Upper Division

6 Jul 2018

Getting to Know the MetalPDB

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation 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.

Prerequisites: 
Corequisites: 
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)
25 Jun 2018

Orbital Overlap and Interactions

Submitted by Jocelyn Pineda Lanorio, Illinois College
Evaluation Methods: 

Evaluation was conducted by the instructor walking around the computer lab to check progress and address the issues students had.

Evaluation Results: 

This LO was implemented once in advanced inorganic chemistry composed of 5 chemistry major students. Students clearly identified the type of orbital interactions and differentiated bonding, nonbonding, and antibonding MOs. Students commented that this is a great in-class activity before the discussion of MOs for diatomic molecules (Chapter 5 of MFT).

Description: 

This is a simple in-class activity that asks students to utilize any of the given available online orbital viewers to help them identify atomic orbital overlap and interactions. 

Learning Goals: 

Following the activity, students will be able to:

  1. draw the s, p, and d atomic orbitals using the given coordinate axes
  2. analyze the orbital interaction by looking at their symmetry and overlap (or lack of)
  3. differentiate s, p, d, and nonbonding molecular orbital

 

Equipment needs: 

Internet connection and computer

Prerequisites: 
Corequisites: 
Implementation Notes: 

This activity should be run in a computer lab.

Time Required: 
15 to 20 minutes
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
Evaluation Methods: 

 A key is provided for the discussion questions. The discussion questions can be collected and graded.

Description: 

The activity is designed to be a literature discussion based on Nicolai Lehnert's Inorganic Chemistry paper, Mechanism of N-N Bond Formation by Transition Metal-Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases.  The discussion questions are designed for an advanced level inorganic course. 

 

Corequisites: 
Course Level: 
Learning Goals: 

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

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

  2. Define and identify non-innocent ligands.

  3. Identify how electron density on the metal center can impact ligand coordination.

  4. Draw molecular orbital diagrams for coordination compounds.

  5. Identify covalency by interpreting molecular orbital diagrams and data.

  6. Define and interpret Enemark-Feltham notation.

  7. Recognize spin multiplicity of the metal and ligand fragments in a complex and how it corresponds to the overall spin multiplicity.

  8. Identify possible electronic structures of {FeNO} complexes.

  9. Describe various characteristics to be considered in the selection of a good reductant.

  10. Explain how occupying bonding versus antibonding orbitals changes the reactivity of a system.

Implementation Notes: 

This is a very involved article with lots of great concepts. It will take a lot of time to read. We suggest giving this as a student group assignment. Give the students a copy of the article and discussion questions. Give them 1-2 weeks to read through the article and complete the discussion questions. Spend one or two 50 min. class periods going over the discussion questions. 

Note: This was developed during the 2018 VIPEr Workshop and has not been implemented, yet. Above instructions are an initial guide, any feedback is welcome and appreciated!

Time Required: 
50-90 min.
23 Jun 2018

Bonding in Tetrahedral Tellurate (updated and expanded)

Submitted by Jocelyn Pineda Lanorio, Illinois College
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 literature discussion is an expansion of a previous LO (https://www.ionicviper.org/literature-discussion/tetrahedral-tellurate) and based on  a 2008 Inorganic Chemistry article http://dx.doi.org/10.1021/ic701578p

Corequisites: 
Prerequisites: 
Learning Goals: 

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

  1. Identify the key aspects of a primary publication including significance, synthetic methods, and product characterization.
  1. Identify isoelectronic species by drawing Lewis Structures.  
  1. Apply standard NMR shielding/deshielding concepts to interpret heteronuclear NMR spectra.
  1. Identify experimental protocols and reaction conditions.
  1. Discuss how the various experimental methods in the article provide evidence of the structure of the compound.
  1. Recognize scientific nomenclature relevant to the research article.
  1. Identify the relationship of telluric acid and tellurate to the related species given in the paper based on periodic trends. (Periodic Acid - isoelectronic; Sulfuric and Selenic acid - same column)
  1. Compare bond lengths for species in the paper.
  1. Identify the point group of the TeO42- with all the same Te-O bond lengths and when with different Te-O bond lengths.
  1. Predict the product(s) and by-products of a chemical reaction.
  1. Identify species and intermolecular interactions in a crystal structure.

 

Related activities: 
Implementation Notes: 

Students are asked to read the paper and answer the discussion questions before coming to class. 

Time Required: 
50 +
22 Jun 2018
Evaluation 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: 
  1. Evaluate the effect of changes in mass on a harmonic oscillator by assembling and observing a simple spring-mass system (Q1 and 2)

  2. Apply these mass-frequency observations to NO and predict IR isotopic shift (14N vs. 15N) (Q3 and 4)

  3. 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).

 

Corequisites: 
Implementation Notes: 

Assemble students into small groups discussions to answer the questions to the activity and collaborate.

 

 

Time Required: 
Approximately 50 minutes
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.
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)
16 May 2018

MetalPDB website

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

I kept track of how much my students used information obtained from this site during their literature presentations.

Evaluation Results: 

The students had little difficulty accessing or using the site. Most of my students used information obtained from the site in their presentations and during in-class dicsussions.

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.

In the past, I have used Metal MACiE to help find metal-containing biological macromolecules and to access information about the metal function and coordination environment. Unfortunately, this site, while still available, has not been updated in several years. I have recently found the MetalPDB website which was created at CERM (University of Florence). This site "collects and allows easy access to the knowledge on metal sites in biological macromolecules" and can be used to explore structures deposited in the PDB.

I also expect my students to use this site to obtain information for their assignments and presentations.

Prerequisites: 
Corequisites: 
Learning Goals: 

When using this website, students are able to:

  • 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.

These learning goals are incorporated in the associated in-class activity, which is posted separately.

Implementation Notes: 

I used this 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, 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.

To learn how to use the site, I assigned an associated activity (posted separately) that I have the students complete before coming to class. This experience allows the students to use the site to get background information about metal geometry and common ligands for their assignments and presentations.

This site utilizes JavaScript and JSmol so students must ensure that Java functions properly in their preferred web browser. I have found no issues accessing this site with any of the browsers used by myself or my students.

 

10 May 2018

3D Sym Op

Submitted by Caroline Saouma, University of Utah
Evaluation Methods: 

None

Description: 

This is a great app that helps students see the symmetry in molecules. It allows you to choose a molecule (by name, structure, or point group) and display a 3D rendition of it. You can then have it display the symmetry elements, and/or apply all the symmetry operations. 

It is available for both android and apple phones: (probably easier to just search for it)

apple: https://itunes.apple.com/us/app/3d-sym-op/id1067556681?mt=8

android: https://play.google.com/store/apps/details?id=com.nus.symmo&hl=en_US

Topics Covered: 
Prerequisites: 
Learning Goals: 

A student should be able to find symmetry elements in molecules. 

Corequisites: 
Implementation Notes: 

In class I project my phone screen so they can see it, and I encourage the students to work along with their phones. I prefer this to models, as it is hard to remember what things looked like before you did the transformation, and moreover, my students have a hard time finding the symmetry elements. 

 

I encourage the students to play with it anytime they have a few spare moments- waiting for the bus, in line for food, etc. 

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