Upper Division

21 May 2019

CompChem 04: Single Point Energies and Geometry Optimizations

Submitted by Joanne Stewart, Hope College
Evaluation Methods: 

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

Evaluation Results: 

Student work is typically complete and correct because they have completed the exercise in class and received feedback as they worked.

Description: 

This is the fourth 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 coordinate scans to explore how changes in bond length, bond angle, and dihedral angle can affect molecular energy. The results allow them to visualize the relationship between the geometry change and molecule's energy.

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 and visualize the potential energy surface of a diatomic molecule.
  2. Calculate and visualize the energy changes in a small molecule during bending.
  3. Calculate and visualize the changes in energy when a small molecule undergoes conformational changes.
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.

Time Required: 
30 minutes
20 May 2019

CompChem 03: Choice of Theoretical Method

Submitted by Joanne Stewart, Hope College
Evaluation Methods: 

This exercise often takes longer than 50 minutes, so I allow students to finish it at home and ask them to turn in the completed handout at the beginning of the next class.

Evaluation Results: 

Student work is typically complete and correct because they have completed most of it in class.

Description: 

This is the third 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 the exercise, students compare the computational results (structures and energies) for different theoretical methods and basis sets.

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. Compare computational results (energies and structures) for different combinations of theoretical method and basis set.
  2. Describe the tradeoff between computational “expense” and accuracy of computational results.
Equipment needs: 

Students need access to a computer, the internet, and WebMO (with Mopac and Gaussian). Students work on their own laptops, or it can be done in a computer lab.

Corequisites: 
Topics Covered: 
Implementation Notes: 

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

Time Required: 
50 minutes
20 May 2019

CompChem 02: Introduction to WebMO

Submitted by Joanne Stewart, Hope College
Evaluation Methods: 

The students write their answers to the questions directly onto the handout. I collect the handout in the next class and check it for completeness (credit/no credit).

Evaluation Results: 

Because the students completed the exercise in class where they could ask questions, their work is typically complete and correct.

Description: 

This is the second 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 was tested on WebMO Version 18 but should work with minimal modification on earlier versions. WebMO is a free web-based interface to computational chemistry packages (www.webmo.net).

The directions assume no prior knowledge of the WebMO interface and provide detailed, click-by-click instructions on building molecules and setting up calculations.

Learning Goals: 

After completing this exercise, students will be able to:

  1.  Draw a molecule in WebMO
  2.  Rotate, translate, and zoom the molecule
  3.  Choose a theory and basis set for calculations
  4.  Optimize the geometry of a molecule
  5.  Determine the bond lengths, bond angle, and dihedral angles in a molecule in WebMO
  6.  Calculate molecular orbitals in WebMO
  7.  Use the Z-matrix editor and coordinate scans to compare the energies of different molecular geometries
Equipment needs: 

Students need access to a computer, the internet, and WebMO (with Mopac). Other computational engines (Gaussian, GAMESS) can be used.

I initially taught this part of the course in a computer lab, but last year all of the students were able to bring their own laptops. I bring an extra laptop to class just in case.

Prerequisites: 
Corequisites: 
Topics Covered: 
Implementation Notes: 

I use this as an in-class exercise. The students are able to follow the directions with little difficulty. Many of them have used the WebMO interface briefly in general chemistry and organic chemistry, so this is not their first exposure.

The students need a reminder of what a dihedral angle is.

Time Required: 
50 minutes
20 May 2019

CompChem 01: Creating a Basis Set

Submitted by Joanne Stewart, Hope College
Evaluation Methods: 

I ask the students to bring printed copies of their graphs and answers to the questions in the student handout to the next class. I collect these and check them for completeness (credit/no credit). 

Evaluation Results: 

Because the students completed the exercise during the previous class, their work is typically complete and correct.

Description: 

This is the first 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).

In the exercise, students learn about simple Gaussian-type basis sets. In an Excel spreadsheet, they compare the Slater function for a 1s orbital to the combination of one, two, or three Gaussian functions. They are also introduced to the Basis Set Exchange website (https://bse.pnl.gov/bse/portal).

 

Learning Goals: 

After completing this exercise, students will be able to:

  1.  Explain why Gaussian-type orbitals (GTOs) are used instead of Slater-type orbitals (STOs) in computational chemistry.
  2.  Use Excel to model the hydrogen STO with GTOs.
  3.  Explain why combining multiple GTOs produces a better approximation of an STO.
  4.  Find alpha values for the STO-3G basis set in an online database.
Equipment needs: 

Students need access to a computer, the internet, and Excel. I initially taught this part of the course in a computer lab, but last year all of the students were able to bring their own laptops. I bring an extra laptop to class just in case.

Prerequisites: 
Corequisites: 
Topics Covered: 
Implementation Notes: 

All of the students had some experience with Excel in their general chemistry course. However, entering the complicated equations into Excel is challenging for many of them. I have found it most effective to simply allow them to help one another with this.

They are typically able to make the graphs without extra assistance, but I walk around the class and help as needed.

Time Required: 
30 minutes
7 Apr 2019

Encapsulation of Small Molecule Guests by a Self-Assembling Superstructure

Submitted by Shirley Lin, United States Naval Academy
Evaluation Methods: 

I have not yet implemented this LO. As with other literature discussions, instructors could collect the completed worksheets (by an individual student or in groups of students) for evaluation.

Evaluation Results: 

I have not yet implemented this LO so there are currently no evaluation results to share.

Description: 

This literature discussion focuses upon two journal articles by the Rebek group on the synthesis and host-guest chemistry observed with the "tennis ball." 

Corequisites: 
Learning Goals: 

After completing this literature discussion, students will be able to:

  • provide examples of supramolecular systems in nature that use reversible, weak noncovalent interactions 
  • define terms in supramolecular chemistry such as host, guest, and self-complementary
  • identify the number and location of hydrogen bonds within the "tennis ball" assembly
  • draw common organic reaction mechanisms for the synthesis of the "tennis ball" subunits
  • describe the physical and spectroscopic/spectrometric techniques used to provide evidence for assembly of a host-guest system
  • explain the observed thermodynamic parameters that are important for encapsulation of small molecule guests by the "tennis ball"
Implementation Notes: 

This LO could be used at the end of a traditional 2-semester organic chemistry sequence as an introduction to organic supramolecular systems, as an organic chemistry example within a discussion about inorganic supramolecular chemistry, or in an upper-division elective course about supramolecular chemistry. The LO topic, the "tennis ball," has a published laboratory experiment in J. Chem. Educ. (found here). Time permitting, instructors could have students read the article and complete the literature discussion before executing the experiment in the lab.

As usual, instructors may wish to mix-and-match questions to suit their learning goals.

Time Required: 
depends upon implementation; minimum of 20-30 minutes for the literature discussion if students read an d answer questions outside of class
26 Mar 2019

Redox-switch polymerization catalysis

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

I am really unsure at this point. I may use the 1FLO version of this as a series of exam quesitons, or I may have the students work on this literature discussion in class. Either way, I am excited to see what they will do with it.

Description: 

This is the full literature discussion based on a communicaiton (J. Am. Chem. Soc. 2011133, 9278). This paper describes a redox-switch yttrium catalyst that is an active catalyst for the polymerization of L-lactide in the reduced form and inactive in the oxidized form. The catalyst contains a ferrocene-based ligand that serves as the redox active site in the catalyst. This full literature discussion is an extension of the one figure literature discussion that is listed below. In addition to presenting all of the same questions as that learning object, this includes interpretation of the XANES spectra presented in the paper. It also asks the students to identify the monomer and polymer in the reaction of interest. A possible extension of this learning object would be to have students examine and take measurements from the crystal structure presented in the paper in order to support the apparently low electron count on the yttrium catalyst. The Covalent Bond Classification system for counting electrons is used in this learning object.

Corequisites: 
Course Level: 
Learning Goals: 

A student should be able to apply their knowledge to 

  1. describe and interpret a plot of conversion vs. time
  2. count electrons and determine valence states in organometallic compounds
  3. determine if an organometallic compound is an oxidizing or reducing agent
  4. decipher a first-order kinetic plot
  5. interpret XANES spectra to determine the valence of iron in the catalyst
Subdiscipline: 
22 Mar 2019

1FLO: Redox-switch polymerization catalysis

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

I am really unsure at this point. I could certainly see this being used as a series of exam questions or have students take a few minutes to think about the questions individually and then have them share with a small group and present their thoughts in class. This is actively interpreting a figure from the literature with almost no context. As such, it is certainly going to be indicative of their understanding of other ideas and concepts.

Description: 

This is what I hope will be a new classification of learning object called a one figure learning object (1FLO). The purpose is to take a single figure from a paper and present students with a series of questions related to interpreting the figure. This literature discussion is based on a paper (J. Am. Chem. Soc. 2011, 133, 9278) from Paula Diaconescu's lab in which a yttrium polymerization catalyst with a ferrocene-based ligand can effectively be rendered active or inactive depeneding on the valence state of the ligand. The figure chosen from the paper shows the conversion of the monomer (L-lactide) to polymer over the course of time. During the reaction, the valence state of the ligand is changed and the rate of polymerization is significantly impacted. While the purpose of this LO was to limit consideration to a single figure, there is so much to mine from this communication that a companion literature discussion was developed to go into more of the details that were presented. Certainly this 1FLO can stand alone or be used in conjunction with the companion literature discussion. The Covalent Bond Classification system for counting electrons is used in this learning object.

Corequisites: 
Subdiscipline: 
Learning Goals: 

A student should be able to apply their knowledge to

  1. describe and interpret a plot of conversion vs. time
  2. count electrons and determine valence states in organometallic compounds
  3. determine if an organometallic compound is an oxidizing or reducing agent
  4. decipher a first-order kinetic plot
Course Level: 
Implementation Notes: 

I have yet to use this but I anticipate doing so in the fall. I hope it works as well as I think it can. It is such a simple plot and yet it is so rich in chemistry. I have a feeling I am going to have a very hard time containing myself to just this LO and not using the companion full Literature Discussion.

Time Required: 
Unknown but I think it could be as short as 15 minutes

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