Spectroscopy and Structural Methods

27 Jun 2019

Porphyrin-Based Metal-Organic Frameworks

Submitted by Amanda Bowman, Colorado College
Evaluation Methods: 

Students completed this activity in small groups, then turned in individual worksheets. Student learning and performance were assessed through 1) in-class group discussion after they had worked on the activity in small groups, and 2) grading the individual worksheets. Participation was most important in the small-group portion.

Evaluation Results: 

In general, students really enjoyed this exercise and felt that it was helpful for visualizing metal-organic frameworks (particularly the extended 3D structure). They also generally felt that it was helpful in visualizing the bonding sites of metal vertices, particularly for thinking about how that influences potential reactivity. We used Mercury as a visualization software for this discussion, and the majority of students felt very comfortable using Mercury and looking at cifs on their own after this activity.

 

The biggest challenge for students seemed to be in relating the 3D structure in the cif to the images and chemicals formulas in the article. They also tended to need some hints about question 5 – to think about what information Mössbauer can provide about oxidation state of the metal, or that you can tell whether or not there are two distinct iron environments. In our class, we do brief units on X-ray crystallography including how to use and interpret cifs, and Mössbauer spectroscopy before this literature discussion. If those topics are not already addressed in a particular class it might be helpful to add them in or directly address those topics for the students as an introduction to the literature discussion.

Description: 

This literature discussion explores the physical structures, electronic structures, and spectroscopic characterization of several porphyrin-based metal-organic frameworks through discussion of “Iron and Porphyrin Metal−Organic Frameworks: Insight into Structural Diversity, Stability, and Porosity,” Fateeva et al. Cryst. Growth Des. 2015, 15, 1819-1826, http://dx.doi.org/doi:10.1021/cg501855k. The activity gives students experience visualizing and interpreting MOF structures, and gives students exposure to some of the methods used to characterize MOFs.

Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to:

  • Interpret and describe the bonding and structural characteristics of MOFs
  • Apply knowledge of ligand field strength to electronic structure of MOFs
  • Analyze X-ray crystallographic data to gain information about structural characteristics of MOFs
  • Interpret Mössbauer spectra to gain information about electronic structure of MOFs
Implementation Notes: 

This literature discussion was designed for use in an advanced (upper-level) inorganic chemistry course, but could be used in a foundational inorganic course if students have already been introduced to d-splitting diagrams and are given some coverage of Mössbauer spectroscopy and X-ray crystallography. When covering MOFs in class, students frequently expressed that visualizing and understanding the bonding sites and extended 3D structures was very challenging. So, this literature discussion was developed specifically to address that. Students completed this activity in small groups. It is very helpful to advise students ahead of time to bring laptops (or instructor should have some available) and to have the cifs from the paper downloaded and ready to go. We used Mercury as a visualization software for this activity. This activity can easily be completed in one class period. It is also helpful if students have been provided with the article ahead of time and encouraged to look it over – otherwise the most time-consuming part of this activity was allowing time for students to examine the MOF structure images in the paper before being able to discuss and answer the questions with their groups.

Note on visualization of MOFs using Mercury: To answer the discussion questions, we used the ‘stick’ or the ‘ball and stick’ style. We also used the default packing scheme (0.4x0.4x0.4) and the 1x1x1 packing scheme. The packing scheme can be changed by selecting Packing/Slicing… in the Calculate menu. I also had students view the 3x3x3 packing scheme – while this is not necessary to answer the discussion questions, it was interesting for students to be able to visualize the extended structure of the MOFs.

 

8 Jun 2019

VIPEr Fellows 2019 Workshop Favorites

Submitted by Barbara Reisner, James Madison University

During our first fellows workshop, the first cohort of VIPEr fellows pulled together learning objects that they've used and liked or want to try the next time they teach their inorganic courses.

6 Jun 2019
Evaluation Methods: 

The guided reading questions may be graded using the answer key. 

Evaluation Results: 

These questions have not yet been assigned to students.

Description: 

Guided reading and in-class discussion questions for "High-Spin Square-Planar Co(II) and Fe(II) Complexes and Reasons for Their Electronic Structure."

Course Level: 
Learning Goals: 

1.  Bring together ligand field theory and symmetry.

  1. Students should be able to identify symmetry of novel molecules in the literature.

  2. Students should be able to explain d-orbital ordering in a coordination complex using ligand field theory.

  3. Students should be able to identify donor/acceptor properties of previously unseen ligands.

  4. Students should be able to apply your knowledge of electronic transitions to the primary literature.

  5. Students should be able to become more familiar with 4-coordinate geometries.

  6. Students should be able to predict magnetic moments of high-spin and low-spin square-planar complexes.

  7. Students should be able to identify properties of ligands that favor formation of the highly unusual high-spin square planar complexes.

2.  Students should comfortable with reading and understanding primary literature.


 

Related activities: 
Implementation Notes: 

You do not have to assign all of the guided reading questions at once.  You may consider assigning questions as they pertain to where you are in your inorganic chemistry class.

Time Required: 
this has not been used yet for in-class discussion.
6 Jun 2019
Evaluation Methods: 

The classroom discussion (participation, answers, etc) may be assessed by the instructor, or alternatively, these questions could be given to students to turn in.

Evaluation Results: 

None yet available.  Please leave yours in the comments!

Description: 

This literature discussion aims to have students in an advanced inorganic chemistry course interpret reaction schemes and electronic spectra, relate chemical formulae to molecular structure, and gain an understanding of how inorganic synthesis is planned and executed.  Students should gain an understanding of how counterions and crown ethers affect structure. Question 7 may be expanded to ask students to why pi-donor ability affects ligand field splitting, or as an introfuction to this topic.

An associated 1FLO based on this paper is linked in the related content.

 

Corequisites: 
Course Level: 
Learning Goals: 
Students will be able to:
  • Interpret reaction schemes and write balanced equations.
  • Rationalize the position of a ligand in the spectrochemical series based upon its π-donor/acceptor properties
  • Relate the electronic structure of tetrahedral d8 complexes to their magnetic properties
  • Analyze the impact of countercations on the geometry and electronic properties of the complexes.
Implementation Notes: 

This LO is intended for an advanced inorganic chemistry course.  Students should read the communication before class with questions above as guidance.  A classroom discussion should insue, in which students gain an insight into inorganic synthesis, and recognize how minor differences between compounds, such as counterions, have significant effects on electronic structure.

 

Time Required: 
50 minutes
6 Jun 2019

1FLO: Relating Electronic Spectra and Ligand Field Strength of [NiX4]2- Anions

Submitted by Wesley S. Farrell, United States Naval Academy
Evaluation Methods: 

Evaluate students' comprehension based on verbal in-class answers and ensuing discussion.

Evaluation Results: 

None yet available.

Description: 

This 1FLO asks students to interpret an electronic spectrum of 5 NiX42- anions.  Students will determine the relative ligand field strength, (re)familiarize themselves with terms such as "redshift" and "blueshift", and consider possible metal complex geometries.

Learning Goals: 
  1. Students (re)familiarize themselves with relationship between wavelength (λ) and wavenumber (cm-1).

  2. Students recall 4-coordinate geometries.

  3. Students define the terms “redshift” and “blueshift.”

  4. Students analyze data to construct a partial spectrochemical series.

Corequisites: 
Course Level: 
Equipment needs: 

None

Implementation Notes: 

This activity could be used as either a guided introduction to the spectrochemical series, or as an in-class activity to review after introduction.  If used as an introduction, question 4 may need modification.

Time Required: 
15 - 20 Minutes
5 Jun 2019

Zinc-Zinc Bonds (Expanded and Updated)

Submitted by Wesley S. Farrell, United States Naval Academy
Evaluation Methods: 

Performance and participation in the discussion will be assessed 

Evaluation Results: 

None collected yet. Evaluation data will be added in the future.

Description: 

This paper in Science reports the synthesis of decamethyldizincocene, a stable compound of Zn(I) with a zinc-zinc bond. In the original LO, the title compound and the starting material, bis(pentamethylcyclopentadienyl)zinc, offer a nice link to metallocene chemistry, electron counting, and different modes of binding of cyclopentadienyl rings as well as more advanced discussions of MO diagrams. More fundamental discussion could focus on the question of what constitutes the evidence for a chemical bond, in this case, the existence of a zinc-zinc bond. In this updated LO, these topics are still covered, however additional topics, such as point group idenitifaction, details regarding the reaction mechanism, electronic structure, and  searching the literature using SciFinder are covered.  Additionally, electron counting is divided into both the covalent and ionic models.

Corequisites: 
Course Level: 
Learning Goals: 
  1. Students should become more confident reading the primary literature

  2. Students should be able to apply existing knowledge to interpret research results.

  3. Students should be able to apply electron counting formalisms to organometallic compounds.

  4. Students should be able to use 1H NMR spectroscopy data to rationalize structure.

  5. Students can rationalize bond distances based on periodic trends in atomic radii

  6. Students use SciFinder to put this work into a larger context.

  7. Students identify redox reactions based on oxidation changes.

  8. Students identify molecular point groups based upon structures.

  9. Students should be able to connect d electron count to observed colors of compounds. 

Related activities: 
Implementation Notes: 

Students are asked to read the paper and the accompanying Perspectives article before class as well as answer the discussion questions. The questions serve as a useful starting point for class discussion. 

Time Required: 
50 minutes
31 May 2019

Helping Students with Visual Impairments See Colors

Submitted by Douglas Balmer, Warwick High School
Evaluation Methods: 

Do these students identify the same colors as the students without visual impairments?

Are their lab results correct? 

Evaluation Results: 

Students were able to accurately describe colors.

Description: 

I have had some students in class have a hard time identifying colors (flame tests, solution color, acid-base indicators, etc.) because of a visual impairment. There are many cell-phone apps that are helpful in aiding these students. "Pixel Picker" allows the students to load a picture from a device (cell phone, ipad). This is helpful because students are now dealing with a "frozen" image. Moving the cross-hair to different parts of the picture changes the R-G-B values. The "Color Blind Pal" app uses a more qualitative approach. It names the color in the cross-hair using various color scales. There are also different options for different types of color blindness. 

Both of these apps are free and availble in the App Store.

Prerequisites: 
Corequisites: 
Course Level: 
Learning Goals: 

A student should be able to correctly identify an unknown metal by the color of its flame.

A student should be able to correctly identify the endpoint in a titration by the indicator's color change.

A student should be able to correctly describe the physical properties (color) of a sample.

A student should be able to correctly predict the visible absorbance spectrum of a solution based on correctly identifying the color of the solution.

Implementation Notes: 

Have the students with visual impairments practice using the app ahead of time to better prepare them to use the app for the first time in class/lab. Students would also need to understand the additive nature of light colors. For example, high R and G values will appear yellow/orange. I would give these students a 1-page handout for their lab notebook with the addative color wheel and various colored circles labeled with their names and RGB values so that students could practice and reference in the lab.

Our lab safety contract actually has students indicate whether they are color blind. This is a good time to introduce these students to the apps.

Time Required: 
15 min
23 May 2019

CompChem 05: Infrared, Thermochemistry, UV-Vis, and NMR

Submitted by Joanne Stewart, Hope College
Evaluation Methods: 

This exercise takes longer than a 50 minute class period, so we get as far as we can in one class and the students complete the exercise as homework. Students write their answers to the questions directly on the handout. Tables are provided for recording numerical results, but because of some (simple) required mathematical manipulations, it is easier if students set up a spreadsheet and record their numerical results there. The handouts with their answers and printed copies of their spreadsheet are collected in the next class.

Evaluation Results: 

In Exercise 1, the vibrational spectrum of formaldehyde is calcuated by three different methods. Because the vibrational modes come out in a different order, energy-wise, in one of the methods, students have trouble keeping track of which vibration is which. Each mode is labeled with the correct symmetry label, which should help them. Plus, they can click on each mode and visualize it.

Exercise 2 involves calcuating delta H for an "isodesmic" reaction: one in which the total number and type of bonds is the same in reactants and products. This helps cancel any systematic errors in the calculations. If this is one of the first time that students have worked in "hartrees," it is helpful to explain that unit to them. Students compare semi-empirical calculations with HF and DFT, and in this example, the HF and DFT calculations give much more accurate results.

Exercise 3 is about calculating UV-Vis spectra, but more importantly it walks students through drawing more complicated molecules. The CIS/ZINDO approach is used for the UV-Vis calcuation, which may not be highly accurate, but is very fast, so students get rapid results that they can compare.

In Exercise 4, students calculate NMR spectra for three different molecules. It teaches students about chemical shifts, but it does not cover coupling constants. If students are experienced with NMR, the averaging of proton resonances (such as the three protons in a methyl group) has become second nature to them. This exercise forces them to think about how those resonances are averaged.

 

Description: 

This is the fifth in a series of exercises used to teach computational chemistry. It has been adapted, with permission, from a Shodor CCCE exercise (http://www.computationalscience.org/ccce). It uses the WebMO interface for drawing structures and visualizing results. WebMO is a free web-based interface to computational chemistry packages (www.webmo.net).

In this exercise, students perform infrared, thermochemistry, UV-Vis, and NMR calculations. They compare the results from different methods and basis sets to experimental values.

The exercise provides detailed instructions, but does assume that students are familiar with WebMO and can build molecules and set up calculations.

Learning Goals: 

Students will be able to:

  1. Calculate an IR spectrum. Visualize the normal modes. Use appropriate scale factors to “correct” the calculated values.
  2. Calculate NMR spectra and average the chemical shift values for the static structures (in 1H NMR) to approximate the experimental spectrum.
  3. Calculate UV-Vis spectra.
Equipment needs: 

Students need access to a computer, the internet, and WebMO (with Mopac and Gaussian). 

Course Level: 
Corequisites: 
Implementation Notes: 

I use this as an in-class exercise. Students bring their own laptops and access our institution's installation of WebMO through wifi.

Time Required: 
2 hours
28 Jan 2019
Evaluation Methods: 

A portion of their grade (20%) is dedicated to literature discussions (4-6 over the course of the semester). The grading rubric involves 3 possible ratings for each question/answer: “excellent”, “acceptable”, or “needs work”.

Concepts covered during literature discussions will be included among exam materials.

Evaluation Results: 

N/A

Description: 

This Guided Literature Discussion was assigned as a course project, and is the result of work originated by students Christopher Lasterand Patrick Wilson.  It is based on the article “Deca-Arylsamarocene: An Unusually Inert Sm(II) Sandwich Complex” by Niels J. C. van Velzen and Sjoerd Harder in Organometallics 201837, 2263−2271. It includes a Reading Guide that will direct students to specific sections of the paper that were emphasized in the discussion.  This article presents a study of the reactivity of bulky CpAr-Et/iPrSm complexes that is contrasted to the more well-known Cp*2Sm.

Course Level: 
Corequisites: 
Learning Goals: 

After reading and discussing this article, a student should be able to…

-      Be more familiar with the chemistry of sandwich samarocene complexes.

-      Understand how bulky ligands affect structure and reactivity in a sandwich complex.

-      Apply the CBC method to identify ligand functions and metal valence number/ligand bond number.

-       Understand how XRD bond distances can help determine a ligand charge.

Implementation Notes: 

I am planning on assigning this LO as a graded in-class group discussion. Students will be given a copy of the article, reading guide, and discussion questions one week in advance. On the day of the discussion, students will be assigned in groups of 2-3. They will then have one lecture period to answer the questions in writing as a group.  [This article is among the free-access ACS Editors’ Choice.]

Time Required: 
1 lecture period, with materials given one week in advance
16 Jan 2019
Evaluation Methods: 

Concepts covered during literature discussions will be included among exam materials.

Evaluation Results: 

N/A

Description: 

This Guided Literature Discussion was assigned as a course project, and is the result of work originated by students Jana Forster and Kristofer Reiser.  It is based on the article “Mechanism of the Platinum(II)-Catalyzed Hydroamination of 4-Pentenylamines” by Christopher F. Bender, Timothy J. Brown, and Ross A. Widenhoefer in Organometallics 2016 35 (2), 113-125. It includes a Reading Guide that will direct students to specific sections of the paper that were emphasized in the discussion.  This article presents a mechanistic study of hydroamination reactions catalyzed by a late transition metal complex.

Course Level: 
Corequisites: 
Learning Goals: 

After reading and discussing this article, a student should be able to…

-  Apply the CBC electron-counting method.

-  Understand how 31P {1H} NMR can help differentiate intermediates.

-  Use information provided by Eyring plots.

-  Understand how a catalyst resting state and turnover-limiting step can be identified.

-  Understand the role of kinetics in mechanistic investigations.

-   Appreciate how proposed reaction mechanisms can be evaluated.

 

Implementation Notes: 

I am planning on assigning this LO as a graded in-class group discussion. Students will be given a copy of the article, reading guide, and discussion questions one week in advance. On the day of the discussion, students will be assigned in groups of 2-3. They will then have one lecture period to answer the questions in writing as a group. A portion of their grade (20%) is dedicated to literature discussions (4-6 over the course of the semester). The grading rubric involves 3 possible ratings for each question/answer: “excellent”, “acceptable”, or “needs work”. [This article is among the free-access ACS Editors’ Choice.]

Time Required: 
1 lecture period, with discussion materials given one week in advance

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