Electronic spectroscopy

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.

9 Jul 2014

5 (or 6) Slides about Biophysical Techniques

Submitted by Sheila Smith, University of Michigan- Dearborn
Description: 

This Five Slides About was prepared specifically for the 2014 IONiC/VIPEr workshop Bioinorganic Applications of Coordination Chemistry held at Northwestern University July 13-18, 2014.  

It covers, in one slide per technique, the techniques of electrochemistry (Cyclic Voltammetry), Electron Paramagnetic Resonance (EPR), Circular Dichroism (CD), X-ray Absorption Spectroscopy (XAS),  NMR (specifically 2D-NMR for structural information), Chemical Exchange Saturation Transfer (CEST).  This may seem an odd list, but it was chosen to prepare participants for the papers covered in the workshop.

It is intended to be paired with a collection of application assessment Questions, posted here on VIPEr, based on actual data from the literature.  I encourage VIPEr users to add your own!

 

These slides contain animations, so they are not very useful for printing out.  

Also, there is a LOT of information (references, teaching hints, etc ) in the NOTES section of the slides.  

Course Level: 
Learning Goals: 
  •  A student should be able to explain the basics of each of the techniques included in this 5 Slides About:  CV, EPR, CEST, NMR, CD, and XAS and to apply these teachniques to the interpretation of real data.
Related activities: 
Implementation Notes: 

This LO is intended to be a quick introduction to the usefulness of these 6 techniques and their application to the characterization of bioinorganic samples.  

Ideally, one would cover each slide (each technique) and then offer students the opportunity to apply their new knowledge to a piece of real data from the literature.  I have posted several sets of Assessment Questions for that purpose.  

Time Required: 
a class period
Evaluation
Evaluation Methods: 

Assessment can be accomplished using the accompanying Assessment Questions linked to this LO and posted here on VIPEr.   I encourage others to add their own sets of Assessment question based on data in the literature.

Evaluation Results: 

This LO has not  been tested.

7 Jul 2014

Dissecting Catalysts for Artificial Photosynthesis

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

Anne’s 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: 

Students’ questions varied from the very specific to the very general.  One wanted to know what the parameter “tau” referred to, and another was confused about the concept of overpotential.  Many students weren’t sure why making carbon monoxide would be a good idea, as they see it as poisonous.  One student wanted to know if these catalysts could ever be used in ambient conditions.  Students were curious to know more about the catalytic mechanism.

Description: 

Anne asked the students in her 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.  Each student chose one article from a list of suggestions provided.  Student Hayley Johnston chose this article describing a Mn-containing catalyst for carbon dioxide reduction (Jonathan M. Smieja, Matthew D. Sampson, Kyle A. Grice, Eric E. Benson, Jesse D. Froehlich, and Clifford P. Kubiak, “Manganese as a Substitute for Rhenium in CO2 Reduction Catalysts: The Importance of Acids” Inorganic Chemistry 2013, 52, 2484-2491. DOI: 10.1021/ic302391u).  The article describes the development of a Mn-based homogeneous catalyst for electrocatalytic CO2 reduction.  Hayley met with Anne for an hour to discuss the article, then generated a list of questions drawn from the article's content.  Using Hayley’s original set of questions as a starting point, Anne and Kyle developed this literature discussion, which is suitable for use in inorganic chemistry courses.

Corequisites: 
Course Level: 
Learning Goals: 

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

  • Describe the value of CO2 reduction catalysts
  • Outline the structure of the catalyst and identify the path electrons take throughout the catalytic cycle
  • Compare and contrast the Mn-based and Re-based catalysts in terms of their CO2 reduction efficiency
Implementation Notes: 

The learning object we've developed contains fifteen questions that cover most of the article's content in great depth.  It's likely too long for an individual assignment, depending on the students' backgrounds.  We encourage instructors to pick and choose from among the questions. 

Before discussing this article, students should be familiar with the concepts of renewable fuels/artificial photosynthesis and maybe also the Keeling curve demonstrating the sharp increase in atmospheric carbon dioxide over the past two hundred years.

Students may not know that CO, carbon monoxide, is very useful. They will likely be most familiar with its dangers, not its importance in industrial chemistry. Instructors could discuss the uses of CO: synthesis of methanol (nearly all industrial methanol comes from CO), synthesis of acetic acid (nearly all of the acetic acid comes from CO and methanol), hydroformylation, and Fischer-Tropsch chemistry (which could be used to make gasoline/diesel – South Africa has used this technology for some time).

A discussion of cyclic voltammetry would also be useful, including discussing the role of ferrocene as an internal reference. We have referenced the “five slides about” LO Cyclic Voltammetry created by Prof. Chip Nataro as a related activity.

In terms of placing this manuscript in context, previous studies included rhenium complexes, which work without added proton sources but are much improved in the presence of proton sources. The seminal work on rhenium complexes was performed by Jean-Marie Lehn (of supramolecular Nobel Prize fame) in the 1980s.

A comprehensive review of the history of these Re and Mn complexes from their discovery up to early 2013 can be found in “Chapter Five  – Recent Studies of Rhenium and Manganese Bipyridine Carbonyl Catalysts for the Electrochemical Reduction of CO2” Kyle A. Grice and Clifford P. Kubiak Advances in Inorganic Chemistry201466, 163-188  (see web resources below).

Several more recent papers have also been published on the Re and Mn systems from the Kubiak group and other groups since early 2013, including mechanistic studies of the Re and Mn systems using a variety of methods. A forward search of the Mn manuscript by Smieja et al. can be used to find these articles.

For more detailed information about IR-SEC, see this reference and references therein: Charles W. Machan, Matthew D. Sampson, Steven A. Chabolla, Tram Dang, and Clifford P. Kubiak Organometallics, 2014, ASAP  (see web resources below).

 

 

Time Required: 
45 minutes
11 Jun 2014

A Jablinko game to promote learning of excited state transitions

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

The learning goals were informally assessed by observing student participation in the class game and through discussion with students during the game. Also, notes taken during the game by the students were used to evaluate if students could make sense of the game.

Evaluation Results: 

Initially, students were shy to volunteer to go up to the board, but after the first round, student involvement increased. It seemed that that response portion of the game was dominated by a few students, so in the future the game may be more effective by dividing the class into teams.

 

Students were unsure how to note the result of one turn on their handout. They would just write down the transition name (e.g. T1 to S0) instead of drawing on the Jablonski diagram. In the future, to help students better connect the game to the Jablonski diagram, the instructor may wish to have a volunteer draw the transition on the chalkboard, for the whole class to see.

 

Over the course of ~10 minutes of playing the game, the students became very quick at answering the name of the transition. However, students did not seem more comfortable drawing the transition, so more time should be spent on helping students to complete the worksheet during the game.

Description: 

The in-class game Jablinko was designed to make learning excited state transitions fun. To play, a student chooses an excited state by placing a game chip at the top of the board, then the chip can “vibrationally cool” by bouncing through the pegs, and finally “transition” to a lower energy state in the bottom row. The students then compete to be the first to name the transition (e.g. S1 to T1 is called intersystem crossing).

Jablinko is intended to be used following an in-class discussion on photochemistry, using the lecture slides provided with these facilitator notes. The Jablonski diagram for [Ru(bpy)3]2+ is central to the discussion on excited state transitions and is relevant as an introduction to upper-level advanced inorganic laboratories that investigate emission or excited state quenching properties.

Learning Goals: 
  • Explain excited state processes through the use of a Jablonski diagram
  • Describe how transitions occur between electronic states
  • Learn how to draw a transition provided from the game on a blank Jablonski diagram
Corequisites: 
Course Level: 
Equipment needs: 

Computer/projector for powerpoint slides. It would be beneficial to have a means of writing on the slides while delivering the information to students, but this is not required.

 

Construction of the Board

A ­­­2’ × 4’, 1/8” thick, holes 3/16” width, standard white pegboard was purchased from a home improvement store for under $20. The board was used as purchased, thus not cutting was required. The holes are 1” apart in all directions. 1-1/4” length, 3/16” width dowel pegs were purchased for less than $2 and used on the board to guide the Jablinko chip. Pegs were inserted leaving three empty holes between sets of pegs, and two empty rows between filled rows in a staggered fashion (see photo). Wells were created at the bottom using peg placement: columns 5 pegs high with a 5-peg-wide gap between. These can be arranged to suit your chip size and it is recommended that you identify your Jablinko chip before placing pegs onto board. Jablinko chips were crafted from the plastic covers used on cardboard poster tubes. Cardstock was used to label the board and paper inserts were created to fit in the caps of the poster tubes. Additional pegs were inserted where needed around the edges of the board to keep the chip from falling off of the board. This entire board was crafted in less than 2 hours.

Implementation Notes: 

Jablinko is intended to be used following an in-class discussion on photochemistry, using the lecture slides provided with these facilitator notes. One suggestion for how to organize the class period is (1) to have the instructor lead the class discussion on slides #1—6, then (2) invite students to play Jablinko, and finally (3) the instructor will finish the class discussion with slide #7. Comments for the instructor are included on each slide to facilitate the transfer of information into your own classroom. Additionally, hidden slides are includes that show hand-written text and drawings that were made during the discussion period with a stylus.

Time Required: 
One 55-minute class period
30 Apr 2014

Inorganic Spectroscopy Introduced Using an Interactive PhET Simulation (Part 1)

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

The learning goals were informally assessed through conversations between the facilitators and students during both class periods (for this and the related LO). Also, student worksheets were collected after class to analyze student responses. Finally, students were asked to complete a survey about the activity and if they feel that the PhET activity should be used in future classes to introduce the topic of inorganic spectroscopy.

Evaluation Results: 

Students were engaged with the Molecules and Light activity which utilized the PhET simulation. Groups of 3-4 students are a good size to encourage all students to be involved in discussion. On the portions of the worksheet that asked for generalizations, the responses were vague and only scratched the surface. In the future, the instructor may wish to lead a class discussion to brainstorm for ideas about which features of molecules make them reactive to the four types of radiation in the simulation.

At the end of the second class period (after the second activity described in the related LO), students were asked to evaluate the PhET simulation and accompanying worksheet. Eleven (out of 16) students responded that the simulation should be used in future classes to provide background before topics about inorganic spectroscopy are discussed. Only one student said that it shouldn't be because it only introduced basic concepts. Four students either did not answer or did not take a definite stance.

Overall, students were satisfied with the PhET simulation and the accompanying worksheets. Also, based on the student responses to the worksheets, the instructors feel that the learning goals were met.

Description: 

A guided-inquiry activity for the interactive PhET simuation "Molecules and Light" was created to introduce upper-level inorganic laboratory students to inorganic spectroscopy. The activity included here is the first part of a two-day discussion. This activity instructs students to use the PhET simulation "Molecules and Light" to explore how various molecules interact with different energies of electromagnetic radiation (microwave, infrared, visible, ultraviolet). This activity can also be used in a general chemistry setting as the topics discussed are very basic.

The PhET simulation "Molecules and Light" was chosen because it integrates with the inorganic laboratory "Linkage isomerism of nitrogen dioxide." The simulation helps students to visualize how nitrogen dioxide gas interacts with infrared light, and in the laboratory, students collect FT-IR spectra of nitrogen dioxide coordinated to a metal.

The second part of the activity ("Inorganic Spectroscopy Introduced Using an Interactive PhET Simulation (Part 2)") builds on topics learned by interacting with the PhET simulation. That activity is most useful for upper level inorganic laboratory students who will be performing spectroscopy experiments. Materials for Part 2 are also shared on VIPER.

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 how a set of example molecules interacts with light of varying energy
  • identify characteristics of molecules that are associated with an interaction with light
  • construct a set of guidelines that generalize how molecules react with light of varying energy (microwave, infrared, visible, ultraviolet)
  • apply these guidelines to predict the reactivity with light for a small molecule which is not in the simulation. The instructor may wish to assign molecules that are shown in another simulation "Molecule Polarity" in order to provide nice visualizations. These include: ammonia, hydrogen cyanide, formaldehyde, methane, CF4, and CH2F2.
Equipment needs: 

In order for students to successfully use the PhET simulation, one computer is suggested per 3-4 students.

 

Prerequisites: 
Corequisites: 
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 their own computer and to download the simulation.

Time Required: 
One 55-minute class period

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