7 ms·

Amazing stuff, feels really good to see that it is exactly the same as we read in textbooks.

andy_ppp 13y ago
When I looked at chemical symbols before seeing this I had always assumed them to be a sort of vague outline of what was really happening. It's amazing to think that the way chemicals bond is the same in reality as drawn in textbooks.
- marcosdumay 13y ago
  They choosed a molecule that was similar to its diagram, but that's not always the case. the main difference is that the diagram is 2D, and molecules are usualy 3D.
  - jcrites 13y ago
    I think you can see some slight 3D effects in the picture: http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve... In the two variants on the right, their edges seem to be curling upward making a bowl shape. Their edges are also brighter, which perhaps means they are closer to the probe than parts that are farther away. Additionally, the hexagons are also not all the same shape. I assume that's due to the curling. I would be interested to know if my interpretation of the image is correct, or if the molecule is really flat and what I'm seeing is an artifact.
    - Komodo9 13y ago
      To answer your question (flat vs. artifact) directly: It's flat. Sorta. Bear with me a moment. If this is confusing, please let me know, and i'll try to clarify. Molecular symmetry isn't my strong point, unfortunately. The trouble with all of this is the "picture" is not an actual picture-made-with-photons picture, but a visualization via computer. That isn't to say it's a poor reflection on reality, but that the limitations of the techniques should be accounted for. In this case, the electron density of the overall molecule is being measured. The brighter signals correspond to an increase in local electron density. In such chemical structures as these, the aromaticity [1] is the main force at play. Without getting too technical, the brighter regions are those with increased electron density. (See figure 4 at the IBM Zurich page on pentacene [2]) The hexagons (and square and pentagons) in fact do not have idealized geometry, but not due to any curling. The unique environment of each carbon is more at play. Symmetry plays a large role; imagine a symmetric vs. unsymmetrical tug-of-war between the carbons with the electrons as the rope. The left hand side and lower right have a dihedral mirror plane, simplifying the density somewhat, where the upper right has a more muddled situation. Getting back to the flatness, the target molecule is 'mounted' on a suitably uniform surface, such that only one side is being scanned/read by the probe. In a vacuum, the tug of war in the Z direction (into the plane) will cancel out between the +Z and -Z vectors, giving a 'flat' molecule. (Depending on your point of view, either because of this or due to this, each of these molecules has a mirror plane in the plane of the molecule, bisecting each atom.) Setting all that aside, the entire process is really #$%*& cool, particularly to a chemist. (Yes, those crazy textbook pictures are often reflected in reality. If only the different atoms were color coded, though!) [1] http://en.wikipedia.org/wiki/Aromaticity http://en.wikipedia.org/wiki/Aromaticity [2] http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.html http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.h...
      - mtdewcmu 13y ago
        "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.
        Komodo9 13y ago
        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.
        mtdewcmu 13y ago
        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.
    - bsg75 13y ago
      I am curious as to the mathematical properties (definitions?) of the hexagonal shape that make it common in natural structures (http://www.space.com/3611-bizarre-hexagon-spotted-saturn.html http://www.space.com/3611-bizarre-hexagon-spotted-saturn.htm...). I probably learned it in some chem course, and later forgot as all my math and science got applied to business :(
      - jfarmer 13y ago
        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 this for a picture: http://en.wikipedia.org/wiki/File:Benzene_Representations.svg http://en.wikipedia.org/wiki/File:Benzene_Representations.sv... So, the electrons in a benzene ring really form more of a cloud around the entire ring. You'd expect this to pull the atoms into a perfect circle with the carbon atoms all being equidistance from each other, all else being equal. However, each carbon atom also has a hydrogen atom attached to it. So now you have a sort of a circle with 6 "strings" attached at points equidistant around the circle all pulling outward, perpendicular to the circle. Imagine a perfectly circular piece of string with 6 strings attached equidistantly around the circle. You apply an equal force perpendicular to the surface of the circle. Hopefully you can see how this would result in the original circular string being "deformed" into a hexagon. It's a far leap from there to say why hexagons are "so common in nature." Are they? Relative to what? I don't know that any of this has anything to do with the shape of that storm you linked to.
        bsg75 13y ago
        > 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 http://en.wikipedia.org/wiki/Giants_Causeway
- mtdewcmu 13y ago
  You can almost make out the tiny C and H on each atom. I honestly thought that was just a notational convenience.

When I looked at chemical symbols before seeing this I had always assumed them to be a sort of vague outline of what was really happening. It's amazing to think that the way chemicals bond is the same in reality as drawn in textbooks.

marcosdumay 13y ago
They choosed a molecule that was similar to its diagram, but that's not always the case. the main difference is that the diagram is 2D, and molecules are usualy 3D.
- jcrites 13y ago
  I think you can see some slight 3D effects in the picture: http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve... In the two variants on the right, their edges seem to be curling upward making a bowl shape. Their edges are also brighter, which perhaps means they are closer to the probe than parts that are farther away. Additionally, the hexagons are also not all the same shape. I assume that's due to the curling. I would be interested to know if my interpretation of the image is correct, or if the molecule is really flat and what I'm seeing is an artifact.
  - Komodo9 13y ago
    To answer your question (flat vs. artifact) directly: It's flat. Sorta. Bear with me a moment. If this is confusing, please let me know, and i'll try to clarify. Molecular symmetry isn't my strong point, unfortunately. The trouble with all of this is the "picture" is not an actual picture-made-with-photons picture, but a visualization via computer. That isn't to say it's a poor reflection on reality, but that the limitations of the techniques should be accounted for. In this case, the electron density of the overall molecule is being measured. The brighter signals correspond to an increase in local electron density. In such chemical structures as these, the aromaticity [1] is the main force at play. Without getting too technical, the brighter regions are those with increased electron density. (See figure 4 at the IBM Zurich page on pentacene [2]) The hexagons (and square and pentagons) in fact do not have idealized geometry, but not due to any curling. The unique environment of each carbon is more at play. Symmetry plays a large role; imagine a symmetric vs. unsymmetrical tug-of-war between the carbons with the electrons as the rope. The left hand side and lower right have a dihedral mirror plane, simplifying the density somewhat, where the upper right has a more muddled situation. Getting back to the flatness, the target molecule is 'mounted' on a suitably uniform surface, such that only one side is being scanned/read by the probe. In a vacuum, the tug of war in the Z direction (into the plane) will cancel out between the +Z and -Z vectors, giving a 'flat' molecule. (Depending on your point of view, either because of this or due to this, each of these molecules has a mirror plane in the plane of the molecule, bisecting each atom.) Setting all that aside, the entire process is really #$%*& cool, particularly to a chemist. (Yes, those crazy textbook pictures are often reflected in reality. If only the different atoms were color coded, though!) [1] http://en.wikipedia.org/wiki/Aromaticity http://en.wikipedia.org/wiki/Aromaticity [2] http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.html http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.h...
    - mtdewcmu 13y ago
      "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.
      - Komodo9 13y ago
        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.
        mtdewcmu 13y ago
        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.
  - bsg75 13y ago
    I am curious as to the mathematical properties (definitions?) of the hexagonal shape that make it common in natural structures (http://www.space.com/3611-bizarre-hexagon-spotted-saturn.html http://www.space.com/3611-bizarre-hexagon-spotted-saturn.htm...). I probably learned it in some chem course, and later forgot as all my math and science got applied to business :(
    - jfarmer 13y ago
      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 this for a picture: http://en.wikipedia.org/wiki/File:Benzene_Representations.svg http://en.wikipedia.org/wiki/File:Benzene_Representations.sv... So, the electrons in a benzene ring really form more of a cloud around the entire ring. You'd expect this to pull the atoms into a perfect circle with the carbon atoms all being equidistance from each other, all else being equal. However, each carbon atom also has a hydrogen atom attached to it. So now you have a sort of a circle with 6 "strings" attached at points equidistant around the circle all pulling outward, perpendicular to the circle. Imagine a perfectly circular piece of string with 6 strings attached equidistantly around the circle. You apply an equal force perpendicular to the surface of the circle. Hopefully you can see how this would result in the original circular string being "deformed" into a hexagon. It's a far leap from there to say why hexagons are "so common in nature." Are they? Relative to what? I don't know that any of this has anything to do with the shape of that storm you linked to.
      - bsg75 13y ago
        > 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 http://en.wikipedia.org/wiki/Giants_Causeway
mtdewcmu 13y ago
You can almost make out the tiny C and H on each atom. I honestly thought that was just a notational convenience.