Computer modeling

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: 
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)
8 Jun 2019

VIPEr Fellows 2019 Workshop Favorites

Submitted by Barbara Reisner, James Madison University

During our first fellows workshop, the first cohort of VIPEr fellows pulled together learning objects that they've used and liked or want to try the next time they teach their inorganic courses.

23 May 2019

Teaching Computational Chemistry

Submitted by Joanne Stewart, Hope College

This is a series of in-class exercises used to teach computational chemistry. The exercises have been updated and adapted, with permission, from the Shodor CCCE exercises (http://www.computationalscience.org/ccce). The directions provided in the student handouts use the WebMO interface for drawing structures and visualizing results. WebMO is a free web-based interface to computational chemistry packages (www.webmo.net).

Prerequisites: 
Corequisites: 
23 May 2019

CompChem 05: Infrared, Thermochemistry, UV-Vis, and NMR

Submitted by Joanne Stewart, Hope College
Evaluation Methods: 

This exercise takes longer than a 50 minute class period, so we get as far as we can in one class and the students complete the exercise as homework. Students write their answers to the questions directly on the handout. Tables are provided for recording numerical results, but because of some (simple) required mathematical manipulations, it is easier if students set up a spreadsheet and record their numerical results there. The handouts with their answers and printed copies of their spreadsheet are collected in the next class.

Evaluation Results: 

In Exercise 1, the vibrational spectrum of formaldehyde is calcuated by three different methods. Because the vibrational modes come out in a different order, energy-wise, in one of the methods, students have trouble keeping track of which vibration is which. Each mode is labeled with the correct symmetry label, which should help them. Plus, they can click on each mode and visualize it.

Exercise 2 involves calcuating delta H for an "isodesmic" reaction: one in which the total number and type of bonds is the same in reactants and products. This helps cancel any systematic errors in the calculations. If this is one of the first time that students have worked in "hartrees," it is helpful to explain that unit to them. Students compare semi-empirical calculations with HF and DFT, and in this example, the HF and DFT calculations give much more accurate results.

Exercise 3 is about calculating UV-Vis spectra, but more importantly it walks students through drawing more complicated molecules. The CIS/ZINDO approach is used for the UV-Vis calcuation, which may not be highly accurate, but is very fast, so students get rapid results that they can compare.

In Exercise 4, students calculate NMR spectra for three different molecules. It teaches students about chemical shifts, but it does not cover coupling constants. If students are experienced with NMR, the averaging of proton resonances (such as the three protons in a methyl group) has become second nature to them. This exercise forces them to think about how those resonances are averaged.

 

Description: 

This is the fifth in a series of exercises used to teach computational chemistry. It has been adapted, with permission, from a Shodor CCCE exercise (http://www.computationalscience.org/ccce). It uses the WebMO interface for drawing structures and visualizing results. WebMO is a free web-based interface to computational chemistry packages (www.webmo.net).

In this exercise, students perform infrared, thermochemistry, UV-Vis, and NMR calculations. They compare the results from different methods and basis sets to experimental values.

The exercise provides detailed instructions, but does assume that students are familiar with WebMO and can build molecules and set up calculations.

Learning Goals: 

Students will be able to:

  1. Calculate an IR spectrum. Visualize the normal modes. Use appropriate scale factors to “correct” the calculated values.
  2. Calculate NMR spectra and average the chemical shift values for the static structures (in 1H NMR) to approximate the experimental spectrum.
  3. Calculate UV-Vis spectra.
Equipment needs: 

Students need access to a computer, the internet, and WebMO (with Mopac and Gaussian). 

Course Level: 
Corequisites: 
Implementation Notes: 

I use this as an in-class exercise. Students bring their own laptops and access our institution's installation of WebMO through wifi.

Time Required: 
2 hours

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