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An introduction to topological chemistry
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2Bibliography
2011, 111, 5434-5464
Angew. Chem. Int. Ed., 2011, 50, 9260-9327
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33Bibliography
2013, 42, 1700
Angew. Chem. Int. Ed., 2015, 54, 6110
Many illustrations present in the slides are taken from these reviews
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4Contents
1- Molecular graph and topological chemistry
2- Synthesis of [2]catenanesa) Historical backgroundb) Sauvage’s template synthesis
3- Sauvage’s strategy for more complex structuresa) Molecular knotsa) Molecular knotsb) Limits and contributions from other groups
4- Borromean rings
5- (Very) short introduction to topological stereochemistry
6- Molecular machines and motors
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Topology
In topology, angles, distances or shapes have no meaningBut the object cannot be cut
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Molecular graph
planar graph
One possible conformation with nocrossing in 2D representation
Representation of the bonds between atoms with no interest in their chemical nature
C60 has a planar graph:
topologically equivalent
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non-planar graph
topological chemistry is the chemistry of molecules having a non planar graph
No possible conformation with nocrossing in 2D representation
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Molecular graph
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Topology in art
Aquilea, Italy
Book of Kells
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Topology in art
SnakesM.C. Escher
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Topology in art
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Topology in nature
Protein chainmail for a virus capside Exonuclease-DNA complex
Nucleic Acid Res, 2003, 31, 1585Science 2000, 289, 2129
Nucleic Acid Res, 2003, 31, 1585
Knotted proteins
FEBS Journal, 2009, 276, 365
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- If two molecules are different only for their graphs, they are topological isomers
a is an isomer of b and c.b and c are topological enantiomers.
- Most popular classes of topological molecules are catenanes and rotaxanes
catenane:
Topological chemistry
catenane:
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rotaxane:
Topological chemistry
rotaxane is not strictly speaking a topological objectbut, in chemistry, there is a good reason to say so:
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Topological chemistry
Loss of the structure by breaking a covalent bond= interaction is strong: not supramolecular chemistry?
BUT: no covalent bond between the two rings!= interaction is weak
mechanical bond
How can this kind of molecules be made?
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Catenane by statistical method
- 1960: statistical synthesis proposed by Wasserman. unsuccessful.
+
Wasserman, J. Am. Chem. Soc.,1960, 82, 4433
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+
- Template synthesis:
interaction
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Catenane by template synthesis
- First work by Schill and Lüttringhaus
Schill and Lüttringhaus, Angew. Chem. Int. Ed. Engl. 1964, 3, 546
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Catenane: copper-template reaction
Sauvage’s contribution: 1983
Dietrich-Buchecker, Sauvage et al. Tet. Lett., 1983, 24, 5095
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Origin of the strategy
Water splitting project with McMillinCopper photocatalyst instead of expensive Ruthenium
Cu+
H2O H2 + ½ O2
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Catenane: copper-template reaction
Sauvage’s contribution: 1983, copper template synthesis.
Sauvage et al. Tet. Lett., 1983, 24, 5095(maximum site occupancy rule)
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Catenane: X-ray structure
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Template synthesis: importance of the closing react ion
ca. 30 %
ca. 80 %
b)
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Catenane: other template syntheses
R=OMe Vögtle, 1992R=H Hunter, 1992Π-stacking, Stoddart, 1989 H-bond-stacking, Stoddart, 1989 H-bond
Hydrophobic effect, Fujita, 1994
↑polarity
↓polarity
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Catenane: other template syntheses
Sauvage’s strategy transposed to an anion template:
Beer et al. Chem. Commun., 2006, 3676
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Rotaxane: active template synthesis
A new template reaction under kinetic control: active template synthesis.The template is not only used for thermodynamic stabilization of a transient speciesbut also for its role in bond formation.
- Many other metal-catalyzed reactions have been employed (Pd(II), Ni(II)…)- This strategy can also be used for the synthesis of catenane
Leigh et al. J. Am. Chem. Soc., 2006, 128, 2186
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Leigh et al. J. Am. Chem. Soc.,2006, 128, 2186
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Beyond the simplest catenane
Xyz: Alexander-Briggs notation
X = minimum crossing points; y = number of components; z = order of the knot
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Molecular knots
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Sauvage’s strategy
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Molecular trefoil knot
-Design: find the good connection
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Molecular trefoil knot
First synthesis achieved by Sauvage et al. in 1989:
X-ray structure
Sauvage et al. Angew. Chem. Int. Ed., 1989, 28, 189
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Molecular Knot
- Similar approach by Hunter :
- Another strategy proposed by Sokolov in 1973:
Hunter et al. Nature. Chem., 2010, 2, 218
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H-bonding template synthesis of a molecular trefoil knot
Vögtle et al., Angew. Chem., Int. Ed., 2000, 39, 1616
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Doubly interlocked [2]catenane – Solomon link
Sauvage et al. Chem Commun., 1999, 615.
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Limit to the strategy based on linear double helice s
NN N N NN N N
RO OR
NN N N NN N N N N
RO OR
R =O O
1: n=32: n=4
n
Sauvage et al. Chem. Eur. J. 2005, 11, 4374
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Circular helix strategy
Inspiration from Lehn’s work
Lehn al. J. Am. Chem. Soc., 1997, 119, 10956
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36Leigh’s triply interlocked [2]catenane - star of Dav id
X-ray
Leigh et al., Nature Chem, 2014, 6, 978
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373737Leigh’s 8 19 knot
Leigh et al., Science, 2017, 355, 159
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3838Leigh’s pentafoil knot
Dynamic covalent bond-metal template and anion template
X-rayLeigh et al., Nature Chem, 2012, 4, 15
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Borromean Rings
One of the most impressive achievement in topological chemistry
Three identical rings. Each ring is inside a second oneand outside the third one. No catenation.
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Borromean Rings
Ring-by-ring synthesis :
ring-in-a-ring
Siegel et al. Angew. Chem. Int. Ed., 2003, 42, 5702
- long synthesis- Borromean rings were not obtained…
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Borromean Rings
- One-step synthesis!!!
control of the synthesis :
- metal-templated- imine bond formation−Π−stacking- geometry and size of the ligandthe ligand
Stoddart et al. Science, 2004, 304, 1308
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N
OO
Borromean Rings
: endo-tridentate
NN
O O
H2N NH2
: exo-bidentate
5-coordinated metalZn(II)
NN
NN
O O
N N
N N
OO
NN
N N
Stoddart et al. Science, 2004, 304, 1308
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Borromean Rings
Formation of 12 imine bondsAssociation of 18 units
X-Ray structure
Stoddart et al. Science, 2004, 304, 1308
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Topological stereochemistry
Catenanes with oriented rings are chiral
Sauvage et al., Angew. Chem. Int. Ed., 1998, 27, 930
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Topological stereochemistry
A knot is chiral and can be resolved
Sauvage et al. J. Am. Chem. Soc., 1996, 118, 10932
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Topological stereochemistry
Diastereoselective synthesis of a molecular knot
Sauvage, von Zelewsky et al., Angew. Chem. Int. Ed., 2004, 43, 4482
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Topological stereochemistry
Diastereoselective synthesis of a molecular knot
Leigh et al., J. Am. Chem. Soc., 2016, 138, 13158
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49Molecular machine powered by an electrochemical fue l
Sauvage et al. J. Am. Chem. Soc., 1994, 116, 9399
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50Molecular machine powered by a chemical fuel
- rotaxane based molecular shuttle- intramolecular process- bistable molecule (1 or 0)
Acid-base powered molecular translation of a ring along a thread :
- bistable molecule (1 or 0)- possibility for high density information storage
High complexity of the molecule:- interlocked system- two orthogonal binding sites on the thread
Balzani et al. Acc. Chem. Res., 2001, 34, 445
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51From switches to motors: toward dissipative systems
Credi et al., Nature Nanotech., 2015, 10, 70