16 years ago TODAY (9/11) at 8:46, the first tower was hit at 9:03, the second tower was hit. Lecture 2 (9/11/17)
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1 16 years ago TODAY (9/11) at 8:46, the first tower was hit at 9:03, the second tower was hit By Anthony Quintano - CC BY 2.0, Lecture 2 (9/11/17) Reading for today: Ch2, Ch2, Problems for today: Ch2 (text) 1,2 Ch2 (study guide) 3,4,5,6,7 NEXT Reading: Ch3; 75 Ch1; Ch4; Problems: Ch1 (text); 13,16 Ch4 (text); 12 1
2 OUTLINE Lecture 2 (9/11/17) WATER Properties The 4 S s Shape Size Solubility Hydrogen Bond Properties explained Molecular Forces Important for Life Other Electrostatic interactions Salt bridges van der Waals Forces (Dispersion or induced dipole induced dipole) Hydrophobic Effect Water (reprise) Last of 4 S s - stability (water as a chemical reagent) Ionization Acids/Bases; ph Examples: Metabolic acidosis Properties of Water 1) Water has a high boiling point and relatively low melting point; its range in the liquid state is large 2) The heat of vaporization is high (more heat to change to vapor state than to raise temperature of the liquid state) 3) Liquid is more dense than the solid (e.g., most metals and other substances the solid is more dense) 4) High viscosity relative to its molecular weight (MW) 5) High surface tension 2
3 Figure 2.15 Surface Tension 3
4 Properties of Water Properties of Water 4
5 WATER The 4 S s for Water: Shape Size Solubility Stability Most of the properties of water are explained or due to its shape, in other words, its structure Shape of Water sp 3 hybridized orbitals: 2 are bonding 2 are filled non-bonding Distorted tetrahedral (equal angles of ): due to repulsion of electrons in filled orbitals 5
6 Shape of Water Permanent DIPOLE Size of Water Very compact structure: 2.0 Å in diameter though van der Waals diameter of oxygen atom is 2.8 Å 2.0 Å The O H bond is relatively short (0.96 Å) though van der Waals diameter of hydrogen atom is 2.4 Å What are these discrepancies due to? ELECTRONEGATIVITY OF OXYGEN 6
7 Solubility of Water: Hydrogen Bonding These dipoles interact with each other in a special kind of non-covalent bond: the hydrogen bond. Bit of a misnomer but named as such because it appears though two oxygen atoms of two water molecules share a hydrogen Its not at all equal: the water with the covalent bond to hydrogen is called the DONOR. The opposite water molecule is called the ACCEPTOR DONOR ACCEPTOR Solubility of Water: Hydrogen Bonding THREE important aspects that make H-bonds unique: 1) Electrostatic: dipoledipole interaction d+ d d d+ 2) Partial electron sharing: partial covalency 3) Directional: geometry 0.96 Å 1.84 Å 2.8 Å This is a stronger bond than this (due to optimizing the covalency) 7
8 Rings of Water Molecules Flickering Clusters of Water Molecules On average, liquid water has about 3.5 hydrogen bonds per molecule Structure of Ice 8
9 Properties of Water 1) Water has a high boiling point and relatively low melting point; its range in the liquid state is large 2) The heat of vaporization is high Ave number of H-bonds in liquid water is ~3.5, but in steam ~0 3) Liquid is more dense than the solid Ave number of H-bonds in liquid water is ~3.5, but in ice its 4, but the geometry takes over 4) High viscosity relative to its molecular weight (MW) liquid water with ~3.5 H-bonds/molecule is sticky 5) High surface tension 6) Water is also a great SOLVENT Solvation of Ions Cations Anions 9
10 Hydrogen Bonding to Polar Molecules by Water Water to ketones/aldehydes Water to alcohols Water to carboxylic acids Water to amines Typical Bond Energies } (kcal mol -1 )
11 Molecular Forces Important for Life The 4 NON-covalent bonds: H-bonds Salt bridges }Electrostatic van der Waal s interactions Hydrophobic effect r r 3 (AKA Salt Bridges) Charge Charge interactions Na + Electrostatic Interactions Cl The strength of all these is governed by Coulomb s Law: Force between two charged particles = k q 1 q 2 D r 2 Where q is the charge on each particle 1 and 2, D is the dielectric constant (unit-less; =1.0 in vacuum, ~80 in water), r is the distance between the two charges, and k is Coulomb s constant (9x10 9 J m/c 2, where C=1.6x10-19 electron charges) r 5 r 6 Induced dipole Induced dipole interactions (AKA Van der Waals interactions) Recalling the relationship between Force and Energy (E = Force x distance): E = k q 1 q 2 D r For partial charges, this distance dependence is exponential 11
12 van der Waals Interactions Induced dipole Induced dipole interactions (AKA Van der Waals interactions) E = k q 1 q 2 D r 6 10 Å / 1 nm van der Waals Interactions 12
13 van der Waals Interactions This is why the issue of COMPLEMENTARITY is so important in biology Typical Bond Energies } (kcal mol -1 ) ~3 Å Van der Waals interactions 0.07 Hydrophobic interactions 13
14 Hydrophobic Interactions Hydrophobic interactions: atoms attracted together due to water structure. Nonpolar Solutes Aggregate in Water Hydrophobic Interactions Transfer of Hydrocarbons to Nonpolar Solvents is Entropically Driven 14
15 Hydrophobic Interactions Structure: Nonpolar Solutes in Water Like ICE Hydrophobic Interactions Figure 2.12 Hydrophilic and Hydrophobic 69 15
16 Hydrophobic Interactions Figure 2.12 Hydrophilic and Hydrophobic x5 70 Hydrophobic Interactions 3 degrees of freedom (DoF) Statistical mechanics has determined that each DoF is equal to 5-6 kcal/mol at 25 C 6 degrees of freedom 56 16
17 For EXAMPLE Hydrophobic Interactions 3 [CH 4 10H 2 O] [(CH 4 ) 3 12H 2 O] + 18H 2 O DG? is definitely NEGATIVE: How? Enthalpy 30 H 2 O x 4 H-bonds each x 5 kcal/mol = 600 kcal/mol to break H-bonds Enthalpy 18 H 2 O x 3.5 H-bonds each x 5 kcal/mol = 315 kcal/mol, plus 12x4x5 = 240 kcal/mol; Total = 555 kcal/mol heat given off to make bonds DH = +45 kcal/mol added in excess to break H- bonds Entropy 3 degrees of freedom (DoF) x 6 kcal/mol at 25 C per DoF = 18 kcal/mol DG = DH TDH = = 51 kcal/mol ENTROPY DRIVEN Entropy 19 degrees of freedom (DoF) x 6 kcal/mol at 25 C per DoF = 114 kcal/mol TDS = +96 kcal/mol in entropic energy gained Bond Energies of Important Noncovalent Interactions } (kcal mol -1 ) ~3 Å Van der Waals interactions Hydrophobic interactions (per CH 2 )
18 Amphipathic Interactions (both hydrophobic and hydrophilic) Example: amphiphiles like Fatty Acid Anions, detergents =O O S O + Na Sodium dodecyl sulfate (C12H 25 O 4 S) (SDS) =O Amphiphiles Form Micelles & Bilayers Structure of a Micelle Protein interiors 18
19 Disrupters of the Hydrophobic Effect Urea Guanidinium-HCl =O H 2 N C NH 2 NH 2 Cl H 2 N + =C NH 2 Physical Properties of Water Learning Goals: Concepts about water Water molecules, which are polar, can form hydrogen bonds with other molecules. In ice, water molecules are hydrogen bonded in a crystalline array, but in liquid water, hydrogen bonds rapidly break and re-form in irregular networks. The attractive forces acting on biological molecules include ionic interactions, hydrogen bonds, and van der Waals interactions. Polar and ionic substances can dissolve in water. The hydrophobic effect explains the exclusion of nonpolar groups as a way to maximize the entropy of water molecules. Amphiphilic substances form micelles or bilayers that hide their hydrophobic groups while exposing their hydrophilic groups to water. 19
20 WATER The 4 S s for Water: Shape Size Solubility Stability The discussion of water s stability is a discussion of its ionization. H 2 O D H + + OH 2H 2 O D H 3 O + + OH Ionization of Water Proton Jumping Occurs Rapidly H The Positive Charge jumps H H H H H + H Proton transfers are very rapid! 2H 2 O D H 3 O + + OH What is the concentration of OH and H 3 O + (protons)? 20
21 Ionization of Water What is the concentration of OH? 2H 2 O D H 3 O + + OH Equilibrium constant (K eq ) is 1.8 x M K eq = 1.8 x M = [H+ ] [OH ] [H 2 O] [H 2 O] 1.8 x M = [H + ] [OH ] [H 2 O] = 55.5 M* 55.5 M x 1.8 x M = [H + ] [OH ] since [H + ] = [OH ] 55.5 M x 1.8 x M = [H + ] x M 2 = [H + ] x 10-7 M = [H + ] Take the log of both sides: 7 = ph call the log[h + ] = ph *1 L water = 1000 g 18 g/mol = 55.5 M Ionization of Water Relationship of ph, [H + ], and [OH - ] 2H 2 O D H 3 O + + OH 21
22 Ionization of Water ph Values of Common Substances Ionization of Water Definitions of Acids and Bases: HA D H + + A If dissociation is >water: ACID HB D H + + B If dissociation is <water: BASE When B associates with protons, it leaves a net difference in [OH ] 2H 2 O D H 3 O + + OH In other words: A proton donor is an Acid (HA) A proton acceptor is a Base (B ) Likewise: The resulting anion from acid dissociation is called the conjugate base (A ) The resulting protonated base is called a conjugate acid (HB) These are Bronsted/Lowry definitions 22
23 Ionization of Water Definitions of Acids and Bases: Strong Acid Strong Base And the [HA] added is the [H + ] in solution. HA H + + A H + + B HB Weak Acid Weak Base Protons come from pulling the water dissociation equilibrium 2H 2 O D H 3 O + + OH And the [B ] added is the [OH ] in solution. HA D H + + A HB D H + + B For weak acids/bases, all 3 species are in measurable Concentrations. How do you calculate these concentrations and how are they related to the ph? Ionization of Water How do you calculate these concentrations and how are they related to the ph? Use the Equilibrium Constant (K eq ) for the dissociation reaction HA D H + + A [H K eq = K d = K a = + ] [A ] [HA] since [H + ] is best expressed as ph, can take log of each side: pk a = ph log [A ] [HA] ph = pk a + log [A ] [HA] This is called the Henderson- Hasselbalch equation 23
24 Ionization of Water Ionization of Water Dissociation Constants and pk a Values of Some Acids 24
25 Ionization of Water Buffers: Titration Curves of Weak Acids } } } NOTICE: Adding protons, but ph not changing very much = BUFFER Ionization of Water Buffers: Titration of a Polyprotic Acid H 3 PO 4 D H + + H H + H + 2 PO 4 + HPO 2 D 4 D + PO 3 4 pk 1 pk 2 pk
26 Biological Buffer Systems Maintenance of intracellular ph is vital to all cells. Enzyme-catalyzed reactions have optimal ph. Solubility of polar molecules depends on H-bond donors and acceptors. Equilibrium between CO 2 gas and dissolved H 2 CO 3 and HCO 3 depends on ph. Buffer systems in vivo are mainly based on: phosphate, concentration in millimolar (mm) range bicarbonate, important for blood plasma; blood ph = 7.40 EXAMPLE: Clinical Importance HCO 3 + H + H 2 CO 3 Bicarbonate =24 mm pka = 6.1 Carbonic Acid =1.2 mm Patient comes to ER with hyperventilation and acidosis (ph = 7.03; [CO 2 ] = 1.1 mm) What is the [HCO 3 ] and what % is used? ph = pk a + log [A ] [HA] 9.36/24 = 61% used What do you do? 7.03 = log [HCO 3 ]/[CO 2 ] 0.93 = log [HCO 3 ]/[CO 2 ] (What is ?) 8.5 = [HCO 3 ]/[CO 2 ] 8.5 = [HCO 3 ]/ mm = [HCO 3 ] 26
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