Pyridine Guest Research Articles

Crystal Structure and Thermodynamic Stability of the [Hg(Pyridine)4(NO3)2] � 2(Pyridine) Inclusion Compound

The studied compound belongs to the family of [MPy4X 2] . 2Py isomorphous clathrates. Its crystal structure exhibits a van der Waals architecture formed by neutral [HgPy4(NO3)2] host molecules, with the guest pyridine molecules included in the cavities of the host lattice. The host complex is formed by coordination of four pyridines, located near the equatorial plane, and two nitrates, located axially, to the Hg(II) cation. One of nitrates ligates as a monodentate ligand and another as a bidentate. The coordination polyhedron is ‘HgN4O3, with average Hg—NPy and Hg—Onitrate distances of 2.38(5) and 2.68(1) A, respectively. The crystal structure is complicated with a superlattice and the crystal symmetry reduced to monoclinic, as compared to the structure usually occurring in the [MPy4X2] . 2Py clathrates. The pyridine vapor pressure over the clathrate was measured in the 293--369 K temperature range by the static tensimetric method. Thermodynamic parameters of the clathrate dissociation were calculated from these data. For the reaction 1/3[HgPy4(NO3)2] . 2Pysolid=1/3[HgPy3(NO3)2] solid + Pygas the parameters are as follows: ΔH0av = 49.4(2) kJ/mol, ΔS 0av = 127(2) J/(mol K) and ΔG0298=11.4(3) kJ/mol. The results are compared with previously reported data on compounds of the [MPy4(NO3)2] . 2Py series.

Rational Design of Metal‐Organic Frameworks Based on 5‐(4‐Pyridyl)tetrazolate: From 2D Grids to 3D Porous Networks

AbstractThe hydrothermal reactions of Zn(ClO4)2·6H2O/Cu(NO3)2·6H2O with 5‐(4‐pyridyl)tetrazole in an ethanol/water or ethanol/water/pyridine medium yield one 2D and one 3D metal‐organic coordination framework [Zn2(OH)(4‐ptz)3] (1) and [Cu(4‐ptz)·0.5(py)] (3) [4‐ptz = 5‐(4‐pyridyl)tetrazolate, py = pyridine], respectively. Complex 1 possesses two identical and independent rectangular grid sheets with twofold parallel interpenetration, in which the four‐connected nodes of the net are provided by Zn2(OH) units connected to one another through 4‐ptz and (4‐ptz)2 bridges. These composite sheets are stacked one on top of another by hydrogen‐bonding interactions to afford a 3D structure. There are many structural similarities between complex 1 and the recently reported 2D layered network [Zn(OH)(4‐ptz)(H2O)] (2), in particular the components of the network, the coordination mode of the 4‐ptz ligand and the in situ formation of hydroxy groups. Complex 2 can be synthesized by the hydrothermal reaction of Zn(ClO4)2·6H2O and 5‐(4‐pyridyl)tetrazole in an ethanol/water/pyridine medium. The structural characterization of complex 3 shows a porous structure that contains the guest pyridine molecules. Additionally, compounds 1 and 2 exhibit strong fluorescence at room temperature in the solid state. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Hydrogen-Bonding Networks in a Bipodal Acyl-thiourea and Its NiII 2:2 Metallamacrocyclic Complex

The crystal structures of 3,3,3‘,3‘-tetra(2-hydroxyethyl)-1,1‘-isophthaloylbis(thiourea) (1) and its green metallamacrocyclic complex cis-[Ni(L-S,O)(pyridine)2]2 (2) are reported in the context of their supramolecular behavior dictated by the use of hydrogen-bonding end-groups on the ligand. In 1, each molecule forms a junction between two 4-fold chiral helices formed by the hydrogen bonding of hydroxyl moieties and sulfur atoms. The structure of 2 is laminar, consisting of layers of water-linked metallamacrocyclic cis-[Ni(L-S,O)(pyridine)2]2 units separated by layers of pyridine guest molecules. Thermogravimetric analysis of 2 shows that on heating the guest pyridine and water molecules are released at ca. 60 °C, followed quickly by the further release of coordinated pyridines from cis-[Ni(L-S,O)(pyridine)2]2 to yield cis-[Ni(L-S,O)]2.

Synthesis and X-ray Structures of Zinc and Cadmium Pyridinecarboxylate Coordination Networks

New zinc(II) and cadmium(II) coordination polymers with 3-[2-(3-pyridyl)ethenyl]benzoato (L) bridging ligands have been synthesized by treating the metal salts and 3-[2-(3-pyridyl)ethenyl]benzonitrile under hydro(solvo)thermal conditions. [Zn(L)2]·(pyridine), 1, adopts a 1D polymeric structure built from mutually perpendicular 22-membered macrocycles. Large open channels formed in 1 are filled with included pyridine guest molecules. Both [Cd2(L)3(NO3)], 2, and [Cd4(L)6(ClO4)2(MeOH)2]·(H2O), 3, adopt complicated 2D polymeric structures that are built from carboxylate-bridged tetracadmium and dicadmium building units, respectively. Crystal data for 1: triclinic space group P1, a = 8.601(1), b = 12.364(1), c = 14.224(1) A, α = 72.687(1), β = 88.118(1), γ = 71.679(1)°, Z = 2. Crystal data for 2: triclinic space group P1, a = 10.675(1), b = 12.671(1), c = 14.838(1) A, α = 74.772(1), β = 88.283(1), γ = 73.671(1)°, Z = 2. Crystal data for 3: monoclinic space group P21, a = 13.165(3), b = 20.119(9), c = 15.4...

A pseudo-honeycomb coordination net formed with 5-sulfoisophthalic acid

The first coordination polymer of a sulfoisophthalic acid isomer is reported. The ligand, 5-sulfoisophthalic acid, L, can be regarded as similar to the much-studied 1,3,5-benzenetricarboxylic acid (BTC) but where a sulfonate group has replaced one of the carboxyl groups on the benzene core. The complex, {[Cu1.5(L)(py)5](py)(H2O)6.76}∞, 1, adopts a pseudo-honeycomb structure with channels occupied by guest solvent molecules. The framework is a pseudo-honeycomb, in contrast to the BTC analogue, owing to the sulfonate lone electron pairs being directed out of the plane of the isophthalic acid moiety. The ruffled stucture of the layers precludes extensive π interactions between adjacent lamellae. However, amongst several disordered guests, one guest pyridine molecule is fixed by both face-to-face and edge-to-face non-covalent interactions.

Cavitand zn(II)-porphyrin capsules with high affinities for pyridines and N-methylimidazole.

Covalent cavitand Zn(II)-porphyrins 17-20 were prepared via multistep syntheses. These host molecules show moderate to excellent binding affinities to N-methylimidazole and pyridine guests. The complexing behavior strongly depends on the spacer's length, number, and rigidity, in addition to the guest size. Cavitand capping and strapping of porphyrins strongly influence the complex formation and result in a 10-700-fold enhancement of the binding strength compared to tetraphenyl Zn(II)-porphyrin.

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) Β, β = 101.03(3)°, V =4805.27(17) Β3. 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· π interaction between the molecules. The hydrogen bonding drives the host macrocycle into a chair-like conformation.

One-Dimensional Coordination Polymers Based upon Bridging Terephthalate Ions

The reaction between transition metal halides MX2 (where M = Co(II) and Ni(II)) in an aqueous solution containing disodium terephthalate along with pyridine-based ligands gives rise to one-dimensional coordination polymers. Both [M(terephthalate)(4-picoline)2(H2O)2]·2(4-picoline) (1) and [M(terephthalate)(pyridine)2(H2O)2]·2(pyridine)·2(H2O) (2) have been isolated. These frameworks exhibit hydrogen bond donors running along the backbone of each polymer, which gives rise to inclusion chemistry between the framework and pyridine guest molecules.

Self-Assembly of Molecular Brick Wall and Molecular Honeycomb from Nickel(II) Macrocycle and 1,3,5-Benzenetricarboxylate: Guest-Dependent Host Structures

Novel multidimensional supramolecular networks with brick wall and honeycomb structures, [Ni(C12H30N6O2)]3[C6H3(COO)3]2·18H2O (1) and [Ni(C12H30N6O2)]3[C6H3(COO)3]2·14H2O·2C5H5N (2), respectively, have been constructed by the self-assembly of S = 0 Ni(II) macrocyclic complex containing hydroxyl pendent chains and 1,3,5-benzenetricarboxylate (BTC3-). The host structures assembled are greatly affected even by the partial change of the guests. X-ray crystal structures indicate that each Ni(II) macrocycle binds two BTC3- in the trans position and each BTC3- coordinates three Ni(II) macrocyclic units via C1 symmetry in 1 and C3 symmetry in 2. The simplest cyclic motif of the two-dimensional (2-D) networks in 1 and 2 is a large ring consisting of six Ni(II) macrocyclic complexes and six BTC3- anions. The rings are extended to form a 2-D layer. The layers are stacked in parallel, separated by 8.850 Å in 1 and 8.973 Å in 2. They are interconnected by the hydrogen-bonding interactions between the hydroxyl pendants of the macrocycle in a layer and the secondary amines of the macrocycle located in the neighboring layers, which gives rise to the three-dimensional structures. The effective cavity size of 1 is ca. 6.7 × 13 Å and that of 2 ca. 11.4 × 11.4 Å. The cavities are filled with guest molecules. In 2, the pyridine guest experiences π−π interaction with the benzene ring of BTC3-. Variable-temperature (2−300 K) magnetic susceptibility measurements indicate that both 1 and 2 exhibit weak anti-ferromagnetic interactions between the S = 1 Ni(II) paramagnetic centers.

X-ray diffraction study of the clathrate [MnPy4(NO3)2)]·2Py and complex [MnPy3(NO3)2] formed in the pyridine (Py)-manganese nitrate system

A clathrate compound [MnPy4(NO3)2]·2Py was synthesized and studied by single-crystal X-ray diffraction analysis (KM-4 diffractometer, CuKα,ω/2ϑ scan mode,ϑ max=78°). The unit cell is base-centered orthorhombic, space group Ccca, a=12.097(4), b=15.197(4), c=17.213(4) A, V=3164(2) A3, Z=4, R=0.072, for 632 reflections and 107 parameters in the least-squares analysis. The host molecule has 222 symmetry. Two monodentate nitrato groups and four pyridine ligands are coordinated to Mn(II) along the symmetry axes (the former via O). The pyridine guest molecules lie in the cavities of the crystal framework. For [MnPy3(NO3)2)], only unit cell parameters were determined: a=12.467(5), b=9.514(2), c=16.383(5) A,β=108.93(4), V=1838(1) A3 space group C2/c or Cc (according to extinctions). The pyridine-manganese nitrate system is shown to be analogous to the previously investigated Co, Ni, Cu, Zn, and Cd systems.

Hexapyridine Addition Compounds of Metal(II) Salts (Nickel and Magnesium Perchlorates, Magnesium Nitrate): Their Supramolecular Nature, and Anion Coordination of the Metal Cation [1

The X-ray structures of [NiPy4(ClO4)2]*2Py (1), [MgPy4(ClO4)2]*2Py (2), and [MgPy4(NO3)2]*2Py (3) are presented. All three compounds are isostructural crystallizing in orthorhombic Ccca space group with 4 formula units per unit cell. For (1) a = 12.344(1), b = 16.104(1), c = 16.932(1) Å; V = 3366 Å3; D calc = 1.445 g cm−1; final R = 0.074 for 1418 observed data. For (2) a = 12.084(1), b = 16.465(1), c = 17.379(1) Å; V = 3458 Å3; D calc = 1.340 g cm−1; final R = 0.053 for 1782 observed data. For (3) a = 12.081(1), b = 15.146(1), c = 17.222(1) Å; V = 3151 Å3; D calc = 1.313g cm−1; final R = 0.063 for 1153 observed data. The compounds consist of host complex molecules with two acido-groups and four pyridine ligands coordinated, and of guest pyridine species included in channels of molecular crystal framework. Coordination of poor acido-ligands in presence of non-bonded pyridine molecules is discussed and possible supramolecular nature of other M(ClO4)2*6Py′ compounds is suggested.

Polymorphous transformation of a clathrate in the pyridinecadmium nitrate system

The polymorphous transformation of the [CdPy 4(NO3)2]·2Py clathrate (Py is pyridine) at 221 K is investigated by analyzing the temperature dependences of the Raman spectra and the lattice parameters in the range 100–293 K The crystal structures of the high- and low-temperature modifications of the clathrate were determined. Above the transition point the clathrate crystallizes in space group Ccca (at 293 K: a = 12.360(4), b = 15.456(3), c = 16.931(3) a, V = 3234(1) a3, Z = 4, R = 0.050 for 879 reflections and 126 refined parameters). Below 221K the unit cell of the clathrate is transformed into the primitive cell, space group Pcca (at 215 K: a = 11.953(3), b = 15.129(3), c = 17.234(3) A, V = 3234(1) a3, Z =4, R = 0.057 for 1596 reflections and 210 refined parameters). In both modifications, the host complex involves four pyridine ligands and two monodentate trans-nitrato groups forming a distorted octahedron around the central atom. The guest pyridine molecules lie in the cavities of the molecular framework of the complex. As the clathrate is cooled, the a and b parameters decrease and the c parameter increases; at transition point, each of these parameters abruptly changes by about 0.2 A. The nitrate ligand undergoes ordering and inclination to the equatorial plane of the complex by 20‡.

Crystal structure of the bis(isothiocyanato)tetrakis(pyridine)nickel(II) clathrate with a pyridine guest [NiPy4(NCS)2]·2Py

The structure of the [NiPy4(NCS)2]·2Py clathrate was determined by single crystal X-ray diffraction analysis (Enraf-Nonius CAD4 diffractometer, λCuKα radiation, Ni filter, ω/2θ scan mode, θmax, 511 reflections, R=0.046). The crystals are tetragonal, space group 141/acd, a=16.079(2), c=27.150(7) A, Z=8 C32H30N8NiS2, dcalc=1.229 g/cm3. The structure is of the island type and consists of distorted octahedral trans-[NiPy4(NCS)2] (host) and pyridine (guest) molecules. The Ni(II) cation is coordinated by six nitrogen atoms and occupies the 222 special position. One of the twofold axes passes axially through the nickel(II) cation and the atoms of the isothiocyanate groups, and the two other axes lie in the equatorial plane of the Ni(NPy)4 complex as diagonals between the Ni−NPy bonds. The Ni−NCS and Ni−NPy distances are 2.033(7) and 2.121(4) A, respectively. The rings of the pyridine ligands form angles of 53.2(2)° with the equatorial plane of the complex. The guest pyridine molecules lie inside the winding channels running along the c axis.

Structure reinterpretation and determination of the clathrate nature of the compounds of the general formula MX2·6Py

Unit cell parameters and space group (Ccca) were determined by X-ray diffraction analysis for 11 compounds of the general formula [MPy4X2]·2Py (M=Cd, Co, Cu, Ni, Zn; X=Br, I, NO3, HCOO). It was found that these compounds, together with the five known compounds, form a large group of clathrates, in which [MPy4X2) (host) complex molecules are packed with pyridine (guest) molecules held in the voids of the crystal framework by van der Waals forces. The results of the study and literature data are analyzed, and it is concluded that there are at least several dozens more clathrates of the molecular formula MX2·6Py that are known but not defined structurally.

Crystal structure of the dinitratotetrakis(pyridine)nickel(II) clathrate with pyridine as guest, [NiPy4(NO3)2]·2Py

The structure of the [NiPy4(NO3)2]·2Py clathrate was determined by single crystal X-ray diffraction analysis (KM-4 diffractometer, λMoKa radiation, graphite monochromator, ω/2θ scan mode, θmax=30°, 640 reflections, R=0.065). Orthorthombic base-centered unit cell, space group Ccca, a=12.148(5), b=15.019(4), c=16.96(1) A, Z=4C30H30N8NiO6, dcalc=1.411 g/cm3. The structure is of island type and consists of distorted octahedral trans-[NiPy4(NO3)2] (host) and pyridine (guest) molecules. The Ni(II) cation coordinated by four nitrogens of the pyridine ligands and two oxygens of the nitrato groups lies in the special position 222; the twofold axes coincide with the directions of the metal-ligand bonds. The guest pyridine molecules lie on the twofold axes that are parallel to the c axes and are oriented in such a way that the total dipole moment of the guest subsystem is zero.

Dynamics of benzene and pyridine guest molecules in their tri-ortho-thymotide inclusion compounds. Solid-state 2H NMR Studies

Dynamic properties of perdeuteriated benzene (C6D6) and perdeuteriated pyridine (C5D5N) guest molecules in their tri-ortho-thymotide (TOT) inclusion compounds have been studied via variable-temperature wide-line solid-state 2H NMR spectroscopy. The temperature dependences of the quadrupole echo 2H NMR lineshape and the 2H NMR spin–lattice relaxation time for C6D6/TOT in the temperature range 96–293 K are interpreted in terms of in-plane rotation (nearest-neighbour 2π/6 jump model) of the benzene molecule, together with restricted wobbling of the molecular plane. The 2H NMR spin–lattice relaxation time measurements suggest that there are two dynamically inequivalent types of benzene molecule (included in structurally different types of tunnel within the TOT host structure), with their activation energies for in-plane rotation estimated to be 4.0 and 5.9 kJ mol–1. For C5D5N/TOT in the temperature range 90–363 K, three types of motion have been identified: (i) in-plane libration; (ii)π jumps of each pyridine molecule about its two-fold symmetry axis; (iii) restricted wobbling of the molecular plane. On the basis of 2H NMR lineshape analysis of 2H NMR spin–lattice relaxation time measurements, the activation energy for motion (ii) is estimated to be ca. 17-20 kJ mol–1.

Complexation with Diol Host Compounds, 12. Synthesis and Solid‐State Inclusion Properties of Bis(diarylhydroxymethyl)1‐Substituted 1,1′‐Binaphthyls. Crystal Structures of a Host and Its Pyridine Clathrate

A series of new clathrate host molecules 1 – 8 containing two bis(diarylhydroxymethyl) groups attached to different positions (2,2′ or 8,8′) of a 1,1′-binaphthyl frame have been synthesized. Their clathrate formation properties with organic guests including alcohols, amines, ketones, and other dipolar aprotic compounds or aromatic hydrocarbons are reported (74 examples of clathrates) together with the results of solvent competition experiments for the parent host compound. The inclusion formation and the clathrate stoichiometries depend on the structure of the host molecules in a systematic manner. The crystal structures of the free parent host 1 and its pyridine clathrate (1 : 3) have been determined by X-ray diffraction. The molecular structure of the host is similar in the two species involving an intramolecular hydrogen bond between the host hydroxyls. No other hydrogen bond is involved in the free host case while in the pyridine inclusion compound the second host hydroxyl forms a hydrogen bond with the nitrogen of one pyridine guest which is surrounded by two unbound pyridine species such as to form clusters of three pyridine guests enclosed in the cavities between the host molecules. Thermal analysis corresponds with the two binding states of the pyridine molecules in the clathrate.

Hydrogen-bonded adducts of ferrocene-1,1′-diylbis-(diphenylmethanol): crystal and molecular structures of adducts with methanol (1 : 1) and pyridine (1 : 2)

Ferrocene-1,1′-diylbis(diphenylmethanol), [Fe(C5H4CPh2OH)2], forms hydrogen-bonded host–guest adducts with a wide range of hydrogen-bond donors and acceptors. Adducts with a diol: guest ratio of 1 : 1 were formed by MeOH, EtOH, Me2SO, Me2NCHO, piperazine, and 4,4′-bipyridyl and 1 : 2 adducts by Me2SO, dioxane, pyridine and piperidine. The 1 : 1 adduct with MeOH has been shown to be triclinic, space group P with a= 8.7624(3), b= 12.2797(6), c= 14.8773(8)A, α= 106.572(4), β= 97.879(4), γ= 100.873(4)° with a final R of 0.044 for 4982 observed reflections. The structure consists of a centrosymmetric assembly of two molecules of the host diol and two molecules of the guest MeOH, hydrogen bonded together to form a chair conformation (OH)6 ring. The 1 : 2 adduct with pyridine has been shown to be monoclinic, space group C2/c with a= 16.6252(10), b= 11.1016(9), c= 20.9440(16)A, β= 107.855(6)° with a final R of 0.042 for 3260 observed reflections. In the structure the diol lies on a two-fold rotation axis with its hydroxyl hydrogens disordered and participating in both intramolecular O–H ⋯ O and intermolecular O–H ⋯ N hydrogen bonding with the two pyridine guest molecules.

Versatility in inclusion hosts. Unusual conformation in the crystal structure of thep-t-butylcalix[8]arene: Pyridine (1:8) clathrate

Crystal structure analysis proves that thep-t-butylcalix[8]arene host sits around a symmetry center in thePI crystal lattice. The triclinic cell parameters and calculated volume are:a = 10.034(2),b = 17.434(2),c = 18.321(2) A,α = 113.86(1)°,β = 93.08(1)°,γ = 92.62(1)°,V = 2919(2) A3. ForZ = 1 and F.W. = 1834.6 the calculated density is 1.04 g/cm3. It is shown that the host macrocycle is in an open chairlike conformation and virtually leaves no cavity to be occupied by the guest molecule. Consequently the pyridine guest molecules are enclathrated through steric barriers into the crystal lattice, having only one of the guests in the asymmetric unit bound to the host. The open conformation of the host is facilitated by a break in the ring of O-O hydrogen bonds on the rim of the would-be calix. This structure also conveys essential information on the possible solution conformations of the host in pyridine.