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In chemistry and materials science, molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly: intermolecular and intramolecular. Commonly, the term molecular self-assembly refers to the former, while the latter is more commonly called folding .
Molecular self-assembly is a key concept in supramolecular chemistry. [6] [7] [8] This is because assembly of molecules in such systems is directed through non-covalent interactions (e.g., hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-stacking interactions, and/or electrostatic) as well as electromagnetic interactions. Common examples include the formation of colloids, biomolecular condensates, micelles, vesicles, liquid crystal phases, and Langmuir monolayers by surfactant molecules. [9] Further examples of supramolecular assemblies demonstrate that a variety of different shapes and sizes can be obtained using molecular self-assembly. [10]
Molecular self-assembly allows the construction of challenging molecular topologies. One example is Borromean rings, interlocking rings wherein removal of one ring unlocks each of the other rings. DNA has been used to prepare a molecular analog of Borromean rings. [11] More recently, a similar structure has been prepared using non-biological building blocks. [12]
Molecular self-assembly underlies the construction of biologic macromolecular assemblies and biomolecular condensates in living organisms, and so is crucial to the function of cells. It is exhibited in the self-assembly of lipids to form the membrane, the formation of double helical DNA through hydrogen bonding of the individual strands, and the assembly of proteins to form quaternary structures. Molecular self-assembly of incorrectly folded proteins into insoluble amyloid fibers is responsible for infectious prion-related neurodegenerative diseases. Molecular self-assembly of nanoscale structures plays a role in the growth of the remarkable β-keratin lamellae/setae/spatulae structures used to give geckos the ability to climb walls and adhere to ceilings and rock overhangs. [13] [14]
When multiple copies of a polypeptide encoded by a gene self-assemble to form a complex, this protein structure is referred to as a "multimer". [15] Genes that encode multimer-forming polypeptides appear to be common. When a multimer is formed from polypeptides produced by two different mutant alleles of a particular gene, the mixed multimer may exhibit greater functional activity than the unmixed multimers formed by each of the mutants alone. In such a case, the phenomenon is referred to as intragenic complementation. [16] Jehle pointed out that, when immersed in a liquid and intermingled with other molecules, charge fluctuation forces favor the association of identical molecules as nearest neighbors. [17]
Molecular self-assembly is an important aspect of bottom-up approaches to nanotechnology. Using molecular self-assembly, the final (desired) structure is programmed in the shape and functional groups of the molecules. Self-assembly is referred to as a 'bottom-up' manufacturing technique in contrast to a 'top-down' technique such as lithography where the desired final structure is carved from a larger block of matter. In the speculative vision of molecular nanotechnology, microchips of the future might be made by molecular self-assembly. An advantage to constructing nanostructure using molecular self-assembly for biological materials is that they will degrade back into individual molecules that can be broken down by the body.
DNA nanotechnology is an area of current research that uses the bottom-up, self-assembly approach for nanotechnological goals. DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties. [18] DNA is thus used as a structural material rather than as a carrier of biological information, to make structures such as complex 2D and 3D lattices (both tile-based as well as using the "DNA origami" method) and three-dimensional structures in the shapes of polyhedra. [19] These DNA structures have also been used as templates in the assembly of other molecules such as gold nanoparticles [20] and streptavidin proteins. [21]
The spontaneous assembly of a single layer of molecules at interfaces is usually referred to as two-dimensional self-assembly. One of the common examples of such assemblies are Langmuir-Blodgett monolayers and multilayers of surfactants. Non-surface active molecules can assemble into ordered structures as well. Early direct proofs showing that non-surface active molecules can assemble into higher-order architectures at solid interfaces came with the development of scanning tunneling microscopy and shortly thereafter. [22] Eventually two strategies became popular for the self-assembly of 2D architectures, namely self-assembly following ultra-high-vacuum deposition and annealing and self-assembly at the solid-liquid interface. [23] The design of molecules and conditions leading to the formation of highly-crystalline architectures is considered today a form of 2D crystal engineering at the nanoscopic scale.
Nanotechnology was defined by the National Nanotechnology Initiative as the manipulation of matter with at least one dimension sized from 1 to 100 nanometers (nm). At this scale, commonly known as the nanoscale, surface area and quantum mechanical effects become important in describing properties of matter. The definition of nanotechnology is inclusive of all types of research and technologies that deal with these special properties. It is therefore common to see the plural form "nanotechnologies" as well as "nanoscale technologies" to refer to the broad range of research and applications whose common trait is size. An earlier description of nanotechnology referred to the particular technological goal of precisely manipulating atoms and molecules for fabrication of macroscale products, also now referred to as molecular nanotechnology.
Molecular engineering is an emerging field of study concerned with the design and testing of molecular properties, behavior and interactions in order to assemble better materials, systems, and processes for specific functions. This approach, in which observable properties of a macroscopic system are influenced by direct alteration of a molecular structure, falls into the broader category of “bottom-up” design.
Self-assembly is a process in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction. When the constitutive components are molecules, the process is termed molecular self-assembly.
A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multidomain enzymes, in which multiple catalytic domains are found in a single polypeptide chain.
Supramolecular chemistry refers to the branch of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. While traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects.
The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, halogen bonding, or resonant interaction effects. In addition to these direct interactions, solvents can play a dominant indirect role in driving molecular recognition in solution. The host and guest involved in molecular recognition exhibit molecular complementarity. Exceptions are molecular containers, including e.g. nanotubes, in which portals essentially control selectivity.
Molecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes. For the last several decades, scientists have attempted, with varying degrees of success, to miniaturize machines found in the macroscopic world. The first example of an artificial molecular machine (AMM) was reported in 1994, featuring a rotaxane with a ring and two different possible binding sites.
In chemistry, a supramolecular assembly is a complex of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules, or a defined number of stoichiometrically interacting molecules within a quaternary complex, it is more often used to denote larger complexes composed of indefinite numbers of molecules that form sphere-, rod-, or sheet-like species. Colloids, liquid crystals, biomolecular condensates, micelles, liposomes and biological membranes are examples of supramolecular assemblies, and their realm of study is known as supramolecular chemistry. The dimensions of supramolecular assemblies can range from nanometers to micrometers. Thus they allow access to nanoscale objects using a bottom-up approach in far fewer steps than a single molecule of similar dimensions.
Nanobiotechnology, bionanotechnology, and nanobiology are terms that refer to the intersection of nanotechnology and biology. Given that the subject is one that has only emerged very recently, bionanotechnology and nanobiotechnology serve as blanket terms for various related technologies.
In chemistry, a resorcinarene is a macrocycle, or a cyclic oligomer, based on the condensation of resorcinol (1,3-dihydroxybenzene) and an aldehyde. Resorcinarenes are a type of calixarene. Other types of resorcinarenes include the related pyrogallolarenes and octahydroxypyridines, derived from pyrogallol and 2,6-dihydroxypyridine, respectively.
DNA origami is the nanoscale folding of DNA to create arbitrary two- and three-dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material, through design of its base sequences. DNA is a well-understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own.
Crystal engineering studies the design and synthesis of solid-state structures with desired properties through deliberate control of intermolecular interactions. It is an interdisciplinary academic field, bridging solid-state and supramolecular chemistry.
In polymer chemistry and materials science, the term "polymer" refers to large molecules whose structure is composed of multiple repeating units. Supramolecular polymers are a new category of polymers that can potentially be used for material applications beyond the limits of conventional polymers. By definition, supramolecular polymers are polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds. These non-covalent interactions include van der Waals interactions, hydrogen bonding, Coulomb or ionic interactions, π-π stacking, metal coordination, halogen bonding, chalcogen bonding, and host–guest interaction. The direction and strength of the interactions are precisely tuned so that the array of molecules behaves as a polymer in dilute and concentrated solution, as well as in the bulk.
Bacillus virus Φ29 is a double-stranded DNA (dsDNA) bacteriophage with a prolate icosahedral head and a short tail that belongs to the genus Salasvirus, order Caudovirales, and family Salasmaviridae. They are in the same order as phages PZA, Φ15, BS32, B103, M2Y (M2), Nf, and GA-1. First discovered in 1965, the Φ29 phage is the smallest Bacillus phage isolated to date and is among the smallest known dsDNA phages.
DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, and functional devices such as molecular machines and DNA computers. The field is beginning to be used as a tool to solve basic science problems in structural biology and biophysics, including applications in X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins to determine structures. Potential applications in molecular scale electronics and nanomedicine are also being investigated.
Nanoparticles are classified as having at least one of its dimensions in the range of 1-100 nanometers (nm). The small size of nanoparticles allows them to have unique characteristics which may not be possible on the macro-scale. Self-assembly is the spontaneous organization of smaller subunits to form larger, well-organized patterns. For nanoparticles, this spontaneous assembly is a consequence of interactions between the particles aimed at achieving a thermodynamic equilibrium and reducing the system’s free energy. The thermodynamics definition of self-assembly was introduced by Professor Nicholas A. Kotov. He describes self-assembly as a process where components of the system acquire non-random spatial distribution with respect to each other and the boundaries of the system. This definition allows one to account for mass and energy fluxes taking place in the self-assembly processes.
Supramolecular catalysis is not a well-defined field but it generally refers to an application of supramolecular chemistry, especially molecular recognition and guest binding, toward catalysis. This field was originally inspired by enzymatic system which, unlike classical organic chemistry reactions, utilizes non-covalent interactions such as hydrogen bonding, cation-pi interaction, and hydrophobic forces to dramatically accelerate rate of reaction and/or allow highly selective reactions to occur. Because enzymes are structurally complex and difficult to modify, supramolecular catalysts offer a simpler model for studying factors involved in catalytic efficiency of the enzyme. Another goal that motivates this field is the development of efficient and practical catalysts that may or may not have an enzyme equivalent in nature.
RNA origami is the nanoscale folding of RNA, enabling the RNA to create particular shapes to organize these molecules. It is a new method that was developed by researchers from Aarhus University and California Institute of Technology. RNA origami is synthesized by enzymes that fold RNA into particular shapes. The folding of the RNA occurs in living cells under natural conditions. RNA origami is represented as a DNA gene, which within cells can be transcribed into RNA by RNA polymerase. Many computer algorithms are present to help with RNA folding, but none can fully predict the folding of RNA of a singular sequence.
Virus nanotechnology is the use of viruses as a source of nanoparticles for biomedical purposes. Viruses are made up of a genome and a capsid; and some viruses are enveloped. Most virus capsids measure between 20-500 nm in diameter. Because of their nanometer size dimensions, viruses have been considered as naturally occurring nanoparticles. Virus nanoparticles have been subject to the nanoscience and nanoengineering disciplines. Viruses can be regarded as prefabricated nanoparticles. Many different viruses have been studied for various applications in nanotechnology: for example, mammalian viruses are being developed as vectors for gene delivery, and bacteriophages and plant viruses have been used in drug delivery and imaging applications as well as in vaccines and immunotherapy intervention.
Roeland J. M. Nolte is a Dutch chemist, known for his work in the fields of organic chemistry, biochemistry, polymer chemistry, and supramolecular chemistry. He is an emeritus Royal Netherlands of Arts and Sciences professor and an emeritus professor of Organic Chemistry at Radboud University in Nijmegen, The Netherlands. Currently, he holds a special chair, i.e. professor of Molecular Nanotechnology, at this university. Nolte is considered to be one of the pioneers of the field of supramolecular chemistry, which encompasses the design and synthesis of new chemical structures from low molecular weight compounds and biopolymers using so-called non-covalent interactions. He published many studies on supramolecular assembly and biomimetic catalysts, which find applications in the field of nanomaterials and medicine.
Gecko "feet and toes are a hierarchical system of complex structures consisting of lamellae, setae, and spatulae. The distinguishing characteristics of the gecko adhesion system have been described [as] (1) anisotropic attachment, (2) high pulloff force to preload ratio, (3) low detachment force, (4) material independence, (5) self-cleaning, (6) anti-self sticking and (7) non-sticky default state. ... The gecko's adhesive structures are made from ß-keratin (modulus of elasticity [approx.] 2 GPa). Such a stiff material is not inherently sticky; however, because of the gecko adhesive's hierarchical nature and extremely small distal features (spatulae are [approx.] 200 nm in size), the gecko's foot is able to intimately conform to the surface and generate significant attraction using van der Waals forces.
