Reaction mechanisms

23 Jun 2018
Evaluation Methods: 

Students answer several questions prior to the in class discussion. These answers can be collected to assess their initial understanding of the paper prior to the class discussion. Assessment of the in class discussion could be based on students’ active participation and/or their written responses to the in class questions.

Evaluation Results: 

This Learning Object was developed as part of the 2018 VIPEr Summer Workshop and has not yet been used in any of our classes, but we will update this section after implementation.

Description: 

This is a literature discussion based on a 2018 Inorganic Chemistry paper from the Lehnert group titled “Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases“(DOI: 10.1021/acs.inorgchem.7b02333). The literature discussion points students to which sections of the paper to read, includes questions for students to complete before coming to class, and in class discussion questions. Several of the questions address content that would be appropriate to discuss in a bioinorganic course. Coordination chemistry and mechanism discussion questions are also included.

 

Corequisites: 
Prerequisites: 
Learning Goals: 

A successful student will be able to:

  • Evaluate structures of metal complexes to identify coordination number, geometry (reasonable suggestion), denticity of a coordinated ligand, and d-electrons in FeII/FeIII centers.

  • Describe the biological relevance of NO.

  • Identify the biological roles of flavodiiron nitric oxide reductases.

  • Identify the cofactors in flavodiiron nitric oxide reductase enzymes and describe their roles in converting NO to N2O.

  • Describe the importance of modeling the FNOR active site and investigating the mechanism of N2O formation through a computational investigation.

  • Explain the importance of studying model complexes in bioinorganic chemistry and analyze the similarities/differences between a model and active site.

  • Write a balanced half reaction for the conversion of NO to N2O and analyze a reaction in terms of bonds broken and bonds formed.

  • Interpret the reaction pathway for the formation of N2O by flavodiiron nitric oxide reductase and identify the reactants, intermediates, transition states, and products.

 

A successful advanced undergrad student will be able to:

  • Explain antiferromagnetic coupling.

  • Apply hard soft acid base theory to examine an intermediate state of the FNOR mechanism and apply the importance of the transition state to product formation of N2O.

  • Apply molecular orbitals of the NO species and determine donor/acceptor properties with the d-orbitals of the diiron center.

Implementation Notes: 

This paper is quite advanced and long, so faculty should direct students to which sections they should read prior to the class discussion. Information about which parts of the paper to read for the discussion are included on the handout. Questions #7 and #8 are more advanced, and may be included/excluded depending on the level of the course.

Time Required: 
In-Class Discussion 1-2 class periods depending on implementation.
23 Jun 2018

Interpreting Reaction Profile Energy Diagrams: Experiment vs. Computation

Submitted by Douglas A. Vander Griend, Calvin College
Evaluation Methods: 

Having not run this yet because it was collaboatively developed as part of a IONIC VIPEr workshop, we suggest grading questions 1-9 for correctness, either during or after class. Students should be tested later with additional questions based on reaction profiles. The final 3 questions should prepare students to constructively discuss the merits/limitations of computational methods. after discussion, students could be asked to submit a 1-minute paper on how well they can describe the benefits/limitations of compuational chemistry.

Evaluation Results: 

Once we use this, we will report back on the results.

Description: 

The associated paper by Lehnert et al. uses DFT to investigate the reaction mechanism whereby a flavodiiron nitric oxide reductase mimic reduces two NO molecules to N2O. While being a rather long and technical paper, it does include several figures that highlight the reaction profile of the 4-step reaction. This LO is designed to help students learn how to recognize and interpret such diagrams, based on free energy in this case. Furthermore, using a simple form of the Arrhenius equation (eq. 8 from the paper) relating activation energy, temperature and rate, the student can make some initial judgements about how well DFT calculations model various aspects of a reaction mechanism such as the structure of intermediates and transition states, and free energy changes.

Learning Goals: 
Upon completing this activity, students will be able to:
  1. Interpret reaction profile energy diagrams.

  2. Use experimental and computational data to calculate half lives from activation energies and vice versa.

  3. Assess the value and limitations of DFT calculations.

Prerequisites: 
Course Level: 
Corequisites: 
Implementation Notes: 

Having not run this with a class, we can only suggest that this activity be run in a single class period.

We presume that students have been exposed to the basic idea of reaction profiles.

Teacher should hand out the paper ahead of time and reassure students that they are not going to be expected to understand many of the details of this dense computational research paper. Instead, students should read just the synopsis included on the handout.Teacher should then spend 5 - 10 minutes summarizing key aspects of paper: 1) it's about a nitric oxide reductase mimic that catalyzes the reaction 2NO → N2O + O; 2) NO is important signaling molecule; 3) DFT is a computational method to model almost any chemical molecule, including hypothetical intermediates and transition states.

Students should work through questions in groups of 2 - 4. The final question (12) is somewhat openended and the teacher should be prepared to lead a wrap up discussion on the benefits and limitations of computational chemistry.

Time Required: 
50 minutes
22 Jun 2018
Evaluation Methods: 

An answer key is included for faculty.

Evaluation Results: 

This LO was developed for the summer 2018 VIPEr workshop, and has not yet been implemented.  Results will be updated after implementation.

Description: 

This acitivty is a foundation level discussion of the Nicolai Lehnert paper, "Mechanism of N-N Bond Formation by Transition Metal-Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases".  Its focus lies in discussing MO theory as it relates to Lewis structures, as well as an analysis of the strucutre of a literature paper.

Prerequisites: 
Corequisites: 
Course Level: 
Learning Goals: 

Upon completion of this activity, students will be able to:

  1. Write a balanced half reaction for the conversion of NO to N2O and analyze a reaction in terms of bonds broken and bonds formed.

  2. Evaluate the structures of metal complexes to identify coordination number, geometry (reasonable suggestion), ligand denticity, and d-electron count in free FeII/FeIII centers.

  3. Recognize spin multiplicity of metal centers and ligand fragments in a complex.

  4. Interpret a reaction pathway and compare the energy requirements for each step in the reaction.

  5. Draw multiple possible Lewis Structures and use formal charges to determine the best structure.

  6. Draw molecular orbital diagrams for diatomic molecules.

  7. Identify the differences in bonding theories (Lewis vs MO), and be able to discuss the strengths and weaknesses of each.

  8. Interpret calculated MO images as σ or π bonds.

  9. Identify bond covalency by interpreting molecular orbital diagrams and data.

  10. Define key technical terms used in an article.

  11. Analyze the structure of a well written abstract.

  12. Identify the overall research goal(s) of the paper.

  13. Discuss the purposes of the different sections of a scientific paper.

Implementation Notes: 

The paper in which this discussion is centered around is very rich in concepts, and will take time for students to digest.  As the technical level is higher than most foundation level course, it is strongly recommended that students focus on the structure of the paper, and not the read the entire paper.  The discussion is modular with focuses on both MO theory drawn form the paper, as well as a general anatomy of how literature papers are organized and what constitutes a good abstract.  Either focus could take a single 50 minute lecture, with two being necessary to complete both aspects.  Instructors can choose either focus, or both depending on their course learning goals.

This was developed during the 2018 VIPEr workshop and has not yet been implemented.  The above instructions are a guide and any feedback is welcome and appreciated!

Time Required: 
One or two 50 minute lectures depending on instructor's desired focus
1 Jun 2018
Evaluation Methods: 

This LO has not been implemented; however, we recommend a few options for evaluating student learning:

  • implement as in-class group work, collect and grade all questions

  • have students complete the literature discussion questions before lecture, then ask them to modify their answers in another pen color as the in-class discussion goes through each questions

  • hold a discussion lecture for the literature questions; then for the following lecture period begin class with a quiz that uses a slightly modified problem.

Evaluation Results: 

This LO has not been implemented yet.

Description: 

In honor of Professor Richard Andersen’s 75th birthday, a small group of IONiC leaders submitted a paper to a special issue of Dalton Transactions about Andersen’s love of teaching with the chemical literature. To accompany the paper, this literature discussion learning object, based on one of Andersen’s recent publications in Dalton, was created. The paper examines an ytterbium-catalyzed isomerization reaction. It uses experimental and computational evidence to support a proton-transfer to a cyclopentadienyl ring mechanism versus an electron-transfer mechanism, which might have seemed more likely.

 

The paper is quite complex, but this learning object focuses on simpler ideas like electron counting and reaction coordinate diagrams. To aid beginning students, we have found it helpful to highlight the parts of the paper that relate to the reading questions. For copyright reasons, we cannot provide the highlighted paper here, but we have included instructions on which sections to highlight if you wish to do that.

 

Corequisites: 
Course Level: 
Learning Goals: 

After completing this literature discussion, students should be able to

  • Count the valence electrons in a lanthanide complex

  • Explain the difference between a stoichiometric and catalytic reaction

  • Predict common alkaline earth and lanthanide oxidation states based on ground state electron configurations  

  • Describe how negative evidence can be used to support or contradict a hypothesis   

  • Describe the energy changes involved in making and breaking bonds

  • On a reaction coordinate diagram, explain the difference between an intermediate and a transition state

  • Explain how calculated reaction coordinate energy diagrams can be used to make mechanistic arguments

Implementation Notes: 

This is a paper that is rich in detail and material. As such, an undergraduate might find it intimidating to pick up and read. We have provided a suggested reading guide that presents certain sections of the paper for the students to read. We suggest the instructor highlight the following sections before providing the paper to the students. While students are certainly encouraged to read the entire paper, this LO will focus on the highlighted sections.  

 

Introduction

            Paragraph 1

            Paragraph 2

            Paragraph 3

            Paragraph 4

First 5 lines ending at the word high (you may encourage students to look up exergonic if that is not a term commonly used in your department)

Line 14 starting with “In that sense,” through the end of the paragraph

            Paragraph 6

From the start through the word “endoergic” in line 22

Line 31 from “oxidation of” to the word “described” in line 33

Line 40 from “These” to the word “dimethylacetylene” in line 45

Paragraph 7

            From the start to the word “appears” in line 4

            The words “to involve” in line 4

            Starting in line 4 with “a Cp*” to “transfer” in line 5

Results and Discussion

            Paragraph 1

            Paragraph 2

            Paragraph 3 from the start through “six hours” in line 10

            Paragraph 4

            Paragraph 5

                        From the start to “solution” in line 3

                        From “This exchange” in line 10 to “allene” in line 11

                        From “Hence” in line 19 through the end of the paragraph

            Paragraph 6 from the start through “infrared spectra” in line 19

            Paragraph 7 from “Hence” in line 4 through the end of the paragraph

Mechanistic aspects for the catalytic isomerisation reaction of buta-1,2-diene to but-2-yne using (Me5C5)2Yb p 2579.

            Paragraph 1

            Paragraph 2

            Paragraph 3

            Paragraph 4

Experimental Section

            Synthesis of (Me5C5)2Yb(η2-MeC≡CMe).

            Synthesis of (Me5C5)2Ca(η2-MeC≡CMe).

Reaction of (Me5C5)2Yb with buta-1,2-diene

 

 

 

Time Required: 
One class period.
10 Jan 2018

What happened to my green solution?

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

I do not do any formal assessment of student learning for this activity, but instead I judge understanding by the quality of the in-class dicussion.

I have also used similar questions on exams in the past to see if the students can apply these ideas to different reactions.

Evaluation Results: 

I have experienced mixed results with this exercise over the three years I have used it. I find that my students have no trouble identifying that a reaction has occurred and they readily recognize that the color change is a consqeuence of the reaction.

My students tend to struggle with the composition of the complex ions in solution. For the CrCl3 solution, students provide many possible compositions of the coordination complex including the neutral complex, [CrCl3(OH2)3], and the hexaaqua complex, [Cr(OH2)6]3+.  More than 2/3 of the students suggest one of the two predominant complex ions that are present in solution. For the Cr(NO3)3 solution, students often want to use the nitrate as a ligand on the chromium center.

All of my students are usually able to write the balanced reactions and explain the changes in the UV-visible spectra once they identify the composition of the complex cations.

Description: 

Students in inorganic chemistry courses are often interested in the colors of transition metal complexes. This in-class activity serves an introduction to reactions of coordination complexes and pushes students to think about the relationship between the color of a complex cation and its structure. Students are provided with pictures of aqueous solutions of two chromium(III) salts [CrCl3*6 H2O and Cr(NO3)3*9 H2O] at two different times and are then asked to explain the changes observed in the solutions. This activity was inspired by a laboratory experiment which was done as part of the inorganic laboratory course for many years ("Determination of Delta_oct in Cr(III) Complexes" from Szafran, Z., Pike, R.M., and Singh, M.M "Microscale Inorganic Chemistry: A Comprehensive Laboratory Experience" Wiley, New York, (c)1991) .

Learning Goals: 

After completing this exercise, students should be able to:

  • describe how the color of a solution is related to the composition of the coordination complex present in solution,
  • explain how the change in color of a solution indicates that a reaction has occured, and
  • determine the identities of the products and reactants of a reaction that has taken place in solution.

If the UV-visible data are also provided, students should also be able to relate the shifts in the peaks observed in the UV-visible spectra to the position of the ligands in the spectrochemical series.

Equipment needs: 

No equipment is needed for this in-class activity. 

Corequisites: 
Subdiscipline: 
Course Level: 
Implementation Notes: 

I usually use this activity to introduce reactions of coordination complexes in lecture, which falls just after a section in my text on the colors of coordination complexes. While my students have seen many transformations in lab, I use this to connect the two portions of the course. For added empahsis you could make the aqueous solutions and bring them to class.

I usually project the pictures on a screen at the front of the class and I therefore need a device to project it from and a projector.

I break up my class into groups and let them work on this activity collaboratively. I usually let them discuss the problem for about 5-10 minutes and I check in with each group individually. If they are having trouble determining the composition of the coordination complexes, I remind them that they need to write out the formulas in the current way that we represent coordiantion complexes. This usually gets them thinking about primary vs. secondary coordination spheres and waters of hydration. I then let them work for another 10 minutes so that they can write the reactions. I then bring the class together to discuss the results. If time allows, I share the UV-visible data with the entire class and as them to explain the observed changes.

Time Required: 
20-30 minutes
14 Aug 2017

Chapter 21--Stanley Organometallics

Submitted by George G. Stanley, Louisiana State University
Description: 

Chapter 21 from George Stanley's organometallics course, Polymerization

 

this chapter covers the history of polymerization reactions.

Unlike the vast majority of the chapters in this series, there are no powerpoint slides for this chapter.

Everyone is more than welcome to edit the materials to suit their own uses, and I would appreciate being notified of any mistakes that are found.


Subdiscipline: 
Corequisites: 
Course Level: 
14 Aug 2017

Chapter 20--Stanley Organometallics

Submitted by George G. Stanley, Louisiana State University
Description: 

Chapter 20 from George Stanley's organometallics course, Metathesis

 

this chapter covers the history of metathesis reactions.

Unlike the vast majority of the chapters in this series, there are no powerpoint slides for this chapter.

Everyone is more than welcome to edit the materials to suit their own uses, and I would appreciate being notified of any mistakes that are found.


Subdiscipline: 
Corequisites: 
Course Level: 
14 Aug 2017

Chapter 19--Stanley Organometaliics

Submitted by George G. Stanley, Louisiana State University
Description: 

Chapter 19 from George Stanley's organometallics course, Polymerization and Metathesis

 

this chapter covers polymerization catalysis and olefin metathesis.

The powerpoint slides contain answers to some of the in-class exercises, so those are behind the "faculty only" wall. I share these with students after the class, but not before.

Everyone is more than welcome to edit the materials to suit their own uses, and I would appreciate being notified of any mistakes that are found.


Subdiscipline: 
Corequisites: 
Course Level: 
14 Aug 2017

Chapter 18--Stanley Organometallics

Submitted by George G. Stanley, Louisiana State University
Description: 

Chapter 18 from George Stanley's organometallics course, Cross-coupling

 

this chapter covers a variety of different named cross-coupling reactions.

The powerpoint slides contain answers to some of the in-class exercises, so those are behind the "faculty only" wall. I share these with students after the class, but not before.

Everyone is more than welcome to edit the materials to suit their own uses, and I would appreciate being notified of any mistakes that are found.


Subdiscipline: 
Corequisites: 
Course Level: 

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