Molecular knot

In chemistry, a molecular knot is a mechanically interlocked molecular architecture that is analogous to a macroscopic knot. Naturally-forming molecular knots are found in organic molecules like DNA, RNA, and proteins. It is not certain that naturally occurring knots are evolutionarily advantageous to nucleic acids or proteins, though knotting is thought to play a role in the structure, stability, and function of knotted biological molecules. The mechanism by which knots naturally form in molecules, and the mechanism by which a molecule is stabilized or improved by knotting, is ambiguous. The study of molecular knots involves the formation and applications of both naturally occurring and chemically synthesized molecular knots. Applying chemical topology and knot theory to molecular knots allows biologists to better understand the structures and synthesis of knotted organic molecules. The term knotane was coined by Vögtle et al. in 2000 to describe molecular knots by analogy with rotaxanes and catenanes, which are other mechanically interlocked molecular architectures. The term has not been broadly adopted by chemists and has not been adopted by IUPAC. Organic molecules containing knots may fall into the categories of slipknots or pseudo-knots. They are not considered mathematical knots because they are not a closed curve, but rather a knot that exists within an otherwise linear chain, with termini at each end. Knotted proteins are thought to form molecular knots during their tertiary structure folding process, and knotted nucleic acids generally form molecular knots during genomic replication and transcription, though details of knotting mechanism continue to be disputed and ambiguous. Molecular simulations are fundamental to the research on molecular knotting mechanisms. Knotted DNA was found first by Liu et al. in 1981, in single-stranded, circular, bacterial DNA, though double-stranded circular DNA has been found to also form knots. Naturally knotted RNA has not yet been reported.

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Catenane

In macromolecular chemistry, a catenane () is a mechanically interlocked molecular architecture consisting of two or more interlocked macrocycles, i.e. a molecule containing two or more intertwined rings. The interlocked rings cannot be separated without breaking the covalent bonds of the macrocycles. They are conceptually related to other mechanically interlocked molecular architectures, such as rotaxanes, molecular knots or molecular Borromean rings.

Molecular knot

Mechanically interlocked molecular architectures

In chemistry, mechanically interlocked molecular architectures (MIMAs) are molecules that are connected as a consequence of their topology. This connection of molecules is analogous to keys on a keychain loop. The keys are not directly connected to the keychain loop but they cannot be separated without breaking the loop. On the molecular level, the interlocked molecules cannot be separated without the breaking of the covalent bonds that comprise the conjoined molecules; this is referred to as a mechanical bond.

The course provides an introduction to supramolecular chemistry. In addition, current trends are discussed using recent publications in this area.

The course aims at providing insight into the cellular and molecular basis of smell and taste with specific emphasis on how molecules are detected by these chemosensory systems.

Molecular Topology: Catenanes and Rotaxanes CH-424: Supramolecular chemistry

Explores the design and synthesis of interlocked molecules like catenanes and rotaxanes, along with the structural and symbolic significance of knots and Borromean rings.

Supramolecular Chemistry: Coordination Cages and Molecular Knots CH-424: Supramolecular chemistry

Explores coordination cages, molecular knots, and their applications in supramolecular chemistry.

Supramolecular Chemistry: Coordination and Topology CH-424: Supramolecular chemistry

Explores supramolecular chemistry, emphasizing metal ion arrays, helicates, and interlocked molecules.