Although students submit their answers in the spreadsheet, I do not grade their answers becuase they worked on this exercise in groups. I usually move through the class and interact with the groups to see how they are progressing.
This is a relatively simple exercise and students have little trouble coming up with the correct answers for these structures. They sometimes have an issue determining the names of the linkage isomers, especially for the SCN- ligand.
Students are confronted with a number of new types of isomerism as they move from organic chemistry into inorganic chemistry. This can be confusing and students often have trouble visualizing structures and differentiating between isomers. In this exercise, students are asked to examine a number of different crystal structures from the Teaching Subset (distributed with Mercury version 3.10, early 2018) of the Cambridge Structural Database. Students have to identify the type of isomerism (geometric, linkage, or optical) exhibited by a complex and then identify the specific isomer (cis/trans, mer/fac, R/S, etc.) observed in the structure.
After completing this exercise, students should be able to:
- access structures from the CCDC using their web-based form,
- visualize the structures using Mercury or other viewer,
- identify the type of isomerism observed in a structure, and
- determine the correct form of the isomer (e.g. cis or trans).
A computer is required to access the Teaching Subset of the Cambridge Structural Database in one of the following ways.
- The freely available viewer (Mercury) can be downloaded from the CCDC [https://www.ccdc.cam.ac.uk/Community/csd-community/FreeMercury/]. The CSD Teaching Subset is included with this download.
- Students may also access the structures online from the Cambridge Crystallographic Date Centre. Structures can be accessed via a web-based form [https://www.ccdc.cam.ac.uk/structures/] or via the Teaching Subset page on the CCDC website [https://www.ccdc.cam.ac.uk/structures/search?compound=Teaching%20Subset]. These pages also work on a tablet.
I have used this exercise as an in-class exercise and and out-of-class assignment and it works equally well in both formats. If this is one of the first times that your students will be using Mercury, then I would suggest employing this as an in-class activity. While in class, I have students work in pairs to complete this exercise.
I usually send out the spreadsheet and have students enter their responses and then return the spreadsheet to me. I have also pushed this out as a Google Sheet and had them fill it out online. I find that it is easier to keep track when using the Google Sheet. (We are a Google campus so I am guaranteed that all of my students have a Google account and can access the G Suite of programs.) If you would like the Google Sheet version of this exercise, please contact me and I will share it with you.
In the spreadsheet, there is a sheet titled "Drop-down list info" and the information on this sheet populates the drop-down lists in the "Isomerism" sheet. This sheet needs to be present for the drop-down lists to work. I usually hide this sheet before distributing the file to my students and I have included instructions how to do this on the sheet.
I assess the student learning by the quality of the discussion generated by this exercise.
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.
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.
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.
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.
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.
In the primary literature, goemetry indices are being used quite often to describe four- and five-coordinate structures adopted by transition metal complexes. This slide deck, which is longer than the intended 5 slides, describes the three common geometry indices (tau4, tau4', and tau5) and provides example calculations for structures that are freely available in the Teaching Subset of the Cambridge Structural Database. (Students can access these structures in Mercury, which is freely available from the CCDC, or via a web request form for which the link is provided below.)
After viewing this presentation, students should be able to:
- recall the common geometries adopted by transition metal centers in four- and five-coordinate structures,
- describe the limiting geometries for each CN,
- recall the formulas for the three geometry indices (tau4, tau4', and tau5),
- calculate the value of the appropriate geometry index for a given structure, and
- identify the geometry exhibited by a TM center.
I have found that this presentation can be used effectively in one of several ways:
- the presentation is given in class and then students complete an exercise in which they calculate the geometry indices for a number of transition metal complexes before the leave class,
- the presentation is given in class and then students complete an exercise in which they calculate the geometry indices for a number of transition metal complexes outside of class (as homework), or
- the presentation is provided to them as a PDF file as part of the pre-class assignment and then students complete an exercise in which they calculate the geometry indices for a number of transition metal complexes when they are in class.