Chemistry 13H
Spring 2000

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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

Secretary: Connie Smith
Office: 222 Davey Laboratory
Phone: (814) 863-0119
AIM: PSUConnie

Grader: Dave Richardson
Phone: (814) 862-7845 Note the newly corrected phone number! E-mail:

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 Brown, Lemay, and Bursten, 7th edition (the same book as used in Chem 12, 12H, and 13), 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 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.
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

Last week's seminars.
Here are this week's seminars for all of the Eberly College of Science!
Here are next week's seminars for the Eberly College of Science.

Monday 10 January 2000 Lecturers: Paul Weiss, Joe Keiser
Introduction (Weiss), Laboratory Introduction (Joe Keiser), Single Molecule Measurements

HW: Find this website (you have did it!). Turn in address on Wednesday 12 January.

How a scanning electron microscope works. (Thanks to Nick H for the link)

Wednesday 12 January 2000
Measurements of Single Molecules in Biology

Further: 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.
Optical tweezers work at NIST. Check out the quicktime movie.
Building simple optical tweezers. HW: Turn in class www site address.

Friday 14 January 2000

Single Molecule Measurements III

HW Problems:
  1. What color is table salt when: in a flame, in a shaker, or spread lightly on a table or piece of paper? Why?
  2. 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 about five sentences describing what the authors were trying to learn. Your article must be printed (whether or not you capture or read it electronically).
    Hint: Try starting with the top journals like Science and Nature.

Monday 17 January 2000

Acids & Bases I

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

Wednesday 19 January 2000

Acids & Bases II

Mass spectroscopy Tutorial including the Magnetic Sector Analyzer figure

HW Problems: 16.3-8, 11-14, 16, 18, 31-34, 82, 91
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 21 January 2000

Acid/base Problem Solving
Optical Trapping

Acids & Bases Reading: 16.6-7 and 16.8-11.
HW: 16.38-50, 55-58, 84, 88, 89. Also, your own problem as described in class.

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

Monday 24 January 2000

Acids and Bases III & Buffers

Check out Prof. Will Castleman's work on solvation in clusters. (Note: I have been having trouble linking to this site over the last few days.)

Wednesday 26 January 2000

Acids & Bases, cont.
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)
Also, your own problem as always.

Friday 28 January 2000
Mass Spectroscopy
HW: 7.6,14,18,26,30, 17.9-12,16,18,19,25-27,29
Find a paper in the literature from 1998 to 2000 that uses one of the techniques mentioned in the class handout on "Single Molecule Measurements" (lectures 1-2) to make single molecule measurements. Critically summarize the article in five to ten sentences. Be sure to include the reference for your article. (For the reference format, use the reference format of the journal.) You will find such articles in both Science and Nature. Attach a copy of the paper.
You may use www resources as a guide in your search, but you must use only the archival literature as your source.

Monday 31 January 2000
Periodic Trends
Read: 7.5-7, 4.5, 17.4-6
HW: 7.43,46,52,54,55
How are the following measured quantitatively: ionization energy, electron affinity?
(This latter problem will be graded in addition to the normal homework.)

Wednesday 2 February 2000
Measurements of Periodic Properties Discusssed & Acid Strength vs. Structure
Read: Sections 19.1-3.
Be prepared to explain the relative acid strengths of:
H2SO4 vs. H2SO3 and
H2SO4 vs. H2SeO4
HW: 17.31-34,40,43,46,51,52,55,56,81,89
How are the following measured quantitatively: covalent & ionic radii?
(This latter problem will be graded in addition to the normal homework.)

Please attend John Hopfield's Lectures this week if you can.
They are:
Wednesday 2 February 2000, 8 PM in 101 Thomas
Brains vs. Electronics: How Do We Think So Fast?

Thursday 3 February 2000, 4 PM in 117 Osmond
Color, Vision, and Smell: "More Is Different" Revisited

Friday 4 February 2000

Monday 7 February 2000

Thermodynamics I:
Spontaneity, Enthalpy, Entropy
Read: Sections 19.4-7
HW: 19.1-2,4-5,14-15,28.

Wednesday 9 February 2000
Exam Review of Material to date
Bring questions/problems
HW: 19.31,34-36,43,44,46-49,54,61,62

Please attend Ger van den Engh's Lecture, if you can.
1115 AM in S5 Osmond
Cell Sorting as a Tool for Genomics

Friday 11 February 2000
Discussion Class with Profs. Ger van den Engh and Barb Trask of the University of Washington Department of Molecular Biotechnology
Genetic Diseases and Their Treatment, Genomics
Bring Questions

Some students have asked if guests can come -- yes.

Please attend Barb Trask's Lecture, if you can.
1115 AM in S5 Osmond
Large duplications: functional complexities of the human genome

(No reading, homework. Use the time to consider discussion topics.)

Sunday 13 February 2000, 915 PM, 104 Osmond Dave Richardson

Special Review Session

Monday 14 February 2000 Happy Valentine's Day!

Exam #1
Covering through the lecture on Friday 11 February

Wednesday 16 February 2000 (Guest Lecturer: Dr. Alex Kandel)
Thermodynamics II:
Free Energy, Equilibrium Constants, and Work

Friday 18 February 2000
Snow day

Monday 21 February 2000
Go over Exam #1
Introduce Electrochemistry

HW: 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.

Read: 8.10, 20.1-4

Wednesday 23 February 2000

Thermodynamics III:
Equilibrium Constants, Work, and Measurements
Electrochemistry I
Project: Select your element for the poster and paper (from a hat!).
Read: 20.8-10
HW: 20.1-3,5,6,8,10,12-14,24,25

(These have not changed.)

Friday 25 February 2000

Electrochemistry II
HW: Assign oxidation states to five molecules or molecular ions, each containing at least three different elements.

Monday 28 February 2000
Electrochemistry III
Batteries, Electrolysis, and Corrosion
Read: 23.7-8

Wednesday 1 March 2000
(Read17.4-6 and 23.7-8, if you have not yet)
HW: 23.31,33-36,38,40

Friday 3 March 2000
Discussion on Chemical and Biological Warfare Agent Detection

4-12 March 2000
Enjoy Spring Break!

Monday 13 March 2000
Transition Metal Ions & Complexes I
Read: 24.1-2

Wednesday 15 March 2000
Transition Metals II: Color & Spin
HW: 24.1-4,9,10

Friday 17 March 2000
Continuation of our Discussion on Chemical and Biological Warfare Agent Detection
and the First Poster
Early Poster:
Cassie Konkle Mg
HW: Turn in abstracts for posters (a few lines each)
Show energy level diagrams for the filling of the d orbitals for d0-d10. Show which electron numbers can have high and low spin complexes and show both the high and low spin electron configurations.

Sunday 19 March 2000
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 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.

Heather Agnew Hg
Zeb Bartels Ni
Jenna Bartz Ca
Kevin Buck Zn
Paul Butterfoss Cl
Jason Clark Li
Edna Clogg Cu
Brian Edwards Fe
Loren Filson Cr
Andrew Glendening K/Na
David Goldstein Tc*
Nick Hartman Sr
Natalie Hepler Pt
Julie Hewett Sn
Samantaha Iivaei Si
Mark Losego F
Dan Lysko Ti
Rick Mellon Mn
Julie Norseen Co
Joanna Paulson Al
Evan Pickett Pb
Ellyn Schuette B
Stephen Segal S
Aaron Shoe Br
Kristin Slagle Se
Jackie Sturgeon Ba
Kristen Tirio I

Monday 20 March 2000
Hydrogen and Oxygen
Read: 23.1-3

Wednesday 22 March 2000 (Guest Lecturer: Lloyd Bumm)
Photography Discussion

Friday 24 March 2000
Nitrogen, Carbon, Fullerenes and Like Molecules
Read: 22.1-2,5-6
HW: 22.5-7,10,11-16,19-20,35-38,40-42,96-98

Monday 27 March 2000
Carbon and the Fullerenes, cont.
Review of Material since Exam #1
Read: 22.7-8
HW: 22.51-53,57-58,60-61,63-64,66-68

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

Identify whether you will take Exam #2 on 29 March or will have a poster on 9 April.

Wednesday 29 March 2000

No class.

Friday 31 March 2000 (Guest Lecturer: Anne Andrews)
Neurotoxicity and Drugs of Abuse

Monday 3 April 2000
Materials and Metallurgy I
Read: 23.1-3

Papers Due (see requirements below)

A talk of possible interest:
Genes and Cancer (Marker Lecture #1 of 2)
Harold E. Varmus, Memorial Sloan-Kettering Cancer Center and Nobel Laureate
8:00 p.m., HUB Auditorium, host: J. Martin Bollinger, Department of Biochemistry and Molecular Biology

Tuesday 4 April 2000
Talks of possible interest:
Mouse Model of Human Cancer (Marker Lecture #2 of 2)
Harold E. Varmus, Memorial Sloan-Kettering Cancer Center and Nobel Laureate
11:15 a.m., HUB Auditorium, host: J. Martin Bollinger, Department of Biochemistry and Molecular Biology
(PLEASE NOTE CHANGE OF TIME AND LOCATION -- Earlier report said: 4:00 p.m., 101 Thomas Building)

Production and Properties of Carbon Nanotubes
Peter Eklund, Penn State, 4:00 p.m., 22 Deike Building
(refreshments at 3:45 p.m. in the Steidle Building museum), Materials Research Institute (863-8407).

Wednesday 5 April 2000
Rare Gases + Materials and Metallurgy II
First Materials Poster

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

Friday 7 April 2000 (Guest lecturer: Phil Bevilacqua)
Surprising Role of Catalysis by RNA
Read: Nobel Prize announcement for Tom Cech: Press Release
and Chapter 14.

Monday 10 April 2000
Materials and Metallurgy III
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.

Wednesday 12 April 2000 (Visit by Friends School 7th and 8th grade class)
Kinetics I
Here is a link to Nadrian Seeman's research at NYU that we discussed in class. You should have already read Chapter 14. Please review it for class.

Friday 14 April 2000
Kinetics II & Materials III
More Materials Posters

Zeb Bartels Depleted Uranium
Natalie Hepler Synthetic Diamonds
Abstracts for second posters due.
HW: 14.2,4,5,9,12,16,17,23,24

Sunday 16 April 2000
600 PM Materials Poster session -- 2nd Floor Osmond/Davey overpass.
Pizza provided.

Heather Agnew Cataracts & The Crystalline Materials Making up the Lens of the Human Eye
Kevin Buck Liquid Crystal Displays
Paul Butterfoss Night Vision
Brian Edwards Three Generations of Night Vision
Loren Filson The Patch for Drug Delivery
Andrew Glendening Fullerenes
David Goldstein Kevlar
Nick Hartman Synthetic Fibers
Samantaha Iivaei Lexan
Cassandra Lynn Konkle Blood-Brain Barrier
Mark Losego Semiconductor Lasers
Dan Lysko Ceramic Films
Rick Mellon Charge-Coupled Devices (CCDs)
Julie Norseen
Joanna Paulson Methane Clathrates
Evan Pickett Thermoelectrics
Ellyn Schuette Shape-Memory Alloys
Stephen Segal Carbon Fibers
Aaron Shoe UV and e-Beam Cured Polymers
Kristin Slagle Teslin -- a silica-based paper
Jackie Sturgeon Space Shuttle Thermal Systems
Kristen Tirio Photochromic Glass

Monday 17 April 2000
Kinetics II, Materials & Polymerization
Last Materials Posters

Jason Clark Solar Cells
Julie Hewett Drug Delivery Using Implanted Microchips
Edna Clogg Martian Meteorites

Wednesday 19 April 2000
Nuclear Chemistry I
Read: 21.1, 21.4-6
(Delayed) HW: 14.27,30,31,35,39,43,44,48,50

Schedule your final exam! Available dates:
Friday 28 April, Monday-Wednesday 1-3 May

Friday 21 April 2000 (Special Guest Lecturer: Prof. Tom Mallouk of the Center for Miscellaneous Chemistry)
Fuel Cells
HW: 21.1-6,12,13,16,19,23,24

Monday 24 April 2000
Nuclear Chemistry II:
Half-Life, Mass-Energy Conversion
and Discussion of Breeder Reactors, Nuclear Waste Handling and Disposal
Read: Chapter 21.7-8.
HW: 21.28-31,34,35,40,43,46,47.

Wednesday 26 April 2000
Nuclear Chemistry III:

Friday 28 April 2000
Final Discussion Class / Review

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

As announced in class, 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!

Friday 28 April 2000
11:15 AM Jenna Bartz
1:00 PM RickMellon
2:00 PM Natalie Hepler
3:00 PM Evan Pickett
3:45 PM Joanna Paulson

Monday 1 May 2000
8:30 AM Jackie Sturgeon
9:15 AM Julie Hewett
10:00 AM Heather Agnew
11:00 AM Jason Clark
1:00 PM Kristin Slagle
3:15 PM David Goldstein
4:00 PM Nick Hartman

Tuesday 2 May 2000
9:15 AM Kristen Tirio
10:00 AM Loren Filson
11:00 AM Mark Losego
1:00 PM Edna Clogg
2:00 PM Julie Norseen
3:00 PM Paul Butterfoss
3:45 PM Dan Lysko

Wednesday 3 May 2000
9:15 AM Stephen Segal
10:00 AM Ellyn Schuette
11:00 AM Aaron Shoe
1:00 PM Zeb Bartels
2:00 PM Samantha Iivari
3:00 PM Kevin Buck
3:45 PM Brian Edwards

Thursday 4 May 2000
10:00 AM Cassie Konkle
11:00 AM Andrew Glendening

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
X-ray Diffraction.
Optical trapping.
Chemical and Biological Warfare Agent Detection.
Fullerenes and like molecules.
Drugs of abuse.
RNA Catalysis
Fuel Cells

Did not get to
The bends in diving.
Nuclear magnetic resonance, and magnetic resonance imaging.


1. Class participation: 20%
2. Homework: 10%
3. Two in-class exams (1 hr. each) or One in-class exam 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 the second poster. 4. 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.
5. Oral final exam: 20%

TOTAL: 100%

27 April 2000