Molecular Structure and Bonding

6 May 2019
Evaluation Methods: 
  • The instuctor walked around the classroom to help students individually as needed for immediate assessment.
  • At the end of the class period, students submitted their work to Blackboard for grading.
  • Assignments were graded based on accuracy and quality of the drawings.
Evaluation Results: 

Students generally were able to determine the molecular formula and generate connectivity drawings of the displayed 3-D structures, but really struggled with 3-D drawing. Although this was developed for a course with second year students who had completed general chemistry, even older students in the course struggled with this component. However, by the end of class, all students greatly improved in their ability to understand, interpret, and convey 3-D structure. 

Many students were surprised and many jokes were made about this being a chemistry art class. Although some students didn't particularly enjoy drawing, all understood the value and felt like they had learned something useful. At the end of the semester, many students remarked that the chemical drawing section was the most useful or interesting. 

Description: 

This in-class activity was designed for a Chemical Communications course with second-year students. It is the first part of a two-week segment in which students learn how to use Chemdraw (or similar drawing software) to create digital drawings of molecules.

In this activity, students are given a blank worksheet and 5 models of molecules were placed around the classroom. Students interpreted the 3-D models to determine molecular formulas, connectivity, and generate drawings that convey the 3-D elements. Once students completed the worksheet by hand, they generated the whole worksheet using Chemdraw.

Learning Goals: 

Students will be able to:

1.    Write the formula for a molecule based on a 3-D structure.

2.    Draw a molecule based on a 3-D structure.

3.    Convey 3-D structure of a molecule in a drawing.

4.    Translate molecular connectivity to a drawing that conveys 3 dimensions.

5.    Create digital drawings of molecules using Chemdraw or similar chemical drawing software.

Equipment needs: 
  • Molecular model set for the instructor to prepare structures before class.
  • One computer per student with chemical drawing software such as Chemdraw.
Course Level: 
Implementation Notes: 

Prior to the activity, students were given a brief presentation with an introduction to basic Chemdraw elements using the Chemdraw manual and existing tutorials (see links provided). VSEPR was also reviewed.

For the activity, students were given 3-D models of molecules, and the color key for atom identity was written on the board (eg. blue = oxygen, black = carbon...). The activity was conducted in a class of 24 students, in which each student had access to a computer. The entire class period was 1 hour 50 min, but the activity could be shortened if fewer molecules are included.

Before class, the instructor built models of molecules using a molecular model kit. It is helpful to have multiple copies of each molecule, especially for a larger class, but not critical. The molecules used for the acitvity can be seen in the faculty-only key, and were chosen to have a range of 3-D structures, but other molecules could be chosen. For example, a coordination chemistry or upper division course could have 3-D printed models of crystal structures used as the starting point. 

Time Required: 
60 min
7 Apr 2019

Encapsulation of Small Molecule Guests by a Self-Assembling Superstructure

Submitted by Shirley Lin, United States Naval Academy
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 two journal articles by the Rebek group on the synthesis and host-guest chemistry observed with the "tennis ball." 

Corequisites: 
Learning Goals: 

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

  • provide examples of supramolecular systems in nature that use reversible, weak noncovalent interactions 
  • define terms in supramolecular chemistry such as host, guest, and self-complementary
  • identify the number and location of hydrogen bonds within the "tennis ball" assembly
  • draw common organic reaction mechanisms for the synthesis of the "tennis ball" subunits
  • describe the physical and spectroscopic/spectrometric techniques used to provide evidence for assembly of a host-guest system
  • explain the observed thermodynamic parameters that are important for encapsulation of small molecule guests by the "tennis ball"
Implementation Notes: 

This LO could be used at the end of a traditional 2-semester organic chemistry sequence as an introduction to organic supramolecular systems, as an organic chemistry example within a discussion about inorganic supramolecular chemistry, or in an upper-division elective course about supramolecular chemistry. The LO topic, the "tennis ball," has a published laboratory experiment in J. Chem. Educ. (found here). Time permitting, instructors could have students read the article and complete the literature discussion before executing the experiment in the lab.

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

Time Required: 
depends upon implementation; minimum of 20-30 minutes for the literature discussion if students read an d answer questions outside of class
31 Jan 2019
Evaluation Methods: 

Students were evaluated informally as I walked around to help the groups as well as during presentations.

Evaluation Results: 

A large majority of the students had no problem making assignments for the simple and intermediate cases.  This outcome is largely a testament to the ease of use of the CBC method.  In fact, students who had no background in inorganic or organometallic chemistry tended to perform a little better because they were less likely to bring in preconceptions about "oxidation state".

Students struggled a bit with the Z-type Ga ligand, which is great because it helped them move forward in understanding the periodic relationship to Al and B.  Students also struggled a bit with the cyclic (alkyl)aminocarbene ligands in the cobalt dimer, since they had not seen those before.

 

Description: 

This in-class group activity extends my original post by providing more examples of varying difficulty for students to assign MLXZ classifications and electron counts to organometallic complexes.  The answers to these are unambiguous within the CBC system, but they provide excellent starting points for conversation with students about bonding formalisms with organometallics.

Learning Goals: 

* Students should be able to use the covalent bond classification method to assign MLXZ classifications to a variety of organometallic complexes.

* Students should be able to defend their assignments using both organic and inorganic views of structure and bonding.

* Students will understand the ambiguities associated with assigning bond orders, valencies, oxidation states, etc., with the hope that their understanding of covalently bonded organometallic systems will become more nuanced.

 

Course Level: 
Corequisites: 
Implementation Notes: 

I split students into groups of 3, as noted in the handout.  Since this was a small class, I used 10 problems (all 7 from this handout and 3 from the earlier activity) and each student presented one answer.  Students took about 25 minutes to work through the problems, and then I had the students present and encouraged questions and challenges to their assignments.  The students brought several interesting insights that deepened their understanding of bonding and the connection between Organic Chemistry (which they have all taken) and Inorganic/Organometallic Chemistry (which most of them have not seen).

 

Time Required: 
45 minutes
31 Jan 2019
Description: 

This set of slides was made for my Organometallics class based on questions about bridging hydrides and specifically the chromium molecule. I decided to make these slides to answer the questions, and do a DFT calc to show the MO's involved in bonding of the hydride. 

 

Corequisites: 
Learning Goals: 

A student will be able to explain bridging hydride bonding

A student will be able to perform electron counting on a chromium comples with a bridging hydride

A student will be able to interepret calculated DFT molecular orbitals. 

Time Required: 
15 min
Evaluation
Evaluation Methods: 

This was provided as supplementary material outside of lecture. 

28 Jan 2019
Evaluation Methods: 

Concepts covered during literature discussions will be included among exam materials.

Evaluation Results: 

N/A

Description: 

This Guided Literature Discussion was assigned as a course project, and is the result of work originated by students Joie Games and Benjamin Melzer.  It is based on the article “Next-Generation Water-Soluble Homogeneous Catalysts for Conversion of Glycerol to Lactic Acid” by Matthew Finn, J. August Ridenour, Jacob Heltzel, Christopher Cahill, and Adelina Voutchkova-Kostal in Organometallics 2018 37 (9), 1400-1409. It includes a Reading Guide that will direct students to specific sections of the paper that were emphasized in the discussion.  This article reports a systematic study of a series of homogeneous catalysts for the conversion of glycerol to lactic acid.

Course Level: 
Corequisites: 
Learning Goals: 

After reading and discussing this article, a student should be able to…

-       Apply the CBC electron-counting method to homogeneous catalysts.

-       Understand the effect of metal and/or metal oxidation state on catalyst activity.

-       Understand the effect of ligand and/or ligand charge on catalyst activity.

-       Understand the differences between microwave and conventional heating.

Implementation Notes: 

I am planning on assigning this LO as a graded in-class group discussion. Students will be given a copy of the article, reading guide, and discussion questions one week in advance. On the day of the discussion, students will be assigned in groups of 2-3. They will then have one lecture period to answer the questions in writing as a group. A portion of their grade (20%) is dedicated to literature discussions (4-6 over the course of the semester). The grading rubric involves 3 possible ratings for each question/answer: “excellent”, “acceptable”, or “needs work”. [This article is among the free-access ACS Editors’ Choice.]

Time Required: 
1 lecture period, with materials given one week in advance
28 Jan 2019
Evaluation Methods: 

A portion of their grade (20%) is dedicated to literature discussions (4-6 over the course of the semester). The grading rubric involves 3 possible ratings for each question/answer: “excellent”, “acceptable”, or “needs work”.

Concepts covered during literature discussions will be included among exam materials.

Evaluation Results: 

N/A

Description: 

This Guided Literature Discussion was assigned as a course project, and is the result of work originated by students Christopher Lasterand Patrick Wilson.  It is based on the article “Deca-Arylsamarocene: An Unusually Inert Sm(II) Sandwich Complex” by Niels J. C. van Velzen and Sjoerd Harder in Organometallics 201837, 2263−2271. It includes a Reading Guide that will direct students to specific sections of the paper that were emphasized in the discussion.  This article presents a study of the reactivity of bulky CpAr-Et/iPrSm complexes that is contrasted to the more well-known Cp*2Sm.

Course Level: 
Corequisites: 
Learning Goals: 

After reading and discussing this article, a student should be able to…

-      Be more familiar with the chemistry of sandwich samarocene complexes.

-      Understand how bulky ligands affect structure and reactivity in a sandwich complex.

-      Apply the CBC method to identify ligand functions and metal valence number/ligand bond number.

-       Understand how XRD bond distances can help determine a ligand charge.

Implementation Notes: 

I am planning on assigning this LO as a graded in-class group discussion. Students will be given a copy of the article, reading guide, and discussion questions one week in advance. On the day of the discussion, students will be assigned in groups of 2-3. They will then have one lecture period to answer the questions in writing as a group.  [This article is among the free-access ACS Editors’ Choice.]

Time Required: 
1 lecture period, with materials given one week in advance
12 Dec 2018

Foundations Inorganic Chemistry for New Faculty

Submitted by Chip Nataro, Lafayette College

What is a foundations inorganic course? Here is a great description

https://pubs.acs.org/doi/abs/10.1021/ed500624t

 

Prerequisites: 
Corequisites: 
Course Level: 
8 Nov 2018

5-ish Slides about Enemark-Feltham Notation

Submitted by Kyle Grice, DePaul University
Description: 

This is a basic introduction to Enemark-Feltham that can be used in conjunction with any literature that has Iron nitrosyls in it. I made this as a follow up to the work that came ouf of the 2018 VIPEr workshop in UM-Dearborn. 

Corequisites: 
Learning Goals: 

A student will be able to detemine the Enemark-Feltham label for a simple iron nitrosyl

A student will be able to describe bonding differences between NO+, NO, and NO- ligands. 

Implementation Notes: 

I haven't used this yet, but It can be a quick lecture module or online module to help students understand Enemark-Feltham before analyzing a paper on iron nitrosyls. 

Time Required: 
10 min
Evaluation
Evaluation Methods: 

I have not used this yet. 

Evaluation Results: 

I have not used this yet. 

25 Jun 2018

Orbital Overlap and Interactions

Submitted by Jocelyn Pineda Lanorio, Illinois College
Evaluation Methods: 

Evaluation was conducted by the instructor walking around the computer lab to check progress and address the issues students had.

Evaluation Results: 

This LO was implemented once in advanced inorganic chemistry composed of 5 chemistry major students. Students clearly identified the type of orbital interactions and differentiated bonding, nonbonding, and antibonding MOs. Students commented that this is a great in-class activity before the discussion of MOs for diatomic molecules (Chapter 5 of MFT).

Description: 

This is a simple in-class activity that asks students to utilize any of the given available online orbital viewers to help them identify atomic orbital overlap and interactions. 

Learning Goals: 

Following the activity, students will be able to:

  1. draw the s, p, and d atomic orbitals using the given coordinate axes
  2. analyze the orbital interaction by looking at their symmetry and overlap (or lack of)
  3. differentiate s, p, d, and nonbonding molecular orbital

 

Equipment needs: 

Internet connection and computer

Prerequisites: 
Corequisites: 
Implementation Notes: 

This activity should be run in a computer lab.

Time Required: 
15 to 20 minutes
23 Jun 2018
Evaluation Methods: 

Students answer several questions prior to the in class discussion. These answers can be collected to assess their initial understanding of the paper prior to the class discussion. Assessment of the in class discussion could be based on students’ active participation and/or their written responses to the in class questions.

Evaluation Results: 

This Learning Object was developed as part of the 2018 VIPEr Summer Workshop and has not yet been used in any of our classes, but we will update this section after implementation.

Description: 

This is a literature discussion based on a 2018 Inorganic Chemistry paper from the Lehnert group titled “Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases“(DOI: 10.1021/acs.inorgchem.7b02333). The literature discussion points students to which sections of the paper to read, includes questions for students to complete before coming to class, and in class discussion questions. Several of the questions address content that would be appropriate to discuss in a bioinorganic course. Coordination chemistry and mechanism discussion questions are also included.

 

Corequisites: 
Prerequisites: 
Learning Goals: 

A successful student will be able to:

  • Evaluate structures of metal complexes to identify coordination number, geometry (reasonable suggestion), denticity of a coordinated ligand, and d-electrons in FeII/FeIII centers.

  • Describe the biological relevance of NO.

  • Identify the biological roles of flavodiiron nitric oxide reductases.

  • Identify the cofactors in flavodiiron nitric oxide reductase enzymes and describe their roles in converting NO to N2O.

  • Describe the importance of modeling the FNOR active site and investigating the mechanism of N2O formation through a computational investigation.

  • Explain the importance of studying model complexes in bioinorganic chemistry and analyze the similarities/differences between a model and active site.

  • Write a balanced half reaction for the conversion of NO to N2O and analyze a reaction in terms of bonds broken and bonds formed.

  • Interpret the reaction pathway for the formation of N2O by flavodiiron nitric oxide reductase and identify the reactants, intermediates, transition states, and products.

 

A successful advanced undergrad student will be able to:

  • Explain antiferromagnetic coupling.

  • Apply hard soft acid base theory to examine an intermediate state of the FNOR mechanism and apply the importance of the transition state to product formation of N2O.

  • Apply molecular orbitals of the NO species and determine donor/acceptor properties with the d-orbitals of the diiron center.

Implementation Notes: 

This paper is quite advanced and long, so faculty should direct students to which sections they should read prior to the class discussion. Information about which parts of the paper to read for the discussion are included on the handout. Questions #7 and #8 are more advanced, and may be included/excluded depending on the level of the course.

Time Required: 
In-Class Discussion 1-2 class periods depending on implementation.

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