Coordination Chemistry

24 Apr 2015

Tanabe Sugano Diagram JAVA Applets

Submitted by Amanda Reig, Ursinus College
Description: 

A series of JAVA applets of Tanbe-Sugano diagrams were developed by Prof. Robert Lancashire at the University of the West Indies.  These diagrams allow students to determine deltao/B values based on ratios of peak energies without the pain of rulers and drawing lines.  There are also features that allow a person to input values and automatically calculate certain parameters.  You can also quickly find values of delta_o and B for certain complexes via a drop-down menu on some of the pages (e.g. Cr3+ complexes).    

Course Level: 
Topics Covered: 
Prerequisites: 
Learning Goals: 

Students will be able to interpret absorption spectra using the provided Tanabe-Sugano diagram applets.

Subdiscipline: 
Implementation Notes: 

I use these applets when teaching Tanabe-Sugano diagrams in my class and students get significant practice with the applets through homework assignments and a lab experiment.

Note that you cannot use Chrome (Firefox or Internet Explorer both work) and you will likely need to add the website to your "safe" list in your JAVA settings in order for the applets to work.

16 Apr 2015

I do not think it means what you think it means.

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

I came across this while working on writing a paper. I think this could make for a very interesting discussion and I am excited to try it in the fall.

Description: 

It is the classic game of telephone (or whatever local varient name you might use). Put a bunch of people in a line. Start by whispering something to the first person and then have them whisper it to the next. This process continues until the last person states out loud what they heard. Usually the starting and ending statements are quite different. When students are reading a paper, it is fairly likely that they feel anything the paper they are reading says about a reference is correct. This is a very dangerous assumption to make and students should learn to always go to the original source. In this activity, students are provided with some background information and then asked to consider the meaning of a specific sentence in a book chapter. They are then sent to the original source to see if that matches up with their original interpretation.

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

Students will learn that it is critical that they always turn to the original source when they are reading the literature.

Implementation Notes: 

There is certainly room for the introduction of many different topics while going through this exercise. Perhaps there is room for the creation of additional LOs from this paper.

17 Mar 2015
Evaluation Methods: 

Students were evaluated informally as I walked around to help the groups as well as during presentations.

Evaluation Results: 

A large majority of the students had no problem making assignments for the simple and intermediate cases.  This outcome is largely a testament to the ease of use of the CBC method.  In fact, students who had no background in inorganic or organometallic chemistry tended to perform a little better because they were less likely to bring in preconceptions about "oxidation state".

For the more difficult problems, I found that students did not have the nuance to be able to come up with good descriptions for the delocalization of charge from Fe onto the bridging N2 unit in #8.  However, they engaged in a lively discussion with me about how we should treat the molecule (this was just a week before Pat Holland came to Carleton to present his research so it was timely!).  On #9, we also had a good discussion because several of the more advanced (and even a few less advanced) students wanted the cycloheptatrienyl ligand to be aromatic but could not figure out how to make it work with the MLXZ system.  As I note, the answer is ambiguous, and I think I disagree with Parkin about the best way to assign it (see the linked J Chem Educ article for his description of a similar system on Ti).  Nevertheless, CBC carried the day and I found that the students with little to no background did extremely well on the next electron-counting homework assignment.

Description: 

This in-class group activity provides several examples of varying difficulty for students to assign MLXZ classifications and electron counts to organometallic complexes.  Though some of the problems are straightforward, some are really ambiguous, and the intent is for student groups to grapple with the issues raised by each one and present their findings to the class to spark further discussion.

Learning Goals: 

* Students should be able to use the covalent bond classification method to assign MLXZ classifications to a variety of organometallic complexes.

* Students should be able to defend their assignments using both organic and inorganic views of structure and bonding.

* Students will understand the ambiguities associated with assigning bond orders, valencies, oxidation states, etc., with the hope that their understanding of covalently bonded organometallic systems will become more nuanced.

Corequisites: 
Implementation Notes: 

I split students into groups of 3-4, as noted in the handout.  Each group was assigned one or two problems that they would need to present to the rest of the class, but all groups were encouraged to work on all of the problems to facilitate discussion later on.

After about 15 minutes, I had the student groups present and encouraged questions and challenges to their assignments.  We had in-depth discussions of problems 8 and 9, which are clearly the most ambiguous.

Time Required: 
45 minutes (can be less, depending on how structured)
8 Mar 2015

Community Challenge #2: Symmetry and MO Theory

Submitted by Nancy Scott Burke Williams, Scripps College, Pitzer College, Claremont McKenna College
Corequisites: 
Prerequisites: 
28 Jan 2015

Literature Introduction to Coordination Complexes

Submitted by Anne Bentley, Lewis & Clark College
Evaluation Methods: 

I have graded this problem on a “complete” vs “incomplete” basis as part of my daily homework system.  (For a description of the system, see the forum discussion here: https://www.ionicviper.org/forum-topic/creative-solutions-homework  )  It turns out that many of the solutions to the problem (ie, metal oxidation state) can often be found in the journal article. This doesn’t bother me too much because my main goals for the problem are to give students the experience of browsing an online journal and to gather complexes for use in future problems.

Evaluation Results: 

Most students do well on this assignment.  I think student performance mostly depends on the amount of time I’ve given the topic in lecture before the problem is assigned.

Description: 

Students are asked to find a coordination complex in the recent literature and analyze its structure. This homework or in-class activity is a great way for the instructor to crowd source the discovery of interesting new complexes to use as material in future exams.

Learning Goals: 

After completing this activity, students should be able to:

  • browse the inorganic literature
  • draw coordination complexes
  • identify a complex’s coordination number
  • identify the oxidation state of a metal and count its d electrons
Corequisites: 
Subdiscipline: 
Prerequisites: 
Related activities: 
Implementation Notes: 

I have assigned this problem as a take-home problem after my first lecture about coordination complexes. However, it could potentially be used as an in-class activity instead.

I compile the students’ complexes into a review document that I give them for extra practice before the exam on coordination complexes. I take images of the structures directly from the journal articles rather than draw them myself, but an instructor could just as easily ask the students to re-draw the structures using Chem Draw as part of the assignment. Some of my students have had little practice using Chem Draw, especially for more complex molecules. After a few years of assigning this problem, I now have a large repository of complexes to draw from in writing exam questions.

I review nomenclature rules in my advanced inorganic class, but I don’t put a lot of emphasis on requiring students to be able to name complexes. They do seem to enjoy making the connection between a long and complicated name and the complex’s structure.

Some students run into trouble accessing the journal from off-campus computers; our campus library does provide a way to do this, but many students need a reminder about how to log in and get permission.

This assignment takes the “ionic” approach to electron counting in coordination complexes, but it could be adapted to ask students to use the “covalent” approach instead.

Time Required: 
20 minutes
22 Jan 2015

Introduction to Mercury

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

As the students work through this exercise, I walk through the classroom and look "over their shoulder" to see how they are doing. Once they complete the exercise, I choose another metal-containing structure and ask them to follow the same process with that structure.

Evaluation Results: 

In looking at the responses from my 13 students, all 13 were able to provide correct answers for all of the questions in the exercise. They had very little trouble following the instructions or interacting with the software. Students were also able to open other structures and perform a similar analysis on their own, with no input or guidance from me.

Description: 

In this exercise, students are introduced to Mercury, a program for visualizing and analyzing crystal structure data.  Students are guided through opening the program for the first time and viewing a structure from the Teaching Subset, a selection of structures from the Cambridge Crystallographic Database (CSD). Activites include changing the representation of the complex, moving the structure around the window, accessing information about the structure, and measuring bond lengths and angles within the structure.

A recent update of the Cambridge Crystallogaphic Data Centre's website has provided free access to the Teaching Subset through a web-based interface. This is ideal for students who use iPads or other tablets. An alternate set of instructions has been added to this learning object. 

Learning Goals: 

After completing this activity, students should be able to:

  • open the teaching subset in Mercury;
  • view a structure included in the teaching subset;
  • manipulate the structure;
  • access basic information about the structure that is included in the datafile;
  • measure bond distances and angles in a structure.
Equipment needs: 

Students can access the structures in two ways.

  • They may use the desktop version of Mercury on a computer that has the software package installed. Mercury is freely available for Mac, Windows, and Linux operating systems. Computers with the Mac OS may also need to install XQuartz, which is also a free download, to run Mecury. 
  • They may also access the structures on an iPad or any computer that has a web browser.

Instructions for both methods of access are included linked to this learning object.

Prerequisites: 
Corequisites: 
Related activities: 
Implementation Notes: 

At Merrimack, it is common practice to not run lab sections the first week of the semester. For a number of years, I have used the lab period in this first week with my sophomore- and junior-level inorganic students to inform them of lab procedures and have them install required software (Mercury) on their laptops. After students install Mercury on their computers, they complete this exercise individually to familiarize themselves with the program.

I usually have the students download and install Mercury while they are in the room with me so I can troubleshoot any downloading or installation issues. The downloads are not that large [MacOS ~ 150 MB; Windows ~ 120 MB], but having a number of students all connecting to the internet through the same access point could slow the download speed. If you are pressed for time or are using it during a 50 minute lecture, it might be better to either ask students to download the installer before coming to class or to have copies on USB drives for those who have trouble downloading the installation file.

More recently, I have had the students use their iPads to access the strucutres and no software must be installed for them to complete this exercise. New instructions for accessing the structures using an iPad have been added to this learning object.

 

Time Required: 
20 minutes to complete exercise; 20 minutes to download and install software
12 Jan 2015

Cobalt-Ammine complexes and theories of bonding in metals

Submitted by Erica Gunn, Simmons College
Evaluation Methods: 

Lab notebooks were collected and graded for all students. In addition to a condensed introduction and thorough lab procedure/observations section, students wrote a short conclusion and discussion of experimental error and answered the postlab questions. Experimental data was compared to literature and classmates' data (where possible), as well as to computational results. 

Evaluation Results: 

See instructor notes document. 

Almost all students were able to synthesize their complexes with little or no difficulty. One student heated too much during the evaporation stage and did not obtain product. Several students obtained low yields for synthesis A, likely due to formation of the cis- instead of the trans product. Reheating the solutions to a higher temperature produced the green trans isomer instead. 

Students were able to obtain UV/VIS and IR data for their complexes, and were interested to compare these experimental results with the computational spectra (Spartan was especially helpful to visualize the vibrational modes to understand how they are connected to symmetry). Our ability to interpret the IR spectra was somewhat limited due to the wavelength range for our instrument and poor preparation of the KBr pellets. We were able to identify some differences in the spectra, but the real identifying peaks fall below 400 cm-1 and were not measurable with our instrument. 

For my iteration of this lab, students also measured the rates of aquation of the three complexes synthesized. This experiment highlighted the dramatic differences in reactivity for the complexes. 

In general, students found this lab straightforward and easy to follow, and these examples served as an anchor for several class discussions (symmetry of vibrational modes, trans effect in kinetics of ligand substitution, isomerism in coordination complexes, etc.). 

Description: 

This is a two-week lab in which students synthesize and then characterize three Werner cobalt complexes using IR, UV/VIS and computer calculations using Spartan. Syntheses are based on procedures from:

Angelici, R. J. Synthesis and Technique in Inorganic Chemistry. University Science Books, 1996, pp 13-17.

Borer, L.L.; Erdman, H.W.; Norris, C.; Williams, J.; Worrell, J. Synthesis of trans-Tetraamminedichlorocobalt (III) chloride, Inorganic Syntheses, Vol 31, 1997, pp 270-271.

Slowinski, E.; Wolsey, W.; Rossi, R. Chemical Principles in the Laboratory 11th ed. Cengage Learning, 2016. 

Students were randomly assigned to synthesize one of the three Co complexes in week 1, and then worked in groups to characterize their complexes in week 2.* They were also required to compare the results for their complex with students in other groups. This latter process was partially completed in lab, and then student data was collected in a shared folder on Google Drive to allow all students access to data that they did not personally collect while writing their lab reports. 

 

* In my iteration of this lab, students also measured the kinetics of aquation of the three complexes, with and without solid state catalysts. That portion of the lab still requires optimization, and was removed for simplicity. See instructor notes for a more thorough discussion.

Corequisites: 
Prerequisites: 
Course Level: 
Learning Goals: 

Students will be introduced to models of bonding in coordination complexes using Werner's cobalt ammine complexes.

Each student will synthesize one cobalt ammine complex, and analyze the product using UV/VIS and IR spectroscopy. 

Students will also carry out computations using Spartan to predict the spectra, view the molecular orbitals, and visualize IR vibrational modes for the molecule, and will compare this data to their experimental results. 

Equipment needs: 

A list of chemicals and equipment required is given in the prep notes (assuming a class of 12 students).

Implementation Notes: 

See Instructor notes document.

Time Required: 
2 4-hour lab periods
5 Jan 2015

The Importance of the Trans Effect in the Synthesis of Novel Anti-Cancer Complexes

Submitted by Sheri Lense, University of Wisconsin Oshkosh
Evaluation Methods: 

A student volunteer from each group was asked to share their answer with the class.  Written answers could also be collected and graded.

Evaluation Results: 

Most students did very well in all parts of this activity, although some students initially had trouble explaining the relative trans-directing ability of the ligands.

Description: 

In this activity, students apply knowledge of the trans effect to the synthesis of planar Pt(II) complexes that contain cis-amine/ammine motifs.  These complexes are of interest as both potential novel chemotherapeutic Pt(II) complexes and as intermediates for promising chemotherapeutic drugs such as satraplatin.  The questions in this LO are based on recent research described in the paper “Improvements in the synthesis and understanding of the iodo-bridged intermediate en route to the Pt(IV) prodrug satraplatin,” by Timothy C. Johnstone and Stephen C. Lippard (Inorganica Chimica Acta, Volume 424, 1 January 2015, Pages 254–259).  Students can be given this paper either prior to class or during class.  Student then work in groups of 3-4 to determine whether the sterochemistry of the Pt(II) complexes synthesized in the paper and in previous work is predicted by the trans effect, as well as whether the bond lengths in a crystal structure of one of these Pt(II) complexes is predicted by the trans influence.

Learning Goals: 

After completing this activity, students should be able to:

  • define the trans effect and trans influence
  • explain what properties of a ligand cause it to have a strong trans effect, and be able to predict the relative trans-directing ability of ligands
  • explain how the trans effect can be utilized to develop synthetic methodologies that produce the desired isomer of a square planar complex
  • apply their knowledge of the trans effect to predict the stereochemistry of a product formed from substitution of a square planar complex
  • explain why the stereochemistry of a product formed substitution of a square-planar complex may differ from that predicted by the trans effect
  • explain the effect of the trans influence on metal-ligand bond lengths
Corequisites: 
Subdiscipline: 
Course Level: 
Equipment needs: 

None

Implementation Notes: 

This was done as an in-class activity in which students worked in groups of 3-4 to complete the assignment.  This LO could also be incorporated into a homework assignment instead.

Time Required: 
20-30 minutes
5 Jan 2015

The Color and Electronic Configurations of Prussian Blue

Submitted by Erica Gunn, Simmons College
Evaluation Methods: 

Student answers to the reading comprehension questions were collected at the beginning of class and graded out of 10 points (largely based on participation and completeness of answers). 

Evaluation Results: 

Most students were able to identify the correct answers from the paper, though some were confused by the last section involving orbital calculations (this was expected, as most of these students have not yet had a course in quantum mechanics). 

Some students also had difficulty following the logic presented in the paper to predict differences in absorption band intensity for the different Fe compounds. Most recognized that the absorption band position was important and some realized that intensity also mattered, but most did not fully follow the arguments for assigning absorption spectra to one particular complex geometry. Most of the class discussion involved recreating the logic behind the peak assignment for the absorption spectra.

Description: 

I used this paper to illustrate several course concepts related to materials structure (crystal lattice structure, coordination number, crystal field theory and orbital splitting, symmetry, electronic spectra, allowed and forbidden transitions). This activity was paired with a laboratory experiment (see related VIPEr objects) in which students synthesized Prussian Blue, and gave students a really in-depth look at what was going on when they mixed those solutions together. Combined with another VIPEr activity that uses a more recent literature example (New Blue Solid, in related links), students gained a broad appreciation for how inorganic chemists can use these concepts to rationally design new materials.

 

 

Corequisites: 
Prerequisites: 
Learning Goals: 

Become familiar with reading chemical literature

Use symmetry and electronic configuration to interpret absorption spectra

Integrate understanding of course concepts to understand a "real life" literature example and enhance student interest 

Implementation Notes: 

These activities were used in a 200-level course, which happened to mostly populated by juniors and seniors. The reading questions were designed mainly to check for basic comprehension. Most students had no difficulty answering the "what" questions about the experiments done and facts presented, but many needed significant guidance to understand why the researchers made these particular measurements, and how they interpreted the data to arrive at the conclusions presented. Most of the class discussion focused on building a "big picture" overview of what was going on. This led to interesting questions about design of experiments and use of evidence in science. Several students were surprised at how much of the scientific argument they had missed in their first reading of the paper, even though they felt like they had a good grasp on the data that the authors had reported.

Time Required: 
1 hour
29 Dec 2014

d-Orbital Splitting Patterns in a Variety of Ligand Geometries

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

There is no formal evaluation done for this in-class activity, but student comprehension is gauged by the quality of the discussion.

Evaluation Results: 

When this activity was assigned as a take-home problem set, most students had very little trouble determining octahedral (covered previously), square planar (3 out of 4), and square pyramidal (3 out of 4) splitting patterns. They had a bit more trouble determining the other splitting patterns, with an average of only 1 out of 4 getting each of the others correct.

I have used this actvity in class for several years (with about 40 students) and have found that the students benefit from the ability to discuss the activity with other students. Their discussions focus on the repulsion that would be felt between electrons in various d orbitals and the ligands in each ligand field. The vast majority of students (greater than 85%) easily determined which orbitals will lie above and below the barycenter. More than two-thirds of the students have been able to distinguish the relative positions of the orbitals based upon ligand-d electron repulsion and pair all of the diagrams with the ligand field correctly after discussing it with their fellow classmates.

Description: 

In this activity, the provided d orbital splitting patterns need to be matched with ligand geometries. Students are provided with the d orbital splitting diagrams for 6 ligand geometries (octahedral, trigonal bipyramidal, square pyramidal, tetrahedral, square planar, and linear). A web browser is used to view an animation (developed by Flick Coleman) which allows for the visualization of the relationship between the positions of the metal d orbitals and the ligands. Given this information, students should then be able to qualitatively rank the orbitals from highest to lowest energy. Once the orbitals are ranked in terms of energy, the pattern can then be matched to the provded splitting diagrams.

Learning Goals: 

After completing this in-class activity, students should be able to:

  • visualize the positions of the ligands relative to the metal's d orbitals;
  • determine the energies of the orbitals based upon electron repulsion relative to the barycenter;
  • qualitatively rank the d orbitals in terms of their energies for a variety of ligand fields;
  • explain why the observed splitting pattern in produced for each ligand geometry.
Equipment needs: 

Each student will need access to a computer or tablet with a web-browser capable of running JavaScript. 

Prerequisites: 
Corequisites: 
Implementation Notes: 

This activity has been used both as an in-class exercise and a homework assignment, and I have found that it works much better as an in-class activity.

In the class previous to the one where the activity is completed, I work through the splitting diagram for an octahedral complex.  The web-based animation is used to show the relative positions of the orbitals and the ligands. While projecting the image on a whiteboard, I illustrate the geometric arrangement of ligands using a cube and I place the metal at the center of the cube and the ligands at the center of each of the 6 faces of the cube. (This allows me to give them an idea about distance between the ligands and the orbitals.) In preparation for the next class, I ask them to think about how the ligand-orbital interactions would be different in a tetrahedral arrangement of ligands. I also remind the students to bring their laptops to the following class.

When arriving in class, I break the students up into groups of two and I ask them to work on the assignment together. They discuss the animations and can consult with other groups or me if they get stuck. The exercise is usually completed in one 50-minute lecture.

Time Required: 
approximately 50 minutes

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