Spectroscopy and Structural Methods

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
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
10 Sep 2017

Inclusive Pedagogy: A Misidentified Molecule and Paper Retraction

Submitted by Sibrina Nichelle Collins, Lawrence Technological University
Evaluation Methods: 

This LO has various options for evaluation. First, a rubric should be prepared based on criteria identified by the student teams for evaluating the team posters. The students will be evaluated based on their ideas and attention to detail for their individual  reponses to the discussion questions. In addition, a 7-question survey is included in the handout for the students. Four of the questions address self-efficacy questions for chemistry majors. These questions were modified from a self-efficacy instrument developed by Baldwin et al for biology students. I have included a link to the model. We should be developing assessment tools that address science identity, sense of belonging, and self-efficacy for chemistry majors. If a student does not feel comfortable in a chemistry course, they will likely not pursue a career as a chemist.

Evaluation Results: 

Will be reported later.

Description: 

This learning object focuses on teaching students how to read and use Chemical and Engineering News for class discussions and critically evaluate the scientific literature. Recently, Chemical and Engineering News published an article about the retraction of a 15-year old paper, which had misidentified a multidentate ligand, which is central to the paper (Ritter, S.K. “Chemist Retract 15-year old paper and publish a revised version.” Chem. Eng. News, 2017, 95, (36), p6). The authors published a revised paper to the journal in 2017, with the correct structure of the ligand along with an x-ray crystal structure. This activity consists of two components, namely the students working in teams to discuss the C &E News article, retracted Inorganic Chemistry paper (DOI:10.1021/acs.inorgchem.7b01932) and the revised paper (DOI:10.1021/acs.inorgchem.7b01117) and preparing a poster for a “Gallery Walk.”

Learning Goals: 

An important learning goal for this learning object is to incorporate practices for creating an inclusive learning environment for students (inclusive pedagogy). The goals for this LO are for students to:

  • Read and use C&E News for student-led discussions
  • Critically evaluate experimental evidence published in the scientific literature
  • Apply concepts learned in previous chemistry courses
  • Gain a better understanding of the peer-review process for publication and retraction
  • Appreciate the importance of structural analysis tools such as X-ray crystallography
  • Prepare a team poster to communicate scientific ideas
Corequisites: 
Equipment needs: 

The students will need 3M Post-IT paper and markers to prepare a poster for the "Gallery Walk."

Prerequisites: 
Course Level: 
Implementation Notes: 

You will need to provide access to the Chemical and Engineering News article, and the two Inorganic Chemistry articles before class. This activity will likely take two class periods The first class period should focus on discussion of the articles and developing a rubric for evaluating the posters with the class. The second class period, the students will be allowed 30 min to prepare a poster for a "Gallery Walk."

Time Required: 
Two 50 min class periods
3 Jun 2017
Evaluation Methods: 

Students were evaluated by the instructor during the activity. The instructor was available throughout the activity to answer questions and guide inquiry. This activity generated good discussion among students and most were able to work their way through. 

Evaluation Results: 

All students completed the activity during the class period and gained a deeper appreciation for metals in biology, protein structure, and using NMR to determine protein structure. Some students needed more guiding through the rationales of metal toxicities and the multi-dimensional NMR experiments than others. 

Description: 

This activity was designed as an in-class group activity, in which students begin by using basic principles to predict relative toxicities and roles of metals in biological systems. Students then learn about the structures of metallothioneins using information from the protein data bank (PDB) and 113Cd NMR data. By the end of the activity, students will have analyzed data to identify and determine bonding models and coordination sites for multiple cadmium centers in metallothioneins. It is based on recent literature, but does not require students to have read the papers before class.

Learning Goals: 

Students will be able to:

  1. Use fundamental principles to predict toxicities of metals
  2. Apply hard-soft acid-base (HSAB) theory to metals in biological systems
  3. Utilize the protein data bank (PDB) to investigate protein-metal interactions
  4. Explain the roles of metallothioneins in biological systems
  5. Evaluate 1-D and 2-D 113Cd NMR to determine structures of Cd bonding sites in metallothioneins
  6. Explain how NMR can be utilized to determine protein structure
Course Level: 
Corequisites: 
Implementation Notes: 

This activity was developed for a Master's level bioinorganic course, but could be utilized in an advanced undergraduate inorganic course. Students were given the worksheet at the beginning of class and worked together in groups to answer the questions. Students did not have access to the paper and had not read any articles previously. Using the PDB was done as a separate in-class activity, so students had some familiarity with the PDB codes and amino acid sequences. 

A brief refresher of [1H-1H] COSY was presented before beginning the activity. 

Time Required: 
60 min
3 Jun 2017

Literature Discussion of R3CH→ SiFR3 Agostic Interactions

Submitted by Tanya Gupta, South Dakota State University
Evaluation Methods: 

Some discussions questions can be taken out and used for exams, quizzes or problem sets.

The instructor can develop a rubric to evaluate these questions based on their needs.

Evaluation Results: 

Monitoring student discussions, or grading student written responses based on implementation.

Description: 

The set of questions in this literature discussion activity is intended to engage students in reading and interpreting scientific literature and to develop a clear and coherent understanding of agostic interactions. The activity is based on a paper by Dorsey & Gabbai (2008). The paper describes agostic interactions in a silicon-based compound (R3C-H→SiFR3). The set of questions in this literature discussion activity is appropriate for an upper division course in inorganic chemistry. The research described in the article ties together concepts of agostic interactions and their impact on the coordination geometry of a Lewis acidic species. The discussion activity includes guided questions for students to understand and determine the presence of agostic interactions experimentally and through computational methods. The activity has specific questions related to bonding, structure, synthesis, characterization, theoretical and computational methods used in the literature. The activity may require reviewing some secondary sources.

Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to..

  • Define an agostic interaction and relate it to other types of bonding.

  • Describe how the agostic interaction affects the coordination geometry of a Lewis acidic atom.

  • Provide examples of how the presence of an agostic interaction can be determined experimentally and through computational methods.

  • Differentiate between computational methods in terms of the information they can provide.

  • Find related sources of information to aid in comprehension of the concepts in the article.

 

Implementation Notes: 

This literature discussion was developed at the VIPEr 2017 workshop at Franklin and Marshall College so it has not yet been implemented. The authors believed that implementation of this article is best for an inorganic course that is post-organic, post-spectroscopy. It could be helpful after a discussion of 3-center 2-electron bonding and/or Lewis acidity/basicity. As with all lit. discussion LOs, this article also provides a valuable experience in reading the literature, including an interpretation and analysis of the experimental section. There are many questions included in this activity and instructors may want to pick and choose these questions and adapt it to their class.

Time Required: 
1 class (50 minutes)
3 Jun 2017

Literature Discussion of "A stable compound of helium and sodium at high pressure"

Submitted by Katherine Nicole Crowder, University of Mary Washington
Evaluation Methods: 

Students could be evaluated based on their participation in the in-class discussion or on their submitted written answers to assigned questions.

Evaluation Results: 

This LO has not been used in a class at this point. Evaluation results will be uploaded as it is used (by Spring 2018 at the latest).

Description: 

This paper describes the synthesis of a stable compound of sodium and helium at very high pressures. The paper uses computational methods to predict likely compounds with helium, then describe a synthetic protocol to make the thermodynamically favored Na2He compound. The compound has a fluorite structure and is an electride with the delocalization of 2e- into the structure.

This paper would be appropriate after discussion of solid state structures and band theory.

The questions are divided into categories and have a wide range of levels.

Dong, X.; Oganov, A. R.; Goncharov, A. F.; Stavrou, E.; Lobanov, S.; Saleh, G.; Qian, G.-R.; Zhu, Q.; Gatti, C.; Deringer, V. L.; et al. A stable compound of helium and sodium at high pressure. Nature Chemistry 2017, 9 (5), 440–445 DOI: 10.1038/nchem.2716.

Corequisites: 
Learning Goals: 

After reading and discussing this paper, students will be able to

  • Describe the solid state structure of a novel compound using their knowledge of unit cells and ionic crystals
  • Apply band theory to a specific material
  • Describe how XRD is used to determine solid state structure
  • Describe the bonding in an electride structure
  • Apply periodic trends to compare/explain reactivity
Implementation Notes: 

The questions are divided into categories (comprehensive questions, atomic and molecular properties, solid state structure, electronic structure and other topics) that may or may not be appropriate for your class. To cover all of the questions, you will probably need at least two class periods. Adapt the assignment as you see fit.

CrystalMaker software can be used to visualize the compound. ICE model kits can also be used to build the compound using the template for a Heusler alloy.

Time Required: 
2 class periods
3 Jun 2017

An ion exchange method to produce metastable wurtzite metal sulfide nanocrystals

Submitted by Janet Schrenk, University of Massachusetts Lowell
Evaluation Methods: 

Evaluation methods are at the discretion of the instructor. For example, you may ask students to provide written answers to the questions, evaluate whether they participated in class discussion, or ask students to present their answers to specific questions to the class.

Description: 

In this literature discussion, students use a paper from the literature to explore the synthesis, structure, characterization (powder XRD, EDS and TEM) and energetics associated with the production of a metastable wurtzite CoS phase. Students also are asked define key terms and acronyms used in the paper; identify the goal of the experiments and determine if the authors met their goal. They examine the fundamental concepts around the key crystal structures available.  

 

Preserving Both Anion and Cation Sublattice Features during a Nanocrystal Cation-Exchange Reaction: Synthesis of a Metastable Wurtzite-Type CoS and MnS

Powell, A.E., Hodges J.M., Schaak, R.E. J. Am. Chem. Soc. 2016, 138, 471-474.

http://pubs.acs.org/doi/abs/10.1021/jacs.5b10624

 

There is an in class activitiy specifically written for this paper. 

Corequisites: 
Prerequisites: 
Learning Goals: 

In answering these questions, a student will be able to…

  • define important scientific terms and acronyms associated with the paper;

  • describe the rocksalt, NiAs, wurtzite, and zinc blende in terms of anion packing and cation coordination;

  • differentiate between the structure types described in the paper;

  • explain the difference between thermodynamically stable and metastable phases and relate it to a free energy diagram; and

  • describe the structural and composition information obtained from EDS, powder XRD, and TEM experiments.

Implementation Notes: 

This learning object was created at the 2017 IONiC Workshop on VIPEr and Literature Discussion. It has not yet been used in class.

Time Required: 
50 minutes
3 Jun 2017

Quantum Dot Growth Mechanisms

Submitted by Chi Nguyen, United States Military Academy
Evaluation Methods: 

The question document attempted by students in preparation for the literature discussion will be due prior to the in-class discussion. In particular, students' performance on the particle-in-a-box question will be evaluated to assess retention from the previously covered course material. The next exam following the discussion will contain specific question(s) (data/figure analysis) addressing these topics. Students' performance difference between the two will be evaluated. The extent to which students improve their post-discussion understanding of the concepts will direct future implementation.

Evaluation Results: 

To be determined. This is a newly proposed literature discussion.

Description: 

This literature article covers a range of topics introduced in a sophomore level course (confinement/particle-in-a-box, spectroscopy, kinetics, mechanism) and would serve as a an end-of-course integrated activity, or as a review activity in an upper level course. The authors of the article employ UV-vis absorption spectroscopy of CdSe quantum dots as a tool to probe the growth mechanism of the nanoparticles, contrasting two pathways.

 

Reference:  DOI 10.1021/ja3079576 J. Am. Chem. Soc. 2012, 134, 17298-17305

 
Corequisites: 
Prerequisites: 
Learning Goals: 

Apply the particle in a box model to interpret absorbance spectra with respect to nanoparticle size.

 

Analyze the step-growth and living chain-growth mechanisms proposed in this paper.

 

Evaluate the kinetics as it applies to the step-addition.

 

Recognize and apply multiple scientific concepts in an integrative manner.
Implementation Notes: 

Sophomore level implementation:  Recommend focusing on select portions (e.g. Figures 1b, 2, 5 with corresponding text) of the paper rather than having students read the entire document.  The learning objects focus on select topics, such as particle-in-a-box, reaction mechanism, and kinetics in conjunction with absorbance spectroscopy.  This would be a good literature discussion resource for an end-of-course integrative experience that encompasses multiple topics from general chemistry and inorganic chemistry.  

 

Advance level implementation:  For an upper division course, incorporate the paper in its entirety early in the course as an assessment on students’ ability to integrate multiple concepts that they should have learned in general chemistry, organic chemistry, and physical chemistry.  To enhance the experience, accompanying the literature discussion on this paper with a laboratory experience by repeating the experimental and characterization procedures presented in the paper, and having students' compare their results with published results.  This also serves to enhance students’ scientific literacy by critically assessing the quality of the paper.

 

Excerpts of the paper and questions can be used on a graded event, or as lesson preparation for in class discussion.

 
Time Required: 
In-class discussion takes approximately 50 minutes with students having already read the paper and submitted their responses to the questions.
3 Jun 2017
Evaluation Methods: 

This was created during the IONiC VIPEr workshop 2017 and has not yet been implemented.

 
Description: 

This module offers students an introductory chemistry or foundational inorganic course exposure to recent literature work. Students will apply their knowledge of VSEPR and basic bonding to predict geometries of complex SiO2-containing structures. Students will gain a basic understanding of how crystallography is used to determine molecular structures and compare experimental crystallographic data to their predictions.

Prerequisites: 
Course Level: 
Corequisites: 
Learning Goals: 

Students will be able to:

  1. Describe the bonding in SiO2 and related compounds
  2. Apply bonding models to compare and contrast bond types
  3. Apply VSEPR to predict bond angles
  4. Utilize crystallographic data to evaluate structures
Implementation Notes: 

Students should have access to the paper and read the first and fourth paragraphs on the first page and the third paragraph on the second page. Students should also reference scheme 1 and figure 1.

 

This module could be either used as a homework assignment or in-class activity.

 
3 Mar 2017

In-class peer review

Submitted by S. Chantal E. Stieber, Cal Poly Pomona
Evaluation Methods: 

Student participation was evaluated during the in-class portion based on the questions students asked. 

The formal peer review homework was evaluated based on completion, level of thought and thoroughness.

Evaluation Results: 

Overall, students were very interested in this topic and had not formally learned about the process before. There was a very lively discussion and a lot of questions were asked. All students received full credit for participation. 

Similarly, once students received their classmate's paper for peer review, they took the process very seriously and carefully went through the paper and answered the worksheet questions. 

I was very impressed by the high quality of the formal peer reviews that were turned in as homework. Students clearly spent a lot of time to carefully think about the paper and craft a reasonable response. Most students received full-credit. 

Description: 

This activity includes questions for students to answer to help guide them through the process of peer review. It was designed to assist students in writing peer reviews for research reports written by their classmates, but could be applied to literature articles as well.

Corequisites: 
Prerequisites: 
Learning Goals: 

A student will be able to:

-Explain how the peer-review process works

-Critically read through a research article

-Carefully review a research article

-Write a professional peer review

Implementation Notes: 

An overview of peer review was given with three powerpoint slides. Students then worked through a modified Q&A of the peer review module "Peer Review - How does it work?" posted by Michael Norris on VIPEr. This provided students with an example of real reviews, along with the resulting article revisions. 

The current worksheet was then passed out to students along with a research report written by one of their classmates (I assigned these and removed names). In class, students answered the questions on the worksheet and were able to ask questions of the editor (the instructor in this case). Following the in-class peer review, students had to write a formal peer review, which was turned in as homework. 

The peer review was a final component of a research report that students had been working on throughout the course. The final report was turned in after students had received the review comments back from their peers. The grade of the final report took into consideration whether or not students had made modifications based on comments by their peer reviewer.

 
Time Required: 
60 min

Pages

Subscribe to RSS - Spectroscopy and Structural Methods