Diverse Proteomimetic Frameworks via Rational Design of π-Stacking Peptide Tectons

Peptide-based frameworks aim to integrate protein architecture into solid-state materials using simpler building blocks. Despite the growing number of peptide frameworks, there are few strategies to rationally engineer essential properties like pore size and shape. Designing peptide assemblies is generally hindered by the difficulty of predicting complex networks of weak intermolecular interactions. Peptides conjugated to polyaromatic groups are a unique case where assembly appears to be strongly driven by π-π interactions, suggesting that rationally adjusting the geometry of the π-stackers could create novel structures. Here, we report peptide elongation as a simple mechanism to predictably tune the angle between the π-stacking groups to produce a remarkable diversity of pore shapes and sizes, including some that are mesoporous. Notably, rapid jumps in pore size and shape can occur with just a single amino acid insertion. The geometry of the π-stacking residues also significantly influences framework structure, representing an additional dimension for tuning. Lastly, sequence identity can also indirectly modulate the π-π interactions. By correlating each of these factors with detailed crystallographic data, we find that, despite the complexity of peptide structure, the shape and polarity of the tectons are straightforward predictors of framework structure. These guidelines are expected to accelerate the development of advanced porous materials with protein-like capabilities.

Stereoselective Amine-omics Using Heavy Atom Isotope Labeled l- and d-Marfey's Reagents

Biological amines and amino acids play essential roles in many biochemical processes. The chemical complexity of biological samples is challenging, and the selective identification and quantification of amines and amino acid stereoisomers would be very useful for amine-focused "amino-omics" studies. Many amines and amino acids are chiral, and their stereoisomers cannot be resolved on achiral media without chiral derivatization. In prior studies, we demonstrated the use of Marfey's reagent─a chiral derivatization reagent for amines and phenolic OH groups─for the LC-MS/MS resolution and quantification of amines and amino acid stereoisomers. In this study, a heavy atom isotope labeled Marfey's reagent approach for the stereoselective detection and quantification of amines and amino acids was developed. Heavy (13C2) l-Marfey's (Hl-Mar) and heavy (2H3) d-Marfey's (Hd-Mar) were synthesized from 13C2-l-Ala and 2H3-d-Ala, respectively. Both light and heavy Marfey's reagents were used to derivatize standard amine mixtures, which were analyzed by LC-QToF-HRMS. Aligned peak lists were comparatively analyzed by light vs heavy Mar mass differences to identify mono-, di-, and tri-Marfey's adducts and then by the retention time difference between l- and d-Mar derivatives to identify stereoisomers. This approach was then applied to identify achiral and chiral amine and amino acid components in a methicillin-resistant Staphylococcus aureus (MRSA) extract. This approach shows high analytical selectivity and reproducibility.

Peptide hydrogen-bonded organic frameworks

Hydrogen-bonded porous frameworks (HPFs) are versatile porous crystalline frameworks with diverse applications. However, designing chiral assemblies or biocompatible materials poses significant challenges. Peptide-based hydrogen-bonded porous frameworks (P-HPFs) are an exciting alternative to conventional HPFs due to their intrinsic chirality, tunability, biocompatibility, and structural diversity. Flexible, ultra-short peptide-based P-HPFs (composed of 3 or fewer amino acids) exhibit adaptable porous topologies that can accommodate a variety of guest molecules and capture hazardous greenhouse gases. Longer, folded peptides present challenges and opportunities in designing P-HPFs. This review highlights recent developments in P-HPFs using ultra-short peptides, folded peptides, and foldamers, showcasing their utility for gas storage, chiral recognition, chiral separation, and medical applications. It also addresses design challenges and future directions in the field.

A New Unnatural Amino Acid Derived from the Modification of 4′-(p-tolyl)-2,2′:6′,2″-terpyridine and Its Mixed-Ligand Complexes with Ruthenium: Synthesis, Characterization, and Photophysical Properties

The modification of the methyl group of 4′-(p-tolyl)-2,2′:6′,2″-terpyridine produced the novel unnatural amino acid 3-(4-([2,2′:6′,2″-terpyridin]-4′-yl)phenyl)-2-aminopropanoic acid (phet). Mononuclear heteroleptic ruthenium complexes of the general formulae [Ru(L1)(L2)](PF6)2 (L1 = 2-acetylamino-2-(4-[2,2′:6′,2″]terpyridine-4′-yl-benzyl)-malonic acid diethyl ester, (phem), 3-(4-([2,2′:6′,2″-terpyridin]-4′-yl)phenyl)-2-aminopropanoic acid, (phet), and L2 = 2,2′:6′,2″-terpyridine (tpy), 4′-phenyl-2,2′:6′,2″-terpyridine (ptpy), 4′-(p-tolyl)-2,2′:6′,2″-terpyridine (mptpy)), as well as the homoleptic [Ru(phem)2](PF6)2 and [Ru(phet)2](PF6)2, were synthesized and characterized by means of NMR spectroscopic techniques, elemental analysis, and high-resolution mass spectrometry. The photophysical properties of the synthesized complexes were also studied.

A Reversibly Porous Supramolecular Peptide Framework

The ability to use bio-inspired building blocks in the assembly of novel supramolecular frameworks is at the forefront of an exciting research field. Herein, we present the first polyproline helix to self-assemble into a reversibly porous, crystalline, supramolecular peptide framework (SPF). This framework is assembled from a short oligoproline, adopting the polyproline II conformation, driven by hydrogen-bonding and dispersion interactions. Thermal activation, guest-induced dynamic porosity and enantioselective guest inclusion have been demonstrated for this novel system. The principles of the self-assembly associated with this SPF will be used as a blueprint allowing for the further development of helical peptide linkers in the rational design of SPFs and metal-peptide frameworks.

Supramolecular helical self-assembly of small peptides

In this highlight, we describe the construction of supramolecular single/double/triple-helical assemblies from small di/tri/tetrapeptides and their applications.

Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials

Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.

One-Pot Biocatalytic Preparation of Enantiopure Unusual α-Amino Acids from α-Hydroxy Acids via a Hydrogen-Borrowing Dual-Enzyme Cascade

Unusual α-amino acids (UAAs) are important fundamental building blocks and play a key role in medicinal chemistry. Here, we constructed a hydrogen-borrowing dual-enzyme cascade for efficient synthesis of UAAs from α-hydroxy acids (α-HAs). D-mandelate dehydrogenase from Lactobacillus brevis (LbMDH) was screened for the catalysis of α-HAs to α-keto acids but with low activity towards aliphatic α-HAs. Therefore, we rational engineered LbMDH to improve its activity towards aliphatic α-HAs. The substitution of residue Leu243 located in the substrate entrance channel with nonpolar amino acids like Met, Trp, and Ile significantly influenced the enzyme activity towards different α-HAs. Compared with wild type (WT), variant L243W showed 103 U/mg activity towards D-α-hydroxybutyric acid, 1.7 times of the WT’s 60.2 U/mg, while its activity towards D-mandelic acid decreased. Variant L243M showed 2.3 times activity towards D-mandelic acid compared to WT, and its half-life at 40 °C increased to 150.2 h comparing with 98.5 h of WT. By combining LbMDH with L-leucine dehydrogenase from Bacillus cereus, the synthesis of structurally diverse range of UAAs from α-HAs was constructed. We achieved 90.7% conversion for L-phenylglycine production and 66.7% conversion for L-α-aminobutyric acid production. This redox self-sufficient cascade provided high catalytic efficiency and generated pure products.

Metal hydrogen-bonded organic frameworks: structure and performance

Although great progress has been made in the design, synthesis, and performance expansion of porous materials, new porous materials with stable structures still need to be explored further. In recent years, porous molecular crystals formed by intermolecular interactions have attracted wide attention from chemists, especially metal hydrogen-bonded organic frameworks (M-HOFs) formed by connecting metal complexes through hydrogen bonds. Metal complexes with specific properties (e.g., magnetism, luminescence, sensing, and catalysis) can expand and develop the application of M-HOFs further. However, the huge volume, irregular shape, complex coordination modes, and interference of coordination bonds pose certain challenges in the synthesis and performance expansion of M-HOFs. In this frontier, we summarize the latest progress in the use of 3d, 4d, and 4f metal complexes for the synthesis of M-HOFs, and briefly introduce the performance expansion of these M-HOFs, which is expected to help expand new porous materials with stable structures and specific functions.

Preparation of Hierarchically Assembled Silver Nanostructures based on the Morphologies of Crystalline Peptide-Silver(I) Complexes

The preparation of a hierarchically assembled Ag nanostructures based on a nanocrystalline assembly was demonstrated using an Ag(I) complex of a dipeptide (AspDap). By heating under N₂ gas, a spherical assembly of a nanocrystalline dipeptide-Ag(I) complex (diameter 4-5 μm), which has a morphology similar to the assembled structure of the dipeptide, was transformed to an assembly of Ag nanostructures, where the micrometre-order crystalline morphology was maintained. In addition, detailed scanning electron microscopy studies revealed that Ag nanoparticles (diameter ca. 10 nm) were formed on the surface of the Ag nanostructure. When the Ag(I) ions were reduced to Ag(0), this phenomenon exhibited surface dependence due to the anisotropic two-dimensional Ag(I) arrangement in the crystals. Thermogravimetric measurements and X-ray photoelectron spectroscopy revealed that the reduction proceeds in a stepwise manner around 200-250 °C, together with the removal of primary and secondary carboxylic groups in the dipeptide. Comparison with the heating process of the crystalline Ag(I) complex of β-alanine indicated that stepwise reduction is key for maintaining the original micrometre-order morphology.

Hydrogen-bonded porous frameworks constructed by rigid π-conjugated molecules with carboxy groups

This review covers construction and properties of porous molecular crystals (PMCs) constructed through hydrogen-bonding of C3-symmetric, rigid, π-conjugated molecular building blocks possessing carboxyaryl groups, which was reported in the last 5 years by the author’s group. PMCs with well-defined, self-standing pores have been attracted attention due to various functionalities provided by selective and reversible inclusion of certain chemical species into the pores. However, it has been recognized for long time that construction of PMCs with permanent porosity is not easy due to weakness of noncovalent intermolecular interactions. Systematic construction of PMCs have been limited so far. To overcome this problem, the author has proposed a unique molecular design concept based on C3-symmetric π-conjugated molecules (C3PIs) possessing o-bis(4-carboxyphenyl)benzene moieties in their periphery and demonstrated that C3PIs systematically yielded hydrogen-bonded organic frameworks (HOFs) composed of H-bonded 2D hexagonal networks (H-HexNets) or interpenetrated 3D pcu-networks, which exhibit permanent porosity, significant thermal stability, polar solvent durability, robustness/flexibility, and/or multifunctionality.

Acid Responsive Hydrogen-Bonded Organic Frameworks

A porous hydrogen-bonded organic framework (HOF) responsive to acid was constructed from a hexaazatrinaphthylene derivative with carboxyphenyl groups (CPHATN). Precise structures of both 1,2,4-trichlorobenzene solvate [CPHATN-1(TCB)] and activated HOF with permanent porosity (CPHATN-1a) were successfully determined by single-crystalline X-ray diffraction analysis. Permanent porosity of CPHATN-1a was evaluated by gas sorption experiments at low temperature. CPHATN-1a also shows significant thermal stability up to 633 K. Its crystals exhibit a rich photochemistry thanks to intramolecular charge-transfer and interunit proton-transfer reactions. Femtosecond (fs) experiments on crystals demonstrate that these events occur in ≤200 fs and 1.2 ps, respectively. Moreover, single-crystal fluorescence microscopy reveals a shift of the emission spectra most probably as a result of defects and a high anisotropic behavior, reflecting an ordered crystalline structure with a preferential orientation of the molecular dipole moments. Remarkably, CPHATN-1a, as a result of the protonation of pyradyl nitrogen atoms embedded in its π-conjugated core, shows reversible vapor acid-induced color changes from yellow to reddish-brown, which can be also followed by an ON/OFF of its emission. To the best of our knowledge, this is the first HOF that exhibits acid-responsive color changes. The present work provides new findings for developing stimuli responsive HOFs.

A double helix of opposite charges to form channels with unique CO2 selectivity and dynamics

Porous molecular materials represent a new front in the endeavor to achieve high-performance sorptive properties and gas transport. Self-assembly of polyfunctional molecules containing multiple charges, namely, tetrahedral tetra-sulfonate anions and bifunctional linear cations, resulted in a permanently porous crystalline material exhibiting tailored sub-nanometer channels with double helices of electrostatic charges that governed the association and transport of CO2 molecules. The charged channels were consolidated by robust hydrogen bonds. Guest recognition by electrostatic interactions remind us of the role played by the dipolar helical channels in regulatory biological membranes. The systematic electrostatic sites provided the perfectly fitting loci of complementary charges in the channels that proved to be extremely selective with respect to N2 (S = 690), a benchmark in the field of porous molecular materials. The unique screwing dynamics of CO2 travelling along the ultramicropores with a step-wise reorientation mechanism was driven by specific host-guest interactions encountered along the helical track. The unusual dynamics with a single-file transport rate of more than 106 steps per second and an energy barrier for the jump to the next site as low as 2.9 kcal mol-1 was revealed unconventionally by complementing in situ 13C NMR anisotropic line-shape analysis with DFT modelling of CO2 diffusing in the crystal channels. The peculiar sorption performances and the extraordinary thermal stability up to 450 °C, combined with the ease of preparation and regeneration, highlight the perspective of applying these materials for selective removal of CO2 from other gases.

Intertwined gababutin-based supramolecular double helix

A dimer-assembly driven supramolecular double helix is observed for the gababutin-based short peptide sequence and this architecture exhibits electrochemical features.

Docking Strategy To Construct Thermostable, Single-Crystalline, Hydrogen-Bonded Organic Framework with High Surface Area

Enhancing thermal and chemical durability and increasing surface area are two main directions for the construction and improvement of the performance of porous hydrogen-bonded organic frameworks (HOFs). Herein, a hexaazatriphenylene (HAT) derivative that possesses six carboxyaryl groups serves as a suitable building block for the systematic construction of thermally and chemically durable HOFs with high surface area through shape-fitted docking between the HAT cores and interpenetrated three-dimensional network. A HAT derivative with carboxybiphenyl groups forms a stable single-crystalline porous HOF that displays protic solvent durability, even in concentrated HCl, heat resistance up to 305 °C, and a high Brunauer-Emmett-Teller surface area [SA_(BET) ] of 1288 m²  g^-1 . A single crystal of this HOF displays anisotropic fluorescence, which suggests that it would be applicable to polarized emitters based on robust functional porous materials.

Hydrophobic dipeptides: the final piece in the puzzle

The crystal structure of L-valyl-L-leucine acetonitrile solvate presented here adds to 24 previously reported structures of dipeptides constructed from the five nonpolar amino acids L-alanine, L-valine, L-isoleucine, L-leucine and L-phenylalanine. It thus constitutes the final piece in the 5 × 5 puzzle of hydrophobic dipeptide structures. This opportunity is taken to review the crystal packing arrangements and hydrogen-bonding preferences of a rather unique group of substances, with updated information on the various hydrogen-bonding patterns and the associated peptide conformations.

Fine Tuning and Specific Binding Sites with a Porous Hydrogen-Bonded Metal-Complex Framework for Gas Selective Separations

Research on hydrogen-bonded organic frameworks (HOFs) has been developed for quite a long time; however, those with both established permanent porosities and functional properties are extremely rare due to weak hydrogen-bonding interactions among molecular organic linkers, which are much more fragile and difficult to stabilize. Herein, through judiciously combining the superiority of both the moderately stable coordination bonds in metal-organic frameworks and hydrogen bonds, we have realized a microporous hydrogen-bonded metal-complex or metallotecton framework HOF-21, which not only shows permanent porosity, but also exhibits highly selective separation performance of C₂H₂/C₂H₄ at room temperature. The outstanding separation performance can be ascribed to sieving effect confined by the fine-tuning pores and the superimposed hydrogen-bonding interaction between C₂H₂ and SiF₆^2- on both ends as validated by both modeling and neutron powder diffraction experiments. More importantly, the collapsed HOF-21 can be restored by simply immersing it into water or salt solution. To the best of our knowledge, such extraordinary water stability and restorability of HOF-21 were observed for the first time in HOFs, underlying the bright perspective of such new HOF materials for their industrial usage.

Expandable porous organic frameworks with built-in amino and hydroxyl functions for CO2and CH4capture

Organic functions built on the node of a porous covalent architecture exhibit excellent affinity for CO₂(54 kJ mol⁻¹) and CH₄(25 kJ mol⁻¹): the interaction of CO₂favorably with amine groups was observed by 2D NMR.

Porous dipeptide crystals as volatile-drug vessels

Anesthetic vapors find temporary hospitality in porous dipeptide crystals, which behave as biologically friendly hosts and carriers.

Understanding the conformational analysis of gababutin based hybrid peptides

A new class of gababutin-based tetrapeptide shows a C₁₂/C₁₀ hydrogen-bonded hybrid turn.

CO2 regulates molecular rotor dynamics in porous materials

Porous molecular crystals contain fast molecular rotors whose dynamics can be controlled by CO₂.

Molecular tectonics: gas adsorption and chiral uptake of (l)- and (d)-tryptophan by homochiral porous coordination polymers

The combination of an enantiomerically pure tecton with a Cu(ii) cation yields robust porous homochiral crystals displaying preferential adsorption ofl-tryptophan.

Dynamic microfluidic control of supramolecular peptide self-assembly

The dynamic nature of supramolecular polymers has a key role in their organization. Yet, the manipulation of their dimensions and polarity remains a challenge. Here, the minimalistic diphenylalanine building block was applied to demonstrate control of nano-assemblies growth and shrinkage using microfluidics. To fine-tune differential local environments, peptide nanotubes were confined by micron-scale pillars and subjected to monomer flows of various saturation levels to control assembly and disassembly. The small-volume device allows the rapid adjustment of conditions within the system. A simplified kinetic model was applied to calculate parameters of the growth mechanism. Direct real-time microscopy analysis revealed that different peptide derivatives show unidirectional or bidirectional axial dimension variation. Atomistic simulations show that unidirectional growth is dictated by the differences in the axial ends, as observed in the crystalline order of symmetry. This work lays foundations for the rational control of nano-materials dimensions for applications in biomedicine and material science.

The organization of supramolecular peptide polymers determines their properties; however, controlling their dimensions still remains a problem. Here, Gazit et al. show the spontaneous elongation and shortening of these polymers at an individual nano-assembly level by using a microfluidic platform.

Molecular Rotors Built in Porous Materials

Molecules and materials can show dynamic structures in which the dominant mechanism is rotary motion. The single mobile elements are defined as "molecular rotors" and exhibit special properties (compared with their static counterparts), being able in perspective to greatly modulate the dielectric response and form the basis for molecular motors that are designed with the idea of making molecules perform a useful mechanical function. The construction of ordered rotary elements into a solid is a necessary feature for such design, because it enables the alignment of rotors and the fine-tuning of their steric and dipolar interactions. Crystal surfaces or bulk crystals are the most suitable to adapt rotors in 2D or 3D arrangements and engineer juxtaposition of the rotors in an ordered way. Nevertheless, it is only in recent times that materials showing porosity and remarkably low density have undergone tremendous development. The characteristics of large free volume combine well with the virtually unhindered motion of the molecular rotors built into their structure. Indeed, the molecular rotors are used as struts in porous covalent and supramolecular architectures, spanning both hybrid and fully organic materials. The modularity of the approach renders possible a variety of rotor geometrical arrangements in both robust frameworks stable up to 850 K and self-assembled molecular materials. A nanosecond (fast dynamics) motional regime can be achieved at temperatures lower than 240 K, enabling rotor arrays operating in the solid state even at low temperatures. Furthermore, in nanoporous materials, molecular rotors can interact with the diffusing chemical species, be they liquids, vapors, or gases. Through this chemical intervention, rotor speed can be modulated at will, enabling a new generation of rotor-containing materials sensitive to guests. In principle, an applied electric field can be the stimulus for chemical release from porous materials. The effort needed to obtain strong dipoles that are noncentrosymmetrically mounted onto rotors and do not hamper rotational motion is a further aspect of this research activity. Thus, materials showing dielectric properties in response to applied electric fields have been fabricated. This may lead to challenging materials that are promptly responsive to an applied electric field, altering the ferroelectric or antiferroelectric ground state by fast dipole reorientation when subjected to electric polarization.