Bond Order Goes under the Microscope

Posted on September 20, 2012 by alan

The 2012 Sept 17 issue of Chemistry & Engineering News ("C&ENews" is what we call it) begins with an article, Bond Order via Microscopy. A team of scientists at IBM's Zurich research center used a scanning probe microscope to investigate electric fields in a large flat aromatic molecule. The images they generate look surprisingly like the bond pattern in the molecule. If you want to get even closer to this project, check out their research publication and microscope images in the 2012 Sept 14 issue of Science magazine.

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Lecture slides (Day 5) for hybrid & molecular orbitals

Posted on September 17, 2012 by alan

You can download the slides that I showed last Wed/Thur (Sept 12/13) here.

I didn't get to show all of the slides, but if I could have, I would have divided the talk into three sections:

  • what you already know (from Chem 101)
  • the creation of MOs by combining AOs (or HOs) and the importance of overlap
  • examples of MOs

There are some really beautiful photos of bonding MOs, and even a few antibonding MOs, in the third section. Please look them over carefully. Make sure you can say the following about each MO:

  • is it bonding or antibonding
  • is it sigma or pi
  • what atoms are involved
  • what atomic (or hybrid) orbitals are involved
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Learning objectives (Day 5) for hybrid & molecular orbitals

Posted on September 16, 2012 by alan

I have prepared a list of learning objectives and study tips for last Wed/Thur's (Sept 12/13) class. You can download them here.

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Challenge Problems + Molecular Modeling Questions = Answers

Posted on September 11, 2012 by alan

I promised that I would post answers to the challenge problems in the learning activities and I have also received requests for 'answers' to the molecular modeling activity (#2). Here are some answers and comments.

Keep in mind: many of the questions in the learning activities are designed to help you build concepts. They are not "problems" in the usual sense and they don't reflect the kinds of problems that might appear on exams. Your book's end-of-chapter problems offer a much better idea of what you can expect exam-wise.

Learning Activity #3 – Answers to Selected Questions & Challenge Problems

Learning Activity #4 – Answers to Selected Questions & Challenge Problems

Molecular Modeling #2 – Answers to Selected Questions

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Beyond Oil and Water

Posted on September 7, 2012 by alan

Organic chemistry is filled with mysteries. The measurements involved in this week's experiment (solubility of alcohols in water) are straightforward, but scientific understanding has not really kept pace. Why do some liquids mix and others separate into distinct phases (that are usually mixtures) is still a mystery with cutting-edge applications.

A perspective article in the 31 Aug 2012 issue of Science magazine (DOI: 10.1126/science.1223728) wonders whether "the organization of cellular compartments may be driven by liquid phase separations". Cell biology meets organic chemistry.

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Vaux Swift Watch 2012

Posted on September 2, 2012 by alan

Chapman ChimneyThis post has nothing to do with o chem, but I think watching 5000+ small Vaux swifts swarm and then roost in the Chapman School chimney is one of the best FREE displays of urban wildlife you will ever see. Fortunately, the timing and location are perfect for Reed students. Head towards the Chapman Elementary school in NW Portland (#15 Bus will get you very close) on any night in early-mid September. Arrive about 30-60 minutes before sunset (7:00-7:30 arrival during Labor Day weekend) if you just want to see birds. Or, bring a picnic and a ball if you want to hang out in the park next to the school before the birds put on their show. The warm late-summer evenings are perfect for an outdoors off-campus adventure.

This event is not to be missed

Some helpful info for swift viewing:

Directions: The chimney is located at the west end (hilly side) of Chapman Elementary school. The school is located next to a park on NW 25th between NW Pettygrove & NW Raleigh. After you see the swifts, you can walk over to NW 23rd for dessert – many many establishments will be happy to serve you between 8-10 PM. Map
Best viewing: Get there about 20 minutes before sunset and watch the birds collect and feed. It takes awhile for all of them to go into the chimney so you'll be there after sunset (full moon tonite). Most people watch from the hillside on NW Pettygrove, but be kind to the neighbors.
Portland Audobon web info

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Learning Activity #2 – Corrections

Posted on August 30, 2012 by alan

Some corrections and clarifications for Learning Activity #2 follow. Let me know if you have other suggestions.

  • #DU. A ring and a double-bond both count as 1 DU. Consider some three-carbon compounds. CH3CH2CH3 is propane, the saturated molecule. CH2=CHCH3 is C3H6. This molecule is one H2 short of saturation (1 DU). Cyclopropane, (CH2)3, contains only single bonds in a three-atom ring. Because its molecular formula is C3H6, it is also one H2 short of saturation (1 DU).
  • Model 4. The definition of alkane might be reworded to make it clearer. Let's try alkane = saturated hydrocarbon.
  • Fact 2.3 gives an incomplete definition of branched alkane. A branched alkane must contain at least one methine (CH) group OR one quaternary C.
  • The right-hand structure in Fig. 2.5 is incorrect. Add another CH3 group to the left end of the molecule so that there are 8 C's in the chain.
  • Re-word Q#19 to read, "Circle each group of C in Fig. 2.5 …". The idea is to draw a single circle around each alkyl substituent.
  • Q#20-22 might lead to some confusion (Sorrell will straighten you out). An alkane is a molecule in which all of the C and H bonding patterns are obeyed. An alkyl group contains one C with only three bonds, a rule violation. Thus, methyl is derived from methane. Q#20-21: the suffix that methyl and ethyl share is 'yl', not 'ethyl'. Applying this in Q#22 leads to CH3CH2CH2 = propyl and so on.

Friday, Aug 31 update. Several students called my attention to an apparent contradiction in Model 6 and Fig. 2.6. The molecule on the left is named 2-ethyl-1,4-dimethylcyclohexane. This name appears to contradict the rule given in Model 6 that states, "C#1 is the ring carbon bonded to the substituent that comes first in the alphabet (prefixes like “di” and “sec-” are ignored)". The rule suggests 'ethyl' is located at C#1, but the name that was provided clearly assigns a methyl to C#1.

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William Perkin? Meet Silas Cook!

Posted on August 28, 2012 by alan

Organic chemistry has a long history. This week we took a look at William Perkin, whose "unsuccessful" preparation of quinine spawned an entire industry, and Silas Cook, Reed '99, who recently supervised the first short "total" synthesis of artemisinin.

A closer look at the following web pages reveals that I reported some dates incorrectly in class: Queen Victoria wore a mauve-colored dress, but not until after the Royal Exhibition of 1851 was just a memory.

A nice book on the subject of Perkin, mauve, etc., is Mauve: How One Man Invented a Color that Changed the World. You can also learn quite a bit at these links:

  • William Perkin, 1838-1907. The teenager who "dyed" Queen Victoria purple
  • August Wilhelm von Hofmann, 1818-1892. The professor who took on a precocious 15-year-old assistant. Wikipedia also describes him as the first lecturer to make use of molecular models
  • Quinine, an early treatment for malaria obtained from the cinchona tree
  • Artemisinin, a "new" treatment for malaria obtained from sweet wormwood
  • Mauveine, the dye that transformed commoners into royalty
  • Silas Cook (Reed '99), Chemistry Department, U. Indiana. His Reed thesis title was: "The synthesis of 3,5-bis(carboranyloxy)benzaldehyde : the precursor to a novel boronated porphyrin for use in boron neutron-capture therapy"
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MUST READ: O-Chem Week #1

Posted on August 26, 2012 by alan

Hi, This is Alan Shusterman, your Chem 201 instructor.

Classes get underway tomorrow and the first o-chem lecture will be in Eliot 314, but o-chem will actually start earlier in the day for some of you. Confusing? Let me tell you exactly what you need to know.

Lecture this week. There are two lecture sections for Chem 201 this year: MW 3:10-4:30 & TuTh 10:30-11:50. Both meet in E314. The caps have been lifted a bit in order to make room for 82 students (45 in MW F01 and 37 in TuTh F02). Please attend only the section that you have registered for. If you are still trying to add this class, you must come see me and persuade me to sign an ADD form because online registration is closed.

CLICKERS this week. I plan to use clickers starting on Day 1. Bring your clicker to every lecture. If your clicker needs to a little tender care or a juicier battery, take it to the Bookstore on Monday morning. If you can't find your clicker, you can buy one at the Bookstore.

>>> LAB THIS WEEK <<< Labs will meet every day this week, starting tomorrow. We have four lab sections for Chem 201 this year: MTuF 1:10-5:00 and Th 12:30-4:20. Lab lecture takes place in Psych 105 for all students on F, 9-9:50. Please attend only the section that the Registrar has placed you in. (Note: the Registrar reassigned several students to new lab sections last Friday nite so your schedule may have changed.) If you were on a waiting list or if you would like to change lab sections, you will need to come see me and persuade me to sign an ADD form. If you absolutely cannot make it to your assigned lab section, then please come to the section that you would like to be in. Here's our tentative lab schedule for this week:

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Preregistration for Fall 2012

Posted on April 17, 2012 by alan

Chem 201 will experiment with a new schedule in Fall 2012 (but Chem 202 will stick with the traditional schedule). So for 201 only:

  • Two lecture sections to choose from: MW 3:10-4:20 OR TuTh 10:30-11:50. They will cover identical material. The only difference is when they meet. Students are asked to attend only the section that they have signed up for, but this rule will be relaxed in case of student illness. So preregister for one section.
  • No conferences (but Chem 202 will have Thursday conferences)
  • Lab days are MTF, 1:10-5:00 (no W lab in the fall). Students are asked to attend only the section that they have signed up for. It is not unusual for students to swap lab sections during the first week of the semester (and if enrollments are sufficiently high, we will add a fourth lab section, but we aren't there yet). Preregister for one lab section.
  • Lab lecture has moved to F 9:00-9:50. Attendance at lab lecture is not required and I will permit students to sign up for other 9 AM classes that might conflict with the lab lecture. That said, you are still responsible for all of the material presented in lab lecture and I strongly discourage students who have a conflict from taking the F afternoon lab.

The prerequisites for Chem 201 are Chem 101/102, lecture + lab, or their equivalent. Students who have not completed the prerequisites cannot preregister for 201. This includes students who plan to take the equivalent of 101/102 during the summer.

Students need to provide evidence of satisfactory completion of summer (or other transfer) courses to Reed's Registrar's Office before SOLAR will allow them to preregister for Chem 201. No exceptions. However, I will allow students to use the following loopholes at the end of the summer/start of the Fall semester so that they can pre-register and settle their schedule and so that we can get a more accurate count of enrollment:

  • End-of-summer loophole #1: if you bring me a signed note on Th-F, Aug 23-4, from your summer introductory chemistry instructor (email is also acceptable) that says you have completed the entire intro chem sequence, lecture and labs, with grades of C- or better, I will override SOLAR's prerequisite requirement so that you can preregister for Chem 201. You will still need to file your transfer documents with the Registrar's Office ASAP.
  • End-of-summer loophole #2: if you are taking intro chem at PSU this summer, your final exam will probably be held Aug 24 so you probably won't have a final grade until classes start at Reed. If you believe that you are earning a passing grade in lecture and lab going in to your final week of PSU classes, simply ask the instructor(s) of your third term lecture and lab to email me your academic status ("status" means confirming that you passed the first two terms of intro chem lecture/lab + confirming that there is a highly likelihood that you will pass the third term lecture/lab). You will still need to file your transfer documents with the Registrar's Office ASAP once they become available.
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