13
Feb
2019
Bioinorganic chemistry
28
Jan
2019
Inorganic Chemistry
Submitted by Kari Young, Centre College
16
Jan
2019
Descriptive Inorganic Chemistry
Submitted by Catherine McCusker, East Tennessee State University
3
Jan
2019
Venn Diagram activity- What is inorganic Chemistry?
Submitted by Sheila Smith, University of Michigan- DearbornEvaluation Methods:
I did not assess this piece, except by participation in the discussion
Evaluation Results:
I asked my students to write an open ended essay to answer the question (asked in that first day exercise): What is Inorganic Chemistry.
Interestingly, 2 of my 15 students drew a version of this Venn Diagram to accompany their essays.
Description:
This Learning Object came to being sort of (In-)organically on the first day of my sophomore level intro to inorganic course. As I always do, I started the course with the IC Top 10 First Day Activity. (https://www.ionicviper.org/classactivity/ic-top-10-first-day-activity). One of the pieces of that In class activity asks students- novices at Inorganic Chemistry- to sort the articles from the Most Read Articles from Inorganic Chemistry into bins of the various subdisciplines of Inorganic Chemistry. As the discussion unfolded, I just sort of started spontaneously drawing a Venn Diagram on the board.
I think Venn diagrams are an excellent logic tool, one that is too little applied these days for anything other than internet memes. This is a nice little add-on activity to the first day.
Your Venn diagram will likely look different from mine. You're right.
Learning Goals:
The successful student should be able to:
- identify the various sub-disciplines of inorganic chemistry.
- apply the rules of logic diagrams to construct overlapping fields of an Venn diagram.
Prerequisites:
Corequisites:
Equipment needs:
colored chalk may be handy but not required.
Topics Covered:
Course Level:
Subdiscipline:
Related activities:
Implementation Notes:
I used this activity in conjuction with a first day activity LO (also published on VIPEr).
I shared a clean copy (this one) with the students after the class where we discussed this.
Time Required:
10-15 minutes
8
Nov
2018
5-ish Slides about Enemark-Feltham Notation
Submitted by Kyle Grice, DePaul UniversityDescription:
This is a basic introduction to Enemark-Feltham that can be used in conjunction with any literature that has Iron nitrosyls in it. I made this as a follow up to the work that came ouf of the 2018 VIPEr workshop in UM-Dearborn.
Corequisites:
Prerequisites:
Topics Covered:
Course Level:
Learning Goals:
A student will be able to detemine the Enemark-Feltham label for a simple iron nitrosyl
A student will be able to describe bonding differences between NO+, NO, and NO- ligands.
Subdiscipline:
Related activities:
Implementation Notes:
I haven't used this yet, but It can be a quick lecture module or online module to help students understand Enemark-Feltham before analyzing a paper on iron nitrosyls.
Time Required:
10 min
6
Jul
2018
Getting to Know the MetalPDB
Submitted by Anthony L. Fernandez, Merrimack CollegeEvaluation Methods:
I reviewed student answers to this assignment and evaluated their contributions to the discussion that took place. I also tried to keep track of how much they used information obtained from this site during their literature presentations.
Evaluation Results:
This assignment is quite straightforward and the 6 of 8 students who completed the assignment had little trouble coming up with correct answers for all of the questions.
At the end of the semester, each student had to give two presentations on bioinorganic topics. They were expected to discuss the metal coordination environment and how "normal" it was, as well as the possibility of substituting another metal into the coordination sphere. One student used information from the MetalPDB in both of her presentations, three students used information in one of their presentations, and four students did not include information from the site in either presentation.
Description:
When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.
I expect my students to use this site to obtain information for their assignments and presentations. This activity is a self-paced introduction to the site that my students complete outside of class. This activity has students use the site to obtain information about metal coordination environments, the common geometries adopted by metals in biological environments, and the common ligands that are used to bind metals.
Learning Goals:
After completing this exercise, students should be able to:
access the MetalPDB site,
obtain statistics pertaining to the number of metal-containing structures in the PDB,
determine the most common geometry observed for a particular metal in a biological structure,
identify the most common ligands attached to the metal when bound in a biological macromolecule, and
find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.
Equipment needs:
Students need access to the internet and a web browser that is capable of running JavaScript and JSmol. This site is accessible on devices running iOS, but the layout of the site works better on a laptop screen.
Topics Covered:
Prerequisites:
Corequisites:
Subdiscipline:
Course Level:
Related activities:
Implementation Notes:
I used the MetalPDB site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules in both my advanced and foundation-level courses, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.
I also have students use the site to get background information about metal geometry and common ligands for their assignments and presentations. I ask them to complete this activity outside of class. I usually distribute this as a Google Doc to my students (through Google Classroom) so that I have access to all of their responses.
For several of the questions/groups of questions, I assign individual members of the class specific geometries (question #5), metals (questions #6-9), or PDB structures (questions #11-13) and we pool their answers in class. We then spend about 30-45 minutes in class discussing the results and search for commonalities and connections to other structures that we have already discussed in class.
Time Required:
1-2 hours (outside of class by student); 30-45 minutes in class (including discussion of related topics)
Web Resources:
23
Jun
2018
Modeling of the Flavodiiron Nitric Oxide Reductase Active Site Literature Discussion- Bioinorganic focus
Submitted by Sarah Shaner, Southeast Missouri State UniversityEvaluation 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:
Course Level:
Topics Covered:
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.
Related activities:
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.
Web Resources:
23
Jun
2018
Interpreting Reaction Profile Energy Diagrams: Experiment vs. Computation
Submitted by Douglas A. Vander Griend, Calvin CollegeEvaluation 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:
Interpret reaction profile energy diagrams.
Use experimental and computational data to calculate half lives from activation energies and vice versa.
Assess the value and limitations of DFT calculations.
Prerequisites:
Course Level:
Corequisites:
Topics Covered:
Related activities:
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
Web Resources:
22
Jun
2018
Using IR Frequencies to Compare Bond Strengths via Harmonic Oscillator Model
Submitted by Amanda Grass, Wayne State UniversityEvaluation Methods:
Discuss students responses with respect to the answer key.
Evaluation Results:
This activty was developed for the IONiC VIPEr summer 2018 workshop, and has not yet been implemented.
Description:
Inorganic chemists often use IR spectroscopy to evaluate bond order of ligands, and as a means of determining the electronic properties of metal fragments. Students can often be confused over what shifts in IR frequencies imply, and how to properly evaluate the information that IR spectroscopy provides in compound characterization. In this class activity, students are initially introduced to IR stretches using simple spring-mass systems. They are then asked to translate these visible models to molecular systems (NO in particular), and predict and calculate how these stretches change with mass (isotope effects, 14N vs 15N). Students are then asked to identify the IR stretch of a related molecule, N2O, and predict whether the stretch provided is the new N≡N triple bond or a highly shifted N-O single bond stretch. Students are lastly asked to generalize how stretching frequencies and bond orders are related based on their results.
Learning Goals:
Evaluate the effect of changes in mass on a harmonic oscillator by assembling and observing a simple spring-mass system (Q1 and 2)
Apply these mass-frequency observations to NO and predict IR isotopic shift (14N vs. 15N) (Q3 and 4)
Predict the identity of the diagnostic IR stretches in small inorganic molecules. (Q5, 6, and 7)
Equipment needs:
Springs, rings, stands, and masses (100 and 200 gram weights for example).
Course Level:
Topics Covered:
Corequisites:
Related activities:
Implementation Notes:
Assemble students into small groups (2-4) discussions to answer the questions to the activity and collaborate.
Time Required:
Approximately 50 minutes
17
May
2018
Characterization and Investigation of a Binuclear Manganese(III)-Peroxo Metastable Intermediate
Submitted by Anthony L. Fernandez, Merrimack CollegeEvaluation 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.
Topics Covered:
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.
Related activities:
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)
Web Resources:
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