Types Of Hydrogen Bonding Interactions Research Articles

Crystal structure and Hirshfeld surface analysis of two iHOFs based on CH...NC hydrogen bonding.

Two ionic hydrogen-bonded organic frameworks (iHOFs) assembled from 4-cyano-N-(4-cyanobenzyl)pyridinium, have been crystallized with Br- and antimony(III) pentabromide, [SbBr5]2-, as counter-ions and characterized. These are 4-cyano-N-(4-cyanobenzyl)pyridinium bromide, C14H10N3+·Br-, and bis[4-cyano-N-(4-cyanobenzyl)pyridinium] antimony(III) pentabromide, (C14H10N3)2[SbBr5]. The CH...NC interactions induced by templating anions construct disparate frameworks. Hirshfeld surface analysis indicated that these crystals exhibit two types of hydrogen-bonding interactions, specifically CH...NC and CH...Br. Consecutive reverse-parallel CH...NC hydrogen-bonding interactions in these crystals induced the formation of a large number of CH...NC bonds which exhibit both cis and trans configurations.

Molecular dynamics simulation study of thermomechanical properties and hydrogen bonding structures of two‐component polyurethanes

AbstractWe investigated the thermomechanical properties and hydrogen bonding (HB) structures of two‐component hexamethylenediisocyanate (HDI)‐poly(tetramethylene oxide) (PTMO) and 4,4′‐methylenediphenyldiisocyanate (MDI)‐PTMO polyurethanes with atomistic molecular dynamics simulations. We used different temperature‐scanning and sampling protocols to estimate the glass transition temperature (Tg) of these two polyurethanes. Our simulation results consistently predicted higher Tg values for MDI‐PTMO than those for HDI‐PTMO, in qualitative agreement with the same trend observed in experiments. We also studied two different types of HB interactions in these polyurethanes. At ambient temperature, more HB contacts between amide‐hydrogens and carbonyl‐oxygens of the carbamate groups along with longer lifetimes were noted in HDI‐PTMO than in MDI‐PTMO, while the latter revealed more HB contacts between amide‐hydrogens and ether‐oxygens of PTMO. MDI‐PTMO, encompassing more rigid chain structures, displayed higher stress values in stress–strain profiles from high strain‐rate tensile deformations at ambient temperature than HDI‐PTMO, which is consistent with a higher Tg value of MDI‐PTMO.

Crystal structure of 2-(methyl-amino)-tropone.

The title compound, 2-(methyl-amino)-cyclo-hepta-2,4,6-trien-1-one, C8H9NO, crystallizes in the monoclinic space group P21/c, with three independent mol-ecules in the asymmetric unit. The planarity of the mol-ecules is indicated by planes fitted through the seven ring carbon atoms. Small deviations from the planes, with an extremal r.m.s. deviation of 0.0345 Å, are present. In complexes of transition metals with similar ligands, the large planar seven-membered aromatic rings have shown to improve the stability of the complex. Two types of hydrogen-bonding inter-actions, C-H⋯O and N-H⋯O, are observed, as well as bifurcation of these inter-actions. The N-H⋯O inter-actions link mol-ecules to form infinite chains. The packing of mol-ecules in the unit cell shows a pattern of overlapping aromatic rings, forming column-like formations. π-π inter-actions are observed between the overlapping aromatic rings at 3.4462 (19) Å from each other.

The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib).

The simplest non-proteinogenic amino acid α-aminoisobutyric acid (Aib), an analogue of glycine and alanine, has been vaporized by laser ablation and probed by high-resolution Fourier transform microwave spectroscopic techniques. Comparison of the experimental rotational and 14 N nuclear quadrupole constants with that predicted ab initio has allowed the identification of three conformers of Aib exhibiting three types of hydrogen-bond interactions I (NH⋅⋅⋅O=C, cis-COOH), II (OH⋅⋅⋅N, trans-COOH), and III (N-H⋅⋅⋅O-H, cis-COOH) within the amino acid backbone. The observation of conformer III, not detected previously for related proteinogenic amino acids with a nonpolar side chain in a supersonic expansion, indicates that the presence of the methyl groups should restrict the conformational relaxation from conformer Aib-III to Aib-I. For conformer Aib-II, the rotational spectra of the 13 C isotopomers reveal a tunneling motion arising from the two equivalent methyl groups in the molecule. The observation of a single spectrum at the midpoint between those predicted for the two 13 C of the methyl groups has been explained by considering a double-minimum potential function with a low-energy interconversion barrier for a large amplitude internal motion. This singular fact has been corroborated by the anomalous centrifugal distortion effects determined in conformer Aib-II.

Isomer-Specific Induced Circular Dichroism Spectroscopy of Jet-Cooled Phenol Complexes with (-)-Methyl l-Lactate.

Induced circular dichroism (ICD) is the CD observed in the absorption of an achiral molecule bound to a transparent chiral molecule through noncovalent interactions. ICD spectroscopy has been used to probe the binding between molecules, such as protein-ligand interactions. However, most ICD spectra have been measured in solution, which only exhibit the averaged CD values of all conformational isomers in solution. Here, we obtained the first isomer-selective ICD spectra by applying resonant two-photon ionization CD spectroscopy to jet-cooled phenol complexes with (-)-methyl l-lactate (PhOH-(-)ML). The well-resolved CD bands in the spectra were assigned to two conformers, which contained different types of hydrogen-bonding interactions between PhOH and (-)ML. The ICD values of the two conformers have different signs and magnitudes, which were explained by differences both in the geometrical asymmetries of PhOH bound to (-)ML and in the electronic coupling strengths between PhOH and (-)ML.

Crystal structure of bis-(1,3-di-amino-propane-κ(2) N,N')bis-[2-(4-nitro-phen-yl)acetato-κO]cadmium.

In the structure of the title compound, [Cd(C8H6NO4)2(C3H10N2)2], the Cd(II) atom is located on a center of symmetry with one independent Cd-O distance of 2.3547 (17) Å and two Cd-N distances of 2.3265 (18) and 2.3449 (19) Å. The Cd(II) atom has an overall octa-hedral coordination environment. Several types of hydrogen-bonding inter-actions are evident. Both intra- and inter-molecular inter-actions occur between the amino groups and the O atoms of the acetate group. These N-H⋯O hydrogen bonds lead to a layered structure extending parallel to the bc plane. In addition, weak inter-molecular C-H⋯O inter-actions involving the nitro groups exist, leading to the formation of a three-dimensional network structure.

Crystal structure of bis-(1,3-di-amino-propane-κ(2) N,N')bis-[2-(4-nitro-phen-yl)acetato-κO]zinc(II).

In the structure of the title compound, [Zn(C8H6NO4)2(C3H10N2)2], the ZnII atom is located on a center of symmetry with one independent Zn—O distance of 2.199 (2) Å, and two Zn—N distances of 2.157 (2) and 2.144 (2) Å. The overall coordination geometry around the ZnII atom is octa­hedral. Several types of hydrogen-bonding inter­actions are evident. Both intra­molecular [2.959 (3) Å] and inter­molecular [3.118 (3) and 3.124 (3) Å inter­actions occur between the O atoms of the acetate group and the amino N atoms, and weak inter­molecular C—H—O inter­actions involving the nitro groups, leading to an extended chain of the molecules aligned along the ac plane.

Diaquabis(propane-1,3-diamine)nickel(II) bis(propane-1,3-diamine)disulfatonickelate(II)

The ionic NiII title complex, [Ni(C3H10N2)2(H2O)2][Ni(SO4)2(C3H10N2)2], is built up of [Ni(dipr)2(H2O)2]2+ complex cations and [Ni(dipr)2(SO4)2]2− complex anions (dipr is propane-1,3-diamine). Both NiII atoms display a slightly distorted octa­hedral coordination and are located on inversion centers. There are several types of hydrogen-bonding inter­actions, which connect complex cations and anions into a two-dimensional network parallel to (010). Hydrogen bonds formed by the axially coordinated water mol­ecule of the complex cation and one of the O atoms of the sulfate groups of the complex anion (first type) link them into chains along the c axis. These chains are linked to each other through hydrogen bonds formed by an O atom (second type) of the SO4 groups and NH2 groups of the ligand of the complex cations from neighboring chains, forming a two-dimensional hydrogen-bonded net perpendicular to the b axis. The third type of O atoms of the sulfate groups of the complex anion are also linked into chains by a combination of both previously described types of H-atom connections.

Four new cobalt(ii) coordination complexes: thermochromic switchable behavior in the process of dehydration and rehydration

Four cobalt(II) coordination complexes, {[Co11(L1)6(HL1)2(H2O)28]·12H2O}n (1), [Co4(H2L1)4(HL1)2(H2O)8]·2H3L1·2H2O (2), {[Co(H2L3)(H2O)3]·2H2O}n (3) and [Co(HL1)(4,4′-bpy)(H2O)2]n (4), (H3L1 = 2,4,6-tri(3-carboxyphenylthio)-1,3,5-triazine, H4L3 = 2,4-bis(3-carboxyphenylthio)-6-(4-carboxyphenylamino -1,3,5-triazine, 4,4′-bpy = 4,4′-bipyridine), was synthesized hydrothermally and characterized by single-crystal X-ray diffraction, powder X-ray diffraction, IR, thermal analysis, UV-vis spectroscopy and magnetic measurements. Complex 1 shows a 2D layer structure composed of three types of secondary building units (SBUs), [M1], [M3] and [M4] bridged by [HL1]2− and [L1]3− linkers. While complex 2 is a tetranuclear compound and further forms a 3D supramolecular network structure based on eight types of hydrogen-bonding interactions between the molecules. The 2D framework of complex 3 can be described as 1D infinite chains interconnected by [H2L3]2− ligands. Furthermore, the hydrogen-bonding interactions between the adjacent layers along the ac plane makes the 2D layer structure extend to a 3D network. The structure of complex 4 can be illustrated as a 1D zigzag infinite chain with 4,4′-bipyridine as the secondary ligand. Additionally, the π⋯π stacking interactions can be observed between the adjacent chains. An aquo-accessible thermochromic change in complexes 1–4 was induced by means of the reversible dehydration and rehydration of the crystals. Magnetic measurements showed antiferromagnetic coupling between the Co2+ ions in all of the four complexes.

Intermolecular dihydrogen- and hydrogen-bonding interactions in diammoniumcloso-decahydrodecaborate sesquihydrate

The asymmetric unit of the title salt, 2NH(4)(+).B(10)H(10)(2-).1.5H(2)O or (NH(4))(2)B(10)H(10).1.5H(2)O, (I), contains two B(10)H(10)(2-) anions, four NH(4)(+) cations and three water molecules. (I) was converted to the anhydrous compound (NH(4))(2)B(10)H(10), (II), by heating to 343 K and its X-ray powder pattern was obtained. The extended structure of (I) shows two types of hydrogen-bonding interactions (N-H...O and O-H...O) and two types of dihydrogen-bonding interactions (N-H...H-B and O-H...H-B). The N-H...H-B dihydrogen bonding forms a two-dimensional sheet structure, and hydrogen bonding (N-H...O and O-H...O) and O-H...H-B dihydrogen bonding link the respective sheets to form a three-dimensional polymeric network structure. Compound (II) has been shown to form a polymer with the accompanying loss of H(2) at a faster rate than (NH(4))(2)B(12)H(12) and we believe that this is due to the stronger dihydrogen-bonding interactions shown in the hydrate (I).

Hydrogen bonding in acetone clusters probed by near-edge x-ray absorption fine structure spectroscopy in the carbon and oxygen K-edge regions

Hydrogen bonding in acetone clusters was investigated using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of the cluster ions were measured as the NEXAFS spectra of acetone clusters. In the carbon K-edge region, the first resonance peak, which was assigned to the C(CO) 1s-->pi( *)(C=O) resonance transition, showed no substantial change in the PIY curves of the acetone clusters, while the C(CH3) 1s-->3ppi(CH(3)) excitation feature was found to be strongly suppressed. The selective suppression of the C(CH3) 1s-->3ppi(CH(3)) resonance transition can be explained by the change in the character of the 3ppi(CH(3)) orbital due to the C=O...H-C type of hydrogen-bonding interaction. On the other hand, the NEXAFS spectra of the acetone molecule and clusters were almost identical in the oxygen K-edge region, except for a small shift in the pi( *)(C=O) resonance of 0.13 eV, because the character of the pi( *)(C=O) orbital remained, regardless of the C=O...H-C hydrogen bonding interaction.

Investigation of intermolecular hydrogen bond interactions in crystalline l-Cysteine by DFT calculations of the oxygen-17, nitrogen-14, and hydrogen-2 EFG tensors and AIM analysis

A systematic computational study is carried out to investigate hydrogen bond (HB) interactions in the real crystalline structures of l-Cysteine at 30 and 298 K by density functional theory (DFT) calculations of electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (monomer) and nine-molecule (cluster) models of l-Cysteine are created by available crystal coordinates at both temperatures and the EFG tensors are calculated for both models to indicate the effect of HB interactions on the tensors. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G⁎⁎ and cc-pVTZ basis sets are converted to those experimentally measurable nuclear quadrupole resonance (NQR) parameters i.e. quadrupole coupling constants (qcc) and asymmetry parameters ( η Q). The evaluated NQR parameters reveal that the EFG tensors of 17O, 14N, and 2H are influenced and show particular trends from monomer to the target molecule in the cluster due to the contribution of target molecule to classic N–H…O, and non-classic S–H…O and S–H…S types of HB interactions. On the other hand, atoms in molecules (AIM) analyses confirm the presence of HB interactions and rationalize the observed EFG trends. The results indicate different contribution of various nuclei to HB interactions in the cluster where O2 and N1 have major contributions. The EFG tensors as well as AIM analysis at the H6 site show that the N1-H6…O2 HB undergoes a significant change from 30 to 298 K where changes in other N–H…O interactions are almost negligible. There is a good agreement between the calculated 14N NQR parameters and reported experimental data.

Unique Interactions Between Diborane and π Orbitals: Blue- or Red-Shifted Hydrogen Bonding?

A new type of hydrogen-bonding interaction in the diborane (B 2H 6)...pi (benzene C 6H 6, 1,3-cyclopentadiene C 5H 6, and cyclobutadiene C 4H 4) system is identified with the natural bond orbital and atoms-in-molecules analyses based on ab initio calculations. In comparison with the symmetric and asymmetric stretching vibrational modes of the bridging hydrogen atoms in free B 2H 6, the frequencies of the symmetric mode are red-shifted for B 2H 6...C 6H 6 and B 2H 6...C 5H 6 but blue-shifted for B 2H 6...C 4H 4. The frequency blue shifts of the asymmetric mode are found for all three complexes; the most significant blue shift is 14.73 cm (-1) for the asymmetric mode in B 2H 6...C 4H 4. In these complexes, the electron-deficient three-center two-electron bond B-H 1-B facing the pi orbital is shortened, while the opposite B-H 2-B bond is elongated.

Hydrogen bond interactions in sulfamerazine: DFT study of the O-17, N-14, and H-2 electric field gradient tensors

Hydrogen bond (HB) interactions are studied in the real crystalline structure of sulfamerazine by density functional theory (DFT) calculations of the electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (single) and four-molecule (cluster) models of sulfamerazine are created by available crystal coordinates and the EFG tensors are calculated in both models to indicate the influence of HB interactions on the tensors. Directly relate to the experiments, the calculated EFG tensors are converted to the experimentally measurable nuclear quadrupole resonance (NQR) parameters, quadrupole coupling constant ( qcc) and asymmetry parameter ( η Q ). The evaluated NQR parameters reveal that due to contribution of the target molecule to N–H⋯N and N–H⋯O types of HB interactions, the EFG tensors at the sites of various nuclei are influenced from single model to the target molecule in cluster. Additionally, O2, N4, and H2 nuclei of the target molecule are significantly influenced by HB interactions, consequently, they have the major contributions to HB interactions in cluster model of sulfamerazine. The calculations are performed employing B3LYP method and 6-311++G∗∗ basis set using GAUSSIAN 98 suite of program.

Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (O [dbnd]C–NH) in crystalline acetamide

A density functional theory (DFT) study was carried out to investigate hydrogen bonding (HB) properties of peptide group (O C–NH) in crystalline acetamide. Since the peptide group in acetamide contributes to N–H⋯O and C–H⋯O types of HB interactions, acetamide is considered as the simplest form of peptide linkage in proteins. The evaluated NMR parameters including quadrupole coupling constants and asymmetry parameters from the calculated electric field gradient (EFG) tensors at the sites of O17, N14 and H2 nuclei and isotropic chemical shieldings from the calculated chemical shielding (CS) tensors at the sites of O17, N15 and H1 nuclei reveal the major contribution of O C–NH group to HB interactions. Although N–H⋯O type of HB interaction play the major role in the HB properties of peptide group in lattice form of crystalline acetamide, however, the role of weaker C–H⋯O type of HB interaction cannot be neglected.

Water Tape Assembled in 1,10-Bis(2-pyrazinylcarbonyl)-1,4,7,10-tetraazadecane via H-Bonding and π−π Stacking

An icelike 2T6(2) water tape was formed in the organic host, 1,10-bis(2-pyrazinylcarbonyl)-1,4,7,10-tetraazadecane (BPTA), and characterized by X-ray diffraction. Each BPTA molecule crystallizes with six water molecules with a molecular formula of BPTA·6H2O. The 2T6(2) water tape is constructed of fused six-membered water rings with chair conformations. The 2T6(2) water tape and BPTA molecules assemble into a network of water tapes sandwiched between BPTA tapes. The network is stabilized by π−π stacking between BPTA molecules and three types of hydrogen-bonding interactions: between BPTA molecules, between the water molecules, and between the water and BPTA molecules.

Computational Study of Noncovalent Complexes between Formamide and Formic Acid

The geometries and binding energies of 1:1, 1:2, and 1:4 formic acid-formamide complexes (FA-FMA) are calculated by quantum chemical procedures. Vibrational spectra and intermolecular distances of the most stable FA-FMA dimers as well as the influence of the basis set superposition error (BSSE) on the geometries and energies of the dimers are also discussed. All FA-FMA dimers are optimized at the B3LYP/cc-pVTZ, the MP2/cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ levels of theory to study the influence of the level of theory on the calculated geometries and energies. CCSD(T)/cc-pVTZ single-point calculations at the MP2/aug-cc-pVTZ-optimized geometries were performed as reference for estimating the quality of lower level calculations. These calculations allow us to qualitatively describe the competition between different types of hydrogen-bonding interactions in FA-FMA complexes. FA-FMA dimers are compared to other formamide complexes and to the FA-FMA crystal structure.

Extended network via hydrogen bond linkages of coordination compounds: synthesis, crystal structure and thermal behaviour of the complexes [M(L)2(NO3)2] (MII=Cu, Co) and [Ni(L)2(H2O)2][(NO3)2] (L=malonamide)

A series of monomeric complexes of general formula [MII(L)2(NO3)2] (MII=Cu, Co) (1), (2, 3), and [NiII(L)2(H2O)2][(NO3)2] (4) with L=malonamide have been isolated and characterized by single crystal X-ray structure. The crystalline structures for all compounds show multi-dimensional arrays or networks structures created by two types of hydrogen-bonding interactions. The first, between hydrogen atoms of the amide moiety and oxygen atoms of malonamide N-H(malonamide)⋯O(malonamide) forming two-dimensional arrays. The second type, between the hydrogen atoms of the amide moiety and the oxygen atoms of the nitrate molecules N-H(malonamide)⋯O(nitrate) generating three-dimensional arrangements. Nevertheless, for the Ni compound two contacts between the oxygen atoms of water molecules and oxygen atoms of nitrate moiety O(water)⋯O(nitrate) are present too. All the compounds have been characterized through thermogravimetric (TG) and calorimetric analyses (DSC).

2-O-Benzoyl-myo-inositol-1,3,5-orthoformate

Protected myo-inositol derivatives are important precursors in the synthesis of phosphorylated myo-inositol derivatives which play a significant role in the cellular signal transduction. The structure of the title compound, C14H14O7, which was prepared from myo-inositol, has been determined by X-ray crystallography. Several types of hydrogen-bonding interactions are involved in the packing of the molecule in the crystal.

The Vibrational Spectra of NH4VO3 at Elevated Temperatures and Pressures

Abstract Results obtained from the vibrational spectra of NH4VO3 and its deuterated analogues show that at least two types of hydrogen bond interactions can be identified at am bient conditions. In accordance with the structural data on NH4VO3 (F. C. Hawthorne and C. Calvo, J. Solid State Chem. 22, 157 (1977)) these interactions are assigned to normal, strong hydrogen bonds and weaker bifurcated ones, respectively. The temperature dependence of some of the N -H bands indicates that the normal hydrogen bonds decrease in strength with increasing temperatures, while the bifurcated ones tend to increase in strength. The NH4 + ions do not show fluxional behaviour at ambient conditions and even the bifurcated hydrogen bonds are of the type that is dominated by acceptor strength of the anions and not by a volume effect. The Ram an active NH4 + vibrations are very weak compared to the V - O modes and could not all be observed in the highpressure diamond anvil cell. The temperature dependence of the V - O Ram an active modes suggests that changes in the crystals of NH4VO3 brought about by the application of heat mainly involve the O -V -O angles, while pressure changes are mostly accommodated by changes in the V -O bridging bonds and O -V -O bridging angles.