Spectroscopy and Structural Methods

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
Prerequisites: 
Equipment needs: 

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

Corequisites: 
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
Corequisites: 
Course Level: 
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: 
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.

Prerequisites: 
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: 
Corequisites: 
Course Level: 
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
21 Feb 2017
Evaluation Methods: 

Graded problems students turned in.

Informal evaluation during discussion.

Evaluation Results: 

Graded assignments: mean of 84, std dev of 12, so a fairly broad range of understandings

Informal: Students really enjoyed getting to evaluate published work critically and were quite engaged in discussions, which helped to bring some of the students who didn't understand the paper as well up to speed.  After the paper, students have felt much more comfortable questioning what is stated in papers, particularly if little or no support is given.

I will definitely use this again!  Unfortunate to find a paper with several important oversights in the literature, but it is a good learning opportunity.

Description: 

This LO is a problem-set-style literature discussion that leads students through a critical analysis of an interesting but flawed paper from the recent chemical literature.  Students use the questions to help them work through the paper prior to class, providing plenty of raw material for an in-class discussion about various aspects of the work from a mechanistic organometallic perspective.  The questions help students critically analyze substrate tables, spectroscopic data, and computational results from DFT.

Corequisites: 
Course Level: 
Learning Goals: 
  • Students will be able to pull out important mechanistic information from substrate tables in an organometallic paper
  • Students will be able to use knowledge of organometallic mechanisms and organic chemistry to rationalize findings in a catalysis paper
  • Students will be able to use knowledge of spectroscopy, particularly NMR, to understand structure and bonding arguments in an organometallic paper
  • Students will critically analyze a paper and learn to feel comfortable questioning assertions by authors, including the major findings of a paper
Implementation Notes: 

I had students prepare answers to these questions ahead of class and bring the answers with them.  To add incentive, I collected them as a homework assignment (though I graded some of the harder ones fairly leniently).  The questions helped prepare them for a class discussion of the paper, which I led with a few slides containing information from the paper and some other useful tidbits (I am happy to send those to you if you like, just contact me).

Time Required: 
1-2 hours student prep (reading paper); 45 minutes in class discussion
17 Jan 2017

Reactions of Cp*2Zr(2,3-dimethylbutadiene)

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

This was developed after the semester in which I teach this material. I look forward to using it next fall and I hope to post some evaluation data at that point. I anticipate having students read the paper prior to coming to class to answer these questions in a group.

Description: 

This literature discussion is based on a paper detailing the structure and reactivity of the title compound (Organometallics, 201635, 3163). The 2,3-dimethylbutadiene ligand is a bit misleading as these typically bond as X type ligands to early transition metals. Students will get a lot of pracitce counting electrons, in particular considering the different ways the 2,3-dimethylbutadiene ligand might be thought of in terms of bonding. These will then be compared to X-ray data to help the students arrive at the proper binding mode. The reactivity of these compounds with carbon monoxide and isonitriles (isocyanides) is examined. Students should be given the paper to read before coming to class for discussion. I use the CBC method of electron counting and that is reflected in the questions on electron counting. Students are taught this at the beginning of a senior level course that is primarily focused on organometallic chemistry.

Course Level: 
Prerequisites: 
Corequisites: 
Learning Goals: 

Upon completing this LO students should be able to

  1. Use the CBC method to count electrons in the zirconium compounds in this paper
  2. Describe the bonding interaction between a metal and a Cp* ligand
  3. Describe the bonding of a 2,3-dimethylbutadiene ligand to zirconium based on the available X-ray data
  4. Classify the reactions of CO and isonitriles with the complexes by reaction type
Time Required: 
50 minutes or so

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