Bioinorganic Chemistry

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
11 Apr 2017

Johnson Matthew Catalytic Reaction Guide

Submitted by Sheila Smith, University of Michigan- Dearborn
Evaluation Methods: 

No evaluation yet

Evaluation Results: 

No results yet

Description: 

This guide, available in print, online and in an app, allows users to look up appropriate catalysts and conditions to accomplish a wide variety of reactions.

 

Prerequisites: 
Course Level: 
Learning Goals: 

A student should be able to use the Catalytic Reaction Guide (CRG) to identify appopriate reaction conditions and catalysts to accomplish a wide variety of reactions.

Implementation Notes: 

I have not yet used this... I just picked up a copy at ACS, but will add to this as I implement it in my classroom.

 

Time Required: 
variable
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
4 Jan 2017
Description: 

This is a great new textbook by George Luther III from the University of Delaware.  The textbook represents the results of a course he has taught for graduate students in chemical oceanography, geochemistry and related disciplines.  It is clear that the point of the book is to provide students with the core material from inorganic chemistry that they will  need to explain inorganic processes in the environment.  However the material is presented in such a clear, logical fashion and builds so directly on fundamental principles of physical inorganic chemistry that the book is actually applicable to a much broader audience.  It provides a very welcome presentation of frontier orbital theory as a guide to predicting and explaining much inorganic chemical reactivity.  There are numerous very  helpful charts and tables and diagrams.  I found myself using the book for a table of effective nuclear charges when I was teaching general chemistry last semester.  The examples are much more interesting that the typical textbook examples and would be easy to embellish and structure a course around.  There is also a helpful companion website that provides powerpoint slides, student exercises and answers.  The book covers some topics not typically seen in inorganic textbooks like the acidity of solids but the presentation of this information makes sense in light of the coherent framework of the text.  We so often tell our students "structure dictates function".  This text really make good on that promise.  My only complaint is that I wish the title were something more generic so that I could use it for a second semester of introductory-esque material that we teach after students have taken a single semester of intro chem and two semesters of organic chemistry.  So much of what is covered in this textbook is precisely what a second semester sophomore chemistry major should know before proceeding on in the major.  But the title makes the book hard to sell to chemistry majors and that is regrettable. 

Prerequisites: 
Course Level: 
27 Jun 2016

Student Oral Presentations of a Communication from the Primary Literature

Submitted by Carmen Works, Sonoma State University
Evaluation Methods: 

see rubric that is attached 

Description: 

In the humanities it is common practice to read a piece of literature and discuss it.  This is also practiced in science and is the purpose of this exercise.  Each student is assigned a communication from the current  literature (inorganic, JACS, organometallics, J. Phys. Chem) and the student presents this paper to the class.  The class will also have the opportunity to read the article prior to the presentation, and I post each paper on my LMS page.  The presenter will be responsible for explaining the paper, and leading a critical discussion.  This is not an easy assignment since these papers are filled with chemical jargon, but an important part of their chemical education is to be able to tackle the literature.  In addition a lot of this jargon is covered during the semester.

  

 

Course Level: 
Learning Goals: 

·      Students will learn to read a paper from the primary literature

·      Students will learn to present the a paper from the primary literature

·      Students will learn to create a group discussion

·      Students will learn how to relate chemical jargon learned throughout the four years of chemistry to the literature

·      Students will learn how to answer exam questions from the primary literature

 

Implementation Notes: 

I hand out selected communications during the second week of class.  Students are allowed to swap papers. They have the entire semester to read the paper and prepare a talk but the talks are during the last 3 weeks of class.  Each student is give 25 min to present their paper to the class.  The assignment is graded using the attached rubric and is worth 15% of their final grade.  I selected about 7 exam questions for the final exam and ask students to answer 5 of these questions.  I try to structure the questions so that they don't have to "know" every paper.  I have attached an example of such a question.  

21 Feb 2016

Ligands that Favor/Force Tetrahedral Geometry

Submitted by Marion E. Cass, Carleton College
Topics Covered: 
Prerequisites: 
Course Level: 
Corequisites: 
Learning Goals: 

Learning Goals:

Learning Objectives:  Going into this exercise:

  1. Students should be able to determine the oxidation state and d electron count for a given set of metal complexes.
  2. Based on the d electron configuration of a metal ion, students should be able to propose whether that metal ion should prefer a tetrahedral or a square planar geometry for a 4 coordinate complex.
  3. Students should have been introduced to the Jahn-Teller distortion.

Following the Presentation/Discussion:

  1. Students should be introduced to the concept that there are ligands that will force (or less successfully distort while trying to force) tetrahedral geometry on metals ions with d electron configurations that prefer to have a different geometry.
  1. Students should be introduced to the concept that by favoring one geometry over another, one oxidation state of a metal can be preferred over another for a given metal.
  1. Students will be introduced to one application of how ligands of this type can be used to facilitate experiments that probe the chemistry of certain metalloproteins.
Time Required: 
15 minutes
22 Aug 2015

Antibacterial Reactivity of Ag(I) Cyanoximate Complexes

Submitted by Kari Young, Centre College
Evaluation Methods: 

Instructors will most likely choose appropriate evaluation method, but instructions are included for the following options:

  1. Writing lab report

  2. Poster

  3. Oral presentation

Evaluation Results: 

In general, students are able to prepare and characterize the complexes.  IR spectroscopy is especially useful in this lab because 1H NMR spectroscopy is not very diagnostic.  One difficulty is removing excess solvent from the ligand, and we recommend using a mechanical vacuum pump after rotovapping.  Some students report that they really enjoy the microbiology/biomedicine application. 

Description: 

In this experiment, students will synthesize and characterize one of three Ag(I) cyanoximate complexes as potential antimicrobial agents for use in dental implants. This experiment combines simple ligand synthesis, metalation and characterization, and a biomedical application. The complexes are both air and light stable. Students apply the Kirby-Bauer disk diffusion test, a common microbiology assay, to determine the antibacterial properties of their complexes. Students will also perform a simple cost analysis as part of the evaluation of the complexes.  This experiment was designed during the June 2015 “Improving Inorganic Chemistry Pedagogy” workshop funded by the Associated Colleges of the South.

Prerequisites: 
Learning Goals: 

A student should be able to:

  • Prepare one of a series of Ag(I) cyanoximate complexes and perform appropriate characterization of identity and purity
  • Measure antimicrobial activity in a semi-quantitative way using the Kirby-Bauer assay, including design and implementation of appropriate control experiments.
  • Evaluate a series of complexes as potential antimicrobials for dental applications based on the criteria of heat stability, water insolubility, and antibacterial activity.
  • Identify most cost effective complex.
Equipment needs: 

FT-IR spectrometer

NMR spectrometer

Melting point apparatus

Microbiology equipment

Implementation Notes: 

We piloted this experiment during the 2015-2016 school year and have made some adjustments based on our experience.  We welcome others in the VIPEr community to help us test this!  If you do try this, please post your comments and/or consider filling out our evaluation survey http://goo.gl/forms/CrP5KJtDtursr5302

 

Students will synthesize and characterize one compound each, but are expected to pool data as a class for a comparative analysis.  The antimicrobial assay requires supplies not commonly found in a chemistry laboratory, and instructors are encouraged to collaborate with a colleague in microbiology.

Time Required: 
Four 3-hour lab sessions
1 Jul 2015

Advanced Inorganic Chemistry Course Videos

Submitted by Kathryn Haas, Saint Mary's College, Notre Dame, IN
Evaluation Methods: 

3 x 1 hour exams, ACS INorganic Chemistry Final Exam.

Description: 

At this website, you will find a link to the syllabus and all lecture videos for a "flipped" version of an Advanced Inorganic Chemistry Course taught at Saint Mary's College (Notre Dame, IN).  I used Shiver & Atkins for this course, and the format is based off of Dr. Franz's course at Duke.  If anyone is interested in the problem sets, I will be happy to share, although much of the material I used is from VIPEr.  

Learning Goals: 

Students will be able to apply fundimental principles of Group Theory, M.O. Theory, Acid/Base Theory, Crystal Field Theory, Kinetic & Thermodynamic trends, and 18e- rule  to understand spectroscopic (Absorption, Vibrational) and magnetic properties and to understand bonding and reactivity of metals.

 

Implementation Notes: 

This was the first iteration of a flipped model, I appologise for any mistakes & innacuracies, but if you spot issues, I'm happy to know about them.  The videos are rather long, and I will say that if I do this again, I will certainly design shorter videos!  Students really like it when the videos are 10-15 min or less.  But, perhaps these can help some beginning teachers prepare for class.  (And if that's you, good luck!)

Time Required: 
1 semester, 3 credit hour course
8 Mar 2015

Community Challenge #2: Symmetry and MO Theory

Submitted by Nancy Scott Burke Williams, Scripps College, Pitzer College, Claremont McKenna College
Corequisites: 
Prerequisites: 
9 Dec 2014
Evaluation Methods: 

I assigned this paper as a 10-point literature activity, intended mostly to expose students to the chemical literature and enhance their interest in class topics. Questions focus largely on reading comprehension, but could easily be expanded for use in a more advanced course (see implementation notes for some suggestions). Students answer the questions listed in the activity sheet to verify that they have read the paper, and I grade them largely based on participation. We took 10-15 minutes in class to discuss the interesting points of the paper (could easily be extended to a longer discussion if you have the time), but this was used as an independent activity to expose them to the ideas and enhance their interest in coordination chemistry. The paper is extremely readable, and students did not appear to have difficulty understanding it on their own. 

 

Evaluation Results: 

Though brief, the in class student discussion indicated a high level of interest in the paper, and excitement about a "real" application of course material. The reading question answers were largely correct and complete, indicating that students had achieved at least basic understanding of the paper, though some students had difficulty explaining how the authors used substitution experiments to infer Mg binding types.

Description: 

I use this literature discussion in my second year inorganic class as a follow-up to a lab experiment where students synthesize Werner complexes and then (with much guidance) analyze their IR spectra using symmetry and group theory arguments. This paper provides an excellent example of how cobalt complexes are used in modern applications, and serves as a bridge to bioinorganic chemistry, which is a central feature later in the course.

Rowinska-Zyrek, M.; Skilandat, M.; Sigel, R. Hexamminecobalt(III) – Probing Metal Ion Binding Sites in Nucleic Acids by NMR Spectroscopy Z. Anorg. Allg. Chem. 2013, 639 (8-9), 1313-1320. DOI: 10.1002/zaac.201300123

Corequisites: 
Course Level: 
Prerequisites: 
Learning Goals: 

In answering these questions, a student will:

- Gain a greater appreciation for the use of transition metal complexes in solving problems of structure and binding in biological systems.

-  Discuss specific features of cobalt hexammine complexes that allow them to substitute for magnesium hexaaqua complexes  when binding to biological molecules

-  Appreciate the effects of metal size, charge, lability, and spectral activity on the ease with which a system can be characterized

-  Identify the advantages and limitations of using a structural mimic to study molecular structure.

Implementation Notes: 

I passed this paper out in the week after students synthesized a series of Werner complexes in the laboratory. Students had been exposed to descriptive inorganic chemistry and periodic trends, symmetry and (rudimentary) group theory prior to this exercise.  In the second half of the laboratory session, they had compared the rates of hydration of hexammine, pentammine, and cis-tetrammine chloride cobalt complexes using UV/VIS, so some students were quite familiar with the stability of the hexammine complex. My students had not yet been introduced to ligand field theory, HSAB theory, redox mechanisms, or the 18-electron rule; incorporation of those ideas would be an interesting extension to the activity if your class has already been prepared to discuss those theories. The paper also explicitly mentions the large number of structures in the RCSB protein data bank that make use of cobalt complexation. This could be another option for extending the exercise for an upper-level course.

Most of the students in my class are juniors or seniors, despite the fact that this is a 200-level course. Many of them have had organic and biochemistry, and several are biochemistry majors. Biological applications are of great interest to them, and bioinorganic chemistry was one of the favorite topics of the course. Students were excited to see class topics applied to current research problems. This paper was a nice example to foreshadow more advanced topics, and later served as a familiar reference point for discussions of inner and outer sphere binding mechanisms, redox chemistry, catalysis, and bioinorganic chemistry.

 

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