The conformation of levopimaric acid investigated by high-level ab initio MO calculations. Possibility of the CH/π hydrogen bond

Ab initio MO calculations were carried out, at the MP2/6-311G(d,p) level of approximation, to investigate the conformation of levopimaric acid. It has been found that the folded conformation is more stable than the extended conformation. The result is consistent with the documented experimental data. The reason for the relative stability of the folded conformation has been sought in the context of the CH/π hydrogen bond. Short non-bond distances have been disclosed between CHs in the 10β angular methyl group and sp² carbons of the conjugated diene ring in the more stable folded conformers of model compounds. We suggest that the folded conformation of levopimaric acid is a consequence of an attractive molecular force, the CH/π hydrogen bond.     

Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study

We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree–Fock (HF)/6‐31G*, HF/6‐31G**, second‐order Møller–Plesset perturbation (MP2)/6‐31G*, and MP2/6‐31G** levels for three Src homology 3 (SH3) domains and five proline‐recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline‐rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline‐rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Intramolecular hydrogen bond C-H⋯N in 1,1′-divinyl-2,2′-diimidazolyl according to the data of ab initio calculations and QTAIM analysis

By non-empirical ab initio quantum chemical calculation the spatial structure of 1,1′-divinyl-2,2′-diimidazolyl is determined and the formation of intramolecular hydrogen bonds of the C-H...N type in it is established. It is evidenced by energy preference for the conformation in which there is a short contact between the α-proton of the vinyl group and the endocyclic nitrogen atom (2.28 Å), creating favorable conditions for the formation of a six-membered chelate cycle. An analysis of the topological characteristics of the electron density and the reduced electron density gradient also give evidence in favor of the formation of a weak intramolecular hydrogen bond C-H...N. The estimation of the hydrogen bond energy by the Espinosa method results in a value below 3 kcal/mol.     

The role of intra- and intermolecular hydrogen bonds in the formation of β-cyclodextrin head-to-head and head-to-tail dimers. The results of ab initio and semiempirical quantum-chemical calculations

The conformation of a free -cyclodextrin molecule optimized by the MNDO/PM3 quantum-chemical calculations has C₇ symmetry. The right orientation of the interglucose hydrogen bonds in -cyclodextrin, in which the 2-OH groups act as the proton donors and the O atoms of the nearby 3"-OH groups function as the proton acceptors, is advantageous for thermodynamic reasons. The ring of seven H bonds thus formed stabilizes the symmetrical form of -cyclodextrin. The -cyclodextrin head-to-head dimer has D ₇ symmetry and consists of molecules whose 2-OH groups partcipate as proton donors in the formation of fourteen complementary intermolecular hydrogen bonds. The energy of H bonds in the -cyclodextrin monomer and dimer was estimated to be 1.0--1.4 kcal mol^–1. Of the two possible -cyclodextrin dimers, the head-to-tail dimer is more thermodynamically stable. The thermodynamic preference of the right orientation of the inter-glucose H bonds in -cyclodextrin was confirmed by the MP2/6-31G(d,p)//6-31G(d,p) ab initio calculations for maltose (-glucodioside). The maltose molecule with inter-glucose H bonds of the type 2-OHO(3")-H is more stable than the structure with the H-(2)OH-O(3") orientation of H bonds with a difference of 2.7 kcal mol^–1. According to the MNDO/PM3 method, the maltose structure with the right H bond orientation is more stable by 3.1 kcal mol^–1.     

The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates

The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.     

Spectra and structure of small ring compounds—LX. Raman and infrared spectra,conformational stability,normal coordinate analysis,and ab initio calculations of cyclobutyl acetylene

The Raman spectra (3400 to 10 cm⁻¹ of gaseous, liquid (with qualitative depolarization values) and solid cyclobutyl acetylene, c-C₄H₇CCH, have been recorded. Additionally, the infrared spectra (3500 to 90 cm⁻¹ of the gas and solid have been obtained. The spectra of the fluid phases are consistent with two stable conformers existing at ambient temperature. These data have been interpreted on the basis that the equatorial conformer is more stable than the high energy axial form in both the gas- and liquid-phases, and is the only conformer present in the solid. Two Q-branches are observed in the low frequency vibrational spectra of the gas at 133 and 118 cm⁻¹ and are assigned to the fundamental ring puckering vibration and an associated upper state transition of the low energy equatorial conformer. These data have been used to approximate the form of the potential function governing ring inversion. Experimental values for the enthalpy difference between the two conformers have been determined for both the gas, 282 ± 49 cm⁻¹, and the liquid, 181 ± 15 cm⁻¹, from relative intensities of a pair of Raman lines over 71 and 100°C temperature ranges, respectively. The structure, conformational stability, inversion barrier and vibrational frequencies have been determined by ab initio calculations using the 3-21G and/or 6-31G* basis sets. These calculated results are discussed in comparison to those determined from experiment and to corresponding quantities for some similar molecules.     

MO investigations on lignin model compounds: IX. A PCILO study of the hydrogen bond O-H…O and O-H…N type formed by phenol with some proton acceptors

A systematic PCILO study has been carried out on the intermolecular hydrogen bond formed by phenol with proton acceptors such as acetone, ether, p-benzoquinone, N,N-dimethylformamide, trimethylamine, pyridine, acetonitrile and acrylonitrile. The complexes studied form hydrogen bonds with energy intervals of 20 − 45 kJ mol⁻¹ at distances R_O…Y = 0.265 − 0.300 nm (Y=N,0). For the system phenol-pyridine both the 1:1 complex PhPy and the 2:1 complex Ph₂Py were also studied. The calculated hydrogen bond energies are compared and discussed with experimental data from the literature. The calculated hydrogen bond and O-H stretching force constants are in range expected.     

Preference of intra- and intermolecular cation-π interaction: cis-trans geometrical effects of amide bond on the interaction mode

An intermolecular cation-π interaction is observed in trans-amide 3, whereas an intramolecular interaction is observed in cis-amide 4, suggesting that cis-trans conformational difference plays a critical role in the preference of the interaction modes.     

The conformation of alkyl cyclohexanones and terpenic ketones. Interpretation for the ‘alkylketone effect’ based on the CH/π(CO) hydrogen bond

Ab initio MO calculations were carried out, at the MP2/6-311++G(d,p)//MP2/6-311G(d,p) level, to investigate the Gibbs free energy of the conformational isomers of 2-alkyl, 3-alkyl, and 4-alkyl cyclohexanones. The calculation gave results consistent with the general trend experimentally found. The genesis of stabilization of the axial conformers in 2- and 3-alkyl cyclohexanones, as compared to the structurally corresponding cyclohexane derivatives, was sought in the context of the attractive CH/π(CO) hydrogen bond. In support of this hypothesis, short nonbonded distances have been noted between CHs in the alkyl group and the carbonyl carbon in the relevant axial conformers. Calculations were also carried out to study the conformational energies of several terpenic ketones. For isomenthone, more than a half molecular fraction (ca. 55%) has been suggested to be in the isopropyl-axial conformation, while for isocarvomenthone ca. 77% has been suggested to be in the axial-isopropyl conformation; this is consistent with bibliographic experimental data. A crystallographic database search has provided results compatible with this conclusion. We suggest that the relative stability of the axial alkyl substituent, often observed in terpenic and steroidal ketones is rationalized in terms of an attractive molecular force, the CH/π(CO) hydrogen bond.     

Clathrate formation of Diels–Alder adduct of phencyclone and acenaphthylene. Key role of CH/π and bidentate CH/O interactions of the phenanthrene ring in construction of host framework

Two clathrate hosts (3a and 3b) were synthesized via the Diels–Alder reaction of phencyclone (1a) and tetracyclone (1b) with acenaphthylene (2), and the clathrate formation properties of these hosts towards a variety of organic guests were investigated. In the presence of aprotic solvents (i.e., aromatic, ketonic and etheric solvents), host 3a formed inclusion complexes with a 2:1 stoichiometric host/guest ratio, whereas 3b primarily formed 1:1 complexes. The desolvation temperatures of the 3a·guest complexes were extremely high in comparison to the boiling points of the pure guest liquids and were also much higher than those of the corresponding 3b·guest complexes, which contain the conformationally flexible stilbene moiety. Structural analyses of the 3a·guest complexes (i.e., 3a·benzene, 3a·toluene, 3a·1,4-dioxane, 3a·acetone and 3a·pentan-3-one) show that the aromatic CH/π (edge-to-face) interactions between phenanthrene and the acenaphthene ring as well as the interaction of the ‘bidentate’ CH/O hydrogen bond between the phenanthrene-ring hydrogen and the bridged carbonyl oxygen play a key role in the construction of the characteristic host ‘column’ structures. The guest molecule of the 3a·benzene complex is held between the stacking columns by aromatic CH/π interactions of the acenaphthene rings of adjacent host molecules. The stable clathrate formation of 3a is discussed based on X-ray structural analyses of six clathrates and PM6 molecular orbital calculations for the clathration model of 3a·benzene.     

The C3-bending vibrational levels of the C3-Kr and C3-Xe van der Waals complexes studied by their Ã-X̃ electronic transitions and by ab initio calculations

Fluorescence excitation spectra and wavelength-resolved emission spectra of the C(3)-Kr and C(3)-Xe van der Waals (vdW) complexes have been recorded near the 2(2-)(0), 2(2+)(0), 2(4-)(0), and 1(1)(0) bands of the A?(1)Π(u)-X?(1)Σ(g)(+) system of the C(3) molecule. In the excitation spectra, the spectral features of the two complexes are red-shifted relative to those of free C(3) by 21.9-38.2 and 34.3-36.1 cm(-1), respectively. The emission spectra from the A? state of the Kr complex consist of progressions in the two C(3)-bending vibrations (ν(2), ν(4)), the vdW stretching (ν(3)), and bending vibrations (ν(6)), suggesting that the equilibrium geometry in the X? state is nonlinear. As in the Ar complex [Zhang et al., J. Chem. Phys. 120, 3189 (2004)], the C(3)-bending vibrational levels of the Kr complex shift progressively to lower energy with respect to those of free C(3) as the bending quantum number increases. Their vibrational structures could be modeled as perturbed harmonic oscillators, with the dipole-induced dipole terms of the Ar and Kr complexes scaled roughly by the polarizabilities of the Ar and Kr atoms. Emission spectra of the Xe complex, excited near the A?, 2(2-) level of free C(3), consist only of progressions in even quanta of the C(3)-bending and vdW modes, implying that the geometry in the higher vibrational levels (υ(bend) ≥ 4, E(vib) ≥ 328 cm(-1)) of the X? state is (vibrationally averaged) linear. In this structure the Xe atom bonds to one of the terminal carbons nearly along the inertial a-axis of bent C(3). Our ab initio calculations of the Xe complex at the level of CCSD(T)∕aug-cc-pVTZ (C) and aug-cc-pVTZ-PP (Xe) predict that its equilibrium geometry is T-shaped (as in the Ar and Kr complexes), and also support the assignment of a stable linear isomer when the amplitude of the C(3) bending vibration is large (υ(4) ≥ 4).     

OH stretching force constants in complexes of water with F−, Cl−, Li+ ions and LiF,LiCl ion pairs by 6-31G ab initio MO calculations

Ab initio MO calculations using 6-31G and 6-31 + G (for complexes with F⁻ and LiF) basis sets have been carried out for complexes of H₂O (monomer and dimer) with F⁻, Cl⁻, Li⁺ ions as well as with LiF and LiCl ion pairs for the evaluation of the OH stretching force constants. The changes in force constants are discussed in terms of molecular interactions, cooperativity effect and interionic electrostatic interactions. It is noticed that the cooperativity effect also operates through ionic bonds in symmetrically hydrated ion pairs and that OH stretching force constants are found to increase in the case of solvent bound ion pairs and symmetrically hydrated halide ions showing anticooperativity effect.     

Does the A.T or G.C base-pair possess enhanced stability? Quantifying the effects of CH...O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations

An empirically based relationship between overall complex stability (-DeltaG degrees ) and various possible component interactions is developed to probe the question of whether the A.T/U and G.C base-pairs exhibit enhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approach suggests ca. 2-2.5 kcal mol-1 in additional stability for A.T owing to a group interaction containing a CH...O contact. Pairing geometry and the role of the CH...O interaction in the A.T base-pair were also probed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicated that Hoogsteen geometry is preferred over Watson-Crick geometry in A.T by ca. 1 kcal mol-1. Factors that might contribute to the preference for Hoogsteen geometry are a shorter CH...O contact, a favorable alignment of dipoles, and greater distances between secondary repulsive sites. The CH...O interaction was also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initio calculations support the result of the phenomenological approach that the A.T base-pair does have enhanced stability relative to hydrogen-bonded complexes with just N-H...N and N-H...O hydrogen bonds.     

Electrogeneration of (Z)-α-aroyloxy-β-aroylthiostilbenes and (Z)-4,5-diaryl-2-arylimino-1,3-oxathioles by cathodic reduction of monothiobenzils in the presence of electrophilic reagents. Computational B3LYP and RI-MP2 study on the relative stability of oxathiole compounds

Electrochemical reductions of monothiobenzils in the presence of either aroyl or carbonimidoyl dichlorides were carried out, yielding products with sulfur retention. Electrolyses in the presence of aroyl chlorides led to previously unknown (Z)-α-aroyloxy-β-aroylthiostilbenes in high to quantitative yields, whereas reactions in the presence of arylcarbonimidoyl dichlorides provided novel 4,5-diaryl-2-arylimino-1,3-oxathioles in fair to high yields. The molecular structures of (Z)-α-benzoyloxy-β-benzoylthio-4,4′-dimethylstilbene and (Z)-2-(2,4-dichlorophenylimino)-4,5-diphenyl-1,3-oxathiole were determined by X-ray crystallography. Also, ab initio HF, density functional B3LYP, and Møller-Plesset RI-MP2 procedures were applied to oxathiole compounds revealing that (Z)-isomers are more stable than (E)-isomers and that both isomers are separated by a relatively low activation barrier.     

Vibronic spectra,ab initio calculations,and structures of conformationally non-rigid molecules of oxalyl halides in the ground and lowest excited electronic states. Part V: Oxalyl chloridefluoride (COCl–COF)

The structure and conformational dynamics of the COCl–COF molecule in the ground and lowest excited electronic states were investigated theoretically by the CASPT2/cc-pVTZ method. The equilibrium geometric parameters, harmonic vibrational frequencies, potential functions of internal rotation, and adiabatic transition energies were obtained. According to the results of calculations, the molecule in the ground electronic state exist as the trans and gauche (dOCCO ~30–40°) conformers with a low potential barrier to gauche–gauche transition therefore it is impossible to exclude existence of the cis conformer (instead of gauche) with a very broad and flat potential minimum. For all the investigated excited electronic states of oxalyl chloridefluoride molecule calculations predicted the trans and cis conformers. The strong coupling of internal rotation around the C–C bond and non-planar vibrations of carbonyl fragments was found for the excited electronic states. The results of calculation were utilized for reanalysis of experimental \( \tilde{A}^{1} A^{\prime \prime} \leftarrow \tilde{X}^{1} A^{\prime} \) and \( \tilde{a}^{3} A^{\prime \prime} \leftarrow \tilde{X}^{1} A^{\prime} \) vibronic spectra reported in Kidd and King (J Mol Spectrosc 50:209–219 (1974), and ibid. 48:592–599 (1973)). The vibrational assignment that does not contradict the vibrational spectroscopy data and results of calculations was obtained.     

Accurate ab initio potential energy surface, thermochemistry, and dynamics of the Cl(2P, 2P(3/2) + CH4 → HCl + CH3 and H + CH3Cl reactions

We report a high-quality, ab initio, full-dimensional global potential energy surface (PES) for the Cl((2)P, (2)P(3/2)) + CH(4) reaction, which describes both the abstraction (HCl + CH(3)) and substitution (H + CH(3)Cl) channels. The analytical PES is a least-squares fit, using a basis of permutationally invariant polynomials, to roughly 16,000 ab initio energy points, obtained by an efficient composite method, including counterpoise and spin-orbit corrections for the entrance channel. This composite method is shown to provide accuracy almost equal to all-electron CCSD(T)/aug-cc-pCVQZ results, but at much lower computational cost. Details of the PES, as well as additional high-level benchmark characterization of structures and energetics are reported. The PES has classical barrier heights of 2650 and 15,060 cm(-1) (relative to Cl((2)P(3/2)) + CH(4)(eq)), respectively, for the abstraction and substitution reactions, in good agreement with the corresponding new computed benchmark values, 2670 and 14,720 cm(-1). The PES also accurately describes the potential wells in the entrance and exit channels for the abstraction reaction. Quasiclassical trajectory calculations using the PES show that (a) the inclusion of the spin-orbit corrections in the PES decreases the cross sections by a factor of 1.5-2.5 at low collision energies (E(coll)); (b) at E(coll) ≈ 13,000 cm(-1) the substitution channel opens and the H/HCl ratio increases rapidly with E(coll); (c) the maximum impact parameter (b(max)) for the abstraction reaction is ~6 bohr; whereas b(max) is only ~2 bohr for the substitution; (d) the HCl and CH(3) products are mainly in the vibrational ground state even at very high E(coll); and (e) the HCl rotational distributions are cold, in excellent agreement with experiment at E(coll) = 1280 cm(-1).     

Cation- and/or anion-directed reaction routes. Could the desolvation pattern of isostructural coordination compounds be related to their molecular structure?

The crystal and molecular structure of [Cu(ampf)(ClO₄)(MeOH)₂]ClO₄, (1), ampf = N,N′-bis(4-acetyl-5-methylpyrazol-3-yl)formamidine, determined by X-ray crystallography is described and compared with the structurally related copper(II) complexes, formed under similar experimental conditions, using Cu^II salts with different anions. The complex formation is discussed in view of the structures of cobalt(II) and nickel(II) complexes with the same organic ligand and different anions, also formed under similar reaction conditions. Solvent molecules coordinated to the central atom play an important role in biologic systems. To get a better insight into the desolvation mechanism, in this study the desolvation pattern of 1 is presented. As in literature little attention is paid to the desolvation mechanism of solvate complexes, the desolvation mechanism of three, potentially biologically active isostructural pairs of octahedral Ni^II and Co^II compounds with ampf and dmpc (3,5-dimethyl-1H-pyrazole-1-carboxamidine) ligands are evaluated and compared with the desolvation of 1. The results of the thermal data are discussed on the basis of structural features of the compounds. The minor differences in structures of the related compounds cannot be straightforwardly connected with the different solvent evaporation mechanism. To explain the differences found in desolvation pattern in isostructural Co^II and Ni^II complexes the Jahn-Teller effect is proposed.     

The resolution of trans-2,2-dichloro-3-methylcyclopropanecarboxylic acid via crystallization of its salts with (+)- and (−)-α-phenylethylamine, and the transformation of the resulting enantiomers into (R)- and (S)-dimethyl 2-methylsuccinates

The resolution of trans-2,2-dichloro-3-methylcyclopropanecarboxylic acid trans-1 was achieved by crystallization of its salts with (+)- and (−)-α-phenylethylamine. The chiral acids were converted into methyl esters 9, which upon reaction with sodium methoxide in methanol underwent a three-carbon ring cleavage, leading to the corresponding mono-orthoester derivatives 10. Acidic hydrolysis then gave the known (R)- and (S)-dimethyl 2-methylsuccinates 12.     

Determination of vibrational parameters of methanol from matrix-isolation infrared spectroscopy and ab initio calculations. Part 1 – Spectral analysis in the domain 11 000–200 cm

Infrared spectra of three isotopic species of methanol (¹²CH₃¹⁶OH, ¹³CH₃¹⁶OH, ¹²CH₃¹⁸OH) trapped in neon and nitrogen matrices have been recorded between 11 000 and 200 cm⁻¹. Their analysis is based on the isotopic effects which slightly modify the frequencies without significantly changing the nature of vibrations nor the band intensities. From the assignment of most of the two quanta transitions 45 out of the 78 anharmonicity coefficients have been deduced. The value of some of them has been confirmed by the identification of three quanta transitions mainly involving the OH stretching mode. The problem of vibrational resonances between methyl bending and stretching modes has been tackled by performing complementary experiments: use of other isotopic species (CH₃OD, CH₂DOH) and acquisition of Raman spectra in the gas phase.     

Investigation of the charge state of heteroatoms in organic compounds of third-row elements by x-ray fluorescence spectroscopy 10. Correlations between values of the shifts of the kα lines of sulfur,phosphorus, and chlorine and the values of the effective charges of these atoms determined from semiempirical quantum-chemical calculations

A set of correlation equations which relate the experimental values of the shifts of the E K lines (E=S, P, Cl) for various classes of E-containing compounds to the values of the effective charges of the atoms of E determined from quantum-chemical calculations by the CNDO/S, CNDO/2, INDO, MINDO/3, and MNDO methods in the minimal basis and the CNDO/S method in an expanded basis has been obtained. It has been established that the INDO method in the minimal basis is best for calibrating the values of (E K) on the basis of the values of the effective charges of the atoms, while the CNDO/2 method and the INDO in the expanded basis are practically unsuitable for determining the values of the effective charges of S and P atoms.For previous communication, see [1].Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 2, pp. 403–410, February, 1991.