Crystal structure of the Hofmann-dma type clathrate

Seven new Hofmann-dma type clathrates Cd(dma)₂Ni(CN)₄-xG (x = 1, G = aniline, 2,3-xylidine, 2,4-xylidine, 2,5-xylidine, 2,6-xylidine, 3,5-xylidine and x = 2, G = 2,4,6-trim ethylaniline) were prepared by replacing the amine in a Hofmann type clathrate Cd(NH₃)₂Ni(CN)₄-2G by dimethylamine (dma). The structure of the Hofmann-dma type clathrate is formed with stacked host two-dimensional metal complexes of Cd(dma)₂ Ni(CN)₄ and guest molecules accommodated in the space between the stacked host complexes. This basic structure scheme is the same as that of the Hofmann type clathrate. However, the guest species accommodated in the Hofmann-dma type clathrate are more various than those of the Hofmann type clathrate, and their crystal structures are classified into four types depending on the geometry of the guest species. In order to clarify the structure of the Hofmann-dma type clathrate, single crystal X-ray diffraction experiments were canied out on the seven new clathrates, and the crystal structures of the o-, m- and p- toluidine clathrates were refined. The X-ray structure analyses showed that the host two-dimensional metal complex of the Hofmann-dma tvpe clathrate has stmctural flexibility to form a puckered structure, which results from the angular distortion of the bond between Cd and N of the cyanide bridge in the host two-dimensional complex. This stmctural flexibility of the host complex leads to the diversity of crystal structures and guest species in Hofmann-dma type clathrates. Translated fromZhurnal Strukturnmoi Khimii, Vol. 40, No. 5, pp. 898–926, September–October, 1999.     

Inclusion Compounds of Bulky Binaphthyl-type Bis-fluorenol Hosts

Inclusion properties of a new family of clathrate hosts (1–4) containing two 9-hydroxy-9-fluorenyl units or chloro-, bromo- and t-butyl-substituted derivatives of this group attached in the 3,3′-position to a basic 2,2′-binaphthyl construction element are reported (115 examples of clathrates). The crystal structures of six selected clathrates, involving dimethylsulfoxide, cyclopentanol, diethylether, benzylamine, chloroform and acetone as the guest, have been determined by X-ray diffraction, showing varied modes of supramolecular interaction dependent on the host and guest constitutions, while the formation of an intramolecular hydrogen bond between the hydroxy groups of the fluorenol units is a common structural feature (except in 3a) controlling twisted conformation of the host molecules.     

N(nPr)4[B5O6(OH)4][B(OH)3]2 and N(nBu)4[B5O6(OH)4][B(OH)3]2: Clathrates with a diamondoid arrangement of hydrogen-bonded pentaborate anions

Single-crystal X-ray structure analyses of N(nPr)₄[B₅O₆(OH)₄][B(OH)₃]₂,1, and N(nBu)₄ [B₅O₆(OH)₄][B(OH)₃]₂,2, reveal that these materials are novel clathrates, the isotypic host structures of which are three-dimensional assemblies of hydrogen-bonded [B₅O₆(OH)₄]^– ionsand B(OH)₃ molecules. The assembly of only the pentaborate anions is a distorted (i.e., along [102] elongated) fourconnected diamond-related network. The N(nPr) ₄ ⁺ and N(nBu) ₄ ⁺ ions are trapped within the complex three-dimensional channel systems of the host frameworks. Both1 and2 crystallize monoclinically with space groupP2₁/c andZ=4. The cell constants are:1:a=13.592(5),b=12.082(2),c=17.355(6) Å, =106.60(2)° (298K);2:a=13.874(3),b=12.585(1),c=17.588(4) Å, =107.04(1)° (238 K). The results obtained by both¹¹B and¹³C MAS NMR spectroscopy are discussed. Thermogravimetric studies under a flowing inert-gas atmosphere suggest that water, stemming from polycondensation of the hydrous borate species, is released from the clathrates at ca. 443 K (1) and 398 K (2) before the decomposition of the organic cations starts at ca. 603 K (1) and 603 K (2).Author for correspondence. Supplementary Data relating to this article are deposited with the British Library as supplementary publication No. SUP 82172 (82 pages).     

6,6′-Dimethoxygossypol: molecular structure,crystal polymorphism,and solvate formation

6,6′-Dimethoxygossypol (DMG) is a naturally occurring derivative of gossypol that is found in relatively high concentration in some Gossypium barbadense cotton varieties. Like gossypol, DMG forms an equimolar solvate with acetic acid, but it was not known if, like gossypol, the compound would also form clathrates with other molecules. To test for this, the compound was crystallized from different solvents. Four new structures of DMG were found that include two polymorphic and two solvated forms. The polymorphs include two monoclinic structures with P2₁/c and C2/c space groups (P1 and P2, respectively). Packing of the DMG molecules P1 is similar to packing of the gossypol molecules in the P1 polymorphic form of gossypol. The DMG molecules in P2 pack in a highly ordered arrangement that has not been previously observed among gossypol structures. DMG forms equimolar solvates with water (S1) and cyclohexanone (S2). Both structures are triclinic with P [`1]P \bar {1} space groups. The DMG molecules in S2 assemble in a manner that is similar to the gossypol molecules of gossypol–cyclohexanone (1:1), and the DMG molecules in S1 pack in a manner that is similar to the DMG molecules in DMG–acetic acid (1:1) as well as the gossypol molecules in gossypol–acetic acid (1:1). Although DMG is not as versatile a host compound as gossypol, it still forms solvates under many crystallization conditions. Consequently, some care is needed to be sure that one understands exactly which form is recovered when the compound is isolated.     

Syntheses and Crystal Structures of Three-Dimensional Cyanocadmate Clathrates with Imidazole

The crystal structures of two clathrates with imidazole (=imH), [Cd₃(CN)₆(imH)₂]·C₆H₁₂, I, and [Cd₃(CN)₆(imH)₂]·C₆H₅Cl, II, have been analyzed by single-crystal X-ray diffraction methods. Clathrate I crystallizes in the monoclinic system, space group P2₁/n with a=13.416(2), b=14.140(2), c=14.151(1)Å, β=105.08(9)°, V=2592.1(5)&Aringsup3;, Z=4, R ₁=0.0360, wR ₂=0.0850 for 5931 independent reflections; II: monoclinic P2₁/n, a=12.369(2), b=14.313(2), c=14.416(4)Å, β=106.04(2)°, V=2452.7(9)&Aringsup3;, Z=4, R ₁=0.0398, wR ₂=0.1105 for 5642 independent reflections. The three-dimensional host structures of clathrates I and II are isostructural with each other. The host framework is built through cyanide bridges among two kinds of Cd ions, tetrahedral and octahedral, in a ratio of 2 : 1. The tetrahedral Cd(1) centre is linked to three octahedral Cd(3) atoms and one tetrahedral Cd(2) atom; the tetrahedral Cd(2) centre is ligated by one unidentate imidazole ligand and linked to one tetrahedral Cd(1) atom and two octahedral Cd(3) atoms; the octahedral Cd(3) centre is ligated by one unidentate imidazole ligand and linked to three tetrahedral Cd(1) atoms and two tetrahedral Cd(2) atoms. The novel host structure provides two types of channels, a large, elongated, rectangular channel and a small rectangular channel. The larger channel is occupied by imidazole ligands coordinated to tetrahedral Cd(2) and octahedral Cd(3). The smaller channel accommodates the guest molecules cyclohexane and chlorobenzene.     

Effect of the size of calixarene macrocycle on the thermodynamic parameters of formation of inclusion compounds in guest vapor—solid host systems

The influence of the calixarene macrocycle size on the thermodynamic parameters of inclusion formation in organic guest vapor—solid host systems was studied in the series of tert-butylcalix[4]arene (1), tert-butylcalix[6]arene (2), and tert-butylcalix[8]arene (3). For this purpose, sorption isotherms of a guest vapor by a solid host were determined using the static method of headspace GC analysis for the systems involving calixarenes 2 and 3 in addition to the earlier obtained data for calixarene 1. Besides, the stoichiometry and decomposition temperatures of saturated clathrates formed in these systems were determined using thermogravimetry. The compositions of some of these clathrates differ substantially from those of clathrates crystallized from a host solution in a liquid guest. For the most guests studied with the thermodynamic activity below 0.6, their uptake by calixarenes 1—3 changes in the series 2 < 1 < 3. As a whole, the trend for each particular parameter of clathrates of hosts 1—3 (stoichiometry, guest activity at 50% saturation of the host) with increasing the size of the calixarene macrocycle is specific for each guest studied. The results obtained are useful for the estimation of receptor properties of calixarenes in quartz microbalance sensors.     

Infrared Spectroscopic Study on the Hofmann-dadn-type and the Td-dahxn-type clathrates

Infrared spectra of M(1,10-diaminodecane)Ni(CN)₄ · 1,5 G (M=Co, Ni or Cd; G=o-xylene, m-xylene, p-xylene) and Cd(l,6-diaminohexane)M(CN)₄ · C₆H₆ (M=Cd or Hg) clathrates are reported. The 1,10-diaminodecane and 1,6-diaminohexane molecules in the host permit the inclusion of bulky guest molecules. The spectral data of clathrates were compared with those of the corresponding host. The spectral features suggest that these compounds are similar in structure to other Hofmann-type and Hofmann-T_d type clathrates, respectively.     

Effect of Guest–Host Hydrogen Bonding on the Structures and Properties of Clathrate Hydrates

To provide improved understanding of guest–host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single‐crystal X‐ray crystallography has been used to detect guest–host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert‐butylamine (tBA) sII clathrate with H₂S/Xe help gases and the pinacolone + H₂S binary sH clathrate. X‐ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 Å from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 Å from the closest water oxygen atom. These distances are compatible with guest–water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X‐ray crystallographic observations. The tBA guest shows long‐lived guest–host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest–host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100–250 K. Guest–host hydrogen bonding leads to the formation of Bjerrum L‐defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen‐bonded guest–host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.     

Inclusion Properties and Crystal Structure of Clathrates Constructed Based on “π-sandwich”

Abstract

Inclusion behavior of structurally similar host compounds, 1,4-bis[1-(9-anthryl)-3-propen-1-on-3-yl]benzene (1) and 1,4-bis[3-(9-anthryl)-3-propen-1-on-1-yl]benzene (2), has been studied. Both hosts preferred cyclic, non-branched small molecules as a guest component, to yield 1:2 clathrates specifically. X-ray powder diffraction studies revealed that those 1:2 clathrates of 1 and 2 were respectively isostructural. X-ray analyses of (1)(THF)₂ (P 1, a = 10.910(2), b = 19.656(5), c = 9.172(4) Å, α = 95.58(3), β = 93.67(2), γ = 103.30(2)°, D _calc = 1.195 g cm^?3, Z = 2, and R = 0.067 for 8644 observed reflections) and (2)(1,4-dioxane)₂, (P2₁/n, a = 5.661(1), b = 17.971(3), c = 18.619(3) Å, β = 91.37(2)°, D _calc = 1.254 g cm^?3, Z = 2, and R = 0.097 for 4353 observed reflections) illuminated that their guest preference should be ascribed to the commonly observed π-sandwich” structure, in which guest molecules are enclathrated between two anthracene planes of the host molecules.     

New crystal structures of β-[Ni(NCS)2(4-methylpyridine)4] clathrates with furan,tetrahydrofuran, methylene chloride,benzene + ethanol and methylcellosolve as guest molecules

Single crystal X-ray structures of clathrates of -[Ni(NCS)₂(4-methylpyridine)₄] with furan, tetrahydrofuran, benzene + ethanol, methylene chloride, and methylcellosolve as guests molecules are reported. The location of the guest molecule in the partially decomposed clathrate with methylene chloride was defined by X-ray diffraction and compared with the fully occupied one. The host lattices of all clathrates studied are tetragonal (I4₁/a) and do not differ significantly from typical -phase clathrates of [M(NCS)₂(4-methylpyridine)₄] (M = divalent metal cation). Arrangements of guest molecules represent different types of packing: one type of guest molecule occupies both possible types of positions, two different guest molecules occupy different positions, with only one type of positions occupied by one type of guest molecule. Possible stoichiometries of clathrates with -type lattices are discussed.Presented at the Sixth International Seminar on Inclusion Compounds, Istanbul, Turkey, 27–31 August 1995.     

Clathrates of organic onium halides,V: preparation of new clathrates and structure of the 1-propanol inclusion of a bis-quinuclidinium salt

Organic onium salts (3–15) are prepared and their inclusion capacity towards solvent molecules is investigated. The crystal structure of the1·propanol·H₂O clathrate ofN,N-[5-tert-butyl-1,3-phenylenebis(methylene)]bis(quinuclidinium)dibromide (4) is reported and compared with the X-ray structures of related clathrates described earlier. Supplementary Data: Details of the crystal structure are available on request from the Fachinformationszentrum Energie-Physik-Mathematik, D-7517 Eggenstein, Leopoldshafen 2, by quoting the depository number CSD 50883, the names of the authors, and the journal citation.     

Clathrate inclusiom compounds of bis(isothiocyanato) tetrakis (4-methylpyridine) nickel II: II. Arrangement of guest molecules in the β-Ni(NCS)2(4-methylpyrldine)4 porous crystals

In this paper crystal structures of three tetragonal 14₁/a β-Ni(NCS)₂(4-Methylpyridine)₄ clathrates containing p-xylene (1:1), m-xylene (1:1) and methanol (2:1 mole of guest/mole of host), respectively, as the guest components are reported and discussed.The guest molecules were found to occupy centrosymmetric cavities in the hoat structure. Non-centrosymmetric m-xylene molecules are disordered to at least two orientations interrelated by inversion; methanol molecules enter the cavities as centrosymmetric pairs.     

CONTACT STABILIZATION OF HOST COMPLEX MOLECULES DURING CLATHRATE FORMATION: THE PYRIDINE-ZINC NITRATE AND THE PYRIDINE-CADMIUM NITRATE SYSTEMS

Abstract

Clathrate formation ranges of the phase diagrams of two binary systems Py-Zn(NO₃)₂ and Py-Cd(NO₃)₂ (Py = pyridine) were studied. A clathrate of composition [MPy₄(NO₃)₂]·2Py (M = Zn, Cd) was observed in each of the systems. The space group Ccca (orthorhombic system) and the parameters of the unit cells of both clathrates were determined by X-ray analysis of their single crystals. The data obtained show them to be isostructural with the clathrate [NiPy₄(NO₃)₂]·2Py whose structure is known and suggest the actual presence of the host molecules trans-[MPy₄(NO₃)₂] (M = Zn,Cd) inside the clathrate phases. Host complexes do not form as separate compounds but can only arise in clathrate phases due to contact stabilization by the guest molecules. Both Zn- and Cd-clathrates are of constant composition and melt incongruently at 62.3(6) and 106.0(5)°C, respectively, yielding the complexes [ZnPy₃(NO₃)₂] and [CdPy₃(NO₃)₂], these melting congruently at 131.4(5) and 169.5(5)°C, respectively. During thermal decomposition under quasi-equilibrium conditions with different pressures of the liberating pyridine both clathrates also decompose in one stage, giving [MPy₃(NO₃)₂] complexes. The results obtained are discussed in relation to a number of other systems with Schaeffer's and Hofmann-lwamoto's clathrates in which contact stabilization occurs or might be expected to occur.     

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. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Institute of Physical Chemistry, Polish Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 6, pp. 1070–1073, November–December 1995. Translated by L. Smolina     

Comparative X-ray structural study of laterally mono-ethyl substituted 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetra-methoxycalix[4]arene and its non-substituted parent compound including guest free and solvated forms. Chemical straightening of guest channels

Three solvate crystal structures of the laterally ethyl substituted tetra-tert-butyltetramethoxycalix[4]arene 1 [(1·THF (1a), 1·CHCl₃ (1b) and 1·CH₂Cl₂ (1c)] are compared to the corresponding solvent-free structure (1) using single crystal X-ray structure determination, isostructurality and molecular isometricity calculations. To study the effect of the lateral substitution, the laterally non-substituted host with the guest THF (2a) is also included to the comparison. The calixarene molecules in the different structures all adopt the partial cone conformation with different affection of the respective guest molecules, always being positioned interstitially. Depending on the lateral substitution and the size of the included guests, the molecular conformation of the calix[4]arene shows small differences relating to the alignment of the arene units. The channels disposable of the solvent guest molecules in the crystal structures straighten as the effect of lateral substitution of the host calix[4]arene. The orthorhombic crystal structures of 1a–c are isostructural irrespective of the included solvent molecules, while 1 and 2a crystallise in the same monoclinic space group.     

On the clathrate structures of syndiotactic poly(m-methylstyrene)

The crystal structures of clathrate forms of syndiotactic poly(m-methylstyrene) containing guest molecules having different steric hindrance (CS₂, benzene and orto-dichlorobenzene) are presented. The structures are all characterized by polymer chains in s (2/1)2 helical conformation and guest molecules packed in an orthorhombic unit cell according to the space group Pcaa. All the presented clathrates belongs to β class indipendently from the dimensions of the guest molecule. In this aspect they differ both from clathrate forms of syndiotactic polystyrene, all belonging to α class, and from clathrate forms of syndiotactic poly(p-methylstyrene) that belong to α or β class according to the steric hindrance of the guest molecule.     

[MPy4(NCO)2]-2Py clathrates (M = M(II) = Mn,Fe, Co,Ni, Cu,Zn, Cd; Py = pyridine)

The title compounds form an iso structural series and are isomorphic with other [MPy₄X₂]-2Py clathrates (XRD, KM4 diffractometer, cell parameters and space group Ccca from 17–80 reflections). In the clathrate [NiPy₄(NCO)₂]-2Py studied in detail (XRD, CAD-4 diffractom eter, λCuK_α, Ω/2θ scan mode, θ_max = 78‡, 990 strong reflections, 104 parameters, R = 0.053), the host molecule has 222 symmetry, and the twofold axes run along the coordination bonds. The transoctahedral environment of nickel consists of six nitrogen atoms of four pyridine and two isocyanate ligands. The coordination polyhedron is slightly distorted due to changes in the bond lengths. The molecule has a propeller conformation. The guest molecules lie in the cavities of the crystal structure in conformity with the van der Waals type of packing. The host complex [NiPy₄(NCO)₂] (XRD, CAD-4 diffractometer, 4615 strong reflections, 560 parameters, R-0.037) crystallizes in the triclinic crystal system (space group P1) with two independent asymmetric molecules in the unit cell. The molecular structure is analogous to that in the ciathrate phase, but the coordination angles are severely distorted; one of the molecules acquires a distorted propeller conformation, and the other, a centrosvmmetric conformation, which is less favorable. While being structurally identical, the [MPy₄(NCO)₂]-2Py clathrates differ heavily in the properties. The first four complexes dissociate to host complexes, and their thermal stability changes in the sequence Mn< Fe< Co< Ni; the Cu and Zn clathrates decompose in one step to dipyridine complexes with decomposition of host complexes. Decomposition of the Cd ciathrate follows one of these patterns depending on conditions. The results are compared with those for other known systems. Synthetic procedures are given. Translated fromZhurnal Strukturnoi Khimii, Vol. 40, No. 5, pp. 935–953, September–October, 1999.     

4-Vinylpyridine-Modified Nickel and Cobalt Dibenzoylmethanates as New Hosts: Inclusions with Carbon Tetrachloride and Chlorobenzene

Abstract

Bis(4-vinylpyridine)bis(dibenzoylmethanato)metal(II), [M(ViPy)₂(DBM)₂] (M = Ni(II), Co(II); ViPy = 4-Vinylpyridine; DBM = C₆H₅COCHCOC₆H₅ ^?, dibenzoylmethanate) is a new metal-complex host. Its inclusions with carbon tetrachloride (host:guest = 1:2; triclinic, P 1, Z = 1) and chlorobenzene (host:guest = 1:1; monoclinic, P2 ₁ /c, Z = 4) are consistent with the van der Waals packing of neutral complex (host) and solvent (guest) molecules. In the host unit, four oxygens from two chelate DBM-units provide a square-planar environment around the metal center that is extended to octahedral coordination by two apical nitrogens from two vinylpyridine moieties in the trans-position. In the carbon tetrachloride inclusions, the host traps two guest molecules in large prolate spheroidal cavities. In the chlorobenzene inclusions, guest species are located inside 8-shaped serpentine channels along the y-axis. The nickel and cobalt versions of the inclusion compounds were found to be very similar.     

The crystal structures ofα,ω-diaminoalkane-cadmium(II) tetracyanonickelate(II) — Aromatic molecule inclusion compounds. VII: Three-dimensional host structures built ofcatena-[cadmium(II) tetra-μ-cyanonickelate(II)] layers and 1,3-diaminopropane, 1,5-diaminopentane or 1,7-diaminoheptane pillar

The crystal structures of four novel Hofmann-diam-type clathrates [Cd(tn)Ni(CN)₄]·1.72(o-MeC₆H₄NH₂),3-o, [Cd(tn)Ni(CN)₄]·0.5(m-ClC₆H₄NH₂),3-m, [Cd(daptn)Ni(CN)₄]·1.5(p-MeC₆H₄NH₂),5-p and [Cd(dahpn)Ni(CN)₄]·1.5(2-MeC₉H₆N),7-q have been determined by single crystal X-ray diffraction method [tn:n=3, daptn:n=5, dahpn:n=7 for NH₂(CH₂) _n NH₂.3-o crystallizes in the monoclinic space groupP2/m,a=7.538(2),b=9.314(5),c=7.670(2) Å, =91.03(2)°,Z=1,R=0.047 for 1252 reflections;3-m: orthorhombicPbam,a=12.1714(7),b=15.798(1),c=7.737(1) Å,Z=4,R=0.044 for 1871;5-p: monoclinicP2₁/a,a=13.736(3),b=22.014(4),c=7.762(3) Å, =91.04(3)°,Z=4,R=0.047 for 5281; and7-q: orthorhombicPbam,a=13.599(2),b=27.938(4),c=7.619(2) Å,Z=4,R=0.054 for 3098. Their host structures are topologically the same to those of the previously reported Hofmann-diam-type clathrates: the two-dimensional [CdNi(CN)₄] networks are spanned by NH₂(CH₂) _n NH₂ at every Cd atom to build up the three-dimensional hosts. The number of cavities available for the guest is regulated by the deformation of the 2D networks and the diamine ligand in the host structure. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82192 (37 pages).