Role of edge-to-face interaction between aromatic rings in clathrate formation of 1-benzoyl-2-hydroxyindoline derivatives with benzene. X-ray crystal and PM6 analyses of the interaction

(4-Nitrophenyl- and 4-chlorophenyl)(2-hydroxy-3,3-dimethylindolin-1-yl)methanone (4a,b) serve as clathrate hosts for benzene guests. X-ray crystal analyses of the inclusion compounds of 4a and 4b with benzene indicate that the ‘edge-to-face interaction’ plays an important role in the formation of the inclusion complexes with benzene as well as in the host-host interactions. PM6 molecular orbital calculations were found to reproduce the characteristic structural features of both intra- and intermolecular edge-to-face interactions.     

The dimeric "hand-shake" motif in complexes and metallo-supramolecular assemblies of cyclotriveratrylene-based ligands

A series of clathrate and metal complexes with cyclotriveratrylene-like molecular host ligands show a similar dimeric homomeric inclusion motif in which a ligand arm of one host is the intra-cavity guest of another and vice versa. This "hand-shake" motif is found in the trinuclear transition metal complex [Cu(3)Cl(6)(1)]CH(3)CN1.5 H(2)O in which 1 is tris(4-[2,2',6',2'-terpyridyl]benzyl)cyclotriguaiacylene; in the self-included M(4)L(4) tetrahedral metallo-supramolecular assembly [Ag(4)(2)(4)] (BF(4))(4) in which 2 is tris-(2-quinolylmethyl)cyclotriguaiacylene; in the 1D coordination chains [Ag(4)]ReO(4) CH(3)CN and [Ag(5)]SbF(6)3 DMFH(2)O in which 4 is tris(1H-imidazol-1-yl)cyclotriguaiacylene and 5 is tris{4-(2-pyridyl)benzyl}cyclotriguaiacylene; and in the acetone clathrate of tris{4-(2-pyridyl)benzyl-amino}cyclotriguaiacylene. Clathrates of ligands 2 and 5 do not show the same dimeric motif, although 2 has an extended homomeric inclusion motif that gives a hexagonal network.     

Gas chromatography on urea-n-hexadecane inclusion compound

Summary The urea-n-hexadecane adduct, as a relatively stable inclusion compound, was studied gas chromatographically in connection with clathrate formation with n-alkanes, branched alkanes as well as with olefins, ketones and n-alcohols. In dependence on the temperature, either the clathrate itself can be used in the GC system, studying the transition phemonena (clathrate decomposition), or its decomposition product, n-hexandecane, be employed as a liquid stationary phase. Analytical usefulness of these phase is also demonstrated.     

球形主体分子的包结性能及其在制备有机非线性光学材料 中的应用

提出了球形主体分子的设计思想,把具有球形结构的分子柏木醇(1)、马钱子碱(2)、三乙烯二胺(1,4-二氮-二环[2.2.2]辛烷(3)作为主体分子,把酚类化合物,诸如苯酚(4)、邻甲苯酚(5)、间甲苯酚(6)、对甲苯酚(7)、对氯苯酚(8)和对硝基苯酚(11)等作为客体分子,进行了主客体分子相素作用实验,采用粉末X射线衍射、1^HNMR等分析手段确认了包结化合物的形成及主客体分子的摩尔比,摩尔比(H/G)分别为(1)+(4)1:1,(1)+(5)1:1,(1)+(6)1:1,(1)+(7)1:1,(1)+(11)1:2,(2)+(11)1:1,(3)+(4)1:2,(3)+(5)1:3,(3)+(6)1:2,(3)+(7)1:2,(3)+(8)1:2,(3)+(11)1:2,对典型包结化合物的单晶,诸如柏木醇和邻甲苯酚、马钱子碱和对硝基苯酚以及三乙烯二胺和对硝基苯酚,进行了四圆X射线衍射结构分析,结果表明,包结化合物的堆砌结构特征随主体分子的体积大小而改变,从隧道型如(1)+(5)和(2)+(11)转变为夹层型如(3)+(11)。用Nd:YAG激光测试晶体的SHG效应,结果表明,大部分包结物晶体具有非线性光学性质。     

Structural Principles and Thermoelectric Properties of Polytypic Group 14 Clathrate‐II Frameworks

We have investigated the structural principles and thermoelectric properties of polytypic group 14 clathrate‐II frameworks using quantum chemical methods. The experimentally known cubic 3C polytype was found to be the energetically most favorable framework, but the studied hexagonal polytypes (2 H, 4 H, 6 H, 8 H, 10 H) lie energetically close to it. In the case of germanium, the energy difference between the 3C and 6H clathrate‐II polytypes is ten times smaller than the difference between the experimentally known 3C‐Ge (α‐Ge) and 4H‐Ge polytypes. The thermoelectric properties of guest‐occupied clathrate‐II structures were investigated for compositions Na–Rb–Ga–Ge and Ge–As–I. The clathrate‐II structures show promising thermoelectric properties and the highest Seebeck coefficients and thermoelectric power factors were predicted for the 3C polytype. The structural anisotropy of the largest studied hexagonal polytypes affects their thermoelectric power factors by over a factor of two.     

Selective preparation of beta-cyclodextrin clathrates by solid-phase exchange of included tetrahydrofurane for volatile guests in absence of water

Solid-phase guest-exchange products, prepared from dehydrated clathrate of beta-cyclodextrin (bCD) with tetrahydrofurane (THF) by its saturation with vapor of second guest, were studied using thermal analysis by thermogravimetry combined with mass-spectrometric detection of evolved vapors. This guest-exchange procedure was found to be effective for inclusion of volatile guests, which otherwise require a difficult optimization of preparation conditions. Besides, a performed solid-phase exchange without liquid/solid-phase contact is a standard, technologically friendly procedure of clathrate preparation, which does not require further drying to provide an end product. An observed exchange of THF in the absence of water is rather selective, with some hydrophobic guests being unable to replace THF in its dried clathrate with bCD. This selectivity together with low toxicity of THF may be an advantage for practical applications of this guest-exchange method.     

The stabilization of thermodynamically disfavoured conformers of chlorocyclohexane in the host lattice of tri-ortho-thymotide. Crystallographic and infrared spectroscopic studies

The clathrate compounds of tri-o-thymotide have been prepared with chlorocyclohexane, bromocyclohexane and 2-chlorotetrahydropyran. The cage-type inclusion complex C₃₃H₃₆O₆ · ₂ ¹ C₆H₁₁Cl (trigonal,P3₁21,a=13.604(1),c=30.605(1) Å,Z=6) contains an axial-Cl chair and an axial-Cl boat conformation of the guest, distributed statistically in the ratio 2 1 over the available sites. The observed conformations have been compared with conformers calculated by force field methods. IR spectra are consistent with the crystal structure results for the tri-o-thymotide/chlorocyclohexane clathrate. They further demonstrate the similar preferential inclusion of axial isomers of bromocyclohexane and 2-chlorotetrahydropyran. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82023 (16 pages).Dedicated to Professor H. M. Powell.     

Enclathration of morpholinium cations by Dianin's compound: salt formation by partial host-to-guest proton transfer

In spite of partial deprotonation upon inclusion of morpholine, Dianin's compound maintains its well-known clathrate structure in the solid state.     

Synthesis of Calix

The formation of p-tert-butylcalix[4]arene mono-, bis-, tris-, and tetrakistriflates 3, 2, 4, and 5, respectively, and their respective reactions, under typical Pd-catalyzed carbonylative, Suzuki-Miyaura coupling, or deoxygenation conditions are described. A novel, nonsolvent-derived 1:1 clathrate (6) of benzophenone and 3 was formed from the palladium-catalyzed carbonylative reaction of phenylboronic acid and 2. The X-ray crystal structure of this first nonsolvent-derived clathrate of a calix[4]arene derivative is reported. Another 1:1 clathrate of triethylamine and 3 was formed during the attempted Pd-catalyzed deoxygenation of 2.     

Enantioselective photocyclization of amides to beta-lactam derivatives in inclusion crystals with an optically active host

Irradiation of inclusion crystals of 2-(N-acyl-N-alkylamino)cyclohex-2-enones and N,N-dimethylphenylglyoxylamide with chiral host molecules gave the optically active N-alkyl-1-azaspiro[3.5]-nonane-2,5-diones and 3-hydroxy-1-methyl-3-phenylazetidin-2-one, respectively. The crystal structure of the 1:1 inclusion complex of N,N-dimethylphenylglyoxylamide with (-)-trans-1,4-bis[3-(o-chlorophenyl)-3-hydroxy-3-phenylprop-1-ynyl]-2,3,5,6- tetrachloro-2,5-cyclohexadiene-1,4-diol was analyzed by X-ray diffraction.     

Spectroscopic observation of critical guest concentration appearing in tert-butyl alcohol clathrate hydrate

The tert-butyl alcohol (TBA) is the most hydrophobic of the simple alcohol and by itself does not form a clathrate hydrate with water. A genuine clathrate hydrate is synthesized by exposing a gaseous guest to solid TBA + H2O powders. Here, we examine three consecutive spectroscopic approaches of (1) the occurrence of a "free" OH stretching band (nu(OH)) signal of TBA molecules representing an absence of hydrogen bonding between the host water and guest TBA, (2) a tuning effect for creating fresh cages via the rearrangement of the host-water lattice, and finally (3) the existence of a critical guest concentration (CGC) that appears only when the TBA concentration is dilute. The present findings from this simple three-step approach can be extended to other alcoholic guest species with the specific modifications to provide the new insights into inclusion chemistry.     

Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

Nonspherical cages in inclusion compounds can result in non‐uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO₂ molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO₂ guests in terms of a polar angle θ and azimuth angle ? and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO₂ sI clathrate. The experimental ¹³C NMR lineshapes of CO₂ guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the ¹³C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.     

Hydrogen encapsulation in a silicon clathrate type I structure: Na5.5(H2)2.15Si46: synthesis and characterization

A hydrogen-encapsulated inorganic clathrate, which is stable at ambient temperature and pressure, has been prepared in high yield. Na5.5(H2)2.15Si46 is a sodium-deficient, hydrogen-encapsulated, type I silicon clathrate. It was prepared by the reaction between NaSi and NH4Br under dynamic vacuum at 300 degrees C. The Rietveld refinement of the powder X-ray diffraction data is consistent with the clathrate type I structure. The type I clathrate structure has two types of cages where the guest species, in this case Na and H2, can reside: a large cage composed of 24 Si, in which the guest resides in the 6d crystallographic position, and a smaller one composed of 20 Si, in which the guest occupies the 2a position. Solid-state 23Na, 1H, and 29Si MAS NMR confirmed the presence of both sodium and hydrogen in the clathrate cages. 23Na NMR shows that sodium completely fills the small cage and is deficient in the larger cage. The 1H NMR spectrum shows a pattern consistent with mobile hydrogen in the large cage. 29Si NMR spectrum is consistent with phase pure type I clathrate framework. Elemental analysis is consistent with the stoichiometry Na5.5(H2.15)2Si46. The sodium occupancy was also examined using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). The high-angle annular dark-field (HAADF) STEM experimental and simulated images indicated that the Na occupancy of the large cage, 6d sites, is less than 2/3, consistent with the NMR and elemental analysis.     

Helical tubulate inclusion compounds

Abstract

The inclusion properties of the first helical tubuland diol hosts 1–5 have been surveyed and are reported. Bicyclic diol 1 forms helical tubulate inclusion compounds with most small solvent molecules, but with certain phenols hydrogen bonded co-crystalline materials are produced instead. Diol 2 yields helical tubulates with larger guest molecules, but if smaller solvents are used then an alternative host system is obtained. This has the guests trapped in ellipsoidal cavities located along constricted canals and is termed the ellipsoidal clathrate type. In some cases both inclusion types can be produced from 2 by varying the experimental conditions. The free volume present in the helical tubuland lattices of 3 and 5 is insufficient for guest inclusion. Diol 4 has the largest void space and can form inclusion compounds with large molecules such as ferrocene and squalene. X-ray crystal structures of representative examples of these compounds are discussed.     

Structure transition and tuning pattern in the double (tetramethylammonium hydroxide + gaseous guests) clathrate hydrates

In this study, we present an extraordinary structural transition accompanying the occurrence of more than two coexisting clathrate hydrate phases in the double (CH4 + tetramethylammonium hydroxide (Me(4)NOH)) and (H2 + Me(4)NOH) ionic clathrate hydrates using solid-state NMR spectroscopy (high-powered decoupling and CP/MAS) and powder X-ray diffraction. It was confirmed that structure-I (sI) and structure-II (sII) hydrates coexist as the water concentration increases. In the Me(4)NOH-depleted region, the unique tuning phenomenon was first observed at a chemical shift of -8.4 ppm where relatively small gaseous CH4 molecules partly occupy the sII large cages (sII-L), pulling out large cationic Me(4)N+ that is considered to be strongly bound with the surrounding host lattices. Moreover, we note that, while pure Me(4)NOH.16H(2)O clathrate hydrates melted at 249 K under atmospheric pressure conditions, the double (CH4 + Me(4)NOH) clathrate hydrate maintained a solid state up to approximately 283 K under 120 bar of CH4 with a conductivity of 0.065 S cm(-1), suggesting its potential use as a solid electrolyte. The present results indicate that ionic contributions must be taken into account for ionic clathrate hydrate systems because of their distinctive guest dynamic behavior and structural patterns. In particular, microscopic analyses of ionic clathrate hydrates for identifying physicochemical characteristics are expected to provide new insights into inclusion chemistry.     

Synthesis and Inclusion Properties of Macrocyclic Polyethers Containing Phosphonic Groups

Abstract

Three novel polyether macrocycles II-IV bearing phosphonic groups have been synthesised in satisfactory yields. Macrocycle II was found to form a 1:1 inclusion compound with cyclohexane and thus was easily isolated from the reaction mixture as a clathrate. The crystal and molecular structure of the cyclohexane solvate has been determined by single crystal X-ray analyses and refined to an R of 0.028 for 3199 reflection. The compound is monoclinic, space group P2₁n with a = 15.886(6) Å, b = 11.657(5) Å, c = 18.621 (6) Å, β = 90.12(3)°, Z = 2. The whole molecule exhibits a great deal of disorder and the different conformations were modelled as consisting of two different primary conformers with population approximately 60:40.     

Clathrate formation of Diels–Alder adduct of phencyclone and acenaphthylene. Key role of CH/π and bidentate CH/O interactions of the phenanthrene ring in construction of host framework

Two clathrate hosts (3a and 3b) were synthesized via the Diels–Alder reaction of phencyclone (1a) and tetracyclone (1b) with acenaphthylene (2), and the clathrate formation properties of these hosts towards a variety of organic guests were investigated. In the presence of aprotic solvents (i.e., aromatic, ketonic and etheric solvents), host 3a formed inclusion complexes with a 2:1 stoichiometric host/guest ratio, whereas 3b primarily formed 1:1 complexes. The desolvation temperatures of the 3a·guest complexes were extremely high in comparison to the boiling points of the pure guest liquids and were also much higher than those of the corresponding 3b·guest complexes, which contain the conformationally flexible stilbene moiety. Structural analyses of the 3a·guest complexes (i.e., 3a·benzene, 3a·toluene, 3a·1,4-dioxane, 3a·acetone and 3a·pentan-3-one) show that the aromatic CH/π (edge-to-face) interactions between phenanthrene and the acenaphthene ring as well as the interaction of the ‘bidentate’ CH/O hydrogen bond between the phenanthrene-ring hydrogen and the bridged carbonyl oxygen play a key role in the construction of the characteristic host ‘column’ structures. The guest molecule of the 3a·benzene complex is held between the stacking columns by aromatic CH/π interactions of the acenaphthene rings of adjacent host molecules. The stable clathrate formation of 3a is discussed based on X-ray structural analyses of six clathrates and PM6 molecular orbital calculations for the clathration model of 3a·benzene.     

DUAL BEHAVIOR OF ACETONITRILE IN A NEW CADMIUM CYANIDE CLATHRATE: CRYSTAL STRUCTURE OF Cd(CH3CN)2Cd(CN)4·2CH3CN

Abstract

We report a new crystal structure of the title clathrate containing tetrahedral and octahedral Cd atoms in a ratio of 1:1. The preparation of the compound is similar to that of the cristobalite-like clathrate Cd(CN)₂·G, where all Cd atoms are tetrahedral. The new inclusion compound crystallizes in the monoclinic space group C2/c, a = 12.337(4), b = 11.964(3), c = 13.594(3) Å, β = 108.60(2)°, Z = 4, R = 0.034 for 1631 reflections. The three-dimensional host framework is built of alternate linkages between the tetrahedral Cd atom of the tetracyanocadmate and the octahedral Cd atom similar to that of the Hofmann-Td and the en-Td types. In the new clathrate dual behavior of acetonitrile, one as a unidentate ligand in the three-dimensional host framework and the other as the guest in the cage-like cavity, has been demonstrated.