1. Atkins & de Paula: Atkins’ Physical Chemistry 9e
Chapter 18: Materials 1: Macromolecules and Self-Assembly

2. Chapter 18: Materials 1: Macromolecules and Self-Assembly
polymer, a compound formed by linking together small molecules.
naturally occurring polymers; Proteins, Nucleic acids, Cellulose, Rubber
synthetic polymers; Nylon, Dacron, Lucite
monomer, the small molecules linked together to form a polymer.

3. Chapter 18: Materials 1: Macromolecules and Self-Assembly
STRUCTURE AND DYNAMICS
 configuration, the structural features that can be changed only by breaking chemical bonds and forming new ones.
 conformation, the spatial arrangement of the different parts of a chain.
18.1 The different levels of structure
 primary structure, the sequence of small molecular residues making up a polymer.
 polypeptide, a macromolecule formed from amino acids .
 peptide link, the group –CONH–.
 sequencing, the determination of primary structure.

4. Chapter 18: Materials 1: Macromolecules and Self-Assembly
 degradation, a disruption of primary structure.
 secondary structure, the (often local) spatial arrangement of a chain.
 denaturation, the loss of secondary structure.
 tertiary structure, the overall three–dimensional structure of a macromolecule.
 quaternary structure, the manner where large molecules are formed by the aggregation

5. Chapter 18: Materials 1: Macromolecules and Self-Assembly
 protein structure; intermolecular forces in a protein molecule.
ionic forces
hydrogen
bonds
dispersion
forces
dipole-dipole

6. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.2 Random coils
 random coil, a conformation in which neighboring groups adopt random angles to each other.
 freely jointed chain, the simplest model of a random coil, a conformation in which any bond is free to make any angle with respect to the preceding one .
Freely jointed chain
Constrained chain

7. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.2 (a) Measures of size
 probability that ends of a long 1-D freely jointed chain (N units of length l) are a distance nl apart (n = NR-NL),
(Further information 18.1(a) & Problem 18.20)
 probability that ends of a long 3-D freely jointed chain lie in the range r to r+dr, f(r)dr
(Further information 18.1(b))

8. Chapter 18: Materials 1: Macromolecules and Self-Assembly
 contour length, Rc, the length of a macromolecule measured along its backbone: Rc = Nl.
 root mean square separation, Rrms, the square root of the mean value of R2: Rrms = N1/2l.
 radius of gyration, Rg, the radius of a thin hollow spherical shell of the same mass and moment of inertia as the molecule: Rg = (N)1/2l. (Justification 18.1 & Problem 18.16)
 Rg for 3-D random coil: Rg = (N/6)1/2l. (Problem 18.17)

9. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.2 (b) Conformational entropy
conformational entropy, the statistical entropy arising from the arrangement of bonds:
ΔS = –½kNln{(1 + v)1+v(1 – v)1–v}, with v = n/N, when a coil of N bonds of length l is stretched or compressed by nl. (Justification 18.2)
18.2 (c) Constrained chains
constrained chains, Rrms & Rg should be multiplied by F= [(1-cosθ)/(1 + cosθ)]1/2
18.2 (d) Partly rigid coils
persistence length, lp; when first monomer-monomer direction is sustained.
(Further information 18.1(c))

10. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.3 The mechanical properties of polymers
 elastic deformation, strain is proportional to the stress and is reversible.
plastic deformation, strain is not proportional to the stress.
yield point, turning point from elastic to plastic deformation.
elastomer, a polymer with a long elastic range.
perfect elastomer, an elastomer where the internal energy is independent of the extension.
restoring force of a perfect elastomer extended or compressed by nl is F = (kT/2l) ln {(1 + v)/(1 – v)}  nkT/Nl when v << 1 (with v = n/N). (Justification 18.3)

11. Chapter 18: Materials 1: Macromolecules and Self-Assembly
melting temperature, Tm, the temperature at which a polymer melts.
glass transition temperature, Tg, the temperature at which a polymer undergoes a transition from a state of high chain mobility to one of low chain mobility.
18.4 The electrical properties of polymers
 conducting polymer, a polymer with extensive conjugation and thereby conducts electricity.
 polaron, a partially localized cation radical in a polymeric solid.
 bipolaron, a di-cation version of a polaron.
 soliton, two separate cations that move independently in a polymeric solid.

12. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.5 The structures of biological macromolecules
18.5(a) Proteins
Corey–Pauling rules, a set of rules that account for the secondary structures of proteins.
1. C, O, N, and H lie in a relatively rigid plane.
2. N, O, and H of a H-bond lie in a straight line.
3. All NH and CO groups are engaged in H-bonding.
restricted rotation
 α-helix, a helical conformation formed by hydrogen bonding between peptide links.
 β-sheet, a planar conformation formed by hydrogen bonding between peptide links .

13. Chapter 18: Materials 1: Macromolecules and Self-Assembly
geometry of polypeptide, specified by φ and ψ
Ramachandran plot, a contour diagram of the conformational energy in which one axis represents φ and the other represents ψ.
nonchiral glycine
Right-handed α-helix (poly-L-glycine)
all φ = 570 and all ψ = -470
chiral L-alanine
Ramachandran plot

14. Chapter 18: Materials 1: Macromolecules and Self-Assembly
 anti-parallel β-sheet, a β-sheet in which φ = –139o, ψ = 113 o, and the N–H–O atoms of the hydrogen bonds form a straight line; very common in proteins.
 parallel β-sheet, a β-sheet in which φ = –119, ψ = 113 and the N–H–O atoms of the hydrogen bonds are not perfectly aligned.

15. Chapter 18: Materials 1: Macromolecules and Self-Assembly
The stability of proteins
 denaturation, the loss of their natural conformation.
cooperative process, a process which becomes more probable the further it proceeds.
melting temp., Tm, where the fraction of unfolded protein is 0.5.

16. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.5 The structures of biological macromolecules
18.5(b) Nucleic acids
polyelectrolyte, a macromolecule with many different charged sites and an overall charge.
base stacking, the organization of the planar π systems of bases by dispersion forces between them.

17. Chapter 18: Materials 1: Macromolecules and Self-Assembly
tRNA

18. Chapter 18: Materials 1: Macromolecules and Self-Assembly
Aggregation & Self-Assembly
Self–assembly, the spontaneous formation of complex structures of molecules or macromolecules held together by molecular interactions.
18.6 Colloids
18.6(a) Classification and preparation
colloid (disperse phase), a dispersion of small particles of one material in another.
sol, a dispersion of a solid in a liquid or of a solid in a solid.
aerosol, a dispersion of a liquid in a gas .
emulsion, a dispersion of a liquid in another liquid.
 lyophilic, solvent attracting.
 lyophobic, solvent repelling.
 hydrophilic, water attracting.
 hydrophobic, water repelling.
 gel, a semirigid mass of a lyophilic sol in which all the dispersion medium has penetrated into the sol particles..
 surfactant, a surface–active agent.
 electrodialysis, dialysis in the presence of an electric field.

19. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.6(c) The electrical double layer
radius of shear, the radius of the sphere that captures a rigid layer of charge around a colloidal particle.
 zeta potential (electrokinetic potential), ζ, the electric potential at the radius of shear relative to its value in the distant, bulk medium .
 electrical double layer, the inner shell of charge and the outer ionic atmosphere around a colloidal particle.
DVLO theory, a thery of the stability of lyophobic dispersions; balance between repulsive interaction between the charges of the electrical double layers and the attractive vdW interactions between the molecules in the particles.
a: particle radius, A & B: constant, R: separation of centers, s: R-2a, rD: thickness of double layer, I: ionic strength, ρ: mass density, bΘ: 1 mol kg-1

20. Chapter 18: Materials 1: Macromolecules and Self-Assembly
flocculation, the reversible aggregation of colloidal particles at high ionic strength.
 coagulation, the irreversible aggregation of colloidal particles.
 Schultze–Hardy rule: hydrophobic colloids are flocculated most efficiently by ions of opposite charge type and high charge number.

21. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.7 Micelles and biological membranes
18.7(a) Micelles formation
 micelle, colloid–sized clusters of molecules.
 critical micelle concentration (CMC), the concentration above which micelles form .
 Krafft temperature, the temperature above which micelles form.

22. Chapter 18: Materials 1: Macromolecules and Self-Assembly
 surfactant parameter, Ns = V/Al (V: volume of hydrophobic tail, A: area of hydrophilic head group, l: maximum length of tail)
 liposome, a vesicle with an inward pointing inner surface of molecules surrounded by an outward pointing outer layer.
lyotropic mesomorph, an orderly arrangement of micelles; a liquid crystalline phase.
reverse micelles, form in nonpolar solvent

23. Chapter 18: Materials 1: Macromolecules and Self-Assembly
Impact on nanotechnology
 Self-Assembly of Mesoscopic Metal-Polymer Amphiphiles
S. Park et al., Science 2004, 303, 348.

24. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.7(b) Bilayers, vesicles, and membranes
 fluid mosaic model, a model of a cell membrane in which the proteins are mobile but have diffusion coefficients much smaller than those of the lipids.

25. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.7(c) Self-assembled monolayers
monolayer, a single layer of molecules on a surface.
Langmuir–Blodgett film, a monolayer that has been transferred to a solid support.
self-assembled monolayer (SAM), an ordered molecular aggregate that form a monolayer of material on a surface.

26. Chapter 18: Materials 1: Macromolecules and Self-Assembly
DETERMINATION OF SIZE AND SHAPE
18.8 Mean molar masses
 monodisperse, a sample with a single, definite molar mass such as proteins.
 polydisperse, a sample with a wide range of molar masses such as synthetic polymers.
number-average molar mass,
 viscosity-average molar mass, the average molar mass obtained from viscosity measurements.
 weight-average molar mass, the average molar mass obtained from light-scattering experiments:
Z-average molar mass, the average molar mass obtained from sedimentation measurements:
 heterogeneity index,
Example 18.1
Typical synthetic materials = 4
Monodisperse synthetic polymer < 1.1
commercial polyethene = 30

27. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.9 The techniques
18.9(a) Mass spectrometry
 matrix–assisted laser desorption/ionization (MALDI), a laser-based technique for ionization of macromolecules.
 electrospray ionization, another technique for ionization of macromolecules.
 MALDI-TOF mass spectrometry, a technique for the determination of molar masses of macromolecules that combines MALDI and time-of-flight mass spectrometry.
trans-3-indoleacrylic acid (matrix) +
NaCl, silver trifluoroacetate

28. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.9(b) Laser light scattering
Rayleigh scattering, the scattering of light by particles with diameters much smaller than the wavelength of the incident radiation.

29. Chapter 18: Materials 1: Macromolecules and Self-Assembly
Example 18.3

30. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.9(c) Sedimentation
 sedimentation, the settling of particles to the foot of a column of solution.
 ultracentrifugation, a sedimentation technique in which particles move under the influence of a centrifugal field.
drift speed, a constant speed through a medium when the driving and retarding forces are balanced.

31. Chapter 18: Materials 1: Macromolecules and Self-Assembly
sedimentation constant
Example 18.4
 sedimentation equilibria, the equilibrium distribution of particles in a gravitational or centrifugal field.

32. Chapter 18: Materials 1: Macromolecules and Self-Assembly
18.9(d) Viscosity
 intrinsic viscosity, the coefficient [η] in η = η0(1+ [η]c + ).
 Ostwald viscometer, a device for measuring viscosity from the time taken for a solution to flow through a capillary and compared with a standard sample..
 rotating rheometer, a device for measuring viscosity that consists of rotating concentric cylinders.
Ostwald viscometer
rotating rheometer

33. Chapter 18: Materials 1: Macromolecules and Self-Assembly
 Mark–Kuhn–Houwink–Sakurada equation for the intrinsic viscosity in terms of the molar mass.
Example 18.5