Exploring and exploiting polar-π interactions with fluorinated aromatic amino acids

Fluorophilic Sigma(σ)-Lock Self-Healable Copolymers

Although F-Containing molecules and macromolecules are often used in molecular biology to increase the binding with Lewis acidic groups by introducing favorable C-F dipoles, there is virtually no experimental evidence and limited understanding of the nature of these interactions, especially their role in synthetic polymeric materials. These studies elucidate the molecular origin of inter- and intra-Chain interactions responsible for self-healing of F-Containing copolymers composed of pentafluorostyrene and n-butyl acrylate units (p(PFS/nBA). Guided by dynamic surface oscillating force (SOF) and spectroscopic measurements supported by molecular dynamics (MD) simulations, these studies show that the reformation of σ-σ orbitals in -C-F of PFS and CH3CH2- of nBA units enables the recovery of entropic energy via fluorophilic-σ-lock van der Waals forces when PFS/nBA molar ratios are ~50/50. The strength of these interactions determined experimentally for self-healable PFS/nBA compositions is in the order ~0.3 kcal/mol which primarily comes from fluorophilic-σ-lock (~70 %) contributions. These interactions are significantly diminished for non-self-healable counterparts. Strongly polarized -C-F σ orbitals create lateral dipolar forces enhancing the affinity towards -C-H orbitals, facilitating energetically favorable interactions. Entropic recovery driven by non-Covalent bonding offers a valuable tool in designing materials with unique functionalities, particularly self-healable batteries and energy storage devices.

Engineering Amino Acid and Peptide Supramolecular Architectures through Fluorination

Fluorinated non-natural amino acids are attracting considerable research interest, especially in the biomedical field and in materials science, thanks to their ability to self-assemble into peculiar supramolecular structures. The conformational changes induced by the presence of fluorine atoms obviously affect their functions, as well as the biological activity of the deriving peptides and proteins. Here, we will briefly describe the main effects of fluorination on the aggregation behavior of such building blocks, focusing in particular on their improved tendency to form fibrils, and gels therefrom. Our aim is to underline the promising potential of fluorination as a tool to affect the self-assembly features of amino acids, both when used alone and when inserted into polypeptide sequences. The ability of fluorine to influence physical, chemical, and structural properties of these substrates offers the possibility to engineer bioinspired materials with specific and tunable functions.

Exploring Favorable Supramolecular Interactions of Multifluorinated Aromatics in Dendronized Push-Pull Chromophores for Electro-Optics

Multifluorinated aromatics serve as supramolecular synthons in the research of organic electro-optic (EO) materials by exploiting π-π stacking interaction between the aromatic hydrocarbon and multifluorinated aromatic groups for performance improvement. However, non-classical hydrogen bonding remains largely unexplored in fluorinated EO dendrimers. In this study, three Fréchet-type generation 1 benzyl ether co-dendrons were synthesized by replacing one benzyl group with 2,3,5,6-tetrafluorobenzyl (p-HF4Bz), pentafluorobenzyl (C6F5Bz), and 2,3,4,5-tetrafluorobenzyl (o-HF4Bz) groups, to afford the benzoic acid derivatives D1, D2, and D3, which were further bonded to the donor and π-bridge moieties to afford three co-dendronized push-pull phenyltetraene chromophores EOD1, EOD2, and EOD3, respectively. The weak C-H⋅⋅⋅X (X=O, F) interactions in the crystal structure of D1 cumulatively add to the benzoic acid dimers to form an extended hydrogen-bonded network, while D2 is crystallized into a centric one-dimensional chain with strong intermolecular interactions. The poled films of EOD1 with PMMA exhibited the largest and most stable EO activity with optical homogeneity among the series. The results identify the effectiveness of weak but favorable hydrogen bonds enabled by the enhanced carbon acidity of p-HF4Bz synthon in D1, over the interactions in D2 and D3, for the rational design of supramolecular EO dendrimers.

Aromatic-Carbonyl Interactions as an Emerging Type of Non-Covalent Interactions

Aromatic-carbonyl (Ar···C═O) interactions, attractive interactions between the arene plane and the carbon atom of carbonyl, are in the infancy as one type of new supramolecular bonding forces. Here the study and functionalization of aromatic-carbonyl interactions in solution is reported. A combination of aromatic-carbonyl interactions and dynamic covalent chemistry provided a versatile avenue. The stabilizing role and mechanism of arene-aldehyde/imine interactions are elucidated through crystal structures, NMR studies, and computational evidence. The movement of imine exchange equilibria further allowed the quantification of the interplay between arene-aldehyde/imine interactions and dynamic imine chemistry, with solvent effects offering another handle and matching the electrostatic feature of the interactions. Moreover, arene-aldehyde/imine interactions enabled the reversal of kinetic and thermodynamic selectivity and sorting of dynamic covalent libraries. To show the functional utility diverse modulation of fluorescence signals is realized with arene-aldehyde/imine interactions. The results should find applications in many aspects, including molecular recognition, assemblies, catalysis, and intelligent materials.

Site-Selective Polyfluoroaryl Modification and Unsymmetric Stapling of Unprotected Peptides

Peptide stapling is recognized as an effective strategy for improving the proteolytic stability and cell permeability of peptides. In this study, we present a novel approach for the site-selective unsymmetric perfluoroaryl stapling of Ser and Cys residues in unprotected peptides. The stapling reaction proceeds smoothly under very mild conditions, exhibiting a remarkably rapid reaction rate. It can furnish stapled products in both liquid and solid phases, and the presence of nucleophilic groups other than Cys thiol within the peptide does not impede the reaction, resulting in uniformly high yields. Importantly, the chemoselective activation of Ser β-C(sp3)-H enables the unreacted -OH to serve as a reactive handle for subsequent divergent modification of the staple moiety with various therapeutic functionalities, including a clickable azido group, a polar moiety, a lipid tag, and a fluorescent dye. In our study, we have also developed a visible-light-induced chemoselective C(sp3)-H polyfluoroarylation of the Ser β-position. This reaction avoids interference with the competitive reaction of Ser -OH, enabling the precise late-stage polyfluoroarylative modification of Ser residues in various unprotected peptides containing other highly reactive amino acid residues. The biological assay suggested that our peptide stapling strategy would potentially enhance the proteolytic stability and cellular permeability of peptides.

Catalyst-free decarboxylative cross-coupling of N-hydroxyphthalimide esters with tert-butyl 2-(trifluoromethyl)acrylate and its application

Here, we demonstrate a practical method toward the facile synthesis of CF3-containing amino acids through visible light promoted decarboxylative cross-coupling of a redox-active ester with tert-butyl 2-(trifluoromethyl)acrylate. The reaction was driven by the photochemical activity of electron donor-acceptor (EDA) complexes that were formed by the non-covalent interaction between a Hantzsch ester and a redox-active ester. The advantages of this protocol are its synthetic simplicity, rich functional group tolerance, and a cost-effective reaction system.

Synthesis of Alkylated Polyfluorobenzenes through Decarboxylative Giese Addition of Aliphatic N-Hydroxyphthalimide Esters with Polyfluorostyrene

Polyfluoroaromatic compounds play crucial roles in medicinal and material science. However, the synthesis of alkylated polyfluoroarenes has been relatively underdeveloped. In this study, we devised a novel decarboxylative coupling reaction between aliphatic N-hydroxyphthalimide esters and polyfluorostyrene, leveraging the photochemical activity of electron donor-acceptor (EDA) complexes. This method offers simple reaction conditions, a broad substrate scope, and excellent functional group tolerance. Furthermore, we have demonstrated the practicality of this protocol through late-stage polyfluoroaryl modification of biologically active molecules using readily available carboxylic acids as starting materials, thus providing an important supplement to the current toolbox for accessing alkylated polyfluoroaryl motifs.

Molecular Dynamics Simulations of Matrix Metalloproteinase 13 and the Analysis of the Specificity Loop and the S1'-Site

The specificity loop of Matrix Metalloproteinases (MMPs) is known to regulate recognition of their substrates, and the S1'-site surrounded by the loop is a unique place to address the selectivity of ligands toward each MMP. Molecular dynamics (MD) simulations of apo-MMP-13 and its complex forms with various ligands were conducted to identify the role of the specificity loop for the ligand binding to MMP-13. The MD simulations showed the dual role of T247 as a hydrogen bond donor to the ligand, as well as a contributor to the formation of the van der Waal surface area, with T245 and K249 on the S1'-site. The hydrophobic surface area mediated by T247 blocks the access of water molecules to the S1'-site of MMP-13 and stabilizes the ligand in the site. The F252 residue is flexible in order to search for the optimum location in the S1'-site of the apo-MMP-13, but once a ligand binds to the S1'-site, it can form offset π-π or edge-to-π stacking interactions with the ligand. Lastly, H222 and Y244 provide the offset π-π and π-CH(Cβ) interactions on each side of the phenyl ring of the ligand, and this sandwiched interaction could be critical for the ligand binding to MMP-13.

Effect of Substituents on the Intramolecular n→π* Interaction in 3-[2-(Dimethylamino) phenyl] propanal: A Computational Study

n→π* non-covalent interaction (NCI) and hydrogen bond have similarity in terms of delocalization of the electron density between the two orbitals involved in the interaction. Hydrogen bond (X-H···Y) involves delocalization of the lone pair electrons (n) on the Y atom into the σ* orbital of the X-H bond. In contrast, the n→π* interaction deals with delocalizing the lone pair electrons (n) on the N, O, or S atom into the π* orbital of a C═O group or aromatic ring. Herein, we have shown a resemblance of this weak n→π* interaction with the relatively stronger hydrogen bond in terms of folding the side chains in flexible molecules. This work reports the study of folding of the flexible side-chain in 3-[2-(dimethylamino) phenyl] propanal (DMAPhP) through a N···C═O n→π* interaction using various computational approaches such as NBO, QTAIM, and NCI analyses. The folding of the molecule by the n→π* interaction observed in this study is found to be similar to that present in the secondary structures of peptides or proteins through hydrogen bonding interactions. Interestingly, the stabilization of the global minimum conformer of DMAPhP by the n→π* interaction demonstrates the importance of this NCI in providing conformational preferences in molecular systems. Another important finding of this study is that the theoretical redshift obtained in the C═O stretching frequency of the most stable conformer of the DMAPhP is contributed mostly by the n→π* interaction as the C═O group is not involved in hyperconjugation with any neighboring heteroatom, which is a common phenomenon in any ester or amide. We have also demonstrated here that the strength of the intramolecular n→π* interaction can be modulated by varying the electronic substituents at the para position of the donor group involved in the interaction.

Mesenchymal Stem Cells Sense the Toughness of Nanomaterials and Interfaces

Stem cells are known to sense and respond to the mechanical properties of biomaterials. In turn, cells exert forces on their environment that can lead to striking changes in shape, size and contraction of associated tissues, and may result in mechanical disruption and functional failure. However, no study has so far correlated stem cell phenotype and biomaterials toughness. Indeed, disentangling toughness-mediated cell response from other mechanosensing processes has remained elusive as it is particularly challenging to uncouple Youngs' or shear moduli from toughness, within a range relevant to cell-generated forces. In this report, it is shown how the design of the macromolecular architecture of polymer nanosheets regulates interfacial toughness, independently of interfacial shear storage modulus, and how this controls the expansion of mesenchymal stem cells at liquid interfaces. The viscoelasticity and toughness of poly(l-lysine) nanosheets assembled at liquid-liquid interfaces is characterised via interfacial shear rheology. The local (microscale) mechanics of nanosheets are characterised via magnetic tweezer-assisted interfacial microrheology and the thickness of these assemblies is determined from in situ ellipsometry. Finally, the response of mesenchymal stem cells to adhesion and culture at corresponding interfaces is investigated via immunostaining and confocal microscopy.

Induced CPL-Active Materials Based on Chiral Supramolecular Co-Assemblies

Circularly polarized luminescence (CPL) has attracted much interest due to its potential applications on chiral photonic techniques and optoelectronic materials science. As known, dissymmetry factor (g_em ) of CPL is one essential factor for evaluating the features of CPL-active materials. Much attention has focused on how to increase the g_em value, which is one of the most important issues for CPL practical applications. Recently, more and more works have demonstrated that chiral supramolecular could provide the significant strategy to improve the g_em value through the orderly helical superstructure of chiral building blocks. Normally, this kind of chiral supramolecular assembly process can be accompanied by chirality transfer and induction mechanism, which can promote the amplification effect on the induced CPL of achiral dyes. In this review, we fully summarized recent advances on the induced CPL-active materials of chiral supramolecular co-assemblies, their applications in circularly polarized organic light-emitting diodes (CP-OLEDs) and current challenges.

Supercharged Protein Nanosheets for Cell Expansion on Bioemulsions

Cell culture at liquid-liquid interfaces, for example, at the surface of oil microdroplets, is an attractive strategy to scale up adherent cell manufacturing while replacing the use of microplastics. Such a process requires the adhesion of cells at interfaces stabilized and reinforced by protein nanosheets displaying not only high elasticity but also presenting cell adhesive ligands able to bind integrin receptors. In this report, supercharged albumins are found to form strong elastic protein nanosheets when co-assembling with the co-surfactant pentafluorobenzoyl chloride (PFBC) and mediate extracellular matrix (ECM) protein adsorption and cell adhesion. The interfacial mechanical properties and elasticity of supercharged nanosheets are characterized by interfacial rheology, and behaviors are compared to those of native bovine serum albumin, human serum albumin, and α-lactalbumin. The impact of PFBC on such assembly is investigated. ECM protein adsorption to resulting supercharged nanosheets is then quantified via surface plasmon resonance and fluorescence microscopy, demonstrating that the dual role supercharged albumins are proposed to play as scaffold protein structuring liquid-liquid interfaces and substrates for the capture of ECM molecules. Finally, the adhesion and proliferation of primary human epidermal stem cells are investigated, at pinned droplets, as well as on bioemulsions stabilized by corresponding supercharged nanosheets. This study demonstrates the potential of supercharged proteins for the engineering of biointerfaces for stem cell manufacturing and draws structure-property relationships that will guide further engineering of associated systems.

Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.

Towards Non-stick Silk: Tuning the Hydrophobicity of Silk Fibroin Protein

Silk fibroin protein is a biomaterial with excellent biocompatibility and low immunogenicity. These properties have catapulted the material as a leader for extensive use in stents, catheters, and wound dressings. Modulation of hydrophobicity of silk fibroin protein to further expand the scope and utility however has been elusive. We report that installing perfluorocarbon chains on the surface of silk fibroin transforms this water-soluble protein into a remarkably hydrophobic polymer that can be solvent-cast. A clear relationship emerged between fluorine content of the modified silk and film hydrophobicity. Water contact angles of the most decorated silk fibroin protein exceeded that of Teflon®. We further show that water uptake in prefabricated silk bars is dramatically reduced, extending their lifetimes, and maintaining mechanical integrity. These results highlight the power of chemistry under moderate conditions to install unnatural groups onto the silk fibroin surface and will enable further exploration into applications of this versatile biomaterial.

A Quantum Chemical Deep-Dive into the π-π Interactions of 3-Methylindole and Its Halogenated Derivatives—Towards an Improved Ligand Design and Tryptophan Stacking

Non-covalent π-π stacking interactions often play a key role in the stability of the secondary and tertiary structures of peptides and proteins, respectively, and can be a means of ensuring the binding of ligands within protein and enzyme binding sites. It is generally accepted that minor structural changes to the aromatic ring, such as substitution, can have a large influence on these interactions. Nevertheless, a thorough understanding of underpinning phenomena guiding these key interactions is still limited. This is especially true for larger aromatic structures. To expand upon this knowledge, elaborate ab initio calculations were performed to investigate the effect of halogenation on the stability of 3-methylindole stacking. 3-Methylindole served as a representation of the tryptophan side chain, and is a frequently used motif in drug design and development. Moreover, an expression is derived that is able to accurately predict the interaction stability of stacked halogenated 3-methylindole dimers as well as halogenated toluene dimers, based on monomer level calculated DFT descriptors. We aim for this expression to provide the field with a straightforward and reliable method to assess the effect of halogenation on the π-π stacking interactions between aromatic scaffolds.

Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches

Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.

Probing Noncovalent Interactions in [3,3]Metaparacyclophanes

Arene-arene interactions are fundamentally important in molecular recognition. To precisely probe arene-arene interactions in cyclophanes, we designed and synthesized (2,6-phenol)paracyclophanes and (2,6-aniline)paracyclophanes that possess two aromatic rings in close proximity. Fine-tuning the aromatic character of one aromatic ring by fluorine substituents enables investigations on the intramolecular interactions between the electron-rich phenol and aniline with tetra-H- and tetra-F-substituted benzene. pK_a measurements revealed that the tetra-F-template increases the acidity of the phenol (ΔpK_a = 0.55). X-ray crystallography and computational analyses demonstrated that all [3,3]metaparacyclophanes adopt cofacial parallel conformations, implying the presence of π-π stacking interactions. Advanced quantum chemical analyses furthermore revealed that both electrostatic interactions and orbital interactions provide the key contribution to the structure and stability of [3,3]metaparacyclophanes.

Aggregation caused quenching to aggregation induced emission transformation: a precise tuning based on BN-doped polycyclic aromatic hydrocarbons toward subcellular organelle specific imaging

Polycyclic aromatic hydrocarbons (PAHs) with boron–nitrogen (BN) moieties have attracted tremendous interest due to their intriguing electronic and optoelectronic properties. However, most of the BN-fused π-systems reported to date are difficult to modify and exhibit traditional aggregation-caused quenching (ACQ) characteristics. This phenomenon greatly limits their scope of application. Thus, continuing efforts to seek novel, structurally distinct and functionally diverse structures are highly desirable. Herein, we proposed a one-stone-two-birds strategy including simultaneous exploration of reactivity and tuning of the optical and electronic properties for BN-containing π-skeletons through flexible regioselective functionalization engineering. In this way, three novel functionalized BN luminogens (DPA-BN-BFT, MeO-DPA-BN-BFT and DMA-DPA-BN-BFT) with similar structures were obtained. Intriguingly, DPA-BN-BFT, MeO-DPA-BN-BFT and DMA-DPA-BN-BFT exhibit completely different emission behaviors. Fluorogens DPA-BN-BFT and MeO-DPA-BN-BFT exhibit a typical ACQ effect; in sharp contrast, DMA-DPA-BN-BFT possesses a prominent aggregation induced emission (AIE) effect. To the best of our knowledge, this is the first report to integrate ACQ and AIE properties into one BN aromatic backbone with subtle modified structures. Comprehensive analysis of the crystal structure and theoretical calculations reveal that relatively large twisting angles, multiple intermolecular interactions and tight crystal packing modes endow DMA-DPA-BN-BFT with strong AIE behavior. More importantly, cell imaging demonstrated that luminescent materials DPA-BN-BFT and DMA-DPA-BN-BFT can highly selectively and sensitively detect lipid droplets (LDs) in living MCF-7 cells. Overall, this work provides a new viewpoint of the rational design and synthesis of advanced BN–polycyclic aromatics with AIE features and triggers the discovery of new functions and properties of azaborine chemistry.

A one-stone-two-birds strategy including simultaneous exploration of reactivity and tuning of the optical and electronic properties for BN-fused polycyclic aromatics through flexible regioselective functionalization engineering is presented.

Elucidating important structural features for the binding affinity of spike - SARS-CoV-2 neutralizing antibody complexes

The coronavirus disease 2019 (COVID-19) has affected the lives of millions of people around the world. In an effort to develop therapeutic interventions and control the pandemic, scientists have isolated several neutralizing antibodies against SARS-CoV-2 from the vaccinated and convalescent individuals. These antibodies can be explored further to understand SARS-CoV-2 specific antigen-antibody interactions and biophysical parameters related to binding affinity, which can be utilized to engineer more potent antibodies for current and emerging SARS-CoV-2 variants. In the present study, we have analyzed the interface between spike protein of SARS-CoV-2 and neutralizing antibodies in terms of amino acid residue propensity, pair preference, and atomic interaction energy. We observed that Tyr residues containing contacts are highly preferred and energetically favorable at the interface of spike protein-antibody complexes. We have also developed a regression model to relate the experimental binding affinity for antibodies using structural features, which showed a correlation of 0.93. Moreover, several mutations at the spike protein-antibody interface were identified, which may lead to immune escape (epitope residues) and improved affinity (paratope residues) in current/emerging variants. Overall, the work provides insights into spike protein-antibody interactions, structural parameters related to binding affinity and mutational effects on binding affinity change, which can be helpful to develop better therapeutics against COVID-19.

Theoretical Approach to Evaluate the Gas-Sensing Performance of Graphene Nanoribbon/Oligothiophene Composites

Composite formation with graphene is an effective approach to increase the sensitivity of polythiophene (nPT) gas sensors. The interaction mechanism between gaseous analytes and graphene/nPT composite systems is still not clear, and density functional theory calculations are used to explore the interaction mechanism between graphene/nPT nanoribbon composites (with n = 3-9 thiophene units) and gaseous analytes CO, NH₃, SO₂, and NO₂. For the studied analytes, the interaction energy ranges from -44.28 kcal/mol for (C₅₄H₃₀-3PT)-NO₂ to -2.37 kcal/mol for (C₅₄H₃₀-3PT)-CO at the counterpoise-corrected ωB97M-V/def2-TZVPD level of theory. The sensing mechanism is further evaluated by geometric analysis, ultraviolet-visible spectroscopy, density of-states analysis, calculation of global reactivity indices, and both frontier and natural bond orbital analyses. The variation in the highest occupied molecular orbital/lowest unoccupied molecular orbital gap of the composite indicates the change in conductivity upon complexation with the analyte. Energy decomposition analysis reveals that dispersion and charge transfer make the largest contributions to the interaction energy. The graphene/oligothiophene composite is more sensitive toward these analytes than either component taken alone due to larger changes in the orbital gap. The computational framework established in the present work can be used to evaluate and design graphene/nPT nanoribbon composite materials for gas sensors.

Nickel-Catalyzed Cross-Coupling of Amino-Acid-Derived Alkylzinc Reagents with Alkyl Bromides/Chlorides: Access to Diverse Unnatural Amino Acids

Unnatural α-amino acids are important synthetic targets in the field of peptide science. Herein we report an efficient, versatile, and straightforward strategy for the synthesis of homophenylalanine derivatives via the nickel-catalyzed Csp3-Csp3 cross-coupling of (fluoro)benzyl bromides/chlorides with natural α-amino-acid-derived alkylzinc reagents. The current protocol features the advantages of a low-cost nickel catalyst system, synthetic convenience, and the tolerance of rich functionality and stereochemistry.

Targeted Chemical Modifications Identify Key Features of Carbohydrate Assemblies and Generate Tailored Carbohydrate Materials

The molecular level description of carbohydrate assemblies is hampered by their structural complexity and the lack of suitable analytical methods. Here, we employed systematic chemical modifications to identify key non-covalent interactions that triggered the supramolecular assembly of a disaccharide model. While some modifications disrupted the supramolecular organization, others were tolerated, delivering important information on the aggregation process. The screening identified new geometries, including nanotubes, and twisted ribbons that were characterized with electron tomography and electron diffraction (ED) methods. This work demonstrates that the combination of synthetic chemistry and ED methods is a powerful tool to draw correlations between the molecular structure and the nanoscale architecture of carbohydrate assemblies.

Higher-order interfiber interactions in the self-assembly of benzene-1,3,5-tricarboxamide-based peptides in water

Mimicking the complexity of biological systems with synthetic supramolecular materials requires a deep understanding of the relationship between the structure of the molecule and its self-assembly pattern. Herein, we report a series of water-soluble benzene-1,3,5-tricarboxamide-based di- and tripeptide derivatives modified with small non-bulky terminal amine salt to induce self-assembly into twisted one-dimensional higher-order nanofibers. The morphology of nanofibers strongly depends on the nature, order, and quantity of amino acids in the short peptide fragments and vary from simple cylindrical to complex helical. From observations of several fiber-splitting events, we detected interfiber interactions that always occur in a pairwise manner, which implies that the C3 symmetry of benzene-1,3,5-tricarboxamide-based molecules in higher-order fibers becomes gradually distorted, thus facilitating hydrophobic contact interactions between fibrils. The proposed mechanism of self-assembly through hydrophobic contact allowed the successful design of a compound with pH-responsive morphology, and may find use in the future development of complex hierarchical architectures with controlled functionality.

3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues

Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ₁, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.

A reactive peptide interface for site-selective cysteine bioconjugation

We report aqueous, site-selective modification of proteins using a reactive peptide interface comprising a nine-residue sequence. This interface is the fastest (second-order rate constant of 152 M-1 s-1) catalyst-free, cysteine-based method for modifying proteins available to date, and enables near-quantitative labeling of antibodies in cell lysate.

Improving the Overall Properties of Circularly Polarized Luminescent Materials Through Arene-Perfluoroarene Interactions

A major trade-off in the field of circularly polarized luminescence (CPL) of pure organic materials is that the large luminescence dissymmetry factor (g_lum ) usually gives rise to the suppression of luminescence efficiency (Φ_PL ). Here, a supramolecular self-assembled system, driven by arene-perfluoroarene (AP) interactions of chiral polycyclic aromatic hydrocarbons (PAHs) and octafluoronaphthalene (OFN), is reported to provide a solution to this problem. Two kinds of chiral PAHs based on pyrene and anthracene could co-assemble with OFN in hybrid solvents to form long-range-ordered AP assemblies. The detailed process of AP interaction driving self-assembly was verified by morphological measurements and fluorescence spectra. The AP assemblies exhibited chirality amplification not only in the excited state but also in the ground state. In addition, the AP assemblies showed an enhanced luminescence efficiency compared with the individual chiral PAHs due to the energy-barrier effect of OFN. The present strategy based on AP interactions could be applied to boost the development of highly efficient CPL-active materials.

Perfluorocarbons in Chemical Biology

Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.

The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation

The hexapeptide hIAPP22-27 (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to β-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.

Access to α,α-Difluoro-γ-amino Acids by Nickel-Catalyzed Reductive Aryldifluoroacetylation of N-Vinylacetamide

A nickel-catalyzed reductive aryldifluoroacetylation of N-vinylacetamide with ethyl chloro(difluoro)acetate and aryl iodides is described. This chelating amide carbonyl group-assisted strategy provides rapid access to a variety of protected α,α-difluoro-γ-amino acids that might have potential applications in peptide chemistry and protein engineering. An advantage of this method is its synthetic simplicity, with no preparation of organometallic reagents.

Selective Activation of Aromatic Aldehydes Promoted by Dispersion Interactions: Steric and Electronic Factors of a π-Pocket within Cage-Shaped Borates for Molecular Recognition

Selective bond formations are one of the most important reactions in organic synthesis. In the Lewis acid mediated electrophile reactions of carbonyls, the selective formation of a carbonyl-acid complex plays a critical role in determining selectivity, which is based on the difference in the coordinative interaction between the carbonyl and Lewis acid center. Although this strategy has attained progress in selective bond formations, the discrimination between similarly sized aromatic and aliphatic carbonyls that have no functional anchors to strongly interact with the metal center still remains a challenging issue. Herein, this work focuses on molecular recognition driven by dispersion interactions within some aromatic moieties. A Lewis acid catalyst with a π-space cavity, which is referred to as a π-pocket, as the recognition site for aromatic carbonyls is designed. Cage-shaped borates 1B with various π-pockets demonstrated significant chemoselectivity for aromatic aldehydes 3 b-f over that of aliphatic 3 a in competitive hetero-Diels-Alder reactions. The effectiveness of our catalysts was also evidenced by intramolecular recognition of the aromatic carbonyl within a dicarbonyl substrate. Mechanistic and theoretical studies demonstrated that the selective activation of aromatic substrates was driven by the preorganization step with a larger dispersion interaction, rather than the rate-determining step of the C-C bond formation, and this was likely to contribute to the preferred activation of aromatic substrates over that of aliphatic ones.

High sensitivity room temperature sulfur dioxide sensor based on conductive poly(p-phenylene)/ZSM-5 nanocomposite

Recently, there has been growing interests in the development of composite materials as the new alternative gas sensing materials for replacing metal oxide based sensors which require the elevated operating temperature. Herein, we reported the fabrication and testing of new sensing composite materials based on the conductive poly(p-phenylene) (PPP) nanoparticle and zeolites for sulfur dioxide (SO₂) detection at room temperature under the effects of doping, zeolite type, zeolite content, SO₂ concentration as well as interferences and humidity. The relative electrical conductivity response depended critically on the doping agent type, doping ratio, and doping temperature. The addition of porous zeolites into the doped-PPP (dPPP) matrix induced the improvement in selectivity and sensing performances towards SO₂ as it promoted more surface area for SO₂ adsorption and its new synergistic effect with the conductive dPPP, related to the additional conductive polymer doping from the dissolution of the SO₂ in intrazeolitic water as identified and reported here. Among all materials, the dPPP/ZSM-5 composite with perchloric acid (HClO₄) as the doping agent, the doping ratio of 50:1, the doping temperature of 70 °C, and the zeolite content of 30% exhibited the highest relative response of 25.42 towards 500 mg L^-1 SO₂ with good repeatability. This composite provided the SO₂ sensitivity of 0.0483 L mg^-1 with R² of 0.9927 and the limit of detection (LOD) of 5 mg L^-1 as determined from the electrical conductivity signal to noise ratio. The present sensing material is a potential candidate in the practical detection of SO₂ at room temperature.

Luminescent Polymorphic Co-crystals: A Promising Way to the Diversity of Molecular Assembly, Fluorescence Polarization, and Optical Waveguide

The design of molecular optoelectronic materials based on fabricating polymorphs and/or co-crystals has received much recent attention in the fields of luminescence, sensors, nonlinear optics, and so on. If the advantages of the two crystal engineering strategies above were combined, the diversity of self-assembly fashions and the tuning of photofunctional performances would be largely extended. However, such multicomponent examples have still been very limited to date. Herein, we report the construction of luminescent polymorphic co-crystals by assembly of tris(pentafluorophenyl)borane (TPFB) with 9,10-dicyanoanthracene (DCA) and acridine (AC) as paradigms. Different stacking modes and arrangement styles based on identical building block units in polymorphic co-crystals result in adjustable crystalline morphologies and variant photophysical properties (such as fluorescence wavelength, lifetimes, and up-conversion luminescence). The optimized photoluminescence quantum yield (63.1%) and lifetime (57.1 ns) are much higher than those of the pristine assembled units. In addition, two polymorphic co-crystals (DCA@TPFB-1 and AC@TPFB-2) present prominent fluorescence polarization and optical waveguide behaviors due to the highly regulated molecular orientation. Their high one-dimensional luminescence anisotropy (0.652) and low optical waveguide loss (0.0079 dB/μm) outperform most state-of-the-art low-dimensional molecular systems and thus endow them with great opportunities for photonic materials and devices. Therefore, this work not only confirms that constructing polymorphic co-crystals can be an effective way to design new photofunctional materials for luminescence and photonic applications but also discloses a deep understanding on the relationship between variant self-assembled fashions and tunable photofunctional properties of new TPFB-based molecular materials.

Fluorinated phenylalanines: synthesis and pharmaceutical applications

Recent advances in the chemistry of peptides containing fluorinated phenylalanines (Phe) represents a hot topic in drug research over the last few decades. ᴅ- or ʟ-fluorinated phenylalanines have had considerable industrial and pharmaceutical applications and they have been expanded also to play an important role as potential enzyme inhibitors as well as therapeutic agents and topography imaging of tumor ecosystems using PET. Incorporation of fluorinated aromatic amino acids into proteins increases their catabolic stability especially in therapeutic proteins and peptide-based vaccines. This review seeks to summarize the different synthetic approaches in the literature to prepare ᴅ- or ʟ-fluorinated phenylalanines and their pharmaceutical applications with a focus on published synthetic methods that introduce fluorine into the phenyl, the β-carbon or the α-carbon of ᴅ-or ʟ-phenylalanines.

Can glycine betaine denature proteins?

Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation-π interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two β-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such non-monotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB's stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation-π binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation-π interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins.

Synthesis, crystal structure, and optical properties of fluorinated poly(pyrazole) ligands and in silico assessment of their affinity for volatile organic compounds

Increasing fluorination of an organic ligand forming porous coordination polymers results in enhanced affinity for volatile organic compounds (VOCs) without affecting the fluorescence properties, thus opening new perspectives for VOC sensing.

Nickel-catalyzed carbodifunctionalization of N-vinylamides enables access to γ-amino acids

A nickel-catalyzed tandem reaction of N-vinylamides with arylboronic acids and bromodifluoroacetate has been developed. The reaction efficiently furnishes a series of protected α,α-difluoro-γ-amino acid esters.

Colocalization Strategy Unveils an Underside Binding Site in the Transmembrane Domain of Smoothened Receptor

We unveiled an underside binding site on smoothened receptor (SMO) by a colocalization strategy using two structurally complementary photoaffinity probes derived from a known ligand Allo-1. Docking study and structural dissection identified key interactions within the site, including hydrogen bonding, π-π interactions, and hydrophobic interactions between Allo-1 and its contacting residues. Taken together, our results reveal the molecular base of Allo-1 binding and provide a basis for the design of new-generation ligands to overcome drug resistance.

Synthetic Methodologies for Perfluoroaryl-Substituted (Diaryl)methylphosphonates, -Phosphinates via SNAr Reaction

The new synthetic methodologies for perfluoroaryl-substituted (diaryl)methylphosphonates, -phosphinates via nucleophilic aromatic substitution (S_NAr) were developed. Benzylphosphonate and α-fluorobenzylphosphonate reacted with a wide variety of perfluoroarenes via S_NAr reaction. The reaction took place quickly and gave perfluoroarylated phosphonates in high yields. Highly diastereoselective S_NAr reaction with binaphthyl-based chiral phosphinates was further carried out.

Photooxidative Generation of Dodecaborate-Based Weakly Coordinating Anions

Redox-active proanions of the type B₁₂(OCH₂Ar)₁₂ [Ar = C₆F₅ (1), 4-CF₃C₆H₄ (2), 3,5-(CF₃)₂C₆H₃ (3)] are introduced in the context of an experimental and computational study of the visible-light-initiated polymerization of a family of styrenes. Neutral, air-stable proanions 1-3 were found to initiate styrene polymerization through single-electron oxidation under blue-light irradiation, resulting in polymers with number-average molecular weights (M_n) ranging from ∼6 to 100 kDa. Shorter polymer products were observed in the majority of experiments, except in the case of monomers containing 4-X (X = F, Cl, Br) substituents on the styrene monomer when polymerized in the presence of 1 in CH₂Cl₂. Only under these specific conditions are longer polymers (>100 kDa) observed, strongly supporting the formulation that reaction conditions significantly modulate the degree of ion pairing between the dodecaborate anion and cationic chain end. This also suggests that 1-3 behave as weakly coordinating anions (WCA) upon one-electron reduction because no incorporation of the cluster-based photoinitiators is observed in the polymeric products analyzed. Overall, this work is a conceptual realization of a single reagent that can serve as a strong photooxidant, subsequently forming a WCA.

Synthesis, structural studies and biological properties of some phosphono-perfluorophenylalanine derivatives formed by SNAr reactions

Several novel phosphono-perfluorophenylalanine derivatives, as mimetics of phenylalanine, were synthesized by subjecting diethyl (2-(perfluorophenyl)-1-(phenylamino)ethyl)-phosphonate to S_NAr reactions with different types of nucleophiles such as thiols, amines and phenols. The structure of the products was confirmed using spectroscopic and spectrometric techniques. For two compounds X-ray single crystal diffraction analysis and DFT investigations were performed providing information in regard to the preferable conformation, hydrogen bonds and other interactions. The antiproliferative potency of some of the new phosphono-perfluorophenylalanine derivatives obtained as well as representatives of previously synthesized perfluorophenyl phosphonate analogues of phenylalanine was studied on selected glioma cell lines. Preliminary evaluation of the compounds drug likeness was examined with respect to Lipinski's and Veber's rules, and showed that they meet the criteria perfectly. MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay results demonstrated that the compounds exhibit moderate activity against the glioblastoma multiforme cell lines (T98G and U-118 MG). Moreover most of the studied S_NAr reaction products displayed significantly higher inhibitory activity against both cancer cell lines than the parent diethyl (2-(perfluorophenyl)-1-(phenylamino)ethyl)phosphonate.

Through-Space Conjugation: A Thriving Alternative for Optoelectronic Materials

Efficient electronic coupling is the key to constructing optoelectronic functional π systems. Generally, the delocalization of π electrons must comply with the framework constructed by covalent bonds (typically σ bonds), representing classic through-bond conjugation. However, through-space conjugation offers an alternative that achieves spatial electron communication with closely stacked π systems instead of covalent bonds thus enabling multidimensional energy and charge transport. Because of the ever-accelerating advances of through-space conjugation studies, researchers are inspired greatly by the beauty of through-space conjugated systems and their potential in high-tech applications. In this mini review, we introduce some representative and newly developed π systems having the through-space conjugation feature. In addition to discussing the profound impacts of through-space conjugation on the luminescence properties and charge transport, we will review some impressive findings of distinctive molecules with attractive characteristics, such as aggregation-induced emission, thermally activated delayed fluorescence, bipolar charge transport, and multichannel. These achievements may bring about new breakthroughs of theory, materials, and devices in the fields of organic electronics and molecular electronics.

Polar-π Interactions Promote Self-assembly of Dipeptides into Laminated Nanofibers

Precise incorporation of functional residues into sequences allows for tailoring the noncovalent interactions between peptides to guide their self-assembly into well-defined nanostructures, thus facilitating creation of artificial functional materials resembling natural systems. Here, we report on the self-assembly of dipeptides consisting of one fluorinated phenylalanine unit (Z residue) and one natural aromatic residue into laminated nanofibers predominately driven by polar-π interactions. On the basis of characterizations using transmission electron microscopy, scanning electron microscopy, atomic force microscopy, circular dichroism, Fourier transform infrared spectroscopy, and thioflavin T binding assay, we found that the face-centered stacking pattern of the dipeptides FZ, ZF, and ZY stabilized by the polar-π interactions and antiparallel β-sheet H-bonding interactions led to lamination of nanofibers and formation of ribbonlike nanostructures. Our findings demonstrate that incorporation of fluorinated aromatic units into short peptides not only promotes of polar-π interactions as alternative self-assembling driving forces but also governs the organizing pattern of peptides, thus benefiting creation of well-defined peptide nanostructures.

Palladium-catalyzed cross-coupling of unactivated alkylzinc reagents with 2-bromo-3,3,3-trifluoropropene and its application in the synthesis of fluorinated amino acids

A palladium-catalyzed cross-coupling of unactivated alkylzinc reagents with 2-bromo-3,3,3-trifluoropropene (BTP) has been developed, which was used as a key step to prepare a series of trifluoromethylated and difluoromethylated amino acids.

Lewis acidic alkaline earth metal complexes with a perfluorinated diphenylamide ligand

Alkaline earth metal chemistry with the anion [N(C₆F₅)₂]⁻ has been explored. Complexes are stabilized by metal⋯F interactions. Mg[N(C₆F₅)₂]₂ is a stronger Lewis acid than B(C₆F₅)₃.

Aromatic interactions in β-hairpin scaffold stability: A historical perspective

Non-covalent interactions between naturally occurring aromatic residues have been widely exploited as scaffold stabilizing agents in de novo designed peptides and in Nature - inspired structures. Our understanding of the factors driving aromatic interactions and their observed interaction geometries have advanced remarkably with improvements in conventional structural studies, availability of novel molecular methods and in silico studies, which have together provided atomistic information on aromatic interactions and interaction strengths. This review attempts to recapitulate the early advances in our understanding of aromatic interactions as stabilizing agents of peptide β-hairpins.