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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The student has a basic understanding of the physical and physicochemical principles which result from the chainlike structure of synthetic macromolecules. The student can predict major characteristic
Explore la conception et la synthèse de molécules imbriquées comme les caténanes et les rotaxanes, ainsi que la signification structurelle et symbolique des nœuds et des anneaux borroméens.
Un caténane est une architecture moléculaire formée d'au moins deux macrocycles imbriqués l'un dans l'autre, formant une sorte de chaine (en latin catena). Deux cycles imbriqués ne peuvent pas être séparés sans casser au moins une liaison covalente d'un des deux cycles. Le concept des caténanes est proche de celui d'autre molécules imbriquées telles les rotaxanes, les nœuds moléculaires ou les nœuds borroméens moléculaires. Une nouvelle terminologie est utilisée pour décrire la connexion entre les cycles d'un caténane : on parle de liaison mécanique.
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.
Un rotaxane est une molécule constituée d'un macrocycle lié mécaniquement à un fragment moléculaire linéaire qui le traverse de part en part. Le nom est dérivé du latin rota signifiant roue et du mot axe. Les deux constituants d'un rotaxane sont cinétiquement piégés par des « bouchons » aux extrémités de l'axe, plus gros que le diamètre interne du cycle. Ainsi les deux composants du rotaxane ne peuvent se dissocier sans rupture d'une liaison covalente, car cette dissociation nécessiterait de trop grandes distorsions des liaisons du cycle.
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