Rotational isomers of small molecules in noble-gas solids: From monomers to hydrogen-bonded complexes

Molecular conformation, quantum tunneling, and hydrogen bonding play important roles in various photochemical processes. We have studied a number of small molecules possessing rotational isomerism (HONO, formic acid, acetic acid, etc.) isolated in noble-gas solid matrices. Selective vibrational excitation efficiently promotes the conformational change in the excited molecule, which allows preparation of higher-energy conformers. Stability of the higher-energy conformers is often limited by quantum tunneling of hydrogen as observed for some carboxylic acids (formic, acetic, etc.). The tunneling mechanism is supported by the strong H/D isotope effect and characteristic temperature dependence with a clear low-temperature limit. The reaction barrier height is an important factor in a tunneling process; however, other factors also play an essential role. The energy mismatch between the initial state of the higher-energy conformer and accepting state of the ground-state conformer is probably important. Hydrogen bonding can change tunneling decay rate of unstable conformers. The trans–cis formic acid dimer was prepared by vibrational excitation of the trans–trans form in neon and argon matrices. Tunneling decay of cis formic acid is substantially slower in the dimeric form compared to monomer, especially in solid neon. This stabilization effect is explained by a complexation-induced increase of reaction barrier, which is confirmed computationally. The complex between cis formic acid and water was prepared in an argon matrix and found to be stable at low-temperatures. These results show that intrinsically unstable conformational structures can be thermodynamically stabilized in asymmetrical hydrogen-bonded network. This effect occurs when the energy difference between conformers is smaller than the hydrogen bond interaction energy, which allows chemistry of unstable conformers to be studied.     

Rotational Spectroscopy of 2-Furoic Acid and Its Dimer: Conformational Distribution and Double Proton Tunneling

Structural and tunneling properties of the 2-furoic acid (FA) monomer and dimer were investigated using rotational spectroscopy and DFT calculations. CREST, a conformational ensemble space exploration tool, was used to identify all possible low-energy conformations of the FA monomer and dimer, followed by the DFT geometry optimization and harmonic frequency calculations. Broadband rotational spectra in the 2–6 and 8–12 GHz regions were recorded in a supersonic jet expansion. The monomeric FA was found to exist dominantly as three different conformers: I , II , and III in a jet, with I and II taking on the cis-COOH configuration while III having the trans-COOH configuration. For the FA dimer, only the I – II conformer was observed experimentally, whereas the symmetric I – I and II – II conformers were not observed because of their zero dipole moments. The analysis of the splittings in the rotational transitions of I – II allowed one to extract the tunneling splitting to be 1056.0(12) MHz. The barrier height was determined to be ∼442 cm⁻¹ using the scaled potential energy scans at several different levels of theory.     

Conformational analysis ofortho-substituted diphenyl ethers and diphenylmethanes with linear substituents

Conformational analysis of di-ortho-substituted diphenylmethanes and Biphenyl ethers containing I, CCH, and CCCCH substituents was carried out by the molecular mechanics method using the MM3 program. Several minima on the potential energy surface, which correspond to thegg, gt, tg, andort conformations, were found. An increase in the length of the linear substituent results in a substantial decrease in the difference in the relative energies of conformers. Barriers to conformational transitions between thegt, tg, andort conformers are less than 2 kcal mol^–1. The transitionort-gg requires expenditure of energy of up to 5 kcal mol^–1. Two valleys of centrosymmetric pairs of thegt, tg, andort conformers are separated by a barrier of up to 6 kcal mol^–1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No, 12, pp, 2882–2885, December, 1996.     

Structure of the 2-isopropylaminoethanol isolated molecule: Conformational analysis and intramolecular interactions

In this paper, a systematic exploration of all the possible conformers of 2-isopropylaminoethanol (2-IPAE) was carried out using the Density Functional Theory (B3LYP) and the 6-311++G(d,p) basis set. At this level, 66 unique conformers within a Gibbs energy range of ca. 31 kJ mol⁻¹ were found in the potential energy surface and their geometrical and thermodynamic properties were determined and discussed. A significant molecular strain was evidenced by the dihedrals and distances between non-bonded hydrogen atoms. According to the geometrical parameters, a O–H···N hydrogen bond was found to be present in the three most stable conformers, representing 68% of the conformational composition at 298.15 K. The energetic and geometrical data derived from the DFT calculations were further complemented by a NBO analysis of the most stable conformers.     

Conformational analysis of 5-substituted 1,3-dioxanes

Quantum-chemical study on the potential energy surface of 5-alkyl- and 5-phenyl-1,3-dioxanes at the RHF/6-31G(d) level of theory revealed two pathways for conformational isomerizations of the equatorial and axial chair conformers. Potential barriers to this process were estimated. The Gibbs conformational energies ΔG° of substituents at C⁵ in the 1,3-dioxane ring were determined on the basis of experimental (¹H NMR) and theoretical vicinal coupling constants, which turned out to be consistent with published data.     

Conformational Behavior of Rigid and Dancing (1,3)(1,4)Cyclophanes

Annelation or substitution of the (1,4)-bridged ring of [2₂](1,3)(1,4)cyclophane 4 , such as in 8 and 9 , respectively, result in two different conformational ground states in each case. Each conformational ground state involves a different destabilizing factor arising from one form of non-bonding interaction. Only the conformers 8b and 9b were isolated experimentally. Their corresponding precursors 11 and 23 were also found to be conformationally rigid. Only the conformers 11a and 23a were isolated indicating an abrupt change in conformational preference going from the dithia[3₂]cyclophanes to the respective [2₂]cyclophanes. The selectively methylated [2₂]cyclophanes 27 , 31 and 32 were, however, found to be conformationally mobile. There is an increase of about 10–15 kJ mol^?1 in conformational energy barrier going from 4 to 27 or 31 . This is consistent with the fact that the presence of the methyl substituents increases the relative conformational ground-state energy more than it would affect the transition-state energy. The conformational barrier of 32 was unexpectedly found to be similar to those of 27 and 31 . This could be explained by a decrease in the transition-state energy due to an inward bending of the (1,4)-bridged ring accompanied by a decrease in conformational ground-state energy due to an outward bending of the methyl groups in 32 .     

Conformational Landscape,Chirality Recognition and Chiral Analyses: Rotational Spectroscopy of Tetrahydro-2-Furoic Acid⋅⋅⋅Propylene Oxide Conformers

A chiral adduct formed between a chiral carboxylic acid, tetrahydro-2-furoic acid (THFA), and a chiral ester, propylene oxide (PO), was investigated using rotational spectroscopy and DFT calculations. Isolated THFA exists dominantly as three different conformers: I , II , and III in a jet, with I and II taking on the trans-COOH configuration and III having the cis-COOH configuration. We utilized CREST, a conformational ensemble space exploration tool, to identify the possible conformations of the binary adduct, THFA⋅⋅⋅PO. Subsequent DFT geometry optimizations predicted about two hundred homochiral and heterochiral binary structures with 28 low energy structures within an energy window of 15 kJ mol⁻¹. A rich broadband rotational spectrum was obtained with a mixture of trace amounts of THFA+PO in neon in a supersonic jet expansion. Six THFA⋅⋅⋅PO conformers were identified experimentally. Kinetically favored binary products which contain trans-COOH I dominate among the observed conformers, while thermodynamically more stable adducts were also detected. Detailed analyses of the structures of the observed conformers show interesting chirality-controlled structural preferences. Such non-covalently bound chiral contact pairs are the foundation of chiral-tag rotational spectroscopy, an exciting new analytical application of rotational spectroscopy for determination of enantiomeric excess. Enantiomeric excess analyses were performed and the results are discussed.     

Interactions intramoléculaires. XXVI—Constantes de couplage et hétérogénéités conformationnelles dans une série de R-3 et R-5 cyano-4 cyclohexènes deutériés (R=méthyl ou t-butyl)

For trans-3-R- and 5-R-1-acetoxy-4-cyanocyclohexene-6,6-d₂ the molar fractions of diequatorial conformers are 0.83 (3-methyl), 0.68 (5-methyl), 0.57 (3-tert-butyl) and 0.55–0.69 (5-tert-butyl). For the last two compounds the values of the coupling constants are in agreement with the hypothesis of an ee?aa equilibrium. For the cis isomers, the molar fractions of equatorial alkyl conformers are 0.76 (3-methyl and 5-methyl) and 1.0 (3-tert-butyl and 5-tert-butyl). The cis-1-acetoxy-3-tert-butyl-4-methoxycarbonyl-cyclohexene presents a conformational heterogeneity. The conformational free energy of the methyl group in position 4 has been evaluated as ?0.6 kcal mol^?1 (2.5 kJ mol^?1).     

Rigorous Conformational Analysis of Pyrrolidine Enamines with Relevance to Organocatalysis

It has been suggested that the origin of regio‐ and stereoselectivity in Michael additions of pyrrolidine enamines is achieved by thermodynamic rather than kinetic control through distinct conformational preferences of the enamines. We assess this proposal by elaboration of a computational protocol that warrants sufficient accuracy. The small energy differences between the conformers necessitate a high accuracy of the electronic structure method which, in addition, must allow for computationally feasible calculations of a large number of conformers. Our protocol is based on density functional theory which we validated against explicitly correlated coupled cluster theory. The results are in agreement with the available experimental data, but illustrate that conformational preferences determined for one enamine are not readily transferable to other types of enamines. We found that an appropriate conformational sampling is inevitable to arrive at meaningful conclusions. Most prominently, s‐cis and s‐trans conformers are similarly stable for aldehyde‐ and ketone‐derived enamines. The regio‐ and stereoselectivity in Michael additions of pyrrolidine‐derived enamines can not be explained by pronounced stability differences of the enamine isomers and conformers in general, disproving the thermodynamic‐control hypothesis. The elucidation of the origin of regio‐ and stereoselectivity requires further theoretical investigations of the elementary steps of Michael additions.     

Conformational composition of the 2,4,6-trimethyl-1,3,2-dioxaborinane stereoisomers

A study of conformational transformations of 2,4,6-trimethyl-1,3,2-dioxaborinane cis- and trans-isomers in non-empirical quantum-chemical HF/6-31G (d) and PBE/3z approximations showed that the transformation routes include the sofa conformers with different orientations of the substituents at the ring atoms C⁴ and C⁶ through the transition states corresponding to diequatorial, axial-equatorial, and dixial conformations of the 2,5-twist form. The calculation and ¹H NMR data show that the conformational equilibrium of cis-isomer is almost entirely shifted to diequatorial sofa, and the trans-form is characterized by the interconversion between the two axial-equatorial sofa conformers.     

Fluorine Substitution Effects on Flexibility and Tunneling Pathways: The Rotational Spectrum of 2‐Fluorobenzylamine

The effect of ring fluorination on the structural and dynamical properties of the flexible model molecule 2‐fluorobenzylamine has been studied by rotational spectroscopy in free‐jet expansion and quantum chemical methods. The complete potential energy surface originating from the flexibility of the aminic side chain has been calculated at the B3LYP/6‐311++G** level of theory and the stable geometries were also characterized with MP2/6‐311++G**. The rotational spectra show the presence of two of the predicted four stable conformers: the global minimum (I), in which the side chain’s dihedral angle with the phenyl plane is almost perpendicular, is stabilized by an intramolecular hydrogen bond between the fluorine atom and one hydrogen of the aminic group; and a second conformer II (E_II?E_I≈5 kJ mol^?1) in which the dihedral angle is smaller and the amino group points towards the aromatic ortho hydrogen atom. This conformation is characterized by a tunneling motion between two equivalent positions of the amino group with respect to the phenyl plane, which splits the rotational transition. The ortho fluorination increases, with respect to benzylamine, the tunneling splitting of this motion by four orders of magnitude. The motion is analyzed with a one‐dimensional flexible model, which allows estimation of the energy barrier for the transition state as approximately 8.0 kJ mol^?1.     

13CMR-Tieftemperatur-Untersuchungen an Cyclooctan-Konformeren

The conformational equilibria of a variety of monosubstituted cyclooctanes is determined by low temperature ¹³CMR spectroscopy. ¹³C shifts allow conclusions to be made regarding the geometry of the conformers. For some conformational processes ΔG^# is obtained by complete line shape analysis.     

Shapes and Internal Dynamics of the 1:1 Adducts of Ammonia with trans and gauche Ethanol: A Rotational Study

Two 1:1 adducts of ammonia with ethanol have been characterized by using pulsed‐jet FT microwave spectroscopy. They are formed with two different (trans and gauche), stable conformers of ethanol. Several internal‐dynamics effects are reflected in the features of the rotational spectra. The trans complex shows the tunneling effects owing to internal rotation of both ammonia and the methyl group. The rotational transitions of the gauche species exhibit a small splitting that is related to tunneling through the potential‐energy barrier between the two equivalent minima.     

Application of J(C,H) coupling constants in conformational analysis

Conformational equilibria for a number of methyl substituted 1,3-dioxanes 1, 1,3-oxathianes 2 and 1,3-dithianes 3 were calculated at the HF and DFT levels of theory. In addition to the chair conformers also the energetically adjacent twist conformers were considered and the positions of the corresponding conformational equilibria estimated. On the basis of the global energy minima of conformers, participating in the conformational equilibria, the ¹J_C,Hax,equ coupling constants were calculated using the GIAO method and compared with the experimental values obtained from ¹³C,¹H coupled ¹³C NMR spectra. The Perlin effect, the influence of the solvent and the suitability of this NMR parameter for assigning the conformational equilibria present are critically discussed.     

The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib)

The simplest non-proteinogenic amino acid α-aminoisobutyric acid (Aib), an analogue of glycine and alanine, has been vaporized by laser ablation and probed by high-resolution Fourier transform microwave spectroscopic techniques. Comparison of the experimental rotational and ¹⁴N nuclear quadrupole constants with that predicted ab initio has allowed the identification of three conformers of Aib exhibiting three types of hydrogen-bond interactions I (NH⋅⋅⋅O=C, cis-COOH), II (OH⋅⋅⋅N, trans-COOH), and III (N−H⋅⋅⋅O−H, cis-COOH) within the amino acid backbone. The observation of conformer III, not detected previously for related proteinogenic amino acids with a nonpolar side chain in a supersonic expansion, indicates that the presence of the methyl groups should restrict the conformational relaxation from conformer Aib-III to Aib-I. For conformer Aib-II, the rotational spectra of the ¹³C isotopomers reveal a tunneling motion arising from the two equivalent methyl groups in the molecule. The observation of a single spectrum at the midpoint between those predicted for the two ¹³C of the methyl groups has been explained by considering a double-minimum potential function with a low-energy interconversion barrier for a large amplitude internal motion. This singular fact has been corroborated by the anomalous centrifugal distortion effects determined in conformer Aib-II.     

Conformational Relaxation of p‐Phenylenevinylene Trimers in Solution Studied by Picosecond Time‐Resolved Fluorescence

Two p‐phenylenevinylene (PV) trimers, containing 3′‐methylbutyloxyl (in MBOPV3) and 2′‐ethylhexyloxyl (in EHOPV3) side chains, are used as model compounds of PV‐based conjugated polymers (PPV) with the purpose of clarifying the origin of fast (picosecond time) components observed in the fluorescence decays of poly[2‐methoxy‐5‐(2′‐ethylhexyloxy)‐p‐phenylenevinylene] (MEH‐PPV). The fluorescence decays of MBOPV3 and EHOPV3 reveal the presence of similar fast components, which are assigned to excited‐state conformational relaxation of the initial population of non‐planar trimer conformers to lower‐energy, more planar conformers. The rate constant of conformational relaxation k_CR is dependent on solvent viscosity and temperature, according to the empirical relationship k_CR=aη_o^?α?exp(?αE_η/RT), where aη_o^?α is the frequency factor, η_o is the pre‐exponential coefficient of viscosity, E_η is the activation energy of viscous flow. The empirical parameter α, relating the solvent microscopic friction involved in the conformational change to the macroscopic solvent friction (α=1), depends on the side chain. The fast component in the fluorescence decays of MEH‐PPV polymers (PPVs), is assigned to resonance energy transfer from short to longer polymer segments. The present results call for revising this assignment/interpretation to account for the occurrence of conformational relaxation, concurrently with energy transfer, in PPVs.     

Conformational analysis of 2-methyl-5-alkyl- and 5-aryl-1,3,2-dioxaborinanes

Quantum chemical study of conformational isomerization of 2-methyl-5-alkyl- and 5-aryl-1,3,2-dioxaborinanes using RHF/6-31G(d) method led to the conclusion that the equilibrium between equatorial and axial sofa conformers is shifted to the latter form. Based on the experimental and theoretically calculated vicinal coupling constants J _HH the quantitative conformational composition and the values of ΔG ⁰ for substituents at the C⁵ ring atom were established.     

A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method

CoMFA analysis, a widely used 3D-QSAR method, has limitations to handle a set of SAR data containing diverse conformational flexibility since it does not explicitly include the conformational entropic effects into the analysis. Here, we present an attempt to incorporate the conformational entropy effects of a molecule into a 3D-QSAR analysis. Our attempt is based on the assumption that the conformational entropic loss of a ligand upon making a ligand-receptor complex is small if the ligand in an unbound state has a conformational propensity to adopt an active conformation in a complex state. For a QSAR analysis, this assumption was interpreted as follows: a potent ligand should have a higher conformational propensity to adopt an `active-conformation'-like structure in an unbound state than an inactive one. The conformational propensity value was defined as the populational ratio, N<sub>active</sub>/N<sub>stable</sub>, of the number of energetically stable conformers, N<sub>stable</sub>, to the number of `active-conformation'-like structures, N_active. The latter number was calculated by counting the number of conformers that satisfied the structural parameters deduced from the active conformation. A set of SAR data of imidazoleglycerol phosphate dehydratase inhibitors containing 20 molecules with different conformational flexibility was used as a training set for developing a 3D structure-activity relationship by a CoMFA analysis with the conformational propensity value. This resulted in a cross-validated squared correlation coefficient of the CoMFA model with the conformational propensity value (R ² _cross = 0.640) higher than that of the standard CoMFA model (R ² _cross = 0.431). Then we evaluated the quality of the CoMFA models by predicting the inhibitory activity for a new molecule.     

Pyrrolizidine alkaloids necine bases: II. Conformational analysis of free bases

Molecular mechanics calculations were applied to the conformational analysis of two diasteroisomers, the pyrrolizidine alkaloids (PAs) retronecine and heliotridine. The application of reoptimized parameters for H bonding corrected the tendency of MM3(92) calculations to give unrealistic H(DOTTED BOND)O distances for intramolecular OH interactions occurring in both diasterisomers. Inversions in the H-bond direction of exo-retronecine and in the relative stability of heliotridine endo–exo conformers were also observed with the application of the new parameters. A set of probable conformers was obtained for each diasterisomer, based on conformational and Boltzmann population analysis. Only exo-puckered conformers were found in the retronecine set, whereas both exo- and endo-puckered conformers were obtained for heliotridine. Transition state conformations supplied arguments supporting the design of models for H-bond interconversion in the case of exo-retronecine and for the exo–endo interconversion of heliotridine. Reactivity behaviors and ¹H-NMR data of both diasterisomers were elucidated in light of the theoretical results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1853–1861, 1998     

Quantum-chemical study of the molecular forms of vanillin

Equilibrium structural parameters, dipole moments, relative energies, vibration spectra, and ionization potentials of various conformers of benzoid (B), p- and o-quinoid (Q), and deprotonated anionic forms of vanillin in a vacuum and in a polarizable medium with dielectric properties of water were calculated by the quantum-chemical method (U)B3LYP/cc-pVTZ. The intramolecular hydrogen bond in free vanillin benzoid molecule B1 is characterized by the energy of 4 kcal mol⁻¹ and by the barrier of cleavage 8 kcal mol⁻¹ that correspond to the conformational transition B1 → B2. The energy of the optimal p-quinoid conformer (Q1) is 22 kcal mol⁻¹ larger than the energy of B1 in a vacuum and 15 kcal mol⁻¹ in water. The p-quinoid forms greatly exceeds the benzoid forms by dipole moment, electrophilicity, and nucleophilicity. The structure calculated for the anion is intermediate between benzoid and p-quinoid forms, and the calculated energy of polarization stabilization in water is 57 kcal mol⁻¹.