BINAP got me excited when I read about it at carbon-based curiosities. It's a molecule worth some calculation time in ArgusLab.
The structure was optimised with semiempirical PM3. I guess this should work fine here. You have to remember though that it is a gas phase calculation which may give strange results in some cases. But I guess it's ok here. In my defense I can say that crystalising a substance for x-ray diffraction may lead to unexpected results as well. Or is benzene not a regular hexagon (Proc. Roy. Soc. A270 (1964) 98-110)?
Anyway this is the structure. jmol is too cool. So I used it again. I am sorry if it takes a long time to load. But it should not make your browser crash if I put only one applet there.
The first thing you notice is that the two naphthalenes are in planes almost perpendicular to each other. It makes sense that they will move out of each other's way. Also the π-bond between the rings would be pretty weak even if the system were planar. You can see that from resonance structures. Or you do it the cool way and calculate the Hückel π-bond order. It is only .40 when every other bond has between .5 and .7.
This enantiomere is apparently called R. You look at the two naphthalene rings: if you want to walk upward you have a right turn. A helix scientist might call it left-handed. If he walks down, he has to turn left. You can also think of it as a lefty tighty, righty loosy screw.
The weird thing is: If you look at the molecule from a different perspective then the turn is the other way. But maybe this doesn't count because you can't walk through without jumping down in between.
Finding disordered residues in an NMR ensemble - Note to self: here's how you identified disordered residues in the NMR ensemble 2KCU.pdb 1. In Pymol: "fetch 2kcu" 2. Action > align > states (*/CA) 3. "...
1 week ago