Download - No Slide Titlecola.kaist.ac.kr/lecture/physchem3/pchem3_ch18.pptx · PPT file · Web view2013-04-10 · Atkins & de Paula: Atkins’ Physical Chemistry 9e. Chapter 18: Materials

Atkins & de Paula:

Atkins’ Physical Chemistry 9e

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.


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


protein structure; intermolecular forces in a protein molecule.

ionic forces

ionic forces

hydrogenbonds

dispersionforces

dispersionforces

dispersionforces

dipole-dipoleforces


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


probability that ends of a long 1-D freely jointed chain (N units of length l) are a distance nl apart (n = NR-NL),

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(a) & Problem 18.20)

(Further information 18.1(b))

18.2 (a) Measures of size

NneN

P 2/2/1

22

2/1

22

3

2/1 23,4)(

22

Nlaerarf ra

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)

22

112

1

,

2

Nlr

rR

N

ii

N

N

jiji

N

ii

N

jiji

rrrrRR

2

0

22)1(2

0

2

0

2

11 Nlr

NRRmrmrmI

N

iig

mNmgtot

N

ii

N

iii

tot


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))

1

01

1 1 N

iip ll

l rrRr

2/12/1 1

2

ll

lNR prms

Chapter 18: Materials 1: Macromolecules and Self-Assembly18.3 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)

NnvvvkN

vv

lkT

vS

NlT

nS

lT

xST

xU

xST

xU

dxTdSdU

vv

TT

TT

TT

/ where},)1()1ln{(

11ln

2

0 elastomer,perfect For

11

21

nlx

S

F

F

F

F


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.


18.5 The structures of biological macromolecules18.5(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 .


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.

Right-handed α-helix (poly-L-glycine) all φ = 570 and all ψ = -470

Ramachandran plot

nonchiral glycine

chiral L-alanine


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-AssemblyThe 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-Assembly18.5 The structures of biological macromolecules18.5(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.


tRNA


Aggregation & Self-Assembly Self–assembly, the spontaneous formation of complex structures of molecules or

macromolecules held together by molecular interactions.

18.6 Colloids18.6(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-Assembly18.6(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.

DDrs

repulsion rawhenIbF

RTrwhereeR

AaV D

,2

,2/1

2/

22

arwheneAaV Drs

repulsionD ),1ln(

21 /2

sBVattraction

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


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-Assembly18.7 Micelles and biological membranes18.7(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

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-Assembly18.7(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.


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.


DETERMINATION OF SIZE AND SHAPE18.8 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,

MMNN

Mi

iin1

MM

MN

MNMMm

mM

iii

iii

WNMNm

iiiW

Aiii

22

/1

2

3

2

3

MM

MN

MNM

iii

iii

Z

2

2

MM

MM

n

WTypical synthetic materials = 4Monodisperse synthetic polymer < 1.1commercial polyethene = 30

Example 18.1

Chapter 18: Materials 1: Macromolecules and Self-Assembly18.9 The techniques18.9(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

Wn MM ,

Chapter 18: Materials 1: Macromolecules and Self-Assembly18.9(b) Laser light scattering Rayleigh scattering, the scattering of light by particles with diameters much smaller than

the wavelength of the incident radiation.

2

2

0sin)(),,(

rIRrI

221222

4

22

2

2

0

3sin16

)()(1)(,

2,)(

sin),,()(,

g

p

r

A

rWp

RpwithpPfactorstructure

dcdn

NnKMKcR

rI

rIRratioRayleigh

gW RM ,


2

22212

1)1(

316

)(sin1

)(1

)()(1

)(1

)(1)(11)(

1)(1

1)(1

)(1 1

g

Wp

Wp

WpWpWp

xx

WpWp

Ra

Ra

MKcR

Rp

MKcR

MKcp

MKcp

MKcRpMKcMcKPR

gRWM

)()(

)()()(

)())(1)((

)()()(

)(/)()()( 2

Rp

Rpp

Rpp

RPp

PRp

MKcp

Wp

Example 18.3

Chapter 18: Materials 1: Macromolecules and Self-Assembly18.9(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.

):,:(1,, soluteofvolumespecificpartialvdensitysolutionvbbmmmasseffective sseff

drift speed, a constant speed through a medium when the driving and retarding forces are balanced.

):(,/22

2 tcoefficienfrictionalff

bmrfrm

srmsfdtdrs effeff

Wn MM ,

Chapter 18: Materials 1: Macromolecules and Self-Assembly sedimentation constant

)cos:,:(6

6,'2 solventofityvisradiusa

NaMbS

fNMb

rsS

A

nafrelationStokes

A

n

Strr

Srdtdr

2

0

2

ln

nMS

sedimentation equilibria, the equilibrium distribution of particles in a gravitational or centrifugal field.

)5.18(ln)(

2

1

222

12

2

ionJustificatcc

brrRTMW

Example 18.4

Chapter 18: Materials 1: Macromolecules and Self-Assembly18.9(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 rheometer00

tt

o

VM


Mark–Kuhn–Houwink–Sakurada equation for the intrinsic viscosity in terms of the molar mass. a

VMK][

)1/(lim)(lim][ 0

00

0

0 cc cc

VM][

Example 18.5

Download - No Slide Titlecola.kaist.ac.kr/lecture/physchem3/pchem3_ch18.pptx · PPT file · Web view2013-04-10 · Atkins & de Paula: Atkins’ Physical Chemistry 9e. Chapter 18: Materials

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