Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

Effect of Substituents in Hydrolyzed Cephalosporins on Intramolecular O–H···N Bond

Russian Journal of Physical Chemistry A - Model molecular systems structurally similar to the transition state of the limiting step of the hydrolysis of cephalosporin antibiotics by the L1...     

Four-membered ring cyclic ketene –O,O–, –O,S–, –O,N–, –S,S–, –S,N–, and –N,N–acetals and their corresponding cations: a computational study

A systematic computational study of four-membered cyclic ketene –O,O–, –O,S–, –O,N–, –S,N– and –N,N-acetals as well as their protonated analogs have been performed at the second order M?ller Plesset level with a polarized triple zeta basis set. The main purpose of this study was to make predictions about the nucleophilicity of these systems and the variations in nucleophilicity with the hetero atoms. Our calculations suggest that all six target molecules are good nucleophiles, and that the N,N analog is the strongest and the S,S analog the weakest nucleophile. Our results include molecular geometries, bond lengths, proton affinities, vibrational frequencies, and calculated charges.     

Co-crystal/salt crystal structure disorder of trichloroacetic acid–N-methylurea complex with double system of homo- and heteronuclear O–H···O/N–H···O hydrogen bonds: X-ray investigation, ab initio and DFT studies

The X-ray diffraction studies revealed disorder of a trichloroacetic acid?CN-methylurea complex crystal structure, connected with a proton transfer via O?CH···O hydrogen bond. The observed structure corresponds to a co-existence of ionic (salt) and neutral (co-crystal) forms of the complex in the solid state in ratio 3:1, respectively. The geometrical analysis based on ab initio and density functional theory methods combined with the experimental research indicated that two different N-methylurea molecular conformations, defined by CNCN torsion angle, correspond to the neutral and the ionic form of the complex, respectively. The conformational changes seem to be connected with stabilization of the ionic structure after a proton transfer, as according to theoretical calculations this form of the complex (the ionic one) was unstable in the gas phase. A particular attention was focused on a system of a double intermolecular hydrogen bonds, O?CH···O and N?CH···O which join molecules into the title complex. The analysis of these interactions performed in terms of their geometry, energetic and topological electron density properties let for their classification into strong and medium strength hydrogen bonds. It was also found that the antibonding hydrogen bonding donor orbital occupation corresponded to the stabilization energy resulting from charge transfer in hydrogen bonds. Hence, it is postulated as a possible indicator of interaction strength.     

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.     

C–H...O and C–H...N interactions in RNA structures

Small molecule studies indicate that C–H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C–H...X angle range increases with an increasing H...X distance. The preferred short C–H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2′(H)...O4′ and C5′(H)...O2′ interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C–H...N interaction has been identified in various structures. Despite the occurrence of short C–H...X contacts their free energy contribution to RNA stability remains to be assessed. Received: 17 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

O–H···C hydrogen bond in the methane–water complex

Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH₄ complex formed by water and methane molecules, in which water is a proton donor and methane carbon (sp³) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial С–H bond of methane directed along the line of the O–H···C hydrogen bridge and the antibonding σ* orbital of the О–H bond of the water molecule. Topological analysis of electron density in the HOH···CH₄ complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O–H···C interaction are typical for Н-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an Н bond of O–H···σ(С–H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).     

N–H···O=P hydrogen-bonded dimers as the main structural motif of aminophosphonate diesters

Abstract  

Crystal and molecular structures of three aminophosphonate diesters, diethyl and dibutyl [α-(quinolin-3-ylamino)-N-benzyl]phosphonates (1 and 2) and dibutyl [α-anilino-(quinolin-3-yl)methyl]phosphonate (3) were reported and comparatively discussed. Characteristic structural features for these compounds are strong N–H···O=P hydrogen bonds that connect two organophosphorus molecules in cyclic centrosymmetric dimer. Phosphoryl oxygen forms additional interaction with a C–H donor from the nearby aromatic group. Dimer formation in solution was also confirmed using electrospray ionization mass spectrometry. Mass spectra of six structurally similar aminophosphonate derivatives, 1–3 along with diethyl [α-anilino-(quinolin-3-yl)methyl]phosphonate (4), diethyl and dibutyl [α-anilino-(quinolin-2-yl)methyl]phosphonates (5 and 6) were studied and dimolecular ions [2M + Na]⁺ and [2M + H]⁺ were observed.     

Theoretical study of N–H· · ·O hydrogen bonding properties and cooperativity effects in linear acetamide clusters

We investigated geometry, energy, ${\nu_{{\text{N--H}}}}$ harmonic frequencies, ¹⁴N nuclear quadrupole coupling tensors, and ${n_{\rm O}\to \sigma _{{\text{N--H}}}^\ast}$ charge transfer properties of (acetamide) _n clusters, with n = 1 ? 7, by means of second-order Møller-Plesset perturbation theory (MP2) and DFT method. Dependency of dimer stabilization energies and equilibrium geometries on various levels of theory was examined. B3LYP/6-311++G** calculations revealed that for acetamide clusters, the average hydrogen-bonding energy per monomer increases from ?26.85 kJ mol^?1 in dimer to ?35.12 kJ mol^?1 in heptamer; i.e., 31% cooperativity enhancement. The n-dependent trend of ${\nu_{{\text{N--H}}}\,{and}\,^{14}}$ N nuclear quadrupole coupling values were reasonably correlated with cooperative effects in ${r_{{\text{N--H}}}}$ bond distance. It was also found that intermolecular ${n_{\rm O}\to \sigma_{{\text{N--H}}}^\ast}$ charge transfer plays a key role in cooperative changes of geometry, binding energy, ${\nu_{{\text{N--H}}}}$ harmonic frequencies, and ¹⁴N electric field gradient tensors of acetamide clusters. There is a good linear correlation between ¹⁴N quadrupole coupling constants, C _Q (¹⁴N), and the strength of Fock matrix elements (F _ij ). Regarding the ${n_{\rm O}\to \sigma_{{\text{N--H}}}^\ast}$ interaction, the capability of the acetamide clusters for electron localization, at the N–H· · ·O bond critical point, depends on the cluster size and thereby leads to cooperative changes in the N–H· · ·O length and strength, N–H stretching frequencies, and ¹⁴N quadrupole coupling tensors.     

Synthesis,crystal structure,and catalytic performance of two 3-D supramolecular compounds: (C7N2H7)3(C7N2H6) · PMo12O40 · 2H2O and (C7N2H7)3(C7N2H6)2 · AsMo12O40 · 3H2O

Two organic–inorganic compounds based on Keggin building blocks have been synthesized by hydrothermal methods, (C₇N₂H₇)₃(C₇N₂H₆)?·?PMo₁₂O_40?·?2H₂O (1) and (C₇N₂H₇)₃(C₇N₂H₆)_2?·?AsMo₁₂O_40?·?3H₂O (2) (C₇N₂H₆?=?benzimidazole). Single-crystal X-ray analysis revealed that 1 crystallized in the triclinic system, P-1 space group with a?=?9.8980(4)?Å, b?=?11.2893(4)?Å, c?=?25.8933(9)?Å, α?=?93.307(2)°, β?=?90.630(2)°, γ?=?108.330(2)°, V?=?2740.68(18)?ų, Z?=?2, R ₁(F)?=?0.0740, ωR ₂(F ²)?=?0.1511, and S?=?1.037; 2 crystallized in the triclinic system, P-1 space group with a?=?12.3353(4)?Å, b?=?13.2649(4)?Å, c?=?20.2878(6)?Å, α?=?95.6630(10)°, β?=?100.1720(10)°, γ?=?99.3940(10)°, V?=?3195.72(17)?ų, Z?=?2, R ₁(F)?= 0.0329, ωR₂ (F ²)?=?0.1236, and S?=?1.088. The two compounds show a layer framework constructed from Keggin-polyoxoanion clusters and benzimidazole via hydrogen bonds and π–π stacking interactions, resulting in a 3-D supramolecular network. Both have high catalytic activity for oxidation of methanol. When the initial concentration of the methanol is 5.37?g?m^?3 in air and the flow velocity is 4.51?mL?min^?1, methanol is completely eliminated at 150°C for 1 (160°C for 2).     

C–H· π Interaction and N·H–O Hydrogen Bonding in the Chair-like p-tert-Butylcalix[8]arene Complex Including Four Pyridine Molecules

Crystal structure analysis shows that the p-tert-butylcalix[8]arene host and its four pyridine guests sit around an inversion center in the P2₁/c crystal lattice. The monoclinic cell parameters and its volume are: a = 19.617(4), b = 9.912(2), c = 25.178(5) , = 101.03(3)°, V =4805.27(17) ³. For Z = 2 and Mw = 1614.18, the calculated density Dcalc = 1.116 g/cm³. A host calixarene molecule includes four pyridine guests in two different ways: by hydrogen bonding and by possible C–H· interaction between the molecules. The hydrogen bonding drives the host macrocycle into a chair-like conformation.     

α（1,2,4—三唑—1—基）—α—苯甲酰基烯酮N,S;N,N;N,O和O,S…

以α（１，２，４三唑－１－基）－α－苯甲酰基烯酮二甲硫缩醛为反应中间体，与取代苯胺、邻苯二胺、乙二胺、乙醇胺和巯基乙醇反应，合成了２７个标题化合物，初步的生物活性测定表明，所合成的部分化合物具有抑菌及植物生长调节活性。     

Theoretical study of the N—H···O red-shifted andblue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO···HNO, HCOOH···HNO, HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F. The geomet- ric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO···HNO and HCOOH···HNO the N—H bond is strongly contracted and N—H···O blue-shifted hydrogen bonds are observed. While in complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F, the N—H bond is elongated and N—H···O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X—H bond length in the X—H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribu- tion, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X—H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO···HNO and HCOOH···HNO, the shortening effects dominate which lead to the blue shift of the N—H stretching frequencies. In complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F where elongating effects are dominant, the N—H···O hydrogen bonds are red-shifted.     

Morpholine adducts of Co, Ni, and Mn benzoylacetonates: isostructurality and C–H···O hydrogen bonding

Morpholine adducts of nickel(II), cobalt(II), and manganese(II) benzoylacetonates, as well as a morpholine solvate of manganese(II) benzoylacetonate, were prepared and characterized by X-ray diffraction and thermal analysis. All four compounds crystallize in the P2₁/c space group with two complex molecules per unit cell. The morpholine solvate, along with the two adduct molecules, also contains four solvent morpholine molecules in the unit cell. The non-solvate compounds are isostructural, with crystal structures comprising 2D networks formed by C–H···O hydrogen bonding between phenyl rings and morpholine oxygen atoms. The topology of these networks can be described as intersecting C₂²(24) chains forming R₄⁴(48) rings. Networks with the same topology are also present in the solvate, but they are heavily distorted due to the presence of solvent morpholine molecules. Thermogravimetric analysis shows similar behavior of the non-solvate compounds upon thermal decomposition, with three degradation steps which can be related to gradual loss of morpholine molecules and subsequent overall decomposition. Decomposition of the solvate also proceeds in several steps, the first of which can be related to loss of solvent morpholine molecules and the further steps are analogous to those in the non-solvate compounds.     

Interaction parameters and (solid + liquid) equilibria calculation for KCl–H2O–HCl–C2H5OH,K2SO4–H2O–H2SO4 and K2SO4–H2O–C2H5OH mixed solvent-electrolyte systems

This work deals with the prediction and experimental measurements of the (solid + liquid) equilibrium (SLE) in acid medium for industrial purposes. Specific systems including KCl–ethanol–water–HCl and K₂SO₄–water–H₂SO₄ were analyzed. At first, a critical discussion of SLE calculations was given, based on the well-known UNIQUAC extended and LIQUAC models. Two new proposals were derived, considering the explicit necessity of a new reference state for SLE calculations for the studied (solvents + acid) mixtures. The solubility of KCl in water–ethanol–HCl mixed solvents was measured in the temperature range of 300.15 to 315.15 K using an analytical gravimetric method. These results combined with some other experimental data reported in the open literature let us to propose a set of parameters for the new models. They included the interaction parameters between ethanol and the H⁺ ion. The prediction capability of the new models, for calculations in acid medium, was illustrated. Experimentally, it was observed that the (K₂SO₄ + water + H₂SO₄) system presented the unusual behavior of increasing K₂SO₄ solubility with an increase in the sulfuric acid concentration. This was accurately predicted by the newly proposed models.     

Thermodynamics,structure and kinetics in the system Ga–O–N

Within the ternary system Ga–O–N we performed experimental and theoretical investigations on the thermodynamics, structure and kinetics of new stable and metastable compounds.We studied the ammonolysis of β-Ga₂O₃ at elevated temperatures by means of ex situ X-ray diffraction, ex situ neutron diffraction, and in situ X-ray absorption spectroscopy (XAS). From total diffraction pattern refinement with the Rietveld method we analyzed the anionic occupancy factors and the lattice parameters of β-Ga₂O₃ during the reaction. Within the detection limits of these methods, we can rule out the existence of a crystalline oxynitride phase that is not derived from wurtzite-type GaN. The nitrogen solubility in β-Ga₂O₃ was found to be below the detection limit of about 2–3 at.% in the anionic sublattice. The kinetics of the ammonolysis of β-Ga₂O₃ to α-GaN and of the oxidation of α-GaN to β-Ga₂O₃ was studied by means of in situ X-ray absorption spectroscopy. In both cases the reaction kinetics could be described well by fitting linear combinations of β-Ga₂O₃ and α-GaN spectra only, excluding that other crystalline or amorphous phases appear during these reactions. The kinetics of the ammonolysis can be described well by an extended Johnson–Mehl–Avrami–Kolmogorow model with nucleation and growth of GaN nuclei, while the oxidation kinetics can be modeled by a shrinking core model where Ga₂O₃ grows as a layer. Investigations by means of TEM and SEM support the assumptions in both models.To investigate the structure and energetics of spinel-type gallium oxynitrides (γ-galons) we performed first-principles calculations using density-functional theory. In addition to the ideal cubic γ-Ga₃O₃N we studied gallium deficient γ-galons within the Constant-Anion-Model.In highly non-stoichiometric, amorphous gallium oxide of approximate composition GaO_1.2 we found at a temperature around 670 K an insulator–metal transition, with a conductivity jump of seven orders of magnitude. We demonstrate through experimental studies and density-functional theory calculations that the conductivity jump takes place at a critical gallium concentration and is induced by crystallization of stoichiometric β-Ga₂O₃ within the metastable oxide matrix. By doping with nitrogen the critical temperature and the conductivity in the highly conducting state can be tuned.     

Ab initio study of the cooperativity between NH···N and NH···C hydrogen bonds in H3N–HNC–HNC complex

Ab initio calculations at the MP2/aug-cc-pVTZ level have been performed to study the cooperativity of hydrogen bonds in homoclusters (HNC–HNC–HNC and HNC–HNC–HNC–HNC) and heteroclusters (H₃N–HNC–HNC and H₃N–HNC–HNC–HNC). The cooperative energies in the HNC–HNC–HNC and H₃N–HNC–HNC trimers are –2.05 and –2.56 kcal/mol, respectively. The result shows that the cooperativity in the heterotrimer is larger than that in the homotrimer. A similar result also happens in the tetramers. The energy decomposition scheme indicates that orbital interaction is a major contribution to the cooperative energy of N···HN hydrogen bond, whereas the electrostatic and orbital interactions to that of C···HN hydrogen bond. The effect of HNC chain length on the strength of N···HN hydrogen bond has also been considered at the MP2/aug-cc-pVDZ level. It is indicated that the interaction energy of N···HN hydrogen bond trends to be a fixed value when the HNC number tends to be infinite, and the strength of N···HN hydrogen bond is regulated mainly through the electrostatic and polarization interactions although the charge transfer interaction also has an effect on it.     

Can the substituent in the para position of anilide ion influence the N−···H–F → N–H···F− switching: a quantum chemical study

The effect of substituents in the para position of anilide ion (An) on the N^?···H–F → N–H···F^? switching in X–An–HF (X = H, Me, CHO, CN, NO, F, NO₂, OH and OMe) complexes was investigated by means of B3LYP and MP2 quantum chemical methods. To delve into the mechanistic details of the proton transfer process, potential energy curve and further geometrical parameters involved in H-bonding during the course of the proton transfer process were evaluated at the MP2/6-311++G(2d,2p) level of theory. The changes in H-bond strength because of variation of substituents were well accompanied by changes in formation energy of complexes, structural parameter, electron density, natural charge and charge transfer between subunits. For X = H, Me, CHO, CN, NO, F and NO₂ substituents, our results at MP2/6-311++G(2d,2p) level showed that the minimum energy structures correspond to the N···HF H-bonded complexes without proton transfer occurring. On the other hand, for electron-donating substituents OH and OMe, proton is transferred from HF to anilide ion and the minimum energy structures are HNH···F^? H-bonded complexes. The nature of HN^?···HF and HN–H···F^? interactions in complexes was characterized by means of atoms in molecules and natural bond orbital analyses.