Organic Chemistry

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
6 Apr 2020

Schlenk Line Survival guide

Submitted by Adam R. Johnson, Harvey Mudd College
Evaluation Methods: 

This is really more of a resource. I have not used it but I have a link to it in my reserach SOP folder. I think it would be good to show the students a general resource before teaching them the specifics of a local line.

Description: 

I feel like I've shared this resource before but I couldn't find it so maybe it will stick this time :)

This is a good resource created by "Dr. Andryj Borys, a main-group chemist, phosphorus fanatic and Schlenk line enthusiast." He is currently a postdoc in Canada, headed back to Europe in 2020 (supposedly..)

this resource describes the use of a Schlenk line in quite a bit of detail, with a variety of standard applications (cannula transfer, sealing NMR tubes).

Topics Covered: 
Prerequisites: 
Corequisites: 
Course Level: 
Learning Goals: 

A student can use this resource to learn general features of a Schlenk line.

6 Apr 2020

Migratory Insertion Guided inquiry

Submitted by Adam R. Johnson, Harvey Mudd College
Evaluation Methods: 

I look to see if students are able to 

1) determine the correct number of IR stretches for the compounds,

2) calculate the labeled IR stretches from the unlabeled ones,

3) correctly predict the product distributions expected for the 3 mechanistic pathways

4) understand/explain the importance of experiment 2, negative evidence, and microscopic reversibility

Evaluation Results: 

Awaiting assessment data at time of submission; will add ASAP.

based on 3 complete submissions (43% response rate, due to COVID)

students generally had no problems with questions 1 and 2, and were able to determine the number/symmetry of IR stretches using group theory, and to predict a vibrational frequency from a areduced mass calculation.

question 3 gave them a lot of trouble. I would normally do this as an in-class exercise and be able to talk them thorugh problems. students were able to draw some of the correct products for the various mechanisms but did not understand the fact that there would be a statistical distribution of products based on the 13C label. However, I spoke with all 3 students and they said that after priming their brains with the exercise, the reading in the textbook made a lot of sense and they understood what they had missed. Perfect!

Students did not generally understand the concept of negative evidence as hoped.

For future years, if I were unable to do this exercise in class, I would want to provide more guidance to get students to think about product distribution. However, if done in class, I think that watching them struggle a bit before helping them over the hurdle would be good.

Description: 

The migratory insertion reaction is one of the "four" main reactions in organometallic chemistry. It involves the formation of an acyl group by insertion of a CO molecule into a metal alkyl bond. The reaction is sometimes called the carbonyl insertion reaction because the product appears to be a result of direct insertion of the CO into the metal alkyl, but that name implies a mechanistic pathway that may not be in operation.

The reaction of methyl pentacarbonyl manganese(I), MeMn(CO)5, was studied extensively by Calderazzo in the mid 1960s. The use of C13 labeled CO and IR spectroscopy allowed for the identification of the mechanism for the reaction among the likely possibilities of direct insertion, alkyl migration, or carbonyl migration. This guided inquiry exercise presents some of the data from the Calderazzo paper and has students interpret it to determine the mechanism of the reaction in this system.

It should be noted that there are examples of all three mechanisms operating in different chemical systems, so this exercise is specific to the manganese substrate, though it is usually more generally applied.

Learning Goals: 

Students will interpret and analyze IR data of metal carbonyls

Students will calculate IR bands for 13C labeled peaks in the IR

Students will predict product distributions for the three likely mechanisms (direct insertion, carbonyl migration, alkyl migration).

Students will compare expected and observed product distributions and identify the mechanism operating

Students will discover and discuss the concept of "negative evidence."

Equipment needs: 

none

Prerequisites: 
Corequisites: 
Subdiscipline: 
Course Level: 
Implementation Notes: 

In my course, we usually cover isotopic labeling and its application to IR spectroscopy. We also use group theoretical methods to predict and assign M-CO stretches the correct symmetry labels and whether they are IR active or not. These two factors could be removed from the guided inquiry and presented as additional data to the students if you don't cover these topics. The rest of the activity is self contained. Access to the paper is not required, as the IR bands are in the document but a reference is provided.

Time Required: 
30-50 minutes
21 Mar 2020

chromium and molybdenum arene complexes (COVID-19 version)

Submitted by Adam R. Johnson, Harvey Mudd College
Evaluation Methods: 

i have no idea.... yet! (growth mindset!)

Evaluation Results: 

I will report this later this spring.

Description: 

The synthesis of (arene)Cr(CO)3 and (arene)Mo(CO)3 complexes are fairly standard experiments in the organometallic curriculum. I present here some student data and experimental descriptions of real procedures carried out at Harvey Mudd College over the previous two to three years. The word document has the answers in it so it is posted under "faculty resources" but the raw data (pdf or png form) is presented for those who need data to support their distance learning classrooms in the Spring of 2020. I also include an input file for Mo(benzene)(CO)3 should you desire to use WebMO or Gaussian to carry out some calculations. 

 

there was a minor mistake in the reported integrations for one of the complexes in the original faculty only file; it has been fixed in the v2 version.

Course Level: 
Prerequisites: 
Corequisites: 
Learning Goals: 

Students will interpret provided data to write their own experimental sections for molecules they were unable to prepare in the lab. The guided inquiry part allows students to use data to predict the outcome of a chemical reaction.

Equipment needs: 

be able to view PDF/PNG files

Implementation Notes: 

I have not used this yet but will be using it spring 2020.

Time Required: 
unknown
21 Mar 2020

Ferrocene acylation - The Covid-19 Version

Submitted by Chip Nataro, Lafayette College
Description: 

This is the classic Chromatography of Ferrocene Derivatives experiment from "Synthesis and Technique in Inorganic Chemistry" 3rd Ed. (1986 pp 157-168) by R. J. Angelici. There are no significant changes from the experiment published in the book so details will not be provided. What is provided are links to some excellent videos showing the experiment and characterization data for students to work with. For the time being this will be a living document. Currently it has 1H, 13C{1H}, COSY, DEPT, HMBC, HSQC IR, UV-Vis, GC-MS and Cyclic Voltammetry raw data files for all compounds for students to work with. It also includes processed 1H, 13C{1H}, COSY, DEPT, HMBC, HSQC, IR, GC-MS and Cyclic Voltammetry data for all compounds. If anyone has any additional means of characterization they would like to include (say Mossbauer) please feel free to contact the author.

Corequisites: 
Learning Goals: 

A student should get an appreciation for what doing this lab would be like by watching videos. In addition, the student will analyze the data provided and learn about the characterization of ferrocene, acetylferrocene and 1,1'-diacetylferrocene.

Equipment needs: 

Nothing.

The NMR data comes from a Bruker instrument and can be opened with TopSpin, MestReNova and perhaps other programs.

Implementation Notes: 

Like most everyone at this time this is going to be a trial by fire.

9 Oct 2019

Fourier Transform IR Spectroscopy of Tetrahedral Borate Ions

Submitted by Zachary Tonzetich, University of Texas at San Antonio
Evaluation Methods: 

The students perpare laboratory reports displaying their data in proper format with each peak labeled. The report must also contain answers to all of the quetions posed in the manual. Student performance and learning is assessed by the qualtity of their written reports and by a separate quiz covering aspects of vibrational spectroscopy. Teaching assistans also ensure that students' data acquisition is performed in a satisfactory manner during the laboratory period.

Evaluation Results: 

Students typically have great difficulty connecting the idea of normal modes, their symmetries, and why we observe IR peaks. They approach IR spectroscopy in much the same way they do NMR spectroscopy (i.e. methane shows four equivalent C-H bonds so I expect one C-H stretching motion) leading to serious misconceptions. This laboratory was designed in part to dispell these misconceptions. Question 1 addresses this issue most directly and many of the class answer incorrectly.

The questions in the laboratory involving harmonic oscialltor analysis are generally more straightforward for students as they just need to use the correct equations. Most of the class answers these correctly.

Likewise, students generally understand that vibrational frequencies are inversely proportional to the mass of the atoms involved in the vibration and are there able to make connections between the observed spectra of BH4-, BD4- and BF4-.

Aspects of functional group analysis are more familiar to students and they generally have little trouble assigning the spectrum of tetraphenylborate.

Description: 

This experiment was developed for an upper division Instrumental Analysis course to give students additional experience with infrared (IR) spectroscopy beyond the routine functional group identification encountered in undergraduate Organic Chemistry courses. It shares some aspects with the analysis of gas phase rovibrational spectra typically performed in Physical Chemistry courses, but places a greater emphasis on more practical considerations including data acquisition (using ATR) and interpretation. The molecular ions used in the experiment also demonstrate tetrahedral symmmetry which allows for topics in Group Theory to be exploited.

The experiment has students record the spectra of several tetrahedral borate ions including the isotopomers NaBH4 and NaBD4. The students then analyze their data in the context of the symmetry of normal modes, the harmonic osciallator model, comparisons with Raman spectra, and functional group composition. Post lab questions guide students through each of the topics and ask them to make quantative and qualitative predictions based on their data and theoretical models of molecular vibration.

Course Level: 
Learning Goals: 

-Students should be able to understand the relationship between molecular structure, normal modes, and peaks in the IR spectrum. This is a major misconception with students as they tend to believe that the presence of four B-H bonds in the borohydride ion will neccessary mean that four peaks (or one since they are equivalent) will be observed by IR. Unlike NMR spectroscopy, there is no 1:1 correspondence between the number of equivalent bonds and the number of peaks observed in the spectrum.

-Students should also be able to apply their knowledge of theoretical models (quantum harmonic oscillator) to quantitaively intrepret IR spectra and predict the energy of transitions that cannot be observed due to instrumental limitations.

-Students should be able to understand at a qualitative level how the masses of atoms affect the energy of molecular vibrations.

Equipment needs: 

The only required piece of equipment beyond the chemicals is an infrared spectrophotometer. At our institution we use an ATR element to acquire the data, but KBr pellets or nujol mulls should work equally well. All chemicals were purchased from Sigma-Aldrich and are of reasonable price.

Implementation Notes: 

See attached file with more details. The data acquisition is very straightforward if ATR sampling is employed. Students need only use the instrument for about 15 - 20 minutes to record all four samples.

Time Required: 
30 minutes to 2 hr depending upon the number of students.
25 Jul 2019

1FLO: One Figure Learning Objects

Submitted by Chip Nataro, Lafayette College
Corequisites: 
9 Jun 2019

Comprehensive literature reading assignment on platinum-based anticancer agents

Submitted by Todsapon Thananatthanachon, University of Evansville
Description: 

Students read two review articles and one research article on platinum-based cancer therapeutic agents.  These articles compresentively discuss various aspects of these drug agents such as discovery, synthesis, mode of function.  Students read the articles and use the knowledge on coordination chemistry (structure, reactivity, bonding, etc.) to explain the information included in the articles. 

 

References:

1) Mudiyanselage,R.; Rajapakse, G.; Dunuweera, S. P. Discovery, Chemistry, Anticancer Action and Targeting of Cisplatin. International Journal of Clinical Oncology and Cancer Research, 2017, 2, 65-74.

2) Takahara, P.; Rosenzweig, A. C.; Frederick, C. A.; Lippard, S. J. Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin. Nature 1995, 377, 649-652.

3) Cai, L.; Yu, C.; Ba, L.; Liu, Q.; Qian, Y.; Yang, B.; Gao, C. Anticancer platinum-based complexes with non-classical structures. Applied Organometallic Chemistry 2018, 32, e4228.

Corequisites: 
Learning Goals: 

After completing the assignment, the students will be able to:

 

1. Explain the function and mechanism of platinum-based compounds as anti-cancer drugs.

2. Apply common concepts in coordination chemistry such as reaction mechanism, hard/soft acids and bases, crystal field stabilization energy, and chelating effect to explain the effectiveness of platinum-based cancer drugs.

Implementation Notes: 

The assignment has been implemented in my fundamental inorganic chemistry class for the past 2 years.  The assignment was assigned toward the end of the coordination chemistry sections as a reading assignment, which is additional to homework assignments.  Students have learned all basic concepts of coordination chemistry (structures, bonding, and reactions) by the time the assignment was assigned.  Students have two weeks to read the three articles and submit the assignment.

Time Required: 
2 weeks

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