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.     

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.     

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).     

The effect of methyl group on the cooperativity between three types of hydrogen bond: O?H···O,C?H···O,and O?H···π

The effect of the methyl group on the cooperativity between three types of hydrogen bond (O H···O, C H···O, and O H···π) in cyclic complex involving an acetylene and two waters has been studied on the basis of high-level ab initio calculations. The total interaction energy of three hydrogen bonds increases as the number of methyl group in the complex increases. The binding distances of O H···π and O H···O hydrogen bonds shorten, while that of C H···O hydrogen bond elongates with increasing methyl group. This indicates that addition of methyl group leads to enhancement of O H···π and O H···O hydrogen bonds, and weakening of C H···O hydrogen bond, as also shown in frequency shift, chemical shifts, charge populations, and stabilization energies of orbital interactions. Although the presence of methyl group has a complicated effect on different type of hydrogen bond, the cooperativity of three hydrogen bonds increases in general with the addition of methyl group. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Density functional investigations on the (H2O)n·CCH and (H2O)n·HCC complexes (n=1–3)

The electronic structures and energies of (H₂O)_n·CCH and (H₂O)_n·HCC complexes (n=1–3) between CCH and water have been theoretically investigated at the UB3LYP/6-311++G(2df,p)//UB3LYP/6-311G(d,p) level. The complexes with n=2–3 are cyclic structures with homodromic hydrogen-bond chain. The (H₂O)_n·CCH (n=1–3) complexes show increasing stabilities towards CCH- or H₂O-eliminations of 2.3, 5.8 and 7.6 kcal/mol and are energetically more stable than the corresponding (H₂O)_n·HCC complexes by 0.8, 2.7 and 3.4 kcal/mol, respectively, due to the charge-separation-enhanced hydrogen bonds within (H₂O)_n·CCH (n=2,3). Strong interactions between CCH and (H₂O)₂ and (H₂O)₃ clusters suggest special solvent effects of water on the chemical behavior of unsaturated radicals.     

Cooperative N–H···N,N–H···O,and O–H···N bonded molecular dimers of two new 3,5-diaryl-1<Emphasis Type="Italic">H</Emphasis>-pyrazoles

Two new 3,5-diaryl-1H-pyrazoles: 3(5)-(4-tert-butylphenyl)-5(3)-(naphthalene-2-yl)-1H-pyrazole (1) and 5-(4-(benzyloxy)phenyl)-3-(furan-2-yl)-1H-pyrazole (2) were synthesized and characterized. Two strong ions peaks [2M]⁺ and [2M + Na]⁺ observed in the ESI–MS spectra are attributed to the dimerization process in solution formed by intermolecular N–H···N hydrogen bonds. The crystal structures have been determined by X-ray crystal structure analysis. Compound 1 exists as a pair of tautomers 1a and 1b, and its dimer [R ₂²(6) motif] is formed by the tautomers 1a and 1b. Compound 2 only exists as a 2a tautomer, and interesting intermolecular N–H···O and O–H···N hydrogen bonds link two pyrazoles and two methanol molecules, leading to the formation of an R ₄⁴(10) dimer motif.     

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...     

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.     

Competition between H···π and H···O interactions in furan heterodimers

Here the interactions of furan with HZ (Z = CCH, CCF, CN, Cl, and F) are studied using a variety of electron correlation methods (MP2, CCSD(T), DFT-SAPT) and correlation-consistent triple- and quadruple-ζ basis sets including complete basis set (CBS) extrapolation. For Fu-HF all methods agree that a n-type structure with a hydrogen bridge between the oxygen lone-pair of furan and the hydrogen atom of HF is the global minimum structure. It is found to be significantly more stable than a π-type structure where the hydrogen atom of HF points toward the π system of furan. For the other four dimers MP2 and DFT-SAPT predict the π-type structure to be somewhat more stable, while CCSD(T) favors the n-type structure as the global minimum for Fu-HCl and predicts both structures as nearly isoenergetic for Fu-HCCH and Fu-HCCF. From a geometrical point of view, the Fu-HCN dimer structures are more related to those of the Fu-HCl complex than to Fu-HCCH. The different behavior of HCCF and HF upon complexation with furan evidence the effect of the presence of a π system in the aggregation of fluorine derivatives. It is shown that aggregates of furan cannot be understood by means of dipole-dipole and electrostatic analysis only. Yet, through a combined and detailed analysis of DFT-SAPT energy contributions and resonance effects on the molecular charge distributions a consistent explanation of the aggregation of furan with both π electron rich molecules and halogen hydrides is provided.     

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.     

An analysis of the vibrational frequencies and amplitudes of the H5O+2 ion in H4SiW12O40·6H2O (TSA·6H2O) and H3PW12O40·6H2O (TPA·6H2O)

The infrared, Raman and inelastic neutron scattering (INS) spectra of TSA·6H₂O and TPA·6H₂O are in agreement with those expected for the presence of H₅O⁺₂ ions. Force fields for different assignment schemes are compared with the observed vibrational frequencies and the INS spectral profile. All but two schemes are eliminated. Whilst low-resolution INS spectroscopy cannot distinguish between these two schemes, the orientations of the vibrational ellipsoids for one scheme are in better agreement with those reported from low-temperature crystallographic studies of the H₅O⁺₂ ion.     

Phase Diagrams of Fullerenol-d–LaCl3–H2O and Fullerenol-d–GdCl3–H2O Systems at 25°С

Russian Journal of Physical Chemistry A - Isothermal phase diagrams of ternary systems fullerenol-d–LaCl3–H2O and fullerenol-d–GdCl3–H2O at 25°C are studied via...     

Intramolecular Rearrangements of >Si(O–C·=O)(CH2–CH3) and >Si(CH2–CH·–CH3)(CH2–CH3) Radicals

Using ESR and IR spectroscopy, the structures of >Si(O–C^·=O)(CH₂–CH₃) (1) and >Si(CH₂–CH^·–CH₃)(CH₂–CH₃) (2) radicals were deciphered. The directions and kinetic parameters of reactions of intramolecular rearrangements in these radicals were determined. The reactions of hydrogen atom abstraction in radical (1) from the CH₂ and CH₃ groups were studied. It was found that the endothermic reaction of hydrogen atom abstraction from the methyl group occurs at a higher rate than the exothermic reaction with the methylene group. The differences are determined by changes in the size of a cyclic transition state. Based on the experimental data, the strengths of separate C–H bonds in surface fragments are compared. The rearrangement >Si(CH₂–CH^·–CH₃)(CH₂–CH₃) >Si(C^·(CH₃)₂)(CH₂–CH₃) was discovered and its mechanism was determined. One of its steps is the skeletal isomerization Si- (2)- _. (1)Si- (1)- _. (2). Experimental data are analyzed using the results of quantum-chemical calculations of model systems.     

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     

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.     

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.