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Freshman Organic Chemistry

Freshman Organic Chemistry - Freshman Organic Chemistry...

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Freshman Organic Chemistry: Lecture 35 Transcript December 5, 2008 << back Professor Michael McBride: At the end last time we asked the question whether molecular mechanics programs are useful? And the answer is yes; in fact, they're really nowadays indispensable for evaluating the energy of molecules and their shapes. But are they true? Are they really fundamentally correct, the same way we believe quantum mechanics to be fundamentally correct? And the answer to that is certainly no. We already saw how they depend on so many arbitrary parameters that are just adjusted to try to fit data from some molecules. And then there's the hope that they'll fit other molecules, and sometimes they do and sometimes they don't. They usually do pretty well, but there can be special cases that differ for some reason, and it's hard to predict those ahead of time. So one has to look at them with a certain grain of salt. Okay? A good example of where they're demonstrably incorrect is in the question of van der Waals radii; for example, the contact between two bromine atoms that are not bonded to one another. So we're going to make a plot showing a bromine attached to carbon, and we're going to do this in the same spirit that Dunitz and his crew looked at amines attacking carbonyls. We're going to look at many, many crystal structures, and we're going to have -- we're going to rotate the various structures so that they have a C-Br bond that lines up right there. And then we're going to see how far it is to the nearest neighboring bromine, from some other molecule. Okay? And now what would we expect? Well there's a certain van der Waals radius for bromine. So the next neighbor should have its bromine in contact with that one. So we should go that radius again, to get to a neighbor. And there should be various directions, of course, where the neighbor could be, but always at that same distance, if they're in contact with one another. Okay? So there should be an arc of a circle, like that. So if we make these -- if we rotate these various crystal structures that have been determined, so the C and Br line up there, and the other Br lies in the plane -- the neighboring Br from another molecule -- then the closest they should get is along that dashed red line. Now, of course, there could be others that are further away, that aren't in contact. And in fact there could be some that are a little bit closer. You'd really expect some to be a little bit closer. Because there's van der Waals attraction, out to infinite distance; at least to great -- to substantial distance, much further than where they're actually in contact. They're attracting one another. So this bromine is part of a molecule that has many atoms in it, and the other bromine is part of a molecule that has many atoms. And all these other atoms are attracting one another, pulling toward one another. Now, of course, it would just collapse, except for the fact that the ones, the closest ones, run into one another. But that means that they should get slightly closer than just precise contact, because they're being pushed together by all the other atoms in those molecules. So we would
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