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Molecular self-assembly

Molecular self-assembly is the spontaneous organization of individual molecules into structurally ordered architectures, driven by noncovalent interactions such as hydrogen bonding, electrostatic forces, π-π stacking, and van der Waals interactions, without external guidance or intervention. This process encodes the final structure within the molecular components themselves, relying on their inherent shapes, functionalities, and environmental conditions to achieve thermodynamic . In biological systems, molecular self-assembly underpins essential structures and functions, including the folding of proteins into functional three-dimensional conformations, the formation of lipid bilayers in cell membranes, and the helical coiling of DNA double strands. Synthetically, it enables the bottom-up fabrication of nanoscale materials through single-step or hierarchical assembly pathways, where simple molecular units progressively form complex superstructures ranging from 10 to 1000 nm in scale. Key principles involve precise molecular design to control assembly kinetics and pathways, often manipulating solution parameters like pH, temperature, or solvent composition to direct outcomes. The significance of molecular self-assembly lies in its potential to produce functional materials with emergent properties, such as conductivity in peptide nanofibers or responsiveness in supramolecular hydrogels, finding applications in nanotechnology for electronics, energy storage devices, drug delivery systems, and sustainable biomaterials. By mimicking nature's billions-of-years-evolved efficiency, this field advances toward scalable, programmable assembly for next-generation technologies.

Fundamentals

Definition and Scope

Molecular self-assembly refers to the spontaneous organization of molecules into structurally ordered aggregates or architectures through non-covalent interactions under equilibrium conditions. This process relies on the inherent chemical properties of the molecules, such as their shape, functionality, and intermolecular forces, to direct the formation of stable, well-defined structures without external intervention. Pioneering work by Jean-Marie Lehn described it as the association of molecules into aggregates joined by noncovalent bonds, emphasizing its role in creating complex entities from simple components. Similarly, George M. Whitesides defined self-assembly as the autonomous organization of components into patterns or structures without human intervention, highlighting its bottom-up nature in contrast to top-down fabrication methods. The scope of molecular self-assembly encompasses a vast range of scales and applications, from nanoscale supramolecular entities to larger functional materials, driven by weak, reversible interactions like hydrogen bonding, van der Waals forces, , and hydrophobic effects. In biological systems, it is fundamental to processes such as , DNA double-helix formation, and , enabling the of life's from molecular building blocks. Synthetically, it extends to and , where it facilitates the design of nanostructures for applications in , sensors, and , often producing architectures unattainable by traditional covalent synthesis. Lehn's framework positioned it as a chemical strategy for , targeting structures in the 1–100 nm range with molecular weights from 10⁴ to 10¹⁰ daltons, bridging and engineered materials. This phenomenon's versatility lies in its reversibility and adaptability, allowing error correction and dynamic reconfiguration in response to environmental cues, which broadens its utility across disciplines including chemistry, physics, and engineering. While naturally occurring in equilibrium-driven biological assembly, synthetic variants often incorporate kinetic control to access non-equilibrium states, expanding the scope to responsive and adaptive systems. Overall, molecular self-assembly represents a paradigm for constructing ordered complexity from disorder, with ongoing research leveraging it for sustainable and scalable fabrication in advanced technologies.

Historical Development

The concept of molecular self-assembly has roots in early 20th-century investigations into organized molecular films. In 1917, Irving Langmuir demonstrated the formation of monolayers of fatty acids at the air-water interface, revealing how amphiphilic molecules spontaneously organize into ordered structures driven by hydrophobic interactions, laying foundational principles for later self-assembly studies. This work, extended by Katherine Blodgett in the 1930s through multilayer deposition techniques, highlighted the potential for controlled molecular organization on surfaces, influencing subsequent developments in supramolecular systems. A pivotal advancement occurred in 1967 when Charles J. Pedersen accidentally discovered crown ethers while synthesizing ligands to stabilize metal catalysts at DuPont; these cyclic polyethers exhibited remarkable selectivity for alkali metal cations through non-covalent encapsulation, marking the birth of host-guest chemistry as a cornerstone of molecular recognition and self-assembly. Building on this, in the 1970s, Donald J. Cram developed spherands—rigid, preorganized cavities for precise guest binding—and Jean-Marie Lehn synthesized cryptands, three-dimensional analogs that enhanced binding affinity via multiple non-covalent interactions. Lehn formalized the field in 1978 by coining the term "supramolecular chemistry" to describe the chemistry of intermolecular bonds leading to organized entities beyond single molecules, emphasizing self-assembly through reversible interactions like hydrogen bonding and coordination. The 1987 Nobel Prize in Chemistry, awarded to Pedersen, Cram, and Lehn, recognized their pioneering work on molecules with selective host sites, catalyzing widespread interest in designing self-assembling systems. In the 1990s, George M. Whitesides advanced the field by promoting molecular self-assembly as a "bottom-up" strategy for , exemplified by self-assembled monolayers (SAMs) of alkanethiols on surfaces, which form ordered, functional films through and van der Waals forces. This approach enabled applications in patterning and sensing, bridging with . Subsequent decades saw expansions into dynamic self-assembly, with contributions from researchers like Fraser Stoddart on rotaxanes and catenanes, and Nadrian Seeman on DNA-based nanostructures, integrating biological motifs for programmable assemblies. By the , the field had matured into a multidisciplinary domain, incorporating computational modeling and advanced characterization to engineer complex architectures like vesicles and gels.

Principles and Mechanisms

Driving Forces

Molecular self-assembly is primarily by non-covalent interactions that provide the thermodynamic favorability for spontaneous organization into ordered structures, balancing enthalpic gains from with entropic costs of . These interactions are reversible and weaker than covalent bonds, allowing and error correction during assembly. The overall process is governed by the minimization of , where the assembled is more than the dissociated components. Key driving forces include the hydrophobic effect, which dominates in aqueous environments by expelling nonpolar moieties from water to reduce unfavorable solvent interactions, as seen in the formation of lipid bilayers and micelles. Hydrogen bonding contributes specificity and directionality, enabling precise molecular recognition, such as in the β-sheet formation of peptides where amide groups align to form nanofibers at concentrations below 1 wt%. Electrostatic interactions, including charge-charge attractions and salt bridges, facilitate ionic self-complementary assemblies, exemplified by peptide systems with alternating charges that drive hydrogel formation. Van der Waals forces and π-π stacking provide cumulative stabilization, particularly in aromatic systems; for instance, π-π interactions in Fmoc-modified dipeptides promote stacking into structures at low concentrations (~0.5 %). Metal-ligand coordination acts as a , directional in supramolecular helicates, where ligand-metal directs helical architectures through self-recognition processes. These forces often cooperate synergistically, as in peptide amphiphiles where hydrophobic tails collapse via the while hydrophilic heads form hydrogen-bonded coronas. Environmental factors like , , and solvent modulate these interactions to control kinetics and .

Types of Self-Assembly

Molecular self-assembly processes are broadly classified into static and dynamic types based on whether the resulting structures form at equilibrium or require continuous energy dissipation. Static self-assembly occurs in systems that reach a global or local energy minimum without ongoing energy input, leading to stable, ordered structures that persist once formed. These processes are driven by reversible non-covalent interactions, such as hydrogen bonding or van der Waals forces, and are common in the formation of molecular crystals, where molecules arrange into lattices to minimize free energy. For example, the folding of globular proteins into their native conformations exemplifies static self-assembly, as the polypeptide chain adopts a thermodynamically favored structure through intramolecular interactions. In contrast, dynamic involves the continuous of to maintain , often resulting in transient or adaptive structures that respond to external stimuli. This type is prevalent in , where from metabolic processes sustains non-equilibrium states, such as the dynamic assembly of in cells that undergo rapid and . Synthetic examples include the of magnetic particles at a liquid-air under a rotating magnetic field, forming swirling patterns that dissipate through motion. Dynamic processes enable complexity and functionality, such as in oscillatory chemical reactions like the Belousov-Zhabotinsky reaction, where spatial patterns emerge from local interactions. Another key classification distinguishes intramolecular self-assembly, where a single folds or organizes internal components into a , from intermolecular self-assembly, involving interactions between multiple molecules to form larger aggregates. Intramolecular self-assembly is akin to the autonomous folding of a into a compact form. This process relies on encoded information within the itself, minimizing entropy while stabilizing the folded state through non-covalent bonds. Intermolecular self-assembly, on the other hand, builds supramolecular architectures from discrete molecular units, often through collective interactions like hydrophobic effects or π-π stacking. A example is the formation of micelles by molecules in , where hydrophobic tails inward to avoid , creating spherical structures that solubilize non-polar . This type scales to larger assemblies, such as lipid bilayers in cell membranes, where phospholipids self-organize into fluid, two-dimensional sheets via intermolecular forces. Hierarchical intermolecular assembly further extends this, as in block copolymer , yielding ordered domains like cylinders or lamellae over multiple length scales. These classifications are not mutually exclusive; for instance, static intramolecular folding can precede dynamic intermolecular interactions in biological systems like virus capsid formation. Understanding these types informs the of , where controlling the balance between equilibrium stability and kinetic adaptability is crucial for applications in and sensors.

Supramolecular Assemblies

Host-Guest Systems

Host-guest systems represent a foundational aspect of , wherein a molecule—typically a macrocyclic or cavitand structure—selectively binds a complementary guest or ion through non-covalent interactions to form a stable complex. This molecular recognition mimics biological processes like enzyme-substrate binding and enables spontaneous self-assembly into discrete or extended structures without covalent bonds. The binding is driven primarily by forces such as hydrogen bonding, hydrophobic effects, electrostatic interactions, π-π stacking, and van der Waals forces, allowing for dynamic and reversible associations. These systems are characterized by high specificity, where the host's cavity size, shape, and functional groups dictate guest selectivity, often achieving association constants ranging from 10² to 10⁸ M⁻¹ depending on the pair. The development of host-guest chemistry traces back to the 1960s, pioneered by Charles J. Pedersen's discovery of crown ethers—cyclic polyethers that selectively complex alkali metal ions based on cavity size, such as 18-crown-6 for potassium ions with a binding constant of approximately 10⁶ M⁻¹ in methanol. Building on this, Donald J. Cram introduced rigid, three-dimensional hosts like spherands for enhanced preorganization and binding affinity, while Jean-Marie Lehn expanded the field to cryptands and supramolecular assemblies, earning them the 1987 Nobel Prize in Chemistry for advancing molecular recognition and self-assembly principles. Subsequent milestones include the elucidation of cyclodextrins (CDs)—oligomeric glucose rings with hydrophobic interiors—as versatile hosts for organic guests via inclusion complexes, and cucurbiturils (CB), pumpkin-shaped macrocycles that form exceptionally tight ion-dipole interactions, exemplified by CB's binding to methylviologen with a constant exceeding 10¹² M⁻¹. Calixarenes, basket-like phenols, further diversify hosts by tuning rim functionality for guest encapsulation. In molecular self-assembly, host-guest interactions extend beyond binary complexes to hierarchical structures, such as pseudorotaxanes and rotaxanes where guests thread through host rings, or supramolecular polymers linked by multiple recognition motifs. For instance, β-cyclodextrin-adamantane pairs self-assemble into vesicles or micelles in aqueous media, driven by hydrophobic inclusion and amphiphilicity, with diameters tunable from 100-500 nm. Cucurbituril-based systems enable out-of-equilibrium assemblies responsive to stimuli like pH or light, forming nanotubes or gels through sequential binding. These dynamics facilitate applications in drug delivery, where host-guest complexes enhance solubility (e.g., paclitaxel with β-CD increasing bioavailability by orders of magnitude) and controlled release, underscoring their role in advancing nanotechnology and materials science.

Micelles and Vesicles

Micelles are spherical aggregates formed by the of amphiphilic molecules in aqueous solutions above a (), where the hydrophobic tails inward to minimize with , while the hydrophilic heads face . This is primarily driven by the , which reduces the of the by sequestering nonpolar segments from the , supplemented by van der Waals and electrostatic repulsions among head groups. Seminal work by Tanford elucidated how this governs micelle formation, emphasizing the of in stabilizing these core-shell structures typically 10–100 in diameter. The geometry of micelles depends on the packing , a ratio of the hydrophobic to the effective head-group area times length, as formalized by Israelachvili; conical shapes (packing <1/3) favor spherical micelles, while cylindrical forms emerge at higher values. Classic examples include sodium dodecyl sulfate (SDS) surfactants, which form normal micelles in water for solubilizing hydrophobic compounds, and reverse micelles like those from cetyl-trimethyl-ammonium bromide in nonpolar solvents, where hydrophilic cores encapsulate water. These assemblies exhibit dynamic equilibrium, with molecules exchanging rapidly, enabling applications in detergency and drug delivery without covalent bonds. Vesicles, or liposomes, represent a more complex self-assembled morphology, consisting of one or more closed lipid bilayers enclosing an aqueous compartment, formed by amphiphiles with packing parameters around 1. Alec Bangham's 1965 discovery demonstrated that phospholipids like lecithin spontaneously swell into multilamellar vesicles upon hydration, driven by hydrophobic interactions and van der Waals forces between tails, with head-group repulsions preventing collapse. Unlike micelles, vesicles can be unilamellar (small: 20–100 nm; large: >100 nm) or multilamellar, providing semipermeable barriers that mimic cell membranes and facilitate compartmentalization. Formation of vesicles involves of planar bilayers that and close due to at edges, with a critical vesicle determined by rigidity; for phospholipids, the minimum diameter is approximately 20 nm, leading to size distributions skewed toward larger vesicles. Beyond biological , synthetic vesicles assemble from single-chain amphiphiles like fatty acids (minimum 8 carbons) or non-lipid molecules such as calixarenes and peptides, often requiring input like sonication for unilamellar structures. These assemblies played a pivotal role in origins-of-life hypotheses, as vesicles from simple amphiphiles could encapsulate RNA and catalyze reactions, promoting primitive cellular evolution. In modern contexts, vesicles enable targeted delivery, with stability enhanced by cholesterol incorporation to modulate fluidity.

Biological Self-Assembly

Protein and Enzyme Complexes

Protein and enzyme complexes represent a of biological , where multiple polypeptide chains spontaneously organize into functional oligomeric or higher-order structures through non-covalent interactions. These assemblies enable functions, such as and substrate channeling, that are unattainable by subunits. In cellular environments, is driven by thermodynamic favorability, with specific subunit interfaces ensuring precise and . For instance, hemoglobin, a consisting of two α and two β subunits, to form a globular that facilitates oxygen and in erythrocytes. The of is stabilized by hydrophobic contacts, hydrogen bonds, and salt bridges at the α-β interfaces, allowing for conformational shifts between tense (T) and relaxed (R) states upon ligand . Multi-enzyme complexes exemplify hierarchical in , where enzymes organize into macromolecular units to enhance catalytic via proximity and channeling of intermediates. The (PDC), a massive in mitochondria and , comprises multiple copies of three enzymes—E1 (), E2 (dihydrolipoyl transacetylase), and E3 (dihydrolipoyl dehydrogenase)—forming a core of 24 E2 subunits surrounded by E1 and E3. In , PDC self-assembles spontaneously from its components, with catalytic activity directly correlating to the of ; dissociated subunits exhibit minimal , while the intact complex achieves high through lipoyl swinging for . is governed by hydrophobic and electrostatic interactions at subunit interfaces, without requiring chaperones, and the structure's cubic symmetry (e.g., approximately 9.5 MDa in eukaryotes) underscores evolutionary conservation for bridging glycolysis and the citric acid cycle. Larger complexes like the proteasome illustrate chaperone-assisted self-assembly to achieve fidelity in complex architectures. The eukaryotic 26S proteasome consists of a 20S core particle (CP) barrel—formed by four stacked heptameric rings of α and β subunits—and two 19S regulatory particles (RPs) that cap the ends for substrate recognition and unfolding. CP assembly proceeds stepwise: α-rings form first, aided by PAC1-PAC2 chaperones to prevent misdimerization; pro-β subunits then incorporate sequentially with Ump1/POMP as a maturation factor, culminating in autocatalytic cleavage of propeptides to activate the catalytic threonines. RP assembly involves distinct chaperones like Nas6, Rpn14, and Nas2 to build the base and lid subcomplexes before docking to the CP. This regulated process ensures the ~2.5 MDa holoenzyme's role in ubiquitin-dependent proteolysis, preventing off-target activity during biogenesis. Driving forces include electrostatic complementarity and hydrophobic collapse, modulated by ATP and cellular conditions. In broader biological contexts, these assemblies often incorporate intrinsically disordered regions (IDRs) for dynamic , forming membraneless organelles that concentrate enzymes for rapid responses. For example, enzymatic complexes in stress granules or metabolic hubs rely on multivalent interactions via low-complexity domains to transiently self-assemble, enhancing reaction rates by orders of . Such highlight self-assembly's in cellular adaptability, with evolutionary pressures favoring robust yet reversible structures.

Nucleic Acid and Membrane Structures

Nucleic acid self-assembly exemplifies molecular recognition and structural precision in biology, primarily through base pairing and folding mechanisms that drive the formation of double helices and higher-order architectures. In DNA, the double helix structure arises spontaneously from the complementary pairing of adenine with thymine and guanine with cytosine via hydrogen bonds, stabilizing two antiparallel polynucleotide chains coiled around a common axis with a pitch of 34 Å and 10 base pairs per turn. This self-assembly process, governed by Watson-Crick base pairing rules, ensures sequence-specific association under physiological conditions, enabling the molecule's role in genetic information storage and replication. RNA self-assembly, in contrast, involves both intra- and intermolecular interactions to form diverse secondary and tertiary structures, often without a complementary strand. RNA molecules fold into complex structures through canonical base pairing and non-canonical interactions. Ribozymes, such as the self-splicing group I , demonstrate catalytic capability through self-assembled tertiary folds stabilized by magnesium ions and base stacking, highlighting RNA's versatility in prebiotic and cellular contexts. These natural motifs, including hairpins, pseudoknots, and kissing loops, serve as modular building blocks for programmable , as seen in the ribosome's large subunit where rRNA folds into a scaffold supporting protein . Membrane structures emerge from the of amphiphilic , where hydrophobic tails to minimize while hydrophilic heads interact with the aqueous , forming a bilayer approximately 40-50 thick. In biological systems, phospholipids like phosphatidylcholine spontaneously organize into bilayers under physiological ionic strengths and temperatures, driven by the and van der Waals forces between acyl chains. The describes this bilayer as a dynamic two-dimensional proteins and , with lateral coefficients around 10^{-8} cm²/ for , allowing adaptive reorganization during cellular processes such as . Non-bilayer , such as phosphatidylethanolamine, can to hexagonal phases under stress, influencing membrane curvature and fusion events essential for vesicle trafficking.

Applications in Nanotechnology and Materials

DNA and RNA Nanotechnology

DNA and RNA nanotechnology harness the programmable base-pairing properties of nucleic acids to direct the self-assembly of nanoscale structures with precise geometries and functions. In DNA nanotechnology, self-assembly relies on Watson-Crick base pairing to form rigid double helices that serve as building blocks for complex architectures, enabling applications in , biosensing, and . RNA nanotechnology extends these principles to single-stranded RNA motifs, which fold into compact 3D shapes via intramolecular interactions, offering advantages in biocompatibility and therapeutic targeting due to RNA's natural roles in cellular processes. The field of DNA nanotechnology originated with Nadrian Seeman's 1982 proposal to use DNA junctions for constructing periodic lattices, addressing challenges in crystallographic analysis of biological macromolecules. This foundational work introduced immobile Holliday junctions as motifs for branching DNA structures, laying the groundwork for programmable beyond linear polymers. Early experimental realizations in the 1990s demonstrated double-crossover (DX) tiles that assemble into two-dimensional arrays, achieving periodic patterns with lattice constants around 30 nm. A major advancement came in 2006 with Paul Rothemund's technique, which folds a long single-stranded DNA scaffold (typically M13 phage DNA, ~7,249 ) using hundreds of short staple strands to create arbitrary two-dimensional shapes, such as disks or smiley faces, with resolutions down to 5 nm. This method has been extended to three-dimensional structures, including voxels and curved surfaces, by layering origami tiles or using blunt-end stacking interactions. DNA nanostructures self-assemble isothermally in solution, often at room temperature, through specific hybridization of sticky ends or toehold-mediated strand , yielding yields exceeding 90% for simple motifs. In applications, DNA origami templates the of inorganic nanoparticles, such as or quantum dots, into plasmonic devices with tunable , as demonstrated in assemblies forming metamaterials. For drug delivery, DNA nanocages encapsulate therapeutic molecules and respond to environmental cues like pH changes for targeted release in cancer cells. Dynamic DNA assemblies, incorporating gates via strand , enable computational nanodevices that process molecular , such as detecting multiple biomarkers simultaneously. RNA nanotechnology builds on the intrinsic folding of RNA into tertiary structures, such as the phi29 DNA packaging motor's pRNA hexamer, which self-assembles via interlocking loop interactions into a ring of approximately 30 nm for motor function. Pioneered in the late 1990s, RNA motifs like hairpins and pseudoknots are designed using computational tools to form stable nanoparticles, often 10-20 nm in size, through intermolecular base pairing. A key method involves reengineering bacteriophage pRNA loops to create multimeric assemblies, allowing site-specific conjugation of siRNA, aptamers, or imaging agents without disrupting folding. Unlike DNA, RNA's 2'-OH group enhances chemical reactivity for modifications, such as 2'-fluoro substitutions to improve serum stability up to 10 hours in vivo. In therapeutic applications, RNA nanoparticles deliver multiple payloads, such as folic acid-targeted pRNA for tumor-specific delivery of chemotherapeutic drugs, achieving up to 50-fold higher efficacy in mouse models compared to free drugs. RNA self-assembly also supports gene silencing, where three-way junction motifs package siRNAs for systemic delivery, reducing tumor growth by over 80% in glioma xenografts. Emerging uses include RNA-based scaffolds for tissue engineering, where self-assembled nanorings promote stem cell differentiation through controlled presentation of growth factors. As of 2024, RNA nanoparticles have entered phase I clinical trials for cancer therapy, demonstrating biocompatibility and targeted delivery. Overall, both DNA and RNA platforms exemplify bottom-up self-assembly, with DNA excelling in structural rigidity and RNA in biological functionality, driving innovations in precision nanomedicine.

Block Copolymers and Colloidal Assemblies

Block copolymers (BCPs) consist of two or more covalently linked polymer chains with distinct chemical compositions, enabling microphase separation driven by the thermodynamic incompatibility of the blocks. This incompatibility, quantified by the Flory-Huggins interaction parameter χ, promotes self-assembly into ordered nanostructures when the product χN exceeds a critical value, where N is the total degree of polymerization. In selective solvents or under confinement, amphiphilic BCPs—featuring hydrophilic and hydrophobic segments—form colloidal particles such as spherical micelles, cylindrical micelles, and vesicles, dictated by the packing parameter p = v/(a₀l_c), where v is the hydrophobic volume, a₀ the headgroup area, and l_c the critical chain length. These assemblies exhibit low critical micelle concentrations (typically <10 mg/L) and sizes ranging from 10 to 100 nm, making them ideal for nanotechnology applications. Colloidal assemblies of BCPs extend beyond simple micelles to hierarchical structures, often achieved through solution-based techniques like crystallization-driven (CDSA) or emulsion confinement. In CDSA, living polymerization enables seeded of monodisperse cylindrical micelles from crystallizable blocks, such as poly(3-hexylthiophene) or poly(ferrocenyldimethylsilane), yielding lengths controllable to hundreds of nanometers with low polydispersity (<1.1). Confined in evaporating emulsion droplets produces nanostructured particles with morphologies like onion-like multilayers or core-shell architectures, governed by the of droplet D to the BCP spacing L₀; for D/L₀ ≈ 2–5, spherical or cylindrical domains emerge. ABC triblock copolymers further enable multicompartment micelles (MCMs), where creates segregated domains for encapsulating multiple incompatible cargos, as demonstrated in polystyrene-polybutadiene-poly() systems forming hierarchical superlattices. In and , BCP serves as a versatile template for fabricating functional nanostructures. For instance, directed of BCPs patterns substrates with sub-10 nm resolution for next-generation , outperforming traditional methods in . Colloidal assemblies from BCPs also guide the of inorganic materials, such as mesoporous or metals, by infiltrating and selectively the ; poly(styrene-block-2-vinylpyridine) templates ordered arrays with tunable plasmonic . In drug , Pluronic-based micelles in SP1049C, a of doxorubicin using PEO-PPO-PEO block copolymers, underwent phase II clinical trials, providing enhanced bioavailability for hydrophobic therapeutics. Polymersomes from poly(ethylene oxide)-block-poly(ε-caprolactone) offer sustained release over weeks. Stimuli-responsive variants, triggered by pH or temperature, enable targeted applications in sensors and responsive coatings, leveraging the reversible assembly-disassembly of polyion complex micelles. As of 2024, BCP directed integrates with extreme ultraviolet for features below 5 nm.

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