Computer modeling

14 Jul 2014

The Synthesis and Characterization of a trans-Dioxorhenium(V) Complex

Submitted by Sibrina Collins, The Charles H. Wright of Museum of African American History
Evaluation Methods: 

One of the learning goals of this is to help the students develop effective writing skills. Thus, after completing the lab work, each student submits a laboratory report in the format of an ACS journal article. This experiment is worth 50 points, namely 35 points for the laboratory report, 10 points for notebook entries, and 5 points for their experimental plan(EP). The EP is their "ticket" for entry to the lab to complete the experiment.

Evaluation Results: 

I have created a rubric to evaluate the laboratory report. I make sure they adhere to formatting guidelines and sophistication of their ideas. I focus on how well they interpret their data. I tell them it is not my responsibility to explain their data! They have to tell a good story.  Approximately 40 students have prepared this compound over the course of two semesters (Spring 2013 and Fall 2013). In general, I have 2-3 "rock stars" per lab that write excellent/very good laboratory reports. Most students write lab reports that are considered good/very good.

Description: 

This experiment involves the preparation of a key starting reactant in high purity and yield for an ongoing research project, specifically for the development of potential photodynamic therapy (PDT) agents. The students synthesize [ReO2(py)4]Cl.2H2O using standard inorganic synthesis techniques. The students visualize the vibrations and electronic properties (e.g. molecular orbitals) of the compound using output files generated from density functional theory (DFT).

Course Level: 
Prerequisites: 
Learning Goals: 

A student will use spectroscopy (UV-vis, IR and 1H NMR) to show they have prepared the target compound.

A student will gain experience visualizing the molecular vibrations using output files generated from DFT.

A student will evaluate and analyze the experimental UV-vis spectra by comparing to the calculated DFT spectra.

A student will write a laboratory report in the format of the ACS journal, Inorganic Chemistry.

Equipment needs: 

CCD Array UV-vis Spectrophotometer, Thermo Scientific Nicolet 6700 FT-IR equipped with an ATR Sampler, Bruker 400 MHz NMR; GaussView software

Implementation Notes: 

The PDT agents I am developing that contain the [ReO2]+ core are based on the prototype, [ReO2(py)4]+(py = pyridine). This is a key reactant for my research efforts. The students enrolled in my inorganic chemistry laboratory synthesize this compound, as part of their curriculum. Thus, I am using classroom teaching as a means to enhance my research efforts. The students work in teams of 2-3 students to synthesize and characterize the compound.  The students are provided with the output of the DFT results to visual MOs and vibrations of the target molecule. I have included the calculated IR and UV-vis spectra in the powerpoint slide (CollinsSynthesis2014.pptx) for the instructors. The idea is for the students to compare their experimental data an compare it to the calculated data and discuss this in their report. I have also included a word document (Collins2014SupportingInformation.docx) that provides the coordinates (xyz) for the optimized geometry.

Time Required: 
Two three hour lab periods.
30 Apr 2014

Inorganic Spectroscopy Introduced Using an Interactive PhET Simulation (Part 1)

Submitted by Alycia Palmer, The Ohio State University
Evaluation Methods: 

The learning goals were informally assessed through conversations between the facilitators and students during both class periods (for this and the related LO). Also, student worksheets were collected after class to analyze student responses. Finally, students were asked to complete a survey about the activity and if they feel that the PhET activity should be used in future classes to introduce the topic of inorganic spectroscopy.

Evaluation Results: 

Students were engaged with the Molecules and Light activity which utilized the PhET simulation. Groups of 3-4 students are a good size to encourage all students to be involved in discussion. On the portions of the worksheet that asked for generalizations, the responses were vague and only scratched the surface. In the future, the instructor may wish to lead a class discussion to brainstorm for ideas about which features of molecules make them reactive to the four types of radiation in the simulation.

At the end of the second class period (after the second activity described in the related LO), students were asked to evaluate the PhET simulation and accompanying worksheet. Eleven (out of 16) students responded that the simulation should be used in future classes to provide background before topics about inorganic spectroscopy are discussed. Only one student said that it shouldn't be because it only introduced basic concepts. Four students either did not answer or did not take a definite stance.

Overall, students were satisfied with the PhET simulation and the accompanying worksheets. Also, based on the student responses to the worksheets, the instructors feel that the learning goals were met.

Description: 

A guided-inquiry activity for the interactive PhET simuation "Molecules and Light" was created to introduce upper-level inorganic laboratory students to inorganic spectroscopy. The activity included here is the first part of a two-day discussion. This activity instructs students to use the PhET simulation "Molecules and Light" to explore how various molecules interact with different energies of electromagnetic radiation (microwave, infrared, visible, ultraviolet). This activity can also be used in a general chemistry setting as the topics discussed are very basic.

The PhET simulation "Molecules and Light" was chosen because it integrates with the inorganic laboratory "Linkage isomerism of nitrogen dioxide." The simulation helps students to visualize how nitrogen dioxide gas interacts with infrared light, and in the laboratory, students collect FT-IR spectra of nitrogen dioxide coordinated to a metal.

The second part of the activity ("Inorganic Spectroscopy Introduced Using an Interactive PhET Simulation (Part 2)") builds on topics learned by interacting with the PhET simulation. That activity is most useful for upper level inorganic laboratory students who will be performing spectroscopy experiments. Materials for Part 2 are also shared on VIPER.

A special thank you goes to the other contributors of these activities: Julia Chamberlain, PhD; Ted Clark, PhD; and Rebecca Ricciardo, PhD

 

Learning Goals: 

Students should be able to:

  • describe how a set of example molecules interacts with light of varying energy
  • identify characteristics of molecules that are associated with an interaction with light
  • construct a set of guidelines that generalize how molecules react with light of varying energy (microwave, infrared, visible, ultraviolet)
  • apply these guidelines to predict the reactivity with light for a small molecule which is not in the simulation. The instructor may wish to assign molecules that are shown in another simulation "Molecule Polarity" in order to provide nice visualizations. These include: ammonia, hydrogen cyanide, formaldehyde, methane, CF4, and CH2F2.
Equipment needs: 

In order for students to successfully use the PhET simulation, one computer is suggested per 3-4 students.

 

Prerequisites: 
Corequisites: 
Implementation Notes: 

Facilitator notes are included as comments on all documents and can be viewed by selecting "Show Comments" under the review tab in Power Point or "Show all markup" under the review tab in Word.

This activity was implemented in a lecture setting with a class of 16 students. The group work was implemented during the 1-hour class that meets weekly and accompanies the 3-hour inorganic laboratory. Students were instructed before class to bring their own computer and to download the simulation.

Time Required: 
One 55-minute class period
25 Mar 2014

'Sophomore' symmetry: Computational analysis

Submitted by Chip Nataro, Lafayette College
Evaluation Methods: 

The lab report had four questions that needed to be addressed.

The MO diagrams constructed using LGOs assessed using the following criteria.

  • Assignment of a point group to the molecule.
  • Assignment of the generator functions.
  • Assignment of the LGOs including determining which orbitals could hold lone pair.
  • The qualitative MO diagram constructed by the students.

 Inclusion of the MO pictures from Spartan ’10 was a point of emphasis.

The final two questions asked the students to compare the computational and LGO results. They were also required to make comparisons between similar molecules. In particular, their ability to notice similarity in orbital shapes, the distribution of MOs and the relative energy of MOs was emphasized.

Evaluation Results: 

In general, students did a very good job with the first two questions. They were able to generate qualitative MO diagrams using LGOs quite effectively. They did struggle a little with the tetrahedral molecules and the three equivalent T2g orbitals. But they did come to my office to ask about that when they had trouble. They also struggled a little with the assigning the lone pair of ammonia. Again, I was able to clarify this when they came to my office with questions.

 

I was disappointed in their ability to compare and contrast their results. None of the groups considered looking at orbital energies from the DFT calculations as a point worthy of consideration. Perhaps that is due to the qualitative aspect of using LGOs. That is a point I will have to emphasize in the future.

Description: 

Having been inspired by a number of wonderful LOs, I introduced group theory in my 'sophomore' inorganic class this spring. In addition to learning to determine the point group of a molecule, students were taught how to construct a qualitative MO diagram though the use of LGOs. While this course can be taken with or without the laboratory component, it seemed only natural to include a lab on this material. A previous lab had introduced the students to computational methods for geometry optimization. This is a natural extension of that lab and a very nice means of visualizing the material being presented in lecture.

Corequisites: 
Prerequisites: 
Course Level: 
Learning Goals: 

Students should be able to

  1. Draw molecules and assign the point group
  2. Use a character table to derive generator functions
  3. Determine LGOs for their molecules
  4. Construct a qualitative MO diagram
  5. Use DFT calculations to generate a MO diagram
Equipment needs: 

Computers with the ability to do DFT calculations

Implementation Notes: 

The calculations should not take too long since the molecules are small.

 

The molecules covered in class are BH3, H2O and PF5. A detailed examination of these can be found in the 'Sophmore' symmetry: Lecture materials LO that can be found in the related activities.

 

 

Time Required: 
3 hrs
5 Feb 2014

Molecular Orbital of Transition Metal Complexes

Submitted by Steven Neshyba, University of Puget Sound
Evaluation Methods: 

Students are asked to summarize their analyses carried out during their investigations. Central to that analysis is identification of the five metal-centered d-orbitals (d-MOs) in the transition metal complex, based on the shape and degeneracies of those MOs. In addition, students are asked to write responses to the following self-assessments:

  1. Define the terms transition metal cation complex, crystal field splitting, metal-centered d-orbitals, sigma antibonding geometry, pi antibonding geometry, doubly degenerate, and triply degenerate.
  2. Describe shape and energy differences between n-d-MO, s*-d-MO, and p*-d-MOs, with an example.
  3. Describe qualitatively how sigma and pi antibonding affect the crystal field splitting (Δo) and the wavelength of absorbed light.

 

Evaluation Results: 

On exams, when shown pictures of transition metal complex MOs, most students were able to pick out those that correspond to the "metal d orbitals", even when those MO contained considerable ligand character. About 1/2 of students were able to accurately distinguish sigma-antibonding vs pi-antibonding character in these MOs.

In conversations, most students also appeared to clearly understand broader ideas associated with MO theory, e.g., the idea that an MO shows how electron density is distributed over various parts of a molecule, and that these orbitals can contain up to two electrons.

During the activity itself, many students initially struggled with mechanics of interpreting the data as presented by Spartan, i.e., what the energy ladder means, where the energies (in eV) are given. For some, more substantive questions arose regarding the difference between the colors associated with different part of an MO (i.e., the phase of the wave function) vs the coloration in an electrostatic potential mapping; as long as enough time is set aside for the activity, these questions provide opportunities for interesting and in-depth discussion.

Description: 

Students construct computer models of two transition metal complexes, solve their electronic structures, and inspect the resulting d-type molecular orbitals to identify which are non-bonding, sigma* antibonding, or pi* antibonding. After constructing a molecular orbital diagram, they determine which of the two complexes is likely to absorb light at a longer wavelength.

Learning Goals: 

Students should be able to

- carry out electronic structure calculations of transition metal cation complexes

- identify d-type orbitals within a transition metal complex

- explain the role of pi-antibonding orbitals in reducing the crystal field splitting

Corequisites: 
Equipment needs: 

The exercise is designed to be run on a laptop with Spartan Student version 5.0.1

Prerequisites: 
Subdiscipline: 
Topics Covered: 
Implementation Notes: 

This learning object is the third in a series of Spartan-based modules in an integrated general chemistry course*. In the preceding two modules, students learn to interpret electrostatic potential mappings of molecules ("Intermolecular forces") and to interpret molecular orbitals ("The MO picture of bonding"). Thus, it is assumed for this activity that students come in already familiar with how to build molecules in Spartan, and how to interpret simple molecular orbitals and orbital diagrams.

*This course is directed at students who took a significant amount of high school chemistry (e.g. AP Chemistry). It is not assumed students have prior expertise in electronic structure calculations, however.

Time Required: 
In-class time is 1-2 hours, assuming 1-2 hours pre-lab work
24 Jan 2014

Student choice literature-based take home exam question

Submitted by Hilary Eppley, DePauw University
Evaluation Methods: 

This question was 30 points on a 100 pt take home exam (the year I did this, there was also a 100 point in class exam as well).   I've included the title page of the take home exam as well as this question.   

The grading scale allowed most of the points for the student chosen course content to highlight.   Of the 30 points, 10 focus on chemical information skills, 20 on summarizing the article and analyzing it using concepts from the class.   

Evaluation Results: 

I gave back a number of the exams before I was able to tally, but of the ones I had remaining: 

60% got full credit on the part a (those who missed neglected to include a summary) 

100% got full credit on part b

60% got full credit on part c (those who missed searched by formula rather than connectivity or provided an insufficient explanation of what they searched on 

100% got full credit on part d

On part e, answers varied widely from 7/17 to 15/17, with an average of 12/17 or a 70%.  

In some cases they lost points for just repeating things verbatim from the paper without explaining them to show they understood the concepts.   The main reason for loss of points however was just a lack of effort at picking apart the paper for parts that were relevant to the course content.   

They were able to successfully apply things such as electron counting and mechanism identification in a catalytic cycle, point groups, descriptions of sigma and pi bonding in ligands.   

 

Description: 

During my junior/senior level inorganic course, we did several guided literature discussions over the course of the semester where the students read papers and answered a series of questions based on them (some from this site!).  As part of my take home final exam, I gave the students an open choice literature analysis question where they had the chance to integrate topics from the semester into their interpretation of a recent paper of their own choice from Inorganic Chemistry, this time with limited guidance.  I also included a number of questions that required them to make use of various literature search tools to show that they had mastered those skills.   I gave them a list of topics that they could incorporate, but based on the poor quality of the responses I received, I encourage you to be more specific in your instructions.  I'd love to see some new versions!      

Corequisites: 
Course Level: 
Prerequisites: 
Learning Goals: 
Students will
  • choose a recent paper that interests them from Inorganic Chemistry
  • summarize why a particular paper is important to the field of inorganic chemistry
  • use literature search tools including Web of Science, Cambridge Structural Database, and SciFinder Scholar to find information aobut cited references, structurally similar compounds, and the authors of the paper
  • integrate ideas such as bonding models, symmetry, spectroscopy structural data, and chemical reactivity from class into a detailed analysis of aspects of the paper

The instructor will

  • get up to date on new literature for possible new literature discussions
  • get a chance to stretch his/her own intellectual muscles on some papers perhaps outside of his/her area of expertise
Implementation Notes: 

The students were given the take home exam about 1 week before it was due (but that was during the final exam period).   The format of the chemical information questions were similar to things they did earlier in the class, however the analysis of the paper was much more open ended, giving them the freedom to choose a paper that interested them and to presumably focus on concepts from the class that they felt comfortable with.   I gave them a date range from April 1 - April 30, 2012 for their paper because those were the most recent issues at the time.  If you use this LO, you will probably want to change those dates to more recent ones.   

Time Required: 
at least an hour, possibly more depending on the student
26 Jun 2013

Chimera - A Molecular Modeling Program

Submitted by Walter Flomer, St. Andrew's University
Description: 

Chimera is a program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can also be generated. Chimera includes documentation and tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera was developed at UCSF and was funded by the National Institute of Health.

Homepage - http://www.cgl.ucsf.edu/chimera/

With Chimera, you can built simple molecules for viewing, which by itself is a good program.  The real power of Chimera is to find, download and view large biomolecules.  With protein structures, you can highlight inidividual amino acids, the alpha chains, or the active site.

The program is open source (freeware).

 

Prerequisites: 
Corequisites: 
Learning Goals: 

Students should be able to build and view the 3-d aspect of small molecules.

Students should be able to download and view biomolecules.

Implementation Notes: 

In using this program in General Chemistry, the students should be able to visualize the structure of simple molecule and understand the bond angles.  The more important use of the program is to bridge biology and chemistry for the first-year students.

25 Jun 2013
Evaluation Methods: 

Students write a formal report which is evaluated with respect to whether each learning goal is achieved.

Evaluation Results: 

Earlier versions of this project have been assigned to approximately 30 students in three senior-level inorganic chemistry courses over a six year period, with substantial revisions made each time. Students were generally able to reproduce the literature results successfully and to gauge which method is expected to be most reliable for first-principles calculations of redox potentials. There was some variability in students’ choice of fullerenes which appropriately span the range of interest. Some students were able to make fairly sophisticated suggestions for future work. 

Description: 

In this project students are asked to reproduce published calculations of molecular orbital energies of a series of derivatized fullerenes and correlate them with published reduction and oxidation potentials obtained from cyclic voltammetry. The particular subset of the derivatives to be studied are chosen by the student and this choice is part of the learning activity. The students then carry out additional calculations using other theoretical models to see whether they improve the correlation between computed and experimental properties. Interpretation of the trends and suggestions for additional work are discussed in a formal report. 

Corequisites: 
Learning Goals: 

After completing this project, students will be able to

  • Summarize the use of cyclic voltammetry to measure redox potentials;
  • Use computer software to build and visualize molecular models of derivatives of buckminsterfullerene;
  • Carry out density functional theory and semiempirical calculations of buckminsterfullerenes;
  • Discuss how derivatization affects the energies of the frontier orbitals;
  • Implement different theoretical models and correctly choose the one which best correlates with the experimental data;
  • Discuss which computational method is likely to be most useful in the prediction of redox potentials from first principles; and
  • Write a formal report describing their findings.
Course Level: 
Equipment needs: 

Modern computer workstation with 6+ GB RAM; molecular structure building and visualization software; quantum mechanics software. Spartan 8 has all of the capabilities required for this project.

 

Implementation Notes: 

The models are built and the calculations are carried out at our institution using Spartan 10, but Gaussian, GAMESS, Q-Chem, NW-Chem or other programs with similar capabilities could be used instead. 

Time Required: 
Students are asked to complete this as an independent project, although the work could be done as a group in one or two laboratory periods if a computer classroom is available.
24 Jun 2013

Symmetry, Group Theory, and Computational Chemistry

Submitted by Joanne Stewart, Hope College

These Learning Objects were used in an advanced undergraduate chemistry course that used computational chemistry as an integrative tool to help students deepen their understanding of structure, bonding, and reactivity and practice their integrative expertise by addressing complex problems in the literature and in their own research.

Corequisites: 
Course Level: 
1 Apr 2013

Online Courses Directory

Submitted by Adam R. Johnson, Harvey Mudd College
Description: 

This website is a free and comprehensive resource that is a collection of open college courses that spans videos, audio lectures, and notes given by professors at a variety of universities. The website is designed to be friendly and designed to be easily accessed on any mobile device.

Course Level: 
Prerequisites: 
Corequisites: 

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