Computer modeling

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
12 Jun 2015

Materials Project

Submitted by Barbara Reisner, James Madison University
Description: 

The Materials Project is part of the Materials Genome Initiative that uses high-througput computing to uncover the properties of inorganic materials.

It's possible to search for materials and their properties

It employs high-throughput computation approaches and IT to create a system that can be used to predict properties and construct phase diagrams andPourbaix diagrams.

Prerequisites: 
Corequisites: 
10 Jun 2015

WebCSD Teaching Database

Submitted by Barbara Reisner, James Madison University
Description: 

Hilary first higlighted this resource as a news item before we had a web resource category. I'd like to bring it back to people's attention as a web resource because of its value. 

The CCDC (Cambridge Crystallographic Data Center) has developed a free version of the CSD (Cambridge Structural Database) that can be used for teaching. There are also several tutorials that are relevant for teaching inorganic chemistry including VSPER, stereochemistry, and hapticity. In addition to the teaching subset of the CCDC database that is available online, you can request the cif for any deposited structure.

A paper on the applications of the CSD in chemical education was published in 2010 and is provided as an IUCr Open Access Article (http://dx.doi.org/10.1107/S0021889810024155).

Prerequisites: 
Corequisites: 
6 Jan 2015

Visualization of Zeolite Structure

Submitted by Erica Gunn, Simmons College
Evaluation Methods: 

Student answers to the activity questions were collected and graded based on participation/completeness.

Evaluation Results: 

Despite some technical difficulties, all students were able to access the site and seemed to find the activity helpful for understanding the zeolite cage structure. Almost all students were able to count the number of cages, identify high-symmetry orientations, and all but a few were able to draw the position of oxygen atoms in the structure successfully. Most identified the pores correctly in the expanded-view structure, though a few students had difficulty orienting the pore direction correctly relative to the unit cell dimensions. 

Description: 

Students use a Java-based website to explore the faujasite zeolite structure. The activity questions guide them through identifying different atomic positions within the structure, and orienting the zeolite pores and "cages" relative to the crystal axes. 

Learning Goals: 

Students will use computer modeling to visualize the 3D crystal structure of a zeolite, and will identify "cage" and pore structures within the solid.

Corequisites: 
Course Level: 
Equipment needs: 

Computer with a web browser capable of running Java 

Prerequisites: 
Related activities: 
Implementation Notes: 

I used this activity as a prelab assignment for a zeolite synthesis experiment (see related activities). Students did the modeling and answered the questions at home, and submitted their answers at the beginning of the lab period. It could be adapted equally well to an in-class activity if desired. 

Several students had technical difficulties allowing Java permission to run in Windows and web browsers. For me, the simplest solution was to:

1) Type "Configure Java" into Windows search bar  

2) Go to security tab

3) Add website to Exception Site list

Beware that this may require administrator privileges, so it's best to have a technology rep handy or test out in advance if you're running this in the classroom! 

Even with this fix, I did have to allow popups multiple times in some browsers (including allowing an out-of-date Java script, I believe) to get the program to run. 

 

Time Required: 
30 mins
12 Sep 2014

Maggie's LOs

Submitted by Chip Nataro, Lafayette College
Corequisites: 
Prerequisites: 
12 Aug 2014

A Tale of Two Structures

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

I have not used this in class yet. I plan on introducing it for the first time in the fall. I think it will be an in class activity. It might make more sense in a lab or homework setting. I don't have a lab in my fall course, so that somewhat limits my options. Hopefully more details will be forthcoming. I certainly would appreciate any feedback from anyone that adopts some or all of this Learning Object.

Description: 

In this activity, students will compare and contrast two closely related structures, [Pd(dcpf)PR3]2+ (dcpf = 1,1'-bis(dicyclohexylphosphino)ferrocene; R = Me or Ph). They will be required to obtain the cif files from the supporting information of a paper. They will then make a variety of measurments in the two stuctures. These measurements can be made using a variety of different freely available programs. Instructions are provided for Mercury 3.3 and Olex2. Finally, students will be required to provide a rationale for the differences in the two structures. Students are expected to have some knowledge of crystallography, sterics vs. electronics and the trans effect.

 

This material is based upon work supported by the National Science Foundation under Grant Number (1057795).

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Learning Goals: 

After performing this activity students should be able to

1) Obtain cif files from the supporting information of an ACS journal

2) Open the cif files in a program that allows them to make measurements on the structures including drawing planes and finding centroids in rings.

3) Explain disorder in crystal structures.

4) Rationalize how electronics and/or sterics impact these particular structures.

Corequisites: 
Course Level: 
Equipment needs: 

A computer with an internet connection.

Prerequisites: 
Implementation Notes: 

The provided instructions have students search for the desired information using the ACS pubs search tools. Certainly SciFinder Scholar could be employed if access is available. I have chosen to provide directions for making measurements using Mercury 3.3 and Olex2. Certainly there are other options. Of the two, Mercury is far more user friendly which is certainly an attractive option in a classroom setting. However, Olex2 provides esd values for non-standard measurements (e.g. those involving centroids) which Mercury does not do (at least as far as I know). It might be valuable to have groups perform the measurements with different programs and then have them discuss their results. There should be little to no difference in the values, but the differences in esd's could be a valuable teaching moment.

4 Aug 2014

Suite of LOs on Biomimetic Modeling

Submitted by Sheila Smith, University of Michigan- Dearborn

This suite of activities can be used as a unit exploring the use of small molecule models and biophysical techniques to illuminate complicated biomolecules.  The Parent LO:  Modeling the FeB center in bacterial Nitric Oxide reductase is a short, data-filled and well-written article that is approachable with an undergraduate's level of understanding.

Course Level: 
17 Jul 2014
Evaluation Methods: 

This learning object was developed for the 2014 VIPEr workshop and has not been evaluated. 

Description: 

This is an in-class PDB exercise based on the paper "Mechanisms Controlling the Cellular Metal Economy" by Gilston and O'Halloran. Students are asked to visualize the metal binding sites of several proteins discussed in the paper, highlighting unusual metal geometries. After identifying the amino acid residues involved in metal binding, students will discuss the bond structure in terms of HSAB theory. 

Learning Goals: 
Students will:
1) Become familiar with reading primary literature and using referenced works.
2) Use the PDB to search for protein structures and create images of metal binding sites.
3) Apply coordination chemistry and HSAB to describe bonding in biological systems
4) Practice drawing chemical structures
Equipment needs: 

Laptop computers with Java installed for accessing the PDB (freely available at www.pdb.org). Instructions for using the PDB can be found in the related activities linked below.

Topics Covered: 
Corequisites: 
Prerequisites: 
Implementation Notes: 

Cys79 is a bridging ligand between Zn402 and Zn401 in ZntR. 

You can highlight two metal atoms in the PDB viewer by holding shift while clicking. 

It is a good idea to pre-test computers that will run the PDB viewer before coming to class, as the viewer runs on Java and may have technological issues. 

 

17 Jul 2014
Evaluation Methods: 

Students will complete the syntheses of the desired compounds, obtain the required instrumental spectra, complete the electronic structure compounds.  Based on these results, students will write a lab report in the style of an inorganic chemistry paper to present the required analyses.  A rubric for the grading of the laboratory report is included. 

Evaluation Results: 

This learning object was developed for the Summer 2014 VIPER workshop, and has not yet been evaluated.

Description: 

In this experiment, students will synthesize a cobalt Schiff base complex with varying axial ligands ([Co(acacen)L2]+). They will characterize the complex using various techniques, and may perform computational modeling to predict spectroscopic properties.

Corequisites: 
Prerequisites: 
Learning Goals: 

Students will be able to:

  • Synthesize a series of cobalt(III) complexes containing acetylacetonatoethylenediimine and ammine and imidazole derivatives.

  • Calculate the percent yield of the complexes synthesized.

  • Determine the steric and electronic effects of the axial ligands on the complex using UV-Vis spectroscopy.

  • Analyze multinuclear NMR spectra to determine the effect of axial ligands on the equatorial ligand.

  • Analyze the IR spectra to confirm the expected structure

  • Create a diagram that illustrates the effect of the axial ligands on the protons of the equatorial ligand.

  • Discuss the binding ability of the complex to biological molecules based on the primary literature.

  • Use Electronic Structure calculations at a minimum of the B3LYP/6-31G(d) level of theory using the PCM model for water to calculate the HOMO, LUMO, vibrational modes, NMR spectra, and UV-Vis spectra.  

  • Compare calculated values to experimental spectra.    

  • Communicate their findings in written and/or oral format.
Equipment needs: 

Standard glassware: Round bottom flask, Stir bar, Vacuum filtration system

Instrumentation: NMR, IR, UV-Vis

A computational package such as Gamess or Gaussian™ capable of electronic structure calculations, and a visualization package such as WebMO, GaussView™, Chem3D™, or Avogadro to visualize input and output files.

Implementation Notes: 

This lab lends itself to many adaptations:

1)   The inorganic chemistry instructor can collaborate with the organic laboratory instructor in the synthesis of the Schift base ligands.  The organic chemistry students will characterize the ligand using proton and carbon-13 NMR.

2)   Each student or pair of students will synthesize the ammine and an imidazole derivative complex.  Students will share the data to investigate effects of the trans ligands on the proton of the acacen ligand.

3)   Co-NMR can also be used to investigate the properties of the trans ligand.

Time Required: 
2-3 weeks. This activity can be done in two-weeks if the TA or the faculty synthesizes the ligand.
17 Jul 2014

Exploring Post-Translational Modification with DFT

Submitted by Gerard Rowe, University of South Carolina Aiken
Evaluation Methods: 

Students will be evaluated based on whether or not they are able to complete the three required calculations with appropriately drawn structures.  They will also be awarded points based on completion of the worksheet and how well they compare their results to their predictions.

A test or quiz question using atomic charges taken from a published calculation on an inorganic would be a nice idea.  

Evaluation Results: 

This activity has not yet been implemented.  Will update when results become available.

Description: 

This activity is designed to give students a deeper understanding of what post-translational modification does in a metalloenzyme using nitrile hydratase (NHase) as a model system.  The metallo-active site of NHase contains a cobalt(III) center that is bound to an unusual coodination sphere containing bis-amidate, cysteinate, sulfenate (RSO-), and sulfinate (RSO2-) ligands.  Using density functional theory calculations on a simple model of the coordination environment of the cobalt, students will carry out geometry optimizations on three compounds that have either a sulfide, sulfenate, or sulfinate ligand.  The students will compare the partial atomic charges on sulfur in the three cases and compare them to their predicted atomic charges based on oxidation number.

Learning Goals: 

The student will use their knowledge of oxidation numbers to determine how electron rich a sulfur-containing ligand atom feels

The student will predict ligand binding strength based on electron richness trends

The student will convert a Lewis structure into a 3-dimensional representation in a molecular modeling program

The student will set and run up a geometry optimization using a computational package like Gaussan

The student will tabulate the results of a computational chemisty calculation

The student will compare their predictions of electron richness and donor strength to the calculated atomic charges and bond distances from their calculation

Equipment needs: 

A fairly hefty computer to carry out the calculations (at least 4 core processor system with 8 GB of ram)

A computational package like Gaussian, Spartan, Gamess*, ADF, or Orca*

A 3-D drawing program like GaussView, Spartan, WebMO*, or Avogadro*

* Free!

Corequisites: 
Prerequisites: 
Implementation Notes: 

This activity takes long enough that it could be used as its lab exercise or as an addition to a synthetic lab.  With a larger class, you will probably need a day or two for all the calculations to finish.  The analysis is very easy, as it is only a few charges and bond angles to jot down.  The charges can also be found as a list in the log file, which can be opened in any text editor.  

If you are pressed for time or have a few students who cannot, for whatever reason, draw the starting structures correctly, Gaussian input files for each of the three compounds are provided.  The structures in each file have already been through several geometry optimization cycles of a successful calculation, so calculations using these files will finish much more quickly  than starting from scratch.

Output files are also available that contain the final data that were used to generate the key.  As an alternative to waiting for everyone's calculations to finish, you can play the "cooking show" game by giving students the completed log files after they successfully create their input files. 

Time Required: 
One 50 minute class + 20 minutes for analysis once calculations are complete (~1.5 h per group)

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