CHEM 212, Fall 2007
News and Updates:
Gradelines for Chem 212, Fall 2007 (Peterson; updated 12/23/07):
The following minimum average scores are required:
A 83
A- 78
B+ 74
B 70
B- 67
C+ 59
C 50
D 35
Saturday, Dec. 22, 2007
The average for the final was 48.4%. Here are the correct answers for the final exam:
Question #, Form A, Form B
1, B, I
2, C, A
3, C, B
4, B, G
5, B, J
6, D, B
7, C, G
8, I, A
9, J, E
10, G, B
11, G, J
12, A, B
13, E, D
14, B, C
15, J, I
16, B, J
17, E, G
18, C, B
19, I, B
20, A, C
21, B, C
22, G, B
23, J, B
24, B, E
25, B, C
Friday, Dec. 14, 2007 (Lecture 44)
Today, we finished discussing pericyclic reactions by discussing how to predict the regiochemistry and stereochemistry of Diels Alder reactions.Good luck on the final exam!
Wednesday, Dec. 12, 2007 (Lecture 43)
Today, we started pericyclic reactions, which includes parts of chapters 14 and 30. We introduced three classes of pericyclic reactions and had a brief review of molecular orbital theory.
Monday, Dec. 10, 2007 (Lecture 42)
We talked about DNA sequencing and solid-phase DNA synthesis.
Friday, Dec. 7, 2007 (Lecture 41)
We continued to talk about Chapter 28 on Heterocycles and Nucleic Acids. The structure of DNA, base pairing and hydrogen bonding between bases, and DNA replication were discussed.We talked about DNA sequencing and briefly discussed DNA synthesis.
Wednesday, Dec. 5, 2007 (Lecture 40)
We started Chapter 28 on Heterocycles and Nucleic Acids. DNA and RNA were introduced today. We discussed heterocyclic bases that are components of these biopolymers as well as the ribose and 2'-deoxyribose sugars that are covalently linked to these bases.
Monday, Dec. 3, 2007 (Lecture 39)
We discussed the biosynthesis of steroids and mechanisms of steroid action.
Friday, Nov. 30, 2007 (Lecture 38)
We continued to discuss lipids and focused on terpenes and the biosynthesis of terpenes. Some new overheads were presented today (and will be presented on Monday). You can download a pdf of these additional overheads by clicking here.
Wednesday, Nov. 28, 2007 (Lecture 37)
We covered a new topic today: Lipids (McMurray Chapter 27). We talked about the structures of fats and oils, how the melting temperature is related to molecular structure, and discussed fatty acids. Lipids enable compartmentalization in cells, and the phospholipids and spingolipids comprise cellular membranes. The supramolecular structure of membranes was introduced.
Monday, Nov. 26, 2007 (Lecture 36)
We finished discussing solution-phase synthesis of peptides, including the mechanism of DCC coupling. Solid-phase synthesis was briefly covered. Proteins were discussed in the context of structure and function. The forces of hydrogen bonding and hydrophobic packing were introduced as factors that influence protein secondary and tertiary structure.
Friday, Nov. 16, 2007 (Lecture 35)
We discussed material from Chapter 26. Amino acid analysis, the Edman degradation, and carboxypeptidase degradation were covered. We started discussing solution-phase peptide synthesis.
Wednesday, Nov. 14, 2007 (Lecture 34)
We primarily discussed in class the synthesis of alpha amino acids. Reductive amination of alpha keto acids, reactions of alpha bromo carboxylic acids, the Strecker synthesis, and the amidomalonate synthesis were discussed. Basic structures of peptides were introduced.
Monday, Nov. 12, 2007 (Lecture 33)
Exam 3 was this evening. The average was 77.8%. Here are the correct answers:
Form A
1. J
2. H
3. G
4. I
5. F
6. C
7. H
8. D
9. C
10. F
11. E
12. G
13. A
14. E
15. D
16. F
17. E
18. D
19. A
20. A
21. G
22. F
23. J
24. A
25. B
Form B
1. E
2. A
3. A
4. E
5. F
6. A
7. J
8. H
9. G
10. I
11. F
12. C
13. D
14. H
15. D
16. C
17. F
18. E
19. G
20. D
21. G
22. F
23. J
24. A
25. B
Friday, Nov. 9, 2007 (Lecture 32)
We started talking today about material from Chapter 26 on Amino acids, Peptides, and Proteins. The structures of several alpha amino acids were introduced, as was the isoelectric point (pI), which corresponds to the pH that yields a neutral (zwitterionic) amino acid.
Wednesday, Nov. 7, 2007 (Lecture 31)
We finished talking about carbohydrates. This is the last of the material to be covered on the third exam. We discussed reactions of monosaccarides such as glycosylation, reduction with NaBH4 to alditols, oxidation of the aldehyde to a carboxylic acid with Br2 in H2O or Ag+ / NH3, oxidation of both the aldehyde and terminal CH2OH to carboxylic acids with dilute nitric acid, the Kilinai-Fischer synthesis, and the Wohl degradation.
Monday, Nov. 5, 2007 (Lecture 30)
We continued talking about carbohydrates (Chapter 25). We began talking about reactions of carbohydrates with a discussion of Haworth projections, the difference between the alpha and beta anomers of glucose, mutarotation and the mechanism of this process.We covered alkylation and acylation of monosaccarides.
Friday, Nov. 2, 2007 (Lecture 29)
We started talking about carbohydrates (Chapter 25) today. We discussed the stereochemical nomenclature of sugars, which includes discriptors such as (+/-), R / S, and D / L. Fisher projections of carbohydrates were discussed, as was the historical basis for the designation "D" sugars and "L" sugars. We discussed carbohydrate enantiomers and distereomers and the configurations of D-aldoses.
Wednesday, Oct. 31, 2007 (Lecture 28)
We discussed the Hofmann elimination, electrophilic aromatic substitution of aromatic amines, and reactions of diazonium salts, which are prepared by treating an aromatic amine with nitrous acid (HNO2) and sulfuric acid. The synthesis of diazonium salts from aromatic amines (the Sandmeyer Reaction) is very useful because these salts can be converted into halogens, nitriles, phenols, or arenes lacking the amino group.
Monday, Oct. 29, 2007 (Lecture 27)
We talked about the Hofmann and Curtus amide rearrangements. These reactions allow one to synthesize amines from carboxylic acid derivatives. The mechanisms of both reactions are similar and they proceed through formation of an electron deficient nitrene, which undergoes a 1,2 shift to afford an electrophilic isocyanate. The Hofmann rearr. is run under basic aqueous conditions, and the isocyanate formed is immediately hydrolyzed to a carbamic acid that loses CO2 to form the product amine. The Curtius rearrangement does not involve aqueous conditions, and the isocyanate formed can be isolated and converted into amines, carbamates, and ureas.
Friday, Oct. 26, 2007 (Lecture 26)
We talked about the synthesis of amines: alkylation of amines, synthesis of amines from azides, the Gabriel amine synthesis from phthalimide, nitrile reduction, and he started to discuss reductive amination.We coverved reductive amination, which is a general synthesis of amines from aldehydes and ketones.
Wednesday, Oct. 24, 2007 (Lecture 25)
We started Chapter 24 on amines. We talked about how the chemistry of amines is dominated by the lone pair on nitrogen, which confers the basicity and nucleophilicy of amines. We introduced the concept of pKb, how it is calculated, and how the pKb relates to the pKa of the conjugate acid.
Monday, Oct. 22, 2007 (Lecture 24)
Exam 2 was this evening. The average was 66.5%. Here are the correct answers
for Exam 2:
Form A
1. F
2. H
3. D
4. E
5. C
6. B
7. E
8. G
9. F
10. B
11. D
12. H
13. F
14. C
15. B
16. D
17. D
18. C
19. A
20. C
21. J
22. G
23. E
24. F
25. H
Form B
1. D
2. A
3. B
4. C
5. E
6. G
7. F
8. B
9. D
10. H
11. C
12. F
13. H
14. D
15. E
16. C
17. B
18. F
19. C
20. J
21. G
22. E
23. F
24. H
25. D
Friday, Oct. 19, 2007 (Lecture 23)
We finished talking about polymers. We discussed fibers, elastomers, and thermosetting resins. We started Chapter 24 on amines.
Wednesday, Oct. 17, 2007 (Lecture 22)
We continued our discussion of polymers in class. We talked about radical-induced branching, copolymers, step growth polymers such as Nylon 66, and we started to discuss polymer morphology (macroscopic physical properties).
Monday, Oct. 15, 2007 (Lecture 21)
Today, we began discussing polymers (Chapter 31). Plesae note that material from this chapter will not be on Exam II. We introduced chain growth polymers today in which the polymer chain becomes longer by the continual addition of monomer units to a reactive end of the chain. We covered the mechanism of anionic polymerization of methylmethacrylate to plexiglass. The Zeigler-Natta catalyst was introduced as a method to prepare stereoregular (isotactic or syndiotactic) polymers.
Friday, Oct. 12, 2007 (Lecture 20)
Jocelyn was a guest lecturer today, and she finished discussing chapter 23. She discussed the Michael reaction, the Stork enamine reaction, and the Robinson annulation. The Michael reaction is a conjugate addition of an enolate on an enone. This reaction is catalytic in base, and is similar in that respect to an Aldol reaction. The Stork enamine reaction is another conjugate addition reaction that uses an enamine as the nucleophile (similar to an enolate). The Robinson annulation is a combination of three reactions: The Michael reaction, the Aldol condensation, and dehydration. Our next exam is on Monday 10/22/07. It will be comprehensive but emphasize material covered since the last exam (Chapters 20-23).
Wednesday, Oct. 10, 2007 (Lecture 19)
Today, we continued discussing Chapter 23 on carbonyl condensation reactions. The Claisen condensation was introduced. This reaction requires a stoichiometric amount of base and yields beta-keto products. Mixed Claisen reactions between two different carbonyl compounds give mixtures of symmetrical and unsymmetrical products. However, the mixed Claisen can work well if one of the carbonyl compounds has no alpha hydrogens (non-enolizable).
Monday, Oct. 8, 2007 (Lecture 18)
We discuss how Aldol reaction products are readily dehydrated under acidic or basic conditions to yield enones . Mixed Aldol reactions between two different aldehydes or ketones tend to give mixtures of products. However, these mixed reactions can work well if one of the carbonyl compounds has no alpha hydrogens or one of the carbonyls is much more acidic than the other (Knovenagel condensation).
Friday, Oct. 5, 2007 (Lecture 17)
We finished discussing Chapter 22 on carbonyl alpha substitution reactions. We talked about enolate alkylation, the malonic ester synthesis, and decarboxylation of beta-keto acids.We talked about the acetoacetic ester synthesis, and direct alkylation of ketones, esters, and nitriles. We started discussing Chapter 23 on carbonyl condensation reactions. The Aldol condensation of aldehydes and ketones was introduced. This reaction requires only a catalytic amount of base and yields beta-hydroxy aldehyde products.
Wednesday, Oct. 3, 2007 (Lecture 16)
We continued discussing Chapter 22 on carbonyl alpha substitution reactions. We covered the haloform reaction of methyl ketones. These compounds are converted into carboxylates by treatment with an excess of NaOH and elemental halogens.
Monday, Oct. 1, 2007 (Lecture 15)
We continued discussing Chapter 22 on carbonyl alpha substitution reactions. Remember that strong bases are usually needed to generate enolates. These bases include NaH, NaNH2, and LDA. One can calculate the exent of deprotonation from the pKa values of the carbonyl compound and the conjugate acid of the base used. Bases always deprotonate the strongest acids preferentially.
Friday, Sept. 28, 2007 (Lecture 14)
We started discussing Chapter 22 on carbonyl alpha substitution reactions. These reactions proceed through enol or enolate intermediates. Enols form readily in acid or base catalyzed reactions, but are typically present in very small amounts (the keto form is more stable). Enols and enolates are nucleophiles that react with electrophiles to generate alpha substitution products. Elemental halogens such as Br2 are electrophilic enough to react with enols in the absence of base. Most other electrophiles require the additon of a strong base to generate the more nucleophilic enolate. Acids, esters, and amides do not enolize sufficiently for direct halogenation to take place. However, carboxylic acids can undergo the Hell-Volhard Zelinskii reaction, which proceeds through an acid halide enol intermediate, to generate alpha halo products.
Wednesday, Sept. 26, 2007 (Lecture 13)
We finished discussing Chapter 21. Grignard reagents react with nitriles to produce ketone products. We talked about reactivity patterns of acid anhydrides, esters, amides, and nitriles. DIBAH can be used to synthesize aldehydes from esters or nitriles. More powerful reducing agents such as LiAlH4 reduce esters to primary alcohols and nitriles to primary amines. We covered the mechanisms of acid and base-induced ester hydrolysis, and the mechanism of the DIBAH aldehyde synthesis.
Monday, Sept. 24, 2007 (Lecture 12)
We started Chapter 21 on carboxylic acid derivatives. We discussed how the nature of the substituents on the carbonyl group affects the stability of the derivative, the electron deficiency of the carbonyl carbon, and its leaving group properties. Acid chlorides are more reactive than anhydrides, which are more reactive than esters, which are more reactive than carboxylic acids in nucleophilic acyl substitution reactions. Steric and electronic effects contribute to control the reactivity of carboxylic acid derivatives. The Fisher synthesis of esters was discussed, as was reactions of acid chlorides, esters, and anhydrides with strong nucleophiles. Keep in mind that strong nucleophiles such as MeMgBr react with these acid derivatives to afford tertiary alcohols. The intermediate ketones cannot be isolated because they are too reactive. The Weinreb ketone synthesis is an approach that allows synthesis of ketones from the addition of strong nucleophiles to acid derivatives.
Friday, Sept. 21, 2007 (Lecture 11)
We finished our discussion of chapter 20 today by talking about the preparation
of carboxylic acids from oxidation of alkylbenzenes, alkenes, alcohols, and
aldehydes. Carboxylic acids can also be prepared from the hydrolysis of nitriles
and the carboxylation of Grignard reagents. These compounds can be reduced
to alcohols with LiAlH4 and BH3.
Wed. Sept. 19, 2007 (Lecture 10)
The average for exam 1 was 74%. Today we started discussing Chapter 20 (Carboxylic acids). We talked about how inductive effects and resonance effects influence the acidity of these compounds. Remember that electron withdrawing groups stabilize the carboxylate to increase the acidity and electron donating groups destabilize the carboxylate to decrease the acidity.
Monday, Sept. 17, 2007 (Lecture 9)
Exam 1 was today. The exam scores will be posted in the lobby of Whitmore (1st floor) as soon as they become available. The scores will be emailed by the UTS to all students. If there are any score discrepancies, please see Mike in 210 Whitmore. Here are the correct answers for Exam 1:
Form A
1. D
2. I
3. C
4. J
5. A
6. G
7. H
8. G
9. C
10. D
11. H
12. C
13. D
14. C
15. A
16. E
17. D
18. B
19. E
20. E
21. F
22. C
23. G
24. E
25. D
Form B
1. D
2. D
3. H
4. C
5. D
6. E
7. D
8. I
9. C
10. J
11. A
12. G
13. H
14. G
15. B
16. C
17. C
18. A
19. E
20. E
21. G
22. E
23. D
24. F
25. C
Friday, Sept. 14, 2007 (Lecture 8)
We finished discussing aldehydes and ketones. We talked about organometallic grignard reagents and organolithium reagents that add irreversibly to aldehydes and ketones to yield alcohols after quenching with acid. We also reviewed the irreversible addition of hydride reagents such as LiAlH4 and NaBH4. We talked about the reversible reactions of hydration and acetal formation. We discussed the addition of amines to both saturated and conjugated ketones and aldehydes. Saturated ketones/aldehydes react with primary amines to yield imines and seconday amines to yield enamines. We also talked about the Wittig reaction in which a ylide is used to generate C=C double bonds. The Wittig reaction allows one to create a new carbon-carbon bond where an aldehyde or ketone carbonyl used to be. We briefly covered conjugate additions to alpha, beta-unsaturated aldehydes and ketones. "Hard" nucleophiles (RMgX, RLi, H- from LiAlH4) prefer 1,2-addition. "Soft" nucleophiles (R2CuLi, RNH2, R2NH, H- from NaBH4) prefer 1,4-addition. The Wolff-Kishner reaction was briefly discussed. This reaction allows one to convert an aldehyde or ketone to a hydrocarbon by reaction with hydrazine (H2N-NH2) and hydroxide.
The room for EXAM1 on Monday 9/17 has been posted (100 Thomas
Bldg.). Please sign up for the conflict exam with Mike in 210 Whitmore if
you have another scheduled activity during the normal exam hours.
The exam will cover all spectroscopic methods (MS, IR, UV-VIS, NMR), spectral
problems, and reactions of aldehydes and ketones (CH. 19). There will be 25
multiple-choice questions on the exam. Two old exams are available for practice
on the web. Tables of spectroscopic data that you will have available during
the exam are on the web. Make sure that you study the combined spectroscopic
problems. There will be several of these on the exam.
Wednesday, Sept. 12, 2007 (Lecture 7)
We started talking about the structure and reactivity of carbonyl
compounds. We will spend several weeks discussing the chemistry of the carbonyl
group, and we will cover a large number of reactions. It is important for
you to understand both general trends and reaction mechanisms. A reaction
list from CHEM 212 is available on the web.
Keep in mind that the electron deficiency of the carbonyl carbon is the reason
for facile nucleophilic attack on carbonyls. This deficiency can be increased
by protonation of the carbonyl oxygen. The nucleophile forms a new bond to
carbon to generate the tetrahedral intermediate. The fate of that intermediate
depends on the nature of the carbonyl compound and the nucleophile.
We started with Chapter 19, which covers aldehydes and ketones. Material from
this chapter will be on the first exam, which is Monday (9/17) from 8:15-10:15
p.m. in 100 Thomas Bldg.
Monday, Sept. 10, 2007 (Lecture 6)
Today we finished discussing proton NMR, and we discussed spectral
problems A and B, which you can download from this web site (go to the testing
center). Please keep in mind the following "trade secrets": (1)
Multiplets of hydrogens coupled with each other show a "roof effect"
in the proton spectrum (they lean toward each other). (2) Hydrogens on O,
N, and S exchange with D2O and disappear from the proton spectrum. (3) The
nitrogen rule states that stable organic compounds with odd molecular masses
must have an odd number of nitrogen atoms. Molecules with even molecular masses
must have an even number of nitrogens (or zero).
On Wednesday we will take a break from spectroscopy and start talking about
aldehydes and ketones (Ch. 19). We will cover many carbonyl reactions within
the next week and they will be on the first exam. You should try to become
an expert in structure determination methods, and go over all of the assigned
book problems and all of the assigned spectral problems (A-J). You should
download the first exam from last semester and look at the spectral tables
at the end of the exam. These tables will be provided as part of Exam 1.
Friday, Sept. 7, 2007 (Lecture 5)
Jocelyn Edathil was a guest lecturer today. She finished our
discussion of 13C NMR by talking about how peak size is related not only to
the number of carbons, but also to the number of attached hydrogens, so integration
is not commonly used in 13C NMR. The 13C technique of DEPT spectroscopy can
be used to determine the number of attached hydrogen atoms.
She also talked in detail about 1H NMR spectroscopy and how functional groups
influence chemical shifts similarly to 13C spectroscopy. In 1H NMR, integration
can be used to determine the relative number of attached hydrogens. Coupling
is observed in 1H NMR, which tells us about the neighborhood that protons
reside in. Here we are talking about the coupling between hydrogens on carbons
that are directly bound to each other. Remember that chemically equivalent
hydrogens do not couple to each other, and (in this class) we are only interested
in vicinal coupling (i.e. coupling between hydrogens separated by three bonds
H-C1-C2-H). Other hydrogens may couple, but we will not analyze such situations
in CHEM 212.
On Monday, we will start talking about how to solve spectral puzzles, and
we will practice with some "real" spectra. Bring the first five
sets (A-E) to class.
Wednesday, Sept. 5, 2007 (Lecture 4)
Today we began discussing the most powerful technique of all
for structure determination: Nuclear Magnetic Resonance (NMR) spectroscopy.
Proton (1H) and carbon-13 (13C) nuclei are magnetically active. Their spins
align both parallel and antiparallel to strong magnetic fields. By irradiating
a sample in the magnet with radio frequencies, the NMR instrument causes the
spins to flip to the higher-energy antiparallel state. The frequency required
to make this transition is measured as parts per million (ppm) with respect
to the standard tetramethylsilane (TMS).
We talked primarily about 13C-NMR and how carbons in different chemical environments
exhibit different chemical shifts. The chemical shift tells us about the chemical
environment of the carbon atom (shielding, deshielding). Nuclei with high
electron density will appear in the high field region of the spectrum (low
ppm values, shielded) and nuclei with diminished electron density will give
peaks in the low field region (high ppm values, deshielded). The number of
peaks in a 13C spectrum tells us the number of chemically different carbon
atoms in the molecule.
For 13C the scale used is from 0 ppm (TMS) to just above 200 ppm (for carbonyl
carbons).
You should start studying Chapter 13. We will also be discussing several of
the spectral problems (A-E) in class, so you should print out copies and bring
them to class.
Friday, August 31, 2007 (Lecture 3)
Today we briefly reviewed UV spectroscopy. UV spectroscopy is used to determine
the extent of conjugation of organic molecules We also taked in much more
detail about infrared (IR) spectroscopy, which is a more powerful technique
because it can be used to identify specific functional groups in molecules.
Different functional groups have characteristic frequencies (expressed in
wavenumbers, i.e. cm-1) that can be observed in the IR spectrum. You should
practice using IR spectra (there are several in the book) to identify functional
groups in molecules.
On Wednesday we will move on to the most powerful structure elucidation technique
of all: Nuclear magnetic resonance (NMR) spectroscopy.
Wednesday, August 29, 2007 (Lecture 2)
Today we started a discussion of methods used to determine the
structures of organic molecules. Mass spectrometery was introduced as a method
to determine the molecular mass of compounds. We talked about the mechanism
of ionization, parent ions (M+), the base peak, and how fragmentation can
yield clues about the presence of substituents such as methyl or ethyl groups
on organic molecules. The most stable cations are usually formed during fragmentation.
We also talked about isotopes, and how they affect the M+1 and M+2 peaks in
the spectrum. These peaks can be used to determine the number of carbon atoms
or detect the presence of chlorine or bromine atoms in a molecule.
Mass spectrometry provides crucial information about the molecular formula,
especially if the mass is determined very precisely. We explored a couple
of examples of mass spectra and you should do more of that on your own in
Chapter 12.
After talking today about blowing up molecules with electron beams, on Friday
we will finish Chapter 12 by discussing how molecular gymnastics (IR spectroscopy)
gives additional information about molecular structures.
Monday, August 27, 2007 (Lecture 1)
Our first class.We went over the syllabus and website today. Be sure to get
a copy of the syllabus! You can download the syllabus from the course webpage.
There are also copies in the undergraduate office (210 Whitmore).
Make sure that you have the 6th or 7th edition of McMurray, the study guide
and the book on nomenclature. I will not spend much time on nomenclature,
so you should consult the nomenclature text whenever we discuss a new functional
group. Please dig out your molecular model set and use it as needed.
Read the webpage section on "How to Study".
Download transparencies for the first section of the syllabus (under the Class
Packet). Get copies of the first five spectra (A-E) from the Testing Center.
Previous "News and Updates" are on a separate page