# Second year

28 May 2019

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:
Course Level:
Subdiscipline:
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).

Topics Covered:
Prerequisites:
Corequisites:
Course Level:
22 May 2019

## Digital Lab Techniques Manual

Submitted by Catherine McCusker, East Tennessee State University
Description:

MIT OpenCourseWare has a great series of videos explaining (synthetic) lab techniques

Course Level:
Prerequisites:
Corequisites:
Implementation Notes:

I have my research students watch these videos before starting to work in the lab.  Many of them have (or remember) very little hands-on lab experience before they start.

Time Required:
Each video is around 10-15 minutes long
22 May 2019

## CompChem 06: Electron Densities, Electrostatic Potentials, and Reactivity Indices

Submitted by Joanne Stewart, Hope College
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).

Course Level:
Prerequisites:
Corequisites:
Related activities:
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
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).

Course Level:
Prerequisites:
Corequisites:
Related activities:
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.

Course Level:
Prerequisites:
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.

Course Level:
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:
Course Level:
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
6 May 2019

## Drawing, visualizing and interpreting 3-D molecular structure (2019 Community Challenge #2)

Submitted by S. Chantal E. Stieber, Cal Poly Pomona
Evaluation Methods:
• The instuctor walked around the classroom to help students individually as needed for immediate assessment.
• At the end of the class period, students submitted their work to Blackboard for grading.
• Assignments were graded based on accuracy and quality of the drawings.
Evaluation Results:

Students generally were able to determine the molecular formula and generate connectivity drawings of the displayed 3-D structures, but really struggled with 3-D drawing. Although this was developed for a course with second year students who had completed general chemistry, even older students in the course struggled with this component. However, by the end of class, all students greatly improved in their ability to understand, interpret, and convey 3-D structure.

Many students were surprised and many jokes were made about this being a chemistry art class. Although some students didn't particularly enjoy drawing, all understood the value and felt like they had learned something useful. At the end of the semester, many students remarked that the chemical drawing section was the most useful or interesting.

Description:

This in-class activity was designed for a Chemical Communications course with second-year students. It is the first part of a two-week segment in which students learn how to use Chemdraw (or similar drawing software) to create digital drawings of molecules.

In this activity, students are given a blank worksheet and 5 models of molecules were placed around the classroom. Students interpreted the 3-D models to determine molecular formulas, connectivity, and generate drawings that convey the 3-D elements. Once students completed the worksheet by hand, they generated the whole worksheet using Chemdraw.

Learning Goals:

Students will be able to:

1.    Write the formula for a molecule based on a 3-D structure.

2.    Draw a molecule based on a 3-D structure.

3.    Convey 3-D structure of a molecule in a drawing.

4.    Translate molecular connectivity to a drawing that conveys 3 dimensions.

5.    Create digital drawings of molecules using Chemdraw or similar chemical drawing software.

Equipment needs:
• Molecular model set for the instructor to prepare structures before class.
• One computer per student with chemical drawing software such as Chemdraw.
Corequisites:
Course Level:
Implementation Notes:

Prior to the activity, students were given a brief presentation with an introduction to basic Chemdraw elements using the Chemdraw manual and existing tutorials (see links provided). VSEPR was also reviewed.

For the activity, students were given 3-D models of molecules, and the color key for atom identity was written on the board (eg. blue = oxygen, black = carbon...). The activity was conducted in a class of 24 students, in which each student had access to a computer. The entire class period was 1 hour 50 min, but the activity could be shortened if fewer molecules are included.

Before class, the instructor built models of molecules using a molecular model kit. It is helpful to have multiple copies of each molecule, especially for a larger class, but not critical. The molecules used for the acitvity can be seen in the faculty-only key, and were chosen to have a range of 3-D structures, but other molecules could be chosen. For example, a coordination chemistry or upper division course could have 3-D printed models of crystal structures used as the starting point.

Time Required:
60 min
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."

Prerequisites:
Corequisites:
Course Level:
Subdiscipline:
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"
Related activities:
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