Knots, Catenanes, and Rotaxanes Flashcards
What does mathematics describe a knot as being?
A circle embedded in 3D space
This applies the molecular compounds because a knot needs to be closed loop otherwise it will wriggle itself undone
Knots exist naturally on the molecular scale as well
They form spontaneously during the synthesis of polymers of…
sufficient length and flexibility
How can knots have symmetry?
What structures can they form with metal centres?
The centre of this knot bares similarities with the chiral metal in helicates
Where we would get three bidentate groups around an octahedral metal ion
E.g. the one of the left is Δ due to spirally down and clockwise
How would we go about synthesising a knot?
- The first step is to synthesise an organic ligand with three bidentate bipyridine groups that is sufficiently flexible to wrap around a single octahedral metal centre
- The ligand backbone is much more flexible than a ligand to form a triple helicate
- It also has a cyclohexyl group which favours the ligand adopting a more curled up conformation
What is the purpose of the primary alcohol groups on the end of the ligands
- These are chosen as they do not interfere wth the metal-ligand bond formation but can be chemically altered afterwards in a suitable reaction
- The wrapping of the ligand around the metal centre places the two alcohol groups close in 3D space
- These are linked through two esterification reaction with a dicarboxylic acid and coupling agent
The tying of the knot must take place under mild reaction conditions, so it does not break the metal-ligand bonds before the knot is tied
This reagent is chosen as it is mild, instead of more typical reagents of catalysts uded to make esters such as…
Conc H₂SO₄ or SOCl₂
what is the relationship between an overhand knot and a trefoil knot
We can make a trefoil knot frm tying the two ends of an overhand knot together
This alternative view of a trefoil knot makes it easier to see how it is possible to tie a trefoil knot using a double helicate, based on…
… two tetrahedral metal centres each with two bidentate ligands
Describe the structure of this knot?
- A dinuclear, double helicate can be constructed from copper(I) and phenanthroline ligands
- The phenol groups and the end of this helicate can be tired together through two nucleophilic substitution (Sₙ²) reactions with a diiodo compound
Why is this metal knot more difficult to make?
- It is crucial that the two top phenol groups are linked, and then the two bottom phenol groups are linked
- If different phenol groups are linked, then the trefoil knot is not formed
- This reaction also has quite harsh conditions meaning so of the metal-ligand bonds break before both links are made
- The yield of the knot is low
One the knot has been tied, the copper metal ions are no longer needed to keep the knot together
They can be removed by the addition of…
KCN
This formed copper(I) cyanide and leaves behind the fully organic ligand
Knots can be drawn in a variety of different ways
The picture shows how the trefoil knot orientation in a double helicate can be move around to make the more common symmetrical orientation
What property of the knot allows this to happen?
due to the flexibility of the backbone
To tie a pentafoil knot from a linear helicate we must tie…
- End 1 and 2
- And end 3 and 4
Why are pentafoil knots difficult to form?
- Due to the length of the ligands, the cloests ends are 1 and 4, and 2 and 3
- Means the ligands are no longer tying the the end closest to it
- (To data, a pentafoil knot has not been made from a linear helicate)
How would we go about forming a pentafoil knot?
- Knots can be tied between the nearby ends of circular helicates
- In circular helicates, the two ends that need to be tied remain close together
- A pentalfoil knot has been tired from a pentanuclear circular triple helicate
- Ring-closing olefin metathesis reaction that is catalysed by Hoveyda-Grubbs 2nd gen catalysis
This reaction requires…
mild conditions which keeps the metal-ligand bonds intact
Hence the yield is high
Once the knot has been fully tied, the metal ions are not needed
They are removed by the addition of
- Na₄EDTA
- EDTA is a hexadentate chelating ligand that is incredibly good at binding transtion metal ions
Interlocked molecules are split into two main classes….
Both structures are said to contain a…
Catenanes and Rotaxanes
contain a mechnical bond
Catenanes consist of…
Interlocked rings
Rotaxanes consist of…
a ring which is locked on a linear rod by bulky stoppers
In the nomenclature of these structures, the name is preceded by a number in square brackets, which describes the number of pieces that are interlocked
How would we name these two structures
- Left: [2]rotaxane
- Right: [3]rotaxane
What is a pseudorotaxane?
- These structures consist of an axle that has been threaded through a macrocycle but has not been stoppered at the ends
- This is not yet a true interlocked molecule
- For the pseudorotaxane to stay together, there must be some favourable interactions which stabilises this arrangement
With catenanes made from three or more pieces, there is the possibility of arranging these pieces in diffferent ways
What are the two ways to orientate [3]catenane?
- We can have both linear and cyclic catenanes
What is the difference between a catenate or a catenane?
- If the motion of the rings is restricted through coordination to a metal ion, we call it a catenate
- If he rings are free to rotate, then it is a catenane
- We have already encountered catenated structures before with [2]catenane in equilibrium with a molecular diamond
- The palladium ions in this structure form parts of the ring and therefore there is no way for them to be removed without the structure falling apart
- Is there structures where this is possible?
- Other catenated strucutres where the metal ions are not part of the ring, this is possible
- The tetrahedral coordination of copper(I) with 2 phenanthroline ligands
- One is part of a macrocycle (ligand A), and one had a free phenol group at each end (ligand B)
How can we remove the copper from this complex?
- Through the addition of cyanide, which forms copper(I) cyanide
- The different conformaton of the [2]catenane means the rings have freedom to rotate
- This conformation leads to more favourable intermolecular interactions such as van der Waals interactions
- If we consider more broadly the use of these double helicates to make either catenanes or knotsm we can see that the structure that forms alternates depending on the number of metal ions
- In these reactions a is always tied to a’ and b is always tired to b’
- An odd number of metal centres gives…
- An even number of metal centres give…
- An odd number of metal centres gives catenanes, with each strand of the helicate tied in its own loop
- An even number of metal centres fives knots with one continous circle made after tying the knot
We will look at capping to form rotaxanes
What does this involve?
- A pseudorotaxane is formed first and then the bulky end group are added later to cap the structure and stop the rings coming off
- Metal coordination is a great way to pre-organise the components into a pseudorotaxane
Three equivalents of ligand A and one equivalent of ligand C self-assemble with three equivalents of copper(I) to form a…
…[4]pseudorotaxane
What other product can form from this reaction and how do you stop it from forming?
- Ligand C can self-assemble with copper(I) to form a (3x3 grid)
- However, if the copper(I) is added in the correct proportions we do not see any grid
- Instead a pseudorotaxane is formed as the ends o ligand C cannot be capped due to lack of reactivity of the methyl groups
- Once of the most common methods for capping a pseudorotaxane into a full rotaxane is with a reaction known as the Huisgen azide-alkyne cycloaddition
- In this reaction an alkyne and an azide react together to made a triazole
- How does it work?
- a [3]pseudorotaxane is first assembled using an axle ligand D with an alkyne group on each end
- The stopped group is synthesised separately - this has an azide group attached at the end
- The capping reaction converts [3]pseudorotaxane into a [3]rotaxane
