Atkins de Paula Atkins Physical Chemistry 9 e

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

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.

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.

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

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

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

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))

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 R 2: Rrms = N 1/2 l. 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)1/2 l. (Justification 18. 1 & Problem 18. 16) Rg for 3 -D random coil: Rg = (N/6)1/2 l. (Problem 18. 17)

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 = –½k. Nln{(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))

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 = (k. T/2 l) ln {(1 + v)/(1 – v)} nk. T/Nl when v << 1 (with v = n/N). (Justification 18. 3)

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.

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.

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

Chapter 18: Materials 1: Macromolecules and Self-Assembly anti-parallel β-sheet, a β-sheet in which φ = – 139 o, 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.

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.

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.

Chapter 18: Materials 1: Macromolecules and Self-Assembly t. RNA

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.

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 vd. W interactions between the molecules in the particles. a: particle radius, A & B: constant, R: separation of centers, s: R-2 a, r. D: thickness of double layer, I: ionic strength, ρ: mass density, bΘ: 1 mol kg-1

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.

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.

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

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.

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.

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.

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: Example 18. 1 heterogeneity index, Typical synthetic materials = 4 Monodisperse synthetic polymer < 1. 1 commercial polyethene = 30

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) + Na. Cl, silver trifluoroacetate

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.

Chapter 18: Materials 1: Macromolecules and Self-Assembly Example 18. 3

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.

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.

Chapter 18: Materials 1: Macromolecules and Self-Assembly 18. 9(d) Viscosity intrinsic viscosity, the coefficient [η] in η = η 0(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

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