Cage-like Complexes Research Articles

Macrobicyclic Dibridgehead Di(trialkyl)pnictogens E((CH2) n )3E (E/n = As/10, As/12, As/14, Sb/14) and Their Cage-like Metal Complexes: Syntheses, Structures, and Homeomorphic Isomerizations.

Photolyses of trans-Fe(CO)3(As((CH2) n )3As) (n = a, 10; b, 12; c, 14) in the presence of PMe3, or reactions of trans-[Fe(CO)2(NO)(As((CH2) n )3As)]+ BF4 - and n-Bu4N+ Cl-, afford the air stable title complexes As((CH2) n )3As (8a-c) in 79-34% yields. With 8a, the in, in and out, out isomers are separable and each is crystallographically characterized. With 8b,c, the isomers rapidly interconvert by homeomorphic isomerization, but each crystallizes (contrathermodynamically) as an out, out isomer. Reactions of 8c with H2O2 or 8b with BH3 give 8c·2O or 8b·2BH3, respectively (85-94%). Reactions of 8c with MCl2 (M = Pt, Pd, Ni), Rh(CO)(Cl), and Fe(CO)3 sources afford the corresponding cage-like complexes trans-ML n (As((CH2)14)3As) (86-51%). The crystal structures of 8c·2O and the PtCl2 and PdCl2 adducts are determined and compared to those of 8a-c and diphosphorus analogs. The corresponding distibine Sb((CH2)14)3Sb is analogously prepared, but precursors necessary for the bismuth analog could not be accessed due to the diminished BiR3 Lewis basicity.

Exploring Host-Guest Interactions within a 600 kDa DegP Protease Cage Complex Using Hydrodynamics Measurements and Methyl-TROSY NMR.

The DegP protease-chaperone operates within the periplasm of Gram-negative bacteria, where it assists in the regulation of protein homeostasis, promotes virulence, and is essential to survival under stress. To carry out these tasks, DegP forms a network of preorganized apo oligomers that facilitate the capture of substrates within distributions of cage-like complexes which expand to encapsulate clients of various sizes. Although the architectures of DegP cage complexes are well understood, little is known about the structures, dynamics, and interactions of client proteins within DegP cages and the relationship between client structural dynamics and function. Here, we probe host-guest interactions within a 600 kDa DegP cage complex throughout the DegP activation cycle using a model α-helical client protein through a combination of hydrodynamics measurements, methyl-transverse relaxation optimized spectroscopy-based solution nuclear magnetic resonance studies, and proteolytic activity assays. We find that in the presence of the client, DegP cages assemble cooperatively with few intermediates. Our data further show that the N-terminal half of the bound client, which projects into the interior of the cages, is predominantly unfolded and flexible, and exchanges between multiple conformational states over a wide range of time scales. Finally, we show that a concerted structural transition of the protease domains of DegP occurs upon client engagement, leading to activation. Together, our findings support a model of DegP as a highly cooperative and dynamic molecular machine that stabilizes unfolded states of clients, primarily via interactions with their C-termini, giving rise to efficient cleavage.

Stability and hydrogen storage properties of Sc6O8 and Y6O8 cage-like complexes

To study the dihydrogen storage capacity of Sc6O8 and Y6O8 complexes, the stability and hydrogen adsorption behavior have been investigated by using density functional theoretical calculations. The lowest-lying isomers are cage-like complexes Sc6O801 and Y6O801, which are energetically much low-lying by at least 40.43 kcal/mol than the other isomers, respectively. Sc6O801 can adsorb 26H2 with gravimetric uptake capacity of 11.64 wt%. The average adsorption energy (ΔEave) is 0.12 eV/H2, which is in the reversible adsorption range. The Y6O801 seem have little ability to adsorb hydrogen molecules, because the ΔEave Y6O801 (1H2) is just only 0.065 eV. However, the binding capacity increases with the number of adsorbed H2 increasing. Y6O801 can adsorb 32H2 with ΔEave of 0.11 eV/H2, and the gravimetric uptake capacity is 8.89 wt%. Various characterization methods indicate that both transition metals and nonmetals in Sc6O801 and Y6O801 can effectively adsorb hydrogen molecules, and these two compounds can be regarded as candidate materials of dihydrogen adsorption under suitable condition.

Luminescent [Cu8I8L6] wheel and [Cu2I2L3] cage assembled from CuI and 3,6-bis(diphenylphosphino)pyridazine

The reaction of CuI and 3,6-bis(diphenylphosphino)pyridazine (dppz) in MeCN leads to the wheel-shaped complex [Cu8I8(dppz)6], assembled from four [Cu2I2] units and six dppz ligands. This complex exhibits thermochromic luminescence with emission colors ranging from red (300 K) to deep red (77 K). When carried out in the presence of PPh3, the reaction of CuI with dppz gives a non-emissive cage-like complex [Cu2I2(dppz)3], in which two CuI units are P,P′-bridged by three dppz ligands.

Understanding the Chloride Affinity of Barbiturates for Anion Receptor Design.

Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C-H bond is as effective as the N-H bond to coordinate chloride. An analysis of the electron charge density at the C-H⋅⋅⋅Cl- and N-H⋅⋅⋅Cl- bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C-H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together with the C-H bond. We finally show how can we use this information to rationally improve the recognition capability of a small cage-like complex that is able to coordinate NaCl.

Green- and red-phosphorescent Mn(II) iodide complexes derived from 1,3-bis(diphenylphosphinyl)propane

The reaction of 1,3-bis(diphenylphosphinyl)propane (dpppO2) with MnI2, depending on the reactants ratio, affords either 1D coordination polymer, [Mn(dpppO2)I2]n (1), or cage-like complex [Mn2(dpppO2)4I2]l2 (2). Polymer 1 contains Mn(II) ions in a tetrahedral [Mn@O2I2] arrangement, while the metal ions of 2 feature a square-pyramidal [Mn@O4I] geometry. At ambient temperature, 1 emits green phosphorescence (λmax = 530 nm) with unusually short lifetime being 50 µs, while 2 displays long-lived red phosphorescence with λmax = 660 nm and the lifetime of 1400 µs.

Green- and Red-Phosphorescent Mn(Ii) Iodide Complexes Derived from 1,3-Bis(Diphenylphosphinyl)Propane

The reaction of 1,3-bis(diphenylphosphinyl)propane (dpppO 2 ) with MnI 2 , depending on the reactants ratio, affords either 1D coordination polymer, [Mn(dpppO 2 )I 2 ] n ( 1 ), or cage-like complex [Mn 2 (dpppO 2 ) 4 I 2 ]l 2 ( 2 ). Polymer 1 contains Mn(II) ions in a tetrahedral [Mn@O 2 I 2 ] arrangement, while the metal ions of 2 feature a square-pyramidal [Mn@O 4 I] geometry. At ambient temperature, 1 emits green phosphorescence (λ max = 530 nm) with unusually short lifetime being 50 µs, while 2 displays long-lived red phosphorescence with λ max = 660 nm and the lifetime of 1400 µs.

Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex

The hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that inside the LdcI-RavA cage, RavA hexamers adopt an asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations. Cryo-EM reconstructions of free RavA reveal two co-existing structural states: an asymmetric spiral, and a flat C2-symmetric closed ring characterised by two nucleotide-free seams. The closed ring RavA state bears close structural similarity to the pseudo two-fold symmetric crystal structure of the AAA+ unfoldase ClpX, suggesting a common ATPase mechanism. Based on these structures, and in light of the current knowledge regarding AAA+ ATPases, we propose different scenarios for the ATP hydrolysis cycle of free RavA and the LdcI-RavA cage-like complex, and extend the comparison to other AAA+ ATPases of clade 7.

Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B.

In response to the growing threat posed by antibiotic-resistant bacterial strains, extensive research is currently focused on developing antimicrobial agents that target lipid II, a vital precursor in the biosynthesis of bacterial cell walls. The lantibiotic nisin and related peptides display unique and highly selective binding to lipid II. A key feature of the nisin–lipid II interaction is the formation of a cage-like complex between the pyrophosphate moiety of lipid II and the two thioether-bridged rings, rings A and B, at the N-terminus of nisin. To understand the important structural factors underlying this highly selective molecular recognition, we have used solid-phase peptide synthesis to prepare individual ring A and B structures from nisin, the related lantibiotic mutacin, and synthetic analogues. Through NMR studies of these rings, we have demonstrated that ring A is preorganized to adopt the correct conformation for binding lipid II in solution and that individual amino acid substitutions in ring A have little effect on the conformation. We have also analyzed the turn structures adopted by these thioether-bridged peptides and show that they do not adopt the tight α-turn or β-turn structures typically found in proteins.

Synthesis, structure and magnetic properties of two mixed-valence icosanuclear nanocages.

The reactions of 3,3'-bis(5-mercapto-1,2,4-triazole) with Co(ii) and Ni(ii) ions, respectively, gave two nanospheric mixed-valence icosanuclear cage-like complexes [M20L12](SO4)2·6DMF·CH3OH·3H2O (M = Co, 1; Ni, 2) with the in situ generated oxalyldithiosemicarbazide (H4L) as ligand. The eight octahedral M(ii) ions and twelve square-planar M(iii) ions in the two complexes are linked by twelve three-connecting linkers of L4- to build an icosanuclear [MII8MIII12L12]4+ nanocage with an inner cubic MII8 cage core. Their cage skeletons are stable in water. The sulphate anions reside over the cage portals. The magnetic measurements of the two complexes revealed the presence of dominant antiferromagnetic interactions between the metal ions in both complexes.

Orientation dependence of energy absorption and relaxation dynamics of C60in fs-laser pulses

By means of nonadiabatic quantum molecular dynamics it is shown that the amount of energy deposited into ${\mathrm{C}}_{60}$ by a short laser field strongly depends on the molecular orientation with respect to the laser polarization direction. In consequence, subsequent electron-vibration coupling leads to different nuclear relaxation mechanisms with mainly three pathways: (1) excitation of giant ${A}_{g}(1)$ modes (``breathing''), (2) formation of deformed cagelike complexes (``isomers''), and (3) fragmentation predominantly into two large pieces (``fission''). The results are in accord with and nicely explain already existing experimental data. Future experiments are proposed to confirm the detailed predictions.

GroEL and CCT are catalytic unfoldases mediating out-of-cage polypeptide refolding without ATP

Chaperonins are cage-like complexes in which nonnative polypeptides prone to aggregation are thought to reach their native state optimally. However, they also may use ATP to unfold stably bound misfolded polypeptides and mediate the out-of-cage native refolding of large proteins. Here, we show that even without ATP and GroES, both GroEL and the eukaryotic chaperonin containing t-complex polypeptide 1 (CCT/TRiC) can unfold stable misfolded polypeptide conformers and readily release them from the access ways to the cage. Reconciling earlier disparate experimental observations to ours, we present a comprehensive model whereby following unfolding on the upper cavity, in-cage confinement is not needed for the released intermediates to slowly reach their native state in solution. As over-sticky intermediates occasionally stall the catalytic unfoldase sites, GroES mobile loops and ATP are necessary to dissociate the inhibitory species and regenerate the unfolding activity. Thus, chaperonin rings are not obligate confining antiaggregation cages. They are polypeptide unfoldases that can iteratively convert stable off-pathway conformers into functional proteins.

Solvothermal preparation of iron phosphonate cages

Three new iron(III) phosphonate cage-like complexes with [Fe4], [Fe9] and [Fe14] cores have been synthesized by solvothermal reaction with various starting materials. Magnetic studies show overall antiferromagnetic interaction presented in these cages.

Possible cage-like nanostructures formed by amino acids

We report possible cage-like nanostructures formed by a representative amino acid, serine octamers and decamers, determined by binding energy calculations and molecular dynamic simulations using the density functional tight-binding method. We used the l-handed serine to construct complex conformers linked by hydrogen bonds. We found the structures linked by -COOH···O=C- to be the most stable conformers and the calculation of the vibrational modes of complexes further illustrated this result. We attempted to apply our cage-like structures to the delivery of C(20) and cycloserine as model molecules. Our results may shed light on the design of cage-like biocompatible complexes for drug delivery.

The cage effect on assembly of cyclic-bis-(zinc porphyrin) with 5,15-dipyridylporphyrin

An inclusion complex of cyclic bis(zinc porphyrin) 1 with 5,15-dipyridylporphyrin derivative 3 has been designed and constructed. The complex formation is induced by Zn-N coordination, and is robust (Kassoc ∼ 106 L/mol) due to the presence of the cage effect of cyclic bis(zinc porphyrin). The cage-like complex as an entity is stable enough, and also convenient to achieve relative movement between the bis(zinc porphyrin) host and the dipyridylporphyrin guest connected by Zn-N coordination. The characteristics of these assemblies have been demonstrated by 1 H NMR, UV-vis, and fluorescence spectra. The results show its potential applications as a molecular gyroscope in molecular machines.

Synthesis and Preferred All‐syn Conformation of C3‐Symmetrical N‐(Hetero)arylmethyl Triindoles

A new series of C(3)-symmetrical N-(hetero)arylmethyl triindoles has been synthesized in a straightforward procedure. The structure and conformation in the solid state have been determined for three derivatives (3, 4, and 6) by X-ray crystallographic analysis. In all three cases, the molecules adopt a tripodal conformation with all of the flexible arms directed towards the same side, thereby delimiting an inner cavity. Compound 6 crystallizes and forms C(3)-symmetric dimeric cagelike complexes. Guest molecules of chloroform and water are confined within the resulting cavities with stabilization by different intermolecular interactions; this highlights the potential of these compounds in the construction of supramolecular systems. A computational analysis has been performed to predict the most stable conformers. As a general trend, a preference for a conformation with all branches directed to the same side has been predicted. Comparison between theoretical and experimental results indicates that the computational level selected for the present study, B3LYP/6-31G*, is able to reproduce both the minimum energy conformations and the rotation barriers about the N--CH(2) bond.

Self‐Assembly and Anion‐Exchange Properties of a Discrete Cage and 3D Coordination Networks Based on Cage Structures

By using tridentate ligand 4-(3-pyridinyl)-1,2,4-triazole (pytrz), cage-like complexes of {[Cu(mu2-pytrz)2](ClO4)(SO4)0.5C2H5OH.0.25 H2O}6 (1), {[Cu3(mu3-pytrz)4(mu2-Cl)2(H2O)2](ClO4)2Cl(2).2 H2O}n (2), and {[Cu3(mu3-pytrz)3(mu3-O)(H2O)3](ClO4)2.5(BF4)(1.5)5.25 H2O}n (3) have been synthesized with different copper(II) salts. Complex 1 represents the second example of a M6L12 metal-organic octahedron with an overall Th symmetry. Complex 2 is constructed from a 3(8) cage-building unit (CBU) and each CBU connects six neighboring cages to give the first 3D metal-organic framework (MOF) based on octahedral M6L12. Complex 3 is built from Cu24(pytrz)12 CBUs with the trinuclear copper clusters serving as second building units (SBUs) and decorating each corner of the M24L12 polyhedron. The Cu24(pytrz)12 building unit is linked by extra ligands to give an extended 3D framework that has the formula Cu24(pytrz)24 and possesses a CaB6 topology. The mixed anions ClO4- and BF4- in 3 are both included in the inner cavity of the cage and can be completely exchanged by ClO4- through the open windows of the cage, as evidenced by the crystal structure of the 3D MOF {[Cu3(mu3-pytrz)3(mu3-O)(H2O)3](ClO4)(4)4.5 H2O}n (4). Complex 4 can also be synthesized when employing 1 as a precursor in an extensive study of the anion-exchange reaction. This represents the first successful conversion of a discrete cage into a 3D coordination network based on a cage structure. Complex 2 remains invariable during anion-exchange reactions because uncoordinated Cl- ions are located in the comparatively small inner cavity.

Syntheses, Structures, and Properties of Novel Cagelike Complexes Based on Dodecanuclear Lanthanide with a Large Cavity

The syntheses, crystal structures, thermal gravimetric analyses (TGA), and magnetic properties of three novel hybrid organic−inorganic dodecanuclear lanthanide-based complexes, [Ln12Na(L)5 (HL) (μ4-NO3)6(μ3-OH)2(μ2-H2O)6(H2O)12]·(H2O)n (Ln = La (1), n = 23.5; Pr (2) and Nd (3), n = 39; L = 2-hydroxy-5-methyl-m-phenylenedimethylenedinitrilotetraacetate anion), are reported. X-ray diffraction analyses revealed that three complexes were isostructural, exhibited C3 symmetry, and crystallized in the rhombohedral crystal system, space group R3. In 1−3, 12 lanthanide atoms regularly arrayed and aggregated into a closed capsule-like cage by anion-bridged ligands containing polycarboxylate, phenolate, nitrate, and hydroxyl groups. Remarkably, these nanosized discrete molecular cages afford large three-compartment cavities with [Na(H2O)6]+ ions encapsulated in the center site.

Cage-like complexes formed by DOTAP, Quil-A and cholesterol

In this note we describe the substitution of the phospholipid component in classical ISCOMs (immune-stimulating complexes) with the cationic lipid dioleoyl-trimethyl-ammonium-propane (DOTAP). The self-assembled colloidal structures formed by DOTAP, Quil-A and cholesterol were characterised using transmission electron microscopy and laser Doppler velocimetry. Samples were prepared using the lipid-film hydration and dialysis techniques. Cage-like structures containing DOTAP were obtained in high numbers using dialysis, but not lipid-film hydration on day 4 post-preparation. The formation of cage-like structures was however only observed at compositions with low weight proportions of DOTAP (less than 25%) resulting in neutral to negative ζ-potentials of the colloidal particles. Compositions with high weight proportions of DOTAP displayed phase separation phenomena. Thus, whilst DOTAP can be incorporated with Quil-A and cholesterol to form cage-like particles, it appears to be unsuitable to prepare cationic equivalents of ISCOMs.

Cationic cage-like complexes formed by DC-cholesterol, Quil-A, and phospholipid

This study describes the formation of cationic, cage-like complexes which have a structure similar to classic anionic ISCOMs. In order to prepare these complexes cholesterol, a major component of classic ISCOM formulations, was substituted with a cationic derivative, 3β-[N-(N′,N′-dimethylaminoethane)-carbamoyl]-cholesterol (DC-CHOL). Colloidal dispersions with varying compositions of DC-CHOL, phosphatidylcholine, and Quil-A, which is a mixture of anionic triterpene saponins, were prepared by the lipid-film hydration method and characterised by transmission electron microscopy and laser Doppler electrophoresis. The colloidal structures obtained are presented in pseudo-ternary phase diagrams with two buffer systems as the pseudo-component. It was found that the formation of cationic, cage-like particles is highly depending on the formulation buffer. With TRIS buffered saline (TBS) pH 7.4, cage-like particles formed at compositions with high proportions of DC-CHOL and had a strongly positive zeta-potential. These could be purified by differential centrifugation. With phosphate buffered saline pH 7.4, the formation of cage-like particles was much reduced. It was shown that the formation of cage-like particles with a positive charge depended on suitable concentrations of TRIS in the hydration buffer.