Computer modeling

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
19 Feb 2016

Build-Your-Own Molecular Orbitals

Submitted by Anne Bentley, Lewis & Clark College
Evaluation Methods: 

I have used this activity twice in my advanced inorganic course for juniors and seniors. In both cases, I allow the students to keep their set of orbitals for further study.

Students seem to enjoy getting a chance to manipulate the orbitals directly. One drawback is that the desks in the room I teach in have very small tables, so students don't have a lot of room to work with. Also, there isn't a way to "reverse" the sign of the orbitals in this activity, so the students don't actually visualize the anti-bonding interactions.  (I suppose one could print one version of each atomic orbital on one side of the paper and the opposite version on the other side, then allowing students to flip their atomic orbitals over to get the anti-bonding interaction...that would be very cool.)

Evaluation Results: 

I haven't directly assessed this activity, but I often include questions on exams that ask students to draw the molecular orbitals, and I hope that this activity helps with the visualization.

Informally, I can say that some students light up at the chance to put down their pens and play with the oribtals. 

Description: 

This is a truly hands-on activity in which students manipulate paper cutouts of carbon atomic orbitals and oxygen group orbitals to identify combinations with identical symmetry and build the carbon dioxide molecular orbital diagram. The activity pairs well with the treatment of MO theory in Miessler, Fischer, and Tarr, Chapter 5. An optional computational modeling component can be added at the end.

Learning Goals: 

After participating in this activity, students will be able to demonstrate the ways in which atmoic orbitals and group orbitals interact to form bonding and anti-bonding molecular orbitals. Students will also be able to use symmetry labels to predict orbital interactions and in the case of no interactions, will be able to identify non-bonding orbitals.

Equipment needs: 

printer, scissors, envelopes

Course Level: 
Corequisites: 
Prerequisites: 
Implementation Notes: 

In my inorganic course, I follow Miessler, Fischer, and Tarr’s presentation of molecular orbitals for larger molecules. This activity is done in class after we have worked through the FHFMO diagram (section 5.4.1). Students have already determined the symmetries of the group orbitals derived from the F atomic orbitals, and they will use these in the activity as we determine the MO diagram for carbon dioxide (section 5.4.2).

The oxygen atomic orbitals combine in the same way that the two F atomic orbitals did in the FHF example. (See the solutions set of images for the correct labels.)

Before class, I print a set of carbon atomic orbitals and oxygen group orbitals for each student and cut them into pieces. (The carbon atomic orbitals will be individual s, px, py, and pz orbitals while the group orbitals from the oxygen atoms consist of pairs of atomic orbitals.) The orbitals are mixed up in an envelope for each student. Note that this implementation is easy for very small classes, but would need to be streamlined for larger classes. (Ask students to bring their own scissors? Cut the orbitals en masse with a paper cutter?)

I hand out the sets of orbitals and ask the students to:

  • Organize your orbitals into “atomic orbitals” and “group orbitals”
  • Label each orbital with the appropriate symmetry label – put the labels on the backside of the paper so they don’t distract you.
  • How many total orbitals do you have? 
  • Identify ways in which your atomic and group orbitals can interact to form molecular orbitals – do this by placing the atomic orbital in the center of the group orbital and assessing whether or not the symmetries match.
  • Check your symmetry labels (on the backside of the paper) to see whether or not the orbitals you matched together really do have the same symmetry.

After the students have had some time to move around their orbitals, we construct the CO2 MO diagram together on the board (see Figure 5.25 in the 5th edition of Miessler, Fischer, and Tarr). Part of the process involves recognizing the oxygen group orbitals that did not “find a match” with any of the atomic orbitals on carbon and assigning these as non-bonding orbitals. In the end, we count the molecular orbitals formed to make sure there are the same number as we started with (n = 12).

I also calculate the molecular orbital surfaces using Spartan and show these to the students after they have developed the MO diagram.

 

Time Required: 
20 minutes
25 Jan 2016

Otterbein Symmetry In-Class Activity/Take home activity

Submitted by Kyle Grice, DePaul University
Evaluation Methods: 

I gave students participation credit for doing this activity, and asked students to comment on the activity during my teaching evaluations. 

Evaluation Results: 

Students commented in the teaching evaluations that they really liked this activity and it helped them understand symmetry a lot better than just reading the text and going to the lectures. 

Description: 

<p>This is an in-class activity I made for my students in a Junior/Senior-level one-quarter inorganic course.&nbsp;</p><p>Unfortunately it was waaay too long for the 1.5 h class (i gave them about 45 min). I recommend taking this and adapting it to a take-home exercise or homework set, which is probably what I will do this coming year.&nbsp;</p><p>Students used Otterbein to look at various structures, starting with low symmetry, working up to very high symmetry structures. I had them go through the &quot;challenge&quot; so they couldn&#39;t see the keys at first, but then go back to check their answers.&nbsp;</p><p>Before class, I had students watch a TED-talk video on symmetry (see web resources) and lectured for about 45 minutes on point groups and symmetry elements. They were also expected to read the chapter on symmetry from MFT.&nbsp;</p>

Learning Goals: 

-          Students will be able to visualize chemical species as 3-dimensional objects

-          Students will practice identifying symmetry elements of chemical species

-          Students will practice determining point groups of chemical species

-          Students will practice recognizing molecules of low and high symmetry

Corequisites: 
Equipment needs: 

I ran this activity in a computer lab. You need internet connection and computers with the proper specs to use Otterbein. Students could bring their own laptops to do the exercise. 

Prerequisites: 
Course Level: 
Implementation Notes: 

Give your students plenty of time, or make this a take-home assignmnet/homework assignment. Stuedents did enjoy this and found it very useful compared to just work on a flat surace. 

Time Required: 
45+ minutes
4 Jul 2015

Orbital Viewer: Visualize atomic and molecular orbitals

Submitted by Kate Plass, Franklin & Marshall College
Evaluation Methods: 

Material is tested in quizzes and exams.

Evaluation Results: 

Never formally assessed, but students like it. It often prompts requests to show other orbitals.

Description: 

Orbital Viewer (http://www.orbitals.com/orb/ov.htm) is a PC-based program that shows electron density calculated from the Schrodinger equation for atoms and molecules. Results can be shown as probability densities or probability surfaces.

Orbital Viewer Program copyright 1986-2004 by David Manthey

Corequisites: 
Prerequisites: 
Learning Goals: 

Students should be able to:
- understand what orbital drawings represent
- understand the connections between quantum numbers n, l, and m and the size, shape, phases, number of nodes, and orientations of atomic orbitals
- understand how atomic orbitals can overlap to form molecular orbitals

Implementation Notes: 

I have used this as an in-class demonstration in general and inorganic chemistry courses. Here are a few ways in which I have found this program particularly useful:
- You can show both probability density and surface probabilities with controlled probability levels. This demonstrates the relationships between the electron density and the shapes chemists draw to represent orbitals nicely.
- You can show several atoms with different orbitals, illustrating the differences in orientation in a rotatable model.
- It allows you to show the nodes and cutaway views. This allows students to visualize the nodal surfaces.
- You can place atoms near each other and generate molecular orbitals.

Time Required: 
~5 min per orbital

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