Editing Rotaxane

{{short description|Interlocked molecular structure resembling a dumbbell}}
[[File:Rotaxane cartoon.jpg|thumb|Graphical representation of a rotaxane]] 
[[Image:Rotaxane Crystal Structure EurJOrgChem page2565 year1998.png|thumb|Structure of a rotaxane that has a [[cyclobis(paraquat-p-phenylene)|cyclobis(paraquat-''p''-phenylene)]] [[macrocycle]].<ref>{{cite journal|title= High Yielding Template-Directed Syntheses of [2]Rotaxanes |year= 1998 |journal= [[Eur. J. Org. Chem.]] |issue= 11 |pages= 2565–2571 |doi= 10.1002/(SICI)1099-0690(199811)1998:11<2565::AID-EJOC2565>3.0.CO;2-8 |volume= 1998|last1= Bravo |first1= José A. |last2= Raymo |first2= Françisco M. |last3= Stoddart |first3= J. Fraser |last4= White |first4= Andrew J. P. |last5= Williams |first5= David J. }}</ref>]]

A '''rotaxane''' ({{ety|la|rota|[[wheel]]||axis|[[axle]]}}) is a [[mechanically interlocked molecular architectures|mechanically interlocked molecular architecture]] consisting of a [[dumbbell]]-shaped molecule which is threaded through a [[macrocycle]] (see graphical representation). 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 [[dissociation (chemistry)|dissociation]] (unthreading) of the components since this would require significant distortion of the [[covalent bond]]s.

Much of the research concerning rotaxanes and other mechanically interlocked molecular architectures, such as [[catenane]]s, has been focused on their efficient [[Chemical synthesis|synthesis]] or their utilization as artificial [[molecular machine]]s. However, examples of rotaxane substructure have been found in naturally occurring [[peptides]], including: [[cystine knot]] peptides, [[cyclotide]]s or lasso-peptides such as microcin J25.

== 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.<ref>{{cite journal |title= Synthesis of a stable complex of a macrocycle and a threaded chain |year= 1967 |journal= [[J. Am. Chem. Soc.]] |volume= 89 |issue= 22 |pages= 5723–5724 |doi= 10.1021/ja00998a052 |last1= Harrison |first1= Ian Thomas. |last2= Harrison |first2= Shuyen. |bibcode= 1967JAChS..89.5723H }}</ref> To obtain a reasonable quantity of rotaxane, the macrocycle was attached to a [[solid-phase synthesis|solid-phase support]] and treated with both halves of the dumbbell 70 times 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 bond]]ing, metal coordination, [[hydrophobic effect|hydrophobic forces]], [[covalent bond]]s, or [[Coulomb force|coulombic interactions]]. The three most common strategies to synthesize rotaxane are "capping", "clipping", and "slipping",<ref>{{Cite book |author= Aricó, F. |title= Templates in Chemistry II |chapter= Templated Synthesis of Interlocked Molecules |year= 2005 |journal= Topics in Current Chemistry |volume= 249 |pages= 203–259 |doi= 10.1007/b104330|isbn= 978-3-540-23087-8 |hdl= 10278/33611 }}</ref> though others do exist.<ref>{{cite journal |title= Threading-Followed-by-Shrinking Protocol for the Synthesis of a [2]Rotaxane Incorporating a Pd(II)-Salophen Moiety |year= 2004 |journal= [[J. Am. Chem. Soc.]] |volume= 126 |issue= 51 |pages= 16740–16741 |doi= 10.1021/ja0464490 |pmid= 15612709|last1= Yoon |first1= I |last2= Narita |first2= M |last3= Shimizu |first3= T |last4= Asakawa |first4= M }}</ref><ref>{{cite journal|title= A novel synthesis of chiral rotaxanes via covalent bond formation |year= 2004 |journal= [[Chem. Commun.]] |issue= 51 |pages= 466–467 |doi= 10.1039/b314744d |pmid= 14765261 |last1= Kameta |first1= N |last2= Hiratani |first2= K |last3= Nagawa |first3= Y }}</ref> Recently, Leigh and co-workers described a new pathway to mechanically interlocked architectures involving a transition-metal center that can catalyse a reaction through the cavity of a macrocycle.<ref>{{cite journal|title= Catalytic "active-metal" template synthesis of [2]rotaxanes, [3]rotaxanes, and molecular shuttles, and some observations on the mechanism of the Cu(I)-catalyzed azide-alkyne 1,3-cycloaddition |year= 2007 |journal= [[J. Am. Chem. Soc.]] |volume= 129 |pages= 11950–11963 |doi= 10.1021/ja073513f |pmid= 17845039 |issue= 39 |last1= Aucagne |first1= V |last2= Berna |first2= J |last3= Crowley |first3= J. D. |last4= Goldup |first4= S. M. |last5= Hänni |first5= K. D. |last6= Leigh |first6= D. A. |last7= Lusby |first7= P. J. |last8= Ronaldson |first8= V. E. |last9= Slawin |first9= A. M. |last10= Viterisi |first10= A |last11= Walker |first11= D. B. }}</ref>

[[File:DNA origami rotaxanes.jpg|thumb|(a) A rotaxane is formed from an open ring (R1) with a flexible hinge and a dumbbell-shaped [[DNA origami]] structure (D1). The hinge of the ring consists of a series of strand crossovers into which additional [[thymine]]s are inserted to provide higher flexibility. Ring and axis subunits are first connected and positioned with respect to each other using 18 [[nucleotide]] long, complementary sticky ends 33 nm away from the center of the axis (blue regions). The ring is then closed around the dumbbell axis using closing strands (red), followed by the addition of release strands that separate dumbbell from ring via toehold-mediated strand displacement. (b) 3D models and corresponding averaged [[Transmission electron microscopy|TEM]] images of the ring and dumbbell structure. (c) TEM images of the completely assembled rotaxanes (R1D1). (d) 3D models, averaged and single-particle TEM images of R2 and D2, subunits of an alternative rotaxane design containing bent structural elements. The TEM images of the ring structure correspond to the closed (top) and open (bottom) configurations. (e) 3D representation and TEM images of the fully assembled R2D2 rotaxane. Scale bar, 50 nm.<ref>{{cite journal|doi=10.1038/ncomms12414|pmid=27492061|pmc=4980458|title=Long-range movement of large mechanically interlocked DNA nanostructures|journal=Nature Communications|volume=7|pages=12414|year=2016|last1=List|first1=Jonathan|last2=Falgenhauer|first2=Elisabeth|last3=Kopperger|first3=Enzo|last4=Pardatscher|first4=Günther|last5=Simmel|first5=Friedrich C.|bibcode=2016NatCo...712414L}}</ref>]]

===Capping===
[[File:Rotaxanes-synthesis-methods.png|thumb|Rotaxane synthesis can be carried out via a "capping," "clipping, "slipping" or "active template" mechanism]]
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, for example rotaxinations with cyclodextrin macrocycles involve exploitation of the hydrophobic effect. This dynamic complex or pseudorotaxane is then converted to the rotaxane by reacting the ends of the threaded guest with large groups, preventing disassociation.<ref>{{cite web|url=https://www.youtube.com/watch?v=7o_-RiMRO6Y|website=youtube.com|title=Rotaxane by capping|date=10 March 2017 }}</ref>

===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 macrocycle. The partial macrocycle then undergoes a [[ring closing reaction]] around the dumbbell-shaped molecule, forming the rotaxane.<ref>{{cite web|last1=Romero|first1=Antonio|title=Rotaxane by capping 3d|url=https://www.youtube.com/watch?v=7o_-RiMRO6Y|website=Rotaxane by capping 3d|date=10 March 2017 |publisher=3D video}}</ref>

===Slipping===
The method of slipping is one which exploits the thermodynamic<ref name="BrunsStoddart2016">{{cite book|author1=Carson J. Bruns|author2=J. Fraser Stoddart|title=The Nature of the Mechanical Bond: From Molecules to Machines|url=https://books.google.com/books?id=xShUDQAAQBAJ&pg=PA271|date=7 November 2016|publisher=John Wiley & Sons|isbn=978-1-119-04400-0|pages=271–}}</ref> 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.

=== Snapping ===
Snapping involves two separate parts of the thread, both containing a bulky group. one part of the thread is then threaded to the macrocycle, forming a semi rotaxane, and end is closed of by the other part of the thread forming the rotaxane.

==="Active template" methodology===
Leigh and co-workers recently began to explore a strategy in which template ions could also play an active role in promoting the crucial final covalent bond forming reaction that captures the interlocked structure (i.e., the metal has a dual function, acting as a template for entwining the precursors and catalyzing covalent bond formation between the reactants).

== Potential applications ==
[[File:Rotaxane Crystal Structure ChemComm page493 2001 commons.jpg|thumb|left|Structure of a rotaxane with an α-[[cyclodextrin]] [[macrocycle]].<ref>{{cite journal |title= Synthesis of fluorescent stilbene and tolan rotaxanes by Suzuki coupling |year= 2001 |journal= [[Chem. Commun.]] |issue= 5 |pages= 493–494 |doi= 10.1039/b010015n|last1= Stanier |first1= Carol A. |last2= o'Connell |first2= Michael J. |last3= Anderson |first3= Harry L. |last4= Clegg |first4= William }}</ref>]]

===Molecular machines===
[[Image:Rot.ogg|thumb|Animation of a pH-controlled molecular rotaxane shuttle]]
Rotaxane-based molecular machines have been of initial interest for their potential use in [[molecular electronics]] as logic [[molecular switch]]ing elements and as [[molecular shuttle]]s.<ref>{{cite journal |title= On the Way to Rotaxane-Based Molecular Motors: Studies in Molecular Mobility and Topological Chirality |year= 2001 |journal= [[Acc. Chem. Res.]] |volume= 34 |issue= 6 |pages= 465–476 |doi= 10.1021/ar000179i |pmid= 11412083 |last1= Schalley |first1= C. A. |last2= Beizai |first2= K |last3= Vögtle |first3= F }}</ref><ref>{{cite journal |author= Sauvage, J. P. |title= Transition Metal-Containing Rotaxanes and Catenanes in Motion: Toward Molecular Machines and Motors |year= 1999 |journal= ChemInform |volume= 30 |issue= 4 |pages= no |doi= 10.1002/chin.199904221}}</ref> These [[molecular motor|molecular machines]] are usually based on the movement of the [[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 a molecular switch, with each possible location of the macrocycle corresponding to a different state. These rotaxane machines can be manipulated both by chemical <ref>{{cite journal |author1=Coutrot, F. |author2=Busseron, E. |title= A New Glycorotaxane Molecular Machine Based on an Anilinium and a Triazolium Station |year= 2008 |journal= [[Chem. Eur. J.]] |volume= 14 |pages= 4784–4787 |doi= 10.1002/chem.200800480 |pmid= 18409178 |issue= 16}}</ref> and photochemical inputs.<ref>{{cite journal |title= Exercising Demons: A Molecular Information Ratchet |year= 2007 |journal= [[Nature (journal)|Nature]] |volume= 445 |pages= 523–527 |doi= 10.1038/nature05452 |pmid= 17268466 |issue= 7127 |bibcode= 2007Natur.445..523S |last1= Serreli |first1= V |last2= Lee |first2= C. F. |last3= Kay |first3= E. R. |last4= Leigh |first4= D. A. |s2cid= 4314051 }}</ref> Rotaxane based systems have also been shown to function as molecular muscles.<ref>{{cite journal  |title= A New pH-Switchable Dimannosyl [c2]Daisy Chain Molecular Machine |year= 2008 |journal= [[Org. Lett.]] |volume= 10 |pages= 3741–3744 |doi= 10.1021/ol801390h |pmid= 18666774 |issue= 17  |last1= Coutrot |first1= F |last2= Romuald |first2= C |last3= Busseron |first3= E }}</ref><ref>{{cite journal |title= Bridging Rotaxanes' wheels – cyclochiral Bonnanes |year= 2006 |journal= [[Angew. Chem. Int. Ed.]] |volume= 45 |pages= 7296–7299 |doi= 10.1002/anie.200602002 |pmid= 17029314 |issue= 43|last1= Radha Kishan |first1= M |last2= Parham |first2= A |last3= Schelhase |first3= F |last4= Yoneva |first4= A |last5= Silva |first5= G |last6= Chen |first6= X |last7= Okamoto |first7= Y |last8= Vögtle |first8= F }}</ref> In 2009, there was a report of a "domino effect" from one extremity to the other in a Glycorotaxane Molecular Machine. In this case, the <sup>4</sup>''C''<sub>1</sub> or <sup>1</sup>''C''<sub>4</sub> chair-like conformation of the manno[[pyranoside]] stopper can be controlled, depending on the localization of the macrocycle.<ref>{{cite journal |author1=Coutrot, F. |author2=Busseron, E. |title= Controlling the Chair Conformation of a Mannopyranose in a Large-Amplitude [2]Rotaxane Molecular Machine |year= 2009 |journal= [[Chem. Eur. J.]] |volume= 15 |pages= 5186–5190 |doi= 10.1002/chem.200900076 |pmid= 19229918 |issue= 21 }}</ref> In 2012, unique pseudo-macrocycles consisting of double-lasso molecular machines (also called rotamacrocycles) were reported in Chem. Sci. These structures can be tightened or loosened depending on pH. A controllable jump rope movement was also observed in these new molecular machines.<ref>{{cite journal |title= Tightening or loosening a pH-sensitive double-lasso molecular machine readily synthesized from an ends-activated [c2]daisy chain |year= 2012 |journal= [[Chem. Sci.]] |volume= 3 |issue= 6 |pages= 1851–1857 |doi= 10.1039/C2SC20072D|last1= Romuald |first1= Camille |last2= Ardá |first2= Ana |last3= Clavel |first3= Caroline |last4= Jiménez-Barbero |first4= Jesús |last5= Coutrot |first5= Frédéric |hdl= 10261/60415 |hdl-access= free }}</ref>

=== Ultrastable dyes ===
Potential application as long-lasting dyes is based on the enhanced stability of the inner portion of the dumbbell-shaped molecule.<ref>{{cite journal|title= Rotaxane-encapsulated cyanine dyes: enhanced fluorescence efficiency and photostability |year= 2000 |journal= [[Chem. Commun.]] |issue= 11 |pages= 905–906 |doi= 10.1039/b001812k |last1= Buston |first1= Jonathan E. H. |last2= Young |first2= James R. |last3= Anderson |first3= Harry L. }}</ref><ref>{{cite journal |title= Rotaxane-Encapsulation Enhances the Stability of an Azo Dye, in Solution and when Bonded to Cellulose |year= 1998 |journal= [[Angew. Chem. Int. Ed.]] |volume= 40 |issue= 6 |pages= 1071–1074 |doi= 10.1002/1521-3773(20010316)40:6<1071::AID-ANIE10710>3.0.CO;2-5 |pmid= 11268077 |last1= Craig |first1= M. R. |last2= Hutchings |first2= M. G. |last3= Claridge |first3= T. D. |last4= Anderson |first4= H. L. |doi-access= free }}</ref> Studies with [[cyclodextrin]]-protected rotaxane [[azo dye]]s established this characteristic. More reactive [[squaraine dye]]s have also been shown to have enhanced stability by preventing [[nucleophile|nucleophilic attack]] of the inner squaraine [[Moiety (chemistry)|moiety]].<ref>{{cite journal |title= Squaraine-Derived Rotaxanes: Sterically Protected Fluorescent Near-IR Dyes |year= 2005 |journal= [[J. Am. Chem. Soc.]] |volume= 127 |issue= 10 |pages= 3288–3289 |doi= 10.1021/ja042404n |pmid= 15755140 |url=http://www.nd.edu/%7Ebsmith3/pdf/JACS2005e.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://www.nd.edu/%7Ebsmith3/pdf/JACS2005e.pdf |archive-date=2022-10-09 |url-status=live|last1= Arunkumar |first1= E |last2= Forbes |first2= C. C. |last3= Noll |first3= B. C. |last4= Smith |first4= B. D. |bibcode= 2005JAChS.127.3288A }}</ref> The enhanced stability 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,<ref>{{cite journal|title= Stable, Reproducible Nanorecording on Rotaxane Thin Films |year= 2005 |journal= [[J. Am. Chem. Soc.]] |volume= 127 |issue= 44 |pages= 15338–15339 |doi= 10.1021/ja054836j |pmid= 16262375 |last1= Feng |first1= M |last2= Guo |first2= X |last3= Lin |first3= X |last4= He |first4= X |last5= Ji |first5= W |last6= Du |first6= S |last7= Zhang |first7= D |last8= Zhu |first8= D |last9= Gao |first9= H |bibcode= 2005JAChS.12715338F }}</ref> a certain rotaxane is deposited as a [[Langmuir–Blodgett film]] on [[indium tin oxide|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 [[conformational isomerism|conformation]] makes the molecules stick out 0.3 [[nanometer]] from the surface. This height difference is sufficient for a [[memory dot]]. It is not yet known how to erase such a nanorecording film.

== Nomenclature ==
Accepted nomenclature is to designate the number of components of the rotaxane in brackets as a prefix.<ref>{{cite journal |title= Nomenclature for Rotaxanes and Pseudorotaxanes (IUPAC Recommendations 2008) |first1= Andrey |last1= Yerin |first2= Edward S. |last2= Wilks |first3= Gerard P. |last3= Moss |first4= Akira |last4= Harada |journal= Pure and Applied Chemistry |year= 2008 |volume= 80 |issue= 9 |pages= 2041–2068 |doi= 10.1351/pac200880092041|doi-access= free }}</ref> Therefore, the rotaxane consisting of a single dumbbell-shaped axial molecule with a single macrocycle around its shaft is called a [2]rotaxane, and two [[cyanostar]] molecules around the central phosphate group of dialkylphosphate is a [3]rotaxane.

==See also==
{{Commons category|Rotaxanes}}
*[[Catenane]]
*[[Mechanically interlocked molecular architecture]]
*[[Molecular Borromean rings]]
*[[Molecular knots]]
*[[Polyrotaxane]]

== References ==
{{reflist|30em}}

[[Category:Supramolecular chemistry]]
[[Category:Molecular electronics]]
[[Category:Organic semiconductors]]
[[Category:Molecular topology]]
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