Chemistry 13H
Spring 2003

This www site is still very much under construction and will be updated continuously throughout the semester.
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Professor Paul S. Weiss
Office: 407 Davey Laboratory
Phone: (814) 865-3693
Instant Messenger: PSWeiss
Office Hours: Drop in or by appointment
Send e-mail to Paul

Aministrative Assistant: Steve Bumbarger
Office: 415 Davey Laboratory
Phone: (814) 865-7817
AIM: catsman4

Grader: Matt Sandel
Phone: (814) 863-8220, (267) 994-6005
AIM: Matt Sandel

Our Amazing Demonstrator: John Cryder
Office 12 Osmond (at the front of the lecture hall)
Phone: (814) 865-5542

We will have excellent guest lecturers. Stay tuned.


While we will use Chemistry: The Central Science, by Brown, LeMay and Burnstein, 9th edition.  We will also use much supplementary material and www links.

Learning in Chem 13H

This is an exciting course for many reasons. We are able to cover many of the highlights of chemistry in a relatively informal way. This introduction is meant to guide you through many future years of scientific thinking and discussion, citizenship, and possibly even more chemistry.

Much of what you learn, you will learn on your own or from each other. This will allow us greater latitude in class. For instance, nearly every Friday class will be a discussion. If you have topics to discuss and know in advance, let us (instructors and classmates) know so that we can prepare for a higher level discussion.

While we will cover everything in the regular (Chem 13) version of this course, we will do it much faster (!) in order to allow us to pursue many other additional topics. This will require a great deal of work on your part. Please be prepared for it and budget the time for it. Anticipate that the lectures, the readings, and the homeworks will be complementary rather than overlapping. You will be responsible for the material from all of these sources. Similarly, your participation in class is required both for discussions and for the education of your classmates and professor. There is little that we plan to say that is so critical that a good classroom discussion would not be preferable.

Unlike other general chemistry classes, we will cover how it is that we know what we think we do and how we test that understanding. We will develop an understanding of what experiments and theory are required to answer fundamental chemical and scientific questions.

Some chemtouristic sites to visit:

The Elements.
Analytical Chemistry Basics
Analytical Chemistry Instrumentation

Portraits of Scientists and Pictures of Instrumentation
Photography Information at Kodak.
Comets from Sky and Telescope magazine.
How a scanning electron microscope works.
The Bends Story
Comment on the bends by Prof. Gold
A little information on rechargeable batteries.
Something on Aluminum.
Quantum control of atoms, etc.
Radon information from the US Geological Survey.
Dupont Nylon page.
Magnetic Resonance Image of a brain.
View biological molecules at NIH's Molecules R Us.
Enzymes -- 3D Views and related links.
Scanning probe microscopy (our research) discussion. See my group's main web page and associated links.
Natural radioactivity and other links.
Feynman Lecture: "There's Plenty of Room at the Bottom"
Energy conversions and Physical Constants from NIST
Stereo images at the exploratorium.

Seminars in the Eberly College of Science.

Monday 13 January 2003 (Lecturers: Paul Weiss, Joe Keiser)
Introduction (Weiss), Laboratory Introduction (Joe Keiser), Single Molecule Measurements

Williams Syndrome information from the Williams Syndrome Foundation.
Fluorescence in situ hybridization (FISH) is used to probe chromosomes using fluorescent labels. We talked about "chromosome paints."

There are commercially available probes. Here is a quick summary on genomics.

Wednesday 15 January 2003
Measurements of Single Molecules in Biology and Chemistry II

HW Due:
Find a journal article from Science or Nature that discusses single molecule measurements.
Provide a summary of the article in ca. 10 sentences. Discuss the goals of the work and the technique(s) used.
Attach a copy of the article to the homework.

Friday 17 January 2003

Single Molecule Measurements III

Optical tweezers work at NIST. Check out the quicktime movie.
Building simple optical tweezers.

HW Due:
Decide on a favorite energy unit.
In this unit give an estimate of or the range for:
Visible photon energy
Typical chemical bond energy
Ionization potential of one common element
Also find the energy range for UV-A and UV-B light

Monday 20 January 2003

Discussion Class on Nanofabrication

(Discussion Monday instead of Friday this week.)

Read: Chapter 15, Sections 4.2-4, 16.1-5.

HW Problems Due:

  1. What region of the spectrum (give both energy and wavelength ranges are useful for:
    Core-level spectroscopies (e.g. X-ray fluorescence discussed in class)
    Valence shell spectroscopies
    Vibrational spectroscopies
    Rotational spectroscopies
  2. What color is table salt when: in a flame, in a shaker, or spread lightly on a table or piece of paper? Why?
  3. Find an article on fluorescence published since 1 January 1999 in an archival journal. Give the full citation including: Author list, journal, volume, page number, and year. Write ca. five sentences describing what the authors were trying to learn. Your article must be printed (whether or not you capture or read it electronically).
    Once again, try starting with the top journals like Science and Nature.

Wednesday 22 January 2003

Acids & Bases I

Mass spectroscopy Tutorial (replacing a broken link).
Mass spectroscopy and some others, too, including nuclear magnetic resonance (nmr).

HW Problems: 16.3-8, 11-14, 16, 17, 28, 31-34, 82, 91, Jenna's extra problem for you!
Additional HW: Make up a problem that you feel best tests your knowledge of Acids & Bases up to now. It should not be a trivial extension of the assigned problems.
(NB- You will do this for every homework assignment and these will always be graded!)

Friday 24 January 2003

Acids & Bases II

Acids & Bases Reading: 16.6-7 and 16.8-11.
HW: 16.38-50 (evens), 55-58, 84, 88, 89. Also, your own problem as described in class.
Jenna's extra problem for you!

Monday 27 January 2003

Acids and Bases III & Buffers

Read: 17.1 (common ion effect),17.2-3 (buffers & titrations), 7.1-4 (periodicity)
HW: 16.59-64, 67-70, 73-75, 78,80.
17.1-3,5-8 (common ion effect & buffers), Allison's famous cheese problem
Also, your own problem as always.

Check out Prof. Will Castleman's work, including solvation in clusters.

Wednesday 29 January 2003

Acids & Bases III
HW: 7.6,14,18,26,30, 17.9-12,16,18,19,25-27,29

Friday 31 January 2003
Buffers and Titrations, cont.

NIST Optical Tweezers Page including the Adhesion Movie
1997 Nobel Physics Prize for Optical Trapping
Mara Prentiss's Optical Tweezers Tutorial

No homework. Sorry...

Monday 3 February 2003
Periodic Trends
Solubility, cont.
Read: 7.5-7, 4.2, 17.4-6
HW: 7.43,46,52,54,55, Hallie's solubility problem, Jenna's pH problem.
How are the following measured quantitatively: ionization energy, electron affinity?
(This latter problem will be graded in addition to the normal homework.)

Wednesday 5 February 2003
Measurements of Periodic Properties Discusssed & Acid Strength vs. Structure
Read: Sections 19.1-3.
Explain the relative acid strengths of:
H2SO4 vs. H2SO3 and
H2SO4 vs. H2SeO4
HW: 17.35-37,40,43,46,49-51,53,55,56,86,89

How are the following measured quantitatively: covalent & ionic radii?
(This latter problem will be graded in addition to the normal homework.)
Find a paper that includes optical trapping measurements that was not mentioned in class, from the years 1998-2003, and is in one of the following journals: Science, Nature, Proceedings of the National Academy of Science, Journal of Biological Chemistry, or Biophysical Journal.
(Hint: if you saw a paper you liked, do a citation search on it.)
Provide a summary of the article in ca. 10 sentences. Discuss the goals of the work and how optical tweezers were used. What other techniques were used and how?
Attach a copy of the article to the homework.

Friday 7 February 2003
Diffraction Discussion

The diffraction demo is from a visitor we had at Penn State: Prof. Amand Lucas, of Namur, Belgium.
He prepared it for a TV show on How X-rays Cracked the Structure of DNA. An elegantly simple optical diffraction demonstration with an inexpensive laser pointer is used to show the way in which x-rays can reveal the structure of crystals in particular the double helix structure of DNA.

Revealing the Backbone Structure of B-DNA from Laser Optical Simulations of Its X-ray Diffraction Diagram, A. A. Lucas, Ph. Lambin, R. Mairesse, and M. Mathot, Journal of Chemical Education 76, 378 (1999).

Monday 10 February 2003

Thermodynamics I:
Spontaneity, Enthalpy, Entropy

Read: Sections 19.4-7
HW: 19.1-2,4-5,14-15,28.
From a table (cite the table): find the C-C bond distances for single, double, and triple bonds.
Give the C-C single, double, and triple bond spacings for a specific molecules for each (say which molecules and cite your sources).

Wednesday 12 February 2003

Thermodynamics II:
Free Energy, Equilibrium Constants, and Work

HW: 19.35-38,43,44,46-49,57-58,61,65

Friday 14 February 2003
Nanoscience that Paul Loves (it is Valentine's Day, after all!)

Find a paper on nanoscience from the years 2000-2003 that is in one of the following journals: Science, Nature, or Proceedings of the National Academy of Science.
(Hint: if you saw a paper you liked, do a citation search on it.)
Provide a summary of the article in ca. 10 sentences. Discuss the goals of the work and how the measurements were performed. What techniques were used and how?
Attach a copy of the article to the homework.

Links of interest:
National Nanotechnology Homepage
The Scientific American Article on Molecular Electronics I mentioned.
The Lieber Group Page at Harvard.

Carlo Montemagno's hybrid biological molecular motors in Scientific American.
More Molecular Motor Links

Monday 17 February 2003 SNOW DAY! Yikes! Good thing we are ahead!
Thermodynamics III
Introduce Electrochemistry

Wednesday 19 February 2003
Thermodynamics IV:
Equilibrium Constants, Work, and Measurements
Electrochemistry II
Project: Select your element for the poster and paper (from a hat!).
Read: Oxidation Numbers pp.121-122, 20.1-4.
Kir's Annie Oakley problem.

Pick out a recent journal article (try Science or Nature) of keen scientific interest to you and write a 5-10 sentence critical synopsis. Choose a topic that involves chemistry in some way. Attach a copy of the paper.

You may use www resources as a guide, but you must use the archival literature as your source.

Friday 21 February 2003

Electrochemistry III: Batteries, Electrolysis, Corrosion

HW: Assign oxidation states to five molecules or molecular ions, each containing at least three different elements.
Read: 20.5-9
HW: 20.1-3,5,6,8,10-14,25,28

Erica's elemental problem.

Monday 24 February 2003
Materials I: Polymers & Ceramics
Read SECTION 24.1-24.5
HW: 24.1-4,7,8
Turn in abstracts for posters (a few lines each)
Show energy level diagrams for the filling of the d orbitals for d0-d10 octahedral complexes. Show which electron numbers can have high and low spin complexes and show both the high and low spin electron configurations.

Wednesday 26 February 2003

Materials II: Semiconductors

Friday 28 February 2003

Exam I Review
Bring questions/problems
As requested, here is a pdf of last year's midterm exam.

Monday 3 March 2003
Exam I

Wednesday 5 March 2003 (Guest Lecturer: Prof. Anne Andrews)
Drugs of Abuse

Friday 7 March 2003 No class! Enjoy spring break. Work on your posters -- bring references with you!
Poster work

10-14 March 2003
Enjoy Spring Break!

Monday 17 March 2003
Go Over Exam
Transition Metal Ions & Complexes I, Metallurgy

Read: 23.7-8
Reread 24.1-24.5


Wednesday 19 March 2003
Transition Metal Ions & Complexes II, Metallurgy

Read 17.4-6.
Describe one enzyme and one therapeutic reagent utilizing a complexed transition metal. Explain in one paragraph for each what it does and where it operates.
Suzanne's carbon monoxide problem.

Thursday 20 March 2003
Poster abstracts due by 5 PM!

Download template here (right click and use SaveAs).
Rename it YourName13H1abs.html

Fill in the title, name, element, and abstract sections, then email to Paul & Steve by clicking here and including the file as an attachment.

Friday 21 March 2003
Transition Metal Ions & Complexes III, Metallurgy
Materials II: Semiconductors

Sunday 23 March 2003
600 PM Elements of Life Poster session -- 2nd Floor Osmond/Davey overpass.
You will have four minutes to present followed by one to two minutes of discussion.

A few thoughts:
Keep a single focus.
Practice your presentation out loud! Work through rough spots repeatedly (memorize words if necessary).
Props and assistants are ok, if justified by your presentation.
Use large, readable fonts. More detail can be in your presentation than on your poster.

Pizza provided.

Mg Kelly Welsh
Ca Lindsay Dickey
Zn David Kalos
Na,K Phil Smith
Li Kim Clemens
Fe Andy Chang
Ni Lisa Dudek
Cu Karl Yaeger
S Regina Heineman
Se Anya Williamson
Si Lauren Versagli
I Susan McCall
Cl Emily Herron
F Christine Olmeda
Pt Kim Downes
Hg Erin Carter
Ba Steve Tumasz
B Fujun Wu
Tc* Christina Cress

Elements of Life Poster session abstracts

Monday 24 March 2003
Hydrogen and Oxygen

Read: 23.1-3

Wednesday 26 March 2003 (Guest Lecturer: Tom Mallouk)
Fuel Cells

Read: 23.4-6
HW: 23.1,9-13,23,24,27

Friday 28 March 2003
Self-Assembly Discussion
Problem: Where do the values for terrestrial abundances of the elements originate, how are they estimated, and what do they estimate?

Read: 22.7-8
HW: 22.45-48,51-55,58-60

Monday 31 March 2003
Nitrogen, Carbon, Fullerenes and Like Molecules
Susan McCall's Iodine Poster.

Read: 22.1-2,5-6
HW: 22.5-7,10,11-16,19-20,31-35,40-42

NSF Fullerene Blurb.
Rick Smalley's www page at Rice University.
New York Times article on fullerenes.

Wednesday 2 April 2003

Kinetics I

Choose a metal that was not discussed in the poster sessions (no transuranium elements without prior permission).
In one page or less:
1) Identify its source (location, chemical identity, impurities).
2) Describe how it is collected.
3) Describe how it is reduced (if required).
4) Describe how it is purified.
5) Find out how much it costs as elemental metal.

Friday 4 April 2003
Materials Discussion
Papers due for +5 point credit

Monday 7 April 2003
Kinetics II
Papers Due (see requirements below).

You should have already read Chapter 14. Please review it for class.

Wednesday 9 April 2003
Kinetics III, Enzymes
Links on reaction dynamics:
H+H2, the simplest reaction. Calculations from Jim Anderson's group at Penn State.
1986 Nobel Prize in Chemistry.
HW: 14.2,4,5,9,12,16,17,23,24

Abstracts for second posters due.

Friday 11 April 2003
Enzymes II: PCR
Nuclear Chemsitry I


Monday 14 April 2003
Nuclear Chemistry II

Read: 21.1, 21.4-6
HW: 21.1-6,12,13,16,19,22,23,25

600 PM Frontiers of Materials Poster session -- 2nd Floor Osmond/Davey overpass.
As before, you will have four minutes to present followed by one to two minutes of discussion.
Dinner provided.

Electroceramics Lauren Versagli
Superhard Silicon Nanospheres Kim Clemens
Smart Silicon Dust Emily Herron
Pyrolytic Carbon Christina Cress
Kevlar Karl Yaeger
Modern Use of Synthetic Polymer: the Properties of Teflon Phil Smith
Polystyrene Lindsay Dickey
Stealth Technologies Steve Tumasz
Organic Polymer Conductors: Polythiophenes Erin Carter
Peapod Nanotubes (Buckyballs in Buckytubes) Lisa Dudek
The Fourth Phase: Liquid Crystal Displays Andy Chang
Shedding Light on Photochromic Lenses Kim Downes
Shape-Memory Alloys David Kalos
Superconducting Niobium Wires Fujun Wu
Olestra: Fat-Free Friend or Foe? Regina Heineman
Dermagraft TC: A New Skin for Burn Victims Susan McCall
Self-Assembled Porous Polymer Cell Scaffolds Kelly Welsh
Plastic, Heal Thyself: Self Healing Polymers Anya Williamson
Disinfected Dorms Without Cleaning?! The Effect of Cationic Polymerized Surfaces on Bacteria Christine Olmeda

Wednesday 16 April 2003
Quantum Mechanics
Introduction to quantum mechanics from the University of Washington.

HW: 14.28-31,34,35,39,40,43,46,47
Allison's problem with Matt (that does not sound right, hmmm).

Friday 18 April 2003
Nuclear Chemistry III
Read: Chapter 21.7-8
HW: 21.28-31,34,35,40,43,46,47

Monday 21 April 2003
Nuclear Chemistry IV:
Half-Life, Mass-Energy Conversion
and Discussion of Breeder Reactors, Nuclear Waste Handling and Disposal

Schedule your final exam! Available dates:
Friday 26 April, Monday 29 April, Tuesday 30 April, and Wednesday 1 May

Wednesday 23 April 2003 (Guest Lecturer: Dr. Charlie Sykes)

Friday 25 April 2003 (Guest Lecturer: Dr. Charlie Sykes)

Monday 28 April 2003
Course Review I
HW: Write a 5-10 sentence description of the function of an enzyme that we did not cover in class or posters. You may include mechanism and structure as appropriate.

Wednesday 30 April 2003
Course Review II

Individual Oral Final Exams

Held in 407 Davey. Expect the exam to take ca. 45 min.
As announced, if you received less than 85% of the homework points, your final exam will be a rigorous test of general chemistry with special emphasis on the homework that you missed!

11:15 AM Christina Cress
1:00 PM Lindsay Dickey
2:00 PM Emily Herron
3:00 PM Andrew Chang
4:00 PM Steve Tumasz
4:45 PM Kelly Welsh

Thursday 1 May 2003
Individual Oral Final Exams

Held in 407 Davey.

10:00 AM Kim Clemens
11:00 AM Fujun Wu
1:00 PM Christine Olmeda
2:00 PM Anya Williamson
3:00 PM Regina Heineman
4:00 PM Karl Yaeger
4:45 PM Susan McCall

Friday 2 May 2003
Final Discussion Class

HW: Summarize in 5-10 sentences the most important thing you learned this semester. Find a related literature reference that goes beyond our discussion. Prepare and answer a question on it.

Individual Oral Final Exams

Held in 407 Davey.

11:15 AM Erin Carter
1:00 PM Kim Downes
2:00 PM Phil Smith
3:00 PM Lauren Versagli
4:00 PM Lisa Dudek
4:45 PM David Kalos

Discussion Topics Suggested

Bring in topics to discuss. These can be aligned to the topics we are covering, but do not need to be. If we can discuss them intelligently, we will do so. If not, we will find some references and cover them next week. Every Friday class will work this way.

Already covered
Optical tweezers.
Single molecule measurements.


1. Class participation: 20%
2. Homework: 10%
3. Paper and poster presentation of researched topic (elements of life -- specific elements will be assigned in class): 20% (10% each)

Paper Requirements:
The paper should be approximately 10 pages in length, double spaced (double spacing is important to leave room for my comments) in a 12 point font, with 1" margins all around. The paper should include figures and complete references (not www references). The figures will not count in the length. Please take into account the comments that you get from your presentation in preparing your paper.
4. One in-class exam (1 hr) and one poster on materials: 30% (15% each)
Note that pre-approved make-up or conflict exams will be oral exams. No paper is required for this second poster. 5. Oral final exam: 20%
If you received less than 85% of the homework points, your final exam will be a rigorous test of general chemistry with special emphasis on the homework that you missed!
Note that my ability to give oral final exams depends upon having 30 or fewer students in the class by the end of the semester.

TOTAL: 100%

All Penn State policies ( regarding ethics and honorable behavior apply to this course.

Homework requirements.

21 April 2003