Molecular Modeling Basics Reviewed on Amazon

Two reviews have appeared on Amazon: one on the Canadian site and one on the American site.  The latter one compares and contrasts MMB to Hincliffe's Molecular Modeling for Beginners.  As always, much appreciated!

Molecular Modeling Basics Reviewed in Journal of Chemical Education

A very nice review of the book (and mention of this blog) by John Shibata in J. Chem. Ed.  Much appreciated!

Molecular Modeling Basics Reviewed in ChemPhysChem

A very nice review of the book (and mention of the blog) by Ralf Tonner in ChemPhysChem.  Much appreciated. 

Computational chemistry exercises

Someone (I'll call him N. O'Boyle ... no, too obvious ... Noel O.) wrote me asking if I had any computational exercises I'd be willing to share. Since I took the trouble of writing him back, it occurred to me that I had free blog material. Here's my reply in a slightly edited form.

When I taught a computational chemistry course in Iowa I used exercises from "A Laboratory Book of Computational Organic Chemistry" by Warren Hehre et al., and Spartan in those pre-Avogadro days. Specifically experiments 4, 11, 34 and 76.  See here for an example.  The computational component of the other half of the course was individual research projects.

I would assign an experiment on a Monday, discuss it the following Monday, and have a write-up due  the Monday after that. I graded the first write-up (of exp 4) very lightly and then gave the student this example write-up of exp 4 so they could see how how to do it.  I also made this check list for a report and a list of questions for each experiment (taken from the book): exp 4, exp 11, exp 34, and exp 76.

Here in Copenhagen I co-teach a similar course with 5 other people, so I just get 1-2 exercises a year, and here I try to fit the content of the exercises in with the other instructors and the topic I cover. I teach the chapter on DFT and here I have developed an exercise using bond energies.

Sometimes I also teach the chapter on geometry optimization and then I use exp 76. Other instructors use Gaussian/Gaussview so that's what the student tend to use here too, so I have made no tutorials to go with the exercises.

"Exercises" in Molecular Modeling Basics: In Chapter 4 I illustrate applications of QM to various chemical problems, and Chapter 5 gives you some details of the underlying GAMESS input and output files (and there are now several blog posts with even more information on the various examples). The intent is that people can reproduce the results I present in Chapter 4 relatively easily.  Depending on the level of the course, reproducing these example may be challenging enough. Otherwise, one could easily come up with additional related problems. Let me know if that is of interest.

Many of the molecules and concepts are very P-chem oriented, i.e. uses small non-organic molecules to illustrate P-chem concepts, but there are some organic molecule/concept examples too: steric strain, hydrogen bonding, amide hydrolysis.  

Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

In this post I summarize the simulations and I have used in teaching thermo and stat mech, and talk a bit about how I use them.

I co-teach two quite similar courses on this topic: one for nano-students and another for chemistry and biochemistry students.  In the nano course we use the book Molecular Driving Forces by Dill and Bromberg, and in the other Quanta, Matter, and Change by Atkins, de Paula, and Friedman.  At the end of this post I have organized the simulations by chapter for each book.

Some of simulations I have made (or modified extensively) and most of these have been discussed in previous blog posts, so I simply give the link to the respective blog post where there is more information.

The other simulations are from the Molecular Workbench (MW) library of models, and here I provide links that will open in MW, so you need to install MW before clicking on the links.  For some of them I also provide a brief description of what concepts try to demonstrate using the simulations.

How do I use the simulations?
All simulations are used during lecture to visualize concepts, start discussions, and motivate equations. I'll take Illustrating energy states as an example: instead of saying "Molecules in a gas translate, rotate, vibrate, and ....", I say "Here is a zoomed-in view of butane gas where you can see the molecules.  You can see that individual molecules move differently.  How do they move differently?  Anyone?  Right, they have different speeds.  This kind of motion is called translation.  What else? ..."

Practical tips
On a very practical note, my own simulations are all on web sites and I make sure to open all of them before the lecture, while I have all the MW simulations for the course indexed on a single MW page (click here to open in MW). It is not possible to embed these simulations in Powerpoint slides, but you can switch between Powerpoint and other applications without quitting Powerpoint (on a Mac you use command-tab and on Windows i believe it is windowskey-tab).  Note that you need access to the internet in the lecture room.

While I have screencasts of most of simulations on the blog posts, I don't use these during lecture.  I think it is too passive, and puts the students to sleep.  But I believe the screencasts are a good way for the students to review the main points of simulations after the lecture.  I put links to the blog posts on the course web site and in the lecture notes.

Is using simulations a good idea?
If possible I try to use a simulation within the first five minutes of a lecture, and have a maximum of 20 minutes between simulations.  I now only have one (45 minute) lecture left where I don't use a single simulation and I can just feel how I loose the student's attention after about 30 minutes.  You can just see it.  That being said, no one has ever mentioned the simulations in their course evaluations (good or bad), so I have no hard evidence that it improves my teaching.  But I can tell you that I enjoy lecturing much more with the simulations, so unless I get complaints I'll keep doing it. 

Making room for simulations in the lecture
I have taught the topics for many years without any simulations, and was never at a loss for material to cover.  Lecture time is precious, and these simulations take time to present and discuss.  You really have to introduce the simulation carefully (don't rush this part!) before you start them, and very often you want the students to speculate about what will happen before you start them.  Furthermore, they tend to stimulate many more questions, that you can hopefully turn into a discussion instead of simply answering them, than derivations - that's the whole point.

So how do you "make room" for the simulations?  I have cut out most of the derivations from the lectures.  To pay for my sins, I provide relatively detailed (typed) lecture notes ahead of lecture (I generally don't use Powerpoint), which include step-by-step derivations. So I'll say things like "Starting with these assumptions we can write down this equation.  This can be rewritten as this equation, which is much simpler.  The details on how we got from here to there are in your notes, but note that in step 3 we assume that ... which is an approximation."  No complaints so far.  If only more progress had been made on simulating derivations ...

Here are the simulations organized by chapter

Molecular Driving Forces by Dill and Bromberg (1st edition)

Ch 6: Entropy and the Boltzmann distribution law
Illustrating entropy

Ch 10: Boltzmann distribution law
Polymer unfolding: The book uses two simple bead models of polymers in this chapter to illustrate micro and macrostates and model protein melting.  I use this example extensively both in lectures and homework problems.  So I made this simulation to illustrate how higher energy macrostates become more likely at higher temperatures.


Ch 11: Statistical mechanics of simple gasses and solids
Illustrating energy states
Energy states in the water molecule: a slightly more complicated molecule than HCl (used in Illustrating energy states) with more than one vibrational mode and 3 rotational degrees of freedom.
Internal energy and molecular motion
Entropy, volume, and temperature


Ch 12: Temperature, heat capacity
The molecular basis of differential scanning calorimetry: heat capacity and energy fluctuations

Ch 13: Chemical equilibria
Seeing chemical equilibrium (opens in MW)
Dalton's law of partial pressure (opens in MW)


Ch 14: Equilibria between solids, liquids, and gasses
Seeing specific and latent heat (opens in MW): I use this simulation to illustrate how the same substance can be solid, liquid, and gas depending on the temperature.
A gas under a piston (opens in MW): I use this simulation to show that, for example, decreasing the pressure can have the same effect as increasing the temperature.
The phase diagram explorer (opens in MW)
Raoult's law: ideal solutions (opens in MW): Here, I use the simulation of the pure liquid to illustrate vapor pressure.


Ch 15: Solution and Mixtures
Mixing gasses, and mixing of ideal and non-ideal liquids
Raoult's law: ideal solutions (opens in MW)
Raoult's law: negative deviation (opens in MW) 
Raoult's law: positive deviation (opens in MW)


Ch 16: Solvation and transfers of molecules between phases
Visualizing osmotic pressure in an osmotic equilibrium (opens in MW)
Desalination using reverse osmosis (opens in MW)




Quanta, Matter, and Change by Atkins, de Paula and Friedman (1st edition)

Ch 13: The Boltzmann distribution
Illustrating energy states
Energy states in the water molecule: a slightly more complicated molecule than HCl (used in Illustrating energy states) with more than one vibrational mode and 3 rotational degrees of freedom.
Internal energy and molecular motion

Ch 14: The first law of thermodynamics#
The molecular basis of differential scanning calorimetry: heat capacity and energy fluctuations
  
Ch 15: The second law of thermodynamics
Illustrating entropy
Entropy, volume, and temperature
  
Ch 16: Physical equilibria
Seeing specific and latent heat (opens in MW): I use this simulation to illustrate how the same substance can be solid, liquid, and gas depending on the temperature.

A gas under a piston (opens in MW): I use this simulation to show that, for example, decreasing the pressure can have the same effect as increasing the temperature.

The phase diagram explorer (opens in MW)
Raoult's law: ideal solutions (opens in MW): Here, I use the simulation of the pure liquid to illustrate vapor pressure.

Raoult's law: negative deviation (opens in MW) 
Raoult's law: positive deviation (opens in MW)

Mixing gasses, and mixing of ideal and non-ideal liquids 

Visualizing osmotic pressure in an osmotic equilibrium (opens in MW)
Desalination using reverse osmosis (opens in MW)

Ch 17: Chemical equilibria#
Seeing chemical equilibrium (opens in MW)
Dalton's law of partial pressure (opens in MW)

# I don't teach this part of the course, but if I did I would use these simulations

Related posts:
An Atkins Diet of Molecular Workbench 
One, Two, Three, MD 
Tunneling and STM (a first stab at using Molecular Workbench to teach quantum mechanics)

Molecular Modeling Basics reviewed in Chemistry World

A very nice review of the book (and blog!) by fellow blogger Henry Rzepa in Chemistry World.  Much appreciated.

The book is out

The book is now available for purchase, at least in the States. You can order it directly from CRC Press or, for example, from Amazon.com (though not yet Amazon.co.uk). And why just one copy? Christmas is practically around the corner.

Shameless book promotion

Things are happening on the book front. A snappy cover (at the top of the blog) and now a promotional flyer - with table of content - which can be downloaded here. The book should be out May 10, complete with non-interactive black-and-white versions of many of the figures found in this blog.

A sense of scale

In chapter 1 of volume 1 of the legendary Feynman Lectures on Physics, Feynman starts by imagining zooming in on a drop of water, past amoeba and so forth, until one can see the water molecules. Starting this way is genius. The tiny length scales and the associated invisibility of atoms and molecules is the single largest barrier to developing a chemical intuition - a barrier that molecular animation can help overcome.

I am often thought of bringing Feynman's imaginary magnification to life by animation, so I as very happy when Nathan Baker brought this site to my attention. The above screencast shows it in action, but the real fun is interacting with it yourself. It's a brilliant piece of interactive animation.

The site brought to mind the granddaddy of them all, Powers of 10, which some kind soul put up on youtube.

A useful equation

(1)

This is a useful equation. Remember it, and your life will change for the better. The equation comes from one of the fundamental equations of statistical mechanics,

(2)

as you can see here

Both equations tell you how the energies of molecule A (E_A) and B (E_B) determine how many molecules of each (n_A and n_B) you will observe at equilibrium.

Eq (1) is simply a much more useful form of (2) for room temperature conditions, because it gives you a feel for what the relative energies mean in terms of chemistry. Yes, with a little practice you will be able to amaze and astound your friends.

An energy difference of 4.5 kcal/mol? Why, that means 0.001 times less B than A. 6.0 kcal/mol? 0.0001! The trick is to recognize that 1.36 is close enough to 1.5, and that 4.5/1.5 = 3 and 6.0/1.5 = 4, meaning that the energies correspond to concentration ratios of roughly 10^-3 and 10^-4, respectively. Respect, indeed! You'll be the life of the party.

You could of course use a calculator to get more accurate results, in which case you might as well use Eq (2). But if you routinely bring a scientific calculator to parties, then you have more serious problems to worry about anyway.

The astute reader will note that I made things pretty easy for myself by picking 4.5 and 6.0 kcal/mol, and that dividing, say, 5, by 1.5 is no mean feat. But at least you'll know that the answer is somewhere between 10^-3 and 10^-4, and that's often all you need.

If you believe in the metric system () you may prefer to work in kJ/mol, in which case 1.36 should be replaced by 5.70 and approximated by 6.

You can do the same party trick with rate constants by using transition state theory,

A barrier of 6 kcal/mol?, why that's a whopping 10⁹ per second! 20 kcal/mol? Here it's a good idea to sip your beer, to stall for time ... 0.1 s^-1, of course! I usually count by 3's (2 times 1.5), 2o is close to 21, 7 times 3, 14 times 1.5, meaning 10^13-14, 10^-1. Get me: I'm Richard Feynman!

On a different note, I firmly believe that animations similar to the screencast in this post could be used to make derivations much more accessible to students. I haven't been able to find any software to do this and I think this is a gaping hole in the world of software. I made the screen cast with Powerpoint, and there were many, many things I would change about if ppt would let me.

In case the notion of animated derivations strikes you as crazy, I leave you with a quote from Richard Feynman's aptly named book What Do You Care What Other People Think:

"When I see equations, I see the letters in colors – I don't know why. As I'm talking, I see vague pictures of Bessel functions from Jahnke and Emde's book, with light-tan j's, slightly violet-bluish n's, and dark brown x's flying around. And I wonder what the hell it must look like to the students."

An Atkins diet of Molecular Workbench

In a recent post I showed an example of how to use Molecular Workbench (MW) in a p-chem lecture. The idea with that post was to keep it simple. Here I'll tell you what I actually prepared for the lectures, but the main point is really to draw your attention to the MW simulations, which are simply wonderful.

I had two back-to-back 45 minute lectures to cover chapter 16 in Atkins et al.'s Quanta, Matter, and Change on physical equilibria, i.e. phase changes and diagrams, chemical potential, colligative properties, ideal solutions, activity, etc.

So, I scoured MW for simulations related to these topics and created a new MW document with a list of the simulations I wanted to show during lecture (the screencast shows how), which can be found here. If you use MW as your "browser" loading new simulations is much faster than, say, powerpoint.

I'll say it again: rhe main point of this post is really to draw your attention to the MW simulations, which are simply wonderful. They really bring rather abstract points (like the deviation from non-ideality) or complex behavior (like osmosis) to life, and helps keep everyone awake (including myself). I should say that thermodynamics was not why I fell in love with science.

Btw, we're using Atkins Quanta for the first time, and I find it a great improvement over his P-Chem book in the thermo-department. Most references to steam engines and phase rules are relegated to various addenda in the back of the chapters. This was clearly a painful decision, as this quote attests to

"One [point] is that one of the most celebrated results in chemical thermodynamics. the phase rule, can be used as a basis of discussing the implications of the phase diagram, but it is not essential. It is described in Further Information 16.1."

I always found lecturing on steam engines and other celebrated results of thermodynamics a bit like Mr. Burn's attempt to send a telegram to the Prussian Embassy in Siam by first aerogyro: a tad dated. And on that note, I believe it is time to 23-skidoo.