Mechanically-interlocked molecular architectures

Mechanically-interlocked molecular architectures are connections of molecules not through traditional bonds, but instead as a consequence of their topology. This connection of molecules is analogous to keys on a key chain loop. The keys are not directly connected to the key chain loop but they cannot be separated without breaking the loop. On the molecular level the interlocked molecules cannot be separated without significant distortion of the covalent bonds that make up the conjoined molecules. Examples of mechanically-interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings.

The synthesis of such entangled architectures has been made efficient through the combination of supramolecular chemistry with traditional covalent synthesis, however mechanically-interlocked molecular architectures have properties that differ from both “supramolecular assemblies” and “covalently-bonded molecules”. Recently the terminology "mechanical bond" has been coined to describe the connection between the components of mechanically-interlocked molecular architectures. Although research into mechanically-interlocked molecular architectures is primarily focused on artificial compounds many examples have been found in biological systems including: cystine knots, cyclotides or lasso-peptides such as microcin J25 are protein, and a variety of peptides. There is a great deal of interest in mechanically-interlocked molecular architectures to develop molecular machines by manipulating the relative position of the components

Molecular self-assembly

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.

Hydrogen bond

A hydrogen bond is the attractive force between one electronegative atom and a hydrogen covalently bonded to another electronegative atom. It results from a dipole-dipole force with a hydrogen atom bonded to nitrogen, oxygen or fluorine (thus the name "hydrogen bond", which must not be confused with a covalent bond to hydrogen). The energy of a hydrogen bond (typically 5 to 30 kJ/mole) is comparable to that of weak covalent bonds (155 kJ/mol), and a typical covalent bond is only 20 times stronger than an intermolecular hydrogen bond. These bonds can occur between molecules (intermolecularly), or within different parts of a single molecule (intramolecularly).^[2] The hydrogen bond is a very strong fixed dipole-dipole van der Waals-Keesom force, but weaker than covalent, or ionic bonds. The hydrogen bond is somewhere between a covalent bond and an electrostatic intermolecular attraction. This type of bond occurs in both inorganic molecules such as water and organic molecules such as DNA.

Intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C). This is because of the strong hydrogen bond, as opposed to other group 16 hydrides. Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids.

Hydrophobic effect

The hydrophobic effect is the property that non-polar molecules tend to form aggregates of like molecules in water and analogous intramolecular interactions. The name arises from the combination of water in Attic Greek hydro- and for fear phobos, which describes the apparent repulsion between water and hydrocarbons. At the macroscopic level, the hydrophobic effect is apparent when oil and water are mixed together and form separate layers or the beading of water on hydrophobic surfaces such as waxy leafs. At the molecular level, the hydrophobic effect is an important driving force for biological structures and responsible for protein folding, protein-protein interactions, formation of lipid bilayer membranes, nucleic acid structures, and protein-small molecule interactions.

According to the solvophobic theory of Reversed Phase Chromatography (RPC), the hydrophobic effect is driven by the loss of hydrogen bonding and the higher entropic cost of forming a cavity around nonpolar molecules. These losses can be minimized by forcing nonpolar molecules together (see Thermodynamics