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This is a report on scores for the first three in-class and take-home quizzes. As I’m sure you realize (and as I have been warning since the beginning of the semester), the material covered by quiz #3 was substantially more difficult than the material on the previous quizzes. This was reflected in the quiz scores which took a substantial and expected downturn. On the other hand, the take-home scores were much higher.

I’ll give you the gory details about quiz #3 in a moment, but I want to say this: students’ first encounter with the acid-base equilibria and chemical reactions (usually nucleophilic substitution reactions) of organic chemistry has been problematic for as long as I have been teaching organic chemistry (over 30 years). I would like to think that there is a better way to teach this material, but I haven’t found it yet. Still, there are some silver linings in all this. Read on.

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As you learned in Hum 110, the ancients were well-acquainted with the ever-changing fortunes of humanity. One day we are raised up, the next day we trip and fall, and who knows what the future will bring? Perhaps the future is even a mystery to the Gods on Olympus?

If you are currently in a financial bind and feel unable to make, or even uncomfortable making, all of your purchases for Chem 201 and your other courses, Reed College is prepared to help you through this! The following instructions were provided by the offices of Student Life and Financial Aid this week, and they are standing by.

Please don’t hesitate to get the assistance we can offer. Remember that clicker usage is totaled up every day of class and two days have slipped past already. Likewise, a few days have already elapsed on the Sapling homework clock for Day 1. But clickers and Sapling need to be purchased, so don’t let a temporary financial problem derail your academic work. Here’s what you do:

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The first 5 or 6 weeks of Chem 201 races through a lot of material you covered in Chem 101/102. In particular, we discuss,

• how molecules are held together (101/102 – atomic structure, electrons, bonds, orbitals)
• how to draw and interpret electron patterns (101/102 – Lewis structures, resonance structures, orbitals)
• how to connect molecular structure to other molecular properties (101/102 – charge distribution, dipole moment, intermolecular forces, molecular energy)
• chemical reactions, beginning with acid-base equilibria (101/102 – pH, pKa, acid/base strength, Keq, reaction thermodynamics (ΔG, ΔH, ΔS))
• chemical reaction kinetics (101/102 – reaction rates, activation energies (Ea, ΔH‡), rate constants (k)).

All of these topics should look at least a little familiar, but how well will you recall and (even more important) be able to use them next fall? One simple way to make sure you get off to a good start in Chem 201 is to review these key topics from 101/102.

Here is a detailed list of topics that you can use to guide your 101/102 review. It includes a large number of pointers regarding key facts, skills, and explanations. To put it another way, it’s a long list so don’t let it overwhelm. Pick-and-choose a few topics for summer study, and we will get the rest of it in 201. (Note: my other two summer review suggestions also cover some of the material on this list.)

(added 8 Aug, 2019) An alternative to my detailed list exists and that is to dive into a smallish (250 page) book, “Preparation for Organic Chemistry” by I. David Reingold. The book is available in paperback and also in a $9.99 Kindle-friendly version. The author describes the book in this way, “Reviews material from general chemistry that is relevant to organic, set in an organic context”. I haven’t seen more of the book than the Table of Contents, but even that limited topic list overlaps well with the topic list that I give you below.

Chem 101/102 Topics that Apply to Organic Chemistry

Lewis Structures

1. Drawing
   1. Know the Chem 201 Atoms of Interest (201 AoI): C/Si, N/P, O/S, F/Cl/Br/I, H/Li/Na/K, Mg, B/Al
   2. Know where the 201 AoI appear on the Periodic Table and know how many valence electrons are held by each type of atom
   3. Know what symbols to use for atoms, bonds, nonbonding electrons, formal charges
   4. Know the rules for constructing plausible Lewis structures (“plausible” means the electron pattern in the Lewis structure is a plausible guide to the electron distribution in the molecule). The three most important rules are:
      1. covalent bond = 2 shared electrons
      2. Lewis octet = ideal electron pattern for each atom
      3. formal charge computation
2. Interpretation
   1. Identify bond orders (single, double, triple)
   2. Identify polar bonds (between atoms of different electronegativity)
      1. Know relative atom electronegativities
      2. Rank bonds from least to more polar
   3. Identify non-zero formal charges (are they plausible?)
   4. Identify atoms that might be associated with strong intermolecular forces
   5. Characterize molecule’s energy as “low” (chemically stable) or “high” (chemically unstable)

Molecular Geometry

1. Bond distances
   1. Know relative atom sizes for 201 AoI
   2. Predict effect of atom size and bond order (from Lewis structure) on relative bond distances
2. Bond angles
   1. Know VSEPR (= electron domain theory) for predicting bond angles around a central atom based on its Lewis structure
      1. Know standard angles
      2. Know how electron pair type (electron domain size) might perturb angles (= deviate from standard values)
   2. Know atom geometry labels: linear, bent, trigonal, tetrahedral, pyramidal, trigonal bipyramidal, square planar, octahedral
3. 3-D Molecular models
   1. Build (plastic, computer) models that accurately reflect VSEPR predictions
   2. Interpret (plastic, computer) models
      1. Label atom geometry (linear, bent, etc.)
      2. Infer steric number (or number of electron domains) that supports the model’s depiction of atom geometry

Resonance Structures (= resonance contributors = resonance forms)

1. Drawing
   1. Use double-headed arrows to “connect” resonance structures
   2. Use partial bonds & partial charges to show electron distribution in resonance hybrid
   3. Push electrons (draw curved arrows) to show how one resonance structure turns into another
2. Interpretation
   1. Identify (and rank) “major” and “minor” resonance contributors
   2. Construct resonance hybrid that reflects rankings of resonance contributors
   3. Predict molecular geometry (adjustments to bond distances, bond angles, and atom geometries required by resonance)
   4. Predict effect of resonance on intermolecular forces (assess location and size of partial charges)
   5. Predict effect of resonance on molecular energy (assess degree of resonance stabilization; small? large?)

Quantum Mechanical Models of Electronic Structure

1. Electrostatic Potential Maps
   1. Identify atoms (and regions near atoms) that are relatively electron-rich (carry a partial negative charge)
   2. Identify atoms (and regions near atoms) that are relatively electron-poor (carry a partial positive charge)
   3. Compare the polarity of two molecules
   4. Compare the degree of charge delocalization (requires resonance) in two molecules
   5. Use location and degree of charge build-up to predict possible intermolecular forces
   6. Use location and degree of charge build-up to predict molecular energy
2. Hybrid Orbitals
   1. Assign atom’s hybridization based on Lewis (or resonance) structure
   2. Identify hybrid orbital (or atomic orbital) that contains nonbonding electrons (lone pairs)
   3. Identify hybrid orbital (or atomic orbital) that contains electrons that participate in a specific covalent bond (sigma & pi bonds are treated differently!)
   4. Use orbital type (atomic: 1s, 2s, 3s, … 2p, 3p, …) (hybrid: sp, sp2, sp3) to identify electrons that are held more tightly/loosely
3. Molecular Orbitals (MO)
   1. Drawing – for any covalent bond in a molecule, construct an orbital mixing diagram
      1. Identify the 2 orbitals (one from each atom) that overlap and share electrons
      2. Draw orbital mixing diagram that shows energy levels of the 2 orbitals that combine, and the 2 MO (bonding, antibonding) that are created by this combining
      3. Label all 4 orbitals (atomic “cartoons” of the overlapping orbitals, and “cartoons” of the MO that can be made by combining these orbitals (one MO is bonding, the other is antibonding)
      4. Draw orbital labels next to each energy level identifying orbital type (see 4.B.iv) (for MO identify as 1) bonding/BMO or antibonding ABMO, and identify as “sigma” or “pi”)
      5. Draw electrons that
      6. Know how relative magnitude of overlap between two orbitals affects energy gap between bonding and antibonding MO, and bond strength (sigma overlap/gap/strength > pi overlap/gap/strength)
      7. Draw an orbital mixing diagram that shows 1) the relative energies of the 2 uncombined and the 2 molecular orbitals, and 2) the electrons that are assigned to each of these orbitals
   2. Predict the overall bond order between two atoms by considering the number of electrons assigned to all anti/bonding orbitals involving both atoms
   3. Predict the effect of MO occupancy (the number of electrons in each MO) on molecular energy

Intermolecular Forces

1. Identify & characterize possible forces
   1. Electrostatic forces
      1. Can be attractive or repulsive
      2. Involves atoms carrying full or partial charges
      3. Hydrogen bonds (attractive, one atom is positively charged H)
   2. London dispersion forces (= van der Waals forces)
      1. Can be attractive or repulsive
      2. Involves “touching” or “overlapping” atoms
2. Express effect of forces on molecular energy
   1. Attractive forces lower molecular energy (stabilize molecules)
   2. Repulsive forces raise molecular energy (destabilize molecules)

Structure-Energy Correlations

1. Attraction = stabilization = low energy
2. Repulsion = destabilization = high energy
3. Stabilizing factors (partial list)
   1. Sharing electrons (strong covalent bonds)
   2. Charges supported by atom electronegativities (surplus electrons located on MORE electronegative atoms; surplus positive charges located on LESS electronegative atoms)
   3. Resonance
   4. Surplus electrons located on more electronegative atoms (related: Surplus positive charges located on less electronegative atoms)
   5. Attractive intermolecular forces (may involve interactions with solvent molecules or ions of opposite charge)
4. Destabilizing factors
   1. Ineffective or insufficient electron sharing (weak covalent bonds, atoms without octets)
   2. Charges NOT supported by atom electronegativities (surplus electrons located on LESS electronegative atoms; surplus positive charges located on MORE electronegative atoms)
   3. Repulsive intermolecular forces

Chemical Equilibria & Concentration

1. Mass-Action Law (equation connecting Keq to reactant/product concentrations)
2. Thermodynamics (equation connecting Keq to ΔG) (equation connecting ΔG to ΔH and ΔS)
   1. Predicting how molecular structure affects molecular energy (see above) and Keq (reaction favorability)
3. Le Chatelier’s Principle (effect of experimental conditions on equilibrium concentrations)
4. Acid-Base equilibria
   1. Convert [H3O+] to pH and to [HO-]
   2. Ka and pKa
      1. relationship between Ka and pKa
      2. relationship between Ka and acid strength
      3. Henderson-Hasselbach equation (connects Ka and [H3O+])

Chemical Reaction Rates (Kinetics)

1. Rate Laws (equations connecting reaction rate – d[Product]/dt – to reactant concentrations)
2. Rate Constants (proportionality constant ‘k’ that appears in rate law) Note: chemists use both of the following equations, but only review what is familiar to you from 101/102
   1. Arrhenius equation ? (equation connecting k to energy barrier, Ea)
   2. Transition state equation ? (equation connecting k to ΔG‡)
3. Reaction Mechanisms
   1. Reaction intermediates
      1. electron-pushing (drawing curved arrows to show how electron patterns & molecular geometries change during a chemical reaction)
   2. Transition states
4. Energy changes & Reaction (or Potential) Energy Diagram
   1. Interpretation
      1. Identify energy minima & maxima
      2. Identify reaction barriers
      3. Identify reaction energies (overall, step-by-step)
      4. Label reactant, product, intermediate(s), transition state(s)
   2. Prediction
      1. Is reaction (overall, step-by-step) favorable or unfavorable?
      2. Given diagrams for two competing (and possibly hypothetical reactions),
         1. Which reaction is more (less) favorable?
         2. Which reaction is faster (slower)?

Organic chemistry is, despite what you may have heard, pretty much the same everywhere, whether MIT or Portland Community College. The courses that science majors and pre-meds take are 2 semesters (3 quarters) long and rely on a commercially produced textbook. There are about a dozen texts to choose from, and they all look pretty much the same: same physical size, same #chapters, same #pages, same content, and (usually) the same topic sequence. (Only the price tag changes!) If this similarity doesn’t persuade you, consider this, the American Chemical Society offers a standardized test for organic chemistry to college professors in order to test their students at the end of the year. (We don’t use this test, but I have no doubt that most of you would do well on it.)

When you think about this degree of standardization, you might guess that just about any college-level material you study will be helpful and you would be exactly right, but as I suggest below, a textbook might not be the best choice for summer work. Instead, I suggest that you find one of the “supplement” style books that I list and work with it instead. Notice that I say, “work,” and not “read.” That’s because all of the supplements are workbooks where you read a little and then do some problems. I think the following two paragraphs (quoted from To the Student in Pushing Electrons) says it best,

“I have only three instructions. First, supply an answer wherever a line appears under a blank space. The correct answer might be a word, a number, a structure, or some arrows. Second, don’t look up the correct answers until you have made a serious try at doing it yourself. Third if you plan to just look up the right answers and transcribe them, return the book and get your money back.

The program uses two effective learning devices: active involvement and repetition. You will participate actively in the learning process. Because so much of the academic experience consists of receiving information, it should be refreshing to work through a program using your own wits. You will see an example of an operation and then carry it out several times as the supporting material is gradually removed. The approach is methodical. Some of you will find that you can accelerate your trip through certain sections. But the program has been written in the hope that none of you will ever feel abandoned. Expect to spend a total of 10 to 14 hours to complete the program.”

4 Books To Consider:

1. Organic Chemistry, 2e by T. Sorrell.
   1. Upsides: This is the Chem 201/2 textbook. It is inexpensive and nearly every chapter offers a few pages of biochemical applications. Cool! Another plus: all of the assigned readings (in sequence) are available on the Chem 201 Classes page. Reading the book is good practice for the reading/study you will have to do in the fall, and the book is loaded with practice problems, summary tables, and other helpful features.
   2. Downsides: The answers to the book’s problems are located in a separate book call the Solutions manual. Both the textbook and solutions manual are huge. Nice adornments for your dorm room, perhaps, but inconvenient to take to a coffee shop or the beach. Also, like all textbooks, this one contains a large number of details and asides that, while essential in the fall, are distractions in the summer.
   3. Bottom-line: Getting familiar with your textbook can only help, but this may be biting off too much for a summer task. One of the following “supplement” books might be a better summer companion.
2. Organic Chemistry I as a Second Language (also listed as Second Language: Organic Chemistry I) by David R. Klein. This can be used for summer prep and also as a supplement throughout the fall.
   1. Upsides: Paperback (just under 400 pages) with answers in the book. The book is written in an informal style that makes it feel like light reading (to a point). The topics covered by volume I parallel those in Chem 201 fairly closely.
   2. Downsides: Obviously, a short book skips material that we will cover in 201. And, while you should learn the author’s explanations/approaches/tricks, you must also be prepared to revise your thinking/drawing habits in the fall because I will provide my own views and instructions.
   3. Bottom-line: This is probably the most comprehensive summer prep book that I can recommend. All editions, new or used, should be fine. Work with Volume I. You do not need Volume II.
3. Pushing Electrons: A Guide for Students of Organic Chemistry, 2e by Daniel P. Weeks. (This is the book that I quoted from above.)
   1. Upsides: Paperback with answers in the book. Much, much shorter than “Second Language” (about 160 pages). Very manageable time investment. (“Expect to spend a total of 10 to 14 hours to complete the program.”)
   2. Downside: The book’s brevity is its chief asset and liability. It consists of only three sections: Lewis Structures, Resonance Structures, Mechanisms. And you will no doubt need to adjust some of your thinking/drawing habits in the fall.
   3. Bottom-line: If you are unsure of how much time you have for your summer prep project, this might be the best way to go. It is the shortest book of all, it reviews at least two key topics from 101/102, and it gets you doing (some of the) things that organic chemists do. Both editions should be fine.
4. Arrow Pushing Organic Chemistry: An EASY Approach to UNDERSTANDING Reaction Mechanisms by Daniel E. Levy. Note: the italics in the title were supplied by the author, not me.
   1. Upsides: Paperback (just under 300 pages) with answers in the book. Significantly shorter than the “Second Language” book, but covers many more topics than the “Pushing Electrons” book. For example, this book contains the occasional drawing of orbitals, whereas “Pushing Electrons” does not.
   2. Downsides: The writing here is much more formal than what you will find in “Second Language”. And, as with the other supplements, you will need to revise some of your thinking/drawing habits in the fall.
   3. Bottom-line: Don’t be fooled by the similarity in titles for #3 and #4, “Pushing Electrons” vs. “Arrow Pushing”. These books are quite different.
5. (added 8 Aug 2019) Preparation for Organic Chemistry by I. David Reingold.
   1. Upsides: Kindle-friendly ($9.99). Manageable content that is explicitly designed for the summer before taking organic. Just 9 chapters (250 pages text + problems).
   2. Downsides: This book is more of a voyage into the sections of general chemistry that are relevant to organic chemistry, rather than a voyage into organic itself. This is supported by the book’s Table of Contents (the only part I have seen) which looks a lot like my list of important Chem 101/102 topics. See Suggestion #1 – Review key topics from Chem 101/102.
   3. Bottom-line: If you are looking for a deep dive into, or just more exposure to, the “new” topics that organic chemistry will introduce, then this isn’t your book because it will cover only the first couple weeks of Chem 201. On the other hand, it could be just the summer preparation you need?

Decisions, decisions. If you have access to only one book (even the textbook), use what you have. If you have access to 2 or 3 supplements, then here’s a way to decide. First, think about time. If you are looking for a small time commitment, choose “Pushing Electrons”. Second, if you are ready to commit to a more substantial summer prep, consider writing style. Read 3-4 pages of “Second Language” and “Arrow Pushing”. Which style meets your needs? Go with that book!

General anesthetics, the chemicals that temporarily ‘put you under,’ have transformed surgery, but doctors and scientists are still learning how these chemicals work.  (more…)

I saw this article (C&ENews, 12 Oct 2015, p. 38) about the molecules that make Halloween pumpkins look and taste and smell the way they do:

You can buy a new molecular model kit from the Chemistry Stockroom ($20), but you have other choices (learn more here), and used model kits are often available at reduced prices from students who have no more use for them. Before you buy a used kit, make sure it contains most of the pieces you need. Here’s a parts list + photo of a new kit.

I received this message from Kristin Bott in CUS. She’s been gathering data about your clickers and she NEEDS YOUR HELP. Read on,

Good afternoon, Chem 201!

A high-five to the 30 of you who have currently registered your clickers. For the remaining near-40 of you, please do so soon! I need to do some data manipulation with that data before Alan can use clickers in class successfully.

To register your clicker, fill out this form.

Your clicker number is a six-digit code on the clicker (see form for examples), a mixture of numbers and letters OR just numbers.

That form requires you to use your Reed credentials. If you are having problems accessing the form,

1. open a NEW browser (if you’re working in Chrome, open Firefox, or Safari, or …)
2. login at weblogin.reed.edu
3. try to access the form again

If that still doesn’t work, you can send me an email with:

• Your full name (First Last)
• Your Reed email handle (everything before @reed.edu)
• Your lecture section
• Your clicker number (six-character code on back of clicker)

If you have any questions or significant confusions, let me know — kbott@reed.edu.

What happens if you cross Lady Gaga with an underpaid biology graduate student? The Hui Zheng lab at the Baylor College of Medicine has the answer and it turns out to be a tricky combination of dominant and recessive genotypes.