You can download a copy of tonight’s lecture here.
Author: alan
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Atomic Force Microscope Takes Pictures of Chemical Bonds
Atomic force microscopy (AFM) is a imaging technique that works on a completely different principle from optical microscopes. Instead of magnifying light waves, an AFM device passes a needle-like probe over a surface and constructs an image of the surface based on subtle variations in the strength of probe-surface forces.
AFM and related imaging techniques generated lots of buzz in the 90’s by providing images of molecules, even individual atoms, on surfaces. AFM has returned to the front page with even higher-resolution images that track the pathways electrons take in chemical bonds, even hydrogen bonds. Compare the white tracks in the AFM image (left) with the pattern of covalent and hydrogen bonds expected from the structural formulas (right) (click image to enlarge).
For an easily digested description, see “Hydrogen Bonds Visualized” in C&ENews, 30 Sept, 2013. Or check out the original research article by J. Zhang et al, “Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy” (Science, 26 Sept 2013, DOI: 10.1126/science.1242603). -
Molecular Modeling Activity Collection
Here are links to all of the molecular modeling activities we have done in class (these links also can be found on the Classes page).
- Activity #1 – Build/sketch models with Spartan ’14
- Activity #2 – Potential maps, intermolecular interactions, hydrogen bonds
- Activity #3 – Orbital shapes (atomic, molecular), HOMO-LUMO gap, electron density surfaces, charge delocalization
Links will be added as needed.
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Office hour canceled for doctor’s appointment
The office hour scheduled for Monday, Sept 23, is canceled. I have a doctor’s appointment in NE Portland at that time. I will be on campus for lab on Monday and will answer questions that you bring there. Normal office hour schedule resumes on Wednesday, Sept 25, 10:30-11:30.
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Bring your model kit to class next week
We are going to be building 5- and 6-carbon rings in class next week. I don’t have enough atoms in my bucket for more than a couple of rings so please bring your own.
The model kits that we used in class this week can be obtained from the Chemistry stockroom for a very modest fee. If you can get gently used models from a previous o chem student, that’s fine too.
Remember, you will want to have a model kit with you when you take the next short exam so why not get one now and start practicing with it?
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Exam #1 – getting ready & what to expect
The first short exam will be in-class Tue-Wed (Sept 17-18). It will run about 25 minutes. The brevity of the exam can make the experience feel a little intense so here are a few notes on how to prepare and what to expect:
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Sample Lab Notebook
The attached file comes from last night’s lab lecture.
Page 1 displays a typical RIGHT-hand page. Blue describes things that need to appear. Red & black show what these things actually look like, i.e., your notebook will look like the red & black stuff only.
Page 2 just lists some features of the notebook. Please read the appendix Keeping a Notebook in the lab manual for more complete information.
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201 Web Site: Changes & Updates
I’ve made a number of changes on the web site this weekend. Let me know if there’s something that you’d like to see.
- Classes page – this replaces the old Syllabus page. Go here to find out what we are covering and when. Also go here to download learning activities, answers, and other in-class handouts. Warnings: 1. I’m still working on the schedule between class #14 (RF before Fall Break) and Thanksgiving. 2. I haven’t found all of the old links to Syllabus yet – if you see one, let me know what URL it appears on.
- Conferences page – Go here to download conference problems and answers
- Exams page – Go here to find exam policies, dates, old exams. The latter part of the exam schedule hasn’t been set – stay tuned.
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Lab schedule for Week #1
Not everyone has found a place in lab yet (see previous post), but that’s OK because we aren’t going to do any ‘wet’ experiments during the first week of classes. Here’s the plan for week #1 broken down by day and lab section:
- Sept 2, M – Labor Day (no class)
- Sept 3, Tu – Tu lab meets at Chemistry loading dock at 1:10 PM for fire extinguisher training. From there go inside to C209 (our lab) for the first half of a safety and lab policy meeting (starts at 1:30). Next, if you haven’t already done so, read the relevant portions of the Chemistry Safety Manual. Complete the Safety Quiz that will be distributed in lab. Sign the Safety Contract. Meet back at C209 at 3:00 to go over the Quiz and turn in your signed Safety Contract and Quiz.
- Sept 4, W – same as Tu
- Sept 5, Th – same as Tu
- Sept 6, F – same as Tu, but meet at loading dock at 2:45 PM and in C209 at 3:15/4:30
If you are enrolled in the Tu or W labs, please attend on your lab day. If you are enrolled in the M lab or if you haven’t yet found a lab, you can attend any day, but W/Th are best and Tu/F are worst.
Wondering what is coming ahead? Check out the lab manual link and the lab calendar link (click on a blue box to see what is scheduled).
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Not in the lab (you want)? Patience…
61 students had signed up for lab lecture as of last Wednesday. As of today (Saturday), there are 68 lab students: 24 students in the M lab, 24 students in the Tu lab, and 14 students in the W lab (and 10 students on wait lists). We have room for 72. There should be room for everybody, but I have learned the hard way that allowing students to sign up for all of the classes they need (or want) independently of other students almost never produces a useful set of enrollments.
I don’t have a solution for any of this yet so I am going to spend the next few days playing ‘wait and see’. Here’s what I think will happen:
- The wait list students will come tell me their stories (why you need to take Chem 201 and why you need to be in the M/Tu lab instead of W)
- Some students will do us all a Big Favor (really!) and switch from M or Tu labs to the W lab
- The wait list students (and maybe others) will ask themselves some existential questions about class schedules: Do I need to take Chem 201 right now or is it something that can wait until another year? Do I need to take the course that conflicts with the W 201 lab right now or can that course wait until another year? Is there more than one way to be happy?
In the meantime some lab periods will slip by and we will approach the Add deadline (Sept 13). Don’t worry about missing lab. We won’t start ‘wet’ experiments in Chem 201 during the first (shortened) week of classes. But that’s the subject of another post …
