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Unformatted text preview: BME 204 Physical Chemistry of Biomacromolecules September 28, 2010 1 Monday, September 27, 2010 Class Business • Discussion will held in 5101 Engineering V, Fridays 1:00-1:50. • Don’s office hours are Mondays from 10 am to 12 pm in 5101 Engineering V. • My office hours are Fridays 8-9 am, or by appointment, in my office (5121 Eng V). • We’ll take a 5 minute break after the first hour of lecture 2 Monday, September 27, 2010 Review • • • • • Polymers are made of monomers Polymers are defined by their molecular weight and molecular weight distribution Polymers may have different architectures Copolymers are polymers that contain more than one monomer 3 Monday, September 27, 2010 Course Overview 1A 1 nm -9 10-10 10-7 10-8 10 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth Lectures 1 and 2: Polymer chains at the 1m 0 10 person molecular scale looking at repeat unit chemistry and orientation O HO O HO O H N O H peptides drugs N H O HO H N NH2 O OH HN H 2N NH 4 Monday, September 27, 2010 Today’s Lecture • Isomers of polymers exist – Structural Isomerism – Cis/trans (geometric) Isomerism – Stereoisomerism • • • • Isomerism can be characterized using techniques such as NMR spectroscopy Different isomers of polymers behave differently (i.e. crystallization) Isomerism is important in both synthetic polymers and natural polymers Isomerism affects chain conformation 5 Monday, September 27, 2010 Polymers are Synthesized from Monomers Vinyl polymerizations Ring opening polymerizations FF F F F F n FF Cl n n O O n O Cl n n n O O H N H Cl O O N n n Cl Cl Cl O n H3C n CH3 O O O n R N H n N n O O O R H N NH2 HO Nn + n-1 H2O n O R O O OH HO O O O O O O O O O HN O O O R O + n-1 H2O n O O O O O Condensation polymerizations N H O O n O n O O O NH O Cl O O OH + HO HO O OH O O OH + H N 2 HO O Monday, September 27, 2010 H N NH2 O + HO R' O OH O O R' n + (n-1)HCl n O O + (n-1)H2O O Cl N Hn + (n-1)H2O 6 Constitutional/Structural Isomers 7 Monday, September 27, 2010 Isomerism • Isomerism – two compounds with same chemical formula can have quite different structures Ex: C8H18 • n-octane d 0.703 g/mL, mp -57 oC, bp 125.5 oC ⇓ • 2-methyl-4-ethyl pentane (isooctane) d 0.688 g/mL, mp -107.4 oC, bp 99.3 oC Chapter 14 Monday, September 27, 2010 8 Forms of glucose in water H OH H H OH H O HO HO OH HH O HO HO OH H H H OH H OH !-D-glucopyranose "-D-glucopyranose 64% in water H HO H H 36% in water CHO OH H OH OH CH2OH open <1% H HOHO HO H H O OH H H OH !-D-Fructofuranose <1% H HOHO HO H H O H H OH OH "-D-Fructofuranose <1% 9 Monday, September 27, 2010 Example: Oligosaccharides Involved in immune defense, fertilization, viral infection, cell growth, cell adhesion, inflammation… OH O HO HO sucrose (sugar): a non-reducing sugar from glucose and fructose H HO CH2 O H H OH OH O HO HO O H H CH2OH OH O HO OH O HO O OH OH β-lactose: milk contains ~5%; without lactase enzyme, humans cannot break down (lactose intolerance) 10 Monday, September 27, 2010 Stereoisomerism 11 Monday, September 27, 2010 Stereoisomerism of Polymers Configurations – to change must break bonds • Stereoisomerism mirror plane Chapter 14 Monday, September 27, 2010 12 cis/trans Isomerism cis trans cis-isoprene (natural rubber) trans-isoprene (gutta percha) bulky groups on same side of chain bulky groups on opposite sides of chain Chapter 14 Monday, September 27, 2010 13 cis/trans isomerism: Gutta Percha and Natural Rubber trans-1,4-polyisoprene cis-1,4-polyisoprene 14 Monday, September 27, 2010 Tacticity Tacticity – stereoregularity of chain isotactic – all R groups on same side of chain syndiotactic – R groups alternate sides atactic – R groups random Chapter 14 Monday, September 27, 2010 15 Analysis of Stereoregularity 16 Monday, September 27, 2010 NMR Characterization of Polymers NMR can be used to quantify: • Number average molecular weight (Mn) • Copolymer composition • Isomerism (sequence, stereo, structural, geometric) 17 Monday, September 27, 2010 Example: PMMA C CH 3 C B CH 2 CO 2CH3 n A B A B’ B C 18 Monday, September 27, 2010 NMR Determination of Tacticity for PMMA C CH 3 A C C B CH 2 CO 2CH3 A n B Predominantly isotactic (anionic polymerization) B Predominantly syndiotactic (radical polymerization) 19 Monday, September 27, 2010 O H2N CHC OH H2N CH2 CH2 CH2 CH2 NH2 lysine K Stereochemistry O O CHC OH H2N CHC OH CH2 CH2 CH2 N CH2 NH NH C NH histadine H NH2 arginine R O H2N CHC OH CH2 OH serine S acidic O H2N CHC OH CH2 CO OH O H2N CHC OH CH2 CH2 CO OH O H2N CHC OH CH2 CO NH2 asparagine N aspartic acid D glutamic acid E O O O H2N CHC OH H2N CHC OH H2N CHC OH H2N CHCH3 CHCH3 CH3 CH3 CH2 alanine A CH3 valine V O CHC OH H2N CH2 CHCH3 CH3 isoleucine I leucine L O CHC O H CH2 CH2 S CH3 cysteine C Monday, September 27, 2010 glycine G threonine T O H2N CHC OH CH2 CH2 CO NH2 glutamine Q O O H2N CHC OH H2N CHC OH CH2 CH2 OH phenylalanine F tyrosine Y methionine M O O H2N CHC OH H2N CHC OH H CH2 SH O H2N CHC OH CHOH CH3 O H2N CHC OH CH2 HN tryptophan W O C OH HN proline P 20 Isomerism of Biological Macromolecules: Polysaccharides H OH H C6H12O6 HO CH2 O HO HO H H OH H OH H HO O OH OH CH2OH H C6H12O6 H !-D-Fructofuranose !-D-glucopyranose glucose fructose "-D-glucopyranose H OH H H HO H H CHO OH H OH OH CH2OH OH OH OH OH O HO OH H OH HO H H H OH H OH O OH OH O HO HO H OH H O HO HO OH HH OH H !-D-glucopyranose "-D-Fructofuranose HO CH2 CH2OH CO HO H H OH H OH CH2OH OH H HO OH OH HO OH OH O CH2OH O H HO H OH OH O HO CH2 O H HO H HO H OH CH2OH !-D-Fructofuranose Monday, September 27, 2010 21 Saccharides • • Fructan, a polymer of fructose, is found in artichokes, asparagus, green beans, leeks, onions, wheat, grass Inulin is a linear fructan polymer linked by β1-2 glycosidic bonds, found in garlic, onion, agave, dandelion, chicory, jicama, wild yam • Levan is a linear fructan polymer with β2-6 glycosidic bonds, • Graminan is a branched fructan polymer linked by both β12 and β2-6 glycosidic bonds, found in grasses H O HO H OH O OH H HO H O H !2-1 OH H OH O H OH H HO O H H O HO H HO H H OH HO H OH H H O OH O HO H OH O HO H O !2-6 HO H O HO OH H 22 Monday, September 27, 2010 Properties of Stereoregular Polymers 23 Monday, September 27, 2010 Properties of Stereoregular Polymers The regularity of polymer structure affects their properties, primarily in their ability to crystallize Atactic polymers are amorphous, soft materials with little or no physical strength Isotactic and syndiotactic polymers tend to be highly crystalline Crystallinity leads to high physical strength and increased solvent and chemical resistance 24 Monday, September 27, 2010 Conformation of stereoregular polymers A 31-helix formed by isotactic polypropylene A 21-helix formed by syndiotactic polypropylene 25 Monday, September 27, 2010 Stereoregularity and Sugar cellulose HO HO OH HO OH CH2OH O O β-1,4 linkages O HO CH2OH O HO OH O HO HO O HO OH O HO HO OH O HO O O HO H OO OH O O HO O HO OH HO OH O HO O CH2OH OH OH O O HO OH O HO OH HO CH2OH O CH2OH OH O HO OH OH O HO OH O HO HO OH O O HO HO O CH2OH O O HO OH HO OH CH2OH α-1,4 linkages O CH2OH O CH2OH OH erthyrodiisotactic OH HO HO O CH2OH cis/equatorial-axial O trans/diequatorial) CH2OH CH2OH amylose OH OH O threodisyndiotactic OH O Straight chain for β-linkage , good for fiber formation α-linkage results in a helix, accessible source of sugar. Mammals do not have cellulases (cannot digest cellulose) O OH HO O OH O HO HO OH O 26 Monday, September 27, 2010 DNA and the double helix: form and function A form: non physiological, dehydrated, or in cells as a pairing with RNA or enzymes; wider right-handed spiral; wide minor groove and narrower and deeper major groove B form: common, physiological form Z form: methylation of bases results in a left-handed spiral; recognized by specific Z-DNA binding proteins, may be involved in regulation of transcription 27 Monday, September 27, 2010 Summary • Isomers of polymers exist – Structural Isomerism – Cis/trans (geometric) Isomerism – Stereoisomerism • • • • Isomerism can be characterized using techniques such as NMR spectroscopy Different isomers of polymers behave differently (i.e. crystallization) Isomerism is important in both synthetic polymers and natural polymers Isomerism affects chain conformation • References: Fundamentals Chpt 1, Essentials Chpt 2, Sperling Chpt 2, Strobl Chpt 1 28 Monday, September 27, 2010 “The Lectin-Binding Properties of Six Generations of Mannose-Functionalized Dendrimers” E.K. Woller and M.J. Cloninger Org. Letters 2002, 4(1), 7-10 G1 and G2 bind monovalently G3 appears to bind via glycoside clustering G4-G6 appear to bind multivalently Modeling confirms experimental results Monday, September 27, 2010 29 “Mannose/Glucose-Functionalized Dendrimers to Investigate the Predictable Tunability of Multivalent Interactions” M.L. Wolfenden and M.J. Cloninger J. Am. Chem. Soc 2005, 127, 12168-12169 glucose mannose 30 Monday, September 27, 2010 “Mannose/Glucose-Functionalized Dendrimers to Investigate the Predictable Tunability of Multivalent Interactions” M.L. Wolfenden and M.J. Cloninger J. Am. Chem. Soc 2005, 127, 12168-12169 31 Monday, September 27, 2010 Next Time: Ideal Chain Conformation References: Fundamentals Chpt 7, Essentials Chpt 8, Strobl Chpt 2 32 Monday, September 27, 2010 ...
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