Covalent Capture: Merging Covalent and Noncovalent Synthesis

The post-synthesis modification (PSM) of MOFs for catalysis

While there are myriad ways to construct metal-organic framework (MOF) based catalysts, the introduction of catalytic functionality via covalent post-synthesis functionalization (PSM) offers multiple advantages: (i) a wide range of different catalyst types are generated from a handful of well-known parent MOFs, (ii) MOF catalyst properties can be systematically tuned while changing few variables, and (iii) catalytically active functional groups that would otherwise interfere with MOF assembly can be introduced facilely. This last advantage is particularly crucial for our quest to generate MOF active sites that are decorated with multiple functional groups capable of cooperative activity, analogous to enzyme active sites.

Calming the Nerves via the Immune Instructive Physiochemical Properties of Self-Assembling Peptide Hydrogels

Current therapies for the devastating damage caused by traumatic brain injuries (TBI) are limited. This is in part due to poor drug efficacy to modulate neuroinflammation, angiogenesis and/or promoting neuroprotection and is the combined result of challenges in getting drugs across the blood brain barrier, in a targeted approach. The negative impact of the injured extracellular matrix (ECM) has been identified as a factor in restricting post-injury plasticity of residual neurons and is shown to reduce the functional integration of grafted cells. Therefore, new strategies are needed to manipulate the extracellular environment at the subacute phase to enhance brain regeneration. In this review, potential strategies are to be discussed for the treatment of TBI by using self-assembling peptide (SAP) hydrogels, fabricated via the rational design of supramolecular peptide scaffolds, as an artificial ECM which under the appropriate conditions yields a supramolecular hydrogel. Sequence selection of the peptides allows the tuning of these hydrogels' physical and biochemical properties such as charge, hydrophobicity, cell adhesiveness, stiffness, factor presentation, degradation profile and responsiveness to (external) stimuli. This review aims to facilitate the development of more intelligent biomaterials in the future to satisfy the parameters, requirements, and opportunities for the effective treatment of TBI.

Exploitation of Catalytic Dyads by Short Peptide-Based Nanotubes for Enantioselective Covalent Catalysis

Extant enzymes with precisely arranged multiple residues in their three-dimensional binding pockets are capable of exhibiting remarkable stereoselectivity towards a racemic mixture of substrates. However, how early protein folds that possibly featured short peptide fragments facilitated enantioselective catalytic transformations important for the emergence of homochirality still remains an intriguing open question. Herein, enantioselective hydrolysis was shown by short peptide-based nanotubes that could exploit multiple solvent-exposed residues to create chiral binding grooves to covalently interact and subsequently hydrolyse one enantiomer preferentially from a racemic pool. Single or double-site chiral mutations led to opposite but diminished and even complete loss of enantioselectivities, suggesting the critical roles of the binding enthalpies from the precise localization of the active site residues, despite the short sequence lengths. This work underpins the enantioselective catalytic prowess of short peptide-based folds and argues their possible role in the emergence of homochiral chemical inventory.

Covalent Capture of a Collagen Mimetic Peptide with an Integrin-Binding Motif

Collagen mimetic peptides (CMPs) are an excellent model to study the structural and biological properties of the extracellular matrix (ECM) due to ease of synthesis and variability in sequence. To ensure that synthetic materials accurately mimic the structure and function of natural collagen in the ECM, it is necessary to conserve the triple helix. However, CMP folding is subject to equilibrium, and frequently peptides exist in solution as both monomer and triple helix. Additionally, the stability of CMPs is highly dependent on peptide length and amino acid composition, leading to suboptimal performance. Here, we report the utility of covalent capture, a method to (a) direct the folding of a supramolecular triple helix and (b) form isopeptide bonds between the helix strands, in the design of an integrin-binding peptide with a GFOGER motif. Covalent capture effectively locked the triple helix and yielded a peptide with high thermal stability and a rapid folding rate. Compared to supramolecular triple helices bearing the same GFOGER-binding site, cell adhesion was substantially increased. In vitro assays using EDTA/Mg²⁺ and an anti-α2β1 antibody demonstrated the preservation of the high specificity of the binding event. This covalently captured integrin-binding peptide provides a template for the future design of bioactive ECM mimics, which can overcome limitations of supramolecular approaches for potential drug and biomaterial designs.

Selective covalent capture of collagen triple helices with a minimal protecting group strategy

A minimal protecting group strategy is developed to allow selective covalent capture of collagen-like triple helices. This allows stabilization of this critical fold while preserving charge–pair interactions critical for biological applications.

Self-assembly of chiral BINOL cages via imine condensation

Condensation of an (S)- or (R)-BINOL-derived dialdehyde and tris(2-aminoethyl)amine produced chiral [2+3] imine cages, which were further reduced to furnish more stable chiral amine cages and applied in the enantioselective recognition of (1R,2R)- and (1S,2S)-1,2-diaminocyclohexane.

Electrochemical sensing behavior of graphdiyne nanoflake towards uric acid: a quantum chemical approach

Though the gas sensing applications of graphdiyne have widely reported; however, the biosensing utility of graphdiyne needs to be explored. This study deals with the sensitivity of graphdiyne nanoflake (GDY) towards the uric acid (UA) within the density functional framework. The uric acid is allowed to interact with graphdiyne nanoflake from all the possible orientations. Based on these interacting geometries, the complexes are differentiated with naming, i.e., UA1@GDY, UA2@GDY, UA3@GDY, and UA4@GDY (Fig. 1). The essence of interface interactions of UA on GDY is derived by computing geometric, energetic, electronic, and optical properties. The adsorbing affinity of complexes is evaluated at ωB97XD/6-31 + G(d, p) level of theory. The stabilities of the complexes are quantified through the interaction energies (E_int) with reasonable accuracy. The calculated E_int of the UA1@GDY, UA2@GDY, UA3@GDY, and UA4@GDY complexes are - 31.13, - 25.87, - 20.59, and - 16.54 kcal/mol, respectively. In comparison with geometries, it is revealed that the higher stability of complexes is facilitated by π-π stacking. Other energetic analyses including symmetry adopted perturbation theory (SAPT), noncovalent interaction index (NCI), and quantum theory of atoms in molecule (QTAIM) provide the evidence of dominating dispersion energy in stabilizing the resultant complexes. The HOMO-LUMO energies, NBO charge transfer, and UV-vis analysis justify the higher electronic transition in UA1@GDY, plays a role of higher sensitivity of GDY towards the π-stacked geometries over all other possible interaction orientations. The present findings bestow the higher sensitivity of GDY towards uric acid via π-stacking interactions. Fig. 1 Optimized geometries (with interaction distances in Å) of UA@GDY complexes.

Enhanced Stability of Peptide Nanofibers Coated with a Conformal Layer of Polydopamine

The susceptibility of self-assembled materials to changes of environmental conditions and mechanical forces often limits their utility for many applications. In this work, the surface of nanofibers formed by β-sheet peptide self-assemblies were coated by polydopamine (PDA) deposition. This conformal coating process rendered the nanofiber dimensions and internal π-stacking chirality impervious to changes in pH, temperature, and physical processing by spin-coating onto a silicon wafer. Whereas sonication-induced shearing of the dopamine/naphthalenediimide-dilysine (DA/NDI-KK) composite irreversibly shortened the nanofibers into 100-200 nm segments, the uncoated nanofibers unraveled into single strands upon similar treatment. Additionally, the PDA-coated nanofibers could be wrapped by an additional layer comprised of a positively charged polyelectrolyte polymer.

Antiparallel Dynamic Covalent Chemistries

The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we introduce the concept of antiparallel chemistries, in which the same functional group can be channeled into one of two reversible chemistries depending on a controllable parameter. Such systems allow both for achieving complexity, by combinatorial chemistry, and addressing it, by switching from one chemistry to another by controlling an external parameter. In our design the two antiparallel chemistries are thiol-disulfide exchange and thio-Michael addition, sharing the thiol as the common building block. By means of oxidation and reduction the system can be reversibly switched from predominantly thio-Michael chemistry to predominantly disulfide chemistry, as well as to any intermediate state. Both chemistries operate in water, at room temperature, and at mildly basic pH, which makes them a suitable platform for further development of systems chemistry.

Control of the reversibility during boronic ester formation: application to the construction of ferrocene dimers and trimers

Equilibration of boronic esters during boronic ester formation was controlled using protic or aprotic solvents under neutral conditions.

Directional Molecular Transportation Based on a Catalytic Stopper-Leaving Rotaxane System

Ratchet mechanism has proved to be a key principle in designing molecular motors and machines that exploit random thermal fluctuations for directional motion with energy input. To integrate ratchet mechanism into artificial systems, precise molecular design is a prerequisite to control the pathway of relative motion between their subcomponents, which is still a formidable challenge. Herein, we report a straightforward method to control the transportation barrier of a macrocycle by selectively detaching one of the two stoppers using a novel DBU-catalyzed stopper-leaving reaction in a rotaxane system. The macrocycle was first allowed to thread onto a semidumbbell axle from the open end and subsequently thermodynamically captured into a nonsymmetrical rotaxane. Then, it was driven energetically uphill until it reached a kinetically trapped state by destroying its interaction with ammonium site, and was finally quantitatively released from the other end when the corresponding stopper barrier was removed. Although the directional transportation at the present system was achieved by discrete chemical reactions for the sake of higher transportation efficiency, it represents a new molecular transportation model by the strategy of using stopper-leavable rotaxane.

A molecular pulley based on a triply interlocked [2]rotaxane

A novel triply interlocked [2]rotaxane was designed and synthesized, which showed pulley-like shuttling motion controlled by acid and base.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Synthesis of polymeric ladders by topochemical polymerization

Two polymeric ladders were synthesized by topochemical polymerization. The critical assemblies with multiple reactive centers were characterized by single crystal X-ray diffraction. Approximately 64% and 70% of the mass of the two polymeric ladders can be derived from biomass, respectively.

Surface modification of supramolecular nanotubes and selective guest capture

Supramolecular nanotubes have been covalently post-modified to show high adsorption capacity and selective adsorption of anionic dyes with easy regeneration.

Relationship between chemical structure and supramolecular effective molarity for formation of intramolecular H-bonds

Effective molarity (EM) is a key parameter that determines the efficiency of a range of supramolecular phenomena from the folding of macromolecules to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramolecular H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramolecular architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the experiments described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chemical double-mutant cycles were used to dissect the thermodynamic contributions of individual H-bond interactions to the overall stabilities of the complexes and hence determine the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramolecular EMs are independent of solvent and intrinsic H-bond strength but depend on supramolecular architecture and geometric complementarity.

On-surface azide-alkyne cycloaddition on Cu(111): does it "click" in ultrahigh vacuum?

Using scanning tunneling microscopy, we demonstrate that the 1,3-dipolar cycloaddition between a terminal alkyne and an azide can be performed under solvent-free ultrahigh vacuum conditions with reactants adsorbed on a Cu(111) surface. XPS shows significant degradation of the azide upon adsorption, which is found to be the limiting factor for the reaction.

Applications of reversible covalent chemistry in analytical sample preparation

Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.

The assessment and application of an approach to noncovalent interactions: the energy decomposition analysis (EDA) in combination with DFT of revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set

An assessment study is presented about energy decomposition analysis (EDA) in combination with DFT including revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set. There has been little knowledge about the performance of the EDA + DFT-D3 concerning STOs. In this assessment such an approach was applied to calculate noncovalent interaction energies and their corresponding components. Complexes in S22 set were used to evaluate the performance of EDA in conjunction with four representative types of GGA-functionals of DFT-D3 (BP86-D3, BLYP-D3, PBE-D3 and SSB-D3) with three STO basis sets ranging in complexity from DZP, TZ2P to QZ4P. The results showed that the approach of EDA + BLYP-D3/TZ2P has a better performance not only in terms of calculating noncovalent interaction energy quantitatively but also in analyzing corresponding energy components qualitatively. This approach (EDA + BLYP-D3/TZ2P) was thus applied further to two representative large-system complexes including porphine dimers and fullerene aggregates to gain a better insight into binding characteristics.

Inter-chain acyl transfer reaction in a peptide six-helical bundle: a chemical method for regulating the interaction between peptides or proteins

An inter-helical acyl transfer specifically occurred between the C-and N-peptides of HIV gp41 after assembly of the six-helical bundle (6HB), forming an inter-helical covalent bond that greatly enhanced 6HB stability. In the reaction, the C-peptide was modified as an acyl donor, and the N-peptide served as an acyl acceptor.