17 Jan 2018

Metal Tropocoronand Complexes

In-Class Activity

Submitted by Anthony L. Fernandez, Merrimack College

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.

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
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.

Creative Commons License: 
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