Self-assembly

Typically, head groups are connected to an alkyl chain in which the terminal end can be functionalized (i.e. adding –OH, -NH3, or –COOH groups) to vary the wetting and interfacial properties. An appropriate substrate is chosen to react with the head group. Substrates can be planar surfaces, such as silicon and metals, or curved surfaces, such as nanoparticles. Thiols and disulfides are the most commonly used on noble metal substrates.

Currently, gold is the standard for these head groups. Gold is an inert and biocompatible material that is easy to acquire. It is also easy to pattern via lithography, a useful feature for applications in nanoelectromechanical systems (NEMS). Additionally, it can withstand harsh chemical cleaning treatments. Silanes are generally used on nonmetallic oxide surfaces. 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, intramolecular self-assembly and intermolecular self-assembly. Most often the term molecular self-assembly refers to intermolecular self-assembly, while the intramolecular analog is more commonly called folding. 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. DNA is thus used as a structural material rather than as a carrier of biological information, to make structures such as two-dimensional periodic lattices (both tile-based as well as using the "DNA origami" method) and three-dimensional structures in the shapes of polyhedra.