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. "When I see equations, I see the letters in colors – I don't know why.
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: I made the screen cast with Powerpoint, and there were many, many things I would change about if ppt would let me.
#HOW DO YOU INSTALL JMOL FOR MAC SOFTWARE#
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.
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. You can do the same party trick with rate constants by using transition state theory,Ī barrier of 6 kcal/mol?, why that's a whopping 10 9 per second! 20 kcal/mol? Here it's a good idea to sip your beer, to stall for time. 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. But at least you'll know that the answer is somewhere between 10 -3 and 10 -4, and that's often all you need. 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 if you routinely bring a scientific calculator to parties, then you have more serious problems to worry about anyway. You could of course use a calculator to get more accurate results, in which case you might as well use Eq (2). Respect, indeed! You'll be the life of the party. 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. Yes, with a little practice you will be able to amaze and astound your friends.Īn energy difference of 4.5 kcal/mol? Why, that means 0.001 times less B than A. Look under the Reactions category in the left-hand column.Įq (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. When I run the input file (which you can find here) that I make at the end of the screencast, GAMESS finds the TS in 20 steps (though I had to remove the $FORCE group which is inserted erroneously by Avogadro).įinally, Steven Bachrachs blog is another good source for TS structures (many images link to a Jmol display of the structure). But because the "TS part" of a TS is usually confined to a few bonds, one can use Avogadro to add substituents and create more complex TSs as well. This is done in the absence of solvent so for some reactions involving ions there is no barrier (and hence no TS) in the gas phase.īecause Jmol is used, the user can interact with the model, rotate, zoom, measure distances, and access the coordinates! That's right, ChemTube3D is also a transition state (TS) repository, and in the screencast I show how use Avogadro to extract the TS structure. Generally speaking, they are obtained by finding the TS of the reaction and then following the atomic forces downhill to reactant and products using the intrinsic reaction coordinate method. In case you are curious how Nick obtained the structures along the reaction path, you can find the detailed instructions here. I wish this has been available when I took organic chemistry, which, somehow, wasn't made any easier by the fact that half the reactions hadn't been discovered yet. This really drives home to the point that the static 2D pictures is meant to represent a dynamic 3D model.
I especially like the way the usual 2D representations of reactions are tied to the 3D animation: you click on 2D structures to see 3D structures and "electron pushing", and on arrows to animate the reaction.
#HOW DO YOU INSTALL JMOL FOR MAC FULL#
And I mean this quite literally, the site is full of wonders: Jmol-animated reaction mechanisms for the most important organic reactions. Nick Greeves has made a wonderful website called ChemTube3D.
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