Computer modeling

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
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
31 Jan 2019
Description: 

This set of slides was made for my Organometallics class based on questions about bridging hydrides and specifically the chromium molecule. I decided to make these slides to answer the questions, and do a DFT calc to show the MO's involved in bonding of the hydride. 

 

Corequisites: 
Learning Goals: 

A student will be able to explain bridging hydride bonding

A student will be able to perform electron counting on a chromium comples with a bridging hydride

A student will be able to interepret calculated DFT molecular orbitals. 

Time Required: 
15 min
Evaluation
Evaluation Methods: 

This was provided as supplementary material outside of lecture. 

23 Jun 2018
Evaluation Methods: 

Students answer several questions prior to the in class discussion. These answers can be collected to assess their initial understanding of the paper prior to the class discussion. Assessment of the in class discussion could be based on students’ active participation and/or their written responses to the in class questions.

Evaluation Results: 

This Learning Object was developed as part of the 2018 VIPEr Summer Workshop and has not yet been used in any of our classes, but we will update this section after implementation.

Description: 

This is a literature discussion based on a 2018 Inorganic Chemistry paper from the Lehnert group titled “Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases“(DOI: 10.1021/acs.inorgchem.7b02333). The literature discussion points students to which sections of the paper to read, includes questions for students to complete before coming to class, and in class discussion questions. Several of the questions address content that would be appropriate to discuss in a bioinorganic course. Coordination chemistry and mechanism discussion questions are also included.

 

Corequisites: 
Prerequisites: 
Learning Goals: 

A successful student will be able to:

  • Evaluate structures of metal complexes to identify coordination number, geometry (reasonable suggestion), denticity of a coordinated ligand, and d-electrons in FeII/FeIII centers.

  • Describe the biological relevance of NO.

  • Identify the biological roles of flavodiiron nitric oxide reductases.

  • Identify the cofactors in flavodiiron nitric oxide reductase enzymes and describe their roles in converting NO to N2O.

  • Describe the importance of modeling the FNOR active site and investigating the mechanism of N2O formation through a computational investigation.

  • Explain the importance of studying model complexes in bioinorganic chemistry and analyze the similarities/differences between a model and active site.

  • Write a balanced half reaction for the conversion of NO to N2O and analyze a reaction in terms of bonds broken and bonds formed.

  • Interpret the reaction pathway for the formation of N2O by flavodiiron nitric oxide reductase and identify the reactants, intermediates, transition states, and products.

 

A successful advanced undergrad student will be able to:

  • Explain antiferromagnetic coupling.

  • Apply hard soft acid base theory to examine an intermediate state of the FNOR mechanism and apply the importance of the transition state to product formation of N2O.

  • Apply molecular orbitals of the NO species and determine donor/acceptor properties with the d-orbitals of the diiron center.

Implementation Notes: 

This paper is quite advanced and long, so faculty should direct students to which sections they should read prior to the class discussion. Information about which parts of the paper to read for the discussion are included on the handout. Questions #7 and #8 are more advanced, and may be included/excluded depending on the level of the course.

Time Required: 
In-Class Discussion 1-2 class periods depending on implementation.
23 Jun 2018

Interpreting Reaction Profile Energy Diagrams: Experiment vs. Computation

Submitted by Douglas A. Vander Griend, Calvin College
Evaluation Methods: 

Having not run this yet because it was collaboatively developed as part of a IONIC VIPEr workshop, we suggest grading questions 1-9 for correctness, either during or after class. Students should be tested later with additional questions based on reaction profiles. The final 3 questions should prepare students to constructively discuss the merits/limitations of computational methods. after discussion, students could be asked to submit a 1-minute paper on how well they can describe the benefits/limitations of compuational chemistry.

Evaluation Results: 

Once we use this, we will report back on the results.

Description: 

The associated paper by Lehnert et al. uses DFT to investigate the reaction mechanism whereby a flavodiiron nitric oxide reductase mimic reduces two NO molecules to N2O. While being a rather long and technical paper, it does include several figures that highlight the reaction profile of the 4-step reaction. This LO is designed to help students learn how to recognize and interpret such diagrams, based on free energy in this case. Furthermore, using a simple form of the Arrhenius equation (eq. 8 from the paper) relating activation energy, temperature and rate, the student can make some initial judgements about how well DFT calculations model various aspects of a reaction mechanism such as the structure of intermediates and transition states, and free energy changes.

Learning Goals: 
Upon completing this activity, students will be able to:
  1. Interpret reaction profile energy diagrams.

  2. Use experimental and computational data to calculate half lives from activation energies and vice versa.

  3. Assess the value and limitations of DFT calculations.

Prerequisites: 
Course Level: 
Corequisites: 
Implementation Notes: 

Having not run this with a class, we can only suggest that this activity be run in a single class period.

We presume that students have been exposed to the basic idea of reaction profiles.

Teacher should hand out the paper ahead of time and reassure students that they are not going to be expected to understand many of the details of this dense computational research paper. Instead, students should read just the synopsis included on the handout.Teacher should then spend 5 - 10 minutes summarizing key aspects of paper: 1) it's about a nitric oxide reductase mimic that catalyzes the reaction 2NO → N2O + O; 2) NO is important signaling molecule; 3) DFT is a computational method to model almost any chemical molecule, including hypothetical intermediates and transition states.

Students should work through questions in groups of 2 - 4. The final question (12) is somewhat openended and the teacher should be prepared to lead a wrap up discussion on the benefits and limitations of computational chemistry.

Time Required: 
50 minutes
22 Jun 2018
Evaluation Methods: 

An answer key is included for faculty.

Evaluation Results: 

This LO was developed for the summer 2018 VIPEr workshop, and has not yet been implemented.  Results will be updated after implementation.

Description: 

This acitivty is a foundation level discussion of the Nicolai Lehnert paper, "Mechanism of N-N Bond Formation by Transition Metal-Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases".  Its focus lies in discussing MO theory as it relates to Lewis structures, as well as an analysis of the strucutre of a literature paper.

Prerequisites: 
Corequisites: 
Course Level: 
Learning Goals: 

Upon completion of this activity, students will be able to:

  1. Write a balanced half reaction for the conversion of NO to N2O and analyze a reaction in terms of bonds broken and bonds formed.

  2. Evaluate the structures of metal complexes to identify coordination number, geometry (reasonable suggestion), ligand denticity, and d-electron count in free FeII/FeIII centers.

  3. Recognize spin multiplicity of metal centers and ligand fragments in a complex.

  4. Interpret a reaction pathway and compare the energy requirements for each step in the reaction.

  5. Draw multiple possible Lewis Structures and use formal charges to determine the best structure.

  6. Draw molecular orbital diagrams for diatomic molecules.

  7. Identify the differences in bonding theories (Lewis vs MO), and be able to discuss the strengths and weaknesses of each.

  8. Interpret calculated MO images as σ or π bonds.

  9. Identify bond covalency by interpreting molecular orbital diagrams and data.

  10. Define key technical terms used in an article.

  11. Analyze the structure of a well written abstract.

  12. Identify the overall research goal(s) of the paper.

  13. Discuss the purposes of the different sections of a scientific paper.

Implementation Notes: 

The paper in which this discussion is centered around is very rich in concepts, and will take time for students to digest.  As the technical level is higher than most foundation level course, it is strongly recommended that students focus on the structure of the paper, and not the read the entire paper.  The discussion is modular with focuses on both MO theory drawn form the paper, as well as a general anatomy of how literature papers are organized and what constitutes a good abstract.  Either focus could take a single 50 minute lecture, with two being necessary to complete both aspects.  Instructors can choose either focus, or both depending on their course learning goals.

This was developed during the 2018 VIPEr workshop and has not yet been implemented.  The above instructions are a guide and any feedback is welcome and appreciated!

Time Required: 
One or two 50 minute lectures depending on instructor's desired focus

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