Molecular structure

1 Jun 2018
Evaluation Methods: 

This LO has not been implemented; however, we recommend a few options for evaluating student learning:

  • implement as in-class group work, collect and grade all questions

  • have students complete the literature discussion questions before lecture, then ask them to modify their answers in another pen color as the in-class discussion goes through each questions

  • hold a discussion lecture for the literature questions; then for the following lecture period begin class with a quiz that uses a slightly modified problem.

Evaluation Results: 

This LO has not been implemented yet.

Description: 

In honor of Professor Richard Andersen’s 75th birthday, a small group of IONiC leaders submitted a paper to a special issue of Dalton Transactions about Andersen’s love of teaching with the chemical literature. To accompany the paper, this literature discussion learning object, based on one of Andersen’s recent publications in Dalton, was created. The paper examines an ytterbium-catalyzed isomerization reaction. It uses experimental and computational evidence to support a proton-transfer to a cyclopentadienyl ring mechanism versus an electron-transfer mechanism, which might have seemed more likely.

 

The paper is quite complex, but this learning object focuses on simpler ideas like electron counting and reaction coordinate diagrams. To aid beginning students, we have found it helpful to highlight the parts of the paper that relate to the reading questions. For copyright reasons, we cannot provide the highlighted paper here, but we have included instructions on which sections to highlight if you wish to do that.

 

Corequisites: 
Course Level: 
Learning Goals: 

After completing this literature discussion, students should be able to

  • Count the valence electrons in a lanthanide complex

  • Explain the difference between a stoichiometric and catalytic reaction

  • Predict common alkaline earth and lanthanide oxidation states based on ground state electron configurations  

  • Describe how negative evidence can be used to support or contradict a hypothesis   

  • Describe the energy changes involved in making and breaking bonds

  • On a reaction coordinate diagram, explain the difference between an intermediate and a transition state

  • Explain how calculated reaction coordinate energy diagrams can be used to make mechanistic arguments

Implementation Notes: 

This is a paper that is rich in detail and material. As such, an undergraduate might find it intimidating to pick up and read. We have provided a suggested reading guide that presents certain sections of the paper for the students to read. We suggest the instructor highlight the following sections before providing the paper to the students. While students are certainly encouraged to read the entire paper, this LO will focus on the highlighted sections.  

 

Introduction

            Paragraph 1

            Paragraph 2

            Paragraph 3

            Paragraph 4

First 5 lines ending at the word high (you may encourage students to look up exergonic if that is not a term commonly used in your department)

Line 14 starting with “In that sense,” through the end of the paragraph

            Paragraph 6

From the start through the word “endoergic” in line 22

Line 31 from “oxidation of” to the word “described” in line 33

Line 40 from “These” to the word “dimethylacetylene” in line 45

Paragraph 7

            From the start to the word “appears” in line 4

            The words “to involve” in line 4

            Starting in line 4 with “a Cp*” to “transfer” in line 5

Results and Discussion

            Paragraph 1

            Paragraph 2

            Paragraph 3 from the start through “six hours” in line 10

            Paragraph 4

            Paragraph 5

                        From the start to “solution” in line 3

                        From “This exchange” in line 10 to “allene” in line 11

                        From “Hence” in line 19 through the end of the paragraph

            Paragraph 6 from the start through “infrared spectra” in line 19

            Paragraph 7 from “Hence” in line 4 through the end of the paragraph

Mechanistic aspects for the catalytic isomerisation reaction of buta-1,2-diene to but-2-yne using (Me5C5)2Yb p 2579.

            Paragraph 1

            Paragraph 2

            Paragraph 3

            Paragraph 4

Experimental Section

            Synthesis of (Me5C5)2Yb(η2-MeC≡CMe).

            Synthesis of (Me5C5)2Ca(η2-MeC≡CMe).

Reaction of (Me5C5)2Yb with buta-1,2-diene

 

 

 

Time Required: 
One class period.
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
10 Jan 2018

What happened to my green solution?

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

I do not do any formal assessment of student learning for this activity, but instead I judge understanding by the quality of the in-class dicussion.

I have also used similar questions on exams in the past to see if the students can apply these ideas to different reactions.

Evaluation Results: 

I have experienced mixed results with this exercise over the three years I have used it. I find that my students have no trouble identifying that a reaction has occurred and they readily recognize that the color change is a consqeuence of the reaction.

My students tend to struggle with the composition of the complex ions in solution. For the CrCl3 solution, students provide many possible compositions of the coordination complex including the neutral complex, [CrCl3(OH2)3], and the hexaaqua complex, [Cr(OH2)6]3+.  More than 2/3 of the students suggest one of the two predominant complex ions that are present in solution. For the Cr(NO3)3 solution, students often want to use the nitrate as a ligand on the chromium center.

All of my students are usually able to write the balanced reactions and explain the changes in the UV-visible spectra once they identify the composition of the complex cations.

Description: 

Students in inorganic chemistry courses are often interested in the colors of transition metal complexes. This in-class activity serves an introduction to reactions of coordination complexes and pushes students to think about the relationship between the color of a complex cation and its structure. Students are provided with pictures of aqueous solutions of two chromium(III) salts [CrCl3*6 H2O and Cr(NO3)3*9 H2O] at two different times and are then asked to explain the changes observed in the solutions. This activity was inspired by a laboratory experiment which was done as part of the inorganic laboratory course for many years ("Determination of Delta_oct in Cr(III) Complexes" from Szafran, Z., Pike, R.M., and Singh, M.M "Microscale Inorganic Chemistry: A Comprehensive Laboratory Experience" Wiley, New York, (c)1991) .

Learning Goals: 

After completing this exercise, students should be able to:

  • describe how the color of a solution is related to the composition of the coordination complex present in solution,
  • explain how the change in color of a solution indicates that a reaction has occured, and
  • determine the identities of the products and reactants of a reaction that has taken place in solution.

If the UV-visible data are also provided, students should also be able to relate the shifts in the peaks observed in the UV-visible spectra to the position of the ligands in the spectrochemical series.

Equipment needs: 

No equipment is needed for this in-class activity. 

Corequisites: 
Subdiscipline: 
Course Level: 
Implementation Notes: 

I usually use this activity to introduce reactions of coordination complexes in lecture, which falls just after a section in my text on the colors of coordination complexes. While my students have seen many transformations in lab, I use this to connect the two portions of the course. For added empahsis you could make the aqueous solutions and bring them to class.

I usually project the pictures on a screen at the front of the class and I therefore need a device to project it from and a projector.

I break up my class into groups and let them work on this activity collaboratively. I usually let them discuss the problem for about 5-10 minutes and I check in with each group individually. If they are having trouble determining the composition of the coordination complexes, I remind them that they need to write out the formulas in the current way that we represent coordiantion complexes. This usually gets them thinking about primary vs. secondary coordination spheres and waters of hydration. I then let them work for another 10 minutes so that they can write the reactions. I then bring the class together to discuss the results. If time allows, I share the UV-visible data with the entire class and as them to explain the observed changes.

Time Required: 
20-30 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
Corequisites: 
Equipment needs: 

The students will need 3M Post-IT paper and markers to prepare a poster for the "Gallery Walk."

Prerequisites: 
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.


Subdiscipline: 
Corequisites: 
Course Level: 
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.


Subdiscipline: 
Corequisites: 
Course Level: 
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.


Subdiscipline: 
Corequisites: 
Course Level: 

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