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D H 0 for some Noncovalent Interactions

D H 0 for some Noncovalent Interactions. Reaction Interaction D H 0 (kJ mol -1 ). Na + (g) + Cl - (g) NaCl(s) Ionic -785 NaCl(s) Na + (aq) + Cl - (aq) Ionic +ion-dipole +4 Ar(g) Ar(s) London (fluctuation dipole) -8 Acetone(g) Acetone(l) London-van der Waals -30

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D H 0 for some Noncovalent Interactions

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  1. DH0 for some Noncovalent Interactions Reaction Interaction DH0(kJ mol-1) Na+(g) + Cl-(g) NaCl(s) Ionic -785 NaCl(s) Na+(aq) + Cl-(aq) Ionic +ion-dipole +4 Ar(g) Ar(s) London (fluctuation dipole) -8 Acetone(g) Acetone(l) London-van der Waals -30 H3C H3C (permanent dipole) 2 O O H O Hydrogen bond -20 H H CH3 H H2NON H H OH2 H2NON Hydrogen bond (aq) -5 H2NONH2 H O(NH2)2 HOH (Urea (aq)) C3H6(l) + H2O(l) C3H6(aq) Hydrophobic -10 (TSWP p. 98)

  2. Protein Unfolding Proteins have a native state. (Really, they tend to have a tight cluster of native states.) Denaturation occurs when heat or denaturants such as guanidine, urea or detergent are added to solution. Also, the pH can affect folding. When performing a denaturation process non-covalent interactions are broken. Ionic, van der-Waals, dipolar, hydrogen bonding, etc. Solvent is reorganized.

  3. Protein Unfolding heat Let’s consider denaturation with heat. We can determine a great deal about the nature of the protein from such a consideration. The experimental technique we use for measuring thermodynamic changes here is the differential scanning calorimeter. Basic experiment: Add heat to sample, measure its temperature change.

  4. Protein Unfolding T1 Heat T2 Protein + Solvent Solvent T1-T2 In differential scanning calorimetry you have two samples: Your material of interest Control You put in an amount of heat to raise the temperature of the control at a constant rate, then measure the rate of change in temperature of the other sample as a function of the input heat. This is a measure of the heat capacity!

  5. Protein Unfolding pH8.0 Bacillus stearothermophilus Rabbit pH6.0 E. coli Data for glyceraldehyde-3-phosphate dehydrogenase. Is the protein more stable at pH 8 or 6? Why is B. stear. more stable?

  6. Protein Unfolding We are given the following data for the denaturation of lysozyme: 10 25 60 100 °C G° kJ/mol 67.4 60.7 27.8 -41.4 H° kJ/mol 137 236 469 732 S° J/ K mol 297 586 1318 2067 TS° kJ/mol 69.9 175 439 771 Where is the denaturation temperature? What then is special about the temperature at which the denaturation is spontaneous?

  7. Nonideal Systems For ideal gases: For all systems define the activity of component A, aA: For a generalized chemical reaction: aA + bB cC + dD

  8. Nonideal Systems • What is the activity of a gas? • For ideal gases it is the partial pressure • For real gases it is related to, but not necessarily equal to the partial pressure: • Since all gases become ideal at low enough pressures, gA = 1 in the limit of low pressure. • Standard state for a real gas is extrapolation of properties at low pressure to 1atm. slope = RT at low pressure

  9. Nonideal Systems • What is the activity of a solid or liquid? • The standard state for a pure solid or liquid is the pure substance at 1atm. • The activity of a pure solid or liquid is 1 at 1atm and changes only slightly with pressure. • For example, consider water: • Molar volume changes slightly with pressure • Can we calculate the activity of water at high pressure from this information?

  10. Nonideal Systems • What is the activity of a solution? • Solutions can be solid or liquid • They can contain many components • The activity of each component will depend on: • Its concentration • The concentrations of everything else in the mixture • The activity coefficient can be expressed in terms of the concentration: • Solvent standard state: aA XA as XA 1. • Or, equivalently, in the limit as XA approaches 1, gA =1. • For dilute solutions, activity of the solvent (e.g. H2O) ~ 1 using the solvent standard state.

  11. 1 aA cA 1 Nonideal Systems • Solute standard state: • The solute standard state for a component is defined as the extrapolated state where the concentration is equal to 1 molar (M) or 1 molal (m), but the properties are those extrapolated from a very dilute solution. • It is a hypothetical 1M (or m) solution of A that is behaving ideally. • The activity becomes equal to the concentration as the concentration goes to zero. Ideal solution Real solution Solute standard state

  12. Nonideal Systems • If the solute is a strong electrolyte (e.g. NaCl) • Activity coefficients • Activity coefficients for divalent ions can be much less than 1,even in the millimolar concentration range. See TSWP p.140.

  13. Nonideal Systems • Biochemist’s standard state • Addresses difficulty of partial dissociation • H3PO4, H2PO4-, HPO42-, PO43- • Distribution of these species depends strongly on pH (moderate equilibrium) • pH = 7 is chosen as the standard condition for aH+ • H+ activity is 1 for [H+] = 10-7 M • Activity of each molecule is set equal to the total concentration of all species of that molecule at pH 7.

  14. Example

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