Chemistry 13H
Spring 2006

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: Nate Hohman
Phone: (814) 863-8220
AIM: nhohman28

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, 10th 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
Using SciFinder Scholar at Penn State
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 9 January 2006 (Including cameo appearances by: Karl Yaeger & Joe Keiser)
Measurements of Single Molecules in Biology and Chemistry I

Wednesday 11 January 2006
Measurements of Single Molecules in Biology and Chemistry II

HW Due:
Find a recent 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 13 January 2006

Single Molecule Measurements III

HW Due:
Your own problem, as described in class.
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 16 January 2006 (Martin Luther King Day, no class. We will combine homeworks as descrived in class.)

Acids & Bases I

Read: Chapter 15, Sections 4.2-4, 16.1-2.
  1. Your own problem, as described in class.
  2. 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
  3. What color is table salt when: in a flame, in a shaker, or spread lightly on a table or piece of paper? Why?
  4. Find an article on fluorescence published since 1 January 2001 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 18 January 2006
Acids & Bases I

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).

Read: Sections 16.3-8.
HW: 16.1, 13-18, 21-24, 26, 27, 38, 41-44, 92, 101
Jenna's extra problem for you!
And, as always, your own problem, as described in class.

Friday 20 January 2006

Discussion Class replaced with Acids and Bases II

Acids & Bases Reading: Sections 16.8-11, 17.1.
HW: 16.48-60 even, 65-68, 94, 98, 99.
Also, your own problem as described in class.

Monday 23 January 2006

Acids & Bases III

Read: 17.1 (common ion effect), 17.2-3 (buffers & titrations), 7.1-4 (periodicity)
HW: 17.5, 9-11, 13-16 (common ion effect & buffers)
Explain the relative acid strengths of:
H2SO4 vs. H2SO3 and
H2SO4 vs. H2SeO4
Problems: 16.69-74, 77-80, 83-85, 88, 90
Allison's famous cheese problem
Also, your own problem as always (and I am going to stop listing it now).

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

Wednesday 25 January 2006

Buffers and Titrations, Solubility

Read: Sections 17.4-6
HW: 7.12, 21, 24, 32, 36
17.17, 18, 22, 24, 25, 35-37, 39

Friday 27 January 2006
Buffers, Solubility, cont.
Acid Strength vs. Structure
Optical Tweezers Discussion

Read: Sections 17.4-6
HW: 7.50, 54, 60, 64, 65

Monday 30 January 2006
Periodic Trends

Read: 7.5-7, 4.2, 17.6-7
Hallie's solubility problem, and
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 1 February 2006
Measurements of Periodic Properties Discusssed
Project: Select your element for the poster and paper (from a hat!).

Read: Sections 19.1-3.
HW: 17.45-47, 50, 53, 56, 59-61, 63, 65, 66, 94, 97

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 2001-2006, 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 3 February 2006
Diffraction and Mass Spectrometry

Monday 6 February 2006

Thermodynamics I:
Spontaneity, Enthalpy, Entropy

Read: Sections 19.4-7
HW: 19.1, 7, 8, 10, 11, 20, 34
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 8 February 2006

Thermodynamics II:
Free Energy, Equilibrium Constants, and Work

HW: 19.44-48, 53, 54, 56-59, 67, 68, 71, 75
Go over your poster topic with me by AIM or email or after class.

Friday 10 February 2006 Guest Lecturer: Beth Anderson
Thermodynamics III & Electrochemistry I

(Paul is at 23rd Annual Houston Conference on Biomedical Engineering Research)

Monday 13 February 2006
Transition Metals
Electrochemistry II: Batteries, Electrolysis, Corrosion
Read: Oxidation Numbers pp. 139-141, 322, and 20.1-4.
Kir's Annie Oakley problem.
Turn in your preliminary versions of your poster abstracts and I will give you feedback on them.

Wednesday 15 February 2006
Electrochemistry III
Metallurgy I
Transition Metals

Read: 20.5-9
HW: 20.9, 10, 13, 15, 16, 18, 20-24, 35, 38
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.

An example elements poster, as requested, from John McManigle of the Chem 13H '05 class.
Grade sheet we will use (pdf).

Thursday 16 February 2006
Please try to mail your poster to Jackie by Wednesday 15 February, if at all possible. You must do this if she is going to print your poster for Friday class. Her email address is:

Final 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 17 February 2006
Transition Metal Ions & Complexes
First posters
Read Sections 23.1-23.8
HW: 23.9, 18-20, 30, 32, 33

Cr Jared Lipton
Pb Stephen Chaves

HW: 20.70, 74, 84-86, 91, 93, 97, 105
Assign oxidation states to five molecules or molecular ions, each containing at least three different elements.
Erica's elemental problem.

Sunday 19 February 2006
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 Hillary Grube
Mg Liz Gratton
Mn Andrew McLean
Tc* Jackie van Pelt
Sr Elizabeth Hicks
Zn Jacob Ross
Na Andrew Shevchuk
K Corrine Thompson
Li Jess Lowery
Co Chandra Richards
Ni Brian Perry
Cu Mackenzie Brady
S Ashley Gibb
Se Leah Giaccotto
Si Sean Russell
Cl Andrew Sinnamon
F Ying-Hsien Huang
He Tory Miksiewicz
Ti Elizabeth Morin
Ba Patrick McClanahan
I Sasha Lewicki
Pt Chris Thompson
B Anna Han
Hg Elyse Amico

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

Monday 20 February 2006
Transition Metal Ions & Complexes II

Wednesday 22 February 2006
Transition Metal Ions & Complexes III
Materials I: Semiconductors

HW: 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.

How is the speed of light measured?

Friday 24 February 2006

Materials II: Polymers & Ceramics
Quantum Mechanics

Read: 24.1-6
HW: 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.

Introduction to quantum mechanics from the University of Washington.

Monday 27 February 2006
Exam I Review
Bring questions/problems
Here is a pdf of a previous midterm exam.

Wednesday 1 March 2006
Exam I

Friday 3 March 2006
Optional Demonstration Class

in which Ashley set off a string of H2 balloons (still),
Patrick lay gun cotton across his arm (still),
Hillary made gummy worms, and
Liz handily won the nylon rope competition.

6-10 March 2006
Enjoy Spring Break!

Monday 13 March 2006
Metallurgy II

Wednesday 15 March 2006
Go Over Exam
Transition Metals III
Materials II: Polymers and Ceramics

Friday 17 March 2006 Guest Lecturer Prof. Anne Andrews
Ecstacy & Neurochemistry Discussion
Papers Due (see requirements below).

Monday 20 March 2006
Complete: Metallurgy, Polymers, Ceramics

Read: 22.7-9 (nonmetals)
HW: 22.55-58, 61-65, 68-70 (nonmetals)

Thermite movie

Wednesday 22 March 2006
Complete: Batteries
Hydrogen and Oxygen

Friday 24 March 2006
Nitrogen, Carbon, and Rare Gases
Read: 22.1-6 (nonmetals)
HW: 22.15-17, 20-26, 29, 41-45, 50-52 (nonmetals)
Where do the values for terrestrial abundances of the elements originate, how are they estimated, and what do they estimate?

Please hold off on Tom Mallouk's Fuel Cell Problems.

Monday 27 March 2006
Kinetics I

Read: 14.1-3
HW: 14.4, 12, 14, 15, 17, 20, 24, 25, 30, 31

Wednesday 29 March 2006

Kinetics II

A video of the clock reaction.

Read: 14-4-5

HW: 14.34-37, 40, 41, 45, 46, 50, 52, 53
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 31 March 2006
Nanoscience Discussion

HW: Find a paper on nanoscience from the years 2001-2006 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.
Lieber Group Page at Harvard.

More Molecular Motor Links

Links of interest:
National Nanotechnology Homepage

Monday 3 April 2006
Kinetics III, Enzymes, PCR

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

Wednesday 5 April 2006

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.

Abstracts for second posters due.

Friday 7 April 2006

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

First Posters:
Carbon Fibers: Synthesis and Applications Chris Thompson
Silver in Metal Prostheses Jackie Van Pelt

Sunday 9 April 2006
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.

Carbon-Nanotube-Strengthened Body Armor Andrew McLean
Boron Carbide and Its Applications Jacob Ross
Kevlar Stephen Chaves
Concrete Ying Huang
Viagra Jared Lipton
Collagen Scaffolds for Tissue Engineering Anna Han
Hydrogel Intervertebral Discs MacKenzie Brady
Stent Coatings Liz Hicks
Spider Silk Liz Morin
Spandex Patrick McLanahan
Piezoelectricity Corinne Thompson
Ceramic Glazes Sasha Lewicki
Superglue Chandra Richards
Life of Mars? Measuring of Meteorites Andrew Sinnamon
Antihydrogen Andrew Shevchuk
Building Blocks of the Solar System Ashley Gibb
Liquid Crystal Displays Liz Gratton
Fluorescent Eye Stains Hillary Grube
Biodiesel Brian Perry
Non-Viral Vectors for Gene Transport Elyse Amico
Botox Leah Giaccotto
Tooth Enamel Jessica Lowery
Organic Light-Emitting Diodes Sean Russell
Silicon Membranes Tory Miksiewicz

Monday 10 April 2006
Nuclear Chemistry II

Read: 21.4-6
HW: 21.32-37, 42, 45, 48, 49

Wednesday 12 April 2006
Nuclear Chemistry III
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 14 April 2006
Nanoscience Discussion II?

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

Monday 17 April 2006
Nuclear Chemistry IV: Half-Life, Mass-Energy Conversion
Breeder Reactors, Nuclear Waste Handling and Disposal
Course Review I

Control rod configuration, as discussed in class.
Also, check this out! Schedule your final exam! Available dates:
Friday 28 April, Monday 1 May, Tuesday 2 May, and Wednesday 3 May

Wednesday 19 April 2006 (Guest Lecturer: Tom Mallouk)
Fuel Cells

Paul is at the Materials Research Society Meeting in San Francisco, CA.

Friday 21 April 2006
Course Review II

Monday 24 April 2006 (Guest Lecturer Beth Anderson)
Quantum Mechanics 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.
Where's Paul? Chairing a meeting at Snowbird, Utah:
Foundations of Nanoscience
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.

Please attend Sunney Xie's Marker Lectures, if you are able:
8 PM 100 Life Science Building: #1, Ever-Fluctuating Enzymes: Lessons from Single-Molecule Studies

Tuesday 25 April 2006 Please attend Sunney Xie's Marker Lectures, if you are able:
1230 PM 102 Chemistry Building: #2, Probing Gene Expression in Live Cells

Please also attend Peter Schulz's Chemerda Lectures, if you are able:
600 PM 100 Life Science Building: #1, Probing Gene Expression in Live Cells

Wednesday 26 April 2006 (Guest Lecturer Beth Anderson)
Quantum Mechanics II

Please attend Peter Schulz's Chemerda Lectures, if you are able:
1200 PM 100 Life Science Building: #2, Synthesis at the Interface of Chemistry and Biology: From Antibodies to Stem Cells

Please attend Sunney Xie's Marker Lectures, if you are able:
400 PM 102 Chemistry Building: #3, Visualizing the Invisibles: CARS (Coherent Anti-Stokes Raman Scattering) Microscopy for Biomedicine

Thursday 27 April 2006
Hear it from the horse's mouth (remember our diffraction lecture?!):
Please attend Prof. Amand Lucas's Physics Colloquium, if you are able:
400 PM 119 Osmond: Diffraction by DNA, Carbon Nanotubes, and other Helical Nanostructures

Friday 28 April 2006
Final Review (II) and 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.

Catalytic degradation of H2O2 by MnO2 movie | Thermite movie 1 | Thermite movie 2 | Last balloon of the year movie

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!

1130 AM Chris Thompson
1215 PM Stephen Chaves
115 PM Jackie van Pelt

Please attend Craig Venter's Eberly Family Lecture, if you are able:
4 PM 100 Thomas: Genomics: From Medicine to the Environment

Sunday 30 April 2006
Individual Oral Final Exams
Held in 407 Davey.

1100 Jacob Ross
1200 PM Sasha Lewicki
1245 PM Brian Perry
130 PM Sean Russell
230 PM Ying Huang

Monday 1 May 2006
Individual Oral Final Exams
Held in 407 Davey.

1100 AM Andrew Sinnamon
130 PM Andrew Shevchuk
215 PM MacKenzie Brady
315 PM Jared Lipton
415 PM Andrew McLean

Tuesday 2 May 2006
Individual Oral Final Exams
Held in 407 Davey.

915 AM Chandra Richards
1000 AM Patrick McClanahan
1100 AM Leah Giaccotto
1215 PM Corinne Thompson
115 PM Ashley Gibb
200 PM Tory Miksiewicz
300 PM Liz Gratton
430 PM Jess Lowery

Wednesday 3 May 2006
Individual Oral Final Exams
Held in 407 Davey.

915 AM Hillary Grube
1000 AM Anna Han
1100 AM Elyse Amico
1215 PM Liz Morin
300 PM Liz Hicks

Some Possible Discussion Topics (from previous years)

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


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.

30 April 2006