Supramolecular Arrangement and DFT analysis of Zinc(II) Schiff Bases: An Insight towards the Influence of Compartmental Ligands on Binding Interaction with Protein

We report, for the first time, a detailed crystallographic study of the supramolecular arrangement for a set of zinc(II) Schiff base complexes containing the ligand 2,6-bis((E)-((2-(dimethylamino)ethyl)imino)methyl)-4-R-phenol], where R=methyl/tert-butyl/chloro. The supramolecular study acts as a pre-screening tool for selecting the compartmental ligand R of the Schiff base for effective binding with a targeted protein, bovine serum albumin (BSA). The most stable hexagonal arrangement of the complex [Zn − Me] (R=Me) stabilises the ligand with the highest FMO energy gap (ΔE=4.22 eV) and lowest number of conformations during binding with BSA. In contrast, formation of unstable 3D columnar vertebra for [Zn − Cl] (R=Cl) tend to activate the system with lowest FMO gap (3.75 eV) with highest spontaneity factor in molecular docking. Molecular docking analyses reported in terms of 2D LigPlot+ identified site A, a cleft of domains IB, IIIA and IIIB, as the most probable protein binding site of BSA. Arg144, Glu424, Ser428, Ile455 and Lys114 form the most probable interactions irrespective of the type of compartmental ligands R of the Schiff base whereas Arg185, Glu519, His145, Ile522 act as the differentiating residues with ΔG=−7.3 kcal mol⁻¹.     

Dynamic Interactions in Synthetic Receptors: A Guest Exchange Saturation Transfer Study

The accumulated knowledge regarding molecular architectures is based on established, reliable, and accessible analytical tools that provide robust structural and functional information on assemblies. However, both the dynamicity and low population of noncovalently interacting moieties within studied molecular systems limit the efficiency and accuracy of traditional methods. Herein, the use of a saturation transfer-based NMR approach to study the dynamic binding characteristics of an anion to a series of synthetic receptors derived from bambusuril macrocycles is demonstrated. The exchange rates of BF₄⁻ are mediated by the side chains on the receptor (100 s⁻¹<k_ex<5000 s⁻¹), which play a critical role in receptor-anion binding dynamics. The signal amplification obtained with this approach allows for the identification of different types of intermolecular interactions between the receptor and the anion, something that could not have been detected by techniques hitherto used to study molecular assemblies. These findings, which are supported by a computational molecular dynamic study, demonstrate the uniqueness and added value of this NMR method.     

Deciphering Internal and External π-Conjugation in C3-Symmetric Multiple Azobenzene Connected Systems in Self-Assembly

Two tripodal C₃-symmetric photoswitchable molecular systems T1 and T2 are reported that have extended conjugation at external and internal positions using an acryl group. The influence of the extended π-bonds in their absorption properties, thermal relaxation of the photoisomers and their propensities in forming supramolecular self-assemblies have been explored through spectroscopy, and microscopic studies. In particular, the investigations on the self-assembly have been carried out using scanning electron microscopy (SEM), transmission electron microscopy (TEM), polarized optical microscopy (POM), X-ray diffraction studies (XRD) and atomic force microscopy (AFM). Remarkably, the position of the acryl group influences the behaviour of the two target molecules in supramolecular assembly, and also in the formation of photoresponsive organic hydrogels or microcrystals.     

The Special “Morse Code” between Solvent Polarity and Morphology Flexibility in a POSS–Dendrimer Supramolecular System

An amazing phenomenon of the relative magnitude of modulus of two liquid-crystal (LC) gels is found inverted under/above their phase transition temperature T_LC-iso, which is further proved to be caused by their diverse morphology flexibility. By testing the polarity of two LCs, gelator POSS-G1-Boc (POSS=polyhedral oligomeric silsesquioxane) was discovered to self-assemble into more flexible structures in a relatively low polar LC, whereas more rigid ones are formed in higher polar LC. Hence, a fitting function to connect morphology flexibility with solvent polarity was established, which can even be generalized to a number of common solvents. Experimental observations and coarse-grained molecular dynamics simulations revealed that solvent polarity mirrors a “Morse code”, with each “code” corresponding to a specific morphology flexibility.     

A Self-Assembled Cage with Endohedral Acid Groups both Catalyzes Substitution Reactions and Controls Their Molecularity

A self-assembled Fe₄L₆ cage complex internally decorated with acid functions is capable of accelerating the thioetherification of activated alcohols, ethers and amines by up to 1000-fold. No product inhibition is seen, and effective supramolecular catalysis can occur with as little as 5 % cage. The substrates are bound in the host with up to micromolar affinities, whereas the products show binding that is an order of magnitude weaker. Most importantly, the cage host alters the molecularity of the reaction: whereas the reaction catalyzed by simple acids is a unimolecular, S_N1-type substitution process, the rate of the host-mediated process is dependent on the concentration of nucleophile. The molecularity of the cage-catalyzed reaction is substrate-dependent, and can be up to bimolecular. In addition, the catalysis can be prevented by a large excess of nucleophile, where substrate inhibition dominates, and the use of tritylated anilines as substrates causes a negative feedback loop, whereby the liberated product destroys the catalyst and stops the reaction.     

Self-Assembly of C3 Symmetric Rigid Macrolactams into Very Polar and Porous Trigonal Crystals

Cyclohexane and cyclotri-β-alanyl have been used as scaffolds for the design of new C₃-symmetric rings incorporating conjugated alkenes and dienes. All three C₃-symmetric lactams share the same triangular shape and their crystal system is trigonal. They all belong to the R3 space group, R3m, R3 and R3c, for the increasingly large 12-, 18- and 24-membered rigid rings, respectively. All lactams stack on top of each other, through H-bonds and van der Waals noncovalent interactions, leading to endless supramolecular cylinders and tubes. The largest member of the family leads to tubes, the central pores of which is wide enough to let water in. A common feature of all the lactams is their very large dipole, of around 9 D, according to DFT calculations. Surprisingly, all the resulting cylinders and tubes pack side by side in the crystals, with all the dipoles pointing to the same direction. As a result, all three crystals are anisotropic and appear to be the first members of a new kind of highly polar crystals.     

Seeded Polymerization of an Amide-Functionalized Diketopyrrolopyrrole Dye in Aqueous Media

The self-assembly of an amide-functionalized dithienyldiketopyrrolopyrrole (DPP) dye in aqueous media was achieved through seed-initiated supramolecular polymerization. Temperature- and time-dependent studies showed that the spontaneous polymerization of the DPP derivative was temporally delayed upon cooling the monomer solution in a methanol/water mixture. Theoretical calculations revealed that an amide-functionalized DPP derivative adopts an energetically favorable folded conformation in the presence of water molecules due to hydration. This conformational change is most likely responsible for the trapping of monomers in the initial stage of the cooperative supramolecular polymerization in aqueous media. However, the monomeric species can selectively interact with externally added fragmented aggregates as seeds through concerted π-stacking and hydrogen-bonding interactions. Consequently, the time course of the supramolecular polymerization and the morphology of the aggregated state can be controlled, and one-dimensional fibers that exhibit a J-aggregate-like bathochromically shifted absorption band can be obtained.     

Exploration of Nano-Saturns: A Spectacular Sphere–Ring Supramolecular System

Saturn-like systems consisting of nanoscale rings and spheres are fascinating motifs in supramolecular chemistry. Several ring molecules are known to include spherical molecules at the center of the cavity via noncovalent attractive interactions. In this Minireview, we generalize the molecular design, the structural features, and the supramolecular chemistry of such “nano-Saturns”, which consist of monocyclic rings and fullerene spheres (mainly C₆₀), on the basis of previous experimental and theoretical studies. Ring molecules are classified into three types (loop, belt, and disk) according to their shapes and possible interactions. Whereas typical belt-shaped rings tend to form tight complexes due to the wide contact area via π–π interactions, flat disk-shaped rings generally form weak complexes due to the narrow contact area mainly via CH–π interactions. In spite of the small association energies, disk-shaped rings are attractive because such rings can mimic the planet Saturn precisely as exemplified by an anthracene cyclic hexamer–C₆₀ complex.     

How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity?

Cucurbit[7]uril (CB[7]) is known to bind strongly to hydrophilic amino saccharide guests with exceptional α‐anomer selectivities under aqueous conditions. Single‐crystal X‐ray crystallography and computational methods were used to elucidate the reason behind this interesting phenomenon. The crystal structures of protonated galactosamine (GalN) and glucosamine (GluN) complexes confirm the inclusion of α anomers inside CB[7] and disclose the details of the host–guest binding. Whereas computed gas‐phase structures agree with these crystal structures, gas‐phase binding free energies show preferences for the β‐anomer complexes over their α counterparts, in striking contrast to the experimental results under aqueous conditions. However, when the solvation effect is considered, the binding structures drastically change and the preference for the α anomers is recovered. The α anomers also tend to bind more tightly and leave less space in the CB[7] cavity toward inclusion of only one water molecule, whereas loosely bound β anomers leave more space toward accommodating two water molecules, with markedly different hydrogen‐bonding natures. Surprisingly, entropy seems to contribute significantly to both anomeric discrimination and binding. This suggests that of all the driving factors for the strong complexation of the hydrophilic amino saccharide guests, water mediation plays a crucial role in the anomer discrimination.     

New Perspectives for Old Clusters: Anderson–Evans Anions as Building Blocks of Large Polyoxometalate Frameworks in a Series of Heterometallic 3 d–4 f Species

A series of nine [Sb₇W₃₆O₁₃₃Ln₃M₂(OAc)(H₂O)₈]^17? heterometallic anions ( Ln₃M₂ ; Ln=La–Gd, M=Co; Ln=Ce, M=Ni and Zn) have been obtained by reacting 3 d metal disubstituted Krebs‐type tungstoantimonates(III) with early lanthanides. Their unique tetrameric structure contains a novel {MW₉O₃₃} capping unit formed by a planar {MW₆O₂₄} fragment to which three {WO₂} groups are condensed to form a tungstate skeleton identical to that of a hypothetical trilacunary derivative of the ?‐Keggin cluster. It is shown, for the first time, that classical Anderson–Evans {MW₆O₂₄} anions can act as building blocks to construct purely inorganic large frameworks. Unprecedented reactivity in the outer ring of these disk‐shaped species is also revealed. The Ln₃M₂ anions possess chirality owing to a {Sb₄O₄} cluster being encapsulated in left‐ or right‐handed orientations. Their ability to self‐associate in blackberry‐type vesicles in solution has been assessed for the Ce₃Co₂ derivative.