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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

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Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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September 3, 2009

Real Molecules

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Posted by Derek

Most of you will have heard about the recent accomplishment at the IBM Zürich labs, using an atomic force microscope with unprecedented resolution. They've imaged individual molecules so well that the atoms and bonds are alarmingly clear. I thought I'd put up one of the less-used images from the paper - here are some pentacene molecules (five fused benzene rings) sitting around on a surface. Not a simulation, not a model: real molecules. It gives me a slight chill, to tell you the truth.

Comments (37) + TrackBacks (0) | Category: General Scientific News


1. SP on September 3, 2009 1:47 PM writes...

So now can they use the AFM tip to move the molecules into position and make or break bonds? There goes all your synthetic methodology (as long as you're happy only getting 10 yoctomoles of product.)

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2. EngelGW on September 3, 2009 2:26 PM writes...

Well, that's definitely impressive indeed. However, I suspect that pentacene molecules are quite perfect for such an experiement. I would be curious to see the same thing with drug-like molecules, more flexible and with different electronic properties...

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3. not a chemist on September 3, 2009 2:28 PM writes...

i had thought bonds were like gravity; they were drawn only for education and illustration purpose.
are they fast moving electrons? why do they prefer the 2 tips (assuming brighter means higher density)?

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4. Peter Metcalfe on September 3, 2009 3:12 PM writes...

Why can't they see the atomic structure of the surface?

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5. Aspirin on September 3, 2009 3:37 PM writes...

Nice! Now let's see something with 8 rotatable bonds and a morpholine ring.

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6. TW Andrews on September 3, 2009 3:44 PM writes...

So how long until they can get video of things reacting in the wild, and slow it down enough to see what's happening?

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7. Phage on September 3, 2009 3:59 PM writes...

Peter Metcalfe: from what I read in the paper, they imaged the pentacene by picking up CO molecules. The carbon end sticks to the metal tip of the probe. The other end supposedly interacts with the pentacene molecular orbitals, therefore amplifying the signal and making the observation possible.

I don't do AFM for a living, so I have no way to verify that statement... nevertheless, that's how I interpret the authors' statement.

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8. retread on September 3, 2009 4:32 PM writes...

Neat pictures -- if the increased signal at the ends of the molecule really represent increased (or decreased) electron density (and not an artifact of the technique_), it should show up in the NMR using either H or 13C (or both). I'm sure the spectra are available. What do they show? What do the computation chemists say? The initial chemical shifts should be pretty simple, ignoring splitting initially -- amazingly there are only 4 types of hydrogen and 4 types of carbon in the molecule.

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9. Anonymous on September 3, 2009 6:12 PM writes...

I just hope this paper will turn IBM into Bell, if you know what I mean.

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10. Schiffs mace on September 3, 2009 9:21 PM writes...

It's called photoshop! I am placing a $50 bet that the authors will be busted in the future.

Tweeking the data so it matches your expectations is weak. Get real.

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11. researchfella on September 3, 2009 9:27 PM writes...

I'm looking forward to the Sony Bravia HD version of this technology, so we can also see the hydrogen atoms, and confirm that carbons are black, hydrogens are white, oxygen is red, nitrogen is blue, etc. And maybe we'll be able to see two lines for a double bond and three lines for a triple bond.

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12. agogmagog on September 4, 2009 3:12 AM writes...

Why do these appear to cast shadows. Was it dawn down in the AFM?

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13. Wim Libaers on September 4, 2009 7:10 AM writes...

I'm not sure how it works in this case, but "shadows" are pretty common in normal AFM images. The tip scans from one side to the other, and when it meets some structure, the rising and falling edge look different. How obvious the effect is depends on scan parameters (mostly scan speed) and the sample.

Some AFM software also enhances the sample topograpgy by casting shadows on it, to make fine detail stand out better. But even in the raw data, steep edges usually show shadow effects.

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14. SJ on September 4, 2009 7:53 AM writes...

Looks like a photoshop effort to me, even though they probably didn't use photoshop to achieve it.

What could that perfectly flat substrate be: metallic hydrogen, perhaps? Maybe neutronium?

Obviously the software that generates the pictures compensates somehow for the roughness of the substrate, and I'd suggest that what Wim says above is true: "software also enhances the sample topography by casting shadows on it".

But what we're left with is a long way from "Not a simulation, not a model: real molecules."

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15. cookingwithsolvents on September 4, 2009 8:40 AM writes...

SJ: surface is single-crystal Cu (100 i think)

retread: there is a very good MO reason for the ends of an aromatic interacting with a surface to be higher up than the middle. a "no prize" to the one who gets it.

No, I don't know if the MO reason is what's being seen (it could be an artifact). We'll have to wait for more data to see if it is repeatable.

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16. Derek Lowe on September 4, 2009 9:43 AM writes...

No folks, this is not Photoshop. Geez, the internet has made everyone so darn suspicious.

The authors mention the shadow effect, and as Wim Libaers mentions above, it's a common sight in AFM imaging. It appears that the CO molecule at the tip of the AFM probe isn't pointed straight down, but is at an angle, so the direction of scanning makes a difference in what you "see". It does make for a nice effect, though.

The slightly dark halo around the molecules in general seems to be due to van der Waals and electrostatic forces, while the atomic resolution is due to Pauli repulsive forces. Density function calculations agree quite well with what they see there - the ends of the molecule aren't poking up, but they have very different electron density.

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17. Vader on September 4, 2009 10:05 AM writes...

Agogmagog beat me to the question, but I'm glad you answered it. I'm surprised there would be a well-defined misaligned state of the imaging CO molecule, though. I would have thought quantum fluctuations would smear it out.

But then the whole imaging thing is amazing.

It will be interesting when the first image comes out pf a molecule with an electron density significantly different from that predicted by the best density functional theory. If that never happens, then of course this is just a stunt, however impressive.

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18. FormerMolecModeler on September 4, 2009 10:34 AM writes...

These images are obviously fake. They were made on a hidden Hollywood set.

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19. Anonymous on September 4, 2009 11:03 AM writes...

Slight chill is a good way to put it - absolutely astounding!

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20. mad on September 4, 2009 12:25 PM writes...

WHy does the Cu surface appear flat and not as a matix. Is it jsut "out of focus" so to speak? Are the molecules in it that much closer than 2 carbons in these rings?


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21. Sili on September 4, 2009 12:31 PM writes...

Thanks for the explanation of the shadows. I love how the internet not only answers my questions, but also asks them for me.

I like this image much better than the 'close-up' that was put up everywhere else (yes, for shame, I did not look for the paper, myself ...). This one really drives home the fact that these are individual molecules. Don't get me wrong, I'm cuckoo about crystallography, but the cries of "yawn - so what else is new?" were annoying me.

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22. pete on September 4, 2009 12:35 PM writes...

It's porn for Chemists :)

But seriously - WOW !

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23. AR on September 5, 2009 8:32 AM writes...

I’ve done AFM on biological specimens, believing once I had image the first alpha helical protein surface. Let me quote what the reviewer said on the articel rejection: ‘Your image looks too much like the text book diagram….” Ditto this.

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24. milkshake on September 5, 2009 8:40 AM writes...

Its photoshopped - the molecules cast shadow!! And the firmament background is perfectly smooth - no atomic resolution there. Quite obviously it was a snapshot of maggots that was re-touched to look more hexagonal

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25. kent on September 5, 2009 6:57 PM writes...

AR: I'd like to talk to you about your AFM imaging of alpha helices, can you shoot me an email at ?

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26. agogmagog on September 6, 2009 6:52 AM writes...

Thanks for the answer to my question. Though the tone was tongue in cheek, I was genuinely interested in the answer.

For some reason when I see this picture, I hear the gentle voice of David Attenborough saying, 'As dawn breaks over the copper flatlands, the herds of pentacene, grazing peacfully, reamin unaware of the predators lying in wait'.

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27. Aspirin on September 6, 2009 9:26 AM writes...

E. coli, yay!

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28. sepisp on September 7, 2009 4:35 AM writes...

What is it about that there are so many willing to claim photoshop, without even checking the article? That's a serious, libelous claim. Many don't seem to even understand what is a scanning tunneling microscope, and why it might produce artifacts. The article is readily falsifiable and it has even height-maps (Fig. 3). Furthermore it refers to previous publications about the same topics.

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29. logic on September 7, 2009 11:04 AM writes...

"What is it about that there are so many willing to claim photoshop, without even checking the article? That's a serious, libelous claim."

Because chemistry is an art rather than a science. So, most chemist's bull-sh*t detectors are set on high. The molecule looks too much like pentacene to be pentacene. This is right up there with the 99% yield, after a 5 column purification.

The authors got a smudge and fiddled with the data or the machine until it matched their preconception. Let's see if dozens of other labs using different machines measure similar data.

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30. DC on September 7, 2009 7:07 PM writes...

@28, 29.

I think I'd agree with milkshake on this one. They are only photoshopped maggots.

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31. undergraduate chemistry student on September 8, 2009 7:51 AM writes...

why pentacene

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32. SRC on September 8, 2009 9:39 PM writes...

To be precise in language, and to underscore my previous rants, IBM has imaged molecules - not compounds. I wish people, especially those ostensibly trained in chemistry, would maintain the distinction: "compound" for the class, "molecule" for each member of the class.

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33. E=mc2 on September 16, 2009 3:01 AM writes...

Would be really useful to know how heavy is the cantilever and how is it build ?

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34. citibank on December 17, 2011 5:36 AM writes...

for 15 Marc Malone:Y'all are missing the most salient point to this survey. To wit: How in the heck did they get so many danged Indies on this survey, and so few Dems?

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35. mztty on March 27, 2012 7:10 PM writes...

If those are visible, what is their backdrop composed of? And I
am sure it is not because of focus.

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36. Joonas V. on January 20, 2013 11:57 AM writes...

It's still a simulation generated by a software based on the data it gathers by detecting the atoms. You can't take a photo of a molecule. The atoms are held together by electrostatic force and there's a "huge" cap between the atom nuclei, so they would probably appear invisible, being too sparse and too small to be visible AND fit to the same picture. Atom nucleus may be hundreds of thousands times smaller than the atom "size" (Depending on the atom) and the only thing remaining are the electrons, which wouldn't appear on the image anyway. (I'm not a physicist, so forgive me if I'm mistaken)

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37. Brian on March 8, 2014 6:36 AM writes...

Joonas, even a photo is not the real thing. They are all projections/reflections/translations causing chemical and/or electromagnetic changes to either chemical sensors (photo plate or film) or electromagnetic (CCD, STM, CRT...)

If you want to move into a more questionable area, then let's investigate doing holographic film development using these advances in miniaturization rather than tired old electromagnetic sensors.

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