Visualization

6 Jul 2018

Getting to Know the MetalPDB

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

I reviewed student answers to this assignment and evaluated their contributions to the discussion that took place. I also tried to keep track of how much they used information obtained from this site during their literature presentations.

 
Evaluation Results: 

This assignment is quite straightforward and the 6 of 8 students who completed the assignment had little trouble coming up with correct answers for all of the questions.

 

At the end of the semester, each student had to give two presentations on bioinorganic topics. They were expected to discuss the metal coordination environment and how "normal" it was, as well as the possibility of substituting another metal into the coordination sphere. One student used information from the MetalPDB in both of her presentations, three students used information in one of their presentations, and four students did not include information from the site in either presentation.

 

Description: 

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

 

I expect my students to use this site to obtain information for their assignments and presentations. This activity is a self-paced introduction to the site that my students complete outside of class. This activity has students use the site to obtain information about metal coordination environments, the common geometries adopted by metals in biological environments, and the common ligands that are used to bind metals.

Learning Goals: 

After completing this exercise, students should be able to:

  • access the MetalPDB site,

  • obtain statistics pertaining to the number of metal-containing structures in the PDB,

  • determine the most common geometry observed for a particular metal in a biological structure,

  • identify the most common ligands attached to the metal when bound in a biological macromolecule, and

  • find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.

Equipment needs: 

Students need access to the internet and a web browser that is capable of running JavaScript and JSmol. This site is accessible on devices running iOS, but the layout of the site works better on a laptop screen.

Prerequisites: 
Corequisites: 
Implementation Notes: 

I used the MetalPDB site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules in both my advanced and foundation-level courses, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.

 

I also have students use the site to get background information about metal geometry and common ligands for their assignments and presentations. I ask them to complete this activity outside of class. I usually distribute this as a Google Doc to my students (through Google Classroom) so that I have access to all of their responses.

 

For several of the questions/groups of questions, I assign individual members of the class specific geometries (question #5), metals (questions #6-9), or PDB structures (questions #11-13) and we pool their answers in class. We then spend about 30-45 minutes in class discussing the results and search for commonalities and connections to other structures that we have already discussed in class.

 
Time Required: 
1-2 hours (outside of class by student); 30-45 minutes in class (including discussion of related topics)
16 May 2018

MetalPDB website

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

I kept track of how much my students used information obtained from this site during their literature presentations.

Evaluation Results: 

The students had little difficulty accessing or using the site. Most of my students used information obtained from the site in their presentations and during in-class dicsussions.

Description: 

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

In the past, I have used Metal MACiE to help find metal-containing biological macromolecules and to access information about the metal function and coordination environment. Unfortunately, this site, while still available, has not been updated in several years. I have recently found the MetalPDB website which was created at CERM (University of Florence). This site "collects and allows easy access to the knowledge on metal sites in biological macromolecules" and can be used to explore structures deposited in the PDB.

I also expect my students to use this site to obtain information for their assignments and presentations.

Prerequisites: 
Corequisites: 
Learning Goals: 

When using this website, students are able to:

  • obtain statistics pertaining to the number of metal-containing structures in the PDB,
  • determine the most common geometry observed for a particular metal in a biological structure,
  • identify the most common ligands attached to the metal when bound in a biological macromolecule, and
  • find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.

These learning goals are incorporated in the associated in-class activity, which is posted separately.

Implementation Notes: 

I used this site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.

To learn how to use the site, I assigned an associated activity (posted separately) that I have the students complete before coming to class. This experience allows the students to use the site to get background information about metal geometry and common ligands for their assignments and presentations.

This site utilizes JavaScript and JSmol so students must ensure that Java functions properly in their preferred web browser. I have found no issues accessing this site with any of the browsers used by myself or my students.

 

18 Jan 2018

Isomerism in Coordination Complexes

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

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.

Evaluation Results: 

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.

Description: 

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.

Learning Goals: 

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).
Corequisites: 
Equipment needs: 

A computer is required to access the Teaching Subset of the Cambridge Structural Database in one of the following ways.

  1. 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.
  2. 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.
Prerequisites: 
Implementation Notes: 

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.

Time Required: 
30 minutes
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.

Prerequisites: 
Corequisites: 
Subdiscipline: 
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
12 Jan 2018

Geometry Indices

Submitted by Anthony L. Fernandez, Merrimack College
Description: 

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.)

Corequisites: 
Prerequisites: 
Learning Goals: 

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.
Implementation Notes: 

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.
Time Required: 
20-30 minutes
Evaluation
Evaluation Methods: 

I use these slides to introduce the concept of geometry indices in class. Since this is a presentation, I do no formal evaluation of the impact of these slides on student learning. 

I do ask students to complete several exercises in which they calculate the geometry indices for a number of transition metal complexes. 

Evaluation Results: 

Over several years, I have observed that students very rarely have trouble completing the assigned exercises correctly after viewing this presentation.

19 Dec 2017

Visual scaffold for stoichiometry

Submitted by Margaret Scheuermann, Western Washington University
Description: 

These five slides are intended to share a visual scaffolding that I developed to help my general chemistry students identify what calculations are needed to solve stoichiometry problems.

 

The visual scaffold involves writing the balanced equation and then under it drawing a table with two rows and enough columns so that there is one column under each reagent in the equation. The top row is labeled as "moles" and the bottom row is labeled as "measurable quantity". Students then write in any information about a specific reagent or product that was given and identify the quantity that the question is asking them to find. They then add a series of arrows to the table to generate a "map" of how to get from the information they are given to the information they need to find with each arrow representating a type of calculation that they have already seen and practiced. Vertical arrows represent a calculation between a measured quantity and a number of moles. Horizontal arrows in the top row represent calculations between moles of one substance and moles of another substance. Horziontal arrows in the "measured quantity" row are not allowed since those unit conversion factors are not readily available. 

 

Corequisites: 
Topics Covered: 
Prerequisites: 
Course Level: 
Learning Goals: 

A student should be able to determine the quantity of a reagent required or the quantity of a product produced in a reaction.

Subdiscipline: 
Related activities: 
Implementation Notes: 

The scaffolding begins with a review of the two types of calculations that are required for basic stoichiometry: converting between grams and moles, and converting between moles of one substance and moles of another substance using the coefficients of a balanced equation as unit conversion factors (slide 1).

Some ABCD card/clicker questions can be added here if students have not practiced these types of problems in class recently.

After introducing the visual scaffold (slide 2) I do an example problem or two on the board/overhead/doc cam (slide 3).

This is a good point to give students an opportunity to work on a practice problem or if the introduction to stoichiometry began part way through a class period, an exit question.

Next I introduce situations where it could take more than one calculation to get from the measured quantity to moles (slide 4). 

An example problem and/or practice problem and/or exit question can be added here.

The visual scaffold is also relevant for limiting reagent problems. I've included an example (slide 5/6) but limiting reagent is usually presented in a subsequent class period after some examples of the limiting reagent concept using sandwiches or something similar. 

Time Required: 
30-50 minutes. varies with the number of examples and practice problems
Evaluation
Evaluation Methods: 

I will usually do an exit question- a stoichiometry problem from the textbook- after either slide 3 or slide 4. I do not require students to use the visual scaffold if they are already comfortable with stoichiometry from a previous class but many choose to use it. Some students will include the tables from the visual scaffold as part of the work they show on exams, again without being prompted or required to do so. 

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