Dynamic Gas-Bridged Bond: An Opportunity of Fabricating Dynamic Assembled Materials with Gas.

Gas molecules, as a family of unique polyatomic building blocks, have long been considered hard to involve in molecular assembly or construct assembled materials due to their structural simplicity yet paucity of defined interacting sites. To solve this non-trivial challenge, a core idea is to break the limit of current ways of bonding gas molecules, endowing them with new modes of interactions that match the basic requirements of molecular assembly. In recent years, a new concept, named the dynamic gas-bridged bond (DGB), has emerged, which allows for gas molecules to constitute a dynamic bridging structure between other building blocks with the aid of frustrated Lewis pairs. This makes it possible to harness gas in a supramolecular or dynamic manner. Herein, this perspective discusses distinct dynamic natures of DGBs and manifests their particular functions in various fields, including the control of molecular/polymeric self-assembly nanostructures, creation of multidimensional assembled materials, and recyclable catalysts. The future research direction and challenges of dynamic gas-bridged chemistry toward gas-programmed self-assembly and gas-constructed adaptive materials are highlighted.

BuildAMol: a versatile Python toolkit for fragment-based molecular design.

In recent years computational methods for molecular modeling have become a prime focus of computational biology and cheminformatics. Many dedicated systems exist for modeling specific classes of molecules such as proteins or small drug-like ligands. These are often heavily tailored toward the automated generation of molecular structures based on some meta-input by the user and are not intended for expert-driven structure assembly. Dedicated manual or semi-automated assembly software tools exist for a variety of molecule classes but are limited in the scope of structures they can produce. In this work we present BuildAMol, a highly flexible and extendable, general-purpose fragment-based molecular assembly toolkit. Written in Python and featuring a well-documented, user-friendly API, BuildAMol empowers researchers with a framework for detailed manual or semi-automated construction of diverse molecular models. Unlike specialized software, BuildAMol caters to a broad range of applications. We demonstrate its versatility across various use cases, encompassing generating metal complexes or the modeling of dendrimers or integrated into a drug discovery pipeline. By providing a robust foundation for expert-driven model building, BuildAMol holds promise as a valuable tool for the continuous integration and advancement of powerful deep learning techniques.Scientific contributionBuildAMol introduces a cutting-edge framework for molecular modeling that seamlessly blends versatility with user-friendly accessibility. This innovative toolkit integrates modeling, modification, optimization, and visualization functions within a unified API, and facilitates collaboration with other cheminformatics libraries. BuildAMol, with its shallow learning curve, serves as a versatile tool for various molecular applications while also laying the groundwork for the development of specialized software tools, contributing to the progress of molecular research and innovation.

Long-range polymer ordering by directional coating to remarkably enhance the charge carrier mobility in PCDTPT-based organic field-effect transistors.

With the wide potential of organic field-effect transistors in all the modern electronic circuitries, researchers are grappling with the challenge of poor charge transport and hence lower mobility in organic polymers. Low-charge carrier mobility is mainly due to disorder in the molecular packing of organic semiconductors along with other factors, such as impurities, defects and interactions between molecules. The current research work has been conducted to align the molecular chains of poly[4-(4,4-dihexadecyl-4H-cyclopenta[1,2-|||b:5,4-|b']|dithiophen-2-yl)-alt-[1,2,5]thiadiazolo-[3,4-c]pyridine] (PCDTPT) using directional coating techniques such as dip coating and brush coating on nano-grooved substrates. Long-range order of polymer chains was clearly observed along the direction of brush coating and nanogrooves in optical and atomic force microscope (AFM) images while transmission spectra confirmed decreased pi-pi stacking for the polymer films deposited by this technique. By comparing the mobility performance of brush-coated devices with other techniques, we found a remarkable mobility enhancement of 90 times that of conventional spin-coated device and 24 times enhancement compared with the dip-coated device for the case when the alignment of polymer chains was parallel to the channel. All the fabrication and characterizations were performed in the ambient environment. This study demonstrates a potential approach to align the polymers on long and short ranges hence providing a route for high-performing devices in ambient conditions.

Liquid-Liquid and Liquid-Solid Interfacial Nanoarchitectonics.

Nanoscale science is becoming increasingly important and prominent, and further development will necessitate integration with other material chemistries. In other words, it involves the construction of a methodology to build up materials based on nanoscale knowledge. This is also the beginning of the concept of post-nanotechnology. This role belongs to nanoarchitectonics, which has been rapidly developing in recent years. However, the scope of application of nanoarchitectonics is wide, and it is somewhat difficult to compile everything. Therefore, this review article will introduce the concepts of liquid and interface, which are the keywords for the organization of functional material systems in biological systems. The target interfaces are liquid-liquid interface, liquid-solid interface, and so on. Recent examples are summarized under the categories of molecular assembly, metal-organic framework and covalent organic framework, and living cell. In addition, the latest research on the liquid interfacial nanoarchitectonics of organic semiconductor film is also discussed. The final conclusive section summarizes these features and discusses the necessary components for the development of liquid interfacial nanoarchitectonics.

Mix and Shake: A Mild Way to Drug-Loaded Lysozyme Nanoparticles.

Biocompatible nanoparticles as drug carriers can improve the therapeutic efficiency of hydrophobic drugs. However, the synthesis of biocompatible and biodegradable polymeric nanoparticles can be time-consuming and often involves toxic solvents. Here, a simple method for protein-based stable drug-loaded particles with a narrow polydispersity is introduced. In this process, lysozyme is mixed with hydrophobic drugs (curcumin, ellipticine, and dasatinib) and fructose to prepare lysozyme-based drug particles of around 150 nm in size. Fructose is mixed with the drug to generate nanoparticles that serve as templates for the lysozyme coating. The effect of lysozyme on the physicochemical properties of these nanoparticles is studied by transmission electron microscopy (TEM) and scattering techniques (e.g., dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS)). We observed that lysozyme significantly stabilized the curcumin fructose particles for 7 days. Moreover, additional drugs, such as ellipticine and dasatinib, can be loaded to form dual-drug particles with narrow polydispersity and spherical morphology. The results also reveal that lysozyme dual ellipticine/dasatinib curcumin particles enhance the cytotoxicity and uptake on MCF-7 cells, RAW 264.7 cells, and U-87 MG cells due to the larger and rigid hydrophobic core. In summary, lysozyme in combination with fructose and curcumin can serve as a powerful combination to form protein-based stable particles for the delivery of hydrophobic drugs.

Cu-chelated polydopamine nanozymes with laccase-like activity for photothermal catalytic degradation of dyes.

The industrial applications of enzymes are usually hindered by the high production cost, intricate reusability, and low stability in terms of thermal, pH, salt, and storage. Therefore, the de novo design of nanozymes that possess the enzyme mimicking biocatalytic functions sheds new light on this field. Here, we propose a facile one-pot synthesis approach to construct Cu-chelated polydopamine nanozymes (PDA-Cu NPs) that can not only catalyze the chromogenic reaction of 2,4-dichlorophenol (2,4-DP) and 4-aminoantipyrine (4-AP), but also present enhanced photothermal catalytic degradation for typical textile dyes. Compared with natural laccase, the designed mimic has higher affinity to the substrate of 2,4-DP with Km of 0.13 mM. Interestingly, PDA-Cu nanoparticles are stable under extreme conditions (temperature, ionic strength, storage), are reusable for 6 cycles with 97 % activity, and exhibit superior substrate universality. Furthermore, PDA-Cu nanozymes show a remarkable acceleration of the catalytic degradation of dyes, malachite green (MG) and methylene blue (MB), under near-infrared (NIR) laser irradiation. These findings offer a promising paradigm on developing novel nanozymes for biomedicine, catalysis, and environmental engineering.

Light-triggered AND logic tetrapeptide dynamic covalent assembly.

We demonstrate light-triggered dynamic covalent assembly of a linear short tetrapeptide containing two terminal cysteine residues in an AND logic manner. A photobase generator is introduced to accomplish light-mediated pH regulation to increase the reduction potential of thiols in the tetrapeptide, which activates its oxidative polymerization through disulfide bonds. Interestingly, it is elucidated that under light irradiation, mere co-existence of photobase generator and the oxidizing agent permits the polymerization performance of this tetrapeptide. Hence, a light-triggered AND logic dynamic covalent assembly of a tetrapeptide is achieved. Further, upon redox response, the reversible aggregation and disaggregation can be transformed for numerous times due to the dynamic covalent feature of disulfide bond. As a comparison, no assembly occurs for a short peptide containing one terminal cysteine residue under the same stimuli condition. This work offers a new approach to remotely control programmable molecular assembly of short linear peptides based on dynamic covalent bond, holding great potential in wide bioapplications.

Charge Photoaccumulation in Covalent Polymer Networks for Boosting Photocatalytic Nitrate Reduction to Ammonia.

In the design of photoelectrocatalytic cells, a key element is effective photogeneration of electron-hole pairs to drive redox activation of catalysts. Despite recent progress in photoelectrocatalysis, experimental realization of a high-performance photocathode for multi-electron reduction of chemicals, such as nitrate reduction to ammonia, has remained a challenge due to difficulty in obtaining efficient electrode configurations for extraction of high-throughput electrons from absorbed photons. This work describes a new design for catalytic photoelectrodes using chromophore assembly-functionalized covalent networks for boosting eight-electron reduction of nitrate to ammonia. Upon sunlight irradiation, the photoelectrode stores a mass of reducing equivalents at the photoexcited chromophore assembly for multielectron reduction of a copper catalyst, enabling efficient nitrate reduction to ammonia. By introducing the new photoelectrode structure, it is demonstrated that the electronic interplay between charge photo-accumulating assembly and multi-electron redox catalysts can be optimized to achieve proper balance between electron transfer dynamics and thermodynamic output of photoelectrocatalytic systems.

A Step-by-Step Guide for the Production of Recombinant Fluorescent TAT-HA-Tagged Proteins and their Transduction into Mammalian Cells.

Investigating the function of target proteins for functional prospection or therapeutic applications typically requires the production and purification of recombinant proteins. The fusion of these proteins with tag peptides and fluorescently derived proteins allows the monitoring of candidate proteins using SDS-PAGE coupled with western blotting and fluorescent microscopy, respectively. However, protein engineering poses a significant challenge for many researchers. In this protocol, we describe step-by-step the engineering of a recombinant protein with various tags: TAT-HA (trans-activator of transduction-hemagglutinin), 6×His and EGFP (enhanced green fluorescent protein) or mCherry. Fusion proteins are produced in E. coli BL21(DE3) cells and purified by immobilized metal affinity chromatography (IMAC) using a Ni-nitrilotriacetic acid (NTA) column. Then, tagged recombinant proteins are introduced into cultured animal cells by using the penetrating peptide TAT-HA. Here, we present a thorough protocol providing a detailed guide encompassing every critical step from plasmid DNA molecular assembly to protein expression and subsequent purification and outlines the conditions necessary for protein transduction technology into animal cells in a comprehensive manner. We believe that this protocol will be a valuable resource for researchers seeking an exhaustive, step-by-step guide for the successful production and purification of recombinant proteins and their entry by transduction within living cells. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA cloning, molecular assembly strategies, and protein production Basic Protocol 2: Protein purification Basic Protocol 3: Protein transduction in mammalian cells.

Molecular architectures of iron complexes for oxygen reduction catalysis-Activity enhancement by hydroxide ions coupling.

Developing cost-effective and high-performance electrocatalysts for oxygen reduction reaction (ORR) is critical for clean energy generation. Here, we propose an approach to the synthesis of iron phthalocyanine nanotubes (FePc NTs) as a highly active and selective electrocatalyst for ORR. The performance is significantly superior to FePc in randomly aggregated and molecularly dispersed states, as well as the commercial Pt/C catalyst. When FePc NTs are anchored on graphene, the resulting architecture shifts the ORR potentials above the redox potentials of Fe2+/3+ sites. This does not obey the redox-mediated mechanism operative on conventional FePc with a Fe2+-N moiety serving as the active sites. Pourbaix analysis shows that the redox of Fe2+/3+ sites couples with HO- ions transfer, forming a HO-Fe3+-N moiety serving as the ORR active sites under the turnover condition. The chemisorption of ORR intermediates is appropriately weakened on the HO-Fe3+-N moiety compared to the Fe2+-N state and thus is intrinsically more ORR active.

Molecular Nanoarchitectonics of Natural Photosensitizers and Their Derivatives Nanostructures for Improved Photodynamic Therapy.

Natural photosensitizers (PSs) and their derivatives have drawn ever-increasing attention in photodynamic therapy (PDT) for their wild range of sources, desirable biocompatibility, and good photosensitivity. Nevertheless, many factors such as poor solubility, high body clearance rate, limited tumor targeting ability, and short excitation wavelengths severely hinder their applications in efficient PDT. In recent years, fabricating nanostructures by utilizing molecular assembly technique is proposed to solve these problems. This technique is easy to put into effect, and the assembled nanostructures could improve the physical properties of the PSs so as to meet the requirement of PDT. In this concept, we focus on the construction of natural PSs and their derivatives nanostructures through molecular assembly technique to enhance PDT efficacy (Figure 1). Furthermore, current challenges and future perspectives of natural PSs and their derivatives for efficient PDT are discussed.

Ferroelectric Organic Semiconductor: [1]Benzothieno[3,2-b][1]benzothiophene-Bearing Hydrogen-Bonding -CONHC14H29 Chain.

An alkylamide-substituted [1]benzothieno[3,2-b][1]benzothiophene (BTBT) derivative of BTBT-CONHC14H29 (1) and C8H17-BTBT-CONHC14H29 (2) were prepared to design the multifunctional organic materials, which can show both ferroelectric and semiconducting properties. Single-crystal X-ray structural analyses of short-chain (-CONHC3H7) derivatives revealed the coexistence of two-dimensional (2D) electronic band structures brought from a herringbone arrangement of the BTBT π core and the one-dimensional (1D) hydrogen-bonding chains of -CONHC3H7 chains. The thin films of 1 and 2 fabricated on the Si/SiO2 substrate surface have monolayer and bilayer structures, respectively, resulting in conducting layers parallel to the substrate surface, which is suitable for a channel layer of organic field-effect transistors (OFETs). The thin film of 1 indicated a hole mobility µFET = 2.4 × 10-5 cm2 V-1 s-1 and threshold voltage VTh = - 29 V, whereas that of 2 showed a µFET = 2.1 × 10-2 cm2 V-1 s-1 and threshold voltage VTh = -9.7 V. Both 1 and 2 formed the smectic E (SmE) phase above 410 and 369 K, respectively, where the existence of a hole transport pathway was confirmed in the SmE phase. The ferroelectric hysteresis behavior was observed in bulk 1 and 2 in the polarization-electric field (P-E) curves at the SmE phase. 1 showed the remanent polarization Pr = 2.3 µC cm-2 and coercive electric field Ec = 5.2 V µm-1, whereas the Pr and Ec of 2 were 3.4 µC cm-2 and 7.0 V µm-1 at the conditions of 453 K and 1 Hz. Introduction of alkylamide units into the BTBT π core has the potential to develop the external stimulus-responsive organic semiconductors brought from both ferroelectricity and semiconducting properties.

Synergistic Combination of Reductive Covalent Functionalization and Atomic Layer Deposition-Towards Spatially Defined Graphene-Organic-Inorganic Heterostructures.

Three-dimensionally (3D) well-ordered and highly integrated graphene hybrid architectures are considered to be next-generation multifunctional graphene materials but still remain elusive. Here, we report the first realization of unprecedented 3D-patterned graphene nano-ensembles composed of a graphene monolayer, a tailor-made structured organophenyl layer, and three metal oxide films, providing the first example of such a hybrid nano-architecture. These spatially resolved and hierarchically structured quinary hybrids are generated via a two-dimensional (2D)-functionalization-mediated atomic layer deposition growth process, involving an initial lateral molecular programming of the graphene lattice via lithography-assisted 2D functionalization and a subsequent stepwise molecular assembly in these regions in the z-direction. Our breakthrough lays the foundation for the construction of emerging 3D-patterned graphene heterostructures.

Pursuing Green and Efficient Agriculture from Molecular Assembly: A Review of Solid-State Forms on Agrochemicals.

Achieving rapid global agricultural development while maintaining ecological harmony is a major challenge of the new millennium. Meeting this challenge requires the development of efficient and environmentally friendly agrochemicals, including pesticides and fertilizers. Molecular assembly, as a promising strategy, has garnered significant attention in recent years for the development of advanced solid-state forms of agrochemicals. In this review, we present the potential and recent advancements of solid-state forms, such as polymorphs, cocrystals/salts, solvates, inclusion compounds, and the amorphous state, for the production of high-efficiency and low-polluting agrochemical products. We provide an overview of the concepts and preparation methods of these solid-state forms, followed by an exploration of their applications in sustainable agriculture. Specifically, we highlight their value in enhancing pesticide solubility, enabling controlled release of chemical fertilizers, and reducing off-target risks. Lastly, we discuss the challenges and prospects associated with the utilization of solid-state forms for the advancement of environmentally friendly and efficient agriculture.

Investigation of the impacts of simple electrolytes and hydrotrope on the interaction of ceftriaxone sodium with cetylpyridinium chloride at numerous study temperatures.

Herein, interactions between cetylpyridinium chloride (CPC) and ceftriaxone sodium (CTS) were investigated applying conductivity technique. Impacts of the nature of additives (e.g. electrolytes or hydrotrope (HDT)), change of temperatures (from 298.15 to 323.15 K), and concentration variation of CTS/additives were assessed on the micellization of CPC + CTS mixture. The conductometric analysis of critical micelle concentration (CMC) with respect to the concentration reveals that the CMC values were increased with the increase in CTS concentration. In terms of using different mediums, CMC did not differ much with the increase in electrolyte salt (NaCl, Na2SO4) concentration, but increased significantly with the rise of HDT (NaBenz) amount. In the presence of electrolyte, CMC showed a gentle increment with temperature, while the HDT showed the opposite trend. Obtained result was further correlated with conventional thermodynamic relationship, where standard Gibb's free energy change (ΔGmo), change of enthalpy (ΔHmo), and change of entropy (ΔSmo) were utilized to investigate. The ΔGmo values were negative for all the mixed systems studied indicating that the micellization process was spontaneous. Finally, the stability of micellization was studied by estimating the intrinsic enthalpy gain (ΔHmo,∗) and compensation temperature (Tc). Here, CPC + CTS mixed system showed more stability in Na2SO4 medium than the NaCl, while in NaBenz exhibited the lowest stability.

Role of Sterically Bulky Azobenzenes in the Molecular Assembly of Pyrene Derivatives: Rectangular Sheet-like Structures and Their Emission Characteristics.

The development of pyrene-based fluorescent assembled systems with desirable emission characteristics by reducing conventional concentration quenching and/or aggregation-induced quenching (ACQ) is highly desirable. In this investigation, we designed a new azobenzene-functionalized pyrene derivative (AzPy) in which sterically bulky azobenzene is linked to pyrene. Absorption and fluorescence spectroscopic results before and after molecular assembly indicate that even in a dilute N,N-dimethylformamide (DMF) solution (~10 µM), AzPy molecules experienced significant concentration quenching, whereas the emission intensities of AzPy DMF-H2O turbid suspensions containing self-assembled aggregates were slightly enhanced and showed similar values regardless of the concentration. The shape and size of sheet-like structures, from incomplete flakes less than one micrometer in size to well-completed rectangular microstructures, could be adjusted by changing the concentration. Importantly, such sheet-like structures exhibit concentration dependence of their emission wavelength from blue to yellow-orange. Comparison with the precursor (PyOH) demonstrates that the introduction of a sterically twisted azobenzene moiety plays an important role in converting the spatial molecular arrangements from H- to J-type aggregation mode. Thus, AzPy chromophores grow into anisotropic microstructures through inclined J-type aggregation and high crystallinity, which are responsible for their unexpected emission characteristics. Our findings provide useful insight into the rational design of fluorescent assembled systems.

Deciphering the Mechanistic Basis for Perfluoroalkyl-Protein Interactions.

Although rarely used in nature, fluorine has emerged as an important elemental ingredient in the design of proteins with altered folding, stability, oligomerization propensities, and bioactivity. Adding to the molecular modification toolbox, here we report the ability of privileged perfluorinated amphiphiles to noncovalently decorate proteins to alter their conformational plasticity and potentiate their dispersion into fluorous phases. Employing a complementary suite of biophysical, in-silico and in-vitro approaches, we establish structure-activity relationships defining these phenomena and investigate their impact on protein structural dynamics and intracellular trafficking. Notably, we show that the lead compound, perfluorononanoic acid, is 106 times more potent in inducing non-native protein secondary structure in select proteins than is the well-known helix inducer trifluoroethanol, and also significantly enhances the cellular uptake of complexed proteins. These findings could advance the rational design of fluorinated proteins, inform on potential modes of toxicity for perfluoroalkyl substances, and guide the development of fluorine-modified biologics with desirable functional properties for drug discovery and delivery applications.

Syntheses, crystal structures and Hirshfeld surface analysis of 4-(4-nitro-phen-yl)piperazin-1-ium tri-fluoro-acetate and 4-(4-nitro-phen-yl)piperazin-1-ium tri-chloro-acetate.

The synthesis and crystal structures of the mol-ecular salts of 4-(4-nitro-phen-yl)piperazine with tri-fluoro-acetate, namely, 4-(4-nitro-phen-yl)piperazin-1-ium tri-fluoro-acetate, C10H14N3O2 +·C2F3O2 - (I), and with tri-chloro-acetate, namely, 4-(4-nitro-phen-yl)piperazin-1-ium tri-chloro-acetate, C10H14N3O2 +·C2Cl3O2 -, (II), are reported and compared. A partial positional disorder of the anions was found. In both structures, the piperazine rings adopt a chair conformation, whereas the positions of the nitro-phenyl group on the piperazine ring differ from bis-ectional in (I) to equatorial in (II). In both structures, the supra-molecular assemblies are mono-periodic on the basis of the chain-of-rings motifs supported by aromatic π-π inter-actions. Hirshfeld surface analysis was used to explore the inter-molecular close contacts in both crystals. The most dominant contacts of the Hirshfeld surface of the cation-anion pairs of the asymmetric units are O⋯H/H⋯O, and those with a contribution of halogen atoms: F⋯H/H⋯F in (I) and Cl⋯H/H⋯Cl in (II), respectively.

Modeling Protein Complexes and Molecular Assemblies Using Computational Methods.

Many biological molecules are assembled into supramolecular complexes that are necessary to perform functions in the cell. Better understanding and characterization of these molecular assemblies are thus essential to further elucidate molecular mechanisms and key protein-protein interactions that could be targeted to modulate the protein binding affinity or develop new binders. Experimental access to structural information on these supramolecular assemblies is often hampered by the size of these systems that make their recombinant production and characterization rather difficult. Computational methods combining both structural data, molecular modeling techniques, and sequence coevolution information can thus offer a good alternative to gain access to the structural organization of protein complexes and assemblies. Herein, we present some computational methods to predict structural models of the protein partners, to search for interacting regions using coevolution information, and to build molecular assemblies. The approach is exemplified using a case study to model the succinate-quinone oxidoreductase heterocomplex.

Electron-Deficient Benzo[de]isoquinolino[1,8-gh]quinoline Diamide π-Electron Systems.

Synthetically versatile electron-deficient π-electron systems are urgently needed for organic electronics, yet their design and synthesis are challenging due to the low reactivity from large electron affinities. In this work, we report a benzo[de]isoquinolino[1,8-gh]quinoline diamide (BQQDA) π-electron system. The electron-rich condensed amide as opposed to the generally-employed imide provides a suitable electronic feature for chemical versatility to tailor the BQQDA π-electron system for various electronic applications. We demonstrate an effective synthetic method to furnish the target BQQDA parent structure, and highly selective functionalization can be performed on bay positions of the π-skeleton. In addition, thionation of BQQDA can be accomplished under mild conditions. Fine-tuning of fundamental properties and supramolecular packing motifs are achieved via chemical modifications, and the cyanated BQQDA organic semiconductor demonstrates a high air-stable electron-carrier mobility.