Rapid screening of a receptor with molecular memory

[reaction: see text] Atropisomeric receptor 1 can change conformation and maintain the new conformation when heated and cooled in the presence of a guest molecule. This molecular memory can be used as a rapid method of screening potential guests. Heating atropisomeric diacid 1 with various hydrogen-bonding guests leads to a shift in the syn/anti ratio that could be easily monitored as it is stable at room temperature even in the absence of the guest molecules.     

7-N,7'-N'-(1",2"-Dithianyl-3",6"-dimethylenyl)bismitomycin C: synthesis and nucleophilic activation of a dimeric mitomycin

Dimeric alkylating agents that modify complementary DNA strands have engendered significant interest. We have prepared the novel dimeric mitomycin, 7-N,7'-N'-(1",2"-dithianyl-3",6"-dimethylenyl)bismitomycin C (9), in which the mitomycins are bridged by a dithiane unit. Dimer 9, like the clinically tested acyclic disulfides KW-2149 (3) and BMS-181174 (4), was designed to activate under nucleophilic and reductive conditions. Successive nucleophile-mediated disulfide cleavage transformations of 9 are expected to generate thiol species ideally positioned to render the two mitomycin systems vulnerable to nucleophilic attack and permit DNA interstrand cross-link formation. The dithiane linker, strategically positioned between the two mitomycins, distinguished 9 from 3 and 4. Nucleophilic activation of this cyclic disulfide permitted both activated mitomycins to remain tethered to one another. We report the synthesis of 9, and show that the nucleophile Et(3)P markedly enhances the activation and consumption of 9, compared with the reference compound 7-N, 7"-N'-(cyclohexanyl-trans-1",4"-dimethylenyl)bismitomycin C (27). We further demonstrated that provides higher levels of DNA interstrand cross-links than either the dimeric reference compounds, and 7-N,7-N'-(2",5"-dihydroxy-1",6"-hexanediyl)bismitomycin C (28), or the monomeric mitomycins, 1 and 3, when Et(3)P is added to solutions containing EcoRI-linearized pBR322 DNA.     

An atropisomeric M2L4 cage mixture displaying guest-induced convergence and strong guest emission in water

Introduction of atropisomeric axes into a bent bispyridine ligand leads to the quantitative formation of a complex mixture of atropisomeric M₂L₄ cages upon treatment with metal ions. Whereas the isomer ratio of the obtained cage mixture, consisting of up to 42 isomers, is insensitive to temperature and solvent, the quantitative convergence from the mixture to a single isomer is accomplished upon encapsulation of a large spherical guest, namely fullerene C₆₀. The observed isomerization with other guests depends largely on their size and shape (e.g., <10 and 82% convergence with planar triphenylene and bowl-shaped corannulene guests, respectively). Besides the unusual guest-induced convergence, the present cage mixture displays the strongest guest emission (Φ_F = 68%) among previously reported M_nL_m cages and capsules, upon encapsulation of a BODIPY dye in water.

A complex mixture of atropisomeric M₂L₄ cages is shown to undergo perfect convergence to a single isomer upon encapsulation of spherical C₆₀ in water. Moreover, the cage mixture displays very strong guest emission upon encapsulation of a BODIPY dye.     

"Pocket dendrimers" as nanoscale receptors for bimolecular guest accommodation

A new series of dendrimer receptors was prepared by combining a (tetraphenylporphinato)zinc(II) core and benzyl ether type dendritic substituents. Since one direction of the (tetraphenylporphinato)zinc(II) was not substituted by a dendritic residue, the resulting unsymmetrical dendrimers have "pockets" available for access of external substrates. Molecular modeling, NMR measurements, and zinc-coordination experiments revealed that the third-generation dendrimer of this type exhibited characteristic inclusion of coordinative pyridine guests. When diamidopyridine moiety was introduced into the dendrimer pocket, a thymine derivative was bound through complementary hydrogen bonding. Two different kinds of substrates, pyridine and thymine derivatives, were simultaneously accommodated in the nanoscale pocket and bimolecular guest accommodation was realized with the designed dendrimer receptor.     

Facile synthesis of Janus "double-concave" tribenzo[a,g,m]coronenes

Hexabutoxytribenzo[a,g,m]coronenes have been prepared in three steps from readily accessible hexabutoxytriphenylene. Single-crystal X-ray diffraction analysis reveals that these molecules can adopt an extraordinary "double-concave" conformation that makes them ideal hosts for the binding of different guest molecules at each face.     

Hyperbranched molecular nanocapsules: comparison of the hyperbranched architecture with the perfect linear analogue

The results of a comparative study of hyperbranched, partially esterified polyglycerols with their linear polyglycerol analogues with respect to molecular encapsulation and phase transfer are reported. Two hyperbranched polyglycerol samples with molecular weights of 3000 and 8000 g/mol (Mw/Mn = 1.3), respectively, have been partially esterified using palmitoyl chloride. The same modification was applied to the structurally analogous linear polyglycerol (3000 g/mol). A detailed UV-vis study correlated with viscosity experiments demonstrated that only the hyperbranched core-shell structures form "nanocapsules", leading to the encapsulation of polar guest molecules. The results underline the crucial role of the hyperbranched topology and the resulting solution conformation for supramolecular guest encapsulation and phase transfer. The unusually compact ("collapsed") structure assumed by the hyperbranched core-shell amphiphiles in apolar media is responsible for the formation of a hydrophilic compartment, capable of irreversibly taking up guest molecules.     

Tetra-TTF calix[4]pyrrole: a rationally designed receptor for electron-deficient neutral guests

A calix[4]pyrrole incorporating four appended tetrathiafulvalene (TTF) units has been synthesized, and its receptor abilities toward neutral electron-deficient guests, such as 1,3,5-trinitrobenzene, tetrafluoro-p-benzoquinone, and tetrachloro-p-benzoquinone, have been studied in solution by UV-vis and 1H NMR spectroscopies as well as in the solid-state by X-ray crystallography. In its 1,3-alternate conformation a 1:2 sandwich-like complex-stabilized by charge transfer and hydrogen bonding interactions-is formed between the tetra-TTF calix[4]pyrrole and the guest molecules. However, upon addition of chloride ions to the complex the 1,3-alternate conformation is changed in favor of a cone conformation which serves to effect a release of the guests from the tetra-TTF calix[4]pyrrole.     

Romancing the "hidden proteome", Anno Domini two zero zero seven

The mechanism of action and properties of a solid-phase ligand library made of hexapeptides, for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins constituting the vast majority of species in any proteome, be it a cell or tissue lysate or a biological fluid, are here reviewed. Mechanisms of adsorption are evaluated, as well as different protocols for en bloc or sequential elution of the captured polypeptides. Examples are given of capture of proteins from serum, human platelet extracts, bacterial extract and egg white. The increment in detection of low-abundance species appears to be of at least four-fold as compared with untreated samples. One particular aspect of this capture is the adsorption of a high proportion of small peptides (in the Mr 600-8000 Da range) that are normally lost upon electrophoretic two-dimensional mapping. Such a peptide population, in human sera, may be of particular importance since it may contain protein cleavage products of diagnostic value.     

Synthesis, aggregation, and binding behavior of synthetic amphiphilic receptors

Amphiphilic bowl-shaped receptor molecules have been synthesized starting from diphenylglycoluril. Upon dispersion in water, these molecules self-assemble to form vesicles that bind neutral guests and alkali metal ions. In the case of bis(alkylester)-modified receptor compound 4, electron microscopy reveals that an increase in the size of the alkali metal ion (from Na(+) or K(+) to Rb(+) and to Cs(+)) leads to a change in the shape of the aggregates, viz. from vesicles to tubules. Monolayer experiments suggest that this behavior is due to a change in the conformation of this amphiphilic receptor. In water, molecules of 4 have an elongated conformation that changes to a sandwich-like one upon binding of alkali metal ions. Binding studies with vesicles from the bis-ammonium receptors 6 and 9 and the guest 4-(4-nitrophenylazo)resorcinol (Magneson) reveal that below the critical aggregation concentration (CAC) of the amphiphile 1:1 host-guest complexes are formed with high host-guest association constants. Above the CAC, a host-guest ratio of 2:1 was observed that indicates that only the cavities on the outside of the vesicle can be occupied. In the case of the naphthalene walled compound 8 changes in the vesicle structure are induced by the organic guest Magneson.     

Cholesteric liquid crystal displays as optical sensors of barbiturate binding

The influence on the optical properties of cholesteric liquid crystal displays (LCDs) was examined for neutral molecule binding by mesogen/receptors in the mesomorphic phase. The motivation was to prepare neutral molecule sensors that use a colour change to signal analyte binding. A receptor that binds barbiturate analytes was modified with two or one cholesteryl groups to yield compounds 2 and 3, respectively. LCDs were prepared by incorporating one of the receptor/mesogen compounds into a cholesteric LC blend along with a potential H-bonding guest. The optical properties of the LCDs were then determined by measuring the absorbance of the displays. For various LCDs, the colour of the display depended upon several factors: the amount of guest molecule used, the number of cholesteryl side chains on the receptor and the mole concentration of receptor/mesogen in the blend. In particular, complementary host/guest binding of H-bonding analytes by the bis(cholesteryl) receptor 2 in a cholesteric LCD caused a change of up to +70 nm, which was observed by the naked eye as a blue-to-orange colour change. Control experiments confirm that the colour of an LCD is a consequence of molecular recognition in the mesomorphic phase.     

Recovery of host crystals from inclusion crystals of <Emphasis Type="Italic">p-tert-</Emphasis>butylcalix[4]arene and <Emphasis Type="Italic">p-tert</Emphasis>-butylthiacalix[4]arene by the treatment with a solvent and/or supercritical CO<Subscript>2</Subscript>

Upon stirring inclusion crystals of p-tert-butylthiacalix[4]arene (2) in solvents with heating, guest compounds were efficiently desorbed to yield guest-free crystals. More specifically, upon treatment with methanol, the exchange of guest compounds with methanol in the crystals, followed by the desorption of the methanol afforded metastable host crystals 2β, whereas, upon treatment with heptane, the dissolution of the inclusion crystals and simultaneous crystallization of compound 2 afforded stable host crystals 2α. Further, a host crystal of p-tert-butylcalix[4]arene (1) was recovered by the treatment of 2:1 (host/guest) inclusion crystals of compound 1 with supercritical carbon dioxide (scCO₂), and through the combination of the guest exchange of 1:1 inclusion crystals of compound 1 with hexane and scCO₂ treatment of the resulting 2:1 inclusion crystals 1₂·hexane. Although the recovered host crystal of compound 1 contained a small amount of CO₂, it could be reused for the inclusion of organic compounds.     

Binding studies of tetrathiafulvalene-calix[4]pyrroles with electron-deficient guests

The neutral meso-octamethylporphyrinogen derivative, tetraTTF-calix[4]pyrrole 1 (TTF=tetrathiafulvalene), acts as a multi-faceted receptor in that it interacts with an assortment of different guests in different ways. The conformation of receptor 1 can be reversibly switched between the 1,3-alternate conformation (i.e., 1, Fig. 1) and the cone conformation (i.e., 1·Cl⁻, Fig. 2) by the repetitive addition of chloride and sodium ions. In this paper, the results of detailed and systematic complexation studies involving both 1 and its chloride-bound complex, 1·Cl⁻, with a variety of guests are described. Receptor 1 binds quasi-planar nitroaromatic guests in its 1,3-alternate conformation, while release of these guests takes place upon addition of chloride anions. On the other hand, spherical fullerene guests are strongly bound by 1·Cl⁻. Finally, it was found that a bidentate guest, consisting of a quasi-planar 2,5,7-trinitro-9-dicyanomethylenefluorene moiety tethered to a spherical C₆₀ fullerene, could be recognized by receptor 1 in either its 1,3-alternate or its chloride-bound cone conformation, albeit through very different binding modes.     

Cholesteric liquid crystal displays as optical sensors of barbiturate binding

The influence on the optical properties of cholesteric liquid crystal displays (LCDs) was examined for neutral molecule binding by mesogen/receptors in the mesomorphic phase. The motivation was to prepare neutral molecule sensors that use a colour change to signal analyte binding. A receptor that binds barbiturate analytes was modified with two or one cholesteryl groups to yield compounds 2 and 3, respectively. LCDs were prepared by incorporating one of the receptor/mesogen compounds into a cholesteric LC blend along with a potential H‐bonding guest. The optical properties of the LCDs were then determined by measuring the absorbance of the displays. For various LCDs, the colour of the display depended upon several factors: the amount of guest molecule used, the number of cholesteryl side chains on the receptor and the mole concentration of receptor/mesogen in the blend. In particular, complementary host/guest binding of H‐bonding analytes by the bis(cholesteryl) receptor 2 in a cholesteric LCD caused a change of up to +70 nm, which was observed by the naked eye as a blue‐to‐orange colour change. Control experiments confirm that the colour of an LCD is a consequence of molecular recognition in the mesomorphic phase.     

Computational analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranose]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) (TSAO) as HIV-1 reverse transcriptase inhibitors: relevance of conformational properties on the inhibitory activity

We have carried out a theoretical analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) by a variety of computational tools, aimed to account for the effect of the endocyclic amino moiety N-2" on the inhibitory activity against HIV-1. Docking studies suggest that compounds substituted at the N-3 and N-2' ' positions present the same binding mode to the [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide)thymine prototype, where the endocyclic amino group remains mostly exposed to the solvent. A careful conformational analysis performed through different theoretical levels, from molecular mechanics to high-level quantum mechanical calculations, provides a rationalization based on conformational preferences, which appears as strongly determined by the substitution at N-2", and on electrostatic effects from the bulk water.     

Significant conformational changes associated with molecular transport in a crystalline solid

Confocal Raman microspectrometry has been applied as an in situ probe of the transport of guest molecules along the one-dimensional tunnels in a crystalline urea inclusion compound, under conditions of guest exchange in which "new" guest molecules (pentadecane) are introduced at one end of the tunnel and displace the "original" guest molecules (1,8-dibromooctane). The Raman spectra, recorded as a function of position along the tunnel direction and as a function of time, demonstrate that the transport process is associated with a significant change in the conformational properties of the original (1,8-dibromooctane) guest molecules. In particular, in the boundary region between the original and new guest molecules, there is a substantial increase in the proportion of 1,8-dibromooctane guest molecules that have the gauche end-group conformation. The wider implications of this observation are discussed in relation to fundamental aspects of the molecular transport process in this material.     

Enhanced shape-selective recognition of anion guests through complexation-induced organization of porphyrin hosts

We present a fortuitous discovery of enhanced shape-selective recognition of anion guests that stems from a complexation-induced conformational change in porphyrin hosts upon anion binding. Porphyrin hosts reported here exist in a conformation that is not favorable to guest binding. Anions that bind strongly are those that can induce a conformational change in the host to allow guest binding. Furthermore, guests that mimic the shape of the newly formed pocket bind the strongest.     

Formation of a Syndiotactic Organic Polymer Inside a MOF by a [2+2] Photo‐Polymerization Reaction

Getting suitable crystals for single‐crystal X‐ray crystallographic analysis still remains an art. Obtaining single crystals of metal–organic frameworks (MOFs) containing organic polymers poses even greater challenges. Here we demonstrate the formation of a syndiotactic organic polymer ligand inside a MOF by quantitative [2+2] photopolymerization reaction in a single‐crystal‐to‐single‐crystal manner. The spacer ligands with trans,trans,trans‐conformation in the pillared‐layer MOF with guest water molecules in the channels, undergo pedal motion to trans,cis,trans‐conformation prior to [2+2] photo‐cycloaddition reaction and yield single crystals of MOF containing two‐dimensional coordination polymers fused with the organic polymer ligands. We also show that the organic polymer in the single crystals can be depolymerized reversibly by cleaving the cyclobutane rings upon heating. These MOFs also show interesting photoluminescent properties and sensing of small organic molecules.     

Modeling and conformation analysis of β-cyclodextrin complexes

Summary A series of -cyclodextrin complexes containing various guest molecules was studied using computer-aided molecular modeling and conformation analysis techniques. The geometry of each complex was studied using crystallographic data. The positions of the glycosidic O4 atoms indicate that the -cyclodextrin molecules are elliptically distorted. This distortion can be related to the van der Waals volume of the guest molecules. This correlation is different for aromatic and non-aromatic guest compounds. Rigid body docking experiments demonstrated that in crystal structures the guest molecule occupies a position in the cavity of nearly minimum interaction energy when there are no other molecules having interactions with the guest molecule. From the crystallographic data several rules could be deduced which seem to determine the conformation of -cyclodextrin molecules in complexes. A procedure was developed to construct -cyclodextrin molecules that are able to encompass guest molecules having a given van der Waals volume.     

Conformational behavior of pyrazine-bridged and mixed-bridged cavitands: a general model for solvent effects on thermal "vase-kite" switching

The controllable switching of suitably bridged resorcin[4]arene cavitands between a "vase" conformation, with a cavity capable of guest inclusion, and a "kite" conformation, featuring an extended flattened surface, provides the basis for ongoing developments of dynamic molecular receptors, sensors, and molecular machines. This paper describes the synthesis, X-ray crystallographic characterization, and NMR analysis of the "vase-kite" switching behavior of a fully pyrazine-bridged cavitand and five other mixed-bridged quinoxaline-bridged cavitands with one methylene, phosphonate, or phosphate bridge. The pyrazine-bridged resorcin[4]arene cavitand displayed an unexpectedly high preference for the kite conformation in nonpolar solvents, relative to the quinoxaline-bridged analogue. This observation led to extensive solvent-dependent switching studies that provide a detailed picture of how solvent affects the thermal vase-kite equilibration. As for any thermodynamic process in the liquid phase, the conformational equilibrium is affected by how the solvent stabilizes the two individual states. Suitably sized solvents (benzene and derivatives) solvate the cavity of the vase form and reduce the propensity for the vase-to-kite transition. Correspondingly, the kite geometry becomes preferred in bulky solvents such as mesitylene, incapable of penetrating the vase cavity. As proposed earlier by Cram, the kite form is preferred at low temperatures due to the more favorable enthalpy of solvation of the enlarged surface. Furthermore, the kite conformation is more preferred in solvents with substantial hydrogen-bonding acidity: weak hydrogen-bonding interactions between the mildly basic quinoxaline and pyrazine nitrogen atoms and solvent molecules are more efficient in the open kite than in the closed vase form. Vase-to-kite conversion is entirely absent in dipolar aprotic solvents lacking any H-bonding acidity. Thermal vase-kite switching requires fully quinoxaline- or pyrazine-bridged cavitands, whereas pH-controlled switching is also applicable to systems incorporating only two or three such bridges.     

Photocontrol of Polar Aromatic Interactions by a Bis‐Hemithioindigo Based Helical Receptor

The first example of a bis‐hemithioindigo (bis‐HTI)‐based molecular receptor was realized. Its folding and selective binding affinity for aromatic guest molecules can be precisely controlled by visible light and heat. The thermodynamically stable state of the bis‐HTI is the s‐shaped planar Z,Z‐configuration. After irradiation with 420 nm light only the E,Z‐configuration is formed in a highly selective photoisomerization. The E,Z‐isomer adopts a helical conformation because of the implementation of repulsive steric interactions. The E,Z‐configured helix is able to recognize electron‐poor aromatic guests exclusively through polar aromatic interactions and also distinguishes between regioisomers. After heating, the Z,Z‐configuration is completely restored and the aromatic guest molecule is efficiently released.