Molecular Structure and Bonding

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

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
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: 

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
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)
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. 

18 Apr 2018

A use for organic textbooks

Submitted by Chip Nataro, Lafayette College
Description: 

This morning before class I was picking on one of my students for having her organic chemistry textbook out on her desk. I believe I said something along the lines of 'how dare you contaminate my classroom with that!' She explained how she had an exam today and I let it drop. That is until later in the class when I was teaching about chelates. I had a sudden inspiration. I asked the student to pick up her organic book with one hand. I then warned her that I was going to smack the book. I did and she dropped it. Based on the size of most organic textbooks, I believe that very few people would be able to hold on to one with one hand while it is being smacked. I then handed her back the book and asked her to hold it with two hands while I smacked it. Sure enough, she was able to maintain her grasp of the book. I think this rather simple deomonstration did a surprisingly good job of driving home the point.

Learning Goals: 

From this in-class activity students will develop a simple appreciation for the chelate effect.

Corequisites: 
Prerequisites: 
Topics Covered: 
Course Level: 
Equipment needs: 

Organic (or p-chem) textbook

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