Capsular Assembly Research Articles

Binding of Linear Anions and Formation of Anion Encapsulated Dimeric Capsular Assembly by Cis‐5,15‐bis(3,5‐trifluoromethylphenyl)calix[4]pyrrole

AbstractCis‐5,15‐bis(3,5‐trifluoromethylphenyl)calix[4]pyrrole (1) forms stable 1/1 complexes with linear anions such as N3−, SCN− and NCO‐ with the highest affinity for NCO− anion in acetonitrile solution. Crystallization of receptor 1 with TBASCN and (TMA)2SO4 resulted in the formation of dimeric capsular assembly, {(TMA)2[12 ⋅ (SCN)2]}, in which two thiocyanate anions are encapsulated. On the other hand, 1 ⋅ OCN(TMA) and 1 ⋅ N3(TMA) complexes form one dimensional columnar structure in the solid state.

Selective recognition and extraction of arsenate by a urea-functionalized tripodal receptor from competitive aqueous media.

A second-generation hydrogen bond donor (HBD) anion receptor with an inner amide cavity and an outer urea cavity can selectively and efficiently extract arsenate (AsO43-) from water in the presence of competitive oxoanions and halides. The X-ray structure showed encapsulation of AsO43- in a π-stacked dimeric capsular assembly of the receptor, the first crystallography-based example of pentavalent AsO43- trianion recognition by a HBD receptor.

Structure directing roles of weak noncovalent interactions and charge-assisted hydrogen bonds in the self-assembly of solvated podands: an example of an anion-assisted dimeric water capsule

A 4-aminopyridinium-functionalized mesitylene-based podand could facilitate the formation of a dimeric capsular assembly due to the complementary hydrogen bonding mediated by bromide counterions and lattice water.

Group B Streptococcus chimeric capsular polysaccharides as novel multivalent vaccine candidates

The capsular polysaccharide of the human pathogen Group B Streptococcus is a key virulence factor and vaccine candidate that induces protective antibodies when conjugated to carrier proteins. It consists of long polymeric chains of oligosaccharide repeating units, and each of the ten capsular serotypes described so far presents a unique chemical structure with distinct antigenic properties; therefore, broad protection against this pathogen could be achieved by a combination of ten glycoconjugates. Capsular polysaccharide biosynthesis and assembly follow a polymerase-dependent pathway that is widespread in encapsulated bacteria and is encoded by a polycistronic operon. Here we exploited the sequence similarity between the capsule operons of types V and IX to generate hybrid polysaccharides incorporating epitopes of both serotypes in a single molecule, by co-expressing their specific CpsM, O, I glycosyltransferases in a single isolate. Physicochemical and immunochemical methods confirmed that an engineered strain produced a high molecular weight chimeric polysaccharide, combining antigenic specificities of both type V and IX. By optimizing the copy number of key glycosyltransferase genes, we were able to modulate the ratio between type-specific epitopes. Finally, vaccination with chimeric glycoconjugates significantly decreased the incidence of disease in pups born from immunized mice challenged with either serotype. This study provides proof of concept for a new generation of glycoconjugate vaccines that combine the antigenic specificity of different polysaccharide variants in a single molecule, eliciting a protective immune response against multiple serotype variants.

Marcus Relationship Maintained During Ultrafast Electron Transfer Across a Supramolecular Capsular Wall.

Photoinduced electron transfer across an organic capsular wall between excited donors and ground-state acceptors is established to occur with rate constants varying in the range 0.32-4.0 × 1011 s-1 in aqueous buffer solution. The donor is encapsulated within an anionic supramolecular capsular host, and the cationic acceptor remains closer to the donor separated by the organic frame through Coulombic attraction. Such an arrangement results in electron transfer proceeding without diffusion. Free energy of the reaction (ΔG°) and the rate of electron transfer show Marcus relation with inversion. From the plot, λ and Vel were estimated to be 1.918 and 0.0058 eV, respectively. Given that the donor remains within the nonpolar solvent-free confined space, and there is not much change in the environment around the acceptor, the observed λ is believed to be because of "internal" reorganization rather than "solvent" reorganization. A similarity exists between the capsular assembly investigated here and glass and crystals at low temperature where the medium is rigid. The estimated electronic coupling (Vel) implies the existence of interaction between the donor and the acceptor through the capsular wall. Existence of such an interaction is also suggested by 1H NMR spectra. Results of this study suggest that molecules present within a confined space could be activated from outside. This provides an opportunity to probe the reactivity and dynamics of radical ions within an organic capsule.

Guest/Host Complexes of Octa Acid and Amphiphilic Benzylidene-3-methylimidazolidinones Exchange Hosts within the NMR Time Scale.

Cavitand octa acid (OA) is established to form a stable capsular assembly with one or two hydrophobic guest molecules (1:2 or 2:2 guest/host complex). Examples are known in which the guest molecule tumbles within the capsule without disrupting the structure of the capsuleplex. This process makes the two OA molecules that form the capsule magnetically equivalent. In this study, we have examined the dynamics of capsules that host amphiphilic benzylidene-3-methylimidazolidinone molecules as guests. In these capsuleplexes, although the guest does not tumble, the two OA molecules become magnetically equivalent because the two OA molecules that form the capsule exchange their positions in the NMR time scale. This is equivalent to the content of the capsule remaining stationary while the capsule swirls around it. Benzylidene-3-methylimidazolidinones form both 1:1 and 1:2 supramolecular complexes with cavitand OA. Two-dimensional NMR, ROESY, and NOESY data suggest that in a 300 ms time scale, the two halves of the capsule exchange between themselves and with free OA. The conclusion drawn here provides valuable information concerning the stability of the OA capsuleplex and cavitandplex that is used as the well-defined space to control the excited-state chemistry and dynamics of confined guest molecules.

Exploring Cryptococcus neoformans capsule structure and assembly with a hydroxylamine-armed fluorescent probe

Chemical biology is an emerging field that enables the study and manipulation of biological systems with probes whose reactivities provide structural insights. The opportunistic fungal pathogen Cryptococcus neoformans possesses a polysaccharide capsule that is a major virulence factor, but is challenging to study. We report here the synthesis of a hydroxylamine-armed fluorescent probe that reacts with reducing glycans and its application to study the architecture of the C. neoformans capsule under a variety of conditions. The probe signal localized intracellularly and at the cell wall-membrane interface, implying the presence of reducing-end glycans at this location where the capsule is attached to the cell body. In contrast, no fluorescence signal was detected in the capsule body. We observed vesicle-like structures containing the reducing-end probe, both intra- and extracellularly, consistent with the importance of vesicles in capsular assembly. Disrupting the capsule with DMSO, ultrasound, or mechanical shear stress resulted in capsule alterations that affected the binding of the probe, as reducing ends were exposed and cell membrane integrity was compromised. Unlike the polysaccharides in the assembled capsule, isolated exopolysaccharides contained reducing ends. The reactivity of the hydroxylamine-armed fluorescent probe suggests a model for capsule assembly whereby reducing ends localize to the cell wall surface, supporting previous findings suggesting that this is an initiation point for capsular assembly. We propose that chemical biology is a promising approach for studying the C. neoformans capsule and its associated polysaccharides to unravel their roles in fungal virulence.

The gfc operon is involved in the formation of the O antigen capsule in Aeromonas hydrophila and contributes to virulence in channel catfish

A hypervirulent A. hydrophila (vAh) pathotype has been identified as the etiologic agent involved in disease outbreaks in farmed carp and catfish species in China and the Southeastern United States, respectively. To assess the role of the LPS O-antigen in vAh virulence, the O-antigen ligase (waaL) and O-antigen polymerase (wzy) genes were deleted. While neither waaL nor wzy were found to be required for vAh virulence, a waaL mutant was found to have a polar effect on an adjacent group 4 capsule (gfc) genetic operon that was predicted to play a role in capsule assembly. Mutations in the gfc operon attenuated vAh virulence in channel catfish, particularly the mutant lacking gfcD that is predicted to encode an outer membrane protein required for capsular polysaccharide export. Furthermore, the vAh gfcD mutant was found to lack significant biofilm-forming capacity or buoyancy compared to wild-type vAh and induced an adaptive immune response that protected catfish from vAh challenge. This study indicates the importance of the capsular polysaccharide assembly process in the pathogenesis of this highly virulent A. hydrophila pathotype.

Encapsulation driven conformational changes in n-alkanes inside a hydrogen-bonded supramolecular cavitand assembly

Molecular chaperones are known to assist proteins in achieving their native state conformations by providing them a confined environment through encapsulation and altering their free energy landscapes. Instances of structural rearrangements in molecules confined to narrow nano-dimensional spaces are often encountered in vivo where the intermolecular interactions play a decisive role in determining the molecular conformations. As a simple analogue, we model a system of n-alkanes encapsulated into a supramolecular host cavitand forming a capsular host-guest assembly of volume less than half a cubic nanometer. Here, we provide a detailed insight of process of host-induced conformational changes in guests by exploring the conformational dynamics. Interestingly, the conformational analysis reveals that the host apart from being able to fold some of the guests into coiled conformations also unfolds a few of the guests while rearranging its hydrogen-bonded network.

Conformational rearrangements in n-alkanes encapsulated within capsular self-assembly of capped carbon nanotubes

Molecular conformations significantly influence the properties of materials. Both internal interactions as well as external impacts can trigger conformational revamping of molecules. By employing molecular dynamics simulations, here we have investigated shift in conformational motifs of n-alkanes confined within a minuscule hydrophobic cavity of self-sustaining capsular assembly of two capped carbon nanotubes. Depending upon relative host-guest dimensions, encapsulated n-alkanes depict either coiling or uncoiling with further adoption of gauche-rich helical structure or trans-dominated extended configuration. Mutual alkane-CNT and CNT-CNT vdw interactions along with the favorable dehydration of their hydrophobic surfaces drive the formation and sustenance of self-assembly. Further segregation of atomistic-level energetic interactions between host-guest molecules revealed that twisting in longer n-alkanes induces a dihedral strain giving an entropic penalty to the strength of formation of self-assembly, which however gets compensated by enhanced vdw interactions between n-alkanes and aromatic surfaces of capped nanotubes.

Mechanistic Insight into Fast and Highly Efficient Organocatalytic Activity of a Tripodal Dimeric Hexaurea Capsular Assembly in Michael Addition Reactions.

A tris(2-aminoethyl)-amine-based dimeric capsular assembly of pentafluorophenyl urea (C1) has been employed as a catalyst in a wide range of Michael addition reactions. This capsular catalyst assembly dramatically accelerates the Michael addition reaction of β-nitrostyrenes (2a–2d) with various Michael donors such as ketoesters (3a, 3e), 1,3-diketones (3b), diesters (3C), and cyanoesters (3d) at room temperature to yield the corresponding nitroalkanes in significantly high yields within a very short reaction time. Significant improvement in solubility and use of conventional organic solvents in reaction along with a drastic decrease in reaction time (high value of the rate constant of the reaction) has been achieved through C1 as compared to the previously reported homologous tripodal monomeric urea catalyst (L1). The addition of enolate to β-nitrostyrenes to generate an anionic intermediate seemed to be highly stabilized by the six urea units of capsular assembly. Control experiments and in situ kinetic studies are performed for this addition reaction and based on the results, a plausible mechanism has been proposed for the formation of Michael adduct inside the capsular cavity.

Steric influence of adamantane substitution in tris-urea receptor: encapsulation of sulphate and fluoride-water cluster

Abstract Tris(2-aminoethyl)amine (tren)-based bulky adamantane group-substituted tris-urea (L) has been developed as the potential tripodal receptor exhibiting strong binding affinities towards small spherical fluoride anion as well as large tetrahedral sulphate anion in its neutral and protonated form, respectively. Structural elucidation reveals that the divalent sulphate ion is fully engulfed inside the complementary space created by two face-to-face oriented symmetry-independent protonated receptors, whereas the smaller fluoride ion is encapsulated as fluoride-water cluster (\(\hbox {F}^{-}\hbox {-H}_{2}\hbox {O}\)) assemblage within the neutral unimolecular capsular assembly of receptor L. GRAPHICAL ABSTRACT SYNOPSIS Entrapment of Sulphate and fluoride-water cluster within the rigid cavity of adamantine-substituted tris-urea.

Ice-like Cyclic Water Hexamer Trapped within a Halide Encapsulated Hexameric Neutral Receptor Core: First Crystallographic Evidence of a Water Cluster Confined within a Receptor-Anion Capsular Assembly

Over the past few decades, the tren [tris(2-aminoethyl)amine] skeleton has materialized as one of the supreme anion binding building blocks demonstrating a strong interplay among topology, complementarity, cooperativity, and coordination. However, anion recognition by modest tren-based unsubstituted aromatic urea has been underexplored, mainly due to the deficiency of π-acidic or electron-withdrawing aryl terminals. This report establishes an infrequent hexameric neutral receptor-anion-water molecular self-assembly, where a conformationally flexible C3v-symmetric halide (F–/Cl–) encapsulated electron-rich naphthyl group containing N-bridged tripodal urea receptor effectively entraps a chair-shaped ice-like neutral cyclic water hexamer within the hexameric cavity of a neutral receptor-halide host–guest assembly.

Cyclic (H2O)6confined hexameric host–guest assemblies and aerial CO2fixation by electron-rich neutral urea/thiourea scaffolds

Neutral capsular assemblies of electron-rich tris-urea/thiourea receptors are formedviacyclic (H2O)6trapping or atmospheric CO2fixation.

Host-guest complexes of C-propyl-2-bromoresorcinarene with aromatic N-oxides

The host-guest complexes of C-propyl-2-bromoresorcinarene with pyridine N-oxide, 3-methylpyridine N-oxide, quinoline N-oxide and isoquinoline N-oxide are studied using single crystal X-ray crystallography and 1H NMR spectroscopy. The C-propyl-2-bromoresorcinarene forms endo-complexes with the aromatic N-oxides in the solid-state when crystallised from either methanol or acetone. In solution, the endo-complexes were observed only in methanol-d4. In DMSO the solvent itself is a good guest, and crystallisation provides only solvate endo-complexes. The C-propyl-2-bromoresorcinarene shows remarkable flexibility when crystallised from either methanol or acetone, and packs into one-dimensional self-included chains. Of special note, crystallising C-propyl-2-bromoresorcinarene with 3-methylpyridine N-oxide from acetone results in a 2:2 dimeric capsular assembly organised through both C−H···πhost and N−O···(H−O)host interactions.

Supramolecular self-assembly of water-soluble cavitands: investigated by molecular dynamics simulation

In this study, we have examined supramolecular self-assembly process of a hydrophobic guest with a water-soluble host known by the trivial name octa acid (OA). Two octa acids form a capsular assembly only in presence of a nonpolar guest(s). Size and shape of the guest control the stoichiometry of the capsular complex. Here, all atom molecular dynamics simulation has been utilized to investigate complex formation mechanisms of a nonpolar guest (nonylbenzene) with two OA cavitands. Nonylbenzene was encapsulated into the nonpolar cavity of OA capsule owing to solvophobic interactions. Upon encapsulation it was twisted and bent due to lack of free space within the capsule. These unusual forms obtained from the simulation study were in accord with experimental findings. The post-complexation attributes of the guest were regulated by the available free space within the OA and favorable non-covalent interactions between the guest and the walls of the OA capsule. In the identical simulation condition two OA cavitands did not form a capsule without a guest, thus indicating requirement of a guest during the self-assembly of OA cavitands.

Genome analysis of E. coli isolated from Crohn\u2019s disease patients

BackgroundEscherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related.ResultsWe performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons.ConclusionsOur findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.

Systematic size mediated trapping of anions of varied dimensionality within a dimeric capsular assembly of a flexible neutral bis-urea platform.

A rationally designed ortho-phenylenediamine based trifluoromethyl meta-disubstituted bis-urea receptor (L) exhibits effective, consistent and systematic binding in its neutral form towards smaller spherical halides (fluoride, chloride, bromide and iodide), and relatively larger planar carbonate and tetrahedral sulphate oxyanions. All the complexes are well characterized both in the solid-state and solution phase. In the presence of excess fluoride anions, the receptor L encapsulates a hydrated cyclic fluoride-water [F2(H2O)2]2- tetramer inside the n-TBA cation sealed dimeric complementary cavity (complex 1). Whereas excess n-TBA/TEA salts of chloride, bromide and iodide result in unusual (Cl-)2, (Br-)2, and (I-)2 doubly encapsulated 2 : 2 dimeric host-guest complexes (2a, 2b, 3 and 4). Two receptor units encapsulate a carbonate ion, via hydroxide induced aerial CO2 fixation (complex 5), and a sulphate anion (complex 6), respectively, in the presence of excess tetrabutylammonium hydroxide and bisulphate salt. 1H NMR titration and 2D NOESY experiments corroborate the solution-state binding and encapsulation of hydrated/non-hydrated halides and oxyanions via N-HA hydrogen bonding.

Hydrogen-bonded molecular capsules: probing the role of water molecules in capsule formation in modified cyclotricatechylene

Pyridine moiety-appended doubly bridged cyclotricatechylene (CTC(Py)2(OH)2) was synthesized and characterized. Solid state studies show that CTC(Py)2(OH)2 forms a capsular assembly in the presence of water but a polymeric assembly in its absence.

Template-directed self-assembly of dynamic covalent capsules with polar interiors.

Chiral polyimine molecular capsules with polar interiors have been prepared through template covalent dynamic self-assembly. An aryl-extended tetraaldehyde calix[4]pyrrole scaffold was condensed with suitable diamines as linkers using templates for efficient self-assembly. The capsular complexes were characterized in solution, gas phase and the solid-state. Unprecedented transfer of asymmetry was observed from a chiral diamine linker to the resulting supramolecular capsular assembly.