Kinetics

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
17 May 2018
Evaluation Methods: 

This assignment is graded based upon effort and not on the submission of correct answers. To receive full credit for this assignment, students must make a honest effort to complete the assignment, turn it in on time, and participate in the in-class discussion. I expect students to attempt to answer almost all of the questions, but I am not concerned if they got every answer completely correct.

I use the in-class discussion to go over student responses and have them guide each other to the correct answers. I judge student understanding by the overall quality of the discussion.

Evaluation Results: 

Of my 8 students, 5 received full credit for the assignment. Of these 5 students, four answered every question and one answered about 3/4 of the questions. These 5 students particpated in the in-class discussion and had little trouble recalling facts from the article or discussing the findings. I was quite pleased overall with the student responses and their preparedness for the dicussion.

When I looked a bit more closely at the submitted answers, I found that students submitted correct or mostly correct answers to the vast majority of the questions. Several of the students struggled with question 18. While they could all calculate the number of unpaired electrons that would give rise to the observed magnetic moment, several struggled to explain the lack of coupling between the the metal centers. (It is worth noting that this is one of the few questions for which the answer could not be found directly in the article.)

In the discussion, it became apparent that while the students provided correct answers for questions 23 & 24 (activation parameters) they did not understand how to calculate them, which was disappointing, or how to use them to infer mechanistic details.

Description: 

In this literature assignment, students are asked to read an article from the primary literature on a binuclear manganese-peroxo complex that is similar to species proposed to be involved in photosynthetic water splitting and DNA biosynthesis. The assignment contains 25 questions that are intended to guide students through the article and help them extract important information about the work. The completed questions are then used as the basis for an in-class discussion of model complexes, which leads to a more advanced discussion on the topic.

While this assignment is geared towards an advanced course, aspects of this assignment (kinetics, structure, electron counting) would be suitable for a foundation-level course.

This literature discussion was created in memory of my friend, Elena Rybak-Akimova (one of the co-authors of the article), just after she passed away. I took a few minutes at the end of the class to talk about Elena and how her skill and knowledge in kinetics made much of this work possible.

Corequisites: 
Course Level: 
Learning Goals: 

After completing this assignment, a student should be able to:

  • extract important information from the primary literature,
  • recall the importance of metal-peroxo complexes,
  • describe how the authors synthesized and characterized the complexes under investigation,
  • explain why unusual techniques needed to be used to study the kinetics of the reaction,
  • rationalize why model complexes are useful in the examination of biologically-active metals.
Implementation Notes: 

The assignment was given to the students about 1 week before the discussion was to take place in class. A Google Doc version of this assignment was distributed using Google Classroom. Students were expected to download the article through our library, read the article, and answer the guiding questions in the assignment. 

In the class preceding our discussion of the article, we covered model complexes, the difference between structural and functional mimics, and why studying the two types of model complexes is important. We also looked at a number of examples: hydrogenase mimics, Collman's picket fence porphyrin, B12 mimics, molybdenum-oxo compounds, B12 model complexes, and engineered metalloeznymes. We also talked about ligand design using examples from Andy Borovik.

This assignment is intended to prepare students for the in-class discussion of the article so students had to submit their answers (via a Google Doc) before the start of class to receive credit for the assignment. The dicussion was based upon student responses. (I peruse the student responses just before class to see what questions they struggled with and which they seem to understand quite well.) We did not go through every question in detail, but instead covered 15-17 questions. Students wanted to discuss the characterization and kinetics questions extensively. I came prepared to talk a bit about stopped flow kinetics and Eyring plots, which was good because students had questions about both of those topics.

After completing our discussion of the assignment, I asked the students to determine the type of model compound that this was and we looked at the proposed mechanism of water splitting by photosystem II. 

Time Required: 
1-2 hours (outside of class by student); 45-60 minutes in class (including discussion of related topics)
3 Jun 2017

An ion exchange method to produce metastable wurtzite metal sulfide nanocrystals

Submitted by Janet Schrenk, University of Massachusetts Lowell
Evaluation Methods: 

Evaluation methods are at the discretion of the instructor. For example, you may ask students to provide written answers to the questions, evaluate whether they participated in class discussion, or ask students to present their answers to specific questions to the class.

Description: 

In this literature discussion, students use a paper from the literature to explore the synthesis, structure, characterization (powder XRD, EDS and TEM) and energetics associated with the production of a metastable wurtzite CoS phase. Students also are asked define key terms and acronyms used in the paper; identify the goal of the experiments and determine if the authors met their goal. They examine the fundamental concepts around the key crystal structures available.  

 

Preserving Both Anion and Cation Sublattice Features during a Nanocrystal Cation-Exchange Reaction: Synthesis of a Metastable Wurtzite-Type CoS and MnS

Powell, A.E., Hodges J.M., Schaak, R.E. J. Am. Chem. Soc. 2016, 138, 471-474.

http://pubs.acs.org/doi/abs/10.1021/jacs.5b10624

 

There is an in class activitiy specifically written for this paper. 

Corequisites: 
Prerequisites: 
Learning Goals: 

In answering these questions, a student will be able to…

  • define important scientific terms and acronyms associated with the paper;

  • describe the rocksalt, NiAs, wurtzite, and zinc blende in terms of anion packing and cation coordination;

  • differentiate between the structure types described in the paper;

  • explain the difference between thermodynamically stable and metastable phases and relate it to a free energy diagram; and

  • describe the structural and composition information obtained from EDS, powder XRD, and TEM experiments.

Implementation Notes: 

This learning object was created at the 2017 IONiC Workshop on VIPEr and Literature Discussion. It has not yet been used in class.

Time Required: 
50 minutes
3 Jun 2017

Quantum Dot Growth Mechanisms

Submitted by Chi Nguyen, United States Military Academy
Evaluation Methods: 

The question document attempted by students in preparation for the literature discussion will be due prior to the in-class discussion. In particular, students' performance on the particle-in-a-box question will be evaluated to assess retention from the previously covered course material. The next exam following the discussion will contain specific question(s) (data/figure analysis) addressing these topics. Students' performance difference between the two will be evaluated. The extent to which students improve their post-discussion understanding of the concepts will direct future implementation.

Evaluation Results: 

To be determined. This is a newly proposed literature discussion.

Description: 

This literature article covers a range of topics introduced in a sophomore level course (confinement/particle-in-a-box, spectroscopy, kinetics, mechanism) and would serve as a an end-of-course integrated activity, or as a review activity in an upper level course. The authors of the article employ UV-vis absorption spectroscopy of CdSe quantum dots as a tool to probe the growth mechanism of the nanoparticles, contrasting two pathways.

 

Reference:  DOI 10.1021/ja3079576 J. Am. Chem. Soc. 2012, 134, 17298-17305

 
Corequisites: 
Prerequisites: 
Learning Goals: 

Apply the particle in a box model to interpret absorbance spectra with respect to nanoparticle size.

 

Analyze the step-growth and living chain-growth mechanisms proposed in this paper.

 

Evaluate the kinetics as it applies to the step-addition.

 

Recognize and apply multiple scientific concepts in an integrative manner.
Implementation Notes: 

Sophomore level implementation:  Recommend focusing on select portions (e.g. Figures 1b, 2, 5 with corresponding text) of the paper rather than having students read the entire document.  The learning objects focus on select topics, such as particle-in-a-box, reaction mechanism, and kinetics in conjunction with absorbance spectroscopy.  This would be a good literature discussion resource for an end-of-course integrative experience that encompasses multiple topics from general chemistry and inorganic chemistry.  

 

Advance level implementation:  For an upper division course, incorporate the paper in its entirety early in the course as an assessment on students’ ability to integrate multiple concepts that they should have learned in general chemistry, organic chemistry, and physical chemistry.  To enhance the experience, accompanying the literature discussion on this paper with a laboratory experience by repeating the experimental and characterization procedures presented in the paper, and having students' compare their results with published results.  This also serves to enhance students’ scientific literacy by critically assessing the quality of the paper.

 

Excerpts of the paper and questions can be used on a graded event, or as lesson preparation for in class discussion.

 
Time Required: 
In-class discussion takes approximately 50 minutes with students having already read the paper and submitted their responses to the questions.
23 May 2017

Ligand based reductive elimination from a thorium compound

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

This was developed after the semester in which I teach this material. I look forward to using it next fall and I hope to post some evaluation data at that point.

Description: 

This literature discussion is based on a paper describing the ligand-based reductive elimination of a diphosphine from a thorium compound (Organometallics2017, ASAP). The thorium compound contains two bidentate NHC ligands providing an opportunity to discuss the coordination of these ligands. The ligand-based reduction is very subtle and would be challenging for students to pick up without some guidance. The compound undergoing reductive elimination also presents an excellent introduction into magnetic nonequivalence and virtual coupling. In addition, the compounds presented in this paper provide the opportunity to do electron counting on f-block compounds. 

Prerequisites: 
Corequisites: 
Learning Goals: 

Upon completing this LO students should be able to

  1. Use the CBC method to count electrons in the thorium compounds in this paper
  2. Describe the bonding interaction between a metal and a NHC ligand
  3. Discuss magnetic nonequivalency and virtual coupling
  4. Describe ligand-based reductive elimination and rationalize how it occurs in this system
Course Level: 
Time Required: 
50 minutes
5 May 2017

SOP4CV - A Web Resource for Cyclic Voltammetry Information

Submitted by Gerard Rowe, University of South Carolina Aiken
Description: 

http://sop4cv.com/

This is a great website created by Dr. Daniel Graham (who has the distinction of publishing a paper featured on TOC ROFL) to give anyone a working understanding of cyclic voltammetry techniques, their physical background, and the interpretation of their results.  

Prerequisites: 
Corequisites: 
Subdiscipline: 
Learning Goals: 

Students will gain experience interpreting the basic features of cyclic voltammograms, including: half-potential, electrochemical reversibility, chemical reversibility, and scan rate dependence

Students will learn the physical origins of the "duck" shape of a reversible CV using the Nernst equation and diffusion concepts

Students will learn what analytical methods are available using CV

Implementation Notes: 

None yet.  I'm considering creating an activity using the information in this website, but for now I just wanted to share this resource.

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