Computer modeling

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
3 Jun 2017

Literature Discussion of "A stable compound of helium and sodium at high pressure"

Submitted by Katherine Nicole Crowder, University of Mary Washington
Evaluation Methods: 

Students could be evaluated based on their participation in the in-class discussion or on their submitted written answers to assigned questions.

Evaluation Results: 

This LO has not been used in a class at this point. Evaluation results will be uploaded as it is used (by Spring 2018 at the latest).

Description: 

This paper describes the synthesis of a stable compound of sodium and helium at very high pressures. The paper uses computational methods to predict likely compounds with helium, then describe a synthetic protocol to make the thermodynamically favored Na2He compound. The compound has a fluorite structure and is an electride with the delocalization of 2e- into the structure.

This paper would be appropriate after discussion of solid state structures and band theory.

The questions are divided into categories and have a wide range of levels.

Dong, X.; Oganov, A. R.; Goncharov, A. F.; Stavrou, E.; Lobanov, S.; Saleh, G.; Qian, G.-R.; Zhu, Q.; Gatti, C.; Deringer, V. L.; et al. A stable compound of helium and sodium at high pressure. Nature Chemistry 2017, 9 (5), 440–445 DOI: 10.1038/nchem.2716.

Corequisites: 
Learning Goals: 

After reading and discussing this paper, students will be able to

  • Describe the solid state structure of a novel compound using their knowledge of unit cells and ionic crystals
  • Apply band theory to a specific material
  • Describe how XRD is used to determine solid state structure
  • Describe the bonding in an electride structure
  • Apply periodic trends to compare/explain reactivity
Implementation Notes: 

The questions are divided into categories (comprehensive questions, atomic and molecular properties, solid state structure, electronic structure and other topics) that may or may not be appropriate for your class. To cover all of the questions, you will probably need at least two class periods. Adapt the assignment as you see fit.

CrystalMaker software can be used to visualize the compound. ICE model kits can also be used to build the compound using the template for a Heusler alloy.

Time Required: 
2 class periods
3 Jun 2017
Evaluation Methods: 

This LO was craeted at the pre-MARM 2017 ViPER workshop and has not been used in the classroom.  The authors will update the evaluation methods after it is used.

Description: 

This module offers students in an introductory chemistry or foundational inorganic course exposure to recent literature work. Students will apply their knowledge of VSEPR, acid-base theory, and thermodynamics to understand the effects of addition of ligands on the stabilities of resulting SiO2-containing complexes. Students will reference results of DFT calculations and gain a basic understanding of how DFT can be used to calculate stabilities of molecules.

 
Prerequisites: 
Corequisites: 
Learning Goals: 

Students should be able to:

  1. Apply VSEPR to determine donor and acceptor orbitals of the ligands

  2. Identify lewis acids and lewis bases

  3. Elucidate energy relationships

  4. Explain how computational chemistry is beneficial to experimentalists

  5. Characterize bond strengths based on ligand donors

Course Level: 
Implementation Notes: 

Students should have access to the paper and have read the first and second paragraphs of the paper. Students should also refer to scheme 2 and table 2.

 

This module could be either used as a homework assignment or in-class activity. This was created during the IONiC VIPEr workshop 2017 and has not yet been implemented.

 
Time Required: 
50 min
25 Mar 2017

KINETICS - Computations vs. Experiment

Submitted by Teresa J Bixby, Lewis University
Evaluation Methods: 

- determine the activation energy of a reaction from an energy diagram

- determine the rate constant for the reaction from the activation energy

- determine the rate law and rate constant for a reaction from experimental data

 

These Learning Objectives will be assessed on a subsequent exam.

Evaluation Results: 

Most students did not have a problem determining the rate constant from the activation energy (from an energy diagram). From what mistakes there were, the most common mistake was choosing the wrong starting energy (choosing the product energy rather than the reactant energy to start). Most students were also able to determine the rate constant from experimental data, especially if there were clearly 2 experiments where only one reactant concentration was doubled for each reactant. Changing the factor by which the reactant concentration changed (1.3 for example), or including experimental data where two reactant concentrations changed at the same time, seemed to cause more problems. 

Description: 

<p>This activity has students use Spartan to build an energy diagram for an SN2 reaction as a function of bond length. The activation energy can then be used to determine the rate constant for the reaction. After a few intoductory questions to orient general chemistry students to the organic reaction (with a short class discussion), the instructions lead them step-by-step to build the energy diagram for CH&lt;sub&gt;3&lt;/sub&gt;Cl + Cl- --&gt; Cl- + CH&lt;sub&gt;3&lt;/sub&gt;Cl. Any questions about how to use the program or descriptions of the levels of theory are given during the class period. The questions, class discussion, and Spartan tutorial for the first reaction can be compelted in one 50 min period.&nbsp;</p><p>The rest of the activity is completed as an assignment. Other anions attack CH&lt;sub&gt;3&lt;/sub&gt;Cl and students consider which product is more stable. They also compare the computational rate constant for OH- attacking with a rate constant determined from experimental data. They find that Spartan is good for molecular modeling but the absolute value of the energies of the transition states are inaccurate.&nbsp;</p><p>SN2 reactions with more complex molecuels may be more illustrative.&nbsp;</p><p>In the future we hope to develop this activity into an in-class prelab where then students can collect the experimental data on their own.&nbsp;</p>

Learning Goals: 

- use Spartan to build molecules and a transition state

- determine the activation energy of a reaction from an energy diagram

- determine the rate constant for the reaction from the activation energy

- determine the rate law and rate constant for a reaction from experimental data

- relate reactant and product energies to leaving group character

- compare computation to experiment

Prerequisites: 
Corequisites: 
Equipment needs: 

Need to have access to Spartan Student.

Topics Covered: 
Course Level: 
Subdiscipline: 
Implementation Notes: 

Building the transition state seems to be the most confusing part for General Chemistry students who have not used Spartan before. Encouraging them to limit twirling the molecule around a lot before they have completed this step seems to help. I intend to clarify these instructions before the next implementation. 

A different base molecule may yield better agreement with experimental data. This will aslo be explored before the next implementation.

Time Required: 
50 min + out-of-class assignment (~5 days)
18 Jan 2017

calistry calculators

Submitted by Adam R. Johnson, Harvey Mudd College
Description: 

I just stumbled on this site while refreshing myself on the use of Slater's rules for calculating Zeff for electrons. There are a variety of calculators on there including some for visualizing lattice planes and diffraction, equilibrium, pH and pKa, equation balancing, Born-Landé, radioactive decay, wavelengths, electronegativities, Curie Law, solution preparation crystal field stabilization energy, and more.

I checked and it calculated Zeff correctly but I can't vouch for the accuracy of any of the other calculators. 

Prerequisites: 
Corequisites: 
Learning Goals: 

This is not a good teaching website but would be good for double checking math

 

Implementation Notes: 

I used this to double check my Slater's rules calculations (and found a mistake in my answer key!)

4 Jan 2017
Description: 

This is a great new textbook by George Luther III from the University of Delaware.  The textbook represents the results of a course he has taught for graduate students in chemical oceanography, geochemistry and related disciplines.  It is clear that the point of the book is to provide students with the core material from inorganic chemistry that they will  need to explain inorganic processes in the environment.  However the material is presented in such a clear, logical fashion and builds so directly on fundamental principles of physical inorganic chemistry that the book is actually applicable to a much broader audience.  It provides a very welcome presentation of frontier orbital theory as a guide to predicting and explaining much inorganic chemical reactivity.  There are numerous very  helpful charts and tables and diagrams.  I found myself using the book for a table of effective nuclear charges when I was teaching general chemistry last semester.  The examples are much more interesting that the typical textbook examples and would be easy to embellish and structure a course around.  There is also a helpful companion website that provides powerpoint slides, student exercises and answers.  The book covers some topics not typically seen in inorganic textbooks like the acidity of solids but the presentation of this information makes sense in light of the coherent framework of the text.  We so often tell our students "structure dictates function".  This text really make good on that promise.  My only complaint is that I wish the title were something more generic so that I could use it for a second semester of introductory-esque material that we teach after students have taken a single semester of intro chem and two semesters of organic chemistry.  So much of what is covered in this textbook is precisely what a second semester sophomore chemistry major should know before proceeding on in the major.  But the title makes the book hard to sell to chemistry majors and that is regrettable. 

Prerequisites: 
Course Level: 
14 May 2016

Crystal Field Theory and Gems--Guided Inquiry

Submitted by Adam R. Johnson, Harvey Mudd College
Evaluation Methods: 

The 2 worksheets were handed in and graded according to the key. I generally used a +, √, - grading scale for the probelms. I gave a single grade for each group. Answer keys are provided as "faculty only" files.

Evaluation Results: 

The day 1 activities were too long and we didn't get to the square planar CFT derivation. For my next offering, I am adding a day to the unit so the students will see all three geometries. Students struggled a bit at first with the software and visualization but were able to figure it out with some assistance. The students in Fall 2015 had already practiced using Crystalmaker in a prior unit; for 2016, this prior unit has been removed so the visualization will probably take more time. I anticipate using 1.5 days for part 1 and 1.5 days for part 2 in Fall 2016.

Description: 

The colors of transition metal compounds are highly variable. Aqueous solutions of nickel are green, of copper are blue, and of vanadium can range from yellow to blue to green to violet. What is the origin of these colors? A simple geometrical model known as crystal field theory can be used to differentiate the 5 d orbitals in energy. When an electron in a low-lying orbital interacts with visible light, the electron can be promoted to a higher-lying orbital with the absorption of a photon. Our brains perceive this as color. Rubies, dark red, and emeralds, brilliant green, are precious gemstones known since antiquity. What causes the color in these beautiful crystals? Using crystal field theory, we can explain the colors in these gemstones.

Learning Goals: 

1.    Derive the crystal field splitting for d orbitals in an octahedral geometry
2.    Predict the magnitude of d orbital splitting
3.    Relate color, energy, wavelength, and crystal field strength
 

Equipment needs: 

Day 1: none

Day 2: access to laptops (one per group or individual) and crystalmaker software (free download avaialbe)

Prerequisites: 
Corequisites: 
Course Level: 
Implementation Notes: 

This LO was used in a first-year chemistry class at Harvey Mudd College in Fall 2015. I started with a brief lecture (see instructor notes) and then turned the class loose in small groups of about 5 students. I walked through the room to answer questions and guide the groups.

The first day’s activities were taken from a J. Chem. Educ. article (J. Chem. Educ., 2015, 92, 1369-1372). This article has a lot of detail that could be adapted for local use. The related activity "metal and Ionic Lattices Guided Inquiry Worksheet" may be appropriate as review/background material, depending on the placement of this activity in your syllabus.

The second day’s activities rely on the use of crystalmaker, a structure visualization program. There is a free demo version available (http://crystalmaker.com/software/index.html)

Fairly detailed instructor notes are included as a "faculty only" file.

The references for the structures I used are here:

Gibbs G V, Breck D W, Meagher E P (1968)  Structural refinement of hydrous and anhydrous synthetic beryl, Al2(Be3Si6)O18 and emerald, Al1.9Cr0.1(Be3Si6)O18 Note: hydrous emerald. Lithos 1:275-285

Wang X, Hubbard C, Alexander K, Becher P (1994)  Neutron diffraction measurements of the residual stresses in Al2O3 - ZrO2 (CeO2) ceramic composites _cod_database_code 1000059. Journal of the American Ceramic Society 77:1569-1575

I relied on a book called "The science of Color" and a website on color theory (linked below) to develop the 2nd days activities.

The Science of Color,” volume 2, edited by Alex Byrne and David R. Hilbert, MIT Press, Cambridge MA, 1997, pp. 10-17.

Time Required: 
2 50 minute class periods

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