Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect

Mesoscale Acid-Base Complexes Display Size-Associated Photophysical Property and Photochemical Activity

The properties of single molecules and molecular aggregates can differ dramatically, leading to a long-standing interest in mesoscale aggregation processes. Herein, a series of acid-base molecular complexes is developed by using a tetraphenylethylene-backboned fluorophore, and investigated the photophysical properties and photochemical activities at different aggregation length scales. This fluorophore, with two basic diethylamine groups and two acidic tetrazole groups, exhibits sparse solubility due to multivalent interactions that cause infinite aggregation. The addition of a third acid leads to the formation of fluorophore/acid complexes with good dispersibility and colloidal stability. This assembly process can be controlled by the use of different acids and their stoichiometry, resulting in aggregates ranging in size from a few to hundreds of nanometers. A crystalline structure is obtained to illustrate the complex properties of the acid-base network. Unlike the single molecule, these complexes show a trend of size-related properties for photoluminescence efficiency and photochemical activity. As the amount of acid added increases, the size of the complexes decreases, the aggregation effect of the complexes on fluorescence emission increases, and the rates of the oxidative photocyclization and photodecomposition slow down. This work may help to understand size-controlled molecular materials at the mesoscale for functional design.

Engineering a polyvinyl butyral hydrogel as a thermochromic interlayer for energy-saving windows

Achieving mastery over light using thermochromic materials is crucial for energy-saving glazing. However, challenges such as high production costs, limited durability, and recyclability issues have hindered their widespread application in buildings. Herein, we develop a glass interlayer made of a polyvinyl butyral-based hydrogel swollen with LiCl solution. In addition to a fast, isochoric, and reversible transparency-to-opacity transition occurring as ambient temperatures exceed thermally comfortable levels, this hydrogel uniquely encompasses multiple features such as frost resistance, recyclability, scalability, and toughness. The combination of these features is achieved through a delicate balance of polyvinyl butyral's amphiphilicity and the suppression of network-forming phase separation. This design endows a nanostructured polyvinyl butyral-LiCl composite gel with swollen molecular segments linked by dispersed cross-linking sites in the form of hydrophobic nano-nodules. Upon laminating this hydrogel (a thickness of 0.3 mm), the resultant glazing product demonstrates approximately 90% luminous transmittance even at sub-zero temperatures, along with a significant modulation of solar and infrared radiation at 80.8% and 68.5%, respectively. Through simulations, we determined that windows equipped with the hydrogel could reduce energy consumption by 36% compared to conventional glass windows in warm seasons. The widespread adoption of polyvinyl butyral in construction underscores the promise of this hydrogel as a thermochromic interlayer for glazing.

Self-assembled nanonization of fatty acid-conjugated vaccine antigen for enhanced thermal stability

The aim of this study was to evaluate the enhanced thermal stability and physicochemical properties of fattigated vaccine antigens. High molecular weight influenza hemagglutinin (Heg) was used as a model antigen because of low heat stability requiring cold chamber. Heg was conjugated with long-chain oleic acid (C18) and short-chain 3-decenoic acid (C10) to prepare fattigated Heg. Circular dichroism analysis revealed no significant changes in the three-dimensional structure post-conjugation. In the liquid state, the fattigated Heg was self-assembled into nanoparticles (NPs) due to its amphiphilic nature, with sizes of 136.27 ± 12.78 nm for oleic acid-conjugated Heg (HOC) and 88.73 ± 3.27 nm for 3-decenoic acid-conjugated Heg (HDC). Accelerated thermal stability studies at 60 °C for 7 days demonstrated that fattigated Heg exhibited higher thermal stability than Heg in various liquid or solid states. The longer-chained HOC showed better thermal stability than HDC in the liquid state, attributed to increased hydrophobic interactions during self-assembly. In bio-mimicking liquid states at 37 °C, HOC exhibited higher thermal stability than Heg. Furthermore, solid-state HOC with cryoprotectants (trehalose, mannitol, and Tween® 80) had significantly increased thermal stability due to reduced exposure of protein surface area via nanonization behavior. The current fattigation platform could be a promising strategy for developing thermostable nano vaccines of heat-labile vaccine antigens.

Steric trapping strategy for studying the folding of helical membrane proteins

Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.

Monophenyl luminescent material with dual-state emission and pH sensitivity for cell imaging

Dual-state emission (DSE) luminescent materials are a newly discovered category of luminescent materials that exhibit efficient light emission in multiple states, including dilute solutions, highly concentrated solutions, aggregated states and solid states. These materials effectively address the aggregation-caused quenching (ACQ) observed in traditional organic luminescent materials with large conjugated planes, as well as the limitations of aggregation-induced emission (AIE) materials, which typically do not emit light in dilute solutions. The design and development of DSE luminescent materials for organelle imaging applications has attracted considerable interest. In this context, this study presents the design and synthesis of a novel luminescent compound, DMSS-AM, characterised by intramolecular hydrogen bonding and a D-π-A structure. As a monophenyl luminescent material, DMSS-AM exhibits DSE properties with fluorescence quantum yields of 22.1% in solution and 14.0% in the solid state. In particular, it exhibits unique pH-responsive properties, facilitating the targeted detection of lysosomal pH changes. Confocal laser scanning microscopy imaging of cells demonstrated that DSE emitters at both low and high concentrations do not affect image quality for bio-imaging applications. This advance is expected to significantly broaden the applicability of DSE luminescent materials in future applications.

Co-aggregation as A Simple Strategy for Preparing Fluorogenic Tetrazine Probes with On-Demand Fluorogen Selection

Life science has progressed with applications of fluorescent probes-fluorophores linked to functional units responding to biological events. To meet the varied demands across experiments, simple organic reactions to connect fluorophores and functional units have been developed, enabling the on-demand selection of fluorophore-functional unit combinations. However, organic synthesis requires professional equipment and skills, standing as a daunting task for life scientists. In this study, we present a simple, fast, and convenient strategy for probe preparation: co-aggregation of hydrophobic molecules. We focused on tetrazine-a difficult-to-prepare yet useful functional unit that provides effective bioorthogonal reactivity and strong fluorogenicity. Simply mixing the tetrazine molecules and aggregation-induced emission (AIE) luminogens in water, co-aggregation is induced, and the emission of AIE luminogens is quenched. Subsequent click reaction bioorthogonally turns on the emission, identifying these coaggregates as fluorogenic probes. Thanks to this bioorthogonal fluorogenicity, we established a new time-gated fluorescence bioimaging technique to distinguish overlapping emission signals, enabling multi-organelle imaging with two same-color fluorophores. Our study showcases the potential of this co-aggregation method for the on-demand preparation of fluorescent probes as well as protocols and molecular design principles in this approach, offering an effective solution to evolving needs in life science research.

Hydrophobic Cross-Linked Chains Regulate High Wet Tissue Adhesion Hydrogel with Toughness, Anti-hydration for Dynamic Tissue Repair

Hydrogel adhesion materials are widely reported for tissue engineering repair applications, however, wet tissue surface moisture can reduce the wet-adhesion properties and mechanical strength of hydrogels limiting their application. Here, anti-hydration gelatin-acrylic acid-ethylene dimethacrylate (GAE) hydrogels with hydrophobic cross-linked chains are constructed. The prepared GAE hydrogel is soaked in PBS (3 days) with a volume change of 0.6 times of the original and the adhesive strength, Young's modulus, toughness, and burst pressure are maintained by ≈70% of the original. A simple and universal method is used to introduce hydrophobic chains as cross-linking points to prepare hydrogels with anti-hydration, toughness, and high wet state adhesion. The hydrophobic cross-linked chains not only restrict the movement of molecular chains but also hinder the intrusion of water molecules. Antihydration GAE hydrogels exhibit good biocompatibility, slow drug release, and dynamic oral wet-state tissue repair properties. Therefore, the anti-hydration hydrogel has excellent toughness, wet tissue adhesion properties, and good prospects for biological applications.

Going Beyond Host Defence Peptides: Horizons of Chemically Engineered Peptides for Multidrug-Resistant Bacteria

Multidrug-resistant (MDR) bacteria are considered a health threat worldwide, and this problem is set to increase over the decades. The ESKAPE, a group of six pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. is the major source of concern due to their high death incidence and nosocomial acquired infection. Host defence peptides (HDPs) are a class of ribosomally synthesised peptides that have shown promising results in combating MDR, including the ESKAPE group, in- and outside bacterial biofilms. However, their poor pharmacokinetics in physiological mediums may impede HDPs from becoming viable clinical candidates. To circumvent this problem, chemical engineering of HDPs has been seen as an emergent approach to not only improve their pharmacokinetics but also their efficacy against pathogens. In this review, we explore several chemical modifications of HDPs that have shown promising results, especially against ESKAPE pathogens, and provide an overview of the current findings with respect to each modification.

Solvation thermodynamics from cavity shapes of amino acids

According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.

Lipid Bilayer Strengthens the Cooperative Network of a Membrane-Integral Enzyme

Lipid bilayer provides a two-dimensional hydrophobic solvent milieu for membrane proteins in cells. Although the native bilayer is widely recognized as an optimal environment for folding and function of membrane proteins, the underlying physical basis remains elusive. Here, employing the intramembrane protease GlpG of Escherichia coli as a model, we elucidate how the bilayer stabilizes a membrane protein and engages the protein's residue interaction network compared to the nonnative hydrophobic medium, micelles. We find that the bilayer enhances GlpG stability by promoting residue burial in the protein interior compared to micelles. Strikingly, while the cooperative residue interactions cluster into multiple distinct regions in micelles, the whole packed regions of the protein act as a single cooperative unit in the bilayer. Molecular dynamics (MD) simulation indicates that lipids less efficiently solvate GlpG than detergents. Thus, the bilayerinduced enhancement of stability and cooperativity likely stems from the dominant intraprotein interactions outcompeting the weak lipid solvation. Our findings reveal a foundational mechanism in the folding, function, and quality control of membrane proteins. The enhanced cooperativity benefits function facilitating propagation of local structural perturbation across the membrane. However, the same phenomenon can render the proteins' conformational integrity vulnerable to missense mutations causing conformational diseases1,2.

Acidic Conditions Impact Hydrophobe Transfer across the Oil-Water Interface in Unusual Ways

Molecular dynamics simulation and enhanced free energy sampling are used to study hydrophobic solute transfer across the water-oil interface with explicit consideration of the effect of different electrolytes: hydronium cation (hydrated excess proton) and sodium cation, both with chloride counterions (i.e., dissociated acid and salt, HCl and NaCl). With the Multistate Empirical Valence Bond (MS-EVB) methodology, we find that, surprisingly, hydronium can to a certain degree stabilize the hydrophobic solute, neopentane, in the aqueous phase and including at the oil-water interface. At the same time, the sodium cation tends to "salt out" the hydrophobic solute in the expected fashion. When it comes to the solvation structure of the hydrophobic solute in the acidic conditions, hydronium shows an affinity to the hydrophobic solute, as suggested by the radial distribution functions (RDFs). Upon consideration of this interfacial effect, we find that the solvation structure of the hydrophobic solute varies at different distances from the oil-liquid interface due to a competition between the bulk oil phase and the hydrophobic solute phase. Together with an observed orientational preference of the hydroniums and the lifetime of water molecules in the first solvation shell of neopentane, we conclude that hydronium stabilizes to a certain degree the dispersal of neopentane in the aqueous phase and eliminates any salting out effect in the acid solution; i.e., the hydronium acts like a surfactant. The present molecular dynamics study provides new insight into the hydrophobic solute transfer across the water-oil interface process, including for acid and salt solutions.

The role of available nitrogen in the adsorption of polystyrene nanoplastics on magnetic materials

Several studies have been conducted on nanoplastics (NPs). However, few studies have investigated the complexity of the interactions between NPs and other aqueous pollutants in multi-solute media. In this study, the adsorption of polystyrene nanoplastics (PSNPs) on magnetic materials (MS) in the presence of available nitrogen (AN) was studied. The results demonstrated that the adsorbed amount of PSNPs increased in the presence of ammonium nitrogen (NH₄⁺-N), whereas no significant difference was detected on the adsorbed amount of PSNPs using nitrate nitrogen (NO₃^--N) as a cosolute. The increase in the adsorbed amount of PSNPs was attributed to the formation of an MS-PSNPs-NH₄⁺-N complex. Scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and zeta potential analyses indicated that the PSNPs with NH₄⁺-N as a cosolute can be bound on the MS surfaces. Moreover, the change in the PSNPs amount adsorbed by MS depends on the valence state, electronegativity of the coexisting ions, and the surface properties and functional groups of PSNPs. Additionally, the ionic strength, dissolved organic matter, solution pH, metal cations and the subsequent release of MS-coated PSNPs and NH₄⁺-N changed considerably in different aquatic systems and artificial nitrating fluids. Among different natural aquatic systems, the PSNPs adsorption on MS was excellent in lake water. The results indicate high potential for the attachment of PSNPs to MS in the presence of AN and further deepen the understanding of removing NPs using magnetic materials in aqueous systems with various coexisting contaminants.

Chiral and Morphological Anisotropy of Supramolecular Polymers Shaped by a Singularity in Solvent Composition

Understanding the role of solvent in translating molecular anisotropy to supramolecular polymers is in the early stages. A solvent's influence on the strength of different noncovalent interactions can explain anisotropic growth in some cases, but its effect on cooperative processes, particularly in mixed solvents, remains obscure. We report the self-assembly of a series of chiral perylene bisimides in water-cosolvent mixtures, and the results highlight the fascinating influence of solvent-solute interactions on supramolecular anisotropy, both chiral and morphological. The initial assembly is agnostic to solvent composition, resulting in weakly chiral, spherical nanostructures. In an extremely narrow solvent composition range, the nanospheres transform into long, prominently chiral supramolecular polymers. Further, chirality can be fully reversed by changing the good (achiral) cosolvent. We elucidate how solvent modulates specific noncovalent interactions and governs the kinetics and thermodynamics of key processes, such as spontaneous phase segregation, secondary nucleation, and cooperative growth. In the context of supramolecular polymerization, our results encourage one to steer the focus away from the physical attributes of a solvent (polarity, phase diagram, etc.) and toward the complexities of solvent-solute interactions.

Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces

The hydrophobicity of an interface determines the magnitude of hydrophobic interactions that drive numerous biological and industrial processes. Chemically heterogeneous interfaces are abundant in these contexts; examples include the surfaces of proteins, functionalized nanomaterials, and polymeric materials. While the hydrophobicity of nonpolar solutes can be predicted and related to the structure of interfacial water molecules, predicting the hydrophobicity of chemically heterogeneous interfaces remains a challenge because of the complex, non-additive contributions to hydrophobicity that depend on the chemical identity and nanoscale spatial arrangements of polar and nonpolar groups. In this work, we utilize atomistic molecular dynamics simulations in conjunction with enhanced sampling and data-centric analysis techniques to quantitatively relate changes in interfacial water structure to the hydration free energy (a thermodynamically well-defined descriptor of hydrophobicity) of chemically heterogeneous interfaces. We analyze a large data set of 58 self-assembled monolayers (SAMs) composed of ligands with nonpolar and polar end groups of different chemical identity (amine, amide, and hydroxyl) in five mole fractions, two spatial patterns, and with scaled partial charges. We find that only five features of interfacial water structure are required to accurately predict hydration free energies. Examination of these features reveals mechanistic insights into the interfacial hydrogen bonding behaviors that distinguish different surface compositions and patterns. This analysis also identifies the probability of highly coordinated water structures as a unique signature of hydrophobicity. These insights provide a physical basis to understand the hydrophobicity of chemically heterogeneous interfaces and connect hydrophobicity to experimentally accessible perturbations of interfacial water structure.

Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein

Two years after SARS-CoV-2 caused the first case of COVID-19, we are now in the "new normal" period, where people's activity has bounced back, followed by the easing of travel policy restrictions. The lesson learned is that the wide availability of accurate and rapid testing procedures is crucial to overcome possible outbreaks in the future. Therefore, many laboratories worldwide have been racing to develop a new point-of-care diagnostic test. To aid continuous innovation, we developed a plasmonic-based biosensor designed explicitly for portable Surface Plasmon Resonance (SPR). In this study, we designed a single chain variable fragment (scFv) from the CR3022 antibody with a particular linker that inserted a cysteine residue at the second position. It caused the linker to have a strong affinity to the gold surface through thiol-coupling and possibly become a ready-to-use bioreceptor toward a portable SPR gold chip without purification steps. The theoretical affinity of this scFv on spike protein was -64.7 kcal/mol, computed using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method from the 100 ns molecular dynamics trajectory. Furthermore, the scFv was produced in Escherichia coli BL21 (DE3) as a soluble protein. The binding activity toward Spike Receptor Binding Domain (RBD) SARS-CoV-2 was confirmed with a spot-test, and the experimental binding free energy of -10.82 kcal/mol was determined using portable SPR spectroscopy. We hope this study will be useful in designing specific and low-cost bioreceptors, particularly early in an outbreak when the information on antibody capture is still limited.

Evolution of Transient Luminescent Assemblies Regulated by Trace Water in Organic Solvents

Trace water in organic solvents can play a crucial role in the construction of supramolecular assemblies, which has not gained enough attention until very recent years. Herein, we demonstrate that residual water in organic solvents plays a decisive role in the regulation of the evolution of assembled structures and their functionality. By adding Mg(ClO₄)₂ into a multi-component organic solution containing terpyridine-based ligand 3Tpy and monodentate imidazole-based ligand M2, the system underwent an unexpected kinetic evolution. Metallo-supramolecular polymers (MSP) formed first by the coordination of 3Tpy and Mg²⁺, but they subsequently decomposed due to the interference of M2, resulting in a transient MSP system. Further investigation revealed that this occurred because residual water in the solvent and M2 cooperatively coordinated with Mg²⁺. This allowed M2 to capture Mg²⁺ from MSP, which led to depolymerization. However, owing to the slow reaction between trace water/M2/Mg²⁺, the formation of MSP still occurred first. Therefore, water regulated both the thermodynamics and kinetics of the system and was the key factor for constructing the transient MSP. Fine-tuning the water content and other assembly motifs regulated the assembly evolution pathway, tuned the MSP lifetime, and made the luminescent color of the system undergo intriguing transition processes over time.

Aggregation of konjac glucomannan by ethanol under low-alkali treatment

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Microstructure of KGM alcogels is distinct from that of normal KGM gels.

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Gel network of EAK_gel is more heterogeneous than that of EK_gel.

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Ethanol arranges the aggregation of deacetylated KGM chains.

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Both structure and function of KGM aggregates are altered by ethanol and alkali.

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Solvent quality deterioration drives the formation of low-alkali KGM alcogels.

Utilizing ethanol in konjac glucomannan (KGM) gelation has important food processing applications. Typically, ethanol positively impacts the formation of low-alkali KGM gels and dramatically changes their physical properties, but the role of ethanol on the aggregation of KGM chains and the resultant gelation is less well understood. This study presents the distinct microstructures of low-alkali KGM gels incorporating ethanol. The fibril diameter and mesh size were determined to be 262.3 ± 22.3 nm and 2.680 ± 0.035 μm in average, contributing to a higher degree of anisotropy of such a gel network. Ethanol favors intermolecular aggregation by increasing the R_g of small-sized aggregates to 2.10 nm. The FTIR and temperature-cycled rheological studies suggest there are hydrophobic interactions stabilizing the gel network with the assistance of hydrogen bonds. The spatial confinement of deacetylated KGM chains as the solvent quality deteriorates by incorporating ethanol may arrange the aggregation and induce the structural reorganization in gel formation.

Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes

Molecular self-assembly provides a bottom-up platform to design supramolecular functional materials, attracting numerous interests in material sciences. The utilization of platinum(II) complexes as building blocks of supramolecular assemblies opens up the unique noncovalent Pt···Pt interaction as one of the driving forces, imparting the supramolecular materials with rich spectroscopic features. However, the exact role of Pt···Pt interactions in molecular assembly remains elusive. The current study combines experimental and computational techniques to elucidate the role of Pt···Pt interactions in the self-assembly process of a representative amphiphilic platinum(II) complex. This work demonstrates the directional role of Pt···Pt interactions in assisting the molecular assembly in an anisotropic manner, achieving the formation of ordered self-assembled structures.

Here, we report the use of an amphiphilic Pt(II) complex, K[Pt{(O₃SCH₂CH₂CH₂)₂bzimpy}Cl] (PtB), as a model to elucidate the key role of Pt···Pt interactions in directing self-assembly by combining temperature-dependent ultraviolet-visible (UV-Vis) spectroscopy, stopped-flow kinetic experiments, quantum mechanics (QM) calculations, and molecular dynamics (MD) simulations. Interestingly, we found that the self-assembly mechanism of PtB in aqueous solution follows a nucleation-free isodesmic model, as revealed by the temperature-dependent UV-Vis experiments. In contrast, a cooperative growth is found for the self-assembly of PtB in acetone–water (7:1, vol/vol) solution, which is further verified by the stopped-flow experiments, which clearly indicates the existence of a nucleation phase in the acetone–water (7:1, vol/vol) solution. To reveal the underlying reasons and driving forces for these self-assembly processes, we performed QM calculations and show that the Pt···Pt interactions arising from the interaction between the p_z and d_z² orbitals play a crucial role in determining the formation of ordered self-assembled structures. In subsequent oligomer MD simulations, we demonstrate that this directional Pt···Pt interaction can indeed facilitate the formation of linear structures packed in a helix-like fashion. Our results suggest that the self-assembly of PtB in acetone–water (7:1, vol/vol) solution is predominantly driven by the directional noncovalent Pt···Pt interaction, leading to the cooperative growth and the formation of fibrous nanostructures. On the contrary, the self-assembly in aqueous solution forms spherical nanostructures of PtB, which is primarily due to the predominant contribution from the less directional hydrophobic interactions over the directional Pt···Pt and π−π interactions that result in an isodesmic growth.

Contiguously hydrophobic sequences are functionally significant throughout the human exome

SignificanceProteins rely on the hydrophobic effect to maintain structure and interactions with the environment. Surprisingly, natural selection on amino acid hydrophobicity has not been detected using modern genetic data. Analyses that treat each amino acid separately do not reveal significant results, which we confirm here. However, because the hydrophobic effect becomes more powerful as more hydrophobic molecules are introduced, we tested whether unbroken stretches of hydrophobic amino acids are under selection. Using genetic variant data from across the human genome, we find evidence that selection increases with the length of the unbroken hydrophobic sequence. These results could lead to improvements in a wide range of genomic tools as well as insights into protein-aggregation disease etiology and protein evolutionary history.

Identifying nonadditive contributions to the hydrophobicity of chemically heterogeneous surfaces via dual-loop active learning

Hydrophobic interactions drive numerous biological and synthetic processes. The materials used in these processes often possess chemically heterogeneous surfaces that are characterized by diverse chemical groups positioned in close proximity at the nanoscale; examples include functionalized nanomaterials and biomolecules, such as proteins and peptides. Nonadditive contributions to the hydrophobicity of such surfaces depend on the chemical identities and spatial patterns of polar and nonpolar groups in ways that remain poorly understood. Here, we develop a dual-loop active learning framework that combines a fast reduced-accuracy method (a convolutional neural network) with a slow higher-accuracy method (molecular dynamics simulations with enhanced sampling) to efficiently predict the hydration free energy, a thermodynamic descriptor of hydrophobicity, for nearly 200 000 chemically heterogeneous self-assembled monolayers (SAMs). Analysis of this dataset reveals that SAMs with distinct polar groups exhibit substantial variations in hydrophobicity as a function of their composition and patterning, but the clustering of nonpolar groups is a common signature of highly hydrophobic patterns. Further molecular dynamics analysis relates such clustering to the perturbation of interfacial water structure. These results provide new insight into the influence of chemical heterogeneity on hydrophobicity via quantitative analysis of a large set of surfaces, enabled by the active learning approach.

Model Folded Hydrophobic Polymers Reside in Highly Branched Voids

By using advanced data analysis techniques, we characterize the shape of the voids surrounding model polymers of different sizes in water, observed in molecular dynamics simulations. We find that even when the model polymer is folded, the voids are extremely rough, with branches that can extend to over 1 nm away from the polymer. Water molecules in contact with the void retain close-to-bulk properties in terms of local structure. The branches disappear, and the voids start resembling the quasispherical shape predicted by dewetting theory only when they surround particles with a radius ∼1 nm, well above the size occupied by a folded hydrophobic polymer. Our results provide fresh insights into the microscopic origins of the vapor-like interfaces underlying dewetting and drying transitions.

Progress on Exploring the Luminescent Properties of Organic Molecular Aggregates by Multiscale Modeling

Luminescent molecular aggregates have attracted worldwide attention because of their potential applications in many fields. The luminescent properties of organic aggregates are complicated and highly morphology-dependent, unraveling the intrinsic mechanism behind is urgent. This review summarizes recent works on investigating the structure-property relationships of organic molecular aggregates at different environments, including crystal, cocrystal, amorphous aggregate, and doped systems by multiscale modeling protocol. We aim to explore the influence of intermolecular non-covalent interactions on molecular packing and their photophysical properties and then pave the effective way to design, synthesize, and develop advanced organic luminescent materials.

Kinetically Controlling the Length of Self-Assembled Polymer Nanofibers Formed by Intermolecular Hydrogen Bonds

Strong directional hydrogen bonds represent a suitable supramolecular force to drive the one-dimensional (1D) aqueous self-assembly of polymeric amphiphiles resulting in cylindrical polymer brushes. However, our understanding of the kinetics in these assembly processes is still limited. We here demonstrate that the obtained morphologies for our recently reported benzene tris-urea and tris-peptide conjugates are strongly pathway-dependent. A controlled transfer from solutions in organic solvents to aqueous environments enabled a rate-dependent formation of kinetically trapped but stable nanostructures ranging from small cylindrical or spherical objects (<50 nm) to remarkably large fibers (>2 μm). A detailed analysis of the underlying assembly mechanism revealed a cooperative nature despite the steric demands of the polymers. Nucleation is induced by hydrophobic interactions crossing a critical water content, followed by an elongation process due to the strong hydrogen bonds. These findings open an interesting new pathway to control the length of 1D polymer nanostructures.

Rapid and selective separation of amyloid beta from its stereoisomeric point mutations implicated in neurodegenerative Alzheimer's disease

Extracellular deposition of amyloid beta (Aβ) peptides are a hallmark of Alzheimer's disease. The isomerization and epimerization of Aβ peptides have been linked to the enhanced deposition of Aβ plaques. Therefore, considerable effort has been expended to create effective methods to distinguish such aberrant Aβ peptides from normal Aβ peptides. Herein, we have developed chromatographic retention U-shaped curves to investigate the hydrophobicity of Aβ 1-38, 1-40, 1-42 and fourteen aberrant Aβ 1-42 peptides. Using this information, we developed the first selective and comprehensive method that can easily detect both aberrant and normal Aβ peptides simultaneously using high performance liquid chromatography-mass spectrometry (HPLC-MS). We show for the first time that D-Ser modifications to Aβ cause the peptide to be more hydrophilic, as does D-Asp and L/D-iso-Asp.

Deciphering the evolution of supramolecular nanofibers in solution and solid-state: a combined microscopic and spectroscopic approach

Supramolecular self-assembly of small organic molecules has emerged as a powerful tool to construct well-defined micro- and nanoarchitecture through fine-tuning a range of intermolecular interactions. The size, shape, and optical properties of these nanostructures largely depend on the specific assembly of the molecular building units, temperature and polarity of the medium, and external stimuli. The engineering of supramolecular self-assembled nanostructures with morphology-dependent tunable emission is in high demand due to the promising scope in nanodevices and molecular machines. However, probing the evolution of molecular aggregates from the solution and directing the self-assembly process in a pre-defined fashion are challenging. In the present study, we have deciphered the sequential evolution of supramolecular nanofibers from solution to spherical and oblong-shaped nanoparticles through the variation of solvent polarity, tuning the hydrophobic-hydrophilic interactions. An intriguing case of molecular self-assembly has been elucidated employing a newly designed π-conjugated thiophene derivative (TPAn) through a combination of steady-state absorption, emission measurements, fluorescence correlation spectroscopy (FCS), and electron microscopy. The FCS analysis and microscopy results revealed that the small-sized nanofibers in the dispersion further agglomerated upon solvent evaporation, resulting in a network of nanofibers. Stimuli-responsive reversible interconversion between a network of nanofibers and spherical nanoaggregates was probed both in dispersion and solvent-evaporated state. The evolution of organic nanofibers and a subtle control over the self-assembly process demonstrated in the current investigation provide a general paradigm to correlate the size, shape, and emission properties of fluorescent molecular aggregates in complex heterogeneous media, including a human cell.

Microcrystal Electron Diffraction Elucidates Water-Specific Polymorphism-Induced Emission Enhancement of Bis-arylacylhydrazone

Aggregation-induced emission (AIE) phenomena have gained intense interest over the last decades because of its importance in solid-state emission. However, the elucidation of a working mechanism is difficult owing to the limited characterization methods on solid-state molecules, further complicated if dynamic structural changes occur. Here, a series of bis-arylacylhydrazones (BAHs) were synthesized, for which their AIE properties are only turned on by the reversible adsorption of water molecules. We used microcrystal electron diffraction (MicroED) to determine the molecular structures of two BAHs directly from bulk powders (without attempting to grow crystals) prepared in the absence or presence of water adsorption. This study reveals the unambiguous characterization of the dependence of crystal packing on the specific cocrystallization with hydrates. The structural analysis demonstrates that water molecules form strong hydrogen bonds with three neighboring BAH-1, resulting in the almost complete planarization and restriction of the intramolecular rotation of the molecule. MicroED plays an important role in providing a decisive clue for the reversible polymorphism changes induced by the adsorption of water molecules, regulating emissive properties.

Interactions between carbon-based nanoparticles and steroid hormone micropollutants in water

The occurrence of micropollutants (MPs) including steroid hormones is a global environmental and health challenge. Carbon-based nanoparticles can be incorporated with water treatment processes to allow MP removal by adsorption. The aim was to compare the suitability of such nanoparticles (graphene, graphene oxide, carbon nanotubes and C₆₀) to adsorb steroid hormones for later incorporation in membrane composites. All nanoparticles displayed fast kinetics; carbon nanotubes and graphene showed high adsorption capacities for hormones undeterminable in isotherm studies (over 10 mg/g). External surface adsorption appears to be the most prominent factor impacting adsorption performance. Structure, conformation, geometry and surface charge of nanoparticles can influence the accessibility of surface area through colloidal instability in aqueous solution. Mechanism inspection shows that adsorption initiates at long ranges (up to 10 nm) through hydrophobic and electrostatic interactions. At relatively short ranges (0.2-0.5 nm), adsorption is enhanced by π/π stacking, XH / π (X = C, O) interactions, van der Waals forces and hydrogen bonding. Both long- and short-range forces transporting hormones from the liquid bulk into the adsorbed phase could control the rate. With relatively short residence time required and high adsorption capacity, carbon nanotubes and graphene are promising for incorporation in a membrane composite.

Aggregate Science: From Structures to Properties

Molecular science entails the study of structures and properties of materials at the level of single molecules or small interacting complexes of molecules. Moving beyond single molecules and well-defined complexes, aggregates (i.e., irregular clusters of many molecules) serve as a particularly useful form of materials that often display modified or wholly new properties compared to their molecular components. Some unique structures and phenomena such as polymorphic aggregates, aggregation-induced symmetry breaking, and cluster excitons are only identified in aggregates, as a few examples of their exotic features. Here, by virtue of the flourishing research on aggregation-induced emission, the concept of "aggregate science" is put forward to fill the gaps between molecules and aggregates. Structures and properties on the aggregate scale are also systematically summarized. The structure-property relationships established for aggregates are expected to contribute to new materials and technological development. Ultimately, aggregate science may become an interdisciplinary research field and serves as a general platform for academic research.

Highly Selective Anion Template Effect in the Synthesis of Constrained Pseudopeptidic Macrocyclic Cyclophanes

Herein, we report the synthesis of a novel family of constrained pseudopeptidic macrocyclic compounds containing the hexahydropyrrolo[3,4-f]isoindolocyclophane scaffold and involving four coupled substitution reactions in the macrocyclization process. Although the increase in the number of steps involved in the macrocyclization could lead to a larger number of possible side products, the optimization of the methodology and the study of the driving forces have made it possible to obtain the desired macrocycles in excellent yields. A thorough computational study has been carried out to understand the macrocyclization process, and the results obtained nicely agree with experimental data. Moreover, the bromide anion had a clear catalytic template effect in the macrocyclization reaction, and surprisingly, the chloride anion had a negative template effect in opposition to the results obtained for analogous macrocycles. The parameters responsible for the specific kinetic template effect observed have been studied in detail.

Precise Molecular Design for High-Performance Luminogens with Aggregation-Induced Emission

Precise design of fluorescent molecules with desired properties has enabled the rapid development of many research fields. Among the different types of optically active materials, luminogens with aggregation-induced emission (AIEgens) have attracted significant interest over the past two decades. The negligible luminescence of AIEgens as a molecular species and high brightness in aggregate states distinguish them from conventional fluorescent dyes, which has galvanized efforts to bring AIEgens to a wide array of multidisciplinary applications. Herein, the useful principles and emerging structure-property relationships for precise molecular design toward AIEgens with desirable properties using concrete examples are revealed. The cutting-edge applications of AIEgens and their excellent performance in enabling new research directions in biomedical theranostics, optoelectronic devices, stimuli-responsive smart materials, and visualization of physical processes are also highlighted.

Phase separation of Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis

Tight control of centriole duplication is critical for normal chromosome segregation and the maintenance of genomic stability. Polo-like kinase 4 (Plk4) is a key regulator of centriole biogenesis. How Plk4 dynamically promotes its symmetry-breaking relocalization and achieves its procentriole-assembly state remains unknown. Here we show that Plk4 is a unique kinase that utilizes its autophosphorylated noncatalytic cryptic polo-box (CPB) to phase separate and generate a nanoscale spherical condensate. Analyses of the crystal structure of a phospho-mimicking, condensation-proficient CPB mutant reveal that a disordered loop at the CPB PB2-tip region is critically required for Plk4 to generate condensates and induce procentriole assembly. CPB phosphorylation also promotes Plk4's dissociation from the Cep152 tether while binding to downstream STIL, thus allowing Plk4 condensate to serve as an assembling body for centriole biogenesis. This study uncovers the mechanism underlying Plk4 activation and may offer strategies for anti-Plk4 intervention against genomic instability and cancer.

Binary Liquid Mixture Contact-Angle Measurements for Precise Estimation of Surface Free Energy

Surface free energy remains a fundamental material property to characterize the interfacial interactions between liquid and solid. Here, we developed a precise approach to determine surface energy by using contact angles of binary mixtures of water-dimethyl sulfoxide (DMSO), water-formamide, water-ethylene glycol, and water-glycerol and analyzed using the Owens-Wendt method. A mixing equation was developed to estimate liquid-dispersive surface tension (γ_L,mix^d) and polar surface tension (γ_L,mix^p) parameters for binary mixtures. To test the approach, two hydrophobic surfaces, flat polydimethylsiloxane (PDMS), and silane-derivatized glass were prepared and the contact angle of mixtures on the surfaces were obtained. Surface energy of PDMS determined by three binary mixtures agrees with that from pure solvents, but the uncertainty decreases to less than 13%; remarkably, the uncertainty drops to around 5% once we combined measured contact angles from all the mixtures, namely, water-DMSO, water-formamide, and water-ethylene glycol. Surface energies of silane-derivatized glass bearing ethyl (C₂), hexyl (C₆), and octadecyl (C₁₈) alkyl chains were determined with water-formamide and water-glycerol mixtures. Measured contact angles fit the Owens-Wendt model, and surface energy value determined from different binary mixtures agree with each other within error. Contact angle measurement of liquid mixtures is a simple method for determination of surface energy that improves the precision of surface energy determined by measurements of multiple pure solvents.

Spatially Heterogeneous Water Properties at Disordered Surfaces Decrease the Hydrophobicity of Nonpolar Self-Assembled Monolayers

Understanding the relationship between hydrophobicity and the properties of functionalized surfaces is vital to the design of materials that interact in aqueous environments. In this Letter, we use atomistic molecular dynamics simulations to investigate the effects of surface order on the hydrophobicity of self-assembled monolayers (SAMs) containing nonpolar ligands. We find that the interfacial hydrophobicity is highly correlated with SAM order and, strikingly, poorly correlated with the solvent-accessible surface area, which typically has been related to interfacial hydrophobicity. Analysis of spatial variations in both SAM and water properties reveals that the SAM-water interface is pinned near regions of disordered SAM surfaces with increased free volume, decreasing the overall interfacial hydrophobicity. Spatial variations in ligand end group positions at disordered SAM surfaces thus translate to spatial variations in hydrophobicity, yielding heterogeneous surface properties. These findings provide new insights into how surface order can alter the hydrophobicity of chemically uniform surfaces.

The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives

Side chain as the main conformational and self-assembly structural factor for C₂-pseudopeptides.

Self-assembled materials and supramolecular chemistry within microfluidic environments: from common thermodynamic states to non-equilibrium structures

Self-assembly is a crucial component in the bottom-up fabrication of hierarchical supramolecular structures and advanced functional materials. Control has traditionally relied on the use of encoded building blocks bearing suitable moieties for recognition and interaction, with targeting of the thermodynamic equilibrium state. On the other hand, nature leverages the control of reaction-diffusion processes to create hierarchically organized materials with surprisingly complex biological functions. Indeed, under non-equilibrium conditions (kinetic control), the spatio-temporal command of chemical gradients and reactant mixing during self-assembly (the creation of non-uniform chemical environments for example) can strongly affect the outcome of the self-assembly process. This directly enables a precise control over material properties and functions. In this tutorial review, we show how the unique physical conditions offered by microfluidic technologies can be advantageously used to control the self-assembly of materials and of supramolecular aggregates in solution, making possible the isolation of intermediate states and unprecedented non-equilibrium structures, as well as the emergence of novel functions. Selected examples from the literature will be used to confirm that microfluidic devices are an invaluable toolbox technology for unveiling, understanding and steering self-assembly pathways to desired structures, properties and functions, as well as advanced processing tools for device fabrication and integration.

Single-Molecule Force Spectroscopy Reveals Self-Assembly Enhanced Surface Binding of Hydrophobins

Hydrophobins have raised lots of interest as powerful surface adhesives. However, it remains largely unexplored how their strong and versatile surface adhesion is linked to their unique amphiphilic structural features. Here, we develop an AFM-based single-molecule force spectroscopy assay to quantitatively measure the binding strength of hydrophobin to various types of surfaces both in isolation and in preformed protein films. We find that individual class II hydrophobins (HFBI) bind strongly to hydrophobic surfaces but weakly to hydrophilic ones. After self-assembly into protein films, they show much stronger binding strength to both surfaces due to the cooperativity of different interactions at nanoscale. Such self-assembly enhanced surface binding may serve as a general design principle for synthetic bioactive adhesives.

Melatonin-directed micellization: a case for tryptophan metabolites and their classical bioisosteres as templates for the self-assembly of bipyridinium-based supramolecular amphiphiles in water

The bulk solution properties of amphiphilic formulations are derivative of their self-assembly into higher ordered supramolecular assemblies known as micelles and of their ordering at the air-water interface. Exerting control over the surface-active properties of amphiphiles and their propensity to aggregate in pure water is most often fine-tuned by covalent modification of their molecular structure. Nevertheless structural constraints which limit the performance of amphiphiles do emerge when trying to develop more sophisticated systems which undergo for example, shape-defined controlled assembly and/or respond to external stimuli. In this regard, the template-modulated assembly of the so-called "supramolecular amphiphiles" continues to make progress ordering molecules that otherwise have very little to no driving force to aggregate in a prescribed manner in aqueous solutions. Herein we describe the template-modulated micellization and ordering at the air-water interface of bipyridinium-based supramolecular amphiphiles triggered by host-guest interactions with high specificity for the neurotransmitter melatonin over its biosynthetic synthon l-tryptophan and the thermodynamic parameters governing the template-modulated micellization process. When bound to the bipyridinium units of micellized surfactant molecules, melatonin effectively serves as "molecular glue" capable of lowering the CMC by 52% as compared to untemplated solutions. Analysis of this system suggests that a hallmark of donor-acceptor template-modulated micellization in water is a strong positively correlated temperature dependence of the CMC and the absence of a U-shaped CMC-temperature curve. Our findings make a case for the incorporation of l-tryptophan-based metabolites and their classical synthetic pharmaceutical bioisosteres as potential targets/components of donor-acceptor CT-based supramolecular amphiphile systems/materials operating in water.

Extent of Surface Force Additivity on Chemically Heterogeneous Substrates at Varied Orientations

Surface interactions between chemically mixed surfaces, as well as those among dissolved biomolecules, comprise distinct contributions from polar and hydrophobic moieties. These contributions are often context dependent. Approximate compliance to the Cassie additivity equation for the wetting free energies on mixed surfaces in water is, however, indicative of similarly additive forces between individual surface elements, suggesting a quadratic interpolation model for total force from the forces between pure surfaces. We use molecular dynamics/umbrella sampling simulations of parallel and nonparallel mixed surfaces with demonstrable Cassie-like behavior to verify how well the total surface force between the heterogeneous, molecularly rough surfaces can be approximated as a combination of forces among the homogeneous ones. When accounting for dissimilar distances of approach between functional groups of different types, our results for graphene surfaces with mixed methyl and nitrile coating show such a superposition to provide a reasonable first order approximation of interactions between the platelets. Deviations from additivity are more prominent in parallel-plate configurations, at high content of hydrophobic groups, and small separations. The inclusion of water polarizability does not visibly alter the observed behavior regardless of platelet orientations. The outcome of this study determines the necessary molecular conditions for observing force additivity that emphasize the context dependence of hydrophobic interaction in the presence of polar groups. This notion provides guidelines for the syntheses of new, chemically heterogeneous materials with tailored function-oriented properties in aqueous media.

Harnessing complexity in molecular self-assembly using computer simulations

In molecular self-assembly, hundreds of thousands of freely-diffusing molecules associate to form ordered and functional architectures in the absence of an actuator. This intriguing phenomenon plays a critical role in biology and has become a powerful tool for the fabrication of advanced nanomaterials. Due to the limited spatial and temporal resolutions of current experimental techniques, computer simulations offer a complementary strategy to explore self-assembly with atomic resolution. Here, we review recent computational studies focusing on both thermodynamic and kinetic aspects. As we shall see, thermodynamic approaches based on modeling and statistical mechanics offer initial guidelines to design nanostructures with modest computational effort. Computationally more intensive analyses based on molecular dynamics simulations and kinetic network models (KNMs) reach beyond it, opening the door to the rational design of self-assembly pathways. Current limitations of these methodologies are discussed. We anticipate that the synergistic use of thermodynamic and kinetic analyses based on computer simulations will provide an important contribution to the de novo design of self-assembly.

Stabilizing Leaf and Branch Compost Cutinase (LCC) with Glycosylation: Mechanism and Effect on PET Hydrolysis

Cutinases are polyester hydrolases that show a remarkable capability to hydrolyze polyethylene terephthalate (PET) to its monomeric units. This revelation has stimulated research aimed at developing sustainable and green cutinase-catalyzed PET recycling methods. Leaf and branch compost cutinase (LCC) is particularly suited toward these ends given its relatively high PET hydrolysis activity and thermostability. Any practical enzymatic PET recycling application will require that the protein have kinetic stability at or above the PET glass transition temperature (T_g, i.e., 70 °C). This paper elucidates the thermodynamics and kinetics of LCC conformational and colloidal stability. Aggregation emerged as a major contributor that reduces LCC kinetic stability. In its native state, LCC is prone to aggregation owing to electrostatic interactions. Further, with increasing temperature, perturbation of LCC's tertiary structure and corresponding exposure of hydrophobic domains leads to rapid aggregation. Glycosylation was employed in an attempt to impede LCC aggregation. Owing to the presence of three putative N-glycosylation sites, expression of native LCC in Pichia pastoris resulted in the production of glycosylated LCC (LCC-G). LCC-G showed improved stability to native state aggregation while increasing the temperature for thermal induced aggregation by 10 °C. Furthermore, stabilization against thermal aggregation resulted in improved catalytic PET hydrolysis both at its optimum temperature and concentration.

Morphology, composition and aggregation mechanisms of soft bioflocs in marine snow and activated sludge: A comparative review

Conditions that lead to marine snow formation and aggregates that constitute the marine snow have similarities with the soft bioflocs that form during wastewater treatment by activated sludge process. Analysis of the conditions and similarities of the soft bioflocs in these two aquatic environments provide insight for the processes that lead to formation and growth of hydrated aggregates consisting of both living and nonliving particles, their chemical and biolocial composition, settling/suspension behavior, and contributing factors for their structure and morphology. This literature review provides a comparative analysis of the soft aggregates that form in marine and wastewater environments to characterize the conditions for formation and growth of highly hydrated aggregates consisting of microorganisms, suspended solids and large molecules. The marine snow and bioflocs that form in wastewater are visually similar and even contain microorganisms that are of similar type (i.e., Zoogloea, filamentous bacteria). During wastewater treatment, the microorganisms are not stressed and exopolymeric substances (EPS) produced have shorter molecules and higher protein content while EPS produced by the marine organisms are significantly larger in molecular size (by orders of magnitude) and have higher carbohydrate content.