Chemistry 13H
Spring 2005

This www site is still very much under construction and will be updated continuously throughout the semester.
Jump to: Next Class | Learning | Chemtourism | Text | Schedule | Finals | Discussion Topics Suggested | Grading

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:

Chemistry's contribution to humanity an ongoing IUPAC project. CRC Handbook Online (you must be logged in through Penn State or another subscribing institution to use this link)
The Elements.

Portraits of Scientists and Pictures of Instrumentation
How a scanning electron microscope works.
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.
Some chemistry demos on video

Seminars in the Eberly College of Science.

Monday 10 January 2005 (Including cameo appearances by: Karl Yaeger & Joe Keiser)
Measurements of Single Molecules in Biology and Chemistry I

Wednesday 12 January 2005
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.
Write and answer your own homework problem, as described in class.

Friday 14 January 2005

Single Molecule Measurements III

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 17 January 2005

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 19 January 2005

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 21 January 2005

Acids & Bases III

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.

Monday 24 January 2005 (Guest Lecturer: Prof. Will Hancock)

Discussion Class on Biomolecular Motors

Read: 17.1 (common ion effect),17.2-3 (buffers & titrations), 7.1-4 (periodicity)
Explain the relative acid strengths of:
H2SO4 vs. H2SO3 and
H2SO4 vs. H2SeO4
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.

Where's Paul? Two meetings:
Winter Conference on Brain Research, Breckenridge, CO
International Conference on Molecular Electronics VII, San Diego, CA (I will chair VIII)

Wednesday 26 January 2005 (Guest Lecturer: Rachel Smith)

Buffers and Titrations

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

Friday 28 January 2005 (Guest Lecturer: Rachel Smith)

Buffers, Solubility, cont.
Acid Strength vs. Structure

Monday 31 January 2005
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.)

Wednesday 2 February 2005
Measurements of Periodic Properties Discusssed
Project: Select your element for the poster and paper (from a hat!).

Read: Sections 19.1-3.
HW: 17.35-37,40,43,46,49-51,53,55,56,86,89

How are the following measured quantitatively: covalent & ionic radii?
(These latter problem will be graded in addition to the normal homework.)
Also, another go at measuring: ionization energy, electron affinity, if you were not happy with your answers for Monday.

Find a paper that includes optical trapping measurements that was not mentioned in class, from the years 1999-2005, 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.

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).

Friday 4 February 2005
Diffraction and Mass Spectrometry

(Guest Lecturer held off: Prof. Mark Horn)
Discussion Class on Nanofabrication

Monday 7 February 2005

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 9 February 2005

Thermodynamics II:
Free Energy, Equilibrium Constants, and Work

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

Friday 11 February 2005
Nanoscience Discussion

Find a paper on nanoscience from the years 2001-2005 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 14 February 2005
Thermodynamics III
Introduce Electrochemistry

Wednesday 16 February 2005
Thermodynamics IV:
Equilibrium Constants, Work, and Measurements
Electrochemistry III: Batteries, Electrolysis, Corrosion
Metallurgy I

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.

Thursday 17 February 2005
POSTER PRINTING INFO (in pdf format))
Please try to mail your poster to Jackie by Wednesday 16 February, if at all possible. You must do this if she is going to print your poster for Friday class. Her email address is:

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 18 February 2005
First posters
Materials I: Semiconductors

First Posters:
Fe Jessie Hershmann
Cu Kasey Holloway
Ti Sarah Krahe
Sr John Sludewski
Pb Mac Pedlow

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.

Sunday 20 February 2005
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.

Ca David Giordano
Zn Ryan Madrak
Na Rocco Panella
K Beth Tirio
Li Lauren Aldinger
Co Matt McCowan
Ni Liz Francis
Mn Laura Hoch
Cr Merika James
S Nikki Williams
Si Eric Myers
Cl Sucharita Mukherjee
Ba Jen Clark
Tc* James Monaco
I John McManigle
Pt Matt Wendahl
B Jocelyn Fitzgerald
Hg Phil Cerami

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

Monday 21 February 2005
Transition Metal Ions & Complexes II
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 23 February 2005 (Guest Lecturer: Dr. Jenny Hampton)

Transition Metal Ions & Complexes I
Quantum Mechanics

Read: 23.7-8

Introduction to quantum mechanics from the University of Washington.

Friday 25 February 2005 (Guest Lecturer: Dr. Jenny Hampton)

Transition Metal Ions & Complexes II

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 28 February 2005
Exam I Review
Bring questions/problems
Here is a pdf of a previous midterm exam.

Wednesday 2 March 2005
Exam I

Friday 4 March 2005 No class
Enjoy spring break

7-11 March 2005
Enjoy Spring Break!

Monday 14 March 2005 (Guest Lecturer: Beth Anderson)
Metallurgy II

Wednesday 16 March 2005
Go Over Exam (average was 82)
Transition Metals III
Materials II: Polymers and Ceramics

Friday 18 March 2005 (Guest Lecturer: Prof. Mark Horn)
Nanotechnology Discussion

Monday 21 March 2005 (Guest Lecturer Beth Anderson -- back by popular demand!)
Hydrogen and Oxygen

Read: 23.1-3

Wednesday 23 March 2005 (Guest Lecturer Tom Mallouk)
Fuel Cells

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

Friday 25 March 2005
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

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 28 March 2005
Kinetics I

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

Wednesday 30 March 2005

Kinetics II

A video of the clock reaction. 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 1 April 2005

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 4 April 2005
Kinetics III, Enzymes, PCR
Rare Gases
Papers Due (see requirements below).

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

Wednesday 6 April 2005

Nuclear Chemistry 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 8 April 2005 (Guest Lecturer: Prof. Anne Andrews)
Brain Imaging

Reading to be announced.

Monday 11 April 2005
Nuclear Chemistry II

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

Wednesday 13 April 2005
Polymers & Ceramics
HW: Do any isotopes undergo both positron emission and electron capture (i.e., one or the other with finite probability)?
Allison's problem with Matt (that does not sound right, hmmm).

Friday 15 April 2005 (Guest Lecturer: Prof. Gary Fosmire, Department of Nutrition)
Food Chemistry Discussion

Read: Chapter 21.7-8
HW: 21.28-31,34,35,40,43,46,47

Sunday 17 April 2005
600 PM Frontiers of Materials Poster session -- 2nd Floor Osmond/Davey overpass (if the weather cooperates, we will move outside for the earlier posters).
As before, you will have four minutes to present followed by one to two minutes of discussion.
Dinner provided. Visitors and alumni welcome.

Caught on Films David Giordano
Electronic Vision from Charge-coupled Devices Eric Myers
Night Vision Goggles Matt McCowan
Keep the Light on for Organic Light-emitting Diodes Jessie Hershmann
Silicon Photovoltaic Cells Mac Pedlow
Scintillator Crystals James Monaco
Conductive Polymers Ryan Modrak
These Elements Never Forget: Nitinol Alloys John McManigle
Clinical Applications of Magentic Resonance Spectroscopic Imaging Sucharita Mukherjee
Superconductivity: Theory Rocco Panella
Superconductivity: Applications Matt Wendahl
Child's Play: The Chemistry of Silly Putty Phil Cerami
I've Got You Under My Skin: Biodegradable Polymers Lauren Aldinger
Synthetic Tooth Enamel Liz Francis
SimMan Is No Dummy Kasey Holloway
Lexan Sarah Krahe
Insulating Aerogels Jen Clark
Phosphorus Pentoxide: The Frizz Detector Merika James
Plastics in Food Packaging Beth Tirio
How Splendid Is Splenda? Nikki Williams
Something to Chew On: The Truth about the Gum Making Process Laura Hoch
Being E-picky about Epoxy Jocelyn Fitzgerald
Polyacrylic Acid John Sladewski

Monday 18 April 2005
Nuclear Chemistry III: Half-Life, Mass-Energy Conversion
Breeder Reactors, Nuclear Waste Handling and Disposal

Remaining Materials Posters
Schedule your final exam! Available dates:
Friday 29 April, Monday 3 May, Tuesday 3 May, and Wednesday 4 May

Wednesday 20 April 2005
Nuclear Chemistry, cont.: Radioactive Dating
Polymers I

Friday 22 April 2005
Course Review I

Monday 25 April 2005 (Guest Lecturer Tom Mallouk)
Solar Energy
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 27 April 2005
Course Review II

Thursday 28 April 2005
Individual Oral Final Exams
Held in 407 Davey.

9 AM Nikki Williams
10 AM Jen Clark
11 AM Phil Cerami
3 PM Matt McCowan
4 PM Jessie Hershmann

Friday 29 April 2005
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!

1115 AM Lauren Aldinger
1 PM Merika James
2 PM Laura Hoch

Monday 2 May 2005
Individual Oral Final Exams
Held in 407 Davey.

915 AM Rocco Panella
10 AM Jocelyn Fitzgerald
11 AM Sarah Krahe
1 PM Matt Wendahl
2 PM John McManigle
3 PM James Monaco
4 PM Mac Pedlow

Tuesday 3 May 2005
Individual Oral Final Exams
Held in 407 Davey.

1015 AM Ryan Modrak
11 AM Beth Tirio
130 PM Eric Myers
230 PM Liz Francis
4 PM Kasey Holloway

Wednesday 4 May 2005
Individual Oral Final Exams
Held in 407 Davey.

11 AM Sucharita Mukherjee
145 PM David Giordano

Discussion Topics Suggested

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

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


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.

2 May 2005