Second year

27 Aug 2018

Interactive Syllabus

Submitted by Amanda Reig, Ursinus College
Description: 

The Interactive Syllabus is a web-based survey delivery of syllabus content to your students prior to the first day of classes.  The web link below explains many of the features and advantages, but in my opinion some of the best benefits are (1) students actually engage with the content on the syllabus in meaningful ways, (2) it saves class time on the first day, and (3) can encourage students to share questions/concerns they may not have been as eager to share in person.

The survey is built on the qualtrics platform, but could be adapted for other programs.  

Prerequisites: 
Corequisites: 
Related activities: 
Implementation Notes: 

I implemented the approach in my General Chemistry I course this fall, and will likely adapt for all future courses.  I based my survey on the one that can be obtained at the website, but did make modifications. I have uploaded a pdf of my version of the survey, and would be happy to share the Qualtric Survey File to anyone interested (it is not an allowed file type so cannot be posted here).

I sent an email to students on Friday before classes began Monday morning containing a PDF of the syllabus and the link to the survey.  I did not assign any points for completion of the survey - just asked them to do so before 8 pm on Sunday (so I would have time to review their answers).  I sent a reminder email mid-day on Sunday.  I had around an 85% response rate.  I estimate it takes around 15 - 20 minutes for a student to work through.  It took around 2 hours for me to adapt the survey to my own preferences based on my syllabus.

6 Jul 2018

Getting to Know the MetalPDB

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

I reviewed student answers to this assignment and evaluated their contributions to the discussion that took place. I also tried to keep track of how much they used information obtained from this site during their literature presentations.

 
Evaluation Results: 

This assignment is quite straightforward and the 6 of 8 students who completed the assignment had little trouble coming up with correct answers for all of the questions.

 

At the end of the semester, each student had to give two presentations on bioinorganic topics. They were expected to discuss the metal coordination environment and how "normal" it was, as well as the possibility of substituting another metal into the coordination sphere. One student used information from the MetalPDB in both of her presentations, three students used information in one of their presentations, and four students did not include information from the site in either presentation.

 

Description: 

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

 

I expect my students to use this site to obtain information for their assignments and presentations. This activity is a self-paced introduction to the site that my students complete outside of class. This activity has students use the site to obtain information about metal coordination environments, the common geometries adopted by metals in biological environments, and the common ligands that are used to bind metals.

Learning Goals: 

After completing this exercise, students should be able to:

  • access the MetalPDB site,

  • obtain statistics pertaining to the number of metal-containing structures in the PDB,

  • determine the most common geometry observed for a particular metal in a biological structure,

  • identify the most common ligands attached to the metal when bound in a biological macromolecule, and

  • find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.

Equipment needs: 

Students need access to the internet and a web browser that is capable of running JavaScript and JSmol. This site is accessible on devices running iOS, but the layout of the site works better on a laptop screen.

Prerequisites: 
Corequisites: 
Implementation Notes: 

I used the MetalPDB site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules in both my advanced and foundation-level courses, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.

 

I also have students use the site to get background information about metal geometry and common ligands for their assignments and presentations. I ask them to complete this activity outside of class. I usually distribute this as a Google Doc to my students (through Google Classroom) so that I have access to all of their responses.

 

For several of the questions/groups of questions, I assign individual members of the class specific geometries (question #5), metals (questions #6-9), or PDB structures (questions #11-13) and we pool their answers in class. We then spend about 30-45 minutes in class discussing the results and search for commonalities and connections to other structures that we have already discussed in class.

 
Time Required: 
1-2 hours (outside of class by student); 30-45 minutes in class (including discussion of related topics)
25 Jun 2018

Orbital Overlap and Interactions

Submitted by Jocelyn Pineda Lanorio, Illinois College
Evaluation Methods: 

Evaluation was conducted by the instructor walking around the computer lab to check progress and address the issues students had.

Evaluation Results: 

This LO was implemented once in advanced inorganic chemistry composed of 5 chemistry major students. Students clearly identified the type of orbital interactions and differentiated bonding, nonbonding, and antibonding MOs. Students commented that this is a great in-class activity before the discussion of MOs for diatomic molecules (Chapter 5 of MFT).

Description: 

This is a simple in-class activity that asks students to utilize any of the given available online orbital viewers to help them identify atomic orbital overlap and interactions. 

Learning Goals: 

Following the activity, students will be able to:

  1. draw the s, p, and d atomic orbitals using the given coordinate axes
  2. analyze the orbital interaction by looking at their symmetry and overlap (or lack of)
  3. differentiate s, p, d, and nonbonding molecular orbital

 

Equipment needs: 

Internet connection and computer

Prerequisites: 
Corequisites: 
Implementation Notes: 

This activity should be run in a computer lab.

Time Required: 
15 to 20 minutes
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
23 Jun 2018

Bonding in Tetrahedral Tellurate (updated and expanded)

Submitted by Jocelyn Pineda Lanorio, Illinois College
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 literature discussion is an expansion of a previous LO (https://www.ionicviper.org/literature-discussion/tetrahedral-tellurate) and based on  a 2008 Inorganic Chemistry article http://dx.doi.org/10.1021/ic701578p

Corequisites: 
Prerequisites: 
Learning Goals: 

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

  1. Identify the key aspects of a primary publication including significance, synthetic methods, and product characterization.
  1. Identify isoelectronic species by drawing Lewis Structures.  
  1. Apply standard NMR shielding/deshielding concepts to interpret heteronuclear NMR spectra.
  1. Identify experimental protocols and reaction conditions.
  1. Discuss how the various experimental methods in the article provide evidence of the structure of the compound.
  1. Recognize scientific nomenclature relevant to the research article.
  1. Identify the relationship of telluric acid and tellurate to the related species given in the paper based on periodic trends. (Periodic Acid - isoelectronic; Sulfuric and Selenic acid - same column)
  1. Compare bond lengths for species in the paper.
  1. Identify the point group of the TeO42- with all the same Te-O bond lengths and when with different Te-O bond lengths.
  1. Predict the product(s) and by-products of a chemical reaction.
  1. Identify species and intermolecular interactions in a crystal structure.

 

Related activities: 
Implementation Notes: 

Students are asked to read the paper and answer the discussion questions before coming to class. 

Time Required: 
50 +
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
22 Jun 2018
Evaluation Methods: 

Discuss students responses with respect to the answer key.

Evaluation Results: 

This activty was developed for the IONiC VIPEr summer 2018 workshop, and has not yet been implemented.

Description: 

Inorganic chemists often use IR spectroscopy to evaluate bond order of ligands, and as a means of determining the electronic properties of metal fragments.  Students can often be confused over what shifts in IR frequencies imply, and how to properly evaluate the information that IR spectroscopy provides in compound characterization.  In this class activity, students are initially introduced to IR stretches using simple spring-mass systems. They are then asked to translate these visible models to molecular systems (NO in particular), and predict and calculate how these stretches change with mass (isotope effects, 14N vs 15N).  Students are then asked to identify the IR stretch of a related molecule, N2O, and predict whether the stretch provided is the new N≡N triple bond or a highly shifted N-O single bond stretch.  Students are lastly asked to generalize how stretching frequencies and bond orders are related based on their results.

 
Learning Goals: 
  1. Evaluate the effect of changes in mass on a harmonic oscillator by assembling and observing a simple spring-mass system (Q1 and 2)

  2. Apply these mass-frequency observations to NO and predict IR isotopic shift (14N vs. 15N) (Q3 and 4)

  3. Predict the identity of the diagnostic IR stretches in small inorganic molecules. (Q5, 6, and 7)

Equipment needs: 

Springs, rings, stands, and masses (100 and 200 gram weights for example).

 

Corequisites: 
Implementation Notes: 

Assemble students into small groups discussions to answer the questions to the activity and collaborate.

 

 

Time Required: 
Approximately 50 minutes
15 Jun 2018
Evaluation Methods: 

I typically evaluate this activity through class participation although the answer key is posted after class to let the students evaluate their own understanding of concepts.  The students do know that they will be tested on the material within the activity and usually I have a density problem on the exam.

Evaluation Results: 

This activity is designed to give the students more freedom as they move from the first density calculation to the last set of calculations.  Within the last set of calculations, they encounter a hexagonal unit cell so that may require some additional intervention to get them to think about how to calculate the volume of a hexagonal unit cell.

Description: 

This activity is designed to relate solid-state structures to the density of materials and then provide a real world example where density is used to design a new method to explore nanotoxicity in human health.  Students can learn how to calculate the density of different materials (gold, cerium oxide, and zinc oxide) using basic principles of solid state chemistry and then compare it to the centrifugation method that was developed to evaluate nanoparticle dose rate and agglomeration in solution.

 

Learning Goals: 

A student should be able to calculate a unit cell volume from structural information, determine the mass of one unit cell, and combine these two parameters to calculate the density for both cubic and hexagonal structures.  In addition, students will have an opportunity to read a scientific article and summarize the major findings, place data in a table, and explain the similarities and differences between the densities calculated in the activity and the experimental values that are reported in the literature.

Corequisites: 
Course Level: 
Equipment needs: 

None

Prerequisites: 
Implementation Notes: 

I have used this activity in our first semester inorganic chemistry course when we cover solid-state materials.  One thing to note is that I do use 2-D projections to describe structures and we cover that in a previous activity.  You could remove 2-D projections from this activity if it is not something that you previously covered.  

 

Time Required: 
This activity usually takes about 40 to 45 minutes.
13 Jun 2018

The Preparation and Characterization of Nanoparticles

Submitted by Kyle Grice, DePaul University
Evaluation Methods: 

Students are evaluated on their participation in lab, lab safety, lab notebook pages, and a lab report turned in a week after the last day of the experiment. 

Evaluation Results: 

This lab was first run in spring of 2016, and again in spring of 2017 and 2018 (a different instructor carried out the lab in 2018). 

In general, students do well on the lab report and seem to enjoy the experiment.They often need guidance when interpreting the Analytical Chemistry article and selecting the correct equations. Discussing their values with them in office hours ("does that make sense?") helps them understand their calculations. 

A sample lab report that scored above 90% is included in the faculty-only files. 

Description: 

This is a nanochemistry lab I developed for my Junior and Senior level Inorganic Chemistry course. I am NOT a nano/matertials person, but I know how important nanochemistry is and I wanted to make something where students could get an interesting introduction to the area. The first time I ran this lab was also the first time I made gold nanoparticles ever! 

We do not have any surface/nano instrumentation here (AFM, SEM/TEM, DLS, etc... we can access them at other universities off-campus but that takes time and scheduling), so that was a key limitation in making this lab. 

While it was made for an upper-division course, I think It could be adapted and implemented at many levels, including gen chem. I do not spend much time on nano in the lecture (none in fact), so this lab was made to have students learn a bit about nanochemistry somewhere in inorganic chemistry. We have one 10-week quarter of inorganic lecture and lab, offered every spring quarter.

This lab takes approximately 2-3 hours if students are well prepared and using their time well, but is usually spread over 2 days. Students are concurrently doing experiments for another lab or two because we have a lab schedule that overlaps multiple labs, and can do these during one day or across two days. The lab space is an organic chemistry laboratory, so we have access to the usual lab synthetic equipment

Students in thelaboratory write lab reports,which are the due the week after the last day of the lab experiment. In the lab report they use their UV-Vis data to calculate information about the AuNP. 

The lab has been posted, as well two photos from students' ferrofluids (these were posted with permission on our departmental blog). A rubric has been posted as a faculty-only file. I have also included a student submission that received over 90% on the lab with their identifying information removed. Students write and introduction and need to cite journal articles in their report, so they are expected to do reading on nanochemistry topics outside of the lab period as they write their reports. 

I am sure the lab can be improved, this was what i came up with the materials and time I had. I plan on continuing to revise and edit it as time goes on. Any suggestions are very welcome! 

Prerequisites: 
Corequisites: 
Learning Goals: 

A student should be able to perform a chemical laboratory experiment safely and follow proper lab notebook protocol.

A student should be able to determine the average size of AuNPs from spectroscopic data and primary literature.

A student should determine atomic and nano-scale information from physical properties.

A student should be able to construct a lab report in the style of an ACS article (Students in my lab wrote lab reports for each experiment). 

Equipment needs: 

For this experiment, you  need

The chemical materials - HAuCl4, trisodium citrate, 

Heating/stirring plates

Glassware

UV-Vis spectrometer (mainly Vis)

A laser pointer

Strong magnets (the stronger and larger the better)

Implementation Notes: 

The syntheses are relatively straightforward, although we've had some problems getting "spikes" for the ferrofluid. Anecdotally, adding the reagents and doing the steps faster tends to give better "spiking". Some students just see a blob moving around in response to the magnet, which was fine in terms of their report. 

The AuNP synthesis can also be done with an ultrasonicator or by addition of sodium borohydride, among other methods. We don't have them make a calibration curve of chloride addition, but that could be a possibility.  

I like having a pre-made solution of a red oroganic dye to shine the laser pointer through to compare versus the laser shining through the AuNP solution. 

One year, the AuNP synthesis was going very slow. We realized it was because the Au(III) was diluted in acid, so it was protonating the citrate. Boiling for a while before adding the citrate solution helped fix this problem.

KAuCl3 is also a good source of Au(III) for this lab. 

Time Required: 
2 hours

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