Reaction mechanisms

15 Jul 2014
Evaluation Methods: 

I make this activity worth 5% of their overall grade to be assessed for originality and level of discussion of how the chemistry part of their lab experiments (in terms of metal-ligand bonding or non-bonding) affected a biological system. Their ability to understand vitamin B12 and its functioning in the body should become apparent in their paper and should be used as the main guide in point distribution.

Evaluation Results: 

Has not been tested yet

Description: 

The students will write a paper in which they analyze the Vitamin B12 co-enzyme from biological, chemical and biochemical perspectives, and will use the guided questions to help show the relevance of an organometallic chemistry experiment to real biochemical systems. This activity is based on a synthetic lab experiment that students would have performed on transition metal-carbon bonds in biology and chemistry (The lab experiment was adapted from third edition of “Inorganic Experiments” by Derek Woollins). The answers to the set of questions in this LO will help guide the students to write the paper. You can choose the style you want the students to use and guide them in that process. 

Students can use information from their lab report, especially the experimental and results/discussion sections. 

 

Corequisites: 
Course Level: 
Learning Goals: 

Students will…

  • Study the chemical structure of vitamin B12 coenzyme and discuss the advantages and/or disadvantages of using cobaloximes as model compounds for vitamin B12 co-enzyme in this experiment.
  • Analyze the chemical reactions they performed in the lab that modelled actual reactions that occur in the human body, and discuss the effects of such chemical transformations. 
Subdiscipline: 
Implementation Notes: 

This term paper is based on a lab experiment that the students did earlier in the semester. I taught the lecture and lab portions concurrently so the students were very familiar with the experiment. They had a one paragraph summary of the lab experiment and a procedure to follow with guided questions to help them write the lab report. They submitted the lab report with the usual experiments, observations, results, discussion and conclusion and received lab credit that was separate from the credit assigned for this activity.

 

Time Required: 
Possibly as a take home assignment due within a week
14 Jul 2014

The Aconitase Enzyme Mechanism

Submitted by Laurel Goj Habgood, Rollins College
Evaluation Methods: 

This activity was not formally assessed but used as part of the participation grade for students.  Participation counts for 10% of their overall grade in the course.

Evaluation Results: 

The activity starts with students pairing up or forming small groups of three to work through the organic mechanism and discuss iron’s role in the process.  After five minutes we return to the class as a whole and the activity debriefed by having students contribute their answers with guidance on my part for the correct and incorrect answers.  Students initially struggled with the acid/base chemistry of amino acids so I now provide the protonated/deprotonated forms pertinent to the mechanism.  Now all the groups are able to complete the organic mechanism.  The two most common speculations for iron interaction amongst the students are the coordination of the deprotonated oxygen on a terminal carboxylic acid and coordination of the iron to the olefin.  The literature currently supports the former interaction.

Description: 

This learning objective focuses on the enzyme aconitase.  The iron-sulfur cluster is used to regulate iron in the cell and isomerize citrate for energy – two very different mechanisms.  The activity consists of an introduction to the enzyme and a student discussion on the mechanism of the isomerization of citrate to isocitrate; starting in a small group setting followed by a class debriefing.  

Learning Goals: 
  1. The student will be able to recognize that the iron-sulfur cluster does not do redox chemistry, the most common function for hemes.
  2. The student will provide the mechanism of citrate isomerization using electron-pushing arrows.
  3. The student will consider how the iron-sulfur cluster in aconitase might interact with the citrate during the isomerization process.
Corequisites: 
Subdiscipline: 
Equipment needs: 

None.

Topics Covered: 
Prerequisites: 
Implementation Notes: 

I use this activity in my inorganic chemistry class, which is the foundational ACS inorganic course typically taken by students in the spring of their junior year in tandem with our foundational biochemistry course.  There are three class days at the end of the semester allotted for bioinorganic chemistry.  The first day is an introduction to the subfield and heme chemistry.  The activity is used to open the second class to show non-heme functions of iron and then progress to copper in biological systems.  Students are not expected to prepare or read anything prior to the activity.  For those interested to learn more about aconitase I mention that it is a former molecule of the month in the protein data bank.

The first slide provides essential talking points for a brief introduction of the enzyme for the students.  The second slide shows a bare bones scheme of the mechanism, the two amino acids involved in the isomerization, and a representation of the iron-sulfur cluster which are my adaptations from published images.  The students are divided into small groups and instructed to use electron-pushing arrows to complete the organic portion of the mechanism and speculate about how the iron is involved in the mechanim.  After about five minutes the groups are disbanded and the activity is debriefed.  A student volunteer is asked to come to the board to fill in the electron-pushing arrows and then we discuss the role of the iron.  The notes section of the slide provides resources to aid the faculty member in the debriefing.

Time Required: 
10-15 minutes in class
3 Jul 2014

Five Slides About Concurrent Tandem Catalysis

Submitted by Shirley Lin, United States Naval Academy
Description: 

This set of slides is adapted from a presentation given at the ACS National Meeting in New Orleans Spring 2013 in the symposium "Undergraduate Research at the Frontiers of Inorganic Chemistry" organized by members of the VIPEr leadership council. The slides are from the introduction to the presentation that takes the audience through how catalytic cycles are depicted and then to the concept of concurrent tandem catalysis (CTC). At the end, there is a slide with references that gives an example of how CTC can be applied to aryl halide substrates to form new C-C and C-H bonds.

A nice feature of the slides is that some of them are animated with how the two catalytic cycles function in CTC versus one-pot, sequential catalysis. Hopefully the animations will download successfully along with the Powerpoint file!

The slides have some notes to help with clarity of presentation.

Corequisites: 
Course Level: 
Subdiscipline: 
Learning Goals: 

After seeing these slides, students should be able to:

1) Follow the visual representation of a single catalytic cycle and identify species in the cycle such as the catalyst, intermediates, substrates, products.

2) Define how concurrent tandem catalysis (CTC) involves 2 catalytic cycles operating at the same time.

3) Follow the progress of substrate to product in a two-cycle CTC mechanism.

4) Compare and contrast CTC to one-pot, sequential catalysis.

Time Required: 
~15 MINUTES
Evaluation
Evaluation Methods: 

No evaluation conducted.

Evaluation Results: 

N/A

10 Jun 2014

Protein Electrochemistry 3rd Bioinorganic Workshop

Submitted by Sheila Smith, University of Michigan- Dearborn
Description: 

This is a 90 minute talk by Fraser Armstrong of Oxford University (http://armstrong.chem.ox.ac.uk) explaining the electrochemistry of proteins immobilized on surfaces.  The talk was presented at the 3rd Bioinorganic Workshop in 2014 at Pennsylvania State University.  The talk contains an excellent basic tutorial on simple electron transfer on immobilized substrates using simple iron sulfur proteins as the primary example.  Talk continues on to more complicated subject matter including trumpet plots, electrocatalysis by enzymes focusing on the hydrogenases as an example.  The talk concludes with case studies presented on NiFe Hydrogenases, FeFe hydrogenases, and CO dehydrogenase.

Course Level: 
Corequisites: 
Learning Goals: 

The student should be able to explain the information available from electrochemistry on immobilized proteins.

Implementation Notes: 

This is an excellent presentation by the developer of many of the modern techniques for electrochemistry on immobilized proteins.  

Time Required: 
90 minute
24 Jan 2014

Student choice literature-based take home exam question

Submitted by Hilary Eppley, DePauw University
Evaluation Methods: 

This question was 30 points on a 100 pt take home exam (the year I did this, there was also a 100 point in class exam as well).   I've included the title page of the take home exam as well as this question.   

The grading scale allowed most of the points for the student chosen course content to highlight.   Of the 30 points, 10 focus on chemical information skills, 20 on summarizing the article and analyzing it using concepts from the class.   

Evaluation Results: 

I gave back a number of the exams before I was able to tally, but of the ones I had remaining: 

60% got full credit on the part a (those who missed neglected to include a summary) 

100% got full credit on part b

60% got full credit on part c (those who missed searched by formula rather than connectivity or provided an insufficient explanation of what they searched on 

100% got full credit on part d

On part e, answers varied widely from 7/17 to 15/17, with an average of 12/17 or a 70%.  

In some cases they lost points for just repeating things verbatim from the paper without explaining them to show they understood the concepts.   The main reason for loss of points however was just a lack of effort at picking apart the paper for parts that were relevant to the course content.   

They were able to successfully apply things such as electron counting and mechanism identification in a catalytic cycle, point groups, descriptions of sigma and pi bonding in ligands.   

 

Description: 

During my junior/senior level inorganic course, we did several guided literature discussions over the course of the semester where the students read papers and answered a series of questions based on them (some from this site!).  As part of my take home final exam, I gave the students an open choice literature analysis question where they had the chance to integrate topics from the semester into their interpretation of a recent paper of their own choice from Inorganic Chemistry, this time with limited guidance.  I also included a number of questions that required them to make use of various literature search tools to show that they had mastered those skills.   I gave them a list of topics that they could incorporate, but based on the poor quality of the responses I received, I encourage you to be more specific in your instructions.  I'd love to see some new versions!      

Corequisites: 
Course Level: 
Prerequisites: 
Learning Goals: 
Students will
  • choose a recent paper that interests them from Inorganic Chemistry
  • summarize why a particular paper is important to the field of inorganic chemistry
  • use literature search tools including Web of Science, Cambridge Structural Database, and SciFinder Scholar to find information aobut cited references, structurally similar compounds, and the authors of the paper
  • integrate ideas such as bonding models, symmetry, spectroscopy structural data, and chemical reactivity from class into a detailed analysis of aspects of the paper

The instructor will

  • get up to date on new literature for possible new literature discussions
  • get a chance to stretch his/her own intellectual muscles on some papers perhaps outside of his/her area of expertise
Implementation Notes: 

The students were given the take home exam about 1 week before it was due (but that was during the final exam period).   The format of the chemical information questions were similar to things they did earlier in the class, however the analysis of the paper was much more open ended, giving them the freedom to choose a paper that interested them and to presumably focus on concepts from the class that they felt comfortable with.   I gave them a date range from April 1 - April 30, 2012 for their paper because those were the most recent issues at the time.  If you use this LO, you will probably want to change those dates to more recent ones.   

Time Required: 
at least an hour, possibly more depending on the student
26 Aug 2013
Evaluation Methods: 

In addition to informal evaluation of lab skills during the weekly meetings, we assess student learning through semi-formal lab reports wherein synthetic and spectral data are reported in journal style and analyzed using knowledge of symmetry and group theory as well as a search of the relevant literature.

A generic rubric for how the points are split up on the lab report is as follows:

  • Analysis of data (40%)
  • Experimental section (35%)
  • Annotated spectra, including assignments (25%)
Evaluation Results: 

Student performance varies quite widely, as might be expected.  In general, the students show a solid understanding of how the glove box works and what kinds of experiments can be performed in a glove box, in addition to the care and special hazards associated with working in a glove box.

Student scores on laboratory reports trend mostly with the amount of time invested by the students in their preparation.  Students with the greatest number of citations for relevant papers from the primary literature also tend to invest the most time in careful reporting of experimental conditions and analysis of the products generated at each step.

Description: 

This laboratory experiment spans three weeks and introduces advanced undergraduates to modern small-scale synthesis techniques involving an inert-atmosphere glove box.  The robust syntheses transform [CpMo(CO3]2 into the methylated CpMo(CO)3(CH3) and examine the phosphine-induced migratory insertion to form various Cp-supported Mo(II) acetyl complexes.  At each step in the synthesis, a combination of IR and multinuclear (1H, 13C, and 31P) NMR spectroscopies allow students to assess the purity of their products and assign molecular geometry and stereochemistry using symmetry and group theory considerations.  We have also adapted the last step of the experiment to allow students to prepare previously unknown acetyl complexes using a variety of phosphines, and in two cases the products have been crystallographically characterized and published.

 

Here we attach a short overview similar to what might be published in J. Chem. Educ. or a related journal, student instructions, full synthetic details including IR and NMR spectra (for instructor reference), implementation notes, and a short handout introducing students to glove box theory and operation.

Prerequisites: 
Corequisites: 
Course Level: 
Subdiscipline: 
Learning Goals: 
  • Students should be able to explain basic principles relating to the operation of an inert-atmosphere glove box and will learn to adapt syntheses performed outside a glove box to run them easily and on small scale inside the box.
  • Students should be able to perform basic small-scale (10-100 mg) manipulations in an inert-atmosphere glove box, particularly those involving use of vacuum for filtrations and solvent removal.
  • Students should be able to apply knowledge of symmetry and group theory in order to rationalize and predict IR and NMR spectroscopic signatures for a series of Mo(II) complexes, paying particular attention to stereochemical implications.
Equipment needs: 
  • Inert-atmosphere glove box (N2 or Ar) equipped with a purge valve and vacuum feedthrough (some details regarding setup for vacuum are included as supplementary material here)
  • Infrared spectrometer and solution IR cells
  • NMR spectrometer capable of performing multinuclear (1H, 13C, 31P) experiments
Implementation Notes: 

More detailed notes are provided in a separate document, but here are a few highlights.  Of course it can be difficult to implement a lab experiment for many students with a single specialized piece of equipment like a glove box.  We have run this experiment with up to 16-18 students in a single term by splitting them into 4 sections (2 each for AM/PM) and having them perform the synthesis in groups of 2-3.  During a single lab period, 2 groups can easily perform the required synthesis and characterization by staggering their start times.  As outlined in the student handout attached, the lab can be completed in 3 weeks:

  • Week 1: Preparation of CpMo(CO)3(CH3)
  • Week 2: Purification and analysis of CpMo(CO)3(CH3), Begin preparation of CpMo(PR3)(CO)2(COCH3)
  • Week 3: Purification and analysis of CpMo(PR3)(CO)2(COCH3)

We have also included lab report guidelines that have worked well for our groups.

Time Required: 
3 weeks (3 laboratory meetings of 3-4 hours each)
26 Jun 2013

Literature summary through student presentation - free choice of topic.

Submitted by Cameron Gren, University of North Alabama
Evaluation Methods: 

I typically weight this assignment as one-half of an exam, i.e. 50 points when exams are worth 100 points each. The question should be worth a portion, perhaps 10 points with the remaining points coming from the presentation. Another option could be, if it would be appropriate for your class, to dedicate a few points to students preparing questions of other presenters. For large classes, they need not all be asked, but simply handed in to you prior to each presentation. then YOU could ask a few of them. As far as a rubric for the presentations, this could vary greatly. I typically count off for things like incorrect information, extremely vague descriptions, or very weak question answering. Specific deductions may vary. Other evaluation options could include student evaluations on each other's presentations, giving a post-presentation quiz (covering all presentations), or possibly including questions on the final exam over the presentations.

Evaluation Results: 

I generally give good grades for this assignment if I can tell the students put in an appropriate amount of work. Students tend to enjoy this assignment (more so after completing it, of course), as they can truly take ownership of their work. They seem to have a good sense of accomplishment after tackling a difficult journal article and breaking it down so they can understand it.

Description: 

(1) Student choses and reads a journal article of his/her choice that is related to a topic we have discussed during the semester. (i.e. atomic structure, MO theory, group theory, solid state structure, band theory, coordination chemistry, organometallics, catalysis). Suggested journals include, but are not limited to JACS, Inorg. Chem., Organometallics, Angew. Chem., JOMC, Chem. Comm.)

(2) Student answers the following questions regarding their chosen article:

    (a) Describe, in 1 or 2 sentences the goal of this work. 

    (b) Define the primary topic(s) from our course that relate to this work. 

    (c) Do you feel the authors achieved their goal? Why or why not?

    (d) What questions remained about the work?

(3) Student prepares a brief (~15 min) PowerPoint (or equivalent program) presentation describing the article. The question set should aid the student in developing the presentation.

(4) Students are encouraged to ask questions following each other student’s presentation.

Course Level: 
Learning Goals: 

• Students will improve their overall reading comprehension with regards to chemical literature.

• Students will be able to identify the relationship between current chemical literature and key concepts in inorganic chemistry.

• Students will improve their ability to present chemical research in a concise but detailed manner.

• Students will become critical observers of other’s presentations, being able to formulate and ask insightful questions.

Implementation Notes: 

I have this assignment due the last few days of the semester. It may be valuable for the students to see the professor summarize an article in this manner first, although I do not do this. It may be valuable to make the journal articles available to the other students prior to the presentations. This might help them formulate insightful questions for the presenters.

Time Required: 
I usually assign this at the beginning of the semester, although ~ 2 weeks might be sufficient prep time. In-class time is about 20 mins per student.
24 Apr 2013

A Visual Isotope Effect (a YouTube video)

Submitted by Dan O'Leary, Pomona College
Description: 

We have prepared a YouTube video demonstrating a visually accessible kinetic isotope effect in the Cr(VI) oxidation process, a reaction commonly encountered in introductory organic chemistry. The demo provides students with an opportunity to see an isotope effect and then understand how it can be used to provide mechanistic evidence for the identification of a rate-determining reaction step.

More information about the demonstration is available in a companion  Journal of Chemical Education article.

Course Level: 
Prerequisites: 
Corequisites: 
1 Apr 2013

Online Courses Directory

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

This website is a free and comprehensive resource that is a collection of open college courses that spans videos, audio lectures, and notes given by professors at a variety of universities. The website is designed to be friendly and designed to be easily accessed on any mobile device.

Course Level: 
Prerequisites: 
Corequisites: 
10 Oct 2012

Metal-Ligand Multiple Bonds and Frustrated Lewis Pairs

Submitted by Matt Whited, Carleton College
Evaluation Methods: 

I suggest evaluating learning through a class discussion where different students (or groups) present answers to different questions and solicit comments and/or responses.  A number of these questions are open-ended enough that there should be room for discussion and disagreement.

The answers I have attached are only starting points.  I suspect that students will have other ideas and valuable insights.

Evaluation Results: 

I have not used this LO yet, though I hope to use a version of it (possibly a shortened version) for my inorganic course next spring.

I have used the review and some related questions for my research students to help them get their heads wrapped around a presentation they were giving on our research (which is related to aspects of the review) last summer.  It seemed to help them understand the concepts of Lewis acidity/basicity and the frontier MO basis for reactivity quite a bit better.

Since this LO is as yet untested, I am very happy to hear feedback!

Description: 

This is a literature-based activity that focuses on a review I recently published as part of a thematic series on C-H activation.

The review highlights similarities between the newly discovered frustrated Lewis pairs and polarized metal-ligand multiple bonds.  There are many ways to use the review, but the attached set of questions focuses on drawing analogies among seemingly diverse types of reactivity using frontier-molecular-orbital considerations.

Corequisites: 
Course Level: 
Learning Goals: 
  • Students should be able to use molecular-orbital theory to rationalize the electronic structure and observed reactivity of species containing polarized metal-ligand multiple bonds
  • Students should be able to draw analogies between the reactivity of organic/main-group molecules and many transition-metal species using frontier molecular-orbital arguments
Implementation Notes: 

I am hoping to use some version of this in my inorganic chemistry class next spring, but it is as yet untested in a classroom setting, though I have had my research students work through the review and some related questions as they prepared a presentation on our work several months ago.  Since it is more or less untested, I am especially happy to hear feedback!

Time Required: 
unknown (probably ~2 hrs outside class + in-class discussion)

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