Reaction mechanisms

2 Jul 2015
Description: 

Upper division literature discussion of a JACS paper on electrocatalysis.  This activity serves as an introductory look at the paper as a homework assignment to prepare the student for a more in depth class discussion.

Course Level: 
Corequisites: 
Learning Goals: 

Learning Objectives

  1. Identify the structure of a research article
  2. Summarize the motivation and major goals of a study.
  3. Recognize the central reaction and catalyst of a paper.
  4. Analyze a catalytic cycle.
  5. Explain how particular conclusions were determined based on experimental data.
  6. Recognize applications of the techniques presented in the paper.
Time Required: 
50 minutes
29 Jun 2015

Synthesis of Aspirin- A Lewis Acid Approach

Submitted by Kathleen Field, WPI
Evaluation Methods: 

Data sheet for intro level courses along with supplemental questions.  

Lab Reports and supplemental questions for uppper classes.  

 

 

Description: 

This is the procedure for a Fe(III) catalyzed synthesis of aspirin, an alternative to the traditionally sulfuric acid catalyzed synthesis of aspirin.  The prep compares and contrasts the Bronsted acid catalyzed esterification reaction with a Lewis acid iron (III) catalyzed pathway.  This can be used in different courses at different levels, but is it written for a general/intro level chemistry course.    

Prerequisites: 
Learning Goals: 

Intro Chemistry

  • Students will be able to compare and contrast Lewis Acids/Bases with Bronsted Acids/Bases
  • Students will be able to calculate the moles of each reactant, the aspirin product, and the percent yield of product.  
  • Students will be able to determine the limiting reagent and calculate amount of excess material

Organic Chemistry

  • Students will characterize aspirin using melting point determination, IR and NMR spectroscopy and be able to distinguish the different structural elements between the starting material (salicylic acid) and the product (aspirin)
  • Students will be able to differentiate between the Fe(III) catalyzed mechanism and the sulfuric acid catalyzed esterification mechanism

Inorganic Chemistry/upper level

  • Students should be able to relate experimental observations (color) to the d-orbital splitting of Fe(III) complexes
  • Students will be able to draw plausible intermediates and propose a mechanism for the iron catalyzed reaction in relation to the observed reaction colors
Equipment needs: 

Erlenmeyer Flasks, Hot Plate, Balance, Vacuum Filtration, NMR and IR spectroscopy

Chemicals: Acetic Anhydride, FeCl3, Salicylic Acid, Water

Implementation Notes: 

Some notes have been included in the uploaded instructor notes.  

We are interested to submit this to the Journal of Chemical Education, so we (the authors) would be very interested in examining any student data that anyone receives if using the procedure as written in addition to any modifications to the procedure for both general/intro level classes and upper level classes/labs.  

Time Required: 
1-3hr class for intro class, 4 hour class for organic, or longer for upper level classes.
29 Jun 2015

Photoredox Dual Catalysis for Decarboxylative Cross Coupling Reaction

Submitted by Keying Ding, Middle Tennessee State University
Evaluation Methods: 

Student performance should be evaluated by the extent to which the students had carefully read the article, their participance in group discussion and their understanding on fundamental organometallic chemistry taught in previous classes. 

 

 

Evaluation Results: 

This LO was developed at the 2015 IONiC/VIPEr workshop and has not yet been evaluated.

Description: 

In this literature discussion, students are asked to read an article describing a type of dual catalytic system in which the synergistic combination of photoredox catalysis and nickel catalysis provides a general method that would exploit naturally abundant, inexpensive organic molecules as coupling partners. This paper addresses several green chemistry principles and serves as a great literature example for teaching organometallic chemistry or green chemistry course. 

Topics Covered: 
Prerequisites: 
Subdiscipline: 
Corequisites: 
Course Level: 
Learning Goals: 

A student should be able to recognize green chemistry principles and familiar with current research trends in sustainable catalysis area.

A student should be familiar with cross coupling reaction, an important type of organometallic reaction, and understand their applications.

A student should be able to develop fundamental understanding of homogeneous photocatalysis mechanism.

The students should be able to use web tools such as Scifinder and explore current research topics such as cross-coupling reactions and homogeneous photocatalytic reactions.

Implementation Notes: 

This paper and the questions will be handed out to students one week ahead of class discussion. It is best to conduct such exercise after discussion of organometallic chemistry in inorganic chemistry course.

The questions are divided into two parts. The first part is for class discussion, and the second is for homework. The students should turn in their homework answers within one week after class discussion. 

Time Required: 
A 55 minute class period
23 Jan 2015

Organometallics course F 2014

Submitted by Adam R. Johnson, Harvey Mudd College

This is a collection of LOs that I used to teach a junior-senior seminar course on organometallics during Fall 2014 at Harvey Mudd College.

Subdiscipline: 
Prerequisites: 
Corequisites: 
Course Level: 
9 Jan 2015

Ligand Effects in Pd-Catalyzed Cross Coupling

Submitted by Matt Whited, Carleton College
Evaluation Methods: 

Student groups presented answers at the front of the room and were questioned by other groups who had worked on the same problems.

Evaluation Results: 

Generally the groups did well and arrived at some form of the correct answer, though the class discussion part was quite important, as some answers were incomplete or focused on less important aspects of the mechanism.

Having students draw competing reaction pathways with likely intermediates was VERY IMPORTANT.

Description: 

This set of questions was used to promote discussion within small groups (3 to 4 students) on how changing ligand properties can have dramatic effects on the product distributions in Pd-catalyzed cross coupling reactions.  The questions are pretty difficult and not always straightforward, partly because they are derived from the primary literature and thus inherently "messy".

Prior to working through these problems, students would be expected to understand the basic steps in cross couplings such as Suzuki, Stille, Negishi, Kumada, Heck, etc.  It will really help if they have seen some examples of how changes in ligand bulk, denticity, and/or electron richness can favor one reaction pathway over another.

NOTE: These could be used equally easily as problem set or exam questions!

Learning Goals: 

* Students should be able to recognize that catalytic chemical reactions often have many possible competitive pathways and come up with hypotheses about relevant mechanisms for a given set of reactions.

* Students should understand the effects that ligand properties (denticity, electron richness, steric bulk) have on cross coupling reactions and make predictions based on this understanding.

Corequisites: 
Subdiscipline: 
Course Level: 
Implementation Notes: 

This activity was for an upper-level undergraduate organometallic chemistry class with about 20 students.

As mentioned above, I split students up into groups of 3 or 4.  These questions sparked some nice discussions and really helped drive home some of the kinetics I was hoping for them to learn.  I had groups volunteer to present answers, and that worked pretty well, although in the future I may just assign groups to go up to the board to draw out answers after they have had time to work on all the problems.

I have used some of these before as problems on an exam or problem set, and they work well for that purpose, too.

Time Required: 
30 minutes
5 Jan 2015

The Importance of the Trans Effect in the Synthesis of Novel Anti-Cancer Complexes

Submitted by Sheri Lense, University of Wisconsin Oshkosh
Evaluation Methods: 

A student volunteer from each group was asked to share their answer with the class.  Written answers could also be collected and graded.

Evaluation Results: 

Most students did very well in all parts of this activity, although some students initially had trouble explaining the relative trans-directing ability of the ligands.

Description: 

In this activity, students apply knowledge of the trans effect to the synthesis of planar Pt(II) complexes that contain cis-amine/ammine motifs.  These complexes are of interest as both potential novel chemotherapeutic Pt(II) complexes and as intermediates for promising chemotherapeutic drugs such as satraplatin.  The questions in this LO are based on recent research described in the paper “Improvements in the synthesis and understanding of the iodo-bridged intermediate en route to the Pt(IV) prodrug satraplatin,” by Timothy C. Johnstone and Stephen C. Lippard (Inorganica Chimica Acta, Volume 424, 1 January 2015, Pages 254–259).  Students can be given this paper either prior to class or during class.  Student then work in groups of 3-4 to determine whether the sterochemistry of the Pt(II) complexes synthesized in the paper and in previous work is predicted by the trans effect, as well as whether the bond lengths in a crystal structure of one of these Pt(II) complexes is predicted by the trans influence.

Learning Goals: 

After completing this activity, students should be able to:

  • define the trans effect and trans influence
  • explain what properties of a ligand cause it to have a strong trans effect, and be able to predict the relative trans-directing ability of ligands
  • explain how the trans effect can be utilized to develop synthetic methodologies that produce the desired isomer of a square planar complex
  • apply their knowledge of the trans effect to predict the stereochemistry of a product formed from substitution of a square planar complex
  • explain why the stereochemistry of a product formed substitution of a square-planar complex may differ from that predicted by the trans effect
  • explain the effect of the trans influence on metal-ligand bond lengths
Corequisites: 
Subdiscipline: 
Course Level: 
Equipment needs: 

None

Implementation Notes: 

This was done as an in-class activity in which students worked in groups of 3-4 to complete the assignment.  This LO could also be incorporated into a homework assignment instead.

Time Required: 
20-30 minutes
12 Nov 2014

Thinking about Mechanisms of Metal Ion Exchange

Submitted by Christian R. Goldsmith, Auburn University
Evaluation Methods: 

I consider the exercise to be a success when there is a high level of discussion. The groups that more animatedly discuss the material usually come up with a more informed answer.

Periodically, some groups will just sit there and wait for other groups to present their thoughts on the exercise. Sometimes, they can be prompted to be more proactive. Other times...

Evaluation Results: 

Typically, the students struggle to weight the two seemingly contradictory bits of information. They know that first-order rate laws are associated with dissociative mechanisms and that negative entropies of activation are associated with associative mechanisms. Many of the examples that they previously encountered had everything agree and didn't require them to evaluate the limitations of the provided data. They are rarely asked to choose.

Many students will realize that the entropy of activation is an imperfect indicator and determine that the rate-determing step involves the loss of the sodium. About one third to one half, however, will not. These students will tend not to settle on a mechanism.

This said, most students have really liked this exercise as it does give them an opportunity to think more critically about the issues discussed in class.

Description: 

Over the past several years, I've been doing this in-class exercise shortly after discussing mechanisms of ligand exchange. The exercise expands on the lecture material by having the students think about metal ions, rather than ligands, exchanging from a coordination complex. The students are encouraged to work in groups of 3-5 and actively discuss the material amongst themselves before we go over it as a class. I do not provide the students with the article ahead of time, so that they may come up with their own conclusions, as opposed to simply repeating those of the authors. I do encourage the class to read the article afterwards.

One item that I stress to my students is that coming up with a working mechanism is not usually a straightforward process. In certain cases, one needs to carefully weight contradicting bits of information, as the authors did in the source manuscript. Further, whichever mechanism one eventually settles on remains, at best, an educated guess.

In the current study, the rate law is inconsistent with an associative-type mechanism in which the iron reacts with the bimetallic complex before the loss of the sodium. This would seemingly be inconsistent with the negative entropy of activation. This parameter, however, will be influenced by solvation, and a more ordered outer-sphere in the transition state would explain this value and obscure a dissociative-type process. It may very well be that the sodium coordinates to water molecules before its dissociates from the ligand.

The exercise is meant for an upper-level class since it requires a solid understanding of kinetic parameters and kinetics. I have presented the exercise after introducing A, D, and I mechanisms for ligand exchange and discussing several case studies involving square planar and octahedral coordination compounds. I typically give the students about 10-15 min to work on this.

Learning Goals: 

The goal would be to get the students to think more critically about the data that one can acquire in a mechanistic study. In the course of the exercise they will need to evaluate how reliable each datum is and put forward a mechanism that is consistent with the entire set of data.

Corequisites: 
Course Level: 
Equipment needs: 

None. This can be done on the board, although a projector would allow the crystal structure of the bimetallic compound to be presented more quickly and clearly.

Subdiscipline: 
Time Required: 
10-15 min
30 Oct 2014

Bio-Organic Reaction Animations (BioORA)

Submitted by Steven A. Fleming, Temple University
Evaluation Methods: 

Through interviews with faculty, focus group interviews, and student surveys, we have explored the following research questions: What are faculty perceptions of BioORA’s impact on student learning? What are student perceptions of BioORA’s impact on their own learning and understanding?

An inductive mode of analysis of qualitative data in which patterns and themes emerge let us discover the specific technical features of BioORA that the instructors and students found useful, as well as the ways in which BioORA increased student engagement and helped students with visualization skills, which both the instructors and students recognized as fundamentally difficult for novices in the fields of biology and chemistry. Additionally, analysis revealed similarities and differences between the perceptions of instructors and students. For example, the instructors emphasized BioORA’s function as a link between specific concepts or principles and the larger context of the class, as well as its function as a link between lectures and lab sections, organic chemistry and biochemistry, what students learn in class and their future work in science, and the individual steps within the reaction.

See: 

“Faculty and Student Perceptions of Student Learning and Experiences with a 3D Simulation Program” Gunersel, A. B.; Fleming, S. A.; J. Chem. Ed., 2013, 90, 988-994.

“Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback” Gunersel, A. B.; Fleming, S. A.; Biochem. Mol. Biol. Ed., 2014, 42, 190-202.

Evaluation Results: 

 

See:

“Faculty and Student Perceptions of Student Learning and Experiences with a 3D Simulation Program” Gunersel, A. B.; Fleming, S. A.; J. Chem. Ed.201390, 988-994.

“Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback” Gunersel, A. B.; Fleming, S. A.; Biochem. Mol. Biol. Ed.201442, 190-202.

Description: 

 

Bio-Organic Reaction Animations (BioORA) can be used as a teaching tool for bio-inorganic courses. BioORA illustrates large biomolecules obtained from crystal structures in the Protein Data Bank using Jmol. The student can manipulate this structure, which is shown on the right-hand side of the screen of BioORA. On the left-hand side of the screen a stripped-down view of the binding site is shown. This stripped down representation can also be manipulated and has three viewing options: ball and stick, tube, and space-filling. The software helps students visualize the three-dimensional aspects of enzyme chemistry. There are more than 25 animations and several of them have coordinating metals involved in the reaction mechanisms that are illustrated.

 

Subdiscipline: 
Prerequisites: 
Corequisites: 
Learning Goals: 

 

BioORA is a visualization program for biochemistry that will focus on molecular events.  The natural tendency has been to substitute acronyms for the biomacromolecules.  This is an understandable result in light of the size of the relevant structures.  However, we have shown that computer imaging technology is sufficiently advanced now to handle animations of the actual molecules involved in the biochemical pathways.  This type of multimedia presentation can provide students with three-dimensional representations of the biomolecules and three-dimensional animations of binding and enzyme catalyzed reactions. 

 

Our goal is to bring the molecular aspects of biochemistry to the forefront.  The chemistry for the bio-organic processes is documented and the 3D visualization software is now accessible.  There is a need for more accurate molecular representation and we are eager to provide it.  We expect that students, regardless of their major, will benefit from this teaching tool.  We hope that it will improve student appreciation of the organic chemistry that occurs in biological systems. 

Course Level: 
12 Sep 2014

Maggie's LOs

Submitted by Chip Nataro, Lafayette College
Corequisites: 
Prerequisites: 
17 Jul 2014

Employing 2D NMR and NOE to assign protons in an organometallic complex

Submitted by Sherzod Madrahimov, Northwestern University
Description: 

The following paper will be given to the students to study at home along with the questions in the attached document. Students will be allowed to discuss their answers in small groups and refine their answers, before the corresct answer is revealed.

The students will not need to see the actual spectra that are in the SI to be able to address the given questions, the spectra can be projected to the class when the answers of the student groups are discussed

Origins of Enantioselectivity during Allylic Substitution Reactions Catalyzed by Metallacyclic Iridium Complexes.

J. Am. Chem. Soc., 2012, 134 (19), pp 8136–8147

DOI: 10.1021/ja212217j

Learning Goals: 

In answering these questions, students will learn to use 2D-NMR and NOE to assign protons in an organometallic complex.

They will also gain some experience in analyzing published material

Prerequisites: 
Course Level: 
Corequisites: 
Equipment needs: 

Computer and projector

Subdiscipline: 
Implementation Notes: 

The paper is quite a long one and students should be given ample time to address the questions and encouraged to skim through the paper.

The students don't need to see the actual spectra that are in the SI, to be able to answer the questions, the spectra (3-4 spectra) can be projected in the class and proton assignments can be discussed

 

Time Required: 
student need to study the paper before coming to class and 10-20 min of class time

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