Chemistry 13H
Spring 2004

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: Karl Yaeger
Phone: (814) 862-6011
AIM: k17yaegermeister

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.

Portraits of Scientists and Pictures of Instrumentation
How a scanning electron microscope works.
The Bends Story
Comment on the bends by Prof. Gold
Dupont Nylon page.
Whole brain atlas.
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 12 January 2004 (Lecturers: Karl Yaeger & Joe Keiser)

Wednesday 14 January 2004
Measurements of Single Molecules in Biology and Chemistry I

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 16 January 2004

Single Molecule Measurements II

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

Draw an energy level diagram for:
Compare the sensitivity and specificity of each.

Monday 19 January 2004

Acids & Bases I

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 21 January 2004

Acids & Bases II

NIST Optical Tweezers Page including the Adhesion Movie

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!

Friday 23 January 2004 (Guest Lecturer: Prof. Will Hancock)

Discussion Class on Biomolecular Motors

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 26 January 2004 (Guest Lecturer: Prof. Mark Horn)

Discussion Class on Nanofabrication

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 28 January 2004

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

Friday 30 January 2004
Buffers and Titrations, cont.

No homework. Sorry...

Monday 2 February 2004
Periodic Trends
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.)

Please attend Prof. Paul Alivasatos's Marker Lectures, if you are able:
8 PM 102 Thomas: Nanocrystals as a New Class of Macromolecule

Tuesday 3 February 2004 Please attend Prof. Paul Alivasatos's Marker Lectures, if you are able:
4 PM S5 Osmond: Shape Control and Structural Properties of Nanocrystals

Wednesday 4 February 2004
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 1998-2004, 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.

Please attend Prof. Paul Alivasatos's Marker Lectures, if you are able:
12 PM S5 Osmond: Optical and Electrical Properties of Nanocrystal Based Materials

Friday 6 February 2004 Class canceled because of ICE!

Monday 9 February 2004

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 11 February 2004

Thermodynamics II:
Free Energy, Equilibrium Constants, and Work

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

Please attend Paul's Research Unplugged Lecture, if you are able:
12 PM Downtown Theatre: Exploring and Controlling the Atomic-Scale World

Friday 13 February 2004

Find a paper on nanoscience from the years 2000-2004 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 Lieber Group Page at Harvard.

More Molecular Motor Links

Monday 16 February 2004
Thermodynamics III
Introduce Electrochemistry

Wednesday 18 February 2004
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 20 February 2004
Electrochemistry III: Batteries, Electrolysis, Corrosion
Materials I: Semiconductors

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 23 February 2004
Materials II: Polymers & Ceramics
Read Sections 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 25 February 2004

Transition Metal Ions & Complexes I, Metallurgy

Read: 23.7-8

Friday 27 February 2004

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.

Monday 1 March 2004
Exam I Review
Bring questions/problems
Here is a pdf of a previous midterm exam.

Wednesday 3 March 2004
Exam I

Friday 5 March 2004 Optional class (come if you have not left for spring break)
Enjoy spring break (by coming to class!)
Work on your posters -- bring references with you!
Discussion and Demonstrations

Yikes! Look what you missed (click for larger images):

Nylon Rope Trick '04 | Nylon Rope Trick '04 | Nylon Rope Trick '04 | Nylon Rope Trick '04 | Nylon Rope Trick '04 | Nylon Rope Trick '04 | Nylon Rope Trick '04

making Gummy Worms '04 | Making Gummy Worms '04

And here is what was left afterwards:

Debris from Demo Competitions '04

8-12 March 2004
Enjoy Spring Break!

Monday 15 March 2004
Go Over Exam
Metallurgy II

Wednesday 17 March 2004
Transition Metals III
Materials II: Polymers and Ceramics

Thursday 18 March 2004
POSTER PRINTING INFO (in pdf format) or (in word format) 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.

Prof. Graham Fleming's seminars (attend if you can):
1215 PM Chemistry Colloquium, S5 Osmond:
The Chemical Physics of Photosynthesis

730 PM Phi Beta Kappa Lecture, 112 Kern:
Photons and Femtoseconds -- How Nature Converts Sunlight into Chemical Energy

Friday 19 March 2004
First poster
Discussion with Phi Beta Kappa Scholar: Prof. Graham Fleming, Department of Chemistry, University of California at Berkeley

First poster:
Tc* Jed Schober

Sunday 21 March 2004
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 Jen Gibson
Ca Stu Greene
Zn Lee Bassett
Na Jimmy Kwon
K Monique Maslak
Li Chris Haggerty
Fe Ryan Urbanski
Co Scott Allen
Ni Matthew Litke
Cu Laura Pucul
Mn Larry Wang
Cr Chad Kuny
S Nikesh Anumula
Se Lou Michalski
Si Allen Naygauzen
Ti Kathleen Carey
I Sherry Yang
Cl Seetal Erramilli
Pt Gaelan Ritter
Hg Tim Braun
B Daniel McKeone

Elements of Life Poster session abstracts Chemical & Engineering News Essays on the Elements

Monday 22 March 2004

Wednesday 24 March 2004 (Guest Lecturer: Dr. Luis Fernandez)
Hydrogen and Oxygen

Read: 23.1-3

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

Friday 26 March 2004
Nitrogen and Carbon
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 29 March 2004 (Guest Lecturer: Dr. Charlie Sykes)
Kinetics I

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

Wednesday 31 March 2004 Guest Lecturer: Matthew Szapacs

Proteomics & Neurochemistry

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 2 April 2004
Kinetics, cont.
Rare Gases
Fullerene & Metcar Discussion
Papers due for +5 point credit

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

Monday 5 April 2004
Kinetics II
Fullerene & Metcar Discussion
Papers Due (see requirements below).

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

Wednesday 7 April 2004
Kinetics III, Enzymes, PCR
Nuclear Chemsitry I
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 9 April 2004 (Guest Lecturer: Prof. Anne Andrews)
Drugs of Abuse

Reading to be announced.

Monday 12 April 2004
Nuclear Chemistry II

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

Wednesday 14 April 2004 (Guest Lecturer: Prof. Anne Andrews)
Drugs of Abuse II
HW: 14.28-31,34,35,39,40,43,46,47
Allison's problem with Matt (that does not sound right, hmmm).

Friday 16 April 2004
Nuclear Chemistry III: Half-Life, Mass-Energy Conversion
Breeder Reactors, Nuclear Waste Handling and Disposal
Read: Chapter 21.7-8
HW: 21.28-31,34,35,40,43,46,47

Monday 19 April 2004
First Materials Posters

The Artificial Body: Tissue and Organ Engineering Sherry Yang
A Silly Mistake With Endless Possiblities Jen Gibson
Safety Glass Stu Greene
The Use of Titanium in Metal Woods for Golf Chad Kuny

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

Please attend Sir John Thomas's Lectures, if you are able:
12 PM HUB Auditorium: The Genius of Michael Faraday

Monday 19 April 2004
720 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.

Materials: Carbon Nanofoam Lee Bassett
Sulfur-induced Cross-Linkages in the Vulcanization of Rubber Nikesh Anumula
Plasticizing PVC Laura Pucul
Diamonds are a Girl's Best Friend Monique Maslak
Organic Electronics Daniel McKeone
Carbon Planes Trains and Automobiles Gaelan Ritter
Plasma Screens: Innovation Using the Fourth State of Matter! Seetal Erramilli
Teflon: Making Life Smoother Larry Wang Space Shuttle Tiles Ryan Urbanski
Radar Absorbing Materials Jed Schober
Magnetic Microstructured Materials Used in Resonance Imaging Louis Michalski
C4 Scott Allen
Bioactive Foam Scaffolds in Tissue Regeneration Matthew D. Litke
The Heart of a Lion Christopher Haggerty
Plastic Organs and the Use of PTFE in Medicine Timothy Braun
Miracle Muscles Kathleen Carey
Polycaprolactone: A Bioactive Alternative to Skull Regeneration Allen Naygauzen
Secrets Behind From Your Flat Monitor [LCD] Screen Jimin Kwon

Tuesday 20 April 2004 Please attend Sir John Thomas">' Lecture, if you are able:
1130 AM S5 Osmond: New Nanoporous and Nanoparticle Catalysts

Wednesday 21 April 2004 (Guest Lecturer: Tom Mallouk)
Fuel Cells

Friday 23 April 2004 (Guest Lecturer: Dr. Charlie Sykes)
Quantum Mechanics
Introduction to quantum mechanics from the University of Washington.

Tom Mallouk's Fuel Cell Problems:
1) Calculate the Carnot efficiency of a H2/O2 engine operating at:
a) T1 = 200 °C
b) T2 = 500 °C

2) What is the maximum possible efficiency of a H2/O2 fuel cell running at 25 °C (=298 K)?

3) a) Balance the steam reforming reactions for coal (mostly C) and oil (assume it is C8H18) for the products H2 and CO2
b) How many moles of H2 do you get per mole of CO2 produced in each case? c) Use the thermochemical tables (back of book) to determine how many kJ of energy you get per mole of C, assuming the H2 is used in a fuel cell at 0.8 V.

Monday 26 April 2004
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 28 April 2004
Course Review II

Thursday 29 April 2004

Individual Oral Final Exams
Held in 407 Davey. Expect the exam to take ca. 45 min.

10:00 AM Jimin Kwon
3:00 PM Scott Allen

If you too would like to move your final to Thursday, please let me know!

Friday 30 April 2004
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!

11:15 AM Kathleen Carey
12:15 PM Seetal Erramilli
1:00 PM Stu Greene

Monday 3 May 2004
Individual Oral Final Exams

Held in 407 Davey.

9:15 AM Sherry Yang
10:00 AM Ryan Urbanski
11:00 AM Tim Braun
1:00 PM Lee Bassett
2:00 PM Lou Michalski
3:00 PM Dan McKeone
4:00 PM Chad Kuny

Tuesday 4 May 2004
Individual Oral Final Exams

Held in 407 Davey.

9:15 AM Larry Wang
10:00 AM Nikesh Anumula
11:00 AM Matt Litke
12:45 PM Allen Naygauzen
1:30 PM Gaelen Ritter
4:00 PM Jed Schober

Wednesday 5 May 2004
Individual Oral Final Exams

Held in 407 Davey.

10:00 AM Jen Gibson
11:00 AM Chris Haggerty
1:00 PM Monique Maslak
2:00 PM Laura Pucul

Discussion Topics Suggested

RNA Catalysis.
Nuclear magnetic resonance.
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
Single molecule measurements.
Single molecule motors.
Directed assembly of molecules and nanoparticles.
Drugs of abuse.
Fuel cells.



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.

28 April 2004