Illustrating enthalpy, entropy, and free energy changes using MD

Here is a video I made that uses an MD simulation I found on Youtube to illustrate enthalpy, entropy, and free energy changes. I also use the simulation in these two videos (here and here) to illustrate enthalpy and entropy changes separately.  The videos are part of a series that I am working on.



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Peer instruction questions for DFT

Peer instruction questions for DFT from molmodbasics

Readers of this blog will know I am a fan of using peer instruction in teaching and I am happy to say that, as of this week, I am using peer instruction instruction in all the courses I contribute to.  This week I covered DFT in our Computational Chemistry course (which is the only week I currently contribute).

In the past I have always lectured, straight from the DFT section in my book, which the students get a copy of beforehand; all because I simply couldn't think of good multiple choice questions.  But now I use Socrative for polling, which has a very nifty "short answer" option: I ask a question, the students discuss and type in their answer, once finished they then get to vote for their favorite answer, and, once finished, I discuss some of the answers (including why some answers are wrong).  You can see the questions I asked above.

Of course this means the students have to prepare for class beforehand.  I had them read the electron correlation and DFT sections from my book, a perspective article by Kieron Burke, and the DFT chapter from Frank Jensen's book.  In addition they had to watch David Sherrill's video lecture on DFT:


I am very happy with the way the process went.  I'll definitely do it this way from now on.

Peer instruction questions for very basic molecular quantum mechanics

As I mentioned in my previous blog post I this year I made some screencasts of lectures to free up time for peer instruction questions.  Here are the peer instruction questions I used.

Peer instructions questions for basic quantum mechanics from molmodbasics

This time I tried Socrative for voting, which allows students to type in short answers to questions.  I can then select some of the questions and have students vote on their favorite.  This is what's happening in slide 13 and 23.

You'll notice I also made use of Molecule Calculator, which is introduced here.  Next year I have to remember also to assign the MolCalc intro video.




This work is licensed under a Creative Commons Attribution 3.0 Unported License.

Peer instruction questions: internal energy

Peer instruction questions: internal energy

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These slides show questions I used when teaching internal energy using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

The slide use a Molecular Workbench simulation you can access here (or download here once you have MW installed), and is further described in this blog post.

I start and carefully explain the simulation on the left, then ask what we will see when we start the simulation on the right.  Then vote, and explain answer.  Then finally run the simulation on the right.  

Related blog posts
See all posts related to peer instruction here.
Internal energy and molecular motion
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Peer instruction: mixing

Peer instruction questions: mixing

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These slides show questions I used when teaching mixing functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slides 1-3 show results from a Molecular Workbench simulation, which you access here.  It is a variation on the simulation I used to illustrate entropy.  If you understand why the gas expands in that example, you also understand why the gasses mix.

Slides 4-10 show results from a Molecular Workbench simulation, which you access here.

Slides 4-5: after two votes there was no clear consensus, but most students likes A "no interactions between molecules".  The second vote came at the end of the first of three back-to-back lectures, so we had a third vote after the break.  There really was intense discussion of this during the break, when most finally settled on B "equal interactions between molecules".   I think A was popular because "ideal solution" conjures up an analogy to "ideal gas", but how can you have a liquid if there are no intermolecular attractions?

Slide 7-8: here is alternated between the simulation and the question a few times.  A better approach would have been to include the question on the web site with the simulation.

Related blog posts
See all posts related to peer instruction here.
Illustrating mixing
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Peer instruction: radial distribution functions

Peer instruction questions for radial distribution functions

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These slides show questions I used when teaching radial distribution functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slide 8: The hint is given after the first vote.

Slides 11-18 show results from two Molecular Workbench exercises, which you can download here and here, once you have installed Molecular Workbench on your computer.

Slide 11: First I run the solid simulation, then pose the question and have a couple of votes, then click on the "show pair correlation function" in the MW simulation.  Note that you have to run for at least 100,000 fs to get good statistics (i.e. relatively smooth curves).  Then I explain the answer (slides 12 and 13)

Slide 14: Same procedure as slide 11, but for the liquid.

Slide 16: No vote, since the answer is pretty obvious, but I do ask where the peak at r = ~1.5 Å comes from.  Of course it comes from the attractive part of the Lennard-Jones potential, and you can clearly see some particles sticking together in the gas simulation.  To check, I change the depth of the well from 0.1 eV to 0.001 eV (simply double-click on any of the particles, and you will see what to do), re-run the simulation, and show the radial distribution function (summarized in slide 17).

See all posts related to peer instruction here.

Peer instruction: entropy

Peer instructions questions on entropy

View more presentations from molmodbasics

These slides show questions I used when teaching entropy using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

The slides refer to two Molecular Workbench simulations, which you can access here and here, and read more about here and here.

Specific comments to the slides
Slides 1-5: Here I start the simulation without removing the separator.  Then pose the question, two rounds of votes (usually not needed for the first simulation with 100 particles, as more than 80 % submit the correct answer), then remove the separator and explain.

Slides 10-15: Here I run the first simulation (small volume, low temperature) and carefully explain what the recorded times mean and how they correlate with probability.  Then I pose the first question (slide 10), two rounds of votes, then run the double volume simulation, then summarize the right answer (slide 11), and explain it (slide 12).  Same process for doubling the temperature.

See all posts related to peer instruction here.

Related blog posts
Illustrating entropy
Entropy, volume, and temperature
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Peer instruction: force fields and energy minimization

Peer instruction questions on force fields and energy minimization

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These slides show questions I used when teaching force fields (slides 1-4) and energy minimization (slides 5-8) using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate.  Many of the equations are discussed in Sections 1.5 and 2.1 of Molecular Modeling Basics.

I also use the Avogadro program when teaching force fields.  See for example this post.

I have made a Jmol model to illustrate energy minimization, as discussed in this post.


See all posts related to peer instruction here.

Molecular modeling and peer instruction

Last Tuesday I had my first go at using peer instruction.  Peer instruction is a fancy term for a relatively simple process:

1. Put up a multiple choice question
2. Ask the students to come up with an answer without talking to each other. Give them 2-3 minutes.
3. Have a vote (more on how below)
4. If 80 % or more get the right answer, show the right answer, give a short explanation, and move on.
5. If less than 80 % get the right answer, ask the students to discuss it with their neighbor. Give them 3-5 minutes.
6. Have another vote.
7. Give them the right answer and explain it.

Voting using Polleverywhere.com

The screencast (best viewed in full-screen mode) shows how I use the website Polleverywhere.com for the voting.  It requires the students to have access to a browser, so I ask them to bring a smartphone or a laptop to class.  It is also possible to submit votes by SMS, but Polleverywhere only provides a British phone number for Europe, so this gets pricey in Denmark.

The free version of Polleverywhere.com can register up to 30 votes.  For larger classes your department needs to buy a six or 12 month subscription, the latter is about $900.  You just create an account on the site, create your poll, and you are ready to go. 

All my questions have four options labelled A, B, C, and D, so I just create one poll per course.  The example in the screencast is used in a course called KemiF1, so the codes for the options are kemif1A - kemif1D.  You do need to create completely unique codes.  The site assigns you numerical codes by default, so you can also just use those.  The website with the question is here.  Option D is "don't know".  It is important to have that option so that everyone casts a vote every time.

I thought it would be cool for the students to see the votes coming in live, but they felt it biased their vote too much, so it is better to leave the question up as they vote, and show the results when the vote is done.  You can monitor the progress on the vote on another device such as a smartphone or iPad.

Why use peer instruction?
Much has been written about peer instruction (just google it), but I find the two videos posted here especially informative.  And think about this: if you lecture on organic chemistry and less than 80 % of your students understand what you mean when you draw a hexagon, is there really any point in going on to more complicated material?


Peer instruction and molecular modeling
The real challenge when using peer instruction is to come up with good questions and I think molecular modeling and visualization can contribute a lot here.  For example, the spinning models in the example  reinforces the fact that cyclohexane is not planar.  Note that the students can go to the page and interact with each model as they mull their options.

I will show more examples of using molecular modeling and peer instruction in future posts.