Take Home Lessons from Lecture 2

ACIDS AND BASES (CONT.)

1. In buffered aqueous solution, an acid will be present predominantly in its deprotonated state if the pH of the solution is a larger value than the pKa of the acid.

KEY EXAMPLES: Amino acids including ones with carboxylic acid, amino, and guanidino functions, phosphodiester groups

2. Lewis acids and Lewis bases will combine to form a complex with a weak covalent bond.

KEY EXAMPLES: BF3 and amines, Al and alkoxides

STEREOCHEMISTRY

3. Chiral objects (or molecules) cannot be superimposed upon their mirror image.

4. Tetrahedral atoms such as carbon with four different substituents are chiral and are called chiral centers.

5. A molecule is not chiral if it contains a plane of symmetry or a center of symmetry.

KEY EXAMPLES: Amino acid, carbohydrates, steroids like cholesterol

6. Enantiomers are nonsuperimposable mirror images of each other and are named using the R,S convention.

7. Samples of enantiomers rotate the plane of plane polarized light to an equal extent, but in opposite directions.

8. There is no absolute link between "R" and "S" and "+" and "-". Sometimes the R enantiomer rotates plane polarized light in the "+" direction, and for other molecules, the S enantiomer rotates plane polarized light in the "+" direction.

KEY EXAMPLES: Amino acids (D and L vs. R and S vs. + and -)

POLAR BONDS

GR2. The most important question in chemistry is "Where are the electrons?" The answer is that electrons are generally in higher amounts around the more electronegative atoms (e.g. F, Cl, O, N). The electronegative atoms pull electron density away from the less electronegative atoms (e.g. C, H) to which they are bonded. Thus, understanding electronegativities provides a simple method of deciding which portions of a molecule have a relatively high electron density, and which portions have a relatively low electron density.

9. Polar covalent bonds (electronegativity difference between 0.5 and 1.9) and nonpolar covalent bonds (electonegativity difference between 0 and 0.5) behave and react totally differently. Understanding where polar covalent bonds are in molecules allows you to predict chemical properties including reactivity.......this is THE KEY to learning, not memorizing chemistry!!!

INTERACTIONS AND PROPERTIES OF MOLECULES

9. Molecules interact with each other (non-covalent interactions) through electrostatic attraction, with the major types of interactions (listed strongest to weakest) being charge-charge (attraction between ions), hydrogen bonding, dipole-dipole, and dispersion (van der Waals) interactions.

KEY EXAMPLES: Boiling point difference between glycerol, propanol, butane

10. The general rule of solvation is "like dissovles like", so polar, hydrogen bonding solvents dissolve polar, charged, or hydrogen bonding molecules and non-polar hydrocarbons dissolve nonpolar hydrocarbons. Non-polar materials do not dissolve in polar solvents because the polar molecules stick to each other too well.

KEY EXAMPLES: Polar protic solvents such as water and acohols vs. polar aprotic solvents such as ethers and dimethylformamide (DMF)

CONFORMATIONS OF MOLECULES

11. The C-C sigma bonds of alkanes rotate rapidly at room temperature, giving rise to conformational isomers, the most extreme of which are called are staggered (more stable) and eclipsed (less stable).

12. The preferred staggered conformation of butane is the "anti" configuration, rather than the "gauche" conformations (the other staggered conformations of butane). The staggered anti conformation is favored due to steric strain also called nonbonded interaction strain (the atoms "crunch" into each other a bit in the gauche conformation). Longer alkanes exist primarily in the zig-zag conformation.

13. Unsubstituted cycloalkane rings pucker to minimize angle and torsional strain as much as possible. Chair cyclohexane is stable because it does not have either kind of strain.

14. The two possible chair forms of cyclohexane can convert into each other rapidly at room temperature via boat like intermediates. During this interconversion the axial positions are switched to equatorial, and vice versa.

15. Groups larger than H prefer to be equatorial because when they are axial there is steric strain (also called non-bonded interaction strain or 1,3 diaxial interactions) with the other axial groups.

KEY EXAMPLES: Carbohydrates and steroids such ascholesterol.

SUMMARY OF SKILLS YOU MUST MASTER FOR THE MCAT:

1) Assign protonation state at different pH values.

2) Identify chiral centers in molecules.

3) Assign "R" and "S" to chiral centers.

4) Recognize when molecules are chiral of if they have a plane or center of symmetry.

5) Define relationship between stereoisomers with more than one chiral center.

6) Predict relative boiling points and solubilities based on the attractions between molecules.

7) Describe alkane conformations on Newman projections using terms such as staggered vs. eclipsed and guache vs. anti.

8) Predict which cyclohexane chair will predominate based on equatorial location of the larger groups attached to the ring.