Double Molecular Encapsulation of Tetrahydrofuran by an Amphiphilic Calix-[4]-arene

The crystal structure of para-octanoylcalix-[4]-arene·2 tetrahydrofuran complex reveals double inclusion of the guest molecules, one deep in the aromatic cavity and the other held in a four-fingered molecular hand formed by the aliphatic chains, the inclusion changes the molecular packing from a bilayer system in the absence of guest, to a head-to-tail antiparallel chain packing.     

Atom-atom potential analysis of the complexing characteristics of cyclodextrins (host) with benzene and p-dihalobenzenes (guest)

Abstract

Intermolecular interaction and modelling calculations on the complexes of α-, β- and γ-cyclodextrins (host) with benzene and p-dihalobenzenes (guest) were performed. The complex formation mechanism between the host and guest molecules was evaluated from three-dimensional potential maps generated by the atom-atom potential method, and the molecular packing of the complexed compounds was visualized by a space-fill representation. Stable inclusion complexes only form when both the host and guest molecules experience a significant decrease in the complexing potential. The host and guest molecules have a maximum molecular surface contact at the minimum potential, which depends on both the cavity size and the molecular volumes of the guest molecules. The calculated interaction energies can be correlated to the association constants of complex formation determined from experiment. The molecular dynamics of the guest molecules are also discussed.     

A New Functional Cyclophane Host. Synthesis, Complex Formation and Crystal Structures of Three Inclusion Compounds

A new macrocyclic host compound 2 having an octamethylsubstituted cyclophane structure with two intra-annular carboxylic acid functions has beensynthesized. The properties of crystalline inclusion formation are studied and X-ray crystalstructures of three inclusion complexes including acetic acid, propionic acid and acetone asthe guest molecules are reported. Inter-host channel formation with complexed guest moleculesaccommodated into the channels are typical features of the acetic acid and acetone 1 : 4 (host : guest) stoichiometric complexes being also hydrated species, while the propionicacid 1 : 2 complex is of the close packing type containing no additional water molecules.Systems of hydrogen bonds involving the host and guest functional groups are common toall structures. In the case of the acetic acid inclusion compound, a complex supramolecularhydrogen-bonded array comprising a bordering tricyclic assembly of eight molecular species exists.     

Importance of packing coefficients of host cavities in the isomerization of open host frameworks: guest-size-dependent isomerization in cholic acid inclusion crystals with monosubstituted benzenes

The crystal structures of inclusion compounds of cholic acid (CA) with 28 monosubstituted benzenes have been systematically investigated. All of the crystals belong to the monoclinic space group P2(1) and have bilayer structures with one-dimensional molecular channels that can include guest compounds. They are classified into four types of host frameworks that depend on the conformations and stacking modes of the host compound. The host frameworks and the host-guest ratios depend primarily on the molecular volumes of the guest compounds. The packing coefficient of the host cavity (PCcavity), which is the volume ratio of the guest compound to the host cavity, is used to clarify the relationship between the guest volume and isomerization of the host frameworks. The value of PCcavity, for stable inclusion compounds lies in the range of 55-70%. Compounds out of this range induce isomerization of the host frameworks. The packing coefficients of other host-guest compounds, in which the guest components are included in the host cavities through steric dimensions and van der Waals forces, are also in this range. These results indicate that PCcavity is a useful parameter correlation for guest recognition and isomerization of the host frameworks.     

Inclusion Compounds Formed from N,N-bis(2-hydroxybenzyl)alkylamine Derivatives and Transition Metal Ions via Molecular Assembly

A series of N,N-bis(2-hydroxybenzyl)alkylamine derivatives (1–5) have been found to form host–guest compounds with transition metal ions. The inclusion phenomena in solution are confirmed from the new peak at 415?nm observed by UV-Vis (ultraviolet-visible) spectroscopy and the aromatic and methylene peak shifts observed by ¹H NMR (proton nuclear magnetic resonance) spectroscopy. Comparative studies on 1–5 by liquid–liquid extraction studies suggest that the bulky group at the aza position of the derivatives obstructs the ion interaction resulting in the decrease in ion extraction ability. Inclusion depends on the interaction of the transition metal ions with the compounds 1–5 at the aza and hydroxyl groups as identified by the two-dimensional nuclear Overhauser enhancement technique (¹H–¹H NOESY). The results from Job's plot and electrospray ionization mass spectroscopy (ESIMS) imply molecular assembly of the host–guest system in a 2:1 ratio. Comparative studies among different ions, i.e., Cu²⁺, Zn²⁺ and Cd²⁺ suggest that the host–guest formation is effective when electron sharing is possible through the outer orbital of the transition metal ions. In the case of inclusion in the solid state, the FTIR (Fourier transform infrared) spectra show the changes in vibrational mode of the functional groups in host molecules whereas the X-ray diffraction (XRD) patterns suggest a change in the packing structure of the host molecules. After host–guest formation, the thermal stability of the host molecules decreases as a result of the change in the packing structure from a hydrogen-bonded network to one of ionic interaction with the guest.     

Isomerization processes in inclusion compounds: Xylenes in deoxycholic acid

The isomerization processes induced by UV photons in inclusion compounds of the host-guest type are examined, with special attention to the photophysics of the energy transfer process between the host and the guest, as well as to the influence of the host molecular cavity symmetry and the guest molecular symmetry. In particular, the experimental study has been carried out on the isomerization processes ofp-,m-, ando-xylene inside the molecular cavities of deoxycholic acid. The results have been compared with those obtained by irradiating the xylenes in an inert solution of hexane. The main difference is the elimination of by-products when the photochemical process is carried out in the solid state inclusion compound; however, the high purity of the isomerization product corresponds to a decrease in its yield with respect to the reaction in solution, due to the energy transfer process from the host to the guest moiety.     

Hydrophobic hydration

The problem of interaction between organic and water moieties (neutral or ionized water molecular species) is of particular interest in chemistry in view of its implications to physico-chemical behavior of chemical and biological systems. Hydration patterns which result from interaction between hydrophilic and hydrophobic species are non trivial in chemistry. The key issue is that water molecules are able to aggregate in extremely large variety of structural modes. Tetrahedral geometry of intermolecular bonding around water molecule is analogous in geometrical terms to that of intramolecular geometry of carbon atom, known as a source of infinite number of organic structures. In general, space filling with hydrogen bonded water molecules is rather low. It may be illustrated in the following way: volume of neonium atoms is comparable to that of water molecules whilst having atomic mass just 10% higher than molecular mass of water. Thus, liquid neonium and liquid water would have similar densities if molecular packing is of comparable efficiency. The real values are much different, however. Liquid neonium at its boiling temperature has density of 1.20 g cm^–3 , thus displaying significantly denser packing that that of water molecules. It certainly means that solid or liquid water has a ‘porous’ structure and may lead to molecular inclusion of foreign (guest) species in the intermolecular space of water framework. This property is not that simple, however, since inclusion of foreign (guest) species is, as a rule, associated with rearrangement of the host framework structure [1]. Anyway, inefficient packing of the mono-component host solid phases may be considered as a prerequisite for its pronounced clathration ability.     

A Solid‐State Fluorescent Host System with a 21‐Helical Column Consisting of Chiral (1R,2S)‐2‐Amino‐1,2‐diphenylethanol and Fluorescent 1‐Pyrenecarboxylic Acid

A solid‐state fluorescent host system was created by self‐assembly of a 2₁‐helical columnar organic fluorophore composed of (1R,2S)‐2‐amino‐1,2‐diphenylethanol and fluorescent 1‐pyrenecarboxylic acid. This host system has a characteristic 2₁‐helical columnar hydrogen‐ and ionic‐bonded network. Channel‐like cavities are formed by self‐assembly of this column, and various guest molecules can be included by tuning the packing of this column. Moreover, the solid‐state fluorescence of this host system can change according to the included guest molecules. This occurs because of the change in the relative arrangement of the pyrene rings as they adjust to the tuning of the packing of the shared 2₁‐helical column, according to the size of the included guest molecules. Therefore, this host system can recognize slight differences in molecular size and shape.     

Inclusion Compound Formation of Amylose by Sealed-Heating with Salicylic Acid Analogues

The inclusion compounds of linear amylose and salicylic acid analogues preparedby sealed-heating were evaluated by using powder X-ray diffraction and infraredspectroscopy. Sealed-heating of amylose and either salicylamide or benzoic acidinduced the amylose structural change from the 6₁- to the 7₁-helix structure, while sealed-heating with o-toluic acid, o-chlorobenzoic acid and o-nitrobenzoic acid induced the change from the 6₁- to the 8₁-helix structure. In contrast to theresults in the salicylic acid system, the amylose helix type of sealed-heated samplewas not varied by the load of the guest compound, but was fixed only by the guestspecies. No change of the helical structure of amylose depending on the amylose molecular weight was observed. From the comparison of inclusion compound formation among different guest systems, it was found that the higher vapor pressure at 100 °C of the guest resulted in faster inclusion compound formation. The vapor pressure of the guest compound would be an important factor affecting the progress of inclusion compound formation.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 2. A new perturbation: the room-temperature crystallographic structure determination for the N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-cyclodextrin complex

Cyclodextrins (CDs) are cyclic oligosaccharides that encapsulate various small organic molecules, forming inclusion complexes. Because CD complexes are held together purely by noncovalent interactions, they function as excellent models for the study of chiral and molecular recognition mechanisms. Recently, room-temperature crystallographic studies of both the 2:2 N-acetyl-L-phenylalanine methyl ester/beta-CD and 2:2 N-acetyl-L-phenylalanine amide/beta-CD complexes were reported. The effect of changes in carboxyl backbone functional group on molecular recognition by the host CD molecule was examined for the nearly isomorphous supramolecular complexes. A new perturbation of the system is now examined, specifically perturbation of the aromatic side chain. We report a room-temperature crystal structure determination for the 2:2 N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-CD inclusion complex. The complex crystallizes isomorphously with the two previously reported examples in space group P1; the asymmetric unit consists of a hydrated head-to-head host dimer with two included guest molecules. The crystal packing provides both a nonconstraining extended hydrophobic pocket and an adjacent hydrophilic region, where hydrogen-bonding interactions can potentially occur with primary hydroxyl groups of neighboring CD molecules and waters of hydration. The rigid host molecules show no sign of conformational disorder, and water of hydration molecules exhibit the same type of disorder observed for the other two complexes, with a few significant differences in locations of water molecules in the hydrophilic region near guest molecules. There is evidence for modest disorder in the guest region of an electron density map. In comparing this system with the two previously reported complexes of phenylalanine derivatives, it is found that the packing of the guest molecules inside the torus of the CD changes upon substitution of a methoxy group at the para position of the aromatic phenyl ring. Backbone hydrogen-bonding interactions for the guest molecules with the CD primary hydroxyls and waters also change. This structure determination is a new and revealing addition to a small but growing database of amino acid and peptidomimetic interactions with carbohydrates.     

Load–Collapse–Release Cascades of Amphiphilic Guest Molecules in Charged Dendronized Polymers through Spatial Separation of Noncovalent Forces

The ability to pack guest molecules into charged dendronized polymers (denpols) and the possibility to release these guest molecules from subsequently densely aggregated denpols in a load–collapse–release cascade is described. Charged denpols, which constitute molecular objects with a persistent, well‐defined envelope and interior, are capable of incorporating large amounts of amphiphilic guest molecules. Simultaneously, multivalent ions can coordinate to the surfaces of charged denpols, leading to counterion‐induced aggregation of the already guest‐loaded host structures. Thus, although the local guest concentration in denpol‐based molecular transport might already be initially high due to the dense guest packing inside the dendritic denpol scaffolding, the “local” guest concentration can nonetheless be further increased by packing (through aggregation) of the host–guest complexes themselves. Subsequent release of guest compounds from densely aggregated dendronized polymers is then possible (e.g., through increasing the solution concentration of imidazolium‐based ions). Augmented with this release possibility, the concept of twofold packing of guests, firstly through hosting itself and secondly through aggregation of the hosts, gives rise to a load–collapse–release cascade that strikingly displays the high potential of dendronized macromolecules for future molecular transport applications.     

Inclusion of Poly(ethylene glycol)s by Crystalline (R)-(1-Naphthyl)glycyl-(R)-phenylglycine

Abstract

Crystallization of (R)-(1-naphthyl)glycyl-(R)-phenyl-glycine [(R,R)-1] in the presence of oligo(ethylene glycol) dimethyl ethers 2(n) or poly(ethylene glycol)s (PEGs, 3(M_n )) afforded inclusion compounds. The ratio of (R,R)-1/the guest polymer (2 or 3) was proportional to the length of the polymer chain. The crystal structure of a hepta(ethylene glycol) dimethyl ether-included compound was disclosed by X-ray crystallography which showed that (R,R)-1 molecules form a sheet and the guest molecule penetrates the crystal lattice of (R,R)-1 through a one-dimensional channel on the sheet. Powder X-ray analysis revealed that, regardless of the length of the guest polymer, the distance between the neighboring sheets remains unchanged (12.0–12.3 Å) in these inclusion crystals. By thermal analysis, it was shown that the decomposition points of these inclusion compounds became higher with the longer PEG included. The inclusion phenomenon enabled the fractionation of PEGs with various molecular weights, among which longer PEG was preferably included.     

Amphiphilic Inclusion Spaces for Various Guests and Regulation of Fluorescence Intensity of 1,8‐Bis(4‐aminophenyl)anthracene Crystals

A host framework for inclusion of various guest molecules was investigated by preparation of inclusion crystals of 1,8‐bis(4‐aminophenyl)anthracene (1,8‐BAPA) with organic solvents. X‐ray crystallographic analysis revealed construction of the same inclusion space incorporating 1,8‐BAPA and eight guest molecules including both non‐polar (benzene) and polar guests (N,N‐dimethylformamide, DMF). Fluorescence efficiencies varied depending on guest molecule polarity; DMF inclusion crystals exhibited the highest fluorescence intensity (Φ_F=0.40), four times as high as that of a benzene inclusion crystal (Φ_F=0.10). According to systematic investigations of inclusion phenomena, strong host–guest interactions and filling of the inclusion space led to a high fluorescence intensity. Temperature‐dependent fluorescence spectral measurements revealed these factors effectively immobilised the host framework. Although hydrogen bonding commonly decreases fluorescence intensity, the present study demonstrated that such strong interactions provide excellent conditions for fluorescence enhancement. Thus, this remarkable behaviour has potential application toward sensing of highly polar molecules, such as biogenic compounds.     

Non-covalent surface modification of metal-macrocycle framework with mono-substituted benzenes

Recently, we have reported a metal-macrocycle framework (MMF) with five enantiomerically paired molecular binding pockets that exhibit site-selective guest arrangement on the nano-channel surface in soaking experiments using a variety of guest molecules. The guest inclusion is based largely on molecular exchange between solvent molecules such as CH₃CN and guest molecules on the surface. Herein, we report that the molecular arrangement on the nano-channel surface varies with size, shape and/or chemical properties of functional groups of guests, mono-substituted benzene derivatives, such as benzonitrile, acetophenone and nitrobenzene. In their inclusion complexes, polar nitrile, acetyl and nitro groups serve as molecular anchors to a macrocyclic cavity through hydrogen bonding. Notably, benzonitrile and benzenesulphonic acid bind only to one pair of enantiomeric binding pockets. Such a highly site-selective binding would enable further multi-component surface modifications in the MMF.     

Molecular dynamics study of host–guest interactions in cyclodextrins: methodology and data analysis for a comparison with solution data and the solid-state structure

A general method is proposed to model the behavior of cyclodextrins (CDs) and of their inclusion compounds through energy minimizations and molecular dynamics (MD) simulations at a constant temperature. In this way, the formation of a host–guest compound is obtained starting from many trial geometries with the guest outside the CD cavity without any a priori assumption. The MD simulation results are analyzed through two functions: (i) the similarity maps of the root-mean-square distances between instantaneous conformations found in the MD runs to recognize different families of conformers; (ii) the pair distribution function PDF, yielding the probability density of finding appropriate atom pairs as a function of their distance at equilibrium. As an example, the inclusion compound formed by β-CD and (−)-menthol-β-d-glucoside is investigated. The lowest-energy inclusion compound is in good agreement with the results of single-crystal X-ray analysis, while at room temperature the MD runs show a closely similar arrangement with thermal fluctuations. In this case, the PDF between diagnostic hydrogen atoms of β-CD and of the guest molecule are fully consistent with the experimental NOE results obtained from NMR measurements in solution.     

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.     

TheO,O′-dibenzoyl derivative of (R,R)-tartaric acid as a host compound for simple organic ethers

TheO, O-dibenzoyl derivative of (R, R)-tartaric acid shows a good inclusion ability for diethyl and di-n-propol ethers. The two crystalline inclusion compounds have 1:1 stoichiometry and reveal isomorphous structures. Hydrogen bonded host molecules form chains running along thez axis of the unit cell and guest molecules join to these chains by short O–H...O hydrogen bonds. Hydrogen bonding in the crystals is characterized by a C(7)D first-order network. The ether molecules are in a fully extended conformation. They are accommodated in channel-like voids running along thex axis. Atomic displacement parameters are significantly larger for diethyl ether than for the di-n-propyl ether molecule reflecting less dense packing for this inclusion compound.Supplementary Data: relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82195 (19 pages)     

Why a hexabromodiquinoline host preferentially includes small aromatic hydrocarbon guests

The preparation and properties of the new hexabromodiquinoline derivative 4 are described. This lattice inclusion host shows a strong preference for trapping small aromatic hydrocarbons. The X-ray crystal structures of the benzene, toluene, o-xylene, and p-xylene compounds are reported, and are analysed from a crystal engineering perspective. Crystallisation of 4 from the dual-nature solvent trifluoromethylbenzene yields the solvent-free material. Comparison of the parent crystal structure with those of its inclusion compounds reveals why inclusion of aromatic hydrocarbon guests is such a favoured process. The high concentration of Br...Br interactions in the structure of pure 4 is diluted and increasingly replaced by aromatic offset face-face (OFF) and aromatic edge-face (EF) interactions in the inclusion compounds, and this results in better lattice packing energies. For toluene, o-xylene, and p-xylene the host-guest ratio is 1:1. Inclusion of the smaller benzene molecule results in a change to 2:3 stoichiometry. This increase in guest content is assisted by replacement of host-host OFF and EF motifs with host-host pi-halogen dimer (PHD) interactions, which provide space for inclusion of the additional guest molecules. These changes result in the most efficient lattice packing of the series for compound (4)2.(benzene)3.     

Pseudorotaxanes of β-Cyclodextrin with Diamino End-functionalized Oligo-phenyl and -benzyl Compounds in Solution and in the Solid State

-Cyclodextrin forms a 1:1 host:guest inclusion complex ([2]pseudorotaxane) with 4-[2-(4-aminophenyl)ethyl]-benzenamine (1) in water as determined by 1D and 2D NMRexperiments. In the crystalline state, the structure of the complex has revealed a 2:2 stoichiometry, with two CD molecules forming head-to-head dimers byH-bonds between the secondary O3 hydroxyl groups and enclosing two molecules of the guest. The packing mode of the present complex is encountered for the first time, since it does not belong to any of the four known packing types of the dimeric CD inclusion complexes. On the other hand,N ¹,N ⁴-bis(4-aminophenyl)-1,4-benzenedimethanamine 2), which is longer than 1 by a phenylene diamine unit, has not afforded any crystals, at present, however it threads into CD in aqueous solution forming most probably [2]- and [3]pseudorotaxanes. The solution structures and the equilibria in this system are investigated.     

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

X‐ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host–guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X‐ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light‐atom‐only crystal. Atomic displacement parameters obtained independently from the X‐ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Ų indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host–guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host–guest interaction (e.g., in protein–drug complexes), at least for polar molecules.