Computer modeling

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.

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
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

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