Physical Chemistry: Thermodynamics

3 Jun 2013

Databases for Kinetics

Submitted by Adam R. Johnson, Harvey Mudd College
Description: 

I recently came across some web resources for teaching kinetics. They are searchable compilations of kinetics data, principally gas-phase. Two of the sites include "recommended" data for use in simulations.

I describe the four sites here and the URLs are here and below.

http://jpldataeval.jpl.nasa.gov/
This is a critical tabulation of the latest kinetic and photochemical data for use by modelers in computer simulations of atmospheric chemistry

http://kinetics.nist.gov/solution/
A compilation of kinetics data on solution-phase reactions

http://kinetics.nist.gov/kinetics/KineticsSearchForm.jsp
gas phase Reaction Database Search Form

http://www.iupac-kinetic.ch.cam.ac.uk/
This website provides kinetic and photochemical data evaluated by the IUPAC Subcommittee for Gas Kinetic Data Evaluation.

Topics Covered: 
Course Level: 
Learning Goals: 

Using these databases, a user can find rate constant data for a chemical reaction.

Implementation Notes: 

I would use these databases to find examples beyond those in the textbook for in-class examples and out-of-class problems.

18 Jul 2012

C(sp3)-F Activation through an Initial C(sp3)-H Activation Mechanism

Submitted by John Lee, University of Tennessee Chattanooga
Evaluation Methods: 

The guided questions can be collected and graded.  In addition, (or alternatively) a qualitative grade can be given for class participation. 

An exam question has also been posted on VIPEr that can be used.

Description: 

This paper is from a Science article from Alan Goldman’s group at Rutgers University. It was one of the literature articles that was assigned during the IONiC VIPEr Workshop in July 2012.  In conjunction with reading the article, workshop participants attended a seminar presented by Alan Goldman on this work.

Here, Goldman’s group showed that C-F bond oxidative addition is possible through an initial C-H bond activation to the (PCP)Ir active complex.  Several key intermediates and Ir complexes were identified using 1H, 13C, 31P and 19F NMR.  LIFDI MS, a soft ionization MS technique, was used to verify the identity of (PCP)Ir(CH3)F.  DFT calculations along with experimental work were used to elucidate a likely mechanism. 

Learning Goals: 

Students should be able to:

  • determine the importance/impact of a paper
  • be able to use cited references within a paper to backtrack both prior and relevant work
  • be able to count electrons for all complexes in this paper
  • be able to describe how spectroscopic techniques are used to characterize new compounds
  • be able to describehow experimental studies are done to determine a reaction mechanism (or disprove a mechanism)
  • be able to describe how computational chemistry, when combined with experimental results, can give more insight into a reaction
Course Level: 
Implementation Notes: 

A copy of the paper (and guided questions) should be made available to students at least one week prior to the scheduled literature discussion.  During class, allow students to break up into small groups and compare answers/discuss the paper.  The instructor can walk around the room answering questions.  Interesting questions, both related and unrelated to the guided questions, should be announced to the entire class to allow for further discussion.

Time Required: 
50 minute lecture
16 Jul 2012

Effects of defects on the properties of single-walled carbon nanotubes

Submitted by Sherri Lovelace-Cameron, Youngstown State University
Evaluation Methods: 

I have students answer all questions and share their answers during class.

Another option is to have students answer all questions and turn them in for grading.

Evaluation Results: 

The entire class participated and completed the sheet.  Question 6 allows for discussion expansion into research topics.  I think the fact that they new an upcoming exam question would come from the assignment they were motivated.

Description: 

I teach advanced inorganic chemistry and wanted to find ways to bring in the primary literature, applications, and current research areas.  Students read the article, "Role of Defects in Single-Walled Carbon Nanotube Chemical Sensors" by Eric S. Snow, Nanoletters 2006, 6 (8) pp. 1747 -1751, on their own.  Students are required to answer guided questions (see file Student_questions_Effects of Defects SWCN.doc) and apply basic concepts they have learned in previous courses to understand current literature.  Students learn terminology related to material defects, relate what they learned about defects to material properties, and find other primary literature papers.

Prerequisites: 
Course Level: 
Learning Goals: 

A student should be able to

  • Define chemisorption and physisorption.
  • Compare and contrast chemisorption and physisorption.
  • Apply their knowledge of defects to the following properties: chemical selectivity, electrical conductance and capacitance.
  • Determine the importance of Langmuir plots in this research.
  • Locate additional articles by the primary author.
  • Connect the science in the paper to a broader research interest.
Implementation Notes: 

Students were given the the paper and a list of questions so they would be prepared for class discussion.  Students come to class prepared to share their answers and will use their handout as a study guide for an upcoming test. Discussion takes 20 minutes of class time.

The attached file, Carbon Nanotube Sensor_resource.pdf, provides background information on this topic.

Time Required: 
20 minutes
16 Jul 2012

Application of Organometallic Chemistry – Breaking the Inert C-H Bond

Submitted by John Lee, University of Tennessee Chattanooga
Evaluation Methods: 

The guided questions can be collected and graded. Alternatively, a qualitative score can be given based on class participation.

Description: 

This learning object is a literature discussion based on a paper published in Nature (Labinger, J. A.; Bercaw, J. E. Nature 2002, 417, 507-514; doi:10.1038/446391a) discussing the mechanisms of C-H activation by transition metal complexes. This is a topic that could be covered at the end of a section on organometallic chemistry that shows a “newer” application. The attached lecture notes start at organic chemistry, then asks a question and is followed by a brief description of the paper showing examples for different mechanisms. The last slide is a thought slide that can easily be removed that asks a question that builds both upon what was discussed in the lecture and previous organometallic lectures. A working knowledge of counting electrons is required before beginning this study.

Learning Goals: 

A student should be able to describe, in limited detail, the “five primary” mechanisms for C-H activation.

A student should be able to distinguish the basic characteristics between oxidative addition, sigma-bond metathesis and electrophilic substitution.

A student should be able to apply his/her knowledge of organometallic reactions to show these reactions in a catalytic cycle for C-H functionalization.

Course Level: 
Equipment needs: 

None

Implementation Notes: 

A copy of the paper and guided questions should be made available to students one week prior to the lecture.  A 15 minute powerpoint lecture is available, if needed.  At the end of the lecture allow the students to break into small groups to take a second attempt at their guided questions. During this time the instructor can walk around helping with both the guided questions and any other questions that might have arisen from the discussion.  Alternatively, if the presentation is not needed you can use the guided questions to lead the class in a discussion.

Time Required: 
50 minute lecture
16 Jul 2012

Solubility and the Need for Bioinorganic Metal Ion Transport and Storage

Submitted by Sheila Smith, University of Michigan- Dearborn
Evaluation Methods: 

 

I generally evaluate success based on the quality of discussion that comes out of the in class activity, since the actual math problem is completed collaboratively. 

Evaluation Results: 

 

Since I provide the van’t Hoff equation, students can typically manage the math of the equation; an understanding of why the calculation is necessary (a reminder that K is temperature dependent) can prove useful.   Students sometimes need some prodding to remember how to do a Qsp vs Ksp problem  ( or to remember that this is what they need to do to answer the question) in the second half.                                                                                                     

Description: 

 

This is an in class exercise that I use to emphasize the need for metal ion transport and storage in biochemistry.  Applying the Van't Hoff equation to the Ksp value at 25°C for ferric hydroxide, students calculate the iron concentration at which ferric hydroxide would begin to precipitate out in the blood.  It' s an interesting problem that requires very little math beyond that used in gen chem, and the answer is in stark contrast to the amount of iron that we actually store in our bodies.  

Learning Goals: 

 

Student should recognize that the balanced chemical equation to which the Ksp can be applied is the precipitation reaction.

Student should be able to write a balanced chemical equation for the precipitation of Ferric hydroxide.

Student should be able to apply Hess’ Law to calculate the enthalpy of reaction for a balanced chemical equation (given DH°f for relevant species).

Student should be able to apply the van’t Hoff equation to predict the equilibrium constant at a temperature other than 25°C (in this case, 37°C).

Student should be able to calculate the [OH-] at a given pH

Student should be able to write the solubility product expression for Fe(OH)3 and use that to calculate the maximum amount of ferric ion that can exist in aqueous solution at a given pH before precipitation occurs. 

Equipment needs: 

calculator

Subdiscipline: 
Course Level: 
Implementation Notes: 

 

I use this at the beginning of class before I start covering Metal transport and storage.  The idea is to draw from the students’ previous knowledge to help them understand the need for transport and storage to avoid accumulation of solid precipitates.  It can also lead, as discussed in the key, to a good discuss of bioavailability. 

Time Required: 
20 minutes of class-time to work and discuss
29 Sep 2011

The Eyring Equation

Submitted by Adam R. Johnson, Harvey Mudd College
Evaluation Methods: 

I would hope a discussion would ensue where different groups of students present the pros and cons of the various forms of data fitting.

Description: 

I was taught (many years ago) the common misconception that fitting the linearized form of the Eyring equation overstates the error in the intercept because on a 1/T axis, the intercept is at infinite temperature, and the intercept is far from the real data. While researching various methods of data fitting, I stumbled across this great article from the New Journal of Chemistry (New J. Chem., 2005, 29, 759–760, doi:  10.1039/b501687h) which proves that in fact, the errors in ∆S and ∆H are the same no matter how you fit the data… but… you must be sure to appropriately weight the data in the non-linear fit.  The supplemental information for the paper includes the real data so that you can examine it in more detail.

The attached Mathematica file was developed by my student Ryan Brewster (HMC, Chem 104, Spring 2010), and he deserves partial author credit for this learning object.  I thank him for working with me and encouraging me to develop this LO.

Learning Goals: 

A student will learn to fit rate data to various forms of the Eyring equation.

A student will be able to explain when weighting of data is necessary.

 

Course Level: 
Equipment needs: 

If done as an in-class activity, computer workstations running Kaleidagraph, Mathematica or other curve-fitting programs would be required. If done as a discussion, the faculty member would need to have access to these programs in order to verify the data presented.

Implementation Notes: 

I have only done this as a lecture and problem set (see the related problem set) but I think it would work very well as an in-class activity.  I look forward to seeing either comments or other implementations. Make sure to look at the supporting information for the article as it includes a dataset for use in class.

Here is a suggested procedure (and language) for implementing this activity as an in-class exercise. Take a kinetics data set (there is usually one in the chapter on ligand substitution reactions, or you could use the dataset in the article) and divide the class into several groups. Have one group of students fit the linearized data, one group fit to the Eyring equation using non-weighted data, and a third group fit to the equation while weighting the data appropriately.

Group 1:  The following data (provided by the instructor) is a series of rate constants at different temperatures for a chemical reaction.  Linearize the data by taking the natural log of each rate constant and plot it vs 1/T (Kelvin temperature!). Fit the linear data to the linearized form of the Eyring equation and extract the activation paramaters from the fit. Report your paramaters on the chalkboard and indicate your group number and how long it took you.

Group 2:  The following data (provided by the instructor) is a series of rate constants at different temperatures for a chemical reaction.  Fit the data to the Eyring equation and extract the activation paramaters from the fit.  Do not weight the data. Report your paramaters on the chalkboard and indicate your group number and how long it took you.

Group 3:  The following data (provided by the instructor) is a series of rate constants at different temperatures for a chemical reaction.  Fit the data to the Eyring equation and extract the activation paramaters from the fit.  Weight the data using the standard weighting scheme in Kaleidagraph (1/k2). Report your paramaters on the chalkboard and indicate your group number and how long it took you.

All groups: After you fit your data, be prepared to discuss the pros and cons of your approach.  How easy was it to fit your data?  How easy was it to extract the activation paramaters?  Do your values match those from the other groups?

 

 

Time Required: 
one 50 minute class period
25 Jun 2011
Description: 

Into the Cool: Energy Flow, Thermodynamics, and Life

Eric D. Schneider, Dorion Sagan

ISBN: 0226739376

In our 4th semester course we cover (among other topics) thermodynamics (about a third of the course).  This is the last course that the pre-medical students have to take, and the course therefore brings with it the typical challenges of students who really don’t particularly want to be there, and want to know why they’re required to think about these topics.  I’ve begun assigning this book as a supplemental required text.  It’s not a regular textbook certainly, but it’s extremely well-written, and provides a very clear and fascinating description of the application of thermodynamic principles to large non-equilibrium systems.  We certainly don’t cover this type of system in this course, but the book is written in such a way that students can really grasp the bigger picture.  While I’ve had a couple of students complain about the additional reading load, most of my students appreciated the larger perspective (and I’ve had students report back to me that they were rereading the book the year after taking the course!) 

 

The book really focuses on the larger implications and meaning of the second law of thermodynamics (rephrased as “Nature abhors a gradient”), and it provides many examples of the second law in action in the real world.  It discusses natural selection,  the complexity of living systems, as well as the trajectories and patterns found in the complexities of ecosystems over time. It touches on cosmology, weather patterns, economics and aging.  I highly recommend this as a supplemental text for those students who may be unconvinced of the fundamental importance, intricacy, and beauty of thermodynamic principles.  It would also make a great central text for a non-majors course, though I haven’t had a chance to offer such a course(yet!)

Prerequisites: 
9 Mar 2008
Evaluation Methods: 

Take home writing assignment and in-class discussion.

Evaluation Results: 

Students found the kinetics a bit difficult to follow, but "got it" after we went over it in class. They picked up on the catalytic cycle right away and came away with some good "suggestions" for future work.

Description: 

This is a literature discussion assignment in which students read a paper, come up with their own answers to the provided questions (and submit them).  This is followed by a general in-class discussion on the paper.  This particular article deals with hydrosilyation of carbonyl compounds by a Re catalyst and describes the mechanism and kinetics in detail.  I found it a good paper to help students connect their P-chem (and inorganic) kinetics with a "real" system.  As part of the literature assignment, I also ask students to draw an MO diagram of a simple substrate (for review).

Subdiscipline: 
Course Level: 
Learning Goals: 

Upon completing this LO students should be able to:

  1. read and extract information from a primary literature article
  2. develop the MO diagram for SiHCl3 using a fragment orbital approach
  3. interpret X-ray crystallographic data to explain bond distances and angles
  4. analyze kinetics data to understand reaction order and kinetic isotope effect for stoichiometric and catalytic reactions
  5. understand and explain how a reaction can be irreversible yet have labile ligands
     
Implementation Notes: 

Students who are currently enrolled in Thermodynamics and Kinetics may need to be paired with a student who has previously completed the course

Time Required: 
2-3 hours writing for students; 50 minutes in-class (could be shorter)

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