Supramolecular catalysis

An enzyme (TEV protease 1lvm) is an example of supramolecular

catalysts in nature. One goal of supramolecular catalysis is to
mimic active site of enzymes.

An early example of enzyme mimics. Crams 1976 crown ether

acyl transfer catalyst.[4]

Supramolecular catalysis is not a well-dened eld but

it generally refers to an application of supramolecular
chemistry, especially molecular recognition and guest
binding, toward catalysis.[1][2] This eld was originally
inspired by enzymatic system which, unlike classical organic chemistry reactions, utilizes non-covalent interactions such as hydrogen bonding, cation-pi interaction, and
hydrophobic forces to dramatically accelerate rate of reaction and/or allow highly selective reactions to occur.
Because enzymes are structurally complex and dicult
to modify, supramolecular catalysts oer a simpler model
for studying factors involved in catalytic eciency of the
enzyme.[3]:1 Another goal that motivates this eld is the
development of ecient and practical catalysts that may
or may not have an enzyme equivalent in nature.
A closely related eld of study is asymmetric catalysis
which requires molecular recognition to dierentiate two
chiral starting material or chiral transition states and thus
it could be categorized as an area of supramolecular catalysis, but supramolecular catalysis however does not necessarily have to involve asymmetric reaction. As there
is another Wikipedia article already written about small
molecule asymmetric catalysts, this article focuses primarily on large catalytic host molecules. Non-discrete
and structurally poorly dened system such as micelle and
dendrimers are not included.

Breslows Regioselective Hydrolysis of Cyclic Phosphate Catalysed by Diimidazole-beta-cyclodextrin[5]

by association of two or more chemical species in his

Nobel lecture in 1987,[6] but the concept of supramolecular catalysis was started way earlier in 1946 by Linus Pauling when he founded the theory of enzymatic catalysis in
which rate acceleration is the result of non-covalent stabilization of the transition state by the enzymes.[7] Nevertheless, it was not until a few decades later that an articial
enzyme was developed. The rst simple enzyme mimics
were based on crown ether and cryptand.[8] In 1976, less
than ten years after the discovery of crown ether, Cram
1 History
et al. developed a functionalized binapthyl crown ether
that catalyze transacylation.[4] The catalyst makes use the
The term supramolecular chemistry is dened by Jean- crown ether motifs ability to capture cation to bind to
Marie Lehn as the chemistry of intermolecular bond, the ammonium ion part of the substrate and subsequently
covering structures and functions of the entities formed employs the nearby thiol motif to cleave the ester.
1

2 MECHANISM OF CATALYSIS

From the early 1970s, cyclodextrins have been extensively studied for its encapsulation properties and used
as binding sites in supramolecular catalyst.[2] Cyclodextrins have rigid ring structure, hydrophilic surface, and
hydrophobic cavity on the inside; therefore, they are
capable of binding organic molecules in aqueous solution. In 1978, with the background knowledge that
the hydrolysis of m-tert-butylphenyl acetate is accelerated in the presence of 2-benzimidazoleacetic acid and
alpha-cyclodextrin,[9] Brewslow et al. developed a catalyst based on a beta-cyclodextrin carrying two imidazole groups. This cyclodextrin catalytic system mimics
ribonuclease A by its use of a neutral imidazole and an
imidazolium cation to selective cleave cyclic phosphate
substrates. The rate of the reaction is catalyzed 120 times
faster, and unlike a hydrolysis by simple base NaOH that
gives a 1:1 mixture of the products, this catalysts yield a
99:1 selectivity for one compound.[5]
In 1993, Rebek et al. developed the rst self-assemble
capsule[10] and in 1997 the so-called tennis ball structure was used to catalyze a Diels-Alder reaction.[11] Selfassembled molecules have an advantage over crown ether
and cyclodextrin in that they can capture signicant larger
molecules or even two molecules at the same time. In
the following decades, many research groups, such as
Makoto Fujita, Ken Raymond, and Jonathan Nitschke,
developed cage-like catalysts also from molecular selfassembly principle.
In 2002, Sanders and coworkers published the use of
dynamic combinatorial library technique to construct a
receptor[12] and in 2003 they employed the technique to
develop a catalyst for Diels-Alder reaction.[13]

Mechanism of catalysis

A chiral substituted crown ether catalyst developed by Jean-Marie

Lehn for ester cleavage. The crown ether binds the aminium ion
so that the labile group (in red) is positioned next to the reactive
group (in blue).[14]

2.2 Raising the eective substrate concentration

Bimolecular reactions are highly dependent on the concentration of substrates. Therefore, when a supramolecular container encapsulates both reactants within its small
cavity, the eective local concentration of the reactants
is increased and, as a result of an entropic eect, the rate
of the reaction is accelerated.[16]:89 That is to say an intramolecular reaction is faster than its corresponding intermolecular reaction.

Although high raise in eective concentration is observed, molecules that employ this mode of catalysis have
tiny rate acceleration compared to that of enzymes. A
proposed explanation is that in a container the substrates
2.1 Orienting reactive and labile groups
are not as tightly bound as in enzyme. The reagents have
room to wiggle in a cavity and so the entropic eect might
A supramolecular host could bind to a guest molecule
not be as important. Even in the case of enzymes, compuin such a way that the guests labile group is positioned
tational studies have shown that the entropic eect might
close to the reactive group of the host. The proximity
also be overestimated.[17]
of the two groups enhances the probability that the reaction could occur and thus the reaction rate is increased. Examples of molecules that work via this mechaThis concept is similar to the principle of preorganization nism are Rebeks tennis ball and Fujitas octahedral
which states that complexation could be improved if the complex.[11][18]
binding motifs are preorganized in a well-dened position
so that the host does not require any major conformational change for complexation.[15] In this case, the cat- 2.3 Stabilizing transition state
alyst is preorganized such that no major conformational
changes is required for the reaction to occur. A notable Supramolecular catalysts can accelerate reactions not
example of catalysts that employ this mechanism is Jean- only by placing the two reactants in close proximity but
Marie Lehns crown ether.[14] In addition, catalysts based also by stabilizing the transition state of the reaction and
on functionalized cyclodextrins often employ this mode reducing activation energy.[16]:89 While this fundamental
principle of catalysis is common in small molecule or hetof catalysis.[16]:88
Three common modes of catalysis are described here.

3.1

Design approach

Hydrogen-bonded glycouril dimer catalyst developed by Julius

Rebek Jr. for Diels-Alder reactions. The catalyst encapsulates
the diene and dienophile, increasing the eective concentration
of reactants.
Porphyrin trimer catalyst developed by Jeremy Sanders for exo
selective Diels-Alder reactions. The catalyst stabilizes the exo
transition state by strategic binding of zinc (II) ion to pyridine
nitrogen atoms on the diene and dienophile.

catalysts are often inspired by the structure of enzymes

with the catalytic group mimicking reactive amino acid
residues, but unlike real enzymes, the binding sites of
these catalysts are rigid structure made from chemical
building blocks.[20] All of the examples in this article are
developed via the design approach.
Generic potential energy diagram showing the eect of a catalyst.

erogeneous catalysts, supramolecular catalysts however

has a dicult time utilizing the concept due to their often
rigid structures. Unlike enzymes that can change shape
to accommodate the substrates, supramolecules do not
have that kind of exibility and so rarely achieve subangstrom adjustment required for perfect transition state
stabilization.[3]:2
An example of catalysts of this type is Sanders porphyrin trimer. A Diels Alder reaction between two pyridine functionalized substrates normally yield a mixture
of endo and exo products. In the presence of the two
catalysts, however, complete endo selectivity or exo selectivity could be obtained. The underlying cause of the
selectivity is the coordination interaction between pyridine and the zinc ion on porphyrin. Depending on the
shape of the catalysts, one product is preferred over the
other.[19]

Jeremy Sanders pointed out that the design approach has

not been successful and has produced very few ecient
catalysts because of rigidity of the supramolecules. He
argued that rigid molecules with a slight mismatch to the
transition state cannot be an ecient catalyst. Rather
than investing so much synthesis eort on one rigid
molecule that we cannot determine its precise geometry
to the sub-angstrom level which is required for good stabilization, Sanders suggested the use of many small exible building blocks with competing weak interactions so
that it is possible for the catalyst to adjust its structure
to accommodate the substrate better.[21] There is a direct trade-o between the enthalpic benet from exible
structure and the entropic benet from rigid structure.[3]:3
Flexible structure could perhaps bind the transition state
better but it allows more room for the substrates to move
and vibrate. Most supramolecular chemists in the past
prefer to build rigid structures out of fear of entropic
cost.[21]

This problem could perhaps be mended by Baker and

Houk's inside-out approach which allows a systematic de novo enzyme development.[22] This computational
3 Approaches
to
making method starts simply with a predicted transition state
structure and slowly builds outward by optimizing the arsupramolecular catalysts
rangement of functional groups to stabilize the transition
state. Then it lls out the remainder of the active site and,
3.1 Design approach
nally, it generates an entire protein scaold that could
contain the designed active site. This method could poThe traditional approach to supramolecular catalysts fo- tentially be applied to supramolecular catalysis, although
cuses on the design of macromolecular receptor with a plethora of chemical building blocks could easily overappropriately placed catalytic functional groups. These whelm the computational model intended to work with

4 PROMINENT EXAMPLES OF SUPRAMOLECULAR CATALYSTS

20 amino acids.

3.2

Transition state analogue

tion/screening approach

needs to be measured directly and also quickly. To develop a high-throughput screen, substrates could be designed to change color or release a uorescent product
selec- upon reaction. For example, Crabtree and coworkers utilized this method in screening for a hydrosylation catalysts for alkene and imine.[23] Unfortunately the prerequisite for such substrates narrow down the range of reactions for study.[20]

3.4 Dynamic combinatorial library approach

A diagram depicting a use of transition state analog selection approach to select a catalytic antibody.

Assuming that catalytic activity largely depends on the

catalysts anity to the transition state, one could synthesize a transition state analog (TSA), a structure that
resembles the transition state of the reaction. Then one
could link the TSA to a solid-support or identiable tag
and use that TSA to select an optimal catalyst from a
mixture of many dierent potential catalysts generated
chemically or biologically by a diversity oriented synthesis. This method allows quick screening of a library of
diverse compounds. It does not require as much synthetic
eort and it allows a study of various catalytic factors simultaneously. Hence the method could potentially yield
an ecient catalyst that we could not have designed with
our current knowledge.[20]
Many catalytic antibodies were developed and studied using this approach.

3.3

Catalytic activity screening approach

A diagram depicting a use of catalytic activity screening approach to screen a catalyst.

A diagram depicting a use of dynamic combinatorial library to

select an optimal receptor.

In contrast to traditional combinatorial synthesis where a

library of catalysts were rst generated and later screened
(as in the two above approaches), dynamic combinatorial library approach utilizes a mixture of multicomponent building blocks that reversibly form library of catalysts. With out a template, the library consists of a
roughly equal mixture of dierent combination of building blocks. In the presence of a template which is either a
starting material or a TSA, the combination that provides
the best binding to the template is thermodynamically favorable and thus that combination is more prevalent than
other library members. The biased ratio of the desired
catalyst to other combinatorial products could then be
frozen by terminating the reversibility of the equilibrium
by means such as change in temperature, pH, or radiation
to yield the optimal catalyst.[20] For example, Lehn et al.
used this method to create a dynamic combinatorial library of imine inhibitor from a set of amines and a set of
aldehydes. After some time, the equilibrium was terminated by an addition of NaBH3 CN to aord the desired
catalyst.[24]

4 Prominent
examples
supramolecular catalysts

of

A problem with transition state analogue selection approach is that catalytic activity is not a screening criteria.
TSAs do not necessarily represent real transition states 4.1 Diederichs pyruvate oxidase mimic
and so a catalyst obtained from screening could just be
the best receptor for a TSA but is not necessarily the best In nature, pyruvate oxidase employs two cofactors
catalyst. To circumvent this problem, catalytic activity thiamine pyrophosphate (ThDP) and Flavin adenine din-

4.3

Raymonds Nazarov cyclization catalyst

ucleotide (FAD) to catalyze a conversion of pyruvate to

acetyl phosphate. First, ThDP mediates a decarboxylation of pyruvate and generates an active aldehyde as a
product. The aldehyde is then oxidized by FAD and is
subsequently attacked by phosphate to yield acetyl phosphate.
Diederich and coworkers mimicked this system with a
supramolecular catalyst based on cyclophane. The catalyst has thiazolium ion, a reactive part of ThDP and avin,
a bare-bones core of FAD, in close proximity and near the
substrate binding site. The catalytic cycle is almost the
same as that in nature, except the substrate is an aromatic
aldehyde rather than pyruvate. First, the catalyst binds
the substrate within its cyclophane ring. Then, it uses thiazolium ion to condense with the substrate generating an A manganese porphyrin catalyst developed by Nolte et al. capaactive aldehyde. This aldehyde is oxidized by avin and ble of successive epoxidation of alkene polymer.
then attacked by methanol to yield a methyl ester.[25]

4.3 Raymonds Nazarov cyclization catalyst

Raymond and coworkers developed a supramolecular
host M4 L6 (4 gallium ions and 6 ligands for each complex) that self-assembles via metal-ligand interaction in
aqueous solution. This container molecule is polyanionic
and thus its tetrahedron-shaped cavity is capable of encapsulating and stabilizing a cationic molecule. Consequently, encapsulated molecule can be easily protonated
as a resulting carbocation from protonation is stabilized
by the surrounding anions. Raymond utilized this propPyruvate oxidase mimic developed by Franois Diederich. The erty to perform acid-catalyzed Nazarov cyclization. The
cyclophane based catalyst utilizes ThDP mimic and FAD mimic catalyst accelerates the reaction by over one million fold,
to accelerate the oxidation of aldehyde into ester.
making it the most ecient supramolecular catalyst to
date. It was proposed that such a high catalytic activity
does not arise just from the increased basicity of the encapsulated substrate but also from the constrictive binding that stabilize the transition state of the cyclization.
4.2 Noltes successive epoxidation catalyst Unfortunately, this catalyst has a problem with product
for alkene polymer
inhibition. To by pass that problem, the product of the
cyclization reaction could be reacted with a dienophile
Processive enzymes are proteins that catalyze consecu- transforming it into a Diels-Alder adduct that no longer
tive reactions without releasing its substrate. An example ts inside the catalyst cavity.[1]
of processive enzymes is RNA polymerase which binds In this case, the supramolecular host was initially deto a DNA strand and repeatedly catalyzes nucleotide signed to simply capture cationic guests. Almost a decade
transfers, eectively synthesizing a corresponding RNA later, it was exploited as a catalyst for Nazarov cyclization.
strand.
Nolte and coworkers developed an articial processive
enzyme in a form of manganese porphyrin rotaxane that
treads along a long polymer of alkene and catalyze multiple rounds of alkene epoxidation. Manganese (III) ion
in the porphyrin is the molecules catalytic center, capable of epoxidation in the presence of an oxygen donor
and an activating ligand. With a small ligand such pyridine that binds manganese from inside the cavity of the
rotaxane, epoxidation happens outside the catalyst. With
a large bulky ligand such as tert-butyl pyridine that does
not t inside the cavity however, epoxidation happens on
the inside of the catalyst.[26]

4.4 Fujitas chiral self-assembled catalyst

for asymmetric [2+2] photoadditions
Fujita and coworkers discovered a self-assemble M6 L4
(6 palladium ions and 4 ligands in each complex)
supramolecular container that could be enhanced into a
chiral supramolecule by an addition of peripheral chiral
auxiliary. In this case, the auxiliary diethyldiaminocyclohexane does not directly activate the catalytic site but
induces a slight deformation of the triazine plane to create chiral cavity inside the container molecule. This

6 PROBLEMS AND LIMITATIONS

A self-assemble gallium catalyst developed by Ken Raymond accelerates Nazarov cyclization by stabilizing the cationic transition
state. The structure drawn here shows only one ligand for simplicity sake, but there are six ligands on the edges of the tetrahedral complex.

container could then be used to asymmetrically catalyze

a [2+2] photoaddition of maleimide and inert aromatic
compound uoranthene, which previously have not been
shown to undergo thermal or photochemical pericyclic
reaction. The catalyst yields an enantiomeric excess of
A chiral constrained Bronsted acid developed by Benjamin List
40%.[27]
works as an asymmetric spiroacetalization catalyst.

5 Supramolecular inhibitors
Supramolecular containers do not only have an application in catalysis but also in the opposite, namely, inhibition. A container molecule could encapsulate a guest
molecule and thus subsequently renders the guest unreactive. A mechanism of inhibition could either be that the
substrate is completely isolated from the reagent or that
the container molecule destabilize the transition state of
the reaction.
An asymmetric [2+2] photoaddition catalyst based on a tetrahedral palladium complex developed by Makoto Fujita. The catalyst has chiral diamine auxiliaries that induces the asymmetric
change in the cavity.

4.5

Nitschke and coworkers invented a self-assembly M4 L6

supramolecular host with a tetrahedral hydrophobic cavity that can encapsulate white phosphorus. Pyrophoric
phosphorus, which could self-combust upon contact with
air, is rendered air-stable within the cavity. Even though
the hole in the cavity is large enough for an oxygen
molecule to enter, the transition state of the combustion
is too large to t wthin the small cage cavity.[29]

Lists conned Bronsted acid as a catalyst for asymmetric spiroacetalization

Inspired by enzymes with deep active site pocket, List

and coworkers designed and constructed a set of conned Bronsted acids with an extremely sterically demanding chiral pocket based on a C2 -symmetric bis(binapthyl)
imidodiphosphoric acid. Within the chiral microenvironment, the catalysts has a geometrically xed bifunctional active site that activates both an electrophilic part
and a nucleophilic part of a substrate. This catalyst
enables stereoselective spiroacetal formation with high
enantiomeric excess for a variety of substrates.[28]

6 Problems and limitations

After many decades since its inception, supramolecular
chemistrys application in practical catalysis remains elusive. Supramolecular catalysis has not yet made significant contribution in the area of industrial chemistry or
synthetic methodology.[21] Here are few problems associated with this eld.

7 See also
Supramolecular Chemistry
Host-Guest Chemistry
Molecular Encapsulation
Articial enzyme
Asymmetric catalysis

8 References

A subcomponent self-assembly tetrahedral capsule developed by

Jonathan Nitschke renders pyrophoric white phosphorus airstable. The structure drawn here shows only one ligand for simplicity sake, but there are six ligands on the edges of the tetrahedral complex.

6.1

Product inhibition

In many supramolecular catalytic systems designed to

work with bimolecular addition reactions like the DielsAlder, the product of the reaction binds more strongly to
the supramolecular host than the two substrates do, consequently leading to inhibition by the product. As a result,
these catalysts has a turnover number of one and are not
truly catalytic. A stoichiometric quantity of the catalysts
is needed for a full conversion.[30]

6.2

Poor transition state stabilization

Most supramolecular catalysts are developed from rigid

building blocks because rigid blocks are less complicated
than exible parts in constructing a desired shape and
placing functional groups where the designer wants. Due
to the rigidity, however, a slight mismatch from the transition state inevitably leads to poor stabilization and thus
poor catalysis. In nature, enzymes are exible and could
change their structures to bind a transition state better
than their native form.[21]

6.3

Diculty in synthesis and further adjustment

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R. G. (2010). Enzymelike Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation. Journal of
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