Organic Chemistry

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

Chem 165 2018

Submitted by Adam R. Johnson, Harvey Mudd College

This is a collection of LOs that I used to teach a junior-senior seminar course on organometallics during Fall 2018 at Harvey Mudd College. There were a total of 9 students in the course. The Junior student (there was only one this year) was taking 2nd semester organic concurrently and had not takein inorganic (as is typical).

Subdiscipline: 
Corequisites: 
Course Level: 
9 Jun 2019

1FLO: PCET and Pourbaix

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

I graded each student’s problems as I would any other homework assignment, and they averaged about 80% on that part of the assignment. The other half of the total points for the assignment came from in-class participation.

Evaluation Results: 

We had a rich conversation about this article in class; it was probably one of the most interesting literature discussion conversations I’ve had. Although this was the only introduction to Pourbaix diagrams in the course, 12 of 15 students correctly interpreted a “standard” Pourbaix diagram on a course assessment.

 

Description: 

This set of questions is based on a single figure from Rountree et al. Inorg. Chem. 2019, 58, 6647. In this article (“Decoding Proton-Coupled Electron Transfer with Potential-pKa Diagrams”), Jillian Dempsey’s group from the University of North Carolina examined the mechanism by which a nickel-containing catalyst brings about the reduction of H+ to form H2 in non-aqueous solvent. Figure 3 in the article presents an excellent introduction to the use of Pourbaix diagrams and cyclic voltammetry to determine the mechanism of a proton-coupled electron transfer reaction central to the production of hydrogen by a nickel-containing catalyst.

Corequisites: 
Course Level: 
Learning Goals: 

Students should be able to:

-  identify atoms in a multidentate ligand that can coordinate to a metal as a Lewis base

-  outline the difference between hydride addition to a metal and protonation of a ligand in terms of changes to the overall charge of the complex

-  analyze a Pourbaix diagram to predict the redox potential and pKa of a species

Subdiscipline: 
Implementation Notes: 

I have discussed the challenge of integrating literature discussions into my inorganic course in a BITeS post and the VIPEr forums. Each spring I try something a little different. This year I used three articles from the literature to frame our review of course material at the end of the semester, with each literature discussion occupying a one-hour class meeting.

In each case, the students completed problems before coming to class. While these problems were based on the journal articles, they did not require the students to read / consult the journal articles in order to complete the assignment. The students brought an electronic or paper copy of the article to class. I usually put students in groups (approximately 3 per group) and gave each group new questions to work on, which did draw from the article. After some time working in groups, each group presented their material to the rest of the class.

In implementing this particular literature discussion, I didn’t have any further questions for them.  I walked through some of the other figures from the article (especially Figure 1).  We discussed the authors’ use of color in creating Figure 3. We also reviewed the significance of horizontal vs vertical vs diagonal lines. Because I had not covered Pourbaix diagrams in the course, the activity was a good introduction to the concept.

Because these problems don’t require consultation with the article, they are suitable to use on an exam.

Time Required: 
varies
9 Jun 2019

Triphenylphosphine: Transformations of a Common Ligand

Submitted by Bradley Wile, Ohio Northern University
Evaluation Methods: 

This lab report is graded using the attached rubric (see faculty files). 

Evaluation Results: 

Over the last four iterations of this lab, the average total score was ~42/50 (n = 21). Students are generally good at recognizing that a redox process is occurring, though some struggle with this realization. Most students generate a Lewis structure with a dative bond, though some do not use the MO diagram to infer a reasonable direction for the dative interaction. I typically work through this with the students, asking them questions like "which orbitals have electrons?" and "what orbitals are interacting in your Lewis depiction?" This has been a good introduction to these synthetic and instrumental methods, and gives the lab partners an opportunity to divide up their responsibilities.

Description: 

This experiment tasks students with preparing triphenylphosphine sulfide, and the corresponding I2 adduct, then characterizing these products using common instrumental methods. Students are asked to consider MOs and tie this to their Lewis bonding depiction for the final product. This discussion is supported by WebMO calculations and tied to the experimental data obtained by the student.

If you would like to use this lab, please complete the feedback form (faculty files) and let me know how you adapt it. I would like to publish this procedure (eventually), and I am open to collaborative projects to get this to the best final form.

Course Level: 
Prerequisites: 
Topics Covered: 
Learning Goals: 
After completing this lab report, students should be able to:
  • Construct an MO diagram for I2, and relate this to the bonding in the Ph3PS-I2 complex
  • Using MO theory as a basis, decide on the best Lewis representation for Ph3PS-I2
  • Discover the wealth of bonding modes within main group species
  • Identify changes in the observable spectra for P(III) and P(V) compounds
  • Search and reference the primary chemical literature using correct ACS reference formatting
 
Subdiscipline: 
Corequisites: 
Equipment needs: 

This experiment is run using our in house instumentation including:

  • NMR spectrometer capable of acquiring 1H and 31P spectra
  • IR spectrometer
  • UV-vis spectrometer (we acquire data on a Spec200 that works just fine for this)
  • GC-MS (optional)

These spectra are provided as faculty files. If you do not have any of these capabilities, the spectra may be given to students as a handout.

Additionally, the experiment will require use of round-bottomed flasks, condensers, beakers, scintillation vials, hot plates, and gravity filtration apparatus (stemless if hot filtration required). Solvents and reagents are typically already present in the department, or may be purchased at reasonable cost.

Implementation Notes: 

I use this lab as the first experiment of the semester, and begin the first week's activity after the introduction and lab safety discussion. 

Prior to running the experiment, I prepare approximately one batch of each product (Ph3PS and Ph3PS-I2) in case of a laboratory mishap. The products are indefinitely stable under ambient conditions.

I do not describe the reaction as a redox process, or suggest a bond order (i.e. I try to write the formula for Ph3PS with an ambiguous bond order, as shown here). 

Depending on the age of your bottle of Ph3P, you may spot a small quantity of Ph3P=O in the 31P spectrum (small peak around 30 ppm in the included spectrum). This may be an opportunity to discuss connections to biochemistry or atmospheric oxidation, or ask students to draw Lewis depictions of these species. 

I teach my students how to manually run their own NMR spectra using TopSpin at this point (they have previously learned 1H and 13C using the autosampler). I typically discuss the differences between 31P{1H} and 31P (non decoupled) spectra at this time. Note that the lab handout has some instructions specific to the Bruker software that may be updated if you use a different spectrometer.

Literature articles describing the crystal structure of the final adduct (and related I2 species) are linked here. I have not typically gone into great detail about this, as the assembled I2 ribbons can confuse the students that are just putting the basic concepts together.

Time Required: 
Two full 3 hour labs, and approximately 1 additional hour (first week). If characterization is done outside of normal lab hours, this could be accomplished in one full 3 hour lab and one additional hour.

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