Axial and equatorial hydrogen bonds: jet-cooled rotational spectrum of the pentamethylene sulfide...hydrogen fluoride complex

Two different axial and equatorial hydrogen-bonded conformers of the complex formed by pentamethylene sulfide and hydrogen fluoride have been generated in a pulsed supersonic expansion and characterised by means of Fourier transform microwave spectroscopy. The ground-state rotational spectra of six isotopomers (C(5)H(10)S...HF, C(5)H(10)S ...DF, C(5)H(10)(34)S ...HF, (13)C(alpha)C(4)H(10)S ...HF, (13)C(beta)C(4)H(10)S...HF and (13)C(gamma)C(4)H(10)S ...HF) have been analysed for both conformers in the frequency range 5.5-18.5 GHz. The rotational parameters were used to derive C(s) structures for the conformers, with hydrogen fluoride pointing to the domain of the nonbonding electron pairs at either the axial or equatorial position of the sulfur atom. The axial form was found to be the more stable, in contrast with the observation for the pentamethylene sulfide...HCl complex. No equatorial-to-axial relaxation was observed when He or Ar were used as the carrier gas. The conformational behaviour is compared with that of related six-membered rings and discussed in terms of the existence of secondary hydrogen bonding between the halogen atom and the nearest H atoms of the methylene groups of the ring. No significant structural distortion of pentamethylene sulfide upon complexation was detected from a comparison with the structure of the isolated monomer. Finally, an ab initio study was carried out to complement the experimental results.     

Proposed fluorination mechanism of CB(5)H(6)(-) and CB(9)H(10)(-) with HF. Evidence of kinetic control in the formation of 2-CB(5)H(5)F(-) and 6-CB(9)H(9)F(-)

Two pathways have been considered in the fluorination of CB(5)H(6)(-) and CB(9)H(10)(-) by HF. In the ionic HF fluorination pathway, the monocarborane anion cage is first protonated in a BBB face followed by H(2) elimination and fluoride anion addition. In the covalent HF fluorination pathway, HF is first coordinated through hydrogen to the BBB face. Next, the fluorine can add to either an axial or equatorial boron atom which opens the cage to a nido structure with an endo fluoride substituent. Endo to exo rearrangement occurs with a small activation barrier followed by H(2) elimination. In both pathways, fluorination at the equatorial boron position is predicted to have smaller activation barriers even though substitution at the axial position leads to the more stable products.     

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.     

Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclopenten-1-ol

The conformations of 2-cyclopenten-1-ol (2CPOL) have been investigated by high-level theoretical computations and infrared spectroscopy. The six conformational minima correspond to specific values of the ring-puckering and OH internal rotation coordinates. The conformation with the lowest energy possesses intramolecular π-type hydrogen bonding. A second conformer with weaker hydrogen bonding has somewhat higher energy. Ab initio coupled-cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the two-dimensional potential energy surface (PES) governing the conformational dynamics along the ring-puckering and internal rotation coordinates. The two conformers with the hydrogen bonding lie about 300 cm⁻¹ (0.8 kcal/mole) lower in energy than the other four conformers. The lowest energy conformation has a calculated distance of 2.68 Å from the hydrogen atom on the OH group to the middle of the C=C double bond. For the other conformers, this distance is at least 0.3 Å longer. The infrared spectrum in the O-H stretching region agrees well with the predicted frequency differences between the conformers and shows the conformers with the hydrogen bonding to have the lowest values. The infrared spectra in other regions arise mostly from the two hydrogen-bonded species.     

Molecular structures of benzoic acid and 2-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations

The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d,p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+G(d,p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol(-1) lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond.     

Chair, boat and twist conformation of dodecamethylcyclohexasilane and undecamethylcyclohexasilane: a combined DFT and Raman spectroscopic study.

The conformations of dodecamethylcyclohexasilane Si6Me12 and undecamethylcyclohexasilane Si6Me11H have been investigated by ab initio calculations employing the B3LYP density functional with a 6-31+G(d) basis set. Local minima as well as transition structures were calculated with imposed symmetry constraints. For Si6Me12, three unique minima, which correspond to the chair, twist and boat conformations were located with relative zero-point-vibration-corrected energies of 0.0, 7.8 and 11.4 kJ mol(-1). A half-chair conformation with four coplanar silicon atoms connects the chair and twisted minima via an energy barrier of 16.0 and 8.2 kJ mol(-1), respectively. A second transition structure with a barrier of 3.9/0.3 kJ mol(-1) connects the twist with the boat structure. Solution Raman spectra of Si6(CH3)12 and Si6(CD3)12 fully corroborate these results. Below -40 degrees C, the symmetric SiSi ring breathing vibration is a single line, which develops a shoulder (originating from the twist conformer) at longer wavelengths whose intensity increases with increasing temperature. From a Van't Hoff plot, the chair/twist enthalpy difference is 6.6+/-1.5 kJ mol(-1) for Si6(CH3)12 and 6.0+/-1.5 kJ mol(-1) for Si6(CD3)12, which is in reasonable agreement with the ab initio results. Due to the low barrier, the boat conformation cannot be observed, because either the lowest torsional vibration level lies above it or a rapid interconversion between the twist and boat conformations occurs, resulting in averaged Raman spectra. For Si6Me11H, six local minima were located. The chair with the hydrogen atom in the axial position (axial chair) is the global minimum, followed by the equatorial chair (+1.9 kJ mol(-1)) and the three twist conformers (+5.3, +8.0 and +8.1 kJ mol(-1)). The highest local minimum (+11.9 kJ mol(-1)) is a C(s) symmetric boat with the hydrogen atom in the equatorial position. Two possible pathways for the chair-to-chair interconversion with barriers of 13.9 and 14.5 kJ mol(-1) have been investigated. The solution Raman spectra in the SiSi ring breathing region clearly show that below -50 degrees C only the axial and equatorial chairs are present, with an experimental deltaH-value of 0.46 kJ mol(-1). With increasing temperature a shoulder develops which is attributed to the combined twist conformers. The experimental deltaH-value is 6.9 kJ mol(-1), in good agreement with the ab initio results. Due to the low interconversion barriers, the various twist conformers cannot be detected separately.     

Spectroscopic and computational studies of the intramolecular hydrogen bonding of 2-indanol

2-Indanol in its most stable form is stabilized by internal hydrogen bonding, which exists between the hydroxyl hydrogen atom and the pi-cloud of the benzene ring. A comprehensive ab initio calculation using the MP2/cc-pVTZ level of theory showed that 2-indanol can exist in four possible conformations, which can interchange through the ring-puckering vibration and the internal rotation of the OH group on the five-membered ring. A potential energy surface in terms of these two vibrational coordinates was calculated. Density functional theory calculations were used to predict the vibrational frequencies and to help in normal mode assignments. Fluorescence excitation spectra of 2-indanol confirm the presence of the four conformers in the electronic ground and excited states. The spectral intensities indicate that, at 90 degrees C, 82% of the molecules exist in its most stable form with the intramolecular hydrogen bonding. The other isomers are present at approximately 11, 5, and 3%. The MP2/6-311++G(d,p) calculation predicts a distribution of 70, 13, 9, and 8% at 90 degrees C, the experimental sample temperature.     

Tautomeric and conformational properties of benzoylacetone, CH3-C(O)-CH2-C(O)-C6H5: gas-phase electron diffraction and quantum chemical study

Tautomeric and structural properties of benzoylacetone, CH(3)-C(O)-CH(2)-C(O)-C(6)H(5), have been studied by gas-phase electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximation with different basis sets up to aug-cc-pVTZ). Analysis of GED intensities resulted in the presence of 100% enol tautomer at 331(5) K. The existence of two possible enol conformers in about equal amounts is confirmed by both GED and quantum chemical results. In both conformers the enol ring possesses C(s) symmetry with a strongly asymmetric hydrogen bond. The experimental geometric parameters are reproduced very closely by the B3LYP/cc-pVTZ method.     

Unexpected conformational properties of 1-trifluoromethyl-1-silacyclohexane, C5H10SiHCF3: gas electron diffraction, low-temperature NMR spectropic studies, and quantum chemical calculations

The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol%/equatorial=42(12) mol%) at T=293 K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length Si--C 1.934(10) A. A low-temperature 19F NMR experiment results in an axial/equatorial ratio of 17(2) mol%:83(2) mol% at 113 K and a DeltaG (not equal) of 5.5(2) kcal mol-1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100-300 K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method.     

Chiral discrimination in the 13C and 2H NMR of the crown and saddle isomers of nonamethoxy-cyclotriveratrylene in chiral liquid-crystalline solutions

We report 2H and 13C NMR spectra of the crown and saddle isomers of nonamethoxy-tribenzocyclononene (1), dissolved in lyotropic achiral and chiral liquid-crystalline solutions based on poly-gamma-benzyl-glutamate and poly-gamma-benzyl-L-glutamate (PBG and PBLG). The 2H-[1H] measurements include spectra of compound 1 deuterated in the ring methylene and in the aromatic sites as well as of the methyl groups in natural abundance. Carbon-13 spectra were recorded in natural abundance as well as in two isotopomers enriched in the ring methylene and one of the methoxy groups. The crown isomer (c-1) is rigid with C3 symmetry and can be separated into its enantiomers using a chiral high-performance liquid chromatography column. The NMR spectra of racemic c-1 in PBLG solutions exhibit two sets of lines due to the enantiomers. The peaks were identified by comparing the spectra with those of the neat enantiomers. Analysis of the 2H quadrupolar splittings and the 13C residual chemical shift anisotropies shows that the dominant factor determining the chiral discrimination is the difference in the ordering of the two enantiomers in the chiral liquid crystals. The saddle isomer (s-1) is highly flexible, undergoing fast pseudorotation between six conformers. The "frozen" conformers have C1 symmetry and are therefore chiral. Three of these comprise one enantiomer, and the other three the second one. However, the rapidly interconverting species has, on the average, a C3h symmetry and is therefore achiral. The methylene groups in the latter are, however, prostereogenic, and their hydrogen/deuterium-carbon bonds constitute enantiotopic pairs. The 2H NMR spectra of the s-1 methylene-deuterated in PBLG solutions exhibit, in fact, enantio-discrimination with two quadrupolar doublets. This is in contrast to rigid prochiral molecules with a threefold symmetry axis, which normally do not show such discrimination. A detailed analysis of the effect is presented, and it is argued that the discrimination observed for s-1 reflects the different ordering of its enantiomers during the pseudorotation cycle.     

The role of hyperconjugation in the conformational analysis of methylcyclohexane and methylheterocyclohexanes

Full geometry optimizations were carried out at the HF/6-31G** and B3LYP/6-31G** levels for methylcyclohexane, 2-, 3-, and 4-methyltetrahydropyran, 2-, 3-, and 4-methylpiperidine, 2-, 3-, and 4-methylthiane, 2-, 4-, and 5-methyl-1,3-dioxane, and 2-, 4-, and 5-methyl-1,3-dithiane and also for S-methyl thianium. Constrained geometry optimizations were carried out for methylcyclohexane, 2-methyl-1,3-dioxane, and the axial conformers of 2- and 3-methyltetrahydropyran and 2- and 3-methylpiperidine. The steric repulsion model, which is believed to account for the conformational energies of the cited compounds, was tested by stretching bonds and bending angles so that the axial methyl group is either forced to approach the ring gamma methylenes or get farther away from them. The calculated energies show that the energy costs of these perturbations are not dependent on the distances between the axial methyl group and the ring gamma methylenes and are not dependent on whether the methyl is axial or equatorial. It is shown that, besides the steric repulsion model, the conformational energies of the compounds studied are dictated by hyperconjugative interactions involving mainly the methine hydrogen. The C[bond]C lengths of the axial and equatorial conformers of methylcyclohexane are shown to be related to hyperconjugation.     

Axial and equatorial hydrogen-bond conformers between (CH2)3S and H(D)F: Fourier transform infrared spectroscopy and ab initio calculations

The coexistence of axial and equatorial hydrogen-bonded conformers of 1?:?1 (CH(2))(3)S-HF (and -DF) has been observed in the same adiabatic expansion of a supersonic jet seeded with argon and in a static absorption cell at room temperature. High level calculations computed the axial conformer to be the most stable one with a small energy difference with respect to the equatorial one, in full agreement with previous microwave experiments. On the grounds of band contour simulations of FTIR spectra and ab initio energetic and anharmonic vibrational calculations, two pairs of ν(s) HF donor stretching bands, observed in a series of jet-FTIR spectra at 3457.9 and 3480.5 cm(-1) have been respectively assigned to the axial and equatorial forms of the 1?:?1 complex. In the jet-FTIR spectra series with HF, the assignment of an additional broad band (about 200 cm(-1) higher in frequency with respect to ν(s)) to a 1?:?2 complex has been supported by theoretical investigations. Experimental detection of both axial and equatorial forms of a cyclic trimer has been confirmed by calculated energetic and vibrational properties. The nature of hydrogen bonding has been examined within topological frameworks. The energetic partitioning within the 1?:?1 dimers has been elucidated with SAPT techniques. Interestingly, the interconversion pathway between two 1?:?1 structures has been explored and it was seen that the formation of the 1?:?1 complex affects the interconversion barrier on the ring puckering motion. The band contour analysis of gas phase FTIR experiments provided a consistent set of vibrational frequencies and anharmonic coupling constants, in good agreement with ab initio anharmonic vibrational calculations. Finally, from a series of cell-FTIR spectra recorded at different partial pressures of (CH(2))(3)S and HF monomers, the absorption signal of the 1?:?1 complex could be isolated which enabled to estimate the equilibrium constant K(p) = 0.023 at 298 K for the dimerization.     

Structures and infrared spectra of fluoride-hydrogen sulfide clusters from ab initio calculations: F(-)-(H2S)n, n = 1-5

Clusters formed between a fluoride anion and several hydrogen sulfide molecules have been investigated via ab initio calculations at the MP2 level of theory, using Dunning's augmented correlation consistent basis sets. Optimised geometries, vibrational frequencies, and enthalpy changes for the ligand association reactions are presented for clusters with up to five H2S ligands interacting with a F- anion. The minimum energy structure for the 1:1 F(-)-H2S complex features proton transfer from the H2S to the F- anion, forming a planar C(s) symmetry FH...SH- structure. For the F(-)-(H2S)2 cluster, the FH...SH- core remains and is solvated by a perturbed H2S ligand. For the larger F(-)-(H2S)(3-5) clusters, in addition to the FH...SH(-)-(H2S)n cluster forms, other minima featuring a 'solvated F-' anion are predicted. Calculated infrared spectra for the minima of each cluster size are presented to aid in assigning spectra from future experimental studies.     

The ring puckering potential function of trimethylene sulfide and trimethylene selenide

The rotational constants A,B and C are functions of the vibrational quantum numbers for the out-of-plane bending modes of trimethylene sulfide and trimethylene selenide. Infrared and microwave spectroscopy have been used to determine the dependence between these parameters. The height and shape of the barrier arising from combination of the ring bending modes is also determined. CNDO/2 calculations are used to predict the position of the hydrogen atoms of the methylene groups in trimethylene sulfide and trimethylene selenide. The four-membered rings are non-planar for several vibrational states of the ring bending modes.     

Electron and hydrogen transfer in small hydrogen fluoride anion clusters

A new stable structure has been found for the anion clusters of hydrogen fluoride. The ab initio method was used to optimize the structures of the (HF)(3)(-), (HF)(4)(-), (HF)(5)(-), and (HF)(6)(-) anion clusters with an excess "solvated" electron. Instead of the well-known "zig-zag" (HF)(n)(-) structure, a new form, (HF)(n-1)F(-)···H, was found with lower energy. In this new form, the terminal hydrogen atom in the (HF)(n)(-) chain is separated from the other part of the cluster and the inner hydrogens transfer along the hydrogen bonds toward the outside fluoride. The negative charge also transfers from the terminal HF molecule of the chain to the center fluoride atoms. The (HF)(n)(-) clusters for n = 4, 5, and 6 have not yet been observed experimentally. These results should assist in the search for these systems and also provide a possible way to study the proton and electron transfer in some large hydrogen bonding systems.     

The ultraviolet photodissociation of axial and equatorial conformers of 3-pyrroline

Resolved sets of photoproducts arising from the photodissociation of axial and equatorial conformers of 3-pyrroline have been observed using H(Rydberg) atom photofragment translational spectroscopy following excitation in the wavelength range of 250-213 nm. 3-pyrroline (alternatively 2,5-dihydropyrrole) is a five membered partially saturated heterocycle in which the bonding around the N atom is pyramidal (sp(3) hybridized) and the N-H bond can lie either axial or equatorial to the ring. Careful analysis of total kinetic energy release data derived from H atom time-of-flight measurements reveals excitation of the 3-pyrrolinyl cofragment consistent with N-H bond fission in both the axial and equatorial conformers. This allows determination of the energy difference between the ground state conformers to be 340±50 cm(-1) and the N-H bond strength for axial and equatorial conformers as 31,610±50 and 31,270±50 cm(-1), respectively.     

Stable dialkyl ether/poly(hydrogen fluoride) complexes: dimethyl ether/poly(hydrogen fluoride), a new,convenient, and effective fluorinating agent

The preparation, (1)H, (13)C, and (19)F NMR structural characterization as well as with DFT-based theoretical calculations of stable dialkyl ether/poly(hydrogen fluoride) complexes are reported. Dimethyl ether/poly(hydrogen fluoride) (DMEPHF), are stable complexes of particular interest and use. The DFT calculations, that are in agreement with NMR data, suggest a cyclic poly(hydrogen fluoride) bridged structure for DMEPHF. The complex, DME-5 HF was found to be a convenient and effective new fluorinating agent with the ease of workup and applied to several fluorination reactions, such as the hydrofluorination and bromofluorination of alkenes, and fluorination of alcohols giving good to excellent yield with high selectivity. Homologous dialkyl ether/poly(hydrogen fluoride) (R(2)O/[HF](n,), R = Et, nPr) systems are also stable and suitable for fluorination reactions.     

Shape of 4S- and 4R-hydroxyproline in gas phase

The alpha-amino acids 4(S)-hydroxyproline and 4(R)-hydroxyproline have been studied under isolation conditions in gas phase using laser-ablation molecular-beam Fourier transform microwave spectroscopy. Two conformers of each molecule have been detected in the jet-cooled rotational spectrum. The most stable conformer in both molecules exhibits an intramolecular N...H-O hydrogen bond (configuration 1) between the hydrogen atom of the carboxylic group and the nitrogen atom. The second conformer is characterized by an intramolecular N-H...O=C hydrogen bond (configuration 2). The conformers of 4(R)-hydroxyproline adopt a C(gamma)-exo puckering, while those of 4(S)-hydroxyproline present a C(gamma)-endo ring conformation. These ring conformations, which show the same propensity observed in collagen-like peptides, are stabilized by additional intramolecular hydrogen bonds involving the 4-hydroxyl group, with the exception of the most stable form of 4(S)-hydroxyproline for which a n-pi interaction between the oxygen atom of the 4-hydroxyl group and the carboxyl group carbon seems to be established. A gauche effect could be also contributing to stabilize the observed conformers.     

Conformation and stability of the hydrogen-bonded complex 6-oxabicyclo

The hydrogen-bonded complex between 6-oxabicyclo[3.1.0]hexane and hydrogen chloride was investigated by microwave spectroscopy in a supersonic jet. A dual flow pulsed valve was used to preclude chemical reaction between the monomers. Only the equatorial conformer was observed and the spectra of three isotopomers, (C5H8O, H35Cl), (C5H8O, H37Cl) and (C5H8O, D35Cl), were measured. The derived structure of the complex has Cs symmetry with the hydrogen chloride pointing to the domain of the equatorial lone pair of electrons at the oxygen atom. The three atoms involved in the hydrogen bond adopt a bent arrangement with a O...H distance of 1.77(4) A, a (O...H-Cl) angle of 115(4)degrees, and a deviation of 15.4(14)degrees of the hydrogen bond from collinearity. In agreement with the experimental results, ab initio calculations predict the equatorial form to be the most stable one.     

Hydrogen-bond interaction in 1:1 complexes of tetrahydrofuran with water, hydrogen fluoride, and ammonia: a theoretical study

Ab initio and density-functional theory electronic structure calculations have been performed for the 1:1 complexes of tetrahydrofuran with water, hydrogen fluoride, and ammonia. Upon hydrogen bonding with H2O and HF, the structure of tetrahydrofuran (THF) remains relatively unchanged with the exception of THF sites involved in hydrogen-bonding interaction. But the similar findings are not true, upon hydrogen bonded with NH3, where the C2 symmetry of THF changed. The hydrogen-bonding strength for the 1:1 complexes of THF with water, HF, and NH3 is found to be in the order HF>H2O>NH3, which is well characterized by the order in bond angles O2H15F14, O2H16O14, and O2H15N14 closer to linearity, respectively, and the redshifted of stretching frequencies of upsilon(FH), upsilon(OH), and upsilon(NH), respectively. This work is an attempt to provide important predictions and to aid in future experimental and theoretical studies towards the understanding of such hydrogen-bonded van der Waals systems.