dimensional network of hydrogen bonds of the liquid 1,2-ethanediol phase.     

On the extent of intramolecular hydrogen bonding in gas-phase and hydrated 1,2-ethanediol

We investigate the quantum dynamical nature of hydrogen bonding in 1,2-ethanediol and monohydrated 1,2-ethanediol using different levels of ab initio theory. Global full-dimensional potential energy surfaces were constructed from PW91/cc-pVDZ, B3LYP/cc-pVDZ, and MP2/cc-pVDZ ab initio data for gas-phase and monohydrated 1,2-ethanediol, using a modified Shepard interpolation scheme. Zero-point energies and nuclear vibrational wave functions were calculated on these surfaces using the quantum diffusion Monte Carlo algorithm. The nature of intra- and intermolecular hydrogen bonding in these molecules was investigated by considering a ground-state nuclear vibrational wavefunction with reduced complete nuclear permutation and inversion (CNPI) symmetry. Separate wavefunction histograms were determined from the ground-state nuclear vibrational wavefunction by projection into bondlength coordinates. The O-H and O-O wavefunction histograms and vibrationally averaged distances were then used to probe the extent of intra- and intermolecular hydrogen bonding. From these data, we conclude that gas-phase ethanediol may possess a weak hydrogen bond, with a relatively short O-O distance but no detectable proton delocalization. Monohydrated ethanediol was found to exhibit no intramolecular hydrogen bonding but instead possessed two intermolecular hydrogen bonds, indicated by both shortening of the O-O distance and significant proton delocalization. The degree of proton delocalization and shortening of the vibrationally averaged O-O distance was found to be dependent on the ab initio method used to generate the potential energy surface (PES) data set.     

Zinc, cadmium, and mercury 1,2-benzenedithiolates with intramolecular NH...S hydrogen bonds

Mononuclear Zn, Cd, and Hg 1,2-benzenedithiolates with intramolecular NH...S hydrogen bonds, [M(II){1,2-S2-3,6-(RCONH)2C6H2}2](2-) (R = CH 3, t-Bu; M = Zn, Cd, Hg), were synthesized and characterized by X-ray analysis and spectral measurements. The presence of intramolecular NH...S hydrogen bonds was established by the IR spectra. (199)Hg and (113)Cd nuclear magnetic resonance showed a stabilized four-thiolate coordinated structure and suggested the influence of the NH...S hydrogen bonds to ppi(Hg)-ppi(S) interactions. The NH stretching bands show that the NH...S hydrogen bonds in Cd and Hg complexes are stronger than those in the corresponding Zn complex. These results are supported by theoretical calculations. The experimental and theoretical results suggested that the NH...S hydrogen bond influences the efficient capture of toxic Cd and Hg ions by metallothioneins.     

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.     

Effects of ionization on N-glycylglycine peptide: influence of intramolecular hydrogen bonds

The ionization effects on 28 conformations of N-glycylglycine are analyzed by means of the hybrid B3LYP and the hybrid meta-MPWB1K density functionals and by single-point calculations at the CCSD(T) level of theory. The most favorable process observed corresponds to the ionization of the only neutral conformation that presents a OH...NH2 intramolecular hydrogen bond, which leads to CO2 elimination after a spontaneous proton transfer from -COOH to NH2. The remaining neutral structures evolve to 20 different conformations of N-glycylglycine radical cation, which lie about 25-40 kcal/mol higher than the decarboxylated [NH3CH2CONHCH2]+*...[CO2] complex. Structural changes induced by ionization depend on the intramolecular hydrogen bonds of the initial conformation, since they determine the nature of the electron hole formed. In most cases, ionization takes place at the terminal -NH2 and -CO of the amide bond, which produces a strengthening of the peptide bond and the formation of new -NH2...OC(amide) and -NH2...OCOH hydrogen bonds. However, if -NH2 and -CO(amide) simultaneously act as proton acceptor in the neutral conformation, ionization is mainly localized at the carboxylic group, which produces a strengthening of the -COOH...OC(amide) bond. Both functionals lead to similar trends and compare well with CCSD(T) results except for a few cases for which B3LYP provides a too delocalized picture of the electron hole and consequently leads to artificial geometry reorganization.     

Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding

A proper understanding of the conformational energetics of 1,2-ethanediol (ethylene glycol) is important to the construction of molecular mechanics force fields for the treatment of carbohydrates since these biologically important molecules have a prevalence of vicinal hydroxyl groups. In the present study, quantum mechanical analysis of the 10 unique minimum-energy conformations of ethylene glycol is performed by using 10 model chemistries ranging from HF/6-311++G(d,p) up to a hybrid method that approximates CCSD(T)/cc-pVQZ. In addition, natural bond orbital (NBO) analysis of these conformations with deletion of pairings of CO bond/antibonding and lone pair/antibonding orbitals is used to investigate contributions from the "gauche" effect to ethylene glycol conformational energetics. MP2 with the "correlation consistent" basis sets and DFT/6-311++G(d,p) do the best job of matching the approximate CCSD(T)/cc-pVQZ energies while MP2/6-31G(d) and Hartree-Fock both fare poorly. NBO analysis shows the conformational energies to be independent of the deletion of matrix elements associated with (i) CO bonding and antibonding orbital interactions and (ii) lone pair and antibonding orbital interactions, whereas the energetic ordering correlates with geometric parameters consistent with internal hydrogen bonds. Thus, the present results suggest that standard molecular mechanics potential energy functional forms, which lack explicit terms to account for stereoelectronic effects, are appropriate for carbohydrates.     

Effects of intramolecular hydrogen bonds on phosphorescence emission: A theoretical perspective

Importing intramolecular hydrogen bond in phosphorescent transition metal complexes has been considered one of the excellent approaches to improve the electroluminescence performance of organic light-emitting diodes in real applications. However, the relationships between such H-bond structure and phosphorescent properties have not been theoretically revealed yet. In this study, two types of intramolecular hydrogen bonds are introduced into the two classes of traditional materials, that is, Pt(II) and Ir(III) complexes ( 1a and 2a ) to completely elucidate their influence on the structures and properties by comparing with the original phosphors ( 1b and 2b ) using density functional theory/time-dependent density functional theory for the first time. A comprehensive analysis of the geometric structures, molecular orbitals, and luminescence properties (including phosphorescence emission wavelengths and radiative and nonradiative decay processes) has been carried out. Our theoretical model highlights that complexes 1a and 2a embedded with H-bonds significantly promote the phosphorescence emission band blue-shifted and restrict molecular deformations compared with the corresponding 1b and 2b , which can provide helpful guidance to regulate and design several aspects of highly efficient blue phosphorescent emitters.     

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.     

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.     

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.     

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.     

The role of intramolecular hydrogen bonds in nucleophilic addition reactions of ketenaminals

Quantum-chemical calculations of the geometries and electronic structures of molecules of ketenaminals 3-(diaminomethylene)-2,4-pentanedione and dimethyl-2-(diaminomethylene)-malonate and calculations of the structures of intermediates in the reaction of the nucleophilic addition of the ketenaminals to the acetonitrile molecule are performed by B3LYP/6-31+G** method. Two possible scenarios of the process are shown, depending on the mutual orientation of reacting molecules. The nucleophilic addition proceeds in two stages. It is found that the rate-limiting stage of the process is the transfer of the proton of the intramolecular hydrogen bond in a ketenaminal molecule. The experimentally observed faster reaction of pyrimidine formation for the 3-(diaminomethylene)-2,4-pentanedione molecule relative to that for dimethyl-2-(diaminomethylene)-malonate is explained by the hydrogen bond being stronger and the barrier of proton transfer from the aminogroup to the ketogroup oxygen falling upon nucleophilic attack in the former molecule.     

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.

---

H-. , .

     

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).     

Conformational analysis of intramolecular bonded amino alcohols : The conformational free energies of some intramolecular OH ⋯ N hydrogen bonds

Equilibrium positions between intramolecular OH ? N hydrogen bonded and free OH forms of some 3-piperidinols, decahydroisoquinolinols, a decahydroquinolinol, lupinine and N-methyl-3-piperidinemethanol have been determined from dilute solution IR spectral data at 33°. Conformational free energies of the H-bonds (ΔG°_OH?N, attractive) have been calculated. The results suggest a linear relationship between the apparent value of ΔG°_OH?N, as defined by the method of calculation, and the strength of the OH ? N bond expressed as Δν, within the limits of 0·5 ± 0·2kcal/mole per 100 cm^?1, from Δν 90 to 350 cm^?1. For cis-decahydroisoquinoline (N-Me or N-H) systems, a 0·4 kcal/mole difference has been calculated between the two possible ring-fused conformations, in favor of the so-called steroid form. For the corresponding cis-decahydroqumoline equilibrium, a 0·8 kcal/mole difference has been calculated, in favor of the nonsteroid form.     

Influence of intramolecular hydrogen bonds on the tautomeric equilibrium of 1,3-diketones

The paper deals with a quantitative characterization of the influence of multiple intramolecular hydrogen bonds on the tautomeric equilibrium of 1,3-diketones by means of NMR-spectroscopy. The contents of the keto- and two enol forms of 1-(o-hydroxyphenyl) -1,3-butandione and 1-(o-methoxyphenyl)-1,3-butandione in tetrachloromethane, deuterochloroforme, acetone-d₆ and acetonitrile-d₃ are compared.The intramolecular hydrogen bond between the phenolic hydroxyl group and the aromatic carbonyl group in 1-(o-hydroxyphenyl)-1,3-butandione shifts are keto-enol equilibrium toward the keto-tautomer and enol-enol equilibrium toward the tautomer with an enolized aliphatic carbonyl group.