Bioinorganic Chemistry

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)
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
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
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.

 

3 Jun 2017
Evaluation Methods: 

Students were evaluated by the instructor during the activity. The instructor was available throughout the activity to answer questions and guide inquiry. This activity generated good discussion among students and most were able to work their way through. 

Evaluation Results: 

All students completed the activity during the class period and gained a deeper appreciation for metals in biology, protein structure, and using NMR to determine protein structure. Some students needed more guiding through the rationales of metal toxicities and the multi-dimensional NMR experiments than others. 

Description: 

This activity was designed as an in-class group activity, in which students begin by using basic principles to predict relative toxicities and roles of metals in biological systems. Students then learn about the structures of metallothioneins using information from the protein data bank (PDB) and 113Cd NMR data. By the end of the activity, students will have analyzed data to identify and determine bonding models and coordination sites for multiple cadmium centers in metallothioneins. It is based on recent literature, but does not require students to have read the papers before class.

Learning Goals: 

Students will be able to:

  1. Use fundamental principles to predict toxicities of metals
  2. Apply hard-soft acid-base (HSAB) theory to metals in biological systems
  3. Utilize the protein data bank (PDB) to investigate protein-metal interactions
  4. Explain the roles of metallothioneins in biological systems
  5. Evaluate 1-D and 2-D 113Cd NMR to determine structures of Cd bonding sites in metallothioneins
  6. Explain how NMR can be utilized to determine protein structure
Course Level: 
Corequisites: 
Implementation Notes: 

This activity was developed for a Master's level bioinorganic course, but could be utilized in an advanced undergraduate inorganic course. Students were given the worksheet at the beginning of class and worked together in groups to answer the questions. Students did not have access to the paper and had not read any articles previously. Using the PDB was done as a separate in-class activity, so students had some familiarity with the PDB codes and amino acid sequences. 

A brief refresher of [1H-1H] COSY was presented before beginning the activity. 

Time Required: 
60 min
11 Apr 2017

Johnson Matthew Catalytic Reaction Guide

Submitted by Sheila Smith, University of Michigan- Dearborn
Evaluation Methods: 

No evaluation yet

Evaluation Results: 

No results yet

Description: 

This guide, available in print, online and in an app, allows users to look up appropriate catalysts and conditions to accomplish a wide variety of reactions.

 

Prerequisites: 
Course Level: 
Learning Goals: 

A student should be able to use the Catalytic Reaction Guide (CRG) to identify appopriate reaction conditions and catalysts to accomplish a wide variety of reactions.

Implementation Notes: 

I have not yet used this... I just picked up a copy at ACS, but will add to this as I implement it in my classroom.

 

Time Required: 
variable
3 Mar 2017

In-class peer review

Submitted by S. Chantal E. Stieber, Cal Poly Pomona
Evaluation Methods: 

Student participation was evaluated during the in-class portion based on the questions students asked. 

The formal peer review homework was evaluated based on completion, level of thought and thoroughness.

Evaluation Results: 

Overall, students were very interested in this topic and had not formally learned about the process before. There was a very lively discussion and a lot of questions were asked. All students received full credit for participation. 

Similarly, once students received their classmate's paper for peer review, they took the process very seriously and carefully went through the paper and answered the worksheet questions. 

I was very impressed by the high quality of the formal peer reviews that were turned in as homework. Students clearly spent a lot of time to carefully think about the paper and craft a reasonable response. Most students received full-credit. 

Description: 

This activity includes questions for students to answer to help guide them through the process of peer review. It was designed to assist students in writing peer reviews for research reports written by their classmates, but could be applied to literature articles as well.

Corequisites: 
Prerequisites: 
Learning Goals: 

A student will be able to:

-Explain how the peer-review process works

-Critically read through a research article

-Carefully review a research article

-Write a professional peer review

Implementation Notes: 

An overview of peer review was given with three powerpoint slides. Students then worked through a modified Q&A of the peer review module "Peer Review - How does it work?" posted by Michael Norris on VIPEr. This provided students with an example of real reviews, along with the resulting article revisions. 

The current worksheet was then passed out to students along with a research report written by one of their classmates (I assigned these and removed names). In class, students answered the questions on the worksheet and were able to ask questions of the editor (the instructor in this case). Following the in-class peer review, students had to write a formal peer review, which was turned in as homework. 

The peer review was a final component of a research report that students had been working on throughout the course. The final report was turned in after students had received the review comments back from their peers. The grade of the final report took into consideration whether or not students had made modifications based on comments by their peer reviewer.

 
Time Required: 
60 min

Pages

Subscribe to RSS - Bioinorganic Chemistry