Rotaxane
A rotaxane is a mechanically-interlocked molecular architecture consisting of a "dumbbell shaped molecule" which is threaded through a "macrocycle" (see graphical representation). The name is derived from the Latin for wheel (rota) and axle (axis). The two components of a rotaxane are kinetically trapped since the ends of the dumbbell (often called stoppers) are larger than the internal diameter of the ring and prevent disassociation (unthreading) of the components since this would require significant distortion of the covalent bonds.
Much of the research concerning rotaxanes and other mechanically-interlocked molecular architectures, such as catenanes, has been focused on their efficient synthesis. However, examples of rotaxane have been found in biological systems including: cystine knots, cyclotides or lasso-peptides such as microcin J25 are protein, and a variety of peptides with rotaxane substructure.

# Synthesis
The earliest reported synthesis of a rotaxane in 1967 relied on the statistical probability that if two halves of a dumbbell shaped molecule were reacted in the presence of a macrocycle that some small percentage would connect through the ring.  To obtain a reasonable quantity of rotaxane the macrocycle was attached to a solid phase support and treated with both halves of the dumbbell 70 time and then severed from the support to give a 6% yield. However, the synthesis of rotaxanes has advanced significantly and efficient yields can be obtained by preorganizing the components utilizing hydrogen bonding, metal coordination, hydrophobic forces, covalent bonds, or coulombic interactions. The three most common strategies to synthesize rotaxane are "capping", "clipping", and "slipping", though others do exist.

## Capping
Synthesis via the capping method relies strongly upon a thermodynamically driven template effect; that is the "thread" is held within the "macrocycle" by non-covalent interactions. This dynamic complex or pseudorotaxane is then converted to the rotaxane by reacting the ends of the threaded guest with large groups preventing disassociation.

## Clipping
The clipping method is similar to the capping reaction except that in this case the dumbbell shaped molecule is complete and is bound to a partial macrocyle. The partial macrocyle then undergoes a ring closing reaction around the dumbbell shaped molecule forming the rotaxane.

## Slipping
The method of slipping is one which exploits the kinetic stability of the rotaxane. If the end groups of the dumbbell are an appropriate size it will be able to reversibly thread through the macrocycle at higher temperatures. By cooling the dynamic complex it becomes kinetically trapped as a rotaxane at the lower temperature.

# Potential applications

## Molecular machines
Rotaxane-based molecular machines have been of initial interest for their potential use in molecular electronics as logic molecular switching elements and as molecular shuttles.  These molecular machines are usually based on the movement of macrocycle on the dumbbell. The macrocycle can rotate around the axis of the dumbbell like a wheel and axle or it can slide along its axis from one site to another. Controlling the position of the macrocycle allows the rotaxane to function as molecular switch with each possible location of the macrocycle corresponding to a different state. These rotaxane machines can be manipulated both by chemical and photochemical inputs. Rotaxane based systems have also been demonstrated as molecular muscles.

## Ultrastable dyes
Potential application as long lasting dyes is based on the enhanced stability of the inner portion of the dumbbell shaped molecule. Studies with cyclodextrin protected rotaxane azo dyes established this characteristic. More reactive squaraine dyes have also been shown to have enhanced stability by preventing nucleophilic attack of the inner squaraine moiety. The enhanced stabilities of rotaxane dyes is attributed to the insulating effect of the macrocycle which is able to block interactions with other molecules.

## Nanorecording
In a nanorecording application a certain rotaxane is deposited as a Langmuir-Blodgett film on ITO coated glass. When a positive voltage is applied with the tip of a scanning tunneling microscope probe, the rotaxane rings in the tip area switch to a different part of the dumbbell and the resulting new conformation makes the molecules stick out from the surface by 0.3 nanometer and this height difference turns out to be sufficient for a memory dot. It is not yet possible to erase such a nanorecording film.

# Nomenclature
Accepted nomenclature is to designate the number of components of the rotaxane in brackets as a prefix. Therefore the graphical representation of rotaxane displayed above would be a rotaxane as it consists of a single dumbbell and a single macrocycle.