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.     

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.     

Platinum precursor of anticancer drug: a structure fixed by long intermolecular N–H···I and C–H···I hydrogen bonds

The title compound 1, cis-[diiodo(1R,2R)-1,2-diaminocyclohexane-κN,κN′]platinum(II), a precursor of a novel platinum-based anticancer complex, was synthesized. High purity (>99%) was determined by HPLC–UV/VIS and its structure was characterized by LC–ESI–MS, FT-IR and X-ray single-crystal diffraction. The molecules of the title compound interact via N–H···I and C–H···I intermolecular (ultra)-long hydrogen–iodine (acceptor) bonds (distances up to 3.1 Å). The crystal structure of the title compound 1 was compared to the structure calculated on the basis of density function theory (DFT). The calculated and measured data varied by a maximum of 0.09 Å in bond lengths and the maximum deviation between the compared angles were less than 2°. Experimentally measured bond lengths in the crystal were observed to be reduced when compared to the theoretical calculation. This was caused by both steric requirements of individual structural units and the presence of hydrogen bonds in real sample, which were confirmed by FT-IR (new bands as well as the band shifts to lower wavelengths).     

The quantum chemical calculation of NMR two-bond spin–spin coupling constants in the N?···H–OH?→?N–H···OH? switching

A quantum chemical study has been carried out to investigate the effects of the size of H₂O cluster and substituents (X = H, Me, OMe, CHO, NO, and NO₂) in the para position of the anilide ion on the two-bond spin–spin coupling constants (SSCCs) ^2h J _N···O across in the N–H–O switching at B3LYP/6-311 ++G(2d,2p) level of theory. The changes in ^2h J _N···O SSCCs due to variation of substituent and H₂O cluster size were well monitored by changes in binding energy, structural parameter, electron density topography, natural charge, charge transfer, and percentage of p-character of N atom in the C–N bond. Linear correlations were found between ^2h J _N···O and above-mentioned properties.     

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.     

Directionality of intermolecular C–F···F–C interactions in crystals: experimental and theoretical charge density study

Bonding intermolecular F···F interactions were analyzed in crystal of a fluorinated benzene derivative using topological analysis of experimental charge density distribution. It was found that the values of electron density and potential energy density in bond critical points of the F···F interactions in crystal depended on the distance between the fluorine atoms, rather than on the corresponding C–F···F angles. The directionality of these F···F interactions was demonstrated by DFT-D and MP2 calculations for model hexafluorobenzene dimers. Possible discrepancies between dimerization energies computed by ab initio methods and via empirical correlations are discussed.     

Nonconventional C–H···Cu Interaction Between Copper Cun Clusters (n = 3–20) and Aromatic Compounds

The present study examines bonding patterns between copper Cu_n clusters (n?=?3–20) and aromatic compounds (benzene, phenol, and benzaldehyde) using a density-functional theory (DFT) approach. Hirshfeld population, natural bond orbital (NBO), molecular orbitals, and quantum theory of atoms in molecules (QTAIM) analyses suggested the formation of two types of interactions Cu–arene and C–H···Cu, in the complexation of copper clusters by an aromatic compound.

     

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.     

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.     

High pressure,a protocol to identify the weak dihydrogen bonds:experimental evidence of C–H···H–B interaction

Pressure, as a thermodynamic parameter, provides an appropriate method to detect weak intermolecular interactions. The C–H···H–B dihydrogen bond is so weak that the experimental evidence of this interaction is still limited. A combination of in situ high pressure Raman spectra and angle-dispersive X-ray diffraction(ADXRD) experiments was utilized to explore the dihydrogen bonds in dimethylamine borane(DMAB). Both Raman and ADXRD measurements suggested that the crystal structure of DMAB is stable in the pressure region from 1 atm(1 atm=1.01325×10~5 Pa) to 0.54 GPa. The red shift of CH stretching and CH_3 distortion modes gave strong evidence for the existence of C–H···H–B dihydrogen bonds. Further analysis of Raman spectra and Hirshfeld surface confirmed our proposal. This work provided a deeper understanding of dihydrogen bonds.And we wish that high pressure could be applied to identify other unconfirmed hydrogen or dihydrogen bond.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

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.     

Simultaneous interactions of pyridine with substituted benzene ring and H–F in X-ben⊥pyr···H–F complexes: a cooperative study

The cooperative effects between T-shape stacking and hydrogen bond interactions in X-ben⊥pyr···H–F complexes were investigated in this work. The results indicate that the electron-withdrawing/donating substituents decrease/increase the magnitude of the binding energies compared to the unsubstituted X-ben⊥pyr···H–F (X = H) complex. The cooperative effects have been studied while using the atoms in molecules (AIM) and natural bond orbital (NBO) methods, allowing us to evaluate the interplay between T-shape stacking and hydrogen bond interactions. There are good relationships among binding energies, Hammett constants, geometrical parameters, and the results of AIM and NBO analysis in X-ben⊥pyr···H–F complexes.     

Supramolecular structures of CdX2-containing coordination compounds constructed by C–H ··· X synthons

Three CdX₂-containing (X = Cl, Br) compounds [CdBr₂(Him)₂] _n (Him = imidazole) (1), [CdCl₂(2,2′-bipy)] _n (2,2′-bipy = 2,2′-bipyridine) (2), and [CdCl₂(phen)] (phen = phenanthroline) (3) have been synthesized through hydrothermal technique. Compound 1 adopts 1-D coordination chain, which is connected to form a 3-D supramolecular network by inter-chain N–H ··· Br and C–H ··· Br hydrogen bonds. Compound 2 also adopts 1-D coordination chain, which is connected to form 3-D supramolecular network by intra- and inter-chain C–H ··· Cl hydrogen bonds; 3 is discrete, linked to form 2-D supramolecular sheets by intra- and inter-molecular C–H ··· Cl hydrogen bonds. The different volume and coordination ability of organic ligands result in the different coordination structure and supramolecular synthons. All these compounds exhibit strong fluorescence emissions at room temperature.     

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.     

Charge-assisted N(+)–H···(−)S hydrogen bonds in the crystal structure of selected diammonium thiophenolates

New salts of thiophenol with three flexible aliphatic diamines H₂N(CH₂)_nNH₂ (n = 2, 4 and 6) have been synthesized and characterized by elemental analyses, IR spectroscopy and X-ray crystallography in order to analyze their supramolecular architecture. Structural analyses indicate that in the crystals, proton transfer has occurred, with the –SH group giving ⁽⁺⁾N–H···S^(?) hydrogen bonding interaction. The structure of compound 1 exhibits a two-dimensional network and compounds 2–3 a three-dimensional supramolecular networks, and each of them is based on hydrogen bonds and CH···π interactions. The transfer of proton from the thiol to the diamines was confirmed by the solid-state FTIR spectra of 1–3.