Preparing for Chem 201 – Summer Study Suggestions

Several students have asked me in the last few years, “What can I do this summer to get ready for Chem 201 next fall?”

A perfectly reasonable question, and one that deserves an instructive response. But I hesitate to answer. Why? Continue reading

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Summer Suggestion #1. Review key topics from Chem 101/102

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)?
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Summer Suggestion #3 – Study Organic Chemistry

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!

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Ring Flipping Apps & YouTube Videos

Understanding what molecules look like, how they move, what relationships exist between atoms, are all challenging mental tasks. Here are two tools that might help.

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Where do I put my CH3 groups in a condensed formula?

I’ve been getting a lot of office visits and emails over the same homework problem. Folks say, “I typed CH3CH2CH(CH3)CH(CH3)CH3” or “I typed CH3(CH3)CHCH…” or “I typed CH3CH(CH3)CH…” and it was marked incorrect. =(

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Molecular Model Kits – Is NOW the time?

The Day 3 materials offered a small taste of where we are headed next: the 3-D world of molecules. Carbon is tetrahedral.

Does this wedge-dashed diagram make sense? Can you rotate it in your head (rotate around any bond or any axis, rotate by any amount 90, 180, 240 degrees)? Can you the rotated figure? Can you reflect it through a plane of symmetry? Can you rotate and reflect and draw? One carbon is just the beginning, my friends!

Model kits are really valuable learning and thinking aids. What is more, I permit you to use models on quizzes and the final exam! (see Exams policies) If you would like to purchase a molecular model kit, I highly recommend the kit shown on the left. You can buy it at the Chemistry stockroom. $20. Cash. Or buy a (slightly, gently used and well-kept) kit from a former o chem student.

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Day 0 – the things you need to do BEFORE your first class

Welcome back to Reed. We have an exciting organic chemistry curriculum planned for Chem 201 and 202, and we will get off to a flying start so here goes…

Day 1 is our first day of classes. It will include a lecture for the MW section at M, Aug 27, 2:20 pm in Eliot 314 (the TuTh section starts the next day at 10:30 am) and a lab lecture for all students at M, Aug 27, 6:10 pm in Psych 105. Your attendance on Day 1 is absolutely required.

The following will tell you what you need to do on Day 0, the time before the first lecture, lab lecture, and lab. Please read and follow these instructions carefully. And see you in class! (Note: the following was sent to all students by email. Check your Inbox.)

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Making Sense of Electrons, Atoms, and Molecules

The discovery of the electron in 1897 was followed just 14 years later by the discovery of the atomic nucleus in 1911. In 1913 Bohr proposed a model of the hydrogen atom in which the electron made perfectly circular orbits around the newly discovered nucleus (proton) only to see his theory replaced by Schrödinger’s more general theory, wave mechanics, in 1926. Wave mechanics has dominated the thinking of chemists ever since, but it has hardly been the last word on the matter. More subatomic particles have been discovered, and other forms of quantum mechanics have been suggested over the years (matrix mechanics, density functional theory, …) including theories (quantum electrodynamics, quantum chromodynamics, …) that go far beyond the simplistic thinking of chemists.

So what really happens when two electrons, or perhaps an electron and a positively charged nucleus, get really, really close to each other? Wave mechanics turns to Coulomb’s law for help, and Coulomb states that the force between these particles varies inversely with the square of the distance between them, that is, the force is proportional to 1/r^2. This would imply that the force (and the potential energy associated with it) approaches infinity as r approaches zero. This can lead to disturbing thoughts (what keeps electrons from ‘falling into’ the nucleus?) and disturbing mathematical problems (how do I work with a formula that busts its way to infinity?).

Nautilus recently emailed me an old article (“The Trouble with Theories of Everything”, 1 Oct 2015) that looks into these disturbing corners of science and concludes, “There is no known physics theory that is true at every scale—there may never be.” Coulomb’s law, wave mechanics, you name it – are designed to explained certain phenomena that appear on certain scales of time, space, energy, and so. It may be possible to extrapolate them to other scales successfully, but there are no guarantees. Caveat extrapolator!

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Elemental Haiku

Carbon, C

Show-stealing diva,

throw yourself at anyone,

decked out in diamonds.

And that pretty much sums it up. Carbon is awesome.

Interested in seeing how the other elements fare when filtered through haiku paper? Check out Elemental Haiku (Science, 4 Aug 2017) or, even easier, find them in this interactive periodic table.

Note: element 119 has not been synthesized yet so the poet has already gone where no scientist has been (yet).

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Protecting Your Eyes During Next Week’s Eclipse and Beyond

What’s so special about the sunlight during an eclipse? Isn’t it the same old sunlight we see the rest of the time?

Yes, it is, but because the event is so interesting to look at, and because the normally blinding solar disk is partly blocked out, the temptation is to look, and look, and look. See “Chemistry explains why you shouldn’t stare at the solar eclipse without proper protection” (C&ENews, print 21 Aug 2017, online 14 Aug 2017).

The article explains the photochemical events that trigger retinal damage (the “heat” of the sunlight is not to blame) and it describes several options for safe viewing of the Sun. Here’s a bit from the article: Continue reading

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