Chemical literature

10 Jun 2020

A copper "Click" catalyst for the synthesis of 1,2,3-triazoles

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

I have not used this in class yet, but anticipate updating this after the fall 2020 semester. This comes as a result of the June 9th LO party.

Description: 

This paper (Gayen, F.R.; Ali, A.A.; Bora, D.; Roy, S.; Saha, S.; Saikia, L.; Goswamee, R.L. and Saha, B. Dalton Trans2020, 49, 6578) describes the synthesis, characterization and catalytic activity of a copper complex with a ferrocene-containing Schiff base ligand. The article is relatively short but packed with information. However, many of the details that are assumed knowledge in the article make for wonderful questions some of which I hope I have captured. The LO includes electron counting using the CBC method, d-orbital splitting, Latimer diagrams and interpretation of catalytic results. There are also opportunities to discuss green chemical practices.

Corequisites: 
Prerequisites: 
Course Level: 
Learning Goals: 

A student should be able

determine the electro count and metal valence in the catalyst

use group theory to determine the number of IR active vibrations in the catalyst

discuss green chemical principles in relation to this article

interpret data from tables and draw conclusions from that data

suggest an additional catalytic experiment that could be performed

Implementation Notes: 

I like the question invoking a Latimer Diagram to get students to rationalize why the copper(I) active catalyst was not isolated. I also enjoyed sneaking in a group theory question. But my favorite quesiton is the last one in which students are asked to go beyond what it presented in the paper and suggest another catalytic reaction to perform. There are some aspects of the paper that were not covered in-depth. In particular the XPS seemed to be a rabbit hole I opted not to go down. The authors do not go into great detail on this topic and perhaps there is a question that could be included, but I opted not to. I also opted not to include anything about the bonding in ferrocene which can be found in many of my other LOs. Also on this list one might include UV-Vis spectroscopy and the computational studies.

Time Required: 
50 minutes
18 May 2020
Evaluation Methods: 

I have not yet implemented this LO. As with other literature discussions, instructors could collect the completed worksheets (by an individual student or in groups of students) for evaluation.

Evaluation Results: 

I have not yet implemented this LO so there are currently no evaluation results to share.

 

 

Description: 

This literature discussion focuses upon the Science article by Coates and Waymouth reporting the synthesis of thermoplastic elastomeric polypropylene by an unbridged zirconocene. This article was the basis for the work done for my PhD thesis in the Waymouth group. The LO was written in May 2020 in honor of Bob Waymouth's 60th birthday. See the BITeS post announcing the LO here

Course Level: 
Corequisites: 
Subdiscipline: 
Learning Goals: 

After completing this literature discussion, students will be able to:

  • describe a thermoplastic elastomer
  • describe the stereochemistry of polypropylene
  • describe the relationship between catalyst structure and polypropylene stereochemistry
  • apply covalent bond classification electron counting to a zirconocene
  • interpret data from figures and tables
  • describe the methods used by the authors to support the synthesis of isotactic-atactic stereoblock polypropylene
Implementation Notes: 

As usual, instructors may wish to mix-and-match questions to suit their learning goals and time constraints.

This article addresses a part of the ACS list of inorganic chemistry macromolecular, supramolecular and nanoscale (MSN) topics:

  • Ziegler-Natta, metallocene catalysts for olefin polymerization - impact on industrial/materials development
Time Required: 
depends upon implementation; minimum of 20-30 minutes for the literature discussion if students read and answer questions outside of class
29 Apr 2020

How to write a (good) paper

Submitted by Adam R. Johnson, Harvey Mudd College
Description: 

This came through my twitter feed today and I thought I would share. I'm linking to McNeil's "Resources" page which has a lot of useful info, but I am specifically talking about the "How to Write a Paper" pdf docuemnt that came from her group taking a few group meetings to discuss what made a good paper. I think this is definitely someting I will keep in mind as I work on my writing this summer!

This pdf gives examples of both good and bad, as well as what her group though about as they made up this resources. It includes secions on titles, abstracts, TOC graphics, introductions, R&D, conclusions, and chemdraw, as well as things to consider for ESI.

 

Topics Covered: 
Course Level: 
Corequisites: 
Learning Goals: 

A student will learn what a real live research group thought about putting together a manuscript, and see some useful tips and pointers for assembling thier own manuscript or report.

Implementation Notes: 

I intend to share this with my summer research studnets and thesis students. Especially as we are moving into a writing phase of research here in summer 2020.

8 Jan 2020

How to Read a Journal Article: Analyzing Author Roles and Article Components

Submitted by Catherine McCusker, East Tennessee State University
Evaluation Methods: 

Follow up small group work with a class discussion of the correct answers. Grade students on participation and completness

Description: 

This literature discussion uses a recently published article on solvatochromic Mo complexes to introduce students to the different components of a research article. The activity is divied into to two parts. Before class students read the paper and focus on defining terms, investigating the "meta" data of the paper, and the different sections iof the paper. In class the students work in groups to investigate the scientific content of the paper

Prerequisites: 
Course Level: 
Corequisites: 
Learning Goals: 

Students should be able to:

  • Interpret the roles that authors play in a research project
  • Recognize the different sections of a research article and the purpose of each section
  • Understand how to access supporting information and the type of information found there
  • Find key conclusions of a research paper and the experimental evidence the author used to make those conclusions
Time Required: 
~30 min (if students complete part 1 before class)
18 Oct 2019

Mechanisms of Mn-catalyzed water oxidation reactions

Submitted by Margaret Scheuermann, Western Washington University
Evaluation Methods: 

I did not grade this activity. 

Evaluation Results: 

Three students out of 14 explicitly mentioned that this activity was helpful on the free response section of the course evaluations.

 

Description: 

This LO is an in-class assignment to prepare students for literature readings involving catalytic cycles in which multiple protons and electrons are transferred. Two catalytic mechanisms, a proposed OEC mechanism and the proposed mechanism of a biomimetic OEC complexes are included. The intermediates are drawn including all charges and oxidation states, details which are sometimes omitted in the primary literature but can be helpful to students who are not accustomed to looking at multistep catalytic cycles. Students are then asked to add in the substrates and products entering and leaving the catalytic cycle. While this is, at its heart, a stoichiometry excercise, it helps calibrate students for the level of attention to detail needed to effectively engage with reading about bioinorganic catalytic mechanisms.

Learning Goals: 

After completing this activity:

A student will be able to follow along with each step in  proposed water oxidation mechanims in the literature.

A student will be able to apply their knowledge of stoichiomety to complex catalytic cycles involving electron transfer.

A student will be able to analyze and compare the details of catalytic cycles.

Corequisites: 
Subdiscipline: 
Prerequisites: 
Implementation Notes: 

I used this activity during a lab lecture before an inorganic laboratory experiment in which students would be preparing and testing an OEC mimic. The procedure we used was roughly based on a published procedure (J. Chem Ed. 2005, 82, 791) linked in web resources. 

I began the class period with a brief introduction to the chemistry of photosynthesis and where water oxidation and PSII fit in the broader picture. I then introduced the mimic that students would be preparing and the chemistry of the Oxone (R) triple salt. 

Students then worked in groups to complete this activity and discuss their structural and mechanistic observations. After the activity they were encouraged to read the papers referenced in the activity and to think about the evidence that supports the proposed mechanism.

 

Other implementation options:

While I used this activity as part of a lab lecture it could also be used to stimulate a discussion comparing structure/mechanism of biological and biomimetic systems in a lecture setting without the accompaning laboratory work.

This could also be modified for use as an equation balancing excercise in a majors or honors general chemistry course.

Time Required: 
10-20 minutes
25 Jul 2019

1FLO: One Figure Learning Objects

Submitted by Chip Nataro, Lafayette College
Corequisites: 
18 Jul 2019

Science Information Literacy Badge--Reading the Literature

Submitted by Michelle Personick, Wesleyan University
Evaluation Methods: 

I use this activity as a "badge," which is self-paced guided skill-building activity that students complete on their own time outside of class. Badges are designed around fundamental chemistry skills that students wouldn’t necessarily acquire from standard course content and lectures. They carry a very small point value (about 2% of the course total per badge) but my students are very motivated by even small amounts of points. I assign points primarily based on completion and effort and also provide brief written feedback for each student. I have my students turn in badges in Moodle, which makes feedback more streamlined.

Description: 

This is an activity designed to introduce general chemistry students to reading the chemistry literature by familiarizing them with the structure of a published article. The activity first presents an article from the Whitesides group at Harvard about writing a scientific manuscript, along with a video about the peer-review process. There are two parts to the questions in the activity, which are based on a specific article from Nature Communications (doi.org/10.1038/s41467-019-08824-8). Part I is focused on the structure of the article and where to find key pieces of information. Part II encourages students to use general audience summaries in combination with the original article to best understand the science while making sure they get a complete and accurate picture of the reported work.

Prerequisites: 
Course Level: 
Corequisites: 
Learning Goals: 

A student should be able to approach the chemistry literature and determine where to find:

  • the authors and their affiliations;
  • the main objective of the research;
  • the main outcomes of the research;
  • why the research is important;
  • experimental details;
  • supplementary figures and other information. 

A student should be able to broadly evaluate the reliability of secondary summaries of scientific articles by comparing them against the key points of the original paper.

Implementation Notes: 

This activity is based on a specific article: "Room temperature CO2 reduction to solid carbon species on liquid metals featuring atomically thin ceria interfaces" (Nat. Commun., 2019, 10, 865. doi.org/10.1038/s41467-019-08824-8). However, it's easily adapted to other articles that are more suited to a particular course, and I've used other articles in previous iterations. This article was chosen because the content is at least partly accessible to students in my second semester general chemistry course, who have already had some electrochemistry/redox chemistry, and who have recently learned about kinetics, reaction mechanisms, and catalysis. The topic of liquid metals is new and interesting to the students, because it's not something the'd normally be exposed to, and the application to CO2 sequestration is something they can connect with. 

 

27 Jun 2019

Porphyrin-Based Metal-Organic Frameworks

Submitted by Amanda Bowman, Colorado College
Evaluation Methods: 

Students completed this activity in small groups, then turned in individual worksheets. Student learning and performance were assessed through 1) in-class group discussion after they had worked on the activity in small groups, and 2) grading the individual worksheets. Participation was most important in the small-group portion.

Evaluation Results: 

In general, students really enjoyed this exercise and felt that it was helpful for visualizing metal-organic frameworks (particularly the extended 3D structure). They also generally felt that it was helpful in visualizing the bonding sites of metal vertices, particularly for thinking about how that influences potential reactivity. We used Mercury as a visualization software for this discussion, and the majority of students felt very comfortable using Mercury and looking at cifs on their own after this activity.

 

The biggest challenge for students seemed to be in relating the 3D structure in the cif to the images and chemicals formulas in the article. They also tended to need some hints about question 5 – to think about what information Mössbauer can provide about oxidation state of the metal, or that you can tell whether or not there are two distinct iron environments. In our class, we do brief units on X-ray crystallography including how to use and interpret cifs, and Mössbauer spectroscopy before this literature discussion. If those topics are not already addressed in a particular class it might be helpful to add them in or directly address those topics for the students as an introduction to the literature discussion.

Description: 

This literature discussion explores the physical structures, electronic structures, and spectroscopic characterization of several porphyrin-based metal-organic frameworks through discussion of “Iron and Porphyrin Metal−Organic Frameworks: Insight into Structural Diversity, Stability, and Porosity,” Fateeva et al. Cryst. Growth Des. 2015, 15, 1819-1826, http://dx.doi.org/doi:10.1021/cg501855k. The activity gives students experience visualizing and interpreting MOF structures, and gives students exposure to some of the methods used to characterize MOFs.

Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to:

  • Interpret and describe the bonding and structural characteristics of MOFs
  • Apply knowledge of ligand field strength to electronic structure of MOFs
  • Analyze X-ray crystallographic data to gain information about structural characteristics of MOFs
  • Interpret Mössbauer spectra to gain information about electronic structure of MOFs
Implementation Notes: 

This literature discussion was designed for use in an advanced (upper-level) inorganic chemistry course, but could be used in a foundational inorganic course if students have already been introduced to d-splitting diagrams and are given some coverage of Mössbauer spectroscopy and X-ray crystallography. When covering MOFs in class, students frequently expressed that visualizing and understanding the bonding sites and extended 3D structures was very challenging. So, this literature discussion was developed specifically to address that. Students completed this activity in small groups. It is very helpful to advise students ahead of time to bring laptops (or instructor should have some available) and to have the cifs from the paper downloaded and ready to go. We used Mercury as a visualization software for this activity. This activity can easily be completed in one class period. It is also helpful if students have been provided with the article ahead of time and encouraged to look it over – otherwise the most time-consuming part of this activity was allowing time for students to examine the MOF structure images in the paper before being able to discuss and answer the questions with their groups.

Note on visualization of MOFs using Mercury: To answer the discussion questions, we used the ‘stick’ or the ‘ball and stick’ style. We also used the default packing scheme (0.4x0.4x0.4) and the 1x1x1 packing scheme. The packing scheme can be changed by selecting Packing/Slicing… in the Calculate menu. I also had students view the 3x3x3 packing scheme – while this is not necessary to answer the discussion questions, it was interesting for students to be able to visualize the extended structure of the MOFs.

 

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