Atkins & de Paula: Atkins’ Physical Chemistry 9e

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

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 • Ramachandranplot, 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 theryof 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., Science2004, 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