Proton-driven conformational change in a 2-aryl-p-carborane constrained by an intramolecular C-H?O hydrogen bond

2-(2-Hydroxyphenyl)-p-carborane forms an intramolecular hydrogen bonding based on the results of X-ray, IR, and ¹H NMR studies. The hydrogen bonding is released by the addition of acid in solution. Density functional theory (DFT) calculations on the phenol, phenolate and protonated phenol structures indicated two stable conformational state, hydrogen bonding form for phenol and phenolate, and dihydrogen bonding form for protonated phenol.     

Hydrogen bonding and molecular vibrations of 2,5-dihydroxy-1,4-benzoquinone

Intramolecular hydrogen bonding in 2,5-dihydroxy-1,4-benzoquinone has been investigated by means of quantumchemical calculations and vibrational spectroscopy. Both computations at the MP2/6-31+G** level as well as FT-IR and FT-Raman spectra are in agreement with the predominance of the C_2h conformer with two intramolecular hydrogen bonding interactions. The spectra were interpreted with the aid of normal coordinate analysis based on a scaled Becke3–Lee–Yang–Parr/6-31G* density functional force field. The general scale factors introduced recently by Rauhut and Pulay for this theoretical level allowed a reliable assignment of most of the fundamentals. The scale factors for vibrations affected strongly by the intramolecular hydrogen bonding interaction needed some adjustment and hence were re-optimized in the present study. The final scaled force field reproduced the experimental frequencies of the molecule by a weighted mean deviation of 8.8 cm⁻¹. Based on the calculated results, 32 from a total of 36 fundamentals were assigned in the vibrational spectra of 2,5-dihydroxy-1,4-benzoquinone revising and extending the assignments of earlier less sophisticated investigations.     

Conformations of 2-aminoindan in a supersonic jet: the role of intramolecular N-H...pi hydrogen bonding

Laser-induced fluorescence (LIF), dispersed fluorescence (DF), mass-resolved one-color resonance enhanced two-photon ionization (RE2PI) and UV-UV hole-burning spectra of 2-aminoindan (2-AI) were measured in a supersonic jet. The hole-burning spectra demonstrated that the congested vibronic structures observed in the LIF excitation spectrum were responsible for three conformers of 2-AI. The origins of the conformers were observed at 36931, 36934, and 36955 cm(-1). The DF spectra obtained by exciting the band origins of the three conformers showed quite similar vibrational structures, with the exception of the bands around 600-900 cm(-1). The molecular structures of the three conformers were assigned with the aid of ab initio calculations at the MP2/6-311+G(d,p) level. An amino hydrogen of the most stable conformer points toward the benzene ring. The stability of the most stable conformer was attributed to an intramolecular N-H...pi hydrogen bonding between the hydrogen atom and the pi-electron of the benzene ring. The other two conformers, devoid of intramolecular hydrogen bonding, were also identified for 2-AI. This suggests weak hydrogen bonding in the most stable conformer. The intramolecular N-H...pi hydrogen bonding in 2-AI was discussed in comparison with other weak hydrogen-bonding systems.     

DFT and FT-IR analyses of hydrogen bonding in 3-substistuted-3-oxo-arylhydrazonopropanenitriles

Ab initio calculations, FT-IR and X-ray crystal analysis, indicated that the most stable configuration of 3-oxo-2-(phenylhydrazono)-3-(thien-2-yl)-propionitrile is the anti phenylhydrazone structure 1. Stability of such a conformation, over the possible E-form, 2, that would be stabilized by intramolecular hydrogen bonding, is due to interaction between electron-pair domains of the N, S and O atoms. However, the simulated and experimental IR frequency data indicated intermolecular hydrogen bonding between NH and CN, the latter being lowered to 2214 cm(-1). Studies on 3-oxo-3-phenyl-2-(phenylhydrazono)-propionitrile showed the same result, as well as, another intramolecular hydrogen association of the type N-H...O. This was clearly indicated by the absorbance of the carbonyl stretch at 1605 cm(-1). These data indicated the existence of a bifurcated hydrogen bond in 1a and a single intermolecular association in 1b.     

Neutralization-Reionization of alkenylammonium cations: An experimental and ab initio study of intramolecular N-H … C=C interactions in cations and hypervalent ammonium radicals

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by collisional electron transfer in the gas phase in an attempt to generate hypervalent ammonium radicals. The radicals dissociated completely on the 4.8–5.4 µs time scale. Radicals in which the hexene double bond was in the 3-, 4-, and 5-positions dissociated by competitive N-H and N=C bond cleavages. Allylic 2-hexen-1-ylammonium and 2-hexen-1-yldimethylammonium radicals underwent predominant cleavages of allylic N-C bonds. Deuterium labeling experiments revealed no intramolecular hydrogen transfer from the hypervalent ammonium group to the hexene double bond. Ab initio and density functional theory calculations showed that alkenylammonium and alkenylmethyloxonium ions preferred hydrogen bonded structures in the gas phase. The stabilization through intramolecular H bonding in 3-buten-1-ylammonium and 3-buten-1-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ mol^?1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-1-yl-methyloxonium radical was calculated to be unbound and predicted to dissociate exothermically by O-H bond cleavage. This dissociation may provide kinetic energy for the hydrogen atom to overcome a small energy barrier for exothermic addition to the double bond. The 3-butten-1-ylammonium and allylammonium radicals were found to be bound and preferred gauche conformations without intramolecular hydrogen bonding. Vertical neutralization of alkenylammonium ions was accompanied by small Franck-Condon effects. The failure to detect stable or metastable hypervalent alkenylammonium radicals was ascribed to the low activation barriers to exothermic dissociations by N-H and N-C bond cleavages.     

Aromaticity-controlled tautomerism and resonance-assisted hydrogen bonding in heterocyclic enaminone-iminoenol systems

The contribution of aromaticity and intramolecular hydrogen bonding to relative stability, for a set of (1H-azahetero-2-ylidene)-acetaldehyde and 2-azahetero-2-yl-ethanol tautomeric pairs, has been investigated by means of quantum chemical DFT and ab initio methods up to the MP4(SDTQ)/AUG-cc-pVDZ and MP2/AUG-cc-pVTZ levels of theory. It is found that the relative energy of the tautomers is governed by the change in the degree of heterocycle aromaticity upon intramolecular hydrogen transfer. An analysis of geometrical parameters of a hydrogen-bonded system reveals a clear relationship between the aromaticity of the heterocycle, the conjugation in a resonant spacer, and the strengths of the intramolecular hydrogen bonds. This allows the conclusion to be drawn that intramolecular N-H...O and O-H...N hydrogen bonds formed are found to be resonance-assisted and their strength is dependent on the pi-donating/accepting properties of the heterocycle. On the basis of the results of the calculations, a simple model describing the mechanism of resonance assistance of hydrogen bonding has been suggested.     

Studies of intramolecular hydrogen bonding in protonated and non-protonated hexahydropyridinobenzodioxins

The conformational stability of hexahydropyridobenzodioxin and related derivatives in both protonated and non-protonated forms have been investigated by means of ab initio molecular orbital methods as well as semi-empirical AM1 and PM3 methods. One of the cis conformers (cis2e) has been found to be most stable due to the formation of an intramolecular hydrogen bond, other conformers including the trans isomer cannot form this interaction but are of different stability because of the orientation of the polar oxygens and the nitrogen. The effect of the intramolecular hydrogen bonding on the stability of hexahydropyridobenzodioxin and its methylated derivatives has been examined using various basis sets levels. In protonated form, both the semi-empirical and ab initio calculations give excellent agreement in energetic order; however, different orderings of conformer stabilities are observed by different computational methods in non-protonated form. The results provide insight into the intramolecular hydrogen bonding in computational studies of biologically important molecules.     

Weak intramolecular interactions in ethylene glycol identified by vapor phase OH-stretching overtone spectroscopy

Vapor phase OH-stretching overtone spectra of ethylene glycol were recorded to investigate weak intramolecular hydrogen bonding. The spectra were recorded with conventional absorption spectroscopy and laser photoacoustic spectroscopy in the first to fourth OH-stretching overtone regions. The room-temperature spectra are dominated by two conformers that show weak intramolecular hydrogen bonding. A less abundant third conformer, with no sign of hydrogen bonding, is also observed. Vapor phase spectra of the ethylene-d(4) glycol isotopomer were also recorded and used to identify an interfering resonance between CH-stretching and OH-stretching states in the fourth overtone. Anharmonic oscillator local mode calculations of the OH-stretching transitions have provided an accurate simulation of the observed spectra. The local mode parameters were calculated with coupled cluster ab initio methods. The calculations facilitate assignment of the different conformers in the spectra and illustrate the effect of the intramolecular hydrogen bonding.     

Competitive hydrogen bonding of cyclopropenium ions: Implications of an anion switch

This work demonstrates how modulating hydrogen bonding between intermolecular, bifurcated, and intramolecular interactions can be used to tune the structural, electronic, and photophysical properties of cyclopropenium ions and their respective fluorophores. The basis of this switchability was examined using X-ray diffraction analysis, ¹H NMR spectroscopy, DFT calculations, and fluorescence spectroscopy.     

Hydrogen-bonding interactions of the trifluoromethyl group: 2-Trifluoromethylvinyl alcohol

As part of our investigation of intramolecular hydrogen bonding and its geometrical consequences, ab initio molecular orbital calculations on 2-trifluoromethylphenol and 2-trifluoromethylvinyl alcohol and their parent structures were performed at the MP2/6–31+G^** level of theory. The intramolecular hydrogen bonding in 2-trifluoromethylvinyl alcohol appears stronger than that in 2-trifluoromethylphenol as witnessed by the shorter F...H interaction (1.96 Å) and the greater bond length changes in the rest of the molecule, as compared with the respective parent molecules. Beyond the geometrical characteristics, the energetics of hypothetical isodesmic reactions and the small shift of the O(SINGLE BOND)H stretching frequency indicate that these C(SINGLE BOND)F...H(SINGLE BOND)O interactions are rather weak. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 645–652, 1997     

Effects of sugar ring puckering, anti-syn interconversion and intramolecular interactions on N-glycosidic bond cleavage in 3-methyl-2��-deoxyadenosine and 2��-deoxyadenosine

The effects of structural parameters and intramolecular interactions on N-glycosidic bond length in 3-methyl-2??- deoxyadenosine (3MDA) and 2??-deoxyadenosine (DA) were investigated employing quantum mechanical methods. All calculations were performed at B3LYP/6-311++G** level in the gas phase. The N-glycosidic bond length strongly depends on sugar configuration; it is shorter in syn conformation relative to anti in many cases where they have the same sugar ring configuration. The sugar conformation can influence the N-glycosidic bond through interaction with the O4?? atom. The impact of intramolecular improper hydrogen bonds and H-H bonding interactions on N-glycosidic bond length was investigated in DA and 3MDA and their modeled structures. Improper hydrogen bonds decrease N-glycosidic bond length while H-H bonding interactions increase it.     

Molecular mechanics investigation of weak complexes: the case of CO:H2O

The structure of the CO:H₂O complex and its isomers have been determined by using the molecular mechanics procedure. The parameters used in atomic pair potentials construction are derived by fitting on ab initio perturbation calculations of atomic or molecular fragments (Symmetry Adapted Perturbation Theory). An intramolecular potential is introduced in order to estimate the frequency shift of the CO stretching mode. Results are compared to recent calculations. The complexes are classified according to the predominant nature of the intermolecular bonding: quasi linear or bifurcated hydrogen bonding, and purely van der Waals bonding.     

Electron propagator theory study of N-/O-methylglycine conformers

The low-lying conformers of N-/O-methylglycine are studied by ab initio calculations at the B3LYP, MP3, and MP4(SDQ) levels of theory with the aug-cc-pVDZ basis set. The conformers having the intramolecular hydrogen bonds N-H...O=C or O-H...N are more stable than the others. Vertical ionization energies for the valence molecular orbitals of each conformer predicted with the electron propagator theory in the partial third-order quasiparticle approximation are in good agreement with the experimental data available in the literatures. The relative energies of the conformers and comparison between the simulated and the experimental photoelectron spectra demonstrate that there are at least three and two conformers of N- and O-methylglycine, respectively, in the gas-phase experiments. The intramolecular hydrogen bonding O-H...N effects on the molecular electronic structures are discussed for the glycine methyl derivatives, on the basis of the ab initio electronic structure calculations, natural orbital bond, and atoms-in-molecules analyses. The intramolecular hydrogen bonding O-H...N interactions hardly affect the electronic structures of the O-NH2-CH2-C(=O)-O-CH3 and alpha-methylated NH2-CH2-C(CH3)OOH conformers, while the similar intramolecular interactions lead to the significantly lower-energy levels of the highest occupied molecular orbitals for the N-(CH3-NH-CH2-COOH) and beta-methylated (NH2-CH2-CH2-COOH) conformers.     

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.     

X-Ray, MP2 and DFT studies of the structure and vibrational spectra of homarinium chloride

The effects of hydrogen bonding, inter- and intramolecular electrostatic interactions on the structure of homarinium chloride, HOMH·Cl, in the crystal and its isolated molecule have been studied by X-ray diffraction, FT-IR, Raman, ¹H and ¹³C NMR spectroscopies, and by the MP2 and DFT theoretical methods. In the crystal, the Cl⁻ anion is connected with protonated homarine via the O–HCl⁻ hydrogen bond of the length of 2.937(4) Å, and two N⁺Cl⁻ intermolecular electrostatic interactions. In the isolated molecule, according to the MP2 and B3LYP calculations, the Cl⁻ anion is engaged in a shorter hydrogen bond (O–HCl⁻ of 2.811–2.861 Å) and in one type of intramolecular electrostatic interactions. The calculated bond lengths and bond angles at the MP2 and B3LYP levels of theory are in good agreement with the X-ray data, except the conformation of the COOH group, which is cis (syn) in the crystal and trans (anti) in the isolated molecule. The tentative assignments for the experimental solid state vibrational spectra of HOMH·Cl and HOMD·Cl have been made on the basis of the B3LYP/6-31G(d,p) calculated frequencies and intensities. The effect of quaternization of picolinic acid on the chemical shifts of the ring protons and carbons is analyzed.     

Intra- vs. intermolecular hydrogen bonding: dimers of alpha-hydroxyesters with methanol

Intermolecular hydrogen bonding competes with an intramolecular hydrogen bond when methanol binds to an alpha-hydroxyester. Disruption of the intramolecular OH...O=C contact in favour of a cooperative OH...OH...O=C sequence is evidenced by FTIR spectroscopy for the addition of methanol to the esters methyl glycolate, methyl lactate and methyl alpha-hydroxyisobutyrate in seeded supersonic jet expansions. Comparison of the OH stretching modes with quantum-chemical harmonic frequency calculations and 18O labelling of methanol unambiguously prove the insertion of methanol into the intramolecular hydrogen bond. This is in marked contrast to UV/IR hole burning studies of the homologous system methyl lactate: (+/-)-2-naphthyl-1-ethanol, where only addition complexes were found and the intramolecular hydrogen bond was conserved. This switch in hydrogen bond pattern from aliphatic to aromatic heterodimers is thought to reflect not only a kinetic propensity but also a thermodynamic preference for addition complexes when dispersion forces become more important in aromatic systems.     

alpha- and beta-FOX-7, polymorphs of a high energy density material, studied by X-ray single crystal and powder investigations in the temperature range from 200 to 423 K

The alpha-beta phase transition in the novel energetic material 1,1-diamino-2,2-dinitroethylene, C2H4N4O4 (FOX-7), has been studied by single-crystal X-ray investigations at five different temperatures over the 200-393 K range. In these investigations, the positions of the hydrogen atoms were experimentally determined without any geometric constraints. In addition, X-ray powder investigations using the Guinier technique have been performed to characterize the beta-phase up to 423 K. The alpha-beta phase transition at 389 K is first order, shows a discontinuous increase of the molar volume and entropy (DeltaV = 1.75 cm3/mol, X-ray investigation; DeltaS = 1.5 cal/K mol, DSC analysis), and can be classified as displacive. The hitherto unknown structure of beta-FOX-7 was solved at 393 K and showed simple structural relations to the alpha-polymorph. The characteristic bonding in wave-shaped layers is now found for beta-FOX-7 (P2(1)2(1)2(1), z = 4, a= 6.9738(7) A, b = 6.635(1) A, c = 11.648(2) A, 393 K), as well as for alpha-FOX-7 (P2(1)/n, z = 4, a = 6.9467(7) A, b = 6.6887(9) A, c = 11.350(1) A, beta = 90.143(13) degrees , 373 K). Interestingly, whereas the intramolecular C-C, C-N, N-O, and N-H bond distances remain nearly unchanged for both polymorphs over the whole temperature range from 200 to 393 K, the two nitro groups deviate strongly from the molecular plane formed by the two carbon and two amino nitrogen atoms. In alpha-FOX-7 at 373 K, the nitro groups are twisted -47 and +6 degrees with respect to the carbon-carbon bond, but in beta-FOX-7 at 393 K, these twist angles are changed to -36 and +20 degrees . Within the layers, the FOX-7 molecules show strong pi-conjugation and extensive intra- and intermolecular hydrogen bonding. In this investigation, we have been able to show that alpha- and beta-FOX-7 build up different nets of intermolecular hydrogen bonds. In alpha-FOX-7, each oxygen atom of the nitro groups is involved in two hydrogen bonds resulting in two intramolecular and six intermolecular hydrogen bonds. But in beta-FOX-7 this coordination changes, and half of the oxygen atoms build up two and the other half build up three hydrogen bonds leading to two intramolecular and eight intermolecular hydrogen bonds. The average intermolecular hydrogen bond distance increases slightly from 2.31 A in alpha-FOX-7 to 2.52 A in beta-FOX-7. The C-NO2 bonds are of particular interest because they are referred to as the detonation trigger. It has been suggested that these bonds could be strengthened by the extensive intermolecular hydrogen bonding within the layers in both polymorphs. Such bond strengthening via cooperative effects was proposed in earlier DFT calculations on FOX-7 and may be one key to understanding its low sensitivity and high activation energy to impact.     

Derivatives of 1-phenyl-3-methylpyrazol-2-in-5-thione and their oxygen analogues in the crystalline phase and their tautomeric transformations in solutions and in the gas phase

1-Phenyl-3-methylpyrazol-2-in-5-thione, crystallised from methanol, was shown to exist in the tautomeric NH-form, stabilised by intermolecular NHS hydrogen bonds. In solutions, however, the molecule is found predominantly as the SH-tautomer, accompanied (in low-polar solvents) by a small amount of the CH-tautomer.

1-Phenyl-3-methyl-4-benzoylpyrazol-2-in-5-thione occurs in the crystal as well as in solution in the SH-tautomeric form, stabilised by an intramolecular SHO bridge. In dimethylsulfoxide solution indications were found for an additional SH-tautomer in a conformation lacking the intramolecular H-bridge.

The structure of 1-phenyl-3-methylpyrazol-2-in-5-one was redetermined by X-ray single crystal diffraction at 120°K in order to obtain more accurate geometry and hydrogen bonding parameters.     

Synthesis, vibrational spectral and nonlinear optical studies of N-(4-hydroxy-phenyl)-2-hydroxybenzaldehyde-imine: a combined experimental and theoretical investigation

The study of imine-bridged organics has been the one hot spot of photo-responsive material sciences in recent years. Herein we make a study of the synthesis, characteristics and potential application of N-(4-hydroxy-phenyl)-2-hydroxy-benzaldehyde-imine (HPHBI), C13H11NO2. The studied compound was synthesized in one step by the condensation reaction of salicylaldehyde and 4-aminophenol in methanol solution, and characterized by single crystal X-ray diffraction, FT-IR and FT-Raman techniques with theoretical calculations at B3LYP/6-31G(d) level. The molecule adopts trans configuration about central CN bond with intramolecular hydrogen bonding, and the adjacent molecules form wave-shaped structure linked by strong intermolecular hydrogen bonding mechanism along b axis. The vibrational spectra have been precisely assigned with the aid of theoretical frequencies. Furthermore, the thermodynamic properties have been obtained by the theoretical vibrational analysis for HPHBI. The total linear polarizability and first-order hyperpolarizabilities calculated on the studied compound respectively present 25.378 ?3 and 1.655×10(-29) cm5/esu, which indicates the compound has relatively good nonlinear optical property.     

A new class of linear tetrapyrroles: acetylenic 10,10a-didehydro-10a-homobilirubins

Novel bilirubin analogues with dipyrrinones conjoined to an acetylene rather than a methylene group were synthesized and examined spectroscopically. Despite the increased separation of the dipyrrinones forced by replacing a -CH(2)- by a -C(triple bond)C- unit, molecular dynamics calculations show that, like bilirubin, they may still engage in intramolecular hydrogen bonding to carboxylic acid groups when the propionic acid chains are slightly lengthened, e.g., butanoic acids. Unlike bilirubin, however, which is bent in the middle and has a ridge-tile shape, the acetylene orients the attached dipyrrinones along a linear path, and intramolecular hydrogen bonding preserves a twisted linear molecular shape. The extended planes of the dipyrrinones intersect along the -C(triple bond)C- axis at an angle of 136 degrees for the conformation stabilized by intramolecular hydrogen bonding in the bis-butyric acid rubin (1b). With shorter acid chains (propionic), only one CO(2)H can engage an opposing dipyrrinone in intramolecular hydrogen bonding, and in this energy-minimum conformation of the linear pigment 1a, the intersection of the extended planes of the dipyrrinones has an angle of 171 degrees. Spectroscopic evidence for such linearized and twisted structures was found in the pigments' NMR spectral data and their exciton UV-vis and induced circular dichroism spectra.