VIPEr

Prerequisites:

Corequisites:

Subdiscipline:

Protein Data Bank - A Beginner's Guide

Course Level:

Related activities:

The Guided Tour of Metalloproteins

Utilizing the PDB and HSAB theory to understand metal specificity in trafficking proteins

Exploring Proteins as Ligands using the Protein Data Bank

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:

MetalPDB

Metal PDB in 2018 article

23 Jun 2018

Modeling of the Flavodiiron Nitric Oxide Reductase Active Site Literature Discussion- Bioinorganic focus

Submitted by Sarah Shaner, Southeast Missouri State University

Additional Authors:

Meng Zhou, Lawrence Technological University

Pavithra Hetti Achchi Kankanamalage, Wayne State University

Sunshine Silver, North Park University

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:

Course Level:

Topics Covered:

Catalysis

Chemical literature

Computer modeling

Reaction mechanisms

Prerequisites:

Biology

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.

Subdiscipline:

Molecular Structure and Bonding

Related activities:

Using IR Frequencies to Compare Bond Strengths via Harmonic Oscillator Model

Molecular Orbital of Transition Metal Complexes

Exploration of Nitrosyl Complexes

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:

Inorg. Chem. 57, 8, 4252-4269.

23 Jun 2018

Interpreting Reaction Profile Energy Diagrams: Experiment vs. Computation

Submitted by Douglas A. Vander Griend, Calvin College

Additional Authors:

Andrea Wallace, College of Coastal Georgia

Cassie Lilly, Meredith College

John DiMeglio, University of Michigan

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:

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:

No Corequisites

Subdiscipline:

Molecular Structure and Bonding

Introductory Chemistry

Topics Covered:

Basics of Computational Chemistry

Related activities:

Manganese carbonyl calculation addition

Energy Content of Fuels--Which fuel is "Best?"

Energetics and mechanisms of reductive elimination from Pt(IV)

Isotope Effects in Arene C-H Bond Activation by Cp*Rh(PMe3)

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:

Lehnert Manuscript

22 Jun 2018

Using IR Frequencies to Compare Bond Strengths via Harmonic Oscillator Model

Submitted by Amanda Grass, Wayne State University

Additional Authors:

James F. Dunne, Central College

Jocelyn Pineda Lanorio, Illinois College

Vince Hradil, Concordia University Chicago

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:

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:

First year

Topics Covered:

Bonding models: Discrete molecules

Chemical literature

Physical methods / analytical techniques

Electronic structure

Molecular structure

Corequisites:

Subdiscipline:

Spectroscopy and Structural Methods

Prerequisites:

First Semester Inorganic Chemistry / Foundation Course in Inorganic Chemistry

Related activities:

Inorganic Chemistry Spectroscopy Tutorial: Theoretical Principles and Applications

Determination of the O-H stretching frequency by isotopic substitution using IR spectroscopy

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

Characterization and Investigation of a Binuclear Manganese(III)-Peroxo Metastable Intermediate

Submitted by Anthony L. Fernandez, Merrimack College

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.

Topics Covered:

First Semester Inorganic Chemistry / Foundation Course in Inorganic Chemistry

Kinetics

Corequisites:

No Corequisites

Prerequisites:

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.

Subdiscipline:

Molecular Structure and Bonding

Related activities:

Suite of LOs on Biomimetic Modeling

Modeling the FeB center in Bacterial Nitric Oxide Reductase: A Reading Guide

Modeling post-translational modification in cobalt nitrile hydratase with a metallopeptide from Anne Jones

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:

Coggins et al. JACS 2013, 135, 5631

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:

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:

Biology

Corequisites:

No Corequisites

Topics Covered:

Visualization

Course Level:

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.

Subdiscipline:

Getting to Know the MetalPDB

Related activities:

Metal MACiE Database

Protein Data Bank - A Beginner's Guide

The Guided Tour of Metalloproteins

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.

Web Resources:

MetalPDB

Metal PDB in 2018 article

17 Jan 2018

Inorganic Chemistry Laboratory

Submitted by Anne Bentley, Lewis & Clark College

17 Jan 2018

Metal Tropocoronand Complexes

Submitted by Anthony L. Fernandez, Merrimack College

Evaluation Methods:

I assess the student learning by the quality of the discussion generated by this exercise.

Evaluation Results:

I have used this exercise several times, but I am reporting the results from the Fall 2017 semester.

Students accessed the structures, measured the bond angles using Mercury, and calculated the tau₄' values without any difficulties (questions 1 and 2).

When they got to the third question, they could describe what they observed, but struggled with the language. They were very concerned about how to name the observed structures. They were not satisfied with using the terms "distorted square planar" and "distorted tetrahedral" to describe the structures. (This then led into the discussion of the tau₄' values and why focusing on the names of the strucutres was limiting.)

All of my students were also able to calculate the LFSE values for the Ni(II) center in the four geometries. They asked about the spin state, but I prodded them to talk it through themselves and think back to previous discussions. They quickly realized that for some of the geometries there is no difference between the HS and LS configurations. They decided to calculate the LFSE for both configuations when they were different. Once their calculations were complete, the students determined that square planar should be the preferred geometry based upon the LFSE.

The last question is the one that threw a monkey wrench into what they thought they knew. They were surprised that a d8 metal center would adopt a tetrahedral geometry since this was contrary to what they had originally learned. I then asked about what other influences would impact the observed geometry. About half of my students said that the steric repulsion of the four donor atoms (and other atoms in the tropocoronand ligand) in a square planar arrangement was greater than that in a tetrahedral arrangement. These students were then able to make the connection to the fact that this must outweigh the LFSE value and favor the geometric transition of the nickel center.

Description:

This exercise looks at the metal complexes of tropocoronand ligands, which were first studied by Nakanishi, Lippard, and coworkers in the 1980s. The size of the metal binding cavity in these macrocyclic ligands can be varied by changing the number of atoms in the linker chains between the aminotroponeimine rings, similar to crown ethers. These tetradentate ligands bind a number of +2 metal centers (Cd, Co, Cu, Ni, and Zn) and the geometry of the donor atoms around the metal center changes with the number of atoms in the linker chains. This exercise focuses on the tropocoronand complexes of Ni(II) and students are asked to quantitatively describe the geometry around the metal using the tau4' geometric parameter. This then leads to a discussion of the factors that influence the geometric arrangement of ligands adopted by a metal center. This exercise is used to introduce the concept of flexible metal coordination geometries in preparation of the discussion of metal binding to biological macromolecules and the entatic effect.

Learning Goals:

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

access structures from the CCDC using their online form,
measure bond angles in a crystal structure using appropriate tools,
calculate the tau4' value for a four-coordinate metal center,
calculate the ligand field stabilization energy for a complex in a number of different geometries,
identify the factors that influence the geometry arrangment of ligands around a metal center, and
explain how the interplay of these factors favor the observed geometry.

Equipment needs:

Students will need to have access to the CIF files containing the structural data. These files are part of the Cambridge Structural Database and can be accessed through that if an institutional subscription has been purchased.

Students can also access these CIF files by requesting the structures from the Cambridge Crystallographic Data Centre (CCDC). The identifiers provided in the faculty-only files can be submitted using the "Access Structures" page (https://www.ccdc.cam.ac.uk/structures/) and the associated CIF files can be viewed or downloaded. Students can then measure the bond angles in the JSmol viewer or in Mercury (which is freely available from the CCDC) after downloading the files.

The CIF files for the copper complexes were not available in the CSD, so I created those CIF files from data found in the linked article.

Topics Covered:

Prerequisites:

Corequisites:

Subdiscipline:

Course Level: