1. Soft Matter
Soft matter is held together by the two weakest types of bonding, the hydrogen bond and the van der Waals bond. It does not exhibit the crystalline order that is characteristic of most hard matter.
Nevertheless, some order remains in soft matter. It is driven by the organization of hydrophobic and hydrophilic molecular groups. That can lead to self-assembly over a wide range of sizes, all the way from nano-structures to human beings.
Pierre-Gilles de Gennes received the 1991 Physics Nobel Prize for bringing order into soft matter, such as polymers and liquid crystals.

2. Micelles Surfactant: Hydrophilic Head + Hydrophobic Tail Phospholipid
= Amphiphilic Molecule
Micelle: Inverse Micelle:
Heads outside, Water outside Heads inside, Water inside
Used for drug delivery Nano-beaker for synthesis of nanocrystals

3. Bilayer Structures
, Vesicle
Part of a Cell Wall

4. Drug Delivery via Liposomes

5. Supramolecular Assemblies

6. This overview figure demonstrates the large variety of ways to mimic life in artificial nanostructures. It is taken from a highly popular study of the National Academy of Sciences which quickly went out of print. A 2008 follow-up study can be found at .

7. Polymers Monomer: A Oligomer: A-A-A-A
Homopolymer: A-A-A-A-A-A-A-A-A-A-A-A-A- …
Heteropolymer = Copolymer: A-B-B-A-B-A-B-A-B-A-A-B-A-B- …
Block Copolymer: A-A-A-A-A-A-A-A-A—B-B-B-B
The volume ratio of the A- and B- blocks, together with the strength of the interaction between A and B determines how they assemble themselves (see Slides 10,11).

8. A Hydrophilic-Hydrophobic Block Copolymer
PMMA PS
(polymethylmethacrylate) (polystyrene)
Negative charge on the Neutral hydrocarbons
oxygen makes it hydrophilic. make it hydrophobic.

9. Identify Polymers by their Molecular Orbitals using X-ray Absorption Spectroscopy
EFermi
Photon
C 1s Core Level

10. Phases of a Diblock Copolymer
Hydrophilic + Hydrophobic
Theory Data
Interaction Strength
Volume Fraction
Volume Fraction
Volume Fraction

11. Triblock Copolymers: Even more Options

12. Biopolymers: DNA

13. Biopolymers: Proteins
The Peptide Bond between Amino Acids in a Protein N
Two amino acids react N forms the bridge.
See the * orbital
of this double bond
in X-ray absorption
covalent ionic N O

14. Need a glycine dimer to establish the peptide bond.
Detect the peptide bond orbital with X-ray absorption spectroscopy at the N 1s edge
Need a glycine dimer to establish the peptide bond.
A. Hitchcock et al.
Photon Energy [eV]

15. The Peptide Bond and Protein Structures
The peptide bond orbital spreads across O=C=N, which produces a planar arrangement.
Hydrophobic
interaction
α-Helix
β-Sheet
Secondary structure
Tertiary structure

16. Protein Folding Hierarchy

17. Schematic of Hemoglobin

18. Protein Infrared Spectroscopy
Vibrations reveal the secondary and tertiary structure.
oxygen
Amide vibrational modes:
Amide I, C=O stretch
secondary structure
a-helix: cm-1
b-sheet: cm-1
Amide II, N-H bend
tertiary structure
HD exchange:
15501450 cm-1
Basics of protein infrared spectroscopy: The main IR signatures observed in proteins come from the C=O and N-H groups. These groups give rise to the amide vibrational modes, of which there are nine. The most useful of the nine bands, from a structural analysis point of view are the amide I and II bands.
The amide I band is primarily due to C=O stretching, and the exact frequency of this band is dependant on the nature of the hydrogen bond experienced by the carbonyl group, which is in turn dictated by the particular secondary structure adopted by the protein. Proteins include various secondary structures, including alpha helices, beta sheets, random coils, and turns. Thus, since most proteins contain all of these structural elements to some degree, the amide I band is actually a composite of several overlapping bands, which are assigned to the various structural elements. For example, alpha helical structure is known to arise between 1649 and 1658 cm-1, while beta sheet structure is found between 1620 and 1635 cm-1.
The amide II band is primarily due to N-H bending. It can provide information on protein tertiary structure because this band is sensitive to deuteration, shifting from 1550 to 1450 upon replacement of the hydrogen with deuterium. The remainder of amide II left after deuteration can tell us something about the accessibilty of the solvent to the peptide backbone. For example, tightly folded structures such as helices, will impede the exchange of the N-H hydrogen.
J. Lipkowski