Three-dimensional Hydrogen-bonded Network Research Articles

Proton transfer mechanism of 1,3,5-tri(2-benzimidazolyl) benzene with a unique triple-stranded hydrogen bond network as studied by DFT-MD simulations

Clarification of proton transfer mechanisms is crucial to the development of proton exchange membrane fuel cells (PEMFCs). Nitrogen-containing heterocyclic compounds (e.g., imidazole derivatives) are well known for their potential to assist proton hopping through hydrogen bond networks at high temperatures. Among the many imidazole derivatives reported thus far, 1,3,5-tri(2-benzimidazolyl)benzene (TBIB) is assumed to be one of the most promising imidazole derivatives because of its triple-stranded three-dimensional hydrogen bond network. In fact, TBIB immersed into a polyphosphoric acid matrix was reported to enhance the proton conductivity to 10−2–10−1S/cm in the high-temperature range up to 170°C. In the present work, the proton transfer mechanism has been investigated using density functional theory (DFT) with a DNP basis set and the GGA exchange-correlation functional BLYP and molecular dynamics simulations (MD) to provide insight into the cause of the remarkable proton conductivity of TBIB. Transition states in the proton hopping process were obtained using two types of models constructed from the X-ray crystal structure: an isolated two-molecule system (type I) and a periodic three-molecule system (type II). Alterations of charge distribution, molecular conformation and molecular orientation were investigated from these models. Further, the diffusion coefficient of proton transfer has been estimated and the mechanisms along three specific channels that favor efficient proton transfer between the layers have been examined in detail. Additionally, the effect of an electric field perturbation was investigated for these two models. The application of an external electric field was found to affect the proton hopping process remarkably, as evidenced by large changes in the activation energies and proton hopping times. In conclusion, the highly organized hydrogen-bonding network observed for TBIB was found to be a key factor in enhancing the efficiency of proton transfer.

Cation-cation interaction in the double Th(IV)/Np(V) nitrate [H3O][Th2(NpO2)3(H2O)9(NO3)12]·2H2O

A new double Th(IV)/Np(V) nitrate, [H3O][Th2(NpO2)3(H2O)9(NO3)12]·2H2O, was isolated in the crystalline form and studied by single crystal X-ray diffraction. Two independent Np atoms in the structure have the coordination polyhedra (CPs) in the form of pentagonal bipyramids with “yl” O atoms in the apical vertices. The equatorial plane of the Np(1) CP is constituted by the O atoms of the bidentate nitrate ion, two water molecules, and “yl” O atom of the adjacent Np(2)O2 group. The equatorial plane of the Np(2) CP is constituted by five water molecules disordered over two positions. The coordination surrounding of the Th4+ cation is formed by the O atoms of five bidentate nitrate ions disordered over two positions and the O atoms of two Np(1)O2 groups; the coordination number of the Th(1) atom is 12. Mixed-element cation-cation (CC) interaction of types NpO 2 + iTh4+ and NpO 2 + iNpO 2 + is observed in the structure. It leads to the formation of corrugated cationic networks. The CC interaction in the crystal is the main structure-forming factor. The hydroxonium ions [H3O]+, coordinated water molecules, and water molecules of crystallization are proton donors in hydrogen bonding. The three-dimensional network of hydrogen bonds additionally stabilizes the crystal packing.

Crystal structure of catena-poly[[[tri-aqua-strontium]-di-μ2-glycinato] dibromide

In the title coordination polymer, {[Sr(C2H5NO2)2(H2O)3]Br2} n , the Sr(2+) ion and one of the water mol-ecules are located on twofold rotation axes. The alkaline earth ion is nine-coordinated by three water O atoms and six O atoms of the carboxyl-ate groups of four glycine ligands, two in a chelating mode and two in a monodentate mode. The glycine mol-ecule exists in a zwitterionic form and bridges the cations into chains parallel to [001]. The Br(-) counter-anions are located between the chains. Inter-molecular hydrogen bonds are formed between the amino and carboxyl-ate groups of neighbouring glycine ligands, generating a head-to-tail sequence. Adjacent head-to-tail sequences are further inter-connected by inter-molecular N-H⋯Br hydrogen-bonding inter-actions into sheets parallel to (100). O-H⋯Br and O-H⋯O hydrogen bonds involving the coordinating water mol-ecules are also present, consolidating the three-dimensional hydrogen-bonding network.

Crystal structure of 4-hy-droxy-pyridin-1-ium 3,5-di-carb-oxy-benzoate.

The structure of the title salt, C5H6NO(+)·C9H5O6 (-), (I), shows that 4-hy-droxy-pyridine has abstracted an H atom from benzene-1,3,5-tri-carb-oxy-lic acid, yielding a pyridinium cation and carboxyl-ate anion. The two ions form an extensive three-dimensional hydrogen-bonded network throughout the crystal. The hydrogen bonds that comprise the core of the network are considered strong, with O-H⋯O and N-H⋯O donor-to-acceptor distances ranging from 2.533 (2) to 2.700 (2) Å. Packing is further enhanced by π-stacking of the cations and anions with like species [centroid-centroid distance = 3.6206 (13) Å].

Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation**Project supported by the National Natural Science Foundation of China (Grant Nos. 61302007 and 60977065), the Fundamental Research Funds for the Central Universities of China (Grant No. FRF-SD-12-016A), and the Engineering Research Center of Industrial Spectrum Imaging of Beijing, China.

The crystal structure of L-glutamine is stabilized by a three-dimensional network of intermolecular hydrogen bonds. We utilize plane-wave density functional theory lattice-dynamics calculations within the generalized-gradient approximation (GGA), Perdew–Burke–Ernzerhof (PBE), PBE for solids (PBEsol), PBE with Wu–Cohen exchange (WC), and dispersion-corrected PBE, to investigate the effect of these intermolecular contacts on the absorption spectra of glutamine in the terahertz frequency range. Among these calculations, the solid-state simulated results obtained using the WC method exhibit a good agreement with the measured absorption spectra, and the absorption features are assigned with the help of WC. This indicates that the vibrational modes of glutamine were related to the combination of intramolecular and intermolecular motions, the intramolecular modes were dominated by rocking or torsion involving functional groups; the intermolecular modes mainly result from the translational motions of individual molecules, and the rocking of the hydrogen-bonded functional groups.

Crystal structure of rilpivirine, C22H18N6

The crystal structure of rilpivirine has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rilpivirine crystallizes in space groupP21/c(#14) witha= 8.39049(3),b= 13.89687(4),c= 16.03960(6) Å,β= 90.9344(3)°,V= 1869.995(11) Å3, andZ= 4. The most prominent features of the structure are N–H···N hydrogen bonds. These form aR2,2(8) pattern which, along withC1,1(12) and longer chains, yield a three-dimensional hydrogen bond network. The powder pattern has been submitted to International Centre for Diffraction Data, ICDD, for inclusion in future releases of the Powder Diffraction File™.

Studies on the synthesis, structural characterization, Hirshfeld analysis and stability of apovincamine (API) and its co-crystal (terephthalic acid: Apovincamine = 1:2)

Apovincamine and the corresponding co-crystal have been synthesized and characterized by single crystal XRD, FT-IR, UV, TGA/DSG. Components of the crystalline phase have also been investigated in terms of their corresponding Hirshfeld surface. In the crystal lattice, a three-dimensional hydrogen-bonded network is observed in the co-crystal, including the formation of a two-dimensional molecular scaffold. Hirshfeld surfaces and fingerprint plots indicate that the structures are stabilized by H⋯H, C−H⋯π, C–H⋯O and O–H⋯N intermolecular interactions. In this work, the co-crystal strategy has been applied successfully to apovincamine. One important parameter, i.e. solubility in water, has also been significantly improved, which proves to be an important factor for bioavailability. Furthermore, DSC/TGA analysis indicates that the co-crystal maintains its crystallinity up to 200°C, suggesting a higher stability of the co-crystal compared to apovincamine.

Chlorometallate-Pyridinium Boronic Acid Salts for Crystal Engineering: Synthesis of One-, Two-, and Three-Dimensional Hydrogen Bond Networks

A series of new crystal structures of salts containing 3- and 4-pyridineboronic acid (3- and 4-pba) with chlorometallate have been prepared: [4-pbaH][MnCl2] (1), [4-pbaH][CdCl2], (2), [4-pbaH]2[CuCl4] (3), [4-pbaH]2[PdCl4] (4), [3-pbaH]2[CdCl4] (5), [3-pbaH][CuCl3(OH2)] (6), and [3-pbaH][PdCl2] (7). In these salts five structural forms for the chlorometallate species are observed: mononuclear square planar [M = Pd (4 and 7)], dimeric square-pyramidal [M = Cu (3)], polymeric square-pyramidal [M = Cu (6)], polymeric trans-edge-sharing octahedral [M = Mn (1), Cd (2)], and polymeric cis-edge-sharing octahedral [M = Cd (5)]. The cyclic R2,2(8) boronic acid dimer is formed in the salt of 1–5. NH···Cl2M synthons A have been exploited in 1–4, 6, and 7. Both NH···Cl2M (sythons A) and B(OH)2···Cl2M (sythons B) interactions give rise to a synthon of form I in 6. The uncommon folded conformation of the NH···Cl2M (synthons A) are formed in 7. The NH or OH donors and consequent branching of the NH···Cl hydrogen-bond network leads to one-, two-, and three-dimensional structures. These structures are further stabilized by CH···O and CH···Cl and π···π stacking interactions.

Isomer-Specific Spectroscopy of Benzene–(H2O)n, n = 6,7: Benzene’s Role in Reshaping Water’s Three-Dimensional Networks

The water hexamer and heptamer are the smallest sized water clusters that support three-dimensional hydrogen-bonded networks, with several competing structures that could be altered by interactions with a solute. Using infrared-ultraviolet double resonance spectroscopy, we record isomer-specific OH stretch infrared spectra of gas-phase benzene-(H2O)(6,7) clusters that demonstrate benzene's surprising role in reshaping (H2O)(6,7). The single observed isomer of benzene-(H2O)6 incorporates an inverted book structure rather than the cage or prism. The main conformer of benzene-(H2O)7 is an inserted-cubic structure in which benzene replaces one water molecule in the S4-symmetry cube of the water octamer, inserting itself into the water cluster by engaging as a π H-bond acceptor with one water and via C-H···O donor interactions with two others. The corresponding D(2d)-symmetry inserted-cube structure is not observed, consistent with the calculated energetic preference for the S4 over the D(2d) inserted cube. A reduced-dimension model that incorporates stretch-bend Fermi resonance accounts for the spectra in detail and sheds light on the hydrogen-bonding networks themselves and on the perturbations imposed on them by benzene.

Syntheses and crystal structures of two magnesium-tetrazole compounds in salt and polymeric forms.

Two alkaline earth-tetrazole compounds, namely catena-poly[[[triaquamagnesium(II)]-μ-5,5'-(azanediyl)ditetrazolato-κ(3)N(1),N(1'):N(5)] hemi{bis[μ-5,5'-(azanediyl)ditetrazolato-κ(3)N(1),N(1'):N(2)]bis[triaquamagnesium(II)]} monohydrate], {[Mg(C(2)HN(9))(H(2)O)(3)][Mg(2)(C(2)HN(9))(2)(H(2)O)(6)]0.5·H(2)O}n, (I), and bis[5-(pyrazin-2-yl)tetrazolate] hexaaquamagnesium(II), (C(5)H(3)N(6))[Mg(H(2)O)(6)], (II), have been prepared under hydrothermal conditions. Compound (I) is a mixed dimer-polymer based on magnesium ion centres and can be regarded as the first example of a magnesium-tetrazolate polymer in the crystalline form. The structure shows a complex three-dimensional hydrogen-bonded network that involves magnesium-tetrazolate dimers, solvent water molecules and one-dimensional magnesium-tetrazolate polymeric chains. The intrinsic cohesion in the polymer chains is ensured by N-H...N hydrogen bonds, which form R(2)(2)(7) rings, thus reinforcing the propagation of the polymer chain along the a axis. The crystal structure of magnesium tetrazole salt (II) reveals a mixed ribbon of hydrogen-bonded rings, of types R(2)(2)(7), R(2)(2)(9) and R(2)(4)(10), running along the c axis, which are linked by R(2)(4)(16) rings, generating a 4,8-c flu net.

Calcium tartrate esahydrate, CaC4H4O6·6H2O: a structural and spectroscopic study.

The crystal structure of calcium tartrate esahydrate, CaC4H4O6·6H2O, has been solved by the charge-flipping method from single-crystal X-ray diffraction data and refined to R = 0.021, based on 1700 unique observed diffractions. Salient crystallographic data are: a = 7.7390 (1), b = 12.8030 (2), c = 5.8290 (1) Å, Z = 2, and space group P2₁2₁2. During the refinement step it was possible to locate all H atoms by difference Fourier synthesis. The tartrate molecule has a (-)-gauche conformation and is coordinated to two calcium ions to form infinite chains along the a axis which alternate Ca polyhedra with tartrate molecules. The chains are interlinked by a three-dimensional network of hydrogen bonds from four water molecules surrounding the Ca ion, reinforced by hydrogen bonds from one interstitial water molecule. Micro-Raman and FT-IR spectroscopic data are provided.

Crystal structures of two deca-vanadates(V) with penta-aqua-manganese(II) pendant groups: (NMe4)2[V10O28{Mn(H2O)5}2]·5H2O and [NH3C(CH2OH)3]2[V10O28{Mn(H2O)5}2]·2H2O.

Two heterometallic deca-vanadate(V) compounds, bis-(tetra-methyl-ammonium) deca-aquadi-μ4-oxido-tetra-μ3-oxido-hexa-deca-μ2-oxido-hexa-oxidodimang-anese(II)-deca-vanadate(V) penta-hydrate, (Me4N)2[V10O28{Mn(H2O)5}2]·5H2O, A, and bis-{[tris-(hy-droxy-meth-yl)meth-yl]ammonium} deca-aquadi-μ4-oxido-tetra-μ3-oxido-hexa-deca-μ2-oxido-hexa-oxidodimanganese(II)deca-vanadate(V) dihydrate, [NH3C(CH2OH)3]2[V10O28{Mn(H2O)5}2]·2H2O, B, have been synthesized under mild reaction conditions in an aqueous medium. Both polyanions present two [Mn(OH2)5](2+) complex units bound to the deca-vanadate cluster through oxide bridges. In A, the deca-vanadate unit has 2/m symmetry, whereas in B it has twofold symmetry. Apart from this, the main differences between A and B rest on the organic cations, tetra-methyl-ammonium and [tris-(hy-droxy-meth-yl)meth-yl]ammonium, respectively, and on the number and arrangement of the water mol-ecules of crystallization. In both compounds, the H atoms from the coordinating water mol-ecules participate in extensive three-dimensional hydrogen-bonding networks, which link the cluster units both directly and through solvent mol-ecules and, in B, through the 'tris-' cation hydroxyl groups. The cation in B also participates in N-H⋯O hydrogen bonds. A number of C-H⋯O inter-actions are also observed in both structures.

Crystal Structures of Two Tetraalkylammonium Salts and One Dihydrate of 4,4′-Dihydroxybenzophenone

Two tetraalkylammonim salts and a dihydrate of 4,4′-dihydroxybenzophenone (DHBP) have been prepared and characterized by X-ray crystallography. In [(CH3)4N](C13H9O3) (1), the DHBP- anions pack to form two-dimensional puckered, hydrogen-bonded layers via O–H···O− hydrogen bonds between the hydroxyl groups. Comparatively, in [(C2H5)4N]2(C13H8O3)·10H2O, the DHBP2− anions act as proton acceptors to link ten water molecules generating two-dimensional planar hydrogen-bonded layers. The tetraalkylammonium cations are located between the hydrogen-bonded layers. Additionally, weak C–H···O hydrogen bonds between the anions and cations are present. The DHBP molecules in 3 ((C13H10O3)·2H2O) are linked to the water molecules forming a three-dimensional hydrogen-bonded network by conventional O–H···O hydrogen bonding. Additionally, theoretical calculations were performed to explore the structural differences among the materials and the results were compared with the corresponding crystal structures. Two tetraalkylammonim salts and one dihydrate of 4,4′-dihydroxybenzophenone (DHBP) have been prepared and characterized by X-ray crystallography. The hydrogen bonding of the structures is presented.

Crystal structure of [Y6(μ6-O)(μ3-OH)8(H2O)24]I8·8H2O.

The crystal structure of the title compound {systematic name: octa-μ3-hydroxido-μ6-oxido-hexa-kis-[tetra-aqua-yttrium(III)] octa-iodide octa-hydrate}, is characterized by the presence of the centrosymmetric mol-ecular entity [Y6(μ6-O)(μ3-OH)8(H2O)24](8+), in which the six Y(3+) cations are arranged octa-hedrally around a μ6-O atom at the centre of the cationic complex. Each of the eight faces of the Y6 octa-hedron is capped by an μ3-OH group in the form of a distorted cube. In the hexa-nuclear entity, the Y(3+) cations are coordinated by the central μ6-O atom, the O atoms of four μ3-OH and of four water mol-ecules. The resulting coordination sphere of the metal ions is a capped square-anti-prism. The crystal packing is quite similar to that of the ortho-rhom-bic [Ln 6(μ6-O)(μ3-OH)8(H2O)24]I8·8H2O structures with Ln = La-Nd, Eu-Tb, Dy, except that the title compound exhibits a slight monoclinic distortion. The proximity of the cationic complexes and the lattice water mol-ecules leads to the formation of a three-dimensional hydrogen-bonded network of medium strength.

Synthesis, structural characterization and Hirshfeld analysis studies of three novel co-crystals of trans-4-[(2-amino-3,5-dibrobenzyl) amino] cyclohexanol with hydroxyl benzoic acids

Combination of active pharmaceutical ingredients, trans-4-[(2-amino-3,5-dibrobenzyl) amino] cyclohexanol (AMB) and some organic acids, e.g., p-hydroxybenzoic acid (PHBA), m-hydroxybenzoic acid (MHBA), and 3,4-dihydroxy benzoic acid (DHBA), yield three novel co-crystals characterized by X-ray single-crystal, Fluorescence spectroscopy and thermal analysis (DSC and TGA), which included co-crystal 1 with 2:2: 1 stoichiometry of AMB, PHBA and H2O, co-crystal 2 with 1:1 stoichiometry of AMB and MHBA, and co-crystal 3 with 1:1:1 stoichiometry of AMB, DHBA and CH3OH. Constituents of the co-crystalline phase were also investigated in terms of Hirshfeld surfaces. In the crystal lattice, a three-dimensional hydrogen-bonded network is observed, including formation of a two-dimensional molecular scaffolding motif. Hirshfeld surfaces and fingerprint plots of three co-crystals show that structures are stabilized by H⋯H, N–H⋯O, H⋯Br and C⋯H intermolecular interactions. Besides, the studies of the solubility showed that this co-crystal strategy could promote the solubility of AMB and follow the order: co-crystal 1<co-crystal 2<co-crystal 3.

Crystal structure of folic acid dihydrate, C29H29N2O6(H2O)2

The crystal structure of folic acid dihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Folic acid dihydrate crystallizes in space groupP212121(#19) witha= 7.275 78(3),b= 8.632 17(4),c= 32.417 19(22) Å,V= 2035.985(18) Å3, andZ= 4. The structure is dominated by a three-dimensional network of hydrogen bonds. The dicarboxylic acid side chain occurs in a bent conformation, helping explain the ability of folate derivatives to coordinate metal cations. The powder pattern has been submitted to ICDD for inclusion in future releases of the Powder Diffraction File™.

Heterocyclic tautomerism: reassignment of two crystal structures of 2-amino-1,3-thiazolidin-4-one derivatives.

The structures of 5-(2-hydroxyethyl)-2-[(pyridin-2-yl)amino]-1,3-thiazolidin-4-one, C10H11N3O2S, (I), and ethyl 4-[(4-oxo-1,3-thiazolidin-2-yl)amino]benzoate, C12H12N2O3S, (II), which are identical to the entries with refcodes GACXOZ [Váňa et al. (2009). J. Heterocycl. Chem. 46, 635-639] and HEGLUC [Behbehani & Ibrahim (2012). Molecules, 17, 6362-6385], respectively, in the Cambridge Structural Database [Allen (2002). Acta Cryst. B58, 380-388], have been redetermined at 130 K. This structural study shows that both investigated compounds exist in their crystal structures as the tautomer with the carbonyl-imine group in the five-membered heterocyclic ring and an exocyclic amine N atom, rather than the previously reported tautomer with a secondary amide group and an exocyclic imine N atom. The physicochemical and spectroscopic data of the two investigated compounds are the same as those of GACXOZ and HEGLUC, respectively. In the thiazolidin-4-one system of (I), the S and chiral C atoms, along with the hydroxyethyl group, are disordered. The thiazolidin-4-one fragment takes up two alternative locations in the crystal structure, which allows the molecule to adopt R and S configurations. The occupancy factors of the disordered atoms are 0.883 (2) (for the R configuration) and 0.117 (2) (for the S configuration). In (I), the main factor that determines the crystal packing is a system of hydrogen bonds, involving both strong N-H...N and O-H...O and weak C-H...O hydrogen bonds, linking the molecules into a three-dimensional hydrogen-bond network. On the other hand, in (II), the molecules are linked via N-H...O hydrogen bonds into chains.

A 16-connected three-dimensional hydrogen-bonding network in tetrakis(4-aminopyridinium) perylene-3,4,9,10-tetracarboxylate octahydrate.

The novel title organic salt, 4C5H7N2(+)·C24H8O8(4-)·8H2O, was obtained from the reaction of perylene-3,4,9,10-tetracarboxylic acid (H4ptca) with 4-aminopyridine (4-ap). The asymmetric unit contains half a perylene-3,4,9,10-tetracarboxylate (ptca(4-)) anion with twofold symmetry, two 4-aminopyridinium (4-Hap(+)) cations and four water molecules. Strong N-H···O hydrogen bonds connect each ptca(4-) anion with four 4-Hap(+) cations to form a one-dimensional linear chain along the [010] direction, decorated by additional 4-Hap(+) cations attached by weak N-H···O hydrogen bonds to the ptca(4-) anions. Intermolecular O-H···O interactions of water molecules with ptca(4-) and 4-Hap(+) ions complete the three-dimensional hydrogen-bonding network. From the viewpoint of topology, each ptca(4-) anion acts as a 16-connected node by hydrogen bonding to six 4-Hap(+) cations and ten water molecules to yield a highly connected hydrogen-bonding framework. π-π interactions between 4-Hap(+) cations, and between 4-Hap(+) cations and ptca(4-) anions, further stabilize the three-dimensional hydrogen-bonding network.

Blackjack water cluster detected

Water Structure Spectroscopy of protonated water clusters has played a pivotal role in elucidating the molecular arrangement of acid solutions. Whereas bulk liquids manifest broad spectral features, the cluster bands tend to be sharper. The 21-membered water cluster has for decades inspired particular interest on account of its stability and its place in the transition from two-dimensional to three-dimensional hydrogen-bonding network motifs, but the spectral signature of its bound proton has proved elusive. Fournier et al. have now detected this long-sought vibrational feature by applying an innovative ion cooling technique. Science , this issue p. [1009][1] [1]: /lookup/doi/10.1126/science.1253788

Vibrational spectral signature of the proton defect in the three-dimensional H⁺(H₂O)₂₁ cluster.

The way in which a three-dimensional network of water molecules accommodates an excess proton is hard to discern from the broad vibrational spectra of dilute acids. The sharper bands displayed by cold gas-phase clusters, H(+)(H2O)n, are therefore useful because they encode the network-dependent speciation of the proton defect and yet are small enough to be accurately treated with electronic structure theory. We identified the previously elusive spectral signature of the proton defect in the three-dimensional cage structure adopted by the particularly stable H(+)(H2O)21 cluster. Cryogenically cooling the ion and tagging it with loosely bound deuterium (D2) enabled detection of its vibrational spectrum over the 600 to 4000 cm(-1) range. The excess charge is consistent with a tricoordinated H3O(+) moiety embedded on the surface of a clathrate-like cage.