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Molecular Mimics: - Nano Text 3/12/02 3:27 PM Page 113
Molecular Mimics: - Nano Text 3/12/02 3:27 PM Page 113
MOLECULAR MIMICS
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 114
114 • N A N OT E C H N O L O G Y
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 115
Figure 5.1
The structure of rotaxanes and catenanes (a) and the mechanism of rotaxane
shuttling (b).
pseudorotaxane
blocking
polymerisation
group
rotaxane polyrotaxane
catenane
polycatenanes
shuttling
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 116
116 • N A N OT E C H N O L O G Y
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 117
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
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118 • N A N OT E C H N O L O G Y
Figure 5.2
Electrically driven molecular switch.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 119
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 120
120 • N A N OT E C H N O L O G Y
Figure 5.3
a) Azobenzene light driven molecular switch,
b) The active unit is a -electron-donating macrocycle polyether, namely bis-p-
phenylene-34-crown ether, and a dumbbell shaped component that contains a
ruthenium polypyridine complex as one of its stoppers.
b
a
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 121
Figure 5.4 a
Synthetic routes
a) Binding
synthesis route to
rotaxanes.
b) Synthesis of [2]
catenane and a
trefoil knot by
cleaving links in
twisted strip-like
molecules. b
Amabilino DB and
Stoddar t JF (1995)
Chemical Reviews
95: 2725–828.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 122
122 • N A N OT E C H N O L O G Y
Figure 5.5
Diagrammatic representation of direct synthesis of catenanes involving template
linkages.
or
Covalent or
Noncovalent Link
Auxiliary Linkage
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 123
Figure 5.6
Actual representation of direct synthesis of catenanes involving template linkages.
Amabilino DB and Stoddar t JF (1995) Chemical Reviews 95: 2725–828.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/13/02 2:48 PM Page 124
124 • N A N OT E C H N O L O G Y
Figure 5.7
The self-assembly by a threading procedure of a [2] rotaxane incorporating a
cyclodextrin. Amabilino DB and Stoddar t JF (1995) Chemical Reviews 95: 2725–828.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 125
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 126
126 • N A N OT E C H N O L O G Y
in the opposite direction. Thus when one ring rotates clockwise the
other must rotate anticlockwise. This arrangement can be used in a
traditional macroscopic manner as paddles.
There are other examples in which molecules resemble everyday
macroscopic rotors. The coupled motions of two structures have been
exploited in the design of molecular gears incorporating 9-triptycyl ring
systems. For example, the gear shown in the middle trace of Figure 5.8
incorporates two 9-triptycyl ring systems bridged by a methylene group.
The aryl rings of the two triptycyl ring systems interdigitate in a manner
reminiscent of the notches of a pair of meshed gears, much like those in
models for carbon based nanotube gears (Chapter 4). As a result, the
rotations of the two 9-triptycyl ring systems about a single bond linked
to a common group are coupled. When one 9-triptycyl ring system
rotates clockwise the other rotates anticlockwise and vice versa.
Figure 5.8
Par ts of molecular
machines: top
trace, paddle;
middle trace,
gears; and bottom
trace, an armature.
The structures
assigned as R are
also shown.
Modified from
Balzani V, Credi A,
Raymo FM and
Stoddar t JF (2000)
Angew. Chemie Int.
Ed. 39: 3348–91.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:27 PM Page 127
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 128
128 • N A N OT E C H N O L O G Y
Figure 5.9
a) Unidirectional propeller and
b) propeller with brake. Modified from Balzani V, Credi A, Raymo FM and Stoddar t
JF (2000) Angew. Chemie Int. Ed. 39: 3348–91.
a
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 129
Figure 5.10
a) Copper, Cu+ on rotating catenane rings
b) Light driven molecular ball and socket molecule. Modified from Balzani V, Credi
A, Raymo FM and Stoddar t JF (2000) Angew. Chemie Int. Ed. 39: 3348–91.
b
a
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 130
130 • N A N OT E C H N O L O G Y
5.9 PRODDERS
We have noted that the azobenzene structure can adopt cis and trans
configurations, and they can be interconverted by irradiation at appro-
priate wavelengths. Thus the geometry is altered by interconversion
from cis to trans. The cyclic structure in Figure 5.10b is called a crown
ether and this particular crown ether has cis and trans forms. The
crown ether compound shown in Figure 5.10b has a charged head. In
the trans form the cation head is away from the crown ether but in the
cis form the head is close to the crown ether. The positive charge is sta-
bilised by intramolecular bonding to the electron rich oxygen atoms in
the crown ether. In the trans form the quaternary ammonium cation
head forms ionic linkages with anions, but in the cis form these ionic
linkages cannot be formed when stuck inside the crown ether. This
device could therefore be used as a light driven detector for anions or
alternatively it could act as a gate, which will release anions only when
photo irradiated. Since the transfer and movement of anions are very
important in biological machines, this device might be useful for cou-
pling with biological material such as membranes.
Another application for the structure in Figure 5.10b is as a prod-
der. If a molecule was situated under the crown ether, then when the
cis form is formed the molecule may be pushed away.
Detached cations make useful molecular syringes, another form of
prodder. In this device (Figure 5.11) a silver ion is coordinated to a
nitrogen atom. However, when the nitrogen atom is protonated with
acid the silver ion is pushed through the tube; upon deprotonation it
is sucked back again. This device could be used to move any free mate-
rial in and below the silver ion. It also acts like a ball valve.
Figure 5.11
A molecular syringe. Modified from Balzani V, Credi A, Raymo FM and Stoddar t JF
(2000) Angew. Chemie Int. Ed. 39: 3348–91.
CH 3
N
O O
O O
CH 3
O
CH 3
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 131
Figure 5.12
The electrically driven ferrocene
plunger. Modified from Balzani V,
Credi A, Raymo FM and Stoddar t
JF (2000) Angew. Chemie Int. Ed.
39: 3348–91.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 132
132 • N A N OT E C H N O L O G Y
5.12 ACTUATORS
Actuators are machines which convert electrical motion to mechanical
energy or vice versa. Nanoactuators may be formed when:
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 133
Figure 5.13
Molecular flippers. a) Light driven and b) light and heat driven. Modified from
Balzani V, Credi A, Raymo FM and Stoddar t JF (2000) Angew. Chemie Int. Ed. 39:
3348–91.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 134
134 • N A N OT E C H N O L O G Y
Figure 5.14
Copper-carr ying molecular train at different stations. Modified from Balzani V, Credi
A, Raymo FM and Stoddar t JF (2000) Angew. Chemie Int. Ed. 39: 3348–91.
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 135
5.13 CONTACTS
The components of nanostructures, such as those compounds dis-
cussed above, will still need to be assembled into a useful structure. A
very good structure is the biological membrane, which is discussed in
Chapter 6. However, there are other structures on which machines can
be built. A very flat surface, such as gold, is preferred since it is very
difficult to assemble a mechanism accurately on an uneven surface,
such as the copper surface in Chapter 2, Figure 2.15.
The nanomachines are not assembled molecule by molecule, as this
would take too long. Rather they are deposited by various means such
as chemical vapour deposition, from a liquid, or electrochemically to
form structures and then contacted.
This involves four steps. In the first step, the molecules of interest
are adsorbed onto the isolating substrate in their millions. Since gold
is a good electrode it can be used as the substrate and then masked
(Chapter 3.4 and in more detail in Chapter 8.4) after the molecules are
added. Whether molecules are covered or destroyed in masking does
not matter since there is a huge inbuilt redundancy. What is important
is that there are clear areas where the molecules are free.
The second step includes the visualisation of the molecule distrib-
ution, mostly by STM. In the third step the molecule is contacted,
either through the scanning tip, which adds molecules (for example,
dip pen technology) or by structuring of electrodes. This can be done
by adding electrode material, by demasking certain areas, or by
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 136
136 • N A N OT E C H N O L O G Y
addition. All of this is very slow and the images from STM are usually
used for localising the molecules of interest. Arrays of electrode pairs
are usually structured from ~100 nm gold (primed with a ~5 nm tita-
nium layer) on a thermally oxidised silicon wafer using lithographic
techniques (Chapter 3.4 and Chapter 8.4). After this, in the fourth
step, electrical characterisation must be achieved. All this needs to be
sped up for practical utilisation. Numerous circuits may be made (as
with silicon chip technology) and only the best kept. These may have
largely non-working systems, but this does not matter since only a few
structures need to work per 100 nm2.
Figure 5.15
Fixing a molecular component to a frame for wiring. Units for wiring are shown in
the table. Modified from Balzani V, Credi A, Raymo FM and Stoddar t JF (2000)
Angew. Chemie Int. Ed. 39: 3348–91.
Au -SH
TiO2 -CO2H
SnO2 -B(OH)2
-OPO2H2
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
•Nano text 3/12/02 3:28 PM Page 137
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
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138 • N A N OT E C H N O L O G Y
5.14 EXERCISES
1 Build four models from Figure 5.13. Use the filled in structures rather
than the molecular structures. Use matchsticks as axles and shape the
structures from pieces of apple or other material. Show that there are
four isomers
2 Build a model of Figure 5.8 top trace from tape, paper and match-
sticks and convince yourself that the diagram shows clockwise and
anticlockwise rotation.
3 Read Balzani V, Credi A, Raymo F and Soddart JF (2000) Angew.
Chem. Int. Ed. 39: 3348–3391. This paper is a brilliant review of the
field.
4 Web search cyclodextrin, nanojunction, ethylene diamine tetra acetic
acid, actuator, and ferrocene.
5 Look up the definition of polycyclic aromatic compounds.
6 Take some string and build the structures shown in Figure 5.4b.
Demonstrate how these structures produce the products shown.
5.15 REFERENCES
1 Amabilino DB & Stoddart JF (1995) Chemical Reviews 95: 2725–828.
2 Bissell RA, Cordova E, Kaifer AE & Stoddart JF (1994) Nature 369: 133.
3 Murakami H, Kawabushi A, Kotoo K, Kunitake M & Nakashima N
(1997) J. Amer. Chem. Soc. 119: 7605–606.
4 Balzani V, Credi A, Raymo FM & Stoddart JF (2000) Angew. Chemie Int.
Ed. 39: 3348–91.
5 Baughaman RH, Cui C, Zakhidov AA, Iqbal Z, Barisci JN, Spinks GM,
© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse
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© 2002 by Michael Wilson, Kamali Kannangara, Geoff Smith, Michelle Simmons, and Burkhard Raguse