Molecular structure

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.

Subdiscipline: 
Corequisites: 
Prerequisites: 
Implementation Notes: 

I have used this activity in a two different ways.

  • In the past, I have assigned this as a homework assignment and have had students complete questions 1-4 outside of our class meeting time. They requested the structures from the CCDC or used our copy of the CSD on their own time. I then facilitated a dicussion of their answers before discussing the last question as a group in class. This approach worked well.
  • This year, I decided to use this exercise as an in-class group activity. I began class with a discussion of geometric indices using the presentation that is also available on the VIPEr site and is included in the "Related activities" section. I then broke my class up into groups of three students and had each group work through the activity. After the students completed the exercise, I then shared the calculations that I did for the zinc complexes so that they could remove the complication of the LFSE values from the discussion. I was much happier with this approach because I was able to focus the discussion a bit more and use the zinc data to reinforce the overall point of the exercise.

Note that in the original articles, the dihedral angle "between the two sets of planes defined by the nickel and two nitrogen atoms of the troponeiminate 5-membered chelate rings" was reported. I have decided to use the more current tau4' parameter in this exercise.

Time Required: 
45-60 minutes
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
14 Aug 2017

Chapter 13--Stanley Organometallics

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

Chapter 13 from George Stanley's organometallics course, Migratory Insertion and Elimination

 

this chapter covers migratory insertion and elimination reactions.

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.


Course Level: 
Subdiscipline: 
Corequisites: 
14 Aug 2017

Chapter 12--Stanley Organometallics

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

Chapter 12 from George Stanley's organometallics course, Oxidative Addition and Reductive Elimination

 

this chapter covers oxidative addition and reductive elimination reactions.

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.


Course Level: 
Subdiscipline: 
Corequisites: 
14 Aug 2017

Chapter 10--Stanley Organometallics

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

Chapter 10 from George Stanley's organometallics course, M-M bonding

 

this chapter covers bonding and structure of metal-metal 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.


Course Level: 
Subdiscipline: 
Corequisites: 
14 Aug 2017

Chapter 9--Stanley Organometallics

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

Chapter 9 from George Stanley's organometallics course, Cp

 

this chapter covers bonding and structure of metal pi-bonds, some descriptive chemistry and some historical context of sandwich compounds..

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.


Course Level: 
Subdiscipline: 
Corequisites: 
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.


Course Level: 
Subdiscipline: 
Corequisites: 
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

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