Bonding models: Discrete molecules

14 Aug 2017

Chapter 8--Stanley Organometallics

Submitted by George G. Stanley, Louisiana State University
Description: 

Chapter 8 from George Stanley's organometallics course, Arenes

 

this chapter covers bonding and structure of metal pi-bonds and some descriptive chemistry.

The powerpoint slides contain answers to some of the in-class exercises, so those are behind the "faculty only" wall. I share these with students after the class, but not before.

Everyone is more than welcome to edit the materials to suit their own uses, and I would appreciate being notified of any mistakes that are found.


Subdiscipline: 
Corequisites: 
Course Level: 
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
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
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: 
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

Course Level: 
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: 
Course Level: 
Corequisites: 
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: 
Course Level: 
Prerequisites: 
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

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. 

Prerequisites: 
Corequisites: 
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
Course Level: 
Time Required: 
50 minutes
1 Mar 2017

Reactivity and Bonding of Complexes with Metal-Metal Bonds

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

Evaluation was conducted by the instructor walking around the classroom and addressing individual problems students had.

Evaluation Results: 

From classroom observations, most students were able to properly count electrons and oxidation states for the metals in the complexes and rationalize the ligand coordination modes. Here, the main source of confusion was how to account for the Z-type Co-Zr interaction. The MO diagrams generated the most discussion and were the most difficult part for students (as was expected). The reactivity was also initially conceptually difficult for students, but once they realized how to treat the M-M bonded system, students were able to apply fundamental organometallic reactions to the system. Many students forgot what they had learned about magnetic moments in the previous quarter, but figured it out and were excited to apply knowledge from the previous course. 

Description: 

This problem set was designed to be an in-class activity for students to practice applying their knowledge of metal-metal bonding (as discussed in the previous lecture) to recently published complexes in the literature. In this activity, complexes from four papers by Christine M. Thomas and coworkers are examined to give students practice in electron counting (CBC method), drawing molecular orbitals, and fundamental organometallic reactions.

Corequisites: 
Course Level: 
Learning Goals: 

Following the activity, a student should be able to:

·      Determine electron counts and oxidation states of complexes with M-M bonds using CBC electron counting method

·      Draw molecular orbital diagrams for M-M bonds

·      Determine M-M bond order

·      Propose mechanisms for reactions at M-M centers

·      Apply fundamental inorganic chemistry to reports in the literature

Implementation Notes: 

This was implemented in the second quarter of advanced inorganic chemistry (4th year level) before the second midterm as an in-class group activity. The worksheet generated a lot of interest from the students and generated good discussions in a class of 23 students. In the previous lecture, we discussed basic metal-metal bonding, including drawing MO diagrams and determining bond order for homobimetallic complexes. This worksheet was a reasonable extension, requiring students to apply this knowledge to more complicated systems.

Time Required: 
65 min
21 Feb 2017
Evaluation Methods: 

Graded problems students turned in.

Informal evaluation during discussion.

Evaluation Results: 

Graded assignments: mean of 84, std dev of 12, so a fairly broad range of understandings

Informal: Students really enjoyed getting to evaluate published work critically and were quite engaged in discussions, which helped to bring some of the students who didn't understand the paper as well up to speed.  After the paper, students have felt much more comfortable questioning what is stated in papers, particularly if little or no support is given.

I will definitely use this again!  Unfortunate to find a paper with several important oversights in the literature, but it is a good learning opportunity.

Description: 

This LO is a problem-set-style literature discussion that leads students through a critical analysis of an interesting but flawed paper from the recent chemical literature.  Students use the questions to help them work through the paper prior to class, providing plenty of raw material for an in-class discussion about various aspects of the work from a mechanistic organometallic perspective.  The questions help students critically analyze substrate tables, spectroscopic data, and computational results from DFT.

Corequisites: 
Course Level: 
Learning Goals: 
  • Students will be able to pull out important mechanistic information from substrate tables in an organometallic paper
  • Students will be able to use knowledge of organometallic mechanisms and organic chemistry to rationalize findings in a catalysis paper
  • Students will be able to use knowledge of spectroscopy, particularly NMR, to understand structure and bonding arguments in an organometallic paper
  • Students will critically analyze a paper and learn to feel comfortable questioning assertions by authors, including the major findings of a paper
Implementation Notes: 

I had students prepare answers to these questions ahead of class and bring the answers with them.  To add incentive, I collected them as a homework assignment (though I graded some of the harder ones fairly leniently).  The questions helped prepare them for a class discussion of the paper, which I led with a few slides containing information from the paper and some other useful tidbits (I am happy to send those to you if you like, just contact me).

Time Required: 
1-2 hours student prep (reading paper); 45 minutes in class discussion

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