Molecular Structure and Bonding

10 Sep 2017

Inclusive Pedagogy: A Misidentified Molecule and Paper Retraction

Submitted by Sibrina Nichelle Collins, Lawrence Technological University
Evaluation Methods: 

This LO has various options for evaluation. First, a rubric should be prepared based on criteria identified by the student teams for evaluating the team posters. The students will be evaluated based on their ideas and attention to detail for their individual  reponses to the discussion questions. In addition, a 7-question survey is included in the handout for the students. Four of the questions address self-efficacy questions for chemistry majors. These questions were modified from a self-efficacy instrument developed by Baldwin et al for biology students. I have included a link to the model. We should be developing assessment tools that address science identity, sense of belonging, and self-efficacy for chemistry majors. If a student does not feel comfortable in a chemistry course, they will likely not pursue a career as a chemist.

Evaluation Results: 

Will be reported later.

Description: 

This learning object focuses on teaching students how to read and use Chemical and Engineering News for class discussions and critically evaluate the scientific literature. Recently, Chemical and Engineering News published an article about the retraction of a 15-year old paper, which had misidentified a multidentate ligand, which is central to the paper (Ritter, S.K. “Chemist Retract 15-year old paper and publish a revised version.” Chem. Eng. News, 2017, 95, (36), p6). The authors published a revised paper to the journal in 2017, with the correct structure of the ligand along with an x-ray crystal structure. This activity consists of two components, namely the students working in teams to discuss the C &E News article, retracted Inorganic Chemistry paper (DOI:10.1021/acs.inorgchem.7b01932) and the revised paper (DOI:10.1021/acs.inorgchem.7b01117) and preparing a poster for a “Gallery Walk.”

Learning Goals: 

An important learning goal for this learning object is to incorporate practices for creating an inclusive learning environment for students (inclusive pedagogy). The goals for this LO are for students to:

  • Read and use C&E News for student-led discussions
  • Critically evaluate experimental evidence published in the scientific literature
  • Apply concepts learned in previous chemistry courses
  • Gain a better understanding of the peer-review process for publication and retraction
  • Appreciate the importance of structural analysis tools such as X-ray crystallography
  • Prepare a team poster to communicate scientific ideas
Prerequisites: 
Equipment needs: 

The students will need 3M Post-IT paper and markers to prepare a poster for the "Gallery Walk."

Corequisites: 
Course Level: 
Implementation Notes: 

You will need to provide access to the Chemical and Engineering News article, and the two Inorganic Chemistry articles before class. This activity will likely take two class periods The first class period should focus on discussion of the articles and developing a rubric for evaluating the posters with the class. The second class period, the students will be allowed 30 min to prepare a poster for a "Gallery Walk."

Time Required: 
Two 50 min class periods
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
Corequisites: 
Course Level: 
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
3 Jun 2017

Introduction to Agostic Interactions

Submitted by Emma Downs, Fitchburg State University
Description: 

A brief introduction to agostic interactions and their importance to common organometallic mechanisms such as beta-hydride elimination. Examples of compounds containing these interactions are discussed and compared to familiar molecules such as diborane. Ways to characterize these interactions are also introduced.

Slides are based on the PNAS review Agostic Interactions in Transition Metal Compounds 

Brookheart, Green, and Parkin Proc. Natl. Acad.Sci. 2007104(7), 6908-6914

 

 
Course Level: 
Corequisites: 
Learning Goals: 

Define an agostic interaction and relate it to other types of bonding.

Provide examples of how the presence of an agostic interaction can be determined experimentally and through computational methods. 

 

Implementation Notes: 

This LO was developed at the VIPEr 2017 workshop at Franklin and Marshall College so it has not yet been implemented. The authors believed that implementation of this LO is best for an inorganic course that is post-organic, post-spectroscopy. It could be helpful after a discussion of 3-center 2-electron bonding and/or Lewis acidity/basicity. A literature discussion on an interesting agostic interaction with silicon was developed in conjunction with this LO and would be appropriate after discussing this five slides about LO.

Time Required: 
20 minutes
3 Jun 2017

Literature Discussion of R3CH→ SiFR3 Agostic Interactions

Submitted by Tanya Gupta, South Dakota State University
Evaluation Methods: 

Some discussions questions can be taken out and used for exams, quizzes or problem sets.

The instructor can develop a rubric to evaluate these questions based on their needs.

Evaluation Results: 

Monitoring student discussions, or grading student written responses based on implementation.

Description: 

The set of questions in this literature discussion activity is intended to engage students in reading and interpreting scientific literature and to develop a clear and coherent understanding of agostic interactions. The activity is based on a paper by Dorsey & Gabbai (2008). The paper describes agostic interactions in a silicon-based compound (R3C-H→SiFR3). The set of questions in this literature discussion activity is appropriate for an upper division course in inorganic chemistry. The research described in the article ties together concepts of agostic interactions and their impact on the coordination geometry of a Lewis acidic species. The discussion activity includes guided questions for students to understand and determine the presence of agostic interactions experimentally and through computational methods. The activity has specific questions related to bonding, structure, synthesis, characterization, theoretical and computational methods used in the literature. The activity may require reviewing some secondary sources.

Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to..

  • Define an agostic interaction and relate it to other types of bonding.

  • Describe how the agostic interaction affects the coordination geometry of a Lewis acidic atom.

  • Provide examples of how the presence of an agostic interaction can be determined experimentally and through computational methods.

  • Differentiate between computational methods in terms of the information they can provide.

  • Find related sources of information to aid in comprehension of the concepts in the article.

 

Implementation Notes: 

This literature discussion was developed at the VIPEr 2017 workshop at Franklin and Marshall College so it has not yet been implemented. The authors believed that implementation of this article is best for an inorganic course that is post-organic, post-spectroscopy. It could be helpful after a discussion of 3-center 2-electron bonding and/or Lewis acidity/basicity. As with all lit. discussion LOs, this article also provides a valuable experience in reading the literature, including an interpretation and analysis of the experimental section. There are many questions included in this activity and instructors may want to pick and choose these questions and adapt it to their class.

Time Required: 
1 class (50 minutes)
3 Jun 2017

Literature Discussion of "A stable compound of helium and sodium at high pressure"

Submitted by Katherine Nicole Crowder, University of Mary Washington
Evaluation Methods: 

Students could be evaluated based on their participation in the in-class discussion or on their submitted written answers to assigned questions.

Evaluation Results: 

This LO has not been used in a class at this point. Evaluation results will be uploaded as it is used (by Spring 2018 at the latest).

Description: 

This paper describes the synthesis of a stable compound of sodium and helium at very high pressures. The paper uses computational methods to predict likely compounds with helium, then describe a synthetic protocol to make the thermodynamically favored Na2He compound. The compound has a fluorite structure and is an electride with the delocalization of 2e- into the structure.

This paper would be appropriate after discussion of solid state structures and band theory.

The questions are divided into categories and have a wide range of levels.

Dong, X.; Oganov, A. R.; Goncharov, A. F.; Stavrou, E.; Lobanov, S.; Saleh, G.; Qian, G.-R.; Zhu, Q.; Gatti, C.; Deringer, V. L.; et al. A stable compound of helium and sodium at high pressure. Nature Chemistry 2017, 9 (5), 440–445 DOI: 10.1038/nchem.2716.

Corequisites: 
Learning Goals: 

After reading and discussing this paper, students will be able to

  • Describe the solid state structure of a novel compound using their knowledge of unit cells and ionic crystals
  • Apply band theory to a specific material
  • Describe how XRD is used to determine solid state structure
  • Describe the bonding in an electride structure
  • Apply periodic trends to compare/explain reactivity
Implementation Notes: 

The questions are divided into categories (comprehensive questions, atomic and molecular properties, solid state structure, electronic structure and other topics) that may or may not be appropriate for your class. To cover all of the questions, you will probably need at least two class periods. Adapt the assignment as you see fit.

CrystalMaker software can be used to visualize the compound. ICE model kits can also be used to build the compound using the template for a Heusler alloy.

Time Required: 
2 class periods
3 Jun 2017
Evaluation Methods: 

This LO was craeted at the pre-MARM 2017 ViPER workshop and has not been used in the classroom.  The authors will update the evaluation methods after it is used.

Description: 

This module offers students in an introductory chemistry or foundational inorganic course exposure to recent literature work. Students will apply their knowledge of VSEPR, acid-base theory, and thermodynamics to understand the effects of addition of ligands on the stabilities of resulting SiO2-containing complexes. Students will reference results of DFT calculations and gain a basic understanding of how DFT can be used to calculate stabilities of molecules.

 
Prerequisites: 
Corequisites: 
Course Level: 
Learning Goals: 

Students should be able to:

  1. Apply VSEPR to determine donor and acceptor orbitals of the ligands

  2. Identify lewis acids and lewis bases

  3. Elucidate energy relationships

  4. Explain how computational chemistry is beneficial to experimentalists

  5. Characterize bond strengths based on ligand donors

Implementation Notes: 

Students should have access to the paper and have read the first and second paragraphs of the paper. Students should also refer to scheme 2 and table 2.

 

This module could be either used as a homework assignment or in-class activity. This was created during the IONiC VIPEr workshop 2017 and has not yet been implemented.

 
Time Required: 
50 min
3 Jun 2017
Evaluation Methods: 

This was created during the IONiC VIPEr workshop 2017 and has not yet been implemented.

 
Description: 

This module offers students an introductory chemistry or foundational inorganic course exposure to recent literature work. Students will apply their knowledge of VSEPR and basic bonding to predict geometries of complex SiO2-containing structures. Students will gain a basic understanding of how crystallography is used to determine molecular structures and compare experimental crystallographic data to their predictions.

Prerequisites: 
Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to:

  1. Describe the bonding in SiO2 and related compounds
  2. Apply bonding models to compare and contrast bond types
  3. Apply VSEPR to predict bond angles
  4. Utilize crystallographic data to evaluate structures
Implementation Notes: 

Students should have access to the paper and read the first and fourth paragraphs on the first page and the third paragraph on the second page. Students should also reference scheme 1 and figure 1.

 

This module could be either used as a homework assignment or in-class activity.

 
3 Jun 2017

Fivefold Bonding in a Cr(I) Dimer Updated and Expanded

Submitted by Thomas Brown, SUNY Oswego
Evaluation Methods: 

Students are asked to answer the questions before coming to class and collected. After discussion students can revise their answers.   

Evaluation Results: 

This is a newly revised learning object so no assessment has been collected yet.  

Description: 

This paper describes the synthesis and characterization of a Cr(I) dimer with a very short Cr-Cr distance. Computational studies support fivefold bonding between the chromium atoms. This paper could be used to introduce metal-metal multiple bonds and discuss the molecular orbital interactions of homonuclear diatomics including d-orbitals. More generally, it is a nice example to stimulate the discussion of what constitutes a bond and the various interpretations of bond order. This version of this learning object is a modified and expanded version of Maggie Geselbracht's original LO. It was prepared colleaboratively at the 2017 VIPEr Literature Discussion workshop.

Corequisites: 
Learning Goals: 
Students should be able to:
  • Identify shapes and orientation of d orbitals

  • Create Lewis structures describing ligand binding type from crystal structures.

  • Apply symmetry concepts to assign orbital symmetries and create molecular orbital diagrams

  • Develop and draw the MO diagram of d-orbital interactions and use it to interpret the bonding involved in metal-metal multiple bonds.

  • Evaluate the relationship between bond order and experimental metal-metal bond distance

  • Evaluate effects of ligand design on molecular stability

  • Apply character tables for associated molecular point groups      

  • Rationalize MO interactions of ligands with metal centers in the presence of a metal-metal multiple bond.

 

Implementation Notes: 

Students are asked to read the paper and answer the discussion questions before coming to class. This could be used in an inorganic course after you have talked about MO theory of diatomics but fairly early in our discussion of transition metal chemistry. There is a Perspectives article in Science that goes along with this paper that gives the MOs more explicitly.   

Time Required: 
50 min +
3 Jun 2017
Evaluation Methods: 

This learning object was created at the pre-MARM workshop in 2017 and as such has not been used in a classroom setting. The authors will update the learning object once they have used it in their classes.

Description: 

This module offers students in an introductory chemistry or foundational inorganic course exposure to recent literature. Students will apply their knowledge of Lewis dot structure theory and basic thermodynamics to compare and contrast bonding in SiO2 and CO2.

Corequisites: 
Learning Goals: 

Students should be able to:

  1. Describe the bonding in SiO2 and related compounds (CO2)

  2. Use Lewis dot structure theory to predict bond orders

  3. Apply bonding models to compare and contrast bond types and bond energies (sigma, pi)

  4. Characterize bond strengths based on ligand donors

Course Level: 
Prerequisites: 
Implementation Notes: 

Students should read the first paragraph of the paper prior to completing this learning object. They can be encouraged to read more of the paper, but the opening paragraph is the focus of this learning object.

Time Required: 
50 min
23 May 2017

Ligand based reductive elimination from a thorium compound

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

This was developed after the semester in which I teach this material. I look forward to using it next fall and I hope to post some evaluation data at that point.

Description: 

This literature discussion is based on a paper describing the ligand-based reductive elimination of a diphosphine from a thorium compound (Organometallics2017, ASAP). The thorium compound contains two bidentate NHC ligands providing an opportunity to discuss the coordination of these ligands. The ligand-based reduction is very subtle and would be challenging for students to pick up without some guidance. The compound undergoing reductive elimination also presents an excellent introduction into magnetic nonequivalence and virtual coupling. In addition, the compounds presented in this paper provide the opportunity to do electron counting on f-block compounds. 

Corequisites: 
Prerequisites: 
Course Level: 
Learning Goals: 

Upon completing this LO students should be able to

  1. Use the CBC method to count electrons in the thorium compounds in this paper
  2. Describe the bonding interaction between a metal and a NHC ligand
  3. Discuss magnetic nonequivalency and virtual coupling
  4. Describe ligand-based reductive elimination and rationalize how it occurs in this system
Time Required: 
50 minutes

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