Electronic spectroscopy

15 Sep 2014

Fe2GeS4 Nanocrystals for Photovoltaics

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

My student led a 20-minute class discussion of this article in the spring of 2014.  The other students in the class were asked to post two questions about the article to moodle before the class meeting, but they were not asked to complete the literature discussion questions due to assignment overload at the end of the semester.

Evaluation Results: 

The six students posted good questions about the article, some of which I have incorporated into the literature discussion. One student asked why Ge was used instead of Si.  (My guess is that Si is too prone to oxidation - it's consistent with redox potentials.)  Another student wanted to know if any articles had been published after this one describing further progress.  At least two asked how the authors could determine that the photocurrent was p-type.

Description: 

I asked the students in my junior/senior inorganic course to develop their own literature discussion learning objects and lead the rest of the class in a discussion of their article.  Student Johann Maradiaga chose this article describing the synthesis and characterization of Fe2GeS4 nanocrystals with potential applications in photovoltaic devices (Sarah J. Fredrick and Amy L. Prieto, “Solution Synthesis and Reactivity of Colloidal Fe2GeS4: A Potential Candidate for Earth Abundant, Nanostructured Photovoltaics” J. Am. Chem. Soc. 2013, 135, 18256-18259. DOI: 10.1021/ja408333y).  The article describes the synthesis in hexadecylamine/octadecene of Fe2GeS4 nanoparticles and their characterization using powder X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, and photocurrent measurements.  Building on Johann’s original set of questions, I developed this literature discussion, which is suitable for use in inorganic chemistry courses. Many thanks to article author Sarah Fredrick for reviewing the assignment and adding some great questions.

Corequisites: 
Course Level: 
Learning Goals: 

After reading and discussing this paper, a student will be able to:

  • Understand how variable growth rates along different crystal planes result in specific shapes, and predict a resulting shape given a particular set of growth rates
  • Compare the oxidation behavior of Fe and Ge over time using XPS data
  • Describe a photocurrent measurement experiment and compare the photocurrent behavior of p-type and n-type semiconductors.
  • Explain the value of a communication as compared to a longer research article

 

Implementation Notes: 

Students do not need to be experts to understand this article, but previous exposure to solid state concepts including semiconductor electronic structure, solid state phases, nanoparticle synthesis, and capping agents will be helpful to them.  Alternatively, the article could be used to introduce these topics.

This JACS communication is fairly short and written clearly, so it could make a good first literature discussion for students without previous experience reading journal articles.

I have included a large number of possible questions in the literature assignment, but as always, users should feel free to pick and choose from the options and/or add their own.

Time Required: 
45 minutes (approximately)
12 Sep 2014

Maggie's LOs

Submitted by Chip Nataro, Lafayette College
Corequisites: 
Prerequisites: 
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: 
22 Jul 2014

The Structure and Function of Transferrin

Submitted by Christopher Bailey, Wells College
Description: 

These Five Slides About examine the structure and function of the iron binding and transport protein transferrin. Students learn that transferrin also acts as an iron buffer and as a potential antimicrobial agent. The structure of the protein is explored in detail; it consists of a single polypeptide (80kDa) folded into two lobes, each of which can bind a single iron in a high affinity region. Changes in the protein as a result of iron uptake is discussed. The iron binding region and the requirement of a bidentate synergistic anion (carbonate) are examined. Finally, the relationship between transferrin and iron-overload is presented.

Prerequisites: 
Corequisites: 
Learning Goals: 

After examining these slides, students should be able to:

  • Discuss the various biological functions of the transferrins and its importance in these roles.
  • Describe the overall structure of the protein.
  • Describe the iron binding sites, including the importance of the synergistic anion.
  • Discuss the importance of this protein in the treatment of iron overload disorders.

 

Implementation Notes: 

These slides can be used at any point that the protein transferrin is discussed. They can be used either for straight lecture or as part of an in-class discussion. I have used them in class as an introduction to the protein prior to assignment of an article from the primary literature.  I also use them for students who who are interested in doing undergraduate research with me.

Although I have not yet tried this, I am planning on using these slides while at the same time having students access the crystal structure of ovotransferrin (1OVT) on the PDB. The ability to "rotate" the protein may make its overall structure and the iron binding sites easier to discern.

Time Required: 
10-20 minutes
Evaluation
Evaluation Methods: 

To date I have used these slides only as an introduction to transferrin, both in class and as part of a research project. Evaluation was based on the understanding of these topics as applied to readings from the primary literature, through discussion, and through inclusion of these background topics in research reports. As described in the implementation notes I intend to connect these slides to an exercise involving the PDB. A more direct means of evaluation should be obtained at that point.

Evaluation Results: 

Although no formal evaluation of the effectiveness of these slides has been undertaken, my experience is that they are a good introduction to the topic---students refer to them correctly in discussions and I find that they understand this background enough to attack articles from the primary literature successfully.

17 Jul 2014

Introduction to Photoinduced Electron Transfer

Submitted by Robert Holbrook, Northwestern University
Description: 

This 5 slides about will introduce students to the concept of photoinduced electron transfer. These slides go over the energics of photoinduced electron transfer, which implements basic concepts of photochemistry and electrochemistry. The photoinduced electron transer properties of ris-(2,2'-bipyridine)-ruthenium(II) is used as an example. 

Prerequisites: 
Course Level: 
Learning Goals: 

Students will be introduced to photoinduced electron transfer and how to determine the driving force between an electron acceptor/donor pair. Students will be able to incororapte photochemistry and electrochemistry to inorganic complexes. Tris-(2,2'-bipyridine)-ruthenium(II) is used as an example. Students should learn the basic concept of photoinduced electron transfer and how to determine the thermodynmics for determining the driving force for PET. This maybe an interesting way to merge concepts of photochemistry and electrochemistry. The excited state of a molecule effects its reduction potentials dramatically (a 2.12 V shift in reduction potential for Ru(bpy)3). This concept is used in a wide variety of research topics from dye-sensitized solar cells to electron transfer in photosystem II.

Implementation Notes: 

These slides can be used in a lecture or a reference to introduce the concept of photoinduced electron transfer. Students must have had an introduction to basics of photochemistry and electrochemistry prior to these notes. 

Evaluation
Evaluation Methods: 

This LO has been developed for the 2014 VIPER workshop and has yet to be tested in the classroom.

17 Jul 2014
Evaluation Methods: 

Students will be assessed qualitatively based on whether they complete the reading guide and how they contribute to a class discussion.  Students can also be assessed using the DFT Post-translational modification activity based on the same paper.

Evaluation Results: 

This LO was created for the 2014 TUES workshop and has not yet been tested in the classroom.

Description: 

In this literature discussion, students read a paper about a cobalt metallopeptide that imitates the active site of the enzyme nitrile hydratase.  Specifically, the model complex is oxidized by air to produce a coordination sphere with both cysteine thiolate and sulfinic acid ligands, much like the post-translationally oxidized cysteine ligands in the biological system.  This paper also provides an introduction to a variety of physical methods used to characterize the structure, including X-ray absorbance spectroscopy, magnetic susceptibility using the Evans method, IR spectroscopy, electronic absorbance spectroscopy, and electron paramagnetic resonance spectroscopy.  This LO was created for the 2014 TUES Viper Workshop on bioinorganic chemistry.

Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to:

  • Identify the oxidation state, coordination number, and approximate geometry of the cobalt complexes presented in this paper

  • Give the overall reaction catalyzed by the enzyme

  • Identify sites of potential ligand coordination in an oligopeptide

  • Compare two cobalt metalloenzyme active sites using the Protein Data Bank

  • Explain how X-ray absorbance spectroscopy can be used to identify the oxidation state of an atom

  • Assign ligand field or LMCT electronic transitions based on molar absorptivity

  • Compare and contrast thiolate, sulfenate, and sulfinate ligands with respect to charge, donor ability, and oxidation state

  • Predict how Lewis basicity and redox potential change as the ligand becomes more oxidized

  • Evaluate the effectiveness of a model complex for reproducing a metalloenzyme active site
Implementation Notes: 

Students should read the paper and complete the reading guide before the literature discussion.  


We hope that instructors will mix and match questions that are appropriate to their classes.  In particular, instructors may want to remove questions 9-12 depending on the desired emphasis on experimental methods. 

17 Jul 2014

Cobalt Schiff Base Zinc Finger Inhibitors

Submitted by Peter Craig, McDaniel College
Evaluation Methods: 

Collection of Reading Guide, evaluation of discussion

Evaluation Results: 

This LO was developed at the 2014 IONiC/VIPEr workshop Bioinorganic Applications of Coordination Chemistry and has not yet been evaluated.

Description: 

This is a literature discussion based on the paper “Spectroscopic Elucidation of the Inhibitory Mechanism of Cys2His2 Zinc Finger Transcription Factors by Cobalt(III) Schiff Base Complexes” by Heffern et. al. In Chemistry: A European Journal http://dx.doi.org/doi:10.1002/chem.201301659

 
Corequisites: 
Learning Goals: 

Students will be able to:

 

  1. read and comprehend the primary literature article
  2. name cobalt coordination complexes
  3. apply HSAB theory to cobalt(III)-Schiff base complexes and metal ion binding of zinc finger proteins
  4. apply the ligand spectrochemical series to determine the spin state of a cobalt(III)-Schiff base complex
  5. verbalize their answers to a series of questions and use these answers to develop answers to more detailed questions that arise during a discussion
  6. interpret and explain the results from various spectroscopies
 
Time Required: 
1 class period
14 Jul 2014

The Synthesis and Characterization of a trans-Dioxorhenium(V) Complex

Submitted by Sibrina Collins, The Charles H. Wright of Museum of African American History
Evaluation Methods: 

One of the learning goals of this is to help the students develop effective writing skills. Thus, after completing the lab work, each student submits a laboratory report in the format of an ACS journal article. This experiment is worth 50 points, namely 35 points for the laboratory report, 10 points for notebook entries, and 5 points for their experimental plan(EP). The EP is their "ticket" for entry to the lab to complete the experiment.

Evaluation Results: 

I have created a rubric to evaluate the laboratory report. I make sure they adhere to formatting guidelines and sophistication of their ideas. I focus on how well they interpret their data. I tell them it is not my responsibility to explain their data! They have to tell a good story.  Approximately 40 students have prepared this compound over the course of two semesters (Spring 2013 and Fall 2013). In general, I have 2-3 "rock stars" per lab that write excellent/very good laboratory reports. Most students write lab reports that are considered good/very good.

Description: 

This experiment involves the preparation of a key starting reactant in high purity and yield for an ongoing research project, specifically for the development of potential photodynamic therapy (PDT) agents. The students synthesize [ReO2(py)4]Cl.2H2O using standard inorganic synthesis techniques. The students visualize the vibrations and electronic properties (e.g. molecular orbitals) of the compound using output files generated from density functional theory (DFT).

Course Level: 
Prerequisites: 
Learning Goals: 

A student will use spectroscopy (UV-vis, IR and 1H NMR) to show they have prepared the target compound.

A student will gain experience visualizing the molecular vibrations using output files generated from DFT.

A student will evaluate and analyze the experimental UV-vis spectra by comparing to the calculated DFT spectra.

A student will write a laboratory report in the format of the ACS journal, Inorganic Chemistry.

Equipment needs: 

CCD Array UV-vis Spectrophotometer, Thermo Scientific Nicolet 6700 FT-IR equipped with an ATR Sampler, Bruker 400 MHz NMR; GaussView software

Implementation Notes: 

The PDT agents I am developing that contain the [ReO2]+ core are based on the prototype, [ReO2(py)4]+(py = pyridine). This is a key reactant for my research efforts. The students enrolled in my inorganic chemistry laboratory synthesize this compound, as part of their curriculum. Thus, I am using classroom teaching as a means to enhance my research efforts. The students work in teams of 2-3 students to synthesize and characterize the compound.  The students are provided with the output of the DFT results to visual MOs and vibrations of the target molecule. I have included the calculated IR and UV-vis spectra in the powerpoint slide (CollinsSynthesis2014.pptx) for the instructors. The idea is for the students to compare their experimental data an compare it to the calculated data and discuss this in their report. I have also included a word document (Collins2014SupportingInformation.docx) that provides the coordinates (xyz) for the optimized geometry.

Time Required: 
Two three hour lab periods.
14 Jul 2014

Inorganic Spectroscopy Introduced Using an Interactive PhET Simulation (Part 2)

Submitted by Alycia Palmer, The Ohio State University
Evaluation Methods: 

Students' worksheets were collected at the end of the class period to analyze student responses.

Evaluation Results: 

Students worked in small groups on Parts 1 and 2, completing these sections quickly and accurately. The third section was more difficult for students, as they were required to search for data in a research paper. This part was more manageable when done as a class, where students worked together to complete the table which was copied on the front chalkboard. This method was useful for the instructor to correct mixed up numbers and to help students understand what each number represents. Students were very confused about how coordination to a metal changes the frequency of a vibration, so much time was spent in clarifying this concept.

Parts 4 and 5 were completed in small groups, and students did not ask many questions while completing these tasks. However, responses on the worksheet for part 5 were not very detailed and could have benefited from more discussion, either with the instructor or as a brainstorming session with involvement from the whole class.

Description: 

This is the second part of a two-day class discussion on molecular and inorganic spectroscopy. In this activity, upper level students learn about spectroscopic tecniques used in inorganic chemistry and then devise an experiment to follow the progress of a hypothetical reaction. The activity also prepares students for the inorganic laboratory "Linkage isomerism of nitrogen dioxide" in which infrared spectroscopy is used to monitor changes to the N-O vibrational stretch upon coordination to a metal. During class students use the primary literature to obtain experimental values that are used in the activity and later during the lab.

The first activity is described in a separated VIPEr submission, Inorganic Spectroscopy Introduced Using and Interactive PhET Sumulation (Part 1), and investigates the interaction of light (microwave, infrared, visible, ultraviolet) with small molecules, including nitrogen dioxide.

A special thank you goes to the other contributors of these activities: Julia Chamberlain, PhD; Ted Clark, PhD; and Rebecca Ricciardo, PhD

Learning Goals: 

Students should be able to:

  • Describe, in general, how each different region of the electromagnetic spectrum influences molecules.
  • Explain how FT-IR can be used to monitor the coordination modes of NO2 on a cobalt complex.
  • Interpret data in a literature article and determine how the results in the literature relate to a laboratory experiment.
  • Design a series of spectroscopic experiments to identify intermediates in an inorganic synthetic pathway.
Equipment needs: 

Parts of the presentation were designed to be used with a stylus during class discussion portions. Drawing and writing examples are included on the hidden slides as an example (available in the "faculty only" file). These slides can be unhidden and adapted for use without a stylus as well.

Corequisites: 
Course Level: 
Implementation Notes: 

Facilitator notes are included as comments on all documents and can be viewed by selecting "Show Comments" under the review tab in Power Point or "Show all markup" under the review tab in Word.

This activity was implemented in a lecture setting with a class of 16 students. The group work was implemented during the 1-hour class that meets weekly and accompanies the 3-hour inorganic laboratory. Students were instructed before class to bring a copy of the article referenced in their laboratory (Penland, Infrared Absorption Spectra of Inorganic Coordination Complexes) and their completed worksheet from the previous week's activity, Inorganic Spectroscopy Introduced Using and Interactive PhET Sumulation (Part 1).

 

Time Required: 
One 55-minute class period
10 Jul 2014

Practical MCD Tutorial- How to collect MCD Data- Lehnert Lab

Submitted by Sheila Smith, University of Michigan- Dearborn
Evaluation Methods: 

An exam question could be asked concerning instrumentation, or sample prep, etc.

Evaluation Results: 

This LO has not been used.

Description: 

Nicolai Lehnert's group recently shared this video they made for the Penn State Bioinorganic Workshops on Youtube.  This is a great practical demonstration of how MCD data is actually collected.

Learning Goals: 

The student will be able to describe the instrumentation and the mechanics involved in the collection of Magnetic Circular Dichroism Data.

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