1. Self-Assembly
Bottom-up assembly generally means making complex nanostructures starting from the random collisions of molecular components in solution.
Entropy plays a large role in the formation of self-assembled structures put together with weak bonds.
Binding enthalpies generally results from the sum of weak interactions.
Self-assembly of complex nanostructures requires achieving the right balance between entropy at a given temperature and binding enthalpies.

2. Copyright Stuart Lindsay 2008
Amphiphiles
Phospholipid
Polar head
Hydrophobic tail
Copyright Stuart Lindsay 2008

3. Self-assembled amphiphilic structures
(From Molecular Cell Biology, 4th ed. By H. Lodish, A. Berk, S.L. Zipursky, P. Matsudara, D. Baltimore, J. Darnell.
© 2000, W.H. Freeman and Company. Used with permission)
Copyright Stuart Lindsay 2008

4. MD Simulation of vesicle formation
1017 DPPC (dipalmitoylphosphatidylcholine) molecules randomly distributed in a box of 106,563 water molecules.
MD simulation was run for 90ns.
(Reprinted with permission from Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail, A.H de Vries et al., A.E. Mark, and S.J. Marrink, J. Am. Chem. Soc : Published 2006 by American Chemical Society)

5. Association Kinetics Single-step aggregation
Aggregate concentration is divided by N to get monomer equivalent.
Association rate
Dissociation rate
In equilibrium the two rates are equal so the equilibrium constant is:

6. In units of mole fraction the total mole fraction of solute is:
The maximum value of C-X1 is unity
Above this critical micelle concentration all added monomer is turned into aggregates

7. When:

9. Chemical potential must be lower in aggregate!
For:
with X1<1
Monomers predominate!

10. Size-dependent chemical potential
The chemical potential depends on the size of the aggregate:
Chemical potential for an infinite N aggregate
Bond energy (in KT units)
p : dimensionality and shape of the aggregate

11. And so:
For a spherical aggregate, the total number of molecules in the sphere is proportional to r3, while those on the surface are proportional to r2. Thus, the chemical potential per particle:
γ = monomer/solvent interfacial energy

12. Critical Micelle Concentration Revisited
Since XN can never exceed 1, X1 cannot exceed exp( -) and:
for a spherical aggregate
For a water/methane interface: γ ≈50mJ·m-2, r≈0.2 nm, T=300K
α ≈ 6

13. For p=1:
Above the cmc:
And for low N:
The concentration of aggregates grows linearly with N (p=1).
For N→∞, XN→0.
For p<1 the aggregate size grows infinitely large above the cmc.
The distribution of aggregate size is sensitive to the geometry of the aggregates.

14. Shape of aggregates Packing effects depend on geometry
lc = length of the hydrocarbon chain
n = volume occupied by the hydrocarbon chain
A0 = area of the head group

15. Long or double hydrocarbon chains
A dimensionless shape factor determining the aggregate geometry
Spherical micelles
Short hydrocarbon chains
Non-spherical micelles
Long or double hydrocarbon chains
Vesicles or bilayers
‘Inverted cones’

16. Copyright Stuart Lindsay 2008
The final folding of a planar bilayer into a spherical vessel is determined by a balance between the excess surface energy associated with the edges of a bilayer and the elastic energy required to fold a planar layer into a sphere.
Copyright Stuart Lindsay 2008

17. Lipid bilayer structure – the mitochondrion
(EM image is reproduced with permission from Chapter 4 of The genetic basis of human disease by G. Wallis published by the Biochemical Society Copyrighted by the Biochemical Society.
Copyright Stuart Lindsay 2008

18. Self-assembled monolayers
Chemisorption of long-chain amphiphilic molecules (both hydrophobic and hydrophilic functionalities) at surfaces.
→ creation of long-range order
active head group for chemisorption
activated surfaces
modification of the hydrophobic/
hydrophilic character of the surface.

19. Organothiols on gold surfaces
long-chain alkanethiolates (SH end group)

20. STM image of a dodecanthiol SAM on Au(111) (40nm·40nm)

21. I step: attachment of the sulfur atom to the gold surface
driving force: Au-S interaction (≈40 kcal·mol-1)
X(CH2)nSH + Au0 → X(CH2)nS- + Au+ + ½H2
Sulfur atoms for long chain alkanethiolates (n>11) formed a hexagonally packed arrangement on the Au(111) surface.
Separation of individual molecules on the surface is ≈5Å (van der Waals radius is around 4.6Å).
Chains tend to tilt at an angle of 30° to fill the available space.

22. Kinetic studies on SAM formation show that the adsorption process is consistent with a first-order Langmuir isotherm: the growth rate is proportional to the number of unoccupied gold sites.

23. II step: lateral organization of the alkyl chains to form a densely packed monolayer.
driving force: Van der Waals lateral interactions
The methylene groups tilt at an angle of 30° degrees from the surface normal to maximize the favorable Van der Waals interactions between adjacent chains.
Bulky or polar groups terminating the alkyl chain may reduce the packing density and overall order of the SAM.
Long-lasting self-healing dynamics

24. A series of STM images of a single octanedithiol molecule inserted into an octanethiol monolayer.
Sulfur with the gold atom attached to it moves over the surface in almost liquid-like manner.
The consequence of the mobility of the sulfur-gold bond is a substantial restructuring of the gold surface resulting in the formation of pits on the surface that are one gold atom in depth.

25. Nanoparticles kinetically trapped
CdSe quantum dots from two phase synthesis with Ostwald ripening (diameter: 8 nm).
(TEM Image)
Ostwald ripening: heating/cooling cycles.
Small crystallites (less stable) dissolve and recrystalize onto more stable existing crystallites to produce a much more uniform size distribution of crystallites.

26. Copyright Stuart Lindsay 2008
Vapor deposition of silicon wires
Si nanowires from Au/Si eutectic seeded on Au NP.
Silicon is incorporated in the gold phase from Si vapors produced by CVD.
Copyright Stuart Lindsay 2008