Specific C-H⋯N intramolecular interactions in the vinyloxy- and vinylthiopyridine series

A weak hydrogen bond with the participation of the vinyl group -hydrogen atom arises in 2-vinyloxypyridine and 2-vinylthiopyridine, which primarily exist in the s-trans-conformation, according to the ¹H and ¹³C NMR data. This interaction does not take place in 2-vinyloxymethyl- and 2-vinyloxyethylpyridines, which primarily exist in the s-cis-conformation. The C-H...N intramolecular interaction also does not occur in o-vinyloxyaniline due to the specific features of the stereoelectronic state of the amino group nitrogen atom.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1077–1081, August, 1991.     

Hydrocarbons as proton donors in C–H⋯N and C–H⋯S hydrogen bonds

C–H?N and C–H?S hydrogen bonds were analyzed in complexes where acetylene, ethylene, methane and their derivatives are proton donors while ammonia and hydrogen sulfide are proton acceptors. Ab initio calculations were performed to analyze those interactions; MP2 method was applied and the following basis sets were used: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. The results showed that hydrogen bonds for complexes with ammonia are systematically stronger than such interactions in complexes with hydrogen sulfide. If the fluorine substituted hydrocarbons are considered then F-substituents enhance the strength of hydrogen bonding. For a few complexes, mainly those where carbon atom in proton donating C–H bond possesses sp³ hybridization, the blue-shifting hydrogen bonds were detected. Additionally, Quantum Theory of ‘Atoms in Molecules’ and Natural Bond Orbitals method were applied to analyze H-bond interactions.     

Crystal and molecular structure analysis of flutamide. Bifurcated helicoidal C-H ⋯ O hydrogen bonds

Crystal structure determination and semiempirical AM1 and PM3 calculations were performed on flutamide {2-methyl-N[4 nitro-3-(trifluoromethyl) phenyl] propamide}, a powerful nonsteroidal androgen antagonist. The molecule is almost planar apart from CF₃, NO₂, and CH₃ groups. The NO₂ plane makes an angle of 36.3(4) with the least-square plane of the phenyl ring. The molecules are intermolecularly linked by one N-H O and one C-H O hydrogen bonds. A bifurcated helicoidal hydrogen bond network is formed by the intermolecular C-H O hydrogen bond together with another intramolecular C-H O hydrogen bond. The calculated structures are in good agreement with the crystallographic conformations. AM1 is more accurate for predicting the intramolecular C-H O hydrogen bond while PM3 gives a better geometry for the crowded nitro group. AM1 and PM3 charges of benzenic hydrogens are used to predict the propensity of these atoms to form hydrogen bonds. The noncentrosymmetric space group of the crystal (Pna2₁), the calculated dipole moment (8.88 D), and the calculated angle between molecular dipoles and the twofold axis (–49) close to the optimal value (54.7) indicate that flutamide might be a possible candidate for nonlinear optical material.     

Cyanide-bridged manganese(II) and chloride-bridged copper(II) complexes with 2-pyridineethanol: synthesis,structural characterization and C-H⋯M interactions

[Mn(hepH)₂Ni(μ-CN)₂(CN)₂]_n (1) and [Cu₂(μ-Cl)₂(μ-hep)₂]_n (2) (2-pyridineethanol abbreviated to hepH) have been synthesized and characterized by FT-IR and Raman spectroscopies, elemental analyses, and single-crystal X-ray diffraction. X-ray single-crystal structure analysis reveals that the structures of 1 and 2 consist of 1-D infinite chains. The coordination environment of Mn(II) was identified as distorted octahedral, whereas Ni(II) has a square planar geometry in 1. Each Cu(II) in 2 adopts a distorted square pyramidal geometry in which the basal plane is constructed by oxygen and nitrogen atoms from hep and a bridging chloride ligand, respectively, and the apical position is occupied by the other chloride. The 1-D chains in 1 and 2 are extended into a 2-D supramolecular network by O?H?N and weak C?H?Cl hydrogen bonds, respectively. Adjacent 2-D layers are further connected by C?H?M interactions resulting in the formation of 3-D supramolecular networks. The most remarkable properties of complexes are the presence of close C–H?M interactions with distance values of 2.58 and 2.93 Å between H?Ni and H?Cu, respectively. The H?Ni interaction distance is shorter than the corresponding values of other tetracyanonickelate(II) complexes.     

Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes

The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.     

Structural variability of Ag(I) metal–organic networks: C–H⋯π and metal⋯π interactions

The synthesis and X-ray structural characterization of two silver(I) coordination polymers, [Ag₂(bpp)₂(Phdac)]·5H₂O (1) and [Ag₂(bpp)(HSSal)] (2), are reported, where bpp = 4,4′-trimethylene dipyridine, H₂Phdac = 1,4-phenylenediacetic acid, and H₃SSal = 5-sulfosalicylic acid. X-ray crystallography reveals that the structures are stabilized through hydrogen bonding interactions. The C–H?π and metal?π interactions of aromatic molecules play a crucial role in building a layered framework. Intricate combinations of the weak non-covalent interactions have been analyzed to explore cooperativity and competitiveness in the solid-state structures.     

Theoretical study of H⋯P and X⋯P interactions of methylphosphines with HSX molecules

Ab initio calculations were used to analyze the interactions between thiohypohalous acids (HSX; X = F, Cl, Br, I) and methylphosphine derivatives (PH _n Me_3?n , n = 0–3) at the MP2/aug-cc-pVDZ level of theory. Interaction of HSX with PH _n Me_3?n leads to both hydrogen bond (HSX–PH _n Me_3?n –HB) as well as halogen bond (HSX–PH _n Me_3?n –XB) complexes. Stabilities of both HB and XB complexes increase with basicity of the phosphines. However, HB complexes of a phosphine molecule with different HSX have the same order of stabilities, but XB complexes of heavier thiohypohalous acids are more stable. Electron densities of complexes were characterized with the atoms in molecules methodology. The charge transfer within dimers was analyzed by means of natural bond orbitals.     

C–H⋯F,C–H⋯O interactions in the crystal structure of 2-(2-nitrophenyl)-3-pentafluorophenyl-oxirane and 2-pentafluorophenyl-3-phenyl-1-(p-tosyl)-aziridine

Existence and nature of C–H?F, C–H?O interactions in 2-(2-nitrophenyl)-3-pentafluorophenyl-oxirane (1) and 2-pentafluorophenyl-3-phenyl-1-(p-tosyl)-aziridine (2) are discussed. In compound 1 with a linear molecule, C–H?F, C–H?O hydrogen bonds assemble adjacent molecules into the two-dimensional layers, F?F, O?F interactions connect adjacent layers into three-dimensional supramolecular networks. Owing to the inductive effect of nitro group, the C–H acidity of nitrophenyl increases and the numbers of C–H?F, C–H?O hydrogen bonds also increase, C–H?F, C–H?O interactions become stronger and more important. 1D ribbons of compound 2 are stabilized by C–H?F, C–H?O intermolecular interactions. Nonplanar tritopic molecule would demand the formation of a π?π packing interactions between benzene rings and pentafluorobenzene rings in 2.     

Palladium-catalyzed oxidative C-H bond and C═C double bond cleavage: C-3 acylation of indolizines with α,β-unsaturated carboxylic acids

A novel palladium-catalyzed C-3 acylation of indolizines with α,β-unsaturated carboxylic acids via C-H bond and C═C double bond cleavage under oxidative conditions is described. The regioselectivity is assisted by the carboxylic group, and the selection of the oxidant is crucial to the reaction.     

2D and 3D supramolecular assemblies of double cyclopalladated azobenzenes realized by C-H?Cl-Pd, π?π and C-H?π interactions

The double cyclopalladated complex with azobenzene, μ-[(E)-1,2-diphenyldiazene-C^2,8, N^1,2]-di-[chloro(dimethylsulfoxide)palladium(II)]; (DMSO)PdCl(μ-C₆H₄NNC₆H₄)(DMSO)PdCl (1) and its analogous complex with DMF as ancillary ligand, (DMF)PdCl(μ-C₆H₄NNC₆H₄)(DMF)PdCl; μ-[(E)-1,2-diphenyldiazene-C^2,8,N^1,2]-di-[chloro(dimethylformamide)palladium(II)] (2a) were synthesized and the function of cyclopalladated moiety in molecular assembling in the solid state is illustrated by their crystal packings. The polymorphism of 2a and 2b is discussed. The crystal structures reveal assemblies with molecular components self-organized by C-H?Cl-Pd hydrogen bonds, π?π, and C-H?π interactions. The double cyclopalladated complexes of azobenzene, with two Pd-Cl moieties participating in the hydrogen bond formation and π-conjugated system involved in the π?π or C-H?π interactions, represent a new class of building blocks for construction of solid state supramolecular assemblies.     

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.     

Manganese-catalyzed bicyclic annulations of imines and α,β-unsaturated esters via C-H activation

A manganese-catalyzed bicyclic annulation of imines with α,β-unsaturated esters via C–H activation is described, which provides an expedient access to fused β-lactams in one-step operation with high efficiency and good functional group tolerance. Of note, both ketimines and aldimines are amenable to this transformation. Mechanistic studies have identified a five-membered azamanganacycle as the key reaction intermediate.     

Features of strong O–H⋯O and N–H⋯O hydrogen bond manifestation in vibrational spectra

The work deals with the establishment of the dependence of the vibrational frequencies of strong O–H?O and N–H?O hydrogen bonds for the diagnosing the bonds themselves. To this end, the Raman spectra of a large number of different normal and deutero-substituted crystals characterized by the presence of strong O–H?O and N–H?O bonds are measured and the quantum chemical calculation is performed for one of these compounds. The dependence of the O–H stretching frequency on the O?O distance is constructed differing from that previously known for short O?O contacts. The mechanisms of significant broadening of the O–H vibration band in strong O–H?O hydrogen bonds are considered. Different dependences of the N–H vibrational frequencies in N–H?O bonds are reported and the causes of this diversity are discussed.     

Computational study of hydrogen-bonded complexes of HOCO with acids: HOCO⋯HCOOH, HOCO⋯H(2)SO(4), and HOCO⋯H(2)CO(3)

Quantum chemistry calculations at the density functional theory (DFT) (B3LYP), MP2, QCISD, QCISD(T), and CCSD(T) levels in conjunction with 6-311++G(2d,2p) and 6-311++G(2df,2p) basis sets have been performed to explore the binding energies of open-shell hydrogen bonded complexes formed between the HOCO radical (both cis-HOCO and trans-HOCO) and trans-HCOOH (formic acid), H(2)SO(4) (sulfuric acid), and cis-cis-H(2)CO(3) (carbonic acid). Calculations at the CCSD(T)∕6-311++G(2df,2p) level predict that these open-shell complexes have relatively large binding energies ranging between 9.4 to 13.5 kcal∕mol and that cis-HOCO (cH) binds more strongly compared to trans-HOCO in these complexes. The zero-point-energy-corrected binding strengths of the cH?Acid complexes are comparable to that of the formic acid homodimer complex (～13-14 kcal∕mol). Infrared fundamental frequencies and intensities of the complexes are computed within the harmonic approximation. Infrared spectroscopy is suggested as a potential useful tool for detection of these HOCO?Acid complexes in the laboratory as well as in various planetary atmospheres since complex formation is found to induce large frequency shifts and intensity enhancement of the H-bonded OH stretching fundamental relative to that of the corresponding parent monomers. Finally, the ability of an acid molecule such as formic acid to catalyze the inter-conversion between the cis- and trans-HOCO isomers in the gas phase is also discussed.     

The interaction strength of intermolecular systems formed by NaH⋯2(HF) and NaH⋯4(HF): Hydrogen bonds,dihydrogen bonds and halogen–hydride bonds

In this paper, a theoretical study of the molecular properties of NaH⋯2(HF) and NaH⋯4(HF) complexes is reported. Based on MP2/6-311++G(d,p) calculations, the dihydrogen bonds (H⋯H), hydrogen bonds (F⋯H) and halogen-hydride bonds (F⋯Na) of these intermolecular systems were fully characterized. The characterization involved the following procedures: the examination of structural parameters, analysis of vibration modes such as frequencies shifted to red or blue in the infrared spectrum, modeling of the electronic topology, quantification of the cooperative energy followed by charge transfer and, finally, natural bond orbital analysis. The results show short intermolecular distances with high electronic density, while the stretch frequencies of the proton donors and acceptors are unusually shifted, and some values reach 1000 cm⁻¹. When all subunits of the complexes are taken into account, in this case the NaH and HF molecules, the high value for the strength of the H⋯H dihydrogen bond in NaH⋯2(HF) suggests the formation of an additional subpart, i.e., the H₂ molecule.     

Nitroaniline Derivatives of 2-Oxo-1-naphthylideneamines—Molecular Self-Assembling <Emphasis Type="Italic">via</Emphasis> C—H⋯O Intermolecular Hydrogen Bonds and Stabilization of O—H⋯N and N—H⋯O Tautomers in Solution and Solid State

Three Schiff-bases of the Ar—CH—N—Ar type were synthesized from 2-hydroxy-1-naphthaldehyde and o- (1), m- (2), and p-nitroaniline (3) in order to investigate the shift of the keto-amine/enol-imine tautomeric equilibrium that arises by the introduction of the electron-withdrawal nitro group. The compounds have been investigated experimentally, in the solid state and in the solution, by IR, NMR, UV spectroscopy, and X-ray single crystal analysis, and theoretically by using density functional theory (DFT). The tautomeric equilibrium is strongly shifted towards the keto-amine form despite of the nitro group position at N-phenyl ring in the solid state of molecular structures of 1, 2, and 3 (especially indicated by C—O and C—N bond distances). The keto-amine tautomeric form of the compounds is characterized by a strong, resonance assisted hydrogen bond (RAHB) of the N—H O type (the N O distances are 2.530(8), 2.554(2) and 2.555(5) Å in 1, 2, and 3, respectively). The molecules are assembled in the crystalline state into a 3D HB network (1), centrosymmetrical dimers (2) or infinite chains (3) by the C—H O intermolecular hydrogen bonds. In contrast, UV/VIS spectra of the chloroform solution of the title compounds reveal predominance of the enol-imine form. The molecular geometries and relative stabilities of the compounds determined by using DFT find good agreement with the experimental data.     

Vibrational overtone spectroscopy, energy levels, and intensities of (CH3)3C-C≡C-H

The vibrational overtone spectra of the acetylenic (Δυ = 4, 5) and methyl (Δυ = 5, 6) C-H stretch transitions of tert-butyl acetylene [(CH(3))(3)C-C≡C-H] were obtained using the phase shift cavity ring down (PS-CRD) technique at 295 K. The C-H stretch fundamental and overtone absorptions of the acetylenic (Δυ = 2 and 3) and methyl (Δυ = 2-4) C-H bonds have been obtained using a Fourier transform infrared and near-infrared spectrophotometer. Harmonic frequency ω(ν(1)) and anharmonicities x(ν(1)) and x(ν(1), ν(24)) are reported for the acetylenic C-H bond. Molecular orbital calculations of geometry and vibrational frequencies were performed. A harmonically coupled anharmonic oscillator (HCAO) model was used to determine the overtone energy levels and assign the absorption bands to vibrational transitions of methyl C-H bonds. Band strength values were obtained experimentally and compared with intensities calculated in terms of the HCAO model where only the C-H modes are considered. No adjustable parameters were used to get order of magnitude agreement with experimental intensities for all pure local mode C-H transitions.     

From strong van der Waals complexes to hydrogen bonding: From CO⋯H2O to CS⋯H2O and SiO⋯H2O complexes

Structures and interaction energies of complexes valence isoelectronic to the important CO?H(2)O complex, namely SiO?H(2)O and CS?H(2)O, have been studied for the first time using high-level ab initio methods. Although CO, SiO, and CS are valence isoelectronic, the structures of their complexes with water differ significantly, owing partially to their widely varied dipole moments. The predicted dissociation energies D(0) are 1.8 (CO?H(2)O), 2.7 (CS?H(2)O), and 4.9 (SiO?H(2)O) kcal∕mol. The implications of these results have been examined in light of the dipole moments of the separate moieties and current concepts of hydrogen bonding. It is hoped that the present results will spark additional interest in these complexes and in the general non-covalent paradigms they represent.     

Influence of OH⋯N and NH⋯O inter- and intramolecular hydrogen bonds in the conformational equilibrium of some 1,3-disubstituted cyclohexanes through NMR spectroscopy and theoretical calculations

The analysis of concentration effects in the (1)H NMR data of cis-3-aminocyclohexanol (ACOL) showed that its diequatorial conformer changes from 60% at 0.01 mol L(-1) to 70% at 0.40 mol L(-1) in acetone-d(6). A similar increase was also observed for the diequatorial conformer of cis-3-N-methylaminocyclohexanol (MCOL), from 32% (CDCl(3) 0.01 mol L(-1)) to 55% (CDCl(3) 0.40 mol L(-1)). The increase in solvent basicity leads to a large stabilization effect for the diequatorial conformer of both compounds too. For ACOL, it changes from 47% (ΔG(eqeq-axax)=0.06 kcal mol(-1)) in CCl(4) to 93% (ΔG(eqeq-axax)=-1.53 kcal mol(-1)) in DMSO, while for MCOL it goes from 7% (ΔG(eqeq-axax)=1.54 kcal mol(-1)) in CCl(4) to 82% (ΔG(eqeq-axax)=-0.88 kcal mol(-1)) in pyridine-d(6). These results indicate that the intramolecular hydrogen bonds (IAHB) OH?N and NH?O stabilize the diaxial conformers of these compounds in a non-polar solvent. For cis-3-amino-1-methoxycyclohexane (ACNE) and cis-3-N-methylamino-1-methoxy-cyclohexane (MCNE) no changes were observed in equilibrium with the variation of solvent polarity. These results indicate for the first time that the IAHB NH?O is not strong enough to stabilize the diaxial conformer of these compounds and that the conformation equilibria of the cis isomers of compounds ACOL and MCOL are influenced only by the IAHB OH?N. Moreover, the presence of a secondary amino group (93% of diaxial conformer in CCl(4)) leads to an IAHB OH?N stronger than in primary and tertiary amino-derivatives (53 and 54% of diaxial conformer, respectively) for 1,3-disubstituted cyclohexanes. Values obtained from the theoretical data through the B3LYP functional are in agreement with the experimental results and indicate that the IAHB strength that influences the conformational equilibrium of these compounds is the IAHB OH?N. Thus, the IAHB NH?O do not stabilize the diaxial conformer of the cis isomer of compounds ACNE and MCNE showing that the diequatorial conformer will always be more stable than the diaxial conformer, independent of concentration or solvent.