Interion and Intermolecular Forces

1. Interion and Intermolecular Forces • Ion-Ion interactions are the strongest interactions • Example of an ion-ion interaction? • Let’s look at the various interactions given in the table

2. Ion-Dipole Interactions • Best example: Hydrated Ions • The polar character of the water molecule allows it to interact with cations or anions • We can describe the interaction energy: z = ion charge µ = Electric dipole moment r = distance

3. Dipole-Dipole interactions • Let’s look at the interactions between polar molecules The Dipole-Dipole interactions force some order in the solution

4. Dipole-Dipole interactions Dipole-Dipole interaction energy: µ1: Dipole moment of molecule 1 µ2: Dipole moment of Molecule 2 The fact that the distance is cubed means that the energy falls of much more rapidly than ion-ion interactions as the interacting species are separated

5. Which molecule has the higher boiling point: p-dichlorobenzene and o-dichlorobenzene Dipole moment for the molecules?

6. Which molecule has the higher boiling point: cis-dichloroethene or trans-dichloroethene?

7. Hydrogen Bonding • A special type of dipole-dipole interaction • Hydrogen bonding only occurs between: N-H O-H and Lone pair e- on N, O, F F-H

8. Hydrogen Bonding • Hydrogen bonds are one of the most important interactions in biological systems • Hydrogen Bonds: • Hold proteins together • Allow DNA base pairs to match up • Allow structural polymers to interact Hydrogen bonds are the strongest type of non-ionic intermolecular force

9. Dipole - Induced Dipole • The presence of a molecule with a strong dipole moment can induce or create a dipole in a non-polar molecule • This depends on the strength of the dipole and the polarizability of the nonpolar molecule 1: Dipole moment of molecule 1 2: Polarizability of molecule 2

10. London Forces • London Forces are attractive forces between non-polar molecules (all molecules have them, but they are much weaker than other types) • These are 1 of the two weakest intermolecular forces • How do these interactions arise?

11. London Forces • The electron clouds are constantly shifting and sometimes the molecule gets a small dipole moment • Neighboring nonpolar molecules will have their electron clouds distorted and will form a dipole of opposite orientation • Then the process starts over (Dipole disappears and reforms) (1x10-16 sec to form and disappear)

12. 1: Polarizability of molecule 1 2: Polarizability of molecule 2 London Forces Very short range effects!! r6 !!!! • What determines Polarizability? • Large atomic radii • Low Zeff • High Polarizability = Large London Interactions

13. Let’s look at London Forces and Polarizability with respect to physical properties As we go down a group, the atomic radius increases and the melting and Boiling points increase (takes More energy)

14. London Forces and Molecular Shape • Because the London Force energy drops off VERY sharply as a function of distance, molecular shape is a major contributor to London Force energy Which has the higher boiling point?

15. Thinking about Biology Chemically • All living organisms use energy • Energy comes from chemical reactions • The energy stored in chemical bonds is harnessed by proteins to catalyze other reactions

16. Functional Groups of Biologically Active Molecules • All the chemistry of life is performed using these chemical entities • We’ll go over these in MUCH greater detail in the next lecture

17. ATP: The Energy Currency of the Cell

18. Formation of Biomolecules • How did the vast array of biologically active molecules come to be? • Initially, it is thought that only NH3, H2S, CO, CO2, CH4, N2, H2 and H2O were present on the early Earth • However, the planet was volcanically active (heat and pressure) and there was significant electrical activity in the atmosphere

19. The Miller-Urey Experiment • Formaldehyde and hydrogen cyanide are usually formed, BUT, after prolonged reaction, so are AMINO ACIDS • The experiment can be taken a step further and be performed with simple amino acids as starting material. • Protein like molecules are formed

20. Biological Polymers and Directionality • Biological Polymers have a specific direction to them based upon their sequence • Proteins: Amino terminus to Carboxy terminus • Nucleic Acids: From 5’ to 3’ • Carbohydrates: From nonreducing terminus to reducing terminus

21. Types of Cells • The different biologically active molecules and polymers arrange themselvs to form cells • The formation of a lipid bilayer is instrumental in this! • We can distinguish between types of cells based upon the presence of organelles, especially the nucleus • Prokaryotic do not have a nucleus or other organelles but Eukaryotic cells do • Organelles are specialized compartments that allow unique reactions to occur within them

22. Types of Cells

23. Types of Cells

24. Section 1.9: Biochemical Energetics • All cells need energy to catalyze the reactions of life • ATP (Adenosine triphosphate) is the energy currency of the cell • The gamma phosphate is hydrolyzed off • This is an example of a high-energy bond

25. Thermodynamics • Let’s review some topics we covered in CHEM105: • Spontaneous Reaction: A reaction that occurs without outside intervention • May be very fast or slow • Free Energy: G, is a measure of the capacity of a system to do thermodynamic work • Only G can be measured • Enthalpy: H, is a measure of the heat stored in a chemical bond • Entropy: S, is a measure of the disorder of a system • G = H - TS

26. Think About It… If all systems in the universe tend towards disorder, how can cells exist in the first place?

27. Biochemical Thermodynamics • The Free Energy of a system decreases in a spontaneous reaction • G < 0 • This is also called an Exergonic reaction • 2. A system at equilibrium has no Free Energy Change at All • G=0 • 3. In a nonspontaneous reaction, energy must be input into the system • G>0 • This is also called an Endergonic reaction

28. Acids, bases and pH • We talked about strong acids and bases last lecture in our discussion of Electrolytes • A strong acid completely dissociates in solution • HA --> H+ + A- • pH = -log [H+] or pH = -log [H3O+] • For a strong acid, the pH will equal the -log[H+] • Remember: Some acids are polyprotic (H2SO4, H3PO4)

29. Acids, Bases and pH • For strong bases, we need to remember that ph and pOH are related: pH + pOH = 14 • Take the negative log of the [OH-] and subtract it from 14 to determine the pH

30. Acids, Bases and pH • Weak acids (and bases) pose a new problem: The fact that they do not completely dissociate in solution • They exist in an equilibrium between the acid and conjugate base HA (aq) + H2O (l) --> H3O+ (aq) + A- (aq)

31. Common Biochemical Acids

32. Henderson-Hasselbach Equation Enzymes have very specific pH ranges in which they will function

33. Henderson-Hasselbach Equation

34. Titration Curves • When we mix an acid and a base together in small increments and then measure the pH, we can make a Titration Curve HA (aq) + OH- (aq)  H2O (l) + A- (aq) • The equivalence or endpoint (EP) is the point in the titration at which all of the acid molecules have reacted with base • Halfway to the EP: [HA]=[A-] • The pH at this point is the pKa. Why? • At the EP: [A-] = Initial [HA] 