Molecular Self-assembly Research Articles

Insights into the molecular self-assembly of urea-functionalized acetylenes.

This study investigates simple acetylenes substituted with phenylurea as a constant H-bonding unit (Alk-R) and varied hydrophobic units (R = H, Phenyl (Ph), Phenylacetylene (PA), Ph-NMe2) to understand self-assembly properties driven by synergistic non-covalent interactions. Our observations reveal hierarchical self-assembled fibrillar networks with luminescent needles, fibers, and flowers on nano- to micro-meter scales. Subtle changes in substituents led to significant differences: H, Ph, PA, and Ph-NMe2 produced needle-like crystals, dendritic nanofibers, microflakes, and no self-assembly, respectively. Alk-Ph-NMe2 likely didn't self-assemble due to reduced hydrophobic interactions and steric hindrance. Interestingly, Alk-Ph exhibited a uniform spherulitic pattern and effectively gelled organic solvents and water. This luminescent gel demonstrated multifunctionality, including white light emission when doped with Rhodamine-B dye and adsorption of organic cationic dyes (methylene blue and crystal violet) from water. This study offers valuable insights into balancing interactions to achieve desired hierarchical networks and understand material properties, guiding future molecular design.

Quantification of solvation forces with amplitude modulation AFM.

Interfacial solvation forces arise from the organisation of liquid molecules near solid surfaces. They are crucial to fundamental phenomena, spanning materials science, molecular biology, and technological applications, yet their molecular details remain poorly understood. Achieving a complete understanding requires imaging techniques, such as three-dimensional atomic force microscopy (3D AFM), to provide atomically resolved images of solid-liquid interfaces (SLIs). However, converting 3D AFM data into accurate tip-sample forces remains challenging, as the process of translating observables into forces is not straightforward. This study compares standard amplitude modulation AFM (AM-AFM) force reconstruction methods (FRMs) and identifies their limitations in reconstructing SLI forces. A novel numerical matrix-based FRM specifically designed for AM-AFM is then introduced, aiming to overcome the limitations and inaccuracies found in standard approaches. The new method is validated through simulations and experimental data obtained at the SLI of silicon oxide and water with 3D AFM. The proposed matrix-based FRM, differently from standard FRMs, can reconstruct the full SLI interaction at the atomic scale, with no loss of information deriving from the specific choice of AFM experimental parameters or the force functional form. This method unlocks the full spectrum of physical phenomena encoded in the tip-sample interaction at the SLI in AFM experiments, greatly advancing our understanding of interfacial properties and their effects on colloid science, including nanoparticle interactions and molecular self-assembly.

Edmundo G. Percástegui.

"My favorite principle is Molecular Self-Assembly. There is beauty in its simplicity, elegance, and the way it creates complexity and functionality… My secret/not-so-secret passion is singing and playing my guitar (it helped to make a few coins back in the day)…" Find out more about Edmundo G. Percástegui in his Introducing… Profile.

Fluorinated and methylated ortho-benzodipyrrole-based acceptors suppressing charge recombination and minimizing energy loss in organic photovoltaics.

The elimination of the A' unit from -type Y6-derivatives has led to the development of a new class of ortho-benzodipyrrole (o-BDP)-based A-DNBND-A-type NFAs. In this work, two new A-DNBND-A-type NFAs, denoted as CFB and CMB, are designed and synthesized, where electron-withdrawing fluorine atoms and electron-donating methyl groups are substituted on the benzene ring of the o-BDP moiety, respectively. CFB exhibits a blue-shifted absorption spectrum, stronger intermolecular interactions, shorter π-π stacking distances, and more ordered 3D intermolecular packing in the neat and blend films, enabling it to effectively suppress charge recombination in the PM6:CFB device showing a higher PCE of 16.55% with an FF of 77.45%. CMB displays a higher HOMO/LUMO energy level, a smaller optical bandgap, and a less ordered 3D packing, which contributes to its superior ability to suppress energy loss in the PM6:CMB device with a high V oc of 0.90 V and a PCE of 16.46%. To leverage the advantages of CFB and CMB, ternary PM6:Y6-16:CFB and PM6:Y6-16:CMB devices are fabricated. The PM6:Y6-16:CFB device exhibits the highest PCE of 17.83% with an increased V oc of 0.86 V and a J sc of 27.32 mA cm-2, while the PM6:Y6-16:CMB device displayed an elevated V oc of 0.87 V and an improved FF of 74.71%, leading to a PCE of 17.44%. The high PCE was achieved using the non-halogenated greener solvent o-xylene, highlighting their potential for facilitating more eco-friendly processing procedures. C-shaped disubstituted o-BDP-based A-D-A type acceptors open up new avenues for tailoring electronic properties and molecular self-assembly, achieving higher OPV performance with enhanced charge recombination suppression and reduced energy loss.

Synthesis of insensitive high-density energetic materials through molecular self-assembly

Synthesis of insensitive high-density energetic materials through molecular self-assembly

Exploration of Fusion and Fission of Molecular Assemblies in Aqueous Solution through a Dynamic Clustering Approach.

To understand the mechanism of self-assembly and to predict the evolutionary pattern of the fusion-fission system over a long period of time, studying the dynamics of these processes is of great significance. The trajectories from molecular dynamics (MD) simulations of self-assembly processes contain numerous latent fusion and fission events. To analyze the fusion and fission events from the simulated trajectory, in this article, a dynamic clustering approach was developed by comparing the changes of monomer composition within clusters over simulated time. The rates of fusion and fission events obtained from dynamic clustering analysis were further coupled with the population balance model (PBM), and the evolution of the molecular assemblies calculated is reasonably consistent with the corresponding MD simulation results. This approach provides a new idea to analyze the big data of molecular self-assembly dynamics obtained from MD simulations, and it offers a computationally achievable approach to connect discrete events at the molecular scale with continuum equations such as the PBM at the macroscale.

Opposite Roles of Cholesterol and Lanosterol in Lipid Membrane on Amyloid-Beta 42 Peptide Nucleation and Fibril Formation.

Molecular self-assembly of amyloid-beta peptides to form fibrillar aggregates is a known cause of Alzheimer's disease. Although homogeneous nucleation of amyloid-beta is unfavorable, heterogeneous nucleation of amyloid-beta in cell membranes plays a key role in fibril formation. We observed these opposite roles in the effects of cholesterol and lanosterol, the precursor of cholesterol in the brain, on nucleation. As previously reported, cholesterol accelerated nucleation, whereas lanosterol decelerated it when mixed with dioleoyl-phosphatidylcholine at 20%. The observed opposite effects of cholesterol and lanosterol on nucleation do not correlate with the differences in the mechanical and thermodynamic nature of mixed membranes. However, the affinity of amyloid-beta to the inner membrane seems to be related to the opposite effects on nucleation kinetics. Cholesterol reduced the insertion of amyloid-beta into the lipid membrane, whereas lanosterol promoted the insertion of amyloid-beta into the membrane, which would make amyloid-beta more tightly bound by lipid molecules and reduce its diffusivity in the membrane and consequently inhibit nucleation. Our study provides insights into the effects of sterol compounds other than the well-investigated cholesterol on the self-assembly of amyloid-beta to clarify the molecular basis underlying Alzheimer's disease pathology and to develop targeted therapeutic strategies.

Binding of a Co(III) Metalloporphyrin to Amines in Water: Influence of the pKa and Aromaticity of the Ligand, and pH-Modulated Allosteric Effect.

Metalloporphyrins have been widely utilized as building blocks for molecular self-assembly in organic solvents, but their application in water is less common due to competition from water molecules for the metal center. However, Co(III) metalloporphyrins are notable for their strong binding to two aromatic amine ligands in aqueous buffers. In this study, we present a comprehensive investigation of the binding behavior of Co(III) tetraphenyl sulfonic acid porphyrin with selected aromatic and aliphatic amines in aqueous solution. Our findings reveal that the ligand affinity is influenced by the pKa values of both the ligand and the porphyrin, as well as the hybridization state of the nitrogen atom, with binding to sp3-hybridized nitrogen being significantly weaker than to sp2-hybridized nitrogen. DFT calculations further suggest that the variations in binding affinities are due to differences in the electrostatic potential at the nitrogen atoms, with aromatic ligands generally exhibiting stronger Co-N coordination due to greater electrostatic attraction. Moreover, our study and the binding model we developed demonstrate that changes in pH affect the affinity for each ligand to varying degrees, sometimes resulting in an allosteric cooperative effect. This effect is linked to electronic changes introduced by the binding of the first ligand. Our model provides a predictive tool for understanding the assembly behavior of these porphyrins in aqueous buffers, with potential applications in developing more efficient catalysts and in the creation of smart materials for fields ranging from catalysis to nanomedicine and optoelectronics.

Octaethyl vs Tetrabenzo Functionalized Ru Porphyrins on Ag(111): Molecular Conformation, Self-Assembly and Electronic Structure.

Metalloporphyrins on interfaces offer a rich playground for functional materials and hence have been subjected to intense scrutiny over the past decades. As the same porphyrin macrocycle on the same surface may exhibit vastly different physicochemical properties depending on the metal center and its substituents, it is vital to have a thorough structural and chemical characterization of such systems. Here, we explore the distinctions arising from coverage and macrocycle substituents on the closely related ruthenium octaethyl porphyrin and ruthenium tetrabenzo porphyrin on Ag(111). Our investigation employs a multitechnique approach in ultrahigh vacuum, combining scanning tunneling microscopy, low-energy electron diffraction, photoelectron spectroscopy, normal incidence X-ray standing wave, and near-edge X-ray absorption fine structure, supported by density functional theory. This methodology allows for a thorough examination of the nuanced differences in the self-assembly, substrate modification, molecular conformation and adsorption height.

Precisely Constructing Superlattices of Soft Giant Molecules via Regulating Volume Asymmetry.

Soft matters, particularly giant molecular self-assembly, have successfully replicated complex structures previously exclusive to metal alloys. These superlattices are constructed from mesoatoms─supramolecular spherical motifs of aggregated molecules, and the formation of superlattices critically depends on the volume distributions of these mesoatoms. Herein, we introduce two general methods to control volume asymmetry (i.e., the volumes' ratio of the largest to smallest mesoatoms, VL/VS) within giant molecular self-assembly. Leveraging the spontaneous increase in the mesoatomic volume ratio in unary systems and self-sorted binary blends, we systematically adjust the volume asymmetry from 1.0 to 9.0 across 24 unary systems and 56 binary blends of giant molecules, uncovering the formation of various superlattices, including BCC, Frank-Kasper A15, σ, Laves C14, C15, NaZn13, AlB2, and notably, the first NaCl like superlattice in homogeneous soft matter self-assembly. A geometric-based analysis, combined with experimental results, further establishes a quantitative relationship between volume asymmetry and the corresponding superlattice formations, thus laying a solid foundation for superlattice engineering within giant molecular systems to mimic and even beyond metal alloys. The lattice parameters of various unit cells range from approximately 5 to 20 nm. Our investigation in giant molecules could guide the advancement of mesoscopic, periodic soft matter materials.

Exploring the Optical Properties of Carotenoid-Based Nanoparticles: The Role of Terminal Groups.

Carotenoids are increasingly used as naturally occurring food colorants. For application as beverage colorants, fat-soluble carotenoids are formulated into dispersion systems via nanoparticle (NP) formation. In recent years, the antioxidant properties of carotenoids have gained immense recognition for their preventive health benefits, thereby highlighting further interest in their development as functional food ingredients. Although functional carotenoids in dispersion-based formulations are desirable, knowledge regarding the structural and optical properties of NPs of carotenoids other than those of β-carotene, and methods to efficiently produce and compare NPs of various carotenoids, remain scarce. In this study, NPs of β-carotene, lycopene, astaxanthin, and lutein were prepared using a simple reprecipitation method, with a focus on understanding the variations in the molecular self-assembly influenced by the quality of solvent used during reprecipitation. This study presents the novel finding that the terminal groups of carotenoids significantly affect the intermolecular interactions, thereby altering the structural and optical properties of the resulting NPs. Our findings are expected to contribute to the development of new technologies for controlling the color of carotenoids based on the crystal structure of the NPs.

Principles and Biomedical Applications of Self-Assembled Peptides: Potential Treatment of Type 2 Diabetes Mellitus.

Type 2 diabetes mellitus (T2DM) is the most prevalent metabolic disorder worldwide. There have been tremendous efforts to find a safe and prolonged effective therapy for its treatment. Peptide hormones, from certain organisms in the human body, as the pharmaceutical agents, have shown outstanding profiles of efficacy and safety in plasma glucose regulation. Their therapeutic promises have undergone intensive investigations via examining their physicochemical and pharmacokinetic properties. Their major drawback is their short half-life in vivo. To address this challenge, researchers have recently started to apply the state-of-the-art molecular self-assembly on peptide hormones to form nanofibrillar structures, as a smart nanotherapeutic drug delivery technique, to tremendously enhance their prolonged bioactivity in vivo. This revolutionary therapeutic approach would significantly improve patient compliance. First, this review provides a comprehensive summary on the pathophysiology of T2DM, various efforts to treat this chronic disorder, and the limitations and drawbacks of these treatment approaches. Next, this review lays out detailed insights on various aspects of peptide self-assembly: adverse effects, potential applications in nanobiotechnology, thermodynamics and kinetics of the process, as well as the molecular structures of the self-assembled configurations. Furthermore, this review elucidates the recent efforts on applying reversible human-derived peptide self-assembly to generate highly organized smart nanostructured drug formulations known as nanofibrils to regulate and prolong the bioactivity of the human gut hormone peptides in vivo to treat T2DM. Finally, this review highlights the future research directions to advance the knowledge on the state-of-the-art peptide self-assembly process to apply the revolutionary smart nanotherapeutics for treatment of chronic disorders such as T2DM with highly improved patient compliance.

Twisted-Planar Molecular Engineering with Sonication-Induced J-Aggregation To Design Near-Infrared J-Aggregates for Enhanced Phototherapy.

J-aggregates show great promise in phototherapy, but are limited to specific molecular skeletons and poor molecular self-assembly controllability. Herein, we report a twisted-planar molecular strategy with sonication-induced J-aggregation to develop donor-acceptor (D-A) type J-aggregates for phototherapy. With propeller aggregation-induced emission (AIE) moieties as the twisted subunits and thiophene as the planar π-bridge, the optimal twisted-planar π-interaction in MTSIC induces appropriate slip angle and J-aggregates formation, redshifting the absorption from 624 nm to 790 nm. In contrast, shorter π-planarity results in amorphous aggregates, and elongation promotes charge transfer (CT) coupled J-aggregates. Sonication was demonstrated to be effective in controlling self-assembly behaviors of MTSIC, which enables the transformation from amorphous aggregates to H-intermediates, and finally to stable J-aggregates. After encapsulation with lipid-PEG, the resultant J-dots show enhanced phototherapeutic effects over amorphous dots, including brightness, reactive oxygen species (ROS) generation, and photothermal conversion, delivering superior cancer phototherapy performance. This work not only advances D-A type J-aggregates design but also provides a promising strategy for supramolecular assembly development.

Molecular self-assembly of stable and small branched DNA nanostructures: Higher than a helical turn is enough for hybridization

The Watson-Crick base pairing property of DNA is widely used for fabricating DNA nanostructures with well-defined geometry. Moreover, DNA nanostructures can be easily modified in terms of shape, size and function at the nanoscale level. Therefore, investigation on smaller and stable branched DNA (bDNA) is of critical significance for biomedical applications. In the present communication, we report smaller and stable branched DNA (bDNA) which is of critical significance for biomedical applications. In this study, a novel strategy has been used in identifying stable bDNA nanostructures with a minimum number of Watson-Crick base pairings. The importance of hybridizing regions and helical twists between multiple oligonucleotides has been explored using various biophysical techniques. The electrophoretic analysis demonstrated that hybridizing regions with ≥12 nt nucleotides can form stable bDNA structures. Substantial negative enthalpic contributions determine the significance of base stacking and the length of oligonucleotides in the hybridization process. Finally, thermal melting investigations confirmed the creation of bDNA nanostructures with ≥12 nt long hybridizing regions. In general, our findings indicate that bDNA oligonucleotides do not undergo hybridization if the number of base pairs is lesser for a single helical turn. Furthermore, the yield and stability of smaller bDNA nanostructures in physiological conditions are comparable with the earlier reported higher-order structures. Hence, smaller bDNAs are more stable which may be preferred over conventional bDNA nanostructures for advanced biomedical applications.

Molecular Engineering in the Semiconductor Industry: Progress and Prospects

Abstract. Along with population growth and economic development, human demand for energy and information will be more than ever, and humans need to rely on semiconductor devices to achieve energy storage, signal and other conversions. So how to design and prepare semiconductor materials with better performance, and industrialise and commercialise the materials has become a new hot topic. Typically, semiconductor materials are nanomaterials, and the current mainstream industrial processing is a top-down process, which raises the cost of production and leads to a waste of resources. Because of this, scientists are starting to believe that molecular engineeringa bottom-up strategy based on molecule self-assembly can save resources, energy, and production costs by constructing semiconductor material structures. This paper examines the bottom-up conceptual approach of molecular engineering and discusses the potential challenges in applying molecular self-assembly technology, which is a crucial method in molecular engineering, to the semiconductor industry. It ultimately concludes that molecular engineering plays a significant role in the semiconductor production process due to its advantages and vast potential for development.

Oleogel formation based on natural insoluble soybean fiber using capillary force: A novel strategy and application

Insoluble dietary fibers can be used as oleogelators to form oleogels via molecular self-assembly following chemical modification. However, the limitations of traditional chemical modifications and oleogel preparation methods significantly restrict their practical application. This study proposed a novel method to directly form edible oleogels using natural soybean insoluble fiber particles as oil-forming agents and water as a secondary fluid via the capillary suspension force between particles. The results showed that when the particle fraction was 15 % and the secondary fluid content was 0.2, a strong capillary suspension force could be formed to maintain the oil holding capacity of oleogels. The sedimentation coefficient analysis suggested that adding particles and secondary fluids significantly affected the oleogel stability. The polarity of the oils, as well as the ionic strength and pH of the secondary fluids, influenced the rheological properties of oleogels, which correlated with the interfacial tension between the secondary fluids and oils. Moreover, the stable oleogels showed their potential as excellent solid fat substitutes in the preparation of breads (specific volume = 2.029 ± 0.114 cm3/g, weight loss = 12.2 ± 2.6 %, and hardness = 3.321 ± 0.055 N). This study highlighted that insoluble dietary fiber can form oleogels via capillary suspension, which is a relatively rapid and simple strategy. Additionally, it provided a solid foundation for the comprehensive utilization of soybean processing byproducts and the transformation of traditional food-specific oils and fats.

Organic BODIPY Based Gels: Optical, Electrochemical and Self-Assembly Properties.

Two novel BODIPY dyes, BOC3 and BC12, were synthesized with variable alkyl chains at terminal amide functional units. BC12, featuring a longer alkyl chain (-C12H25), formed a gel compared to BOC3, which has a shorter alkyl chain (< C->CH2OCH3), due to supra molecular self-assembly in film. Both dyes exhibited absorption peaks around 530 nm in the visible region, with a red shift of about 30 nm in the film state, essential for organic electronic applications. Concentration variation studies revealed π-π stacking/aggregates in the solid state causing red shifts in absorption and emission. BC12 exhibited more significant red shifts in film compared to its solution state due to supra molecular self-assembly. Electronic structure analysis using density functional theories (BMK and O3LYP) showed better correlation with absorption using the O3LYP method. Both dyes displayed quasi-irreversible oxidation and reduction couples with suitable HOMO (5.46 eV) and LUMO (3.32 eV) energy levels for organic electronic applications. Transient photoluminescence studies indicated a longer lifetime for BC12 (5.28 ns) than BOC3 (4.50 ns), suggesting π-π aggregation and supra molecular self-assembly. BC12's gelation, attributed to its long alkyl chain and two-dimensional motifs of the BODIPY core, forms spherical-shaped nano networks. These findings underscore the potential of molecularly tuned dyes with alkyl chains for nano-sized self-assembly in organic electronic devices. Red shifts were observed due to combination of aggregation, stacking and columnar meso-phase formation in supramolecular assembly. Absorption spectra of dyes in toluene with various concentrations showed the formation of Aggregation/π-π stacking might be due to head to tailing interactions.

Molecular Dynamics and Self-Assembly in Double Hydrophilic Block and Random Copolymers.

We investigate the self-assembly and dynamics of double hydrophilic block copolymers (DHBCs) composed of densely grafted poly[oligo(ethylene glycol) methacrylate] (POEGMA) and poly(vinyl benzyl trimethylammonium chloride) (PVBTMAC) parent blocks by means of calorimetry, small- and wide-angle X-ray scattering (SAXS/WAXS), and dielectric spectroscopy. A weak segregation strength is evident from X-ray measurements, implying a disordered state and reflecting the inherent miscibility between the host homopolymers. The presence of intermixed POEGMA/PVBTMAC nanodomains results in homogeneous molecular dynamics, as evidenced through isothermal dielectric and temperature-modulated DSC measurements. The intermixed process undergoes a glass transition at a temperature approximately 40 K higher than the vitrification of bulk POEGMA segments, and it shifts to an even higher temperature by increasing the content of the hard block. At temperatures below the intermixed glass transition temperature, the confined POEGMA segments between the glassy intermixed regions contribute to a segmental process featuring (i) reduced glass transition temperature (Tg), (ii) reduced dielectric strength, (iii) broader distribution of relaxation times, and (iv) reduced fragility compared to the POEGMA homopolymer. We also observe two glass transition temperatures of dry PVBTMAC, which we attribute to the backbone and side chain segmental relaxation. To the best of our knowledge, this is the first time in the literature that these glass transitions of dry PVBTMAC have been reported. Finally, this study shows that excellent mixing of the two homopolymers is obtained, and this implies that different properties of this copolymer system can be tailored by adjusting the concentration of each homopolymer.

Unravelling the Complexity of Amyloid Peptide Core Interfaces.

Amyloids, large intermolecular sandwiched β-sheet structures, underlie several protein misfolding diseases but have also been shown to have functional roles and can be a basis for designing smart and responsive nanomaterials. Short segments of proteins, called aggregation-prone regions (APRs), have been identified that nucleate amyloid formation. Here we present the database of 173 APR crystal structures currently available in the PDB, and a tool, ACW, for analyzing their topologies and the 267 inter-β-sheet interfaces of zipper regions assigned in these structures. We defined a new descriptor of zipper interfaces, the surface detail index (SDi), which quantifies the intertwining between the side chains of both β-sheets of the zipper, an important factor for the molecular recognition and self-assembly of these mesostructures. This allowed a comparative analysis of the zipper interfaces and identification of 6 clusters with different intertwining, steric fit, and size characteristics using three complementary descriptors, SDi, shape complementarity, and buried surface area. 60% of the APR structures are formed by parallel β-sheets, of which 52% belong to the topological class 1. This could be explained by the better fit and a deeper entanglement of the zipper regions of the parallel structures than of the antiparallel structures, as the analysis showed that both their shape complementarity (0.79 vs 0.70) and SDi (1.53 vs 1.32) were higher. The higher abundance of certain residues (Asn and Gln in parallel and Leu and Ala in antiparallel β-sheets) can be explained by their ability to form different ladder-like secondary interaction patterns within β-sheets. Analogous to the hierarchy of protein structure, we interpreted the primary, secondary, tertiary, and quaternary structure levels of APRs revealing different characteristics of the zipper regions for both parallel and antiparallel β-sheet structures, which may provide clues to the structural conditions of amyloid core formation and the rational design of amyloid polymorphs.

Steerable Structural Evolvement and Adsorption Behavior of Metastable Polyoxovanadate-Based Metal-Organic Polyhedra.

Promoting the advancement of the structure and function of metastable substances is challenging but worthwhile. In particular, how to harness the entangled state and evolution path of labile porous structures has been at the forefront of research in molecular self-assembly. In this work, the metastable structures of polyoxovanadate-based metal-organic polyhedra (VMOPs) can be manually regulated, including separation of the interlocked aggregate by a ligand-widening approach as well as transformation from a tetrahedral to capsule-like scaffold via a vertice-remodeling strategy. In these processes, intra- and intermolecular π···π and C-H···π interactions have been recognized as the primary driving forces. Besides being responsible for commanding the structural evolvement of VMOPs, such weak interactions were able to program their spatial arrangements and hence the adsorption performances for dye and iodine. The successful use of such a weak force-dominated design concept beacons a feasible route for customization of the function-oriented metastable structures. Separation and transformation of the interlocked metastable VMOPs have been achieved via the respective ligand-widening approach and vertice-remodeling strategy. Not only their structures but also adsorption features could be well regulated by such a weak force-dominated design concept.