Spectroscopy and Structural Methods

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. 

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.

20 Mar 2020

virtual inorganic lab experiments with data

Submitted by Adam R. Johnson, Harvey Mudd College

This collection includes new and/or updated lab experiments useful for online/distance learning. To be included in this collection, data should be provided for others to use in their new virtual laboratory courses. This collection was prepared as part of my response to the COVID-19 pandemic.

Prerequisites: 
Corequisites: 
Course Level: 
19 Mar 2020

Job's Method - The Covid-19 Version

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

Students are generally asked to write a full lab report including an abstract, brief introduction, experimental and results/discussion. I will likely not ask them to do that in this virtual lab. However, they will be asked to determine the value for n for the various [Ni(en)x] solutions as well as questions 1 and 2 from Angelici's book. In addition, I typically ask them to do some literature searching questions, but I am not sure if they will have access to SciFinder so I may have to bypass that or provide them the original papers I have them look at. Links to those papers are included.

Evaluation Results: 

I'll use this in a few weeks and see how it goes.

Description: 

This is the classic Job's Method experiment from "Synthesis and Technique in Inorganic Chemistry" 3rd Ed. (1986 pp 108-114) 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 a series of pictures and videos showing the experiment being performed. Also included are the raw files of the absorbance spectra in EXCEL. It is not perfect but given the situation many of us are facing at the time this is published, it is better than nothing. I was extremely rushed given that the governor essentially closed the state down the evening I did this, so please forgive any errors. This also includes literature searching questions.

Prerequisites: 
Course Level: 
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 determine the species present in solutions containing various mole fractions of ethylenediamine and Ni(II).

Equipment needs: 

Nothing

Implementation Notes: 

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

9 Jan 2020

Marvin suite from ChemAxon

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

As my students draw structures, I usually observe them and make suggestions to improve their drawings. 

Evaluation Results: 

While I do no formal assessment of this activity, I have observed that students seem to learn how to use the program fairly quickly and then use it without much difficulty for the rest of the semester.

Description: 

It is important for students to be able to effectively communicate the results of their scientific work. This does not only inlcude written and oral communication, but the creation of appropriate representations of the complexes they have investigated. It is crucial that students learn how to draw molecules using electronic structure drawing programs, but site licenses for structure drawing programs can be prohibitive for some institutions.

Marvin suite is a software package from ChemAxon that is freely avaialble for educational institutions. It contains a structure drawing program (MarvinSketch) and a viewer (MarvinView), as well as tools that allow for the calculation of many molecular and spectroscopic properties of molecules. This is a very useful suite of programs that can be used by all students and faculty at an instituion once an Academic License is obtained.

A set of directions for drawing a coordination complex in MarvinSketch is also included as part of this learning object. These directions will guide the user as they draw the structure of a square-planar coordination complex, trans-[Ni(NCS)2(PMe3)2].

Corequisites: 
Prerequisites: 
Learning Goals: 

After following the instructions, students should be able to draw a chemical structure electronically using a chemical structure drawing program.

Once the structure in drawn in the program, a user would then be able to access the many other functions available in the software.

Implementation Notes: 

During the first week of our semester, lab sections are usually not held for courses so that student enrollment issues can be sorted out. In an advanced course such as Inorganic Chemistry, I want to take advantage of every week that I can so I use the first lab meeting time to have students learn how to use several software programs that they wil use over the course of the semester. 

I post the download link and the license file for the software on the course LMS before the lab period and I ask the students to download and install the software. You should make sure that students update their Java installation before installing the Marvin suite. (I also place a link to the Java download site on the course LMS as well, but students tend to ignore it.) Aside from the Java issue, I have found that there are no real issues encountered by students when they install the software. 

When we meet, I ask the students to follow the linked instructions to create a drawing of a coordination complex. Once they complete that successfully, I ask them to draw several other structures. I do not  have any specific structures that I use, but I try to choose complexes with different geometries (octahedral, tetrahedral, square pyramidal, etc.) around the metal center.

The Marvin suite of programs provides the students with a number of useful tools, not just a structure drawing progam. Students use this to calculate or estimate a number of different things, such as the molecular mass, the elemental analysis, a mass spectrum, 1H and 13C NMR, and charge distribution.

To obtain a license file, the faculty member must log into the ChemAxon site and request an Academic License. Once approved, the instituion is allowed to use the software for 2 years and the license can be easily renewed when it expires.

 

Time Required: 
30 minutes
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)
9 Oct 2019

2019 Nobel Prize - Li-ion battery LOs

Submitted by Barbara Reisner, James Madison University

Congratulations to the 2019 recipients of the Nobel Prize - John B. Goodenough, M. Stan Whittingham and Akira Yoshino. It's a well deserved honor!

There are several LOs on VIPEr that talk about lithium ion batteries and related systems. The 2019 Nobel is a great opportunity to include something about these batteries in your class.

I hope to see more LOs in the coming weeks so we can bring this chemistry into our classrooms!

Prerequisites: 
Corequisites: 
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: 
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.

 

Pages

Subscribe to RSS - Spectroscopy and Structural Methods