High-resolution images of a molecule as it breaks and reforms chemical bonds • Hacker News Board

Re: High-resolution images of a molecule as it breaks and reforms chemical bonds

#31

Post by RDeckard » Sun, Jun 02, 2013, 7:34 AM UTC

Komodo9 wrote: post #26

mtdewcmu wrote: post #20

Earlier quoted context omitted.

The short answer for why benzene rings are common is aromaticity, which makes it a very stable structure. Rings with fewer than 6 members are uncommon in chemistry, because the angles are not what the bonds naturally want to be and so they are increasingly unstable. As for nature in general, you could probably come up with a convincing argument that boils down to: 6 is a nice round number. It has 2 and 3 as factors.

>Rings with fewer than 6 members are uncommon in chemistry In chemistry, or in nature? five membered rings show up all over the place, both aromatic and otherwise. Granted, cyclobutyl (4 member, square) and cyclopropyl (3 membered, triangle) suffer from ring strain and are uncommon, but 5, 6, 7, (or higher) rings show up all over the place. Examples off the top of my head are the cyclopentadienyl ion pervasive in ino…

Are you a chemist?

Re: High-resolution images of a molecule as it breaks and reforms chemical bonds

#32

Post by mtdewcmu » Mon, Jun 03, 2013, 8:03 AM UTC

Komodo9 wrote: post #27

mtdewcmu wrote: post #21

Earlier quoted context omitted.

"In this case, the electron density of the overall molecule is being measured." It seemed to me that it was more directly measuring the bond energies, which, of course, is related to electron density.

True. Even having a decent grasp on the topic (or perhaps, because having a decent grasp), I find it difficult to try to peel apart bond energy, electron density, bond length, etc, from each other; They're all effectively functions of each other and the entire system.

It sounds like you might be more up on this stuff than I am. Since the probe measures force, I was picturing it sort of pushing on the bond and registering the resistance, i.e. the bond energy. But that was just an impression, and I'm certainly no authority on this.

Re: High-resolution images of a molecule as it breaks and reforms chemical bonds

#33

Post by [deleted] » Mon, Jun 03, 2013, 8:16 AM UTC

Komodo9 wrote: post #26

mtdewcmu wrote: post #20

Earlier quoted context omitted.

The short answer for why benzene rings are common is aromaticity, which makes it a very stable structure. Rings with fewer than 6 members are uncommon in chemistry, because the angles are not what the bonds naturally want to be and so they are increasingly unstable. As for nature in general, you could probably come up with a convincing argument that boils down to: 6 is a nice round number. It has 2 and 3 as factors.

>Rings with fewer than 6 members are uncommon in chemistry In chemistry, or in nature? five membered rings show up all over the place, both aromatic and otherwise. Granted, cyclobutyl (4 member, square) and cyclopropyl (3 membered, triangle) suffer from ring strain and are uncommon, but 5, 6, 7, (or higher) rings show up all over the place. Examples off the top of my head are the cyclopentadienyl ion pervasive in ino…

[deleted]

Re: High-resolution images of a molecule as it breaks and reforms chemical bonds

#34

Post by mtdewcmu » Wed, Jun 05, 2013, 5:14 PM UTC

bsg75 wrote: post #23

jfarmer wrote: post #19

Earlier quoted context omitted.

You don't really need much math to see why this is happening. First, the bonds in a benzene ring aren't discrete like we draw them, alternating between single bonds and double bonds. It's also important to realize that although we typically represent benzene in 2D all molecules really have a 3D geometry. Electron orbitals can overlap in different ways depending on the geometry of the atom and its electronics. See thi…

> It's a far leap from there to say why hexagons are "so common in nature." I was thinking of things (compared to other geometric shapes) like the storm, honey bee cells (honeycombs), basalt columns [1], turtle shells (although irregular), and a common snowflake shape. [1] http://en.wikipedia.org/wiki/Giants_Causeway

Snowflakes come out hexagonal because of the way water crystallizes: http://en.wikipedia.org/wiki/File:Hex_ice.GIF

It has to do with the bond angles in water molecules. The bond angles are, in turn, determined by quantum mechanical wave functions. These quantum mechanical wave functions apply to all of chemistry, including benzene rings. So the shapes of snowflakes and the shapes of benzene rings are not totally independent events.