Atkins & de Paula: Atkins’ Physical Chemistry 9e 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 hydrogen bonds dispersion forces dipole-dipole

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 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)

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))

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)

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 = –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.

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 tRNA

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 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

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:  heterogeneity index, Example 18.1 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) + NaCl, 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 = 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

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