Chemistry 13H
Spring 2002

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

Grader: Matt Sandel
Phone: (814) 237-0616
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 Molecular Science, by Moore, Stanitski, and Jurs, 1st 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 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 7 January 2002 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 9 January 2002
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 11 January 2002

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 14 January 2002 (Guest Lecturer: Prof. Mark Horn of Engineering Science and Mechanics, Former Associate Director of the Penn State Nanofabrication Facility)

Discussion Class on Nanofabrication

(Discussion Monday instead of Friday this week.)

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 16 January 2002

Acids & Bases I

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

Read: Chapter 16
HW Problems Due:
From Chapter 16: 12, 14, 17, 19, 21, 24, 25, 27, 29, 31, 35, 37, 39, 41, 43
Make up a problem that you feel best tests your knowledge of Acids & Bases up to now. Answer it. This 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 18 January 2002

Acids & Bases II

HW Problems Due:
From Chapter 16: 45, 47, 49, 51, 52, 53, 56, 58, 59, 62, 63, 67, 68, 69-71
Jenna's extra problem for you!

Monday 21 January 2002

Acids and Bases III & Buffers

HW Problems Due:
From Chapter 16: 73, 75-77, 79, 81, 82,84, 86, 88, 89, 91, 93, 95, 97, 98, 100
Allison's famous cheese problem

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

Wednesday 23 January 2002

Acids & Bases III
Read: Chapter 17
HW: 51, 53, 55, 58, 59, 62, 63, 66, 69, 71, 72, 74, 86, 88, 89

Friday 25 January 2002
Optical Trapping

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 28 January 2002
Periodic Trends
Solubility, cont.
Read: pp. 296-307
HW Problems Due: 7.99, 101, 103, 107-111, 114

How are the following measured quantitatively: ionization energy, electron affinity?
(This latter problem will be graded in addition to the normal homework.)
Hallie's solubility problem
Jenna's pH problem

Wednesday 30 January 2002
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

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 1998-2002, 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 1 February 2002 (with assistance from Prof. Mike Sailor of UCSD)
Chemical Sensors Discussion

Please attend Prof. Sailor's talk, if you are able:
Chemistry of Nanocrystalline Silicon for Chemical and Biological Sensors and Biomedical Applications
1115 AM in S5 Osmond

Monday 4 February 2002

Exam I Review
Bring questions/problems

Wednesday 6 February 2002 (Administered by Matt)
Exam I

Friday 8 February 2002 (Guest Lecturer Will Hancock, PSU Bioengineering)
Molecular Motors

Monday 11 February 2002

Go over Exam I
Thermodynamics I:
Spontaneity, Enthalpy, Entropy

Reading: pp. 223-236; 813-827

Find a paper biomolecular motors that was not mentioned in class, from the years 1998-2002, and is in one of the following journals: Science, Nature, Proceedings of the National Academy of Science, 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 the measurements were performed. What techniques were used and how?
Attach a copy of the article to the homework.

Wednesday 13 February 2002

Thermodynamics II:
Free Energy, Equilibrium Constants, and Work

Reading: pp. 827-838 Problems: 6.22-25, 6.46, 6.48; 18.21, 26, 29, 31, 39, 40, 47, 49, 57

Friday 15 February 2002 (Guest Lecturer: Andy Ewing, Head of the Chemistry Department)
Neurochemistry Discussion

Reading: pp. 827-838
Problems: 18.62, 64, 72, 73, 79, 84, 86, 89, 90, 93, 95

Monday 18 February 2002
Thermodynamics III
Introduce Electrochemistry
Reading: pp. 839-851, Ch. 19
Understand Review Questions, and pp. 868-871
Problems: 18.99, 100, 105, 107

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.

Wednesday 20 February 2002

Thermodynamics IV:
Equilibrium Constants, Work, and Measurements
Electrochemistry II
Project: Select your element for the poster and paper (from a hat!).
19.7, 10, 11, 13, 14, 16, 17, 20, 22, 25, 26-28, 31, 35, 38
Kir's Annie Oakley problem.

Friday 22 February 2002

Electrochemistry III: Batteries, Electrolysis
HW: Assign oxidation states to five molecules or molecular ions, each containing at least three different elements.
19.39, 43, 45, 48, 50, 51, 53, 57-59, 64, 69, 71, 73, 75, 78, 81
Erica's elemental problem.

Monday 25 February 2002
Electrochemistry IV: Corrosion
Transition Metal Ions & Complexes I
Read Chapter 22
Problems 22.42, 43, 47, 66, 67, 68, 73, 77

Wednesday 27 February 2002
Transition Metal Ions & Complexes II, Metallurgy

The first poster (but no pizza):
Al Arwen Wilson

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

Friday 1 March 2002 No class! Enjoy spring break. Work on your posters -- bring references with you!
Poster work

2-10 March 2002
Enjoy Spring Break!

Monday 11 March 2002 (Guest Lecturer: Dr. Mahnaz El-Kouedi)
Materials I: Polymers & Ceramics
Reading: pp. 487-503, 543-565
Problems: 11.63-65, 67, 68, 70, 72, 73; 12.55, 59, 62, 69, 70, 77

Wednesday 13 March 2002
Materials II: Semiconductors

Friday 15 March 2002
Fullerene Discussion
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.
(More to be added here)

Sunday 17 March 2002
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 Guy Barbato
Ca Jason Robosky
Fe Amra Tabakovic
Zn Marta Ventura -- delayed
Na Sam Pliska
K Si Lobdell
Ni Cristina Feather
Cu Chelsey Giardina
Co Sheila Bal
Sr Aimee Kumer
S Laurie Kemmere
Se Aryn Gabai
I Hillary Herendeen
F Hans Arora
Br Meghan Smith
Li Ben Wong
Pt Colleen Creuz
Sn Michelle Gandhi
Ti Mariah Giardina
Si Christina Guice
Ba Vincent Ho
Ba Oliver Chen
B Jeff Paulsen
Hg Sean Commins
Pb Alex Radovic-Moreno
Al Arwen Wilson -- delayed for Arwen's return

Monday 18 March 2002
Hydrogen and Oxygen

Wednesday 20 March 2002
Nitrogen, Carbon, Fullerenes and Like Molecules
Reading: pp. 955-967
Problems: 21.1, 11, 25

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

Friday 22 March 2002
Self-Assembly Discussion
Problem: Where do the values for terrestrial abundances of the elements originate, how are they estimated, and what do they estimate?

Monday 25 March 2002 (Guest Lecturer Prof. Tom Mallouk of the Center for Miscellaneous Chemistry)
Fuel Cells

Please attend Dr. Craig Venter's talk this evening in the Distinguished Speaker Lecture Series. You will need tickets.

Tuesday 26 March 2002

Please attend Dr. Craig Venter's Kohout Lecture at 1030 AM in the HUB Auditorium: Sequencing the Human Genome.

Wednesday 27 March 2002
Kinetics I

Delayed Elements of Life Poster:
Zn Marta Ventura

Reading: Review Chapter 13, understand review Qs.

Friday 29 March 2002
Papers due for +5 point credit

Monday 1 April 2002 (Uh oh. Paul's favorite day of the year.)
Kinetics II
Papers Due, no kidding (see requirements below)

Wednesday 3 April 2002
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.
Reading: Chapter 17.
Problems: 17.17-19, 26, 29, 33, 39, 43, 48, 56, 61, 63, 71, 78, 80, 86, 93, 114 (oops)

Friday 5 April 2002 (Guest lecturer: Tom Pearl)
Quantum Mechanics II/font>

Problems: 13.17-19, 26, 29, 33, 39, 43, 48, 56, 61, 63, 71, 78, 80, 86, 93, 114
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.

Monday 8 April 2002 (Guest lecturer: Tom Pearl)
Quantum Mechanics II/font>
Introduction to quantum mechanics from the University of Washington.

Wednesday 10 April 2002
Nuclear Chemistry I

Reading: pp. 919-944
Problems: 20.1, 3-8, 11, 13, 15, 17, 18, 25, 33, 35, 36
Allison's problem with Matt (that does not sound right, hmmm).

Friday 12 April 2002
Nuclear Chemistry II

Sunday 14 April 2002
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.
Calzones for dinner.

TiN Coatings Jeff Paulsen
Superefractory Materials Si Lobdell
Heat Shields on the Space Shuttle Oliver Chen
Polymer Healing Sean Commins
Self-Healing Plastic Laurie Kemmere
Kevlar Sheila Bal
Structures Built from DNA Guy Barbato
Polymer-Encapsulated DNA for Drug Delivery Arwen Wilson
Tissue Engineering Amra Tabakovic
Tissue Engineering Christina Guice
Nanoparticles in Medicine Marta Ventura
Bionic Arm Jason Robosky
Joint Replacements Ben Wong
Artificial Muscles Chelsey Giardina
Biodegradable Polymers for Induced Skin Tissue Regeneration Meghan Smith
Protein Folding Mariah Giardina
Self-Contained Breathing Apparatus Aryn Gabai
Superconductors Colleen Creuz
C60: The New Superconductor Aimee Kumer
Synthetic Flavors Hillary Herendeen
Olestra Michelle Gandhi
Goretex Vincent Ho
Nafion: Solid Electrolyte Polymer Alex Radovic-Moreno
Liquid Crystal Displays Hans Arora
Photonic Crystals Cristina Feather
Electrochromic Devices Sam Pliska

Monday 15 April 2002
Nuclear Chemistry III:
Half-Life, Mass-Energy Conversion
and Discussion of Breeder Reactors, Nuclear Waste Handling and Disposal

Abstracts for second posters due.

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

Wednesday 17 April 2002

Friday 19 April 2002

Monday 22 April 2002
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 24 April 2002
Course Review II

Friday 26 April 2002
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. 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!

Friday 26 April 2002 - Thursday 2 May 2002 Oral Final Exams
11:15 AM Ben Wong
1:00 PM Christina Guice
2:00 PM Sean Commins
3:00 PM Meghan Smith
4:00 PM Sheila Bal

Monday 29 April 2002
8:30 AM Colleen Creuz
9:15 AM Jason Robosky
10:00 AM Hillary Herendeen
11:00 AM Aryn Gabai
12:00 noon Arwen Wilson
2:15 PM Hans Arora
3:00 PM Michelle Ghandi

Tuesday 30 April 2002
9:15 AM Samantha Pliska
10:00 AM Alex Radovic-Moreno
11:00 AM Vincent Ho
1:00 PM Amra Tabakovic
2:00 PM Cristina Feather
3:00 PM Laurie Kemmere
3:45 PM Jeffrey Paulson
4:30 PM Oliver Chen

Wednesday 1 May 2002
9:00 AM Chelsea Giardina
10:00 AM Mariah Giardina
11:00 AM Simon Lobdell
1:00 PM Guy Barbato
2:15 PM Marta Ventura
3:00 PM Aimee Kumer

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.
Chemical and biological warfare agent detection -- sensors


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%

Homework requirements.

28 April 2002