Ck80 Organic Nanochemistry

Self-assembly
Organic Nanochemistry

Spring 2006

Kurt Gothelf
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Nanotechnology – my first encounter

Engines of Creation: The Coming Era of Nanotechnology

K. E. Drexler, Fourth Estate, 1990
Nanosystems: Molecular Maschinery, Manufacturing, and Computation
K. E. Drexler, John Wiley and Sons, 1992

K. E. Drexler
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Design and fabrication of nano-structures

• Miniaturization of known systems

• Apply methods resembling nature
• Develop new methods
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“Bottom up” versus “Top down”

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NANOTECHNOLOGY APPROACHES

Top-down

Bottom-up
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Self-assembly
Molecular self-assembly is the spontaneous association of molecules
under equilibrium conditions into stable, structurally well defined
aggregates joined by non-covalent bonds.
Whitesides et al. Science 254 1312 (1991).

Non-covalent interactions: Hydrogen bonds

Metal coordination complexes
Van der Waals interactions
Hydrophobic interactions
Electrostatic interactions

Equilibrium conditions: Rejects defects

(Assembly by many reversible weak interactions) Self-healing
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Self-assembled structures of nature

Egg and sperm

Governor of California
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Function of the cell is based on

self-assembly
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Building molecular nanostructures

• Traditional organic synthesis

• Polymer chemistry
• Self-organization into polydisperse aggregates
(Self-organization)
• Self-assembly into monodisperse aggregates
(Molecular self-assembly)
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Molecular interaction leading to

molecular organization

Self-organization

Molecular self-
assembly
(Specific molecular
recognition)

Forming monodisperse assemblies

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Examples
• Polydisperse structures
– membranes, micelles and vesicles
– self-assembled monolayers
– monolayers on colloides
– coordination chemistry on surfaces
– polymers
– crystals

• Monodisperse structures
– compounds made by conventional organic synthesis
– dendrimers
– supramolecular chemistry (closed shell structures)
– molecular recognition by DNA and analoges
– countles other interactions in biologial systems
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Cell membrane
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Selv-organisring

Hydrophobic and hydrophilic interactions

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Arrangement of phospholipides
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Cell membrane
Flexibility of membranes
Inside cell Outside cell

Vesicle containing
waste material
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LM-techn
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Ultrathin Organic Films

a) Langmuir film: film at the water-air interface

b) Langmuir-Blodgett film (LB): mono- or multi-layers transferred from the

water-air interface onto a solid substrate.

c) Self-assembled monolayers: molecular assemblies that are formed

spontaneously on a surface by the immersion into a solution of an active
surfactant in an organic solvent
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Nature – the master of

self-assembly
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The central dogma

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DNA
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Using DNA as an encoding material

to assemble nanostructures

C G C G
C G C G
T A T A
A T A T
C G C G
G C G C
A T A T
C G C G
T A T A
A T A T
A T A T
A T A T
G C G C
T A T A
T A T A

Forskellige DNA-kæder
med 15 baser = 415 DNA-helix
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Information i DNA

1g rent DNA
indeholder information svarende til
1012 compact discs!
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Example: Kinetics of DNA hybridization

Steed & Atwood Supramolecular Chemistry

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Proteins
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Ribosomet aflæser mRNA og

udfører proteinsyntese
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Ribosomer er ca. 28 nm i diameter,

og kan ses ved elektronmikroskopi

Ribosomer mRNA Proteinkæde

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Ribosomet studeres i dag i atomar detalje

“en plet” “en klump” 200.000 atomer

Ref. Poul Nissen, iNANO
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Ribosomets indre
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Whitesides’ definitions
1) Self-assembly involves association by many weak, reversible, interactions to obtain
a final structure that represents a thermodynamic, minimum. Incorrect structural
units are rejected in the dynamic, equilibrium assembly. This equilibration allows
high fidelity in the process.
2) Self-assembly occurs by a modular process. The formation of stable subassemblies
by sequential covalent processes precedes their assembly into the final structure.
This mechanism allows for efficient assembly from the preformed units [a
"convergent synthesis," in the therms of organic chemistry].
3) Only a small number of types of molecules are normally involved in modular self-
assembly. Consequently, a limited set of binding interactions is required to cause
the final structure to form. This principle minimizes the amount of information
required for a particular structure.
4) Self-assembly often displays positive cooperativity.
5) Complementarity in molecular shape provides the foundation for the association
between components. Shape-dependent association based on van der Waals and
hydrophobic interactions can be made more specific and stronger, by hydrogen
bonding and electrostatic interactions.
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Self-assembly at the meso-scale

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Mesoscopic Self-assembly

Whitesides and co-workers, SCIENCE, 284 948 (1999)

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Self-assembled electrical network

Whitesides and co-workers

SCIENCE 289 1170 (2000).