Upper Division

2 Jun 2019

Hyperphysics

Submitted by Barbara Reisner, James Madison University
Description: 

The hyperphysics website uses concept maps as a way to organize physics content knowledge: http://hyperphysics.phy-astr.gsu.edu/hbase/hframe.html (condensed matter). I cam across this website while doing a review of the literature on what students know about semiconductors. There are nice explanations of many of the topics associated with semiconductors and they are organized in an unique way.

Prerequisites: 
Corequisites: 
Learning Goals: 

I haven't used this in teaching, but think it is a valuable resource for teaching bonding in the solid state.

28 May 2019

Quadruple Bond Acrobatics

Submitted by Lori Watson, Earlham College
Evaluation Methods: 

Students are typically asked one multiple chose or short answer question where they identify which d orbitals are involved in metal-metal quadruple bonding and/or idetify/draw the interaction.  They will also use these concepts in a more applied way in both problem set and exam in depth questions where they must explain particular structural or spectroscopic evidence using, for example, the ligand geometry forced by the eclipsed conformation of the dx2-y2 remaining d orbital.

Evaluation Results: 

Students generally perform very well on the basic identification/d-orbital interaction question that mostly tests recal of the facts.  There is a range of performance on more complex application problems, though students usually correctly identify the role of the quadruple bond orbitals and geometry as a factor.  Common challenges involve misidentification of axes, and an inability to think through how changes to variables like metal identity or oxidation state, or ligand sterics, may further contribute to observed bonding or structural data.

Description: 

Four pairs of students represent quadruple bonding in metal complexes by "forming bonds" with a variety of physical methods involving actions like facing each other while holding hands (sigma bond), touch hands and feet of their partner "above and below" the plane (two pi bonds), touching hands and feet while facing each other (delta bond).  This results in a "Twister"-like pile of students resembling the quadruple bonding interaction

 

Procedure:

1. Ask for 8 volunteers who are comfortable touching each other (holding hands, touching foot to foot)
2. Start with the shortest pair of students, and proceed through all four pairs having them do the following:

  • Sigma bond: have two students face each other at a comfortable distance, holding both hands.  The held hands represent electron density along the internuclear axis.  This is dz2
  • Pi bonds: have two pairs of students form the dxz and dyz bonds by having two students stand behind each of the first pair. They will represent pi electron density above and below the internuclear axis by touching hands together on either side (dxz) or a hand and foot above and below the axis respectively (dyz), where the y axis points toward the ceiling.  Unless your students can levitate, one foot must remain on the floor at all times--so the dxz orbital interaction is challenging, and one "lobe" (represented by the foot stick out toward the back) will not be properly represented.  
  • Delta bond: have the tallest students face each other, one behind each of the previous three students on their side.  Have them spread out their feet and hands at approximate right angles to each other, and then touch both hands palm to palm together above the z axis, and both feet together below th z axis.  To do this, the previous pairs of students will have to move even closer together, and the dxy orbitals will need to "bend" toward each other.  Students will observe that it's difficult to make good contact palm to palm.  Quadruple bonds are weaker!

3. Let the class dissolve into giggles, and then debrief.  How did each group of students have to move? Which orbital was "left out"? How would be expect incoming ligands to bind? Why? Could you have quintuple bonds? (Hint: yes) What would happen if the incoming ligands were too large to be eclipsed? (Hint: will tend to form staggered, triple bonded metal-metal complexes instead).

4. Give the class time to sketch out all four orbitals involved in a metal-metal quadruple bond in their notes.

Learning Goals: 

A student should be able to identify and draw the d orbitals involved in quadruple bonding, including their interactions.  They should be able to explain why quadruple bonds are shorter than corresponding triple bonds and where and which d orbital will be involved in bonding to ligands.

Prerequisites: 
Equipment needs: 

8 willing students who consent to physical contact with each other (holding hands, touching foot to foot).  It works best to begin with the shortest pair of students and proceed toward the tallest pair of students.

Corequisites: 
Implementation Notes: 

This works best when begining with the shortest pair of students and proceeding toward the tallest pair of students.

 

Please see attached pictures for a step-by-step guide to movement.

Time Required: 
5 minutes, plus 5 minutes debrief
23 May 2019

Teaching Computational Chemistry

Submitted by Joanne Stewart, Hope College

This is a series of in-class exercises used to teach computational chemistry. The exercises have been updated and adapted, with permission, from the Shodor CCCE exercises (http://www.computationalscience.org/ccce). The directions provided in the student handouts use the WebMO interface for drawing structures and visualizing results. WebMO is a free web-based interface to computational chemistry packages (www.webmo.net).

Prerequisites: 
Corequisites: 
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
22 May 2019
Evaluation Methods: 

This exercise usually takes longer than a 50 minute class period. Students record their answers directly onto their handouts, and I collect the handouts at the beginning of the next class.

 

Evaluation Results: 

Some common student struggles:

In Exercise 2, students don't always understand how to use simple electrostatic arguments to explain the possible packing of benzene molecules in the solid.

In Exercise 3, students are confused by the fact that the PM3 and DFT calculations give them different answers.

In Exercise 4, students find it challenging to sketch how the HOMO and LUMO come together in the Diels-Alder reaction.

Description: 

This is the sixth 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 molecular orbital calculations, which generate electron densities, electrostatic potentials, and reactivity indices. They compare electron distribution in H2, HF, and LiH. They learn about electrophilic and nucleophilic reactivity indices. They use HOMO and LUMO shapes and energies to predict reactivity in a Diels-Alder reaction.

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

 

Learning Goals: 

After completing this exercise, students will be able to:

  1. Calculate and visualize electron densities, electrostatic potentials, HOMO/LUMO, and reactivity indices.
  2. Use these visualizations to predict or understand reactivity.
Equipment needs: 

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

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.

In Exercise 1, students compare the electron density distributions in H2, HF, and LiH. It is not always obvious to them that these can be considered models for covalent, polar covalent, and ionic bonding, so I debrief those concepts after they have completed the exercise.

In Exercise 2, students compare electron density distributions in benzene and pyridine. Although they have studied aromatic compounds in organic, they are still somewhat surprised by the benzene results, with its negative region in the middle of the ring and positive region around the outside of the ring. They are reluctant to suggest T-shaped packing in the solid state.

In Exercise 3, students are introduced to the concept of reactivity indices and asked to consider the "Electrophilic (HOMO) Frontier Density," which is used to predict where an electrophile might attack. There are several interesting discoveries for students here. First, they are happy to see that the methoxybenzene calculation predicts an ortho, para preference for electrophilic substituion, which is what they learned in organic chemistry. Second, they see that semi-empirical calculations can sometimes be misleading, when their PM3 thiophene calcuation gives them the "wrong" result, but a DFT calculation gives them the "right" result. The DFT calculation clearly predicts that electrophilic subsitution is most likely at the alpha-carbon atoms. (The PM3 calculation gets the "wrong" order for the HOMO and LUMO, so the electrophilic (HOMO) frontier density ends up on sulfur instead of on the alpha carbons.

It is worth mentioning that the WebMO colors for the electrophilic (HOMO) frontier density may seem counterintuitive. We are used to visualizing electrostatic potentials, where red means negative and blue means positive. Intuitively, we might think that the site for electrophilic attack would be red because it is electron-rich. However, it is blue.

In Exercise 4, students visualize the HOMOs and LUMOs for the diene and dienophile in a Diels-Alder reaction. This exericise takes students longer than you might think. First, they must figure out which orbitals are the HOMOs and LUMOs, by looking at the long list of orbitals and finding the last full one and the first empthy one. Also, it is difficult for them to visualize/understand the orbitals and twist the molecules into useful views.

Time Required: 
1.5 hours

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