Sciencemadness Discussion Board

Single molecule, one million times smaller than a grain of sand, pictured for first time

argyrium - 30-8-2009 at 08:34

Pretty cool.

http://tinyurl.com/knhsmt

"....
Scientists from IBM used an atomic force microscope (AFM) to reveal the chemical bonds within a molecule.

'This is the first time that all the atoms in a molecule have been imaged,' lead researcher Leo Gross said....."

Now if they only add color and better focus - I'd buy two ;)




article-1209726-063617DB000005DC-474_468x241.jpg - 16kB
pentacene


[Edited on 30-8-2009 by argyrium]

hissingnoise - 30-8-2009 at 08:43

I think M Rothko beat them to it?
But seriously, it is mindblowing to know you're actually seeing the fused rings, soft-focus though they are. . .

[Edited on 30-8-2009 by hissingnoise]

Klute - 31-8-2009 at 14:49

Incredible.

I wonder how they fixed that single molecule of carbon monoxide at the exact point of a metallic pyramide.. How do you construct such nanomaterial at one molecule close?

chemoleo - 31-8-2009 at 16:47

I wonder though how this could be used for anything more advanced- for structures of chemical compounds - very difficult as they may not be planar, and as soon as they stick off the plane, multiple rotational 'snapshots' need to be taken to get an idea of the overall structure. Also no atom information is given with this method. With complex structures, such as large biological macromolecules (proteins, lipids, carbohydrates and their infinite combinations), all you'll ever get is the surface, and focus will be an issue with showing a 3D molecule (unlike the 2D pentacene molecular structure). And for getting the surface texture of complex molecules (albeit at a lower res) there are plenty of existing methods.
Not only that, for any more complex molecules such as proteins (where this would be of most profound use), there's still the issue of having a large molecule sitting on a sticky plane (with no water, salt, buffer etc keeping them happy, stable, folded and active)- and almost certainly it will not look like the molecule in solution. There'll be artefacts much much worse than with crystals of proteins (also worse than with electron microscopy)

Nonetheless, it is pretty cool!

Didn't they do this with gold atoms already btw?

[Edited on 1-9-2009 by chemoleo]

psychokinetic - 31-8-2009 at 17:04

Can't Berkley already see individual atoms?

JohnWW - 31-8-2009 at 18:01

Quote: Originally posted by psychokinetic  
Can't Berkley already see individual atoms?
Yes, with an electron microscope, but only of conducting materials like metals.

Ozone - 31-8-2009 at 18:40

IIRC they spelled out "IBM" with xenon (which are very large, for atoms) atoms :

http://www.fourmilab.ch/autofile/www/section2_84_14.html

http://www.nanooze.org/english/interviews/doneigler.html

Wish I could find my copy of Time Science:Matter, which has a nicer B/W of the image than I could find on the web. It suddenly occurs to me that media format is part of the problem with relaying science to the masses. They go into how wonderful and mischeviously complex "extreme scientificky X thing" is, but forget? to put the cool image in the article.

Result: very few care enough to read the article.

The picture says it all--put it to press (regardless of the extra cost), damnit.

[edit] Oh yes (re. pentacene), remember that atoms are not perfectly hard spheres. They are tiny nuclei surrounded at a (relatively) great (read immense) distance by an electron cloud. The fact that it is not a peanut-shaped blob is pretty impressive to me (particularly considering the electron delocalization in this system). I think that the picture was quite crisp. Quite cool.

Cheers,

O3


[Edited on 1-9-2009 by Ozone]

Magpie - 31-8-2009 at 18:47

I was awed by this picture. It is just fantastic to be able to see something that small. Thanks for posting this, argyrium.

And what a wonderful confirmation of the atomic theory and molecular bonding. Ever since the Greeks came up with the concept of atoms we have only been able to gather inferential evidence. Now we can see them!

Sedit - 31-8-2009 at 18:51

I must ask the noob question of whats the difference between this picture and those imaged thru the use of a SEM? I admit I have not read the link yet so bear with me.

Ozone - 31-8-2009 at 19:23

Looks like this to me:

0. AFM with a single molecule (CO) probe.
1. Carbon is much smaller than the Xe or metal atoms that they have been pushing around.
2. The connectivity (and planar nature of this particular system) of the atoms, and, it looks like, the pi e- delocalization in an aromatic system were unambiguously imaged (Interesting how the signals are so much greater on the "ends"; I wonder if that is real or if it is an artifact).

I need to get the paper (the blurb is in C&EN, this week).

Heady stuff,

O3

watson.fawkes - 31-8-2009 at 19:43

Quote: Originally posted by Ozone  
the pi e- delocalization in an aromatic system were unambiguously imaged (Interesting how the signals are so much greater on the "ends"; I wonder if that is real or if it is an artifact).
Sure looks real to me. Think of Gauss's Law applied at the microscale. Excess charge has migrated to the surface of a conductor. In this case the surface has two ends. I even suspect the difference in intensity between the two ends is real, given that the charge distribution is almost-certainly quantized, yielding local minima and metastable states.

psychokinetic - 31-8-2009 at 19:49

Quote: Originally posted by JohnWW  
Quote: Originally posted by psychokinetic  
Can't Berkley already see individual atoms?
Yes, with an electron microscope, but only of conducting materials like metals.


Here we go: Link to video of the microscope and its use

turd - 31-8-2009 at 23:04

Quote: Originally posted by JohnWW  
Quote: Originally posted by psychokinetic  
Can't Berkley already see individual atoms?
Yes, with an electron microscope, but only of conducting materials like metals.

Um, no. You're probably thinking about a TEM or STEM microscope and these work with insulators as well. Also, while the lateral resolution is smaller than an atom, technically what you're seeing is a column of atoms. You're not going to mount a single atom layer into your sample holder. And, while the images look very neat, interpretation is not as easy as you might believe at first. That's why the HRTEM guys do lots of simulation.

OTOH, single atoms of solid state compounds have been pictured with AFM in the 1980s, but that's much easier than single molecules since, with a typical AFM, you would just move those around or destroy them. While the pictures produced with AFM look great, its actually a quite annoying method. The tip quickly gets dirty and makes the image quality decrease. Lots of work until you get the one picture you want!

PS: If I was rich, a 200 kV TECNAI TEM would be one of the first things I'd buy. This is just too cool of an instrument.

psychokinetic - 1-9-2009 at 12:41

Quote: Originally posted by turd  


PS: If I was rich, a 200 kV TECNAI TEM would be one of the first things I'd buy. This is just too cool of an instrument.


*drools*

hinz - 1-9-2009 at 13:17

Quote: Originally posted by turd  

PS: If I was rich, a 200 kV TECNAI TEM would be one of the first things I'd buy. This is just too cool of an instrument.


Bah, TEM sample preparation is quite complex, at least if you want to see more advanced things than metal structures.

The grinding of the sample is quite time consuming, you can easily spend a half a day grinding your sample to a thickness of about 100nm (to get it electron transparent) by using finer and finer grinding paper. And if you don´t pay attention, your sample gets flushed down the drain if the glue mounting to the tripod fails. Or you grind to much and there´s no more sample

If your sample is brittle, like semiconductors, glass or ceramics, the sample also likes to break.
So if you need to prepare samples from these materials you´ll need a FIB (Focussed Ion Beam), which is also real expensive.
For SEM you´ll only need a sputtering/carbon coating machine

So if there is the alternative between SEM and TEM, I would always prefere the SEM and only use the TEM if the magnification is very important. IMHO a SEM is much more universal and cheaper than a TEM.

[Edited on 1-9-2009 by hinz]

sparkgap - 1-9-2009 at 18:35

Quote:
The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy
Leo Gross, Fabian Mohn, Nikolaj Moll, Peter Liljeroth, Gerhard Meyer
Science,2009, 325 (5944), pp 1110–1114/i]


Abstract
Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because the tunneling current is primarily sensitive to the local electron density of states close to the Fermi level. We demonstrate imaging of molecules with unprecedented atomic resolution by probing the short-range chemical forces with use of noncontact atomic force microscopy. The key step is functionalizing the microscope’s tip apex with suitable, atomically well-defined terminations, such as CO molecules. Our experimental findings are corroborated by ab initio density functional theory calculations. Comparison with theory shows that Pauli repulsion is the source of the atomic resolution, whereas van der Waals and electrostatic forces only add a diffuse attractive background.


They have been playing with pentacene for a long time, after all...

sparky (~_~)

Attachment: pentapic.pdf (973kB)
This file has been downloaded 839 times

turd - 2-9-2009 at 03:55

Quote: Originally posted by hinz  
Bah, TEM sample preparation is quite complex, at least if you want to see more advanced things than metal structures.

What could be easier than putting a drop of an emulsion on a carbon grid and dry it?
Of course you are right about the tediousness of preparing solid samples.

Quote: Originally posted by hinz  
If your sample is brittle, like semiconductors, glass or ceramics, the sample also likes to break.
So if you need to prepare samples from these materials you´ll need a FIB (Focussed Ion Beam), which is also real expensive.

Indeed, that's why next to most TEMs you'll have a SEM/FIB machine. To prepare samples. ;)
Quote: Originally posted by hinz  
So if there is the alternative between SEM and TEM, I would always prefere the SEM and only use the TEM if the magnification is very important. IMHO a SEM is much more universal and cheaper than a TEM.

I think you completely miss the point of TEM: simultaneous imaging and diffraction.

Formatik - 3-9-2009 at 07:36

Pretty amazing to see a molecule like this, and good to see some theory further verified.

franklyn - 3-9-2009 at 22:42

Honestly you're all going off the deep end here.
Nothing is being " seen ". Feeling around in the
dark is a better description. This is perhaps a
bit better technique than crystallography which
actually " sees " the shadow cast by molecules.
What is interesting is not the experimental
affirmation of postulated structure but what
can be learned at a size where quantum effects
become pronounced.

Because they are set unusually far apart , atoms
of uranium in its oxide have been imaged by
electron microscopy many years ago.

.

turd - 3-9-2009 at 23:27

Quote: Originally posted by franklyn  
Honestly you're all going off the deep end here. Nothing is being " seen ". Feeling around in the dark is a better description. This is perhaps a bit better technique than crystallography which actually " sees " the shadow cast by molecules.

These two methods are so different in their application and their results that saying one or the other is better makes no sense at all.
Crystallography works on three dimensional crystalline (more or less) compounds and has an insanely high accuracy, whereas AFM is purely a surface method. Try solving the structure of a protein, a metal-organic compound or even an inorganic solid-state compound with AFM or "picturing" the structure of a single molecule or mono-layer with XRD. Good luck.

Also I highly object the use of the word "shadow" to describe diffraction. There's a point when simplification for the masses becomes oversimplification and this is way past it. A shadow cast by the sun is a projection of 3-dimensional space on 2-dimensional space, therefore throwing away 3d information. What you measure in crystallography is the Fourier transform of the electron density, but only intensity without the phase data. So in a way, if you wish to call it so, the "shadow" of the Fourier transform. But, in practically all cases, the missing phase data can be recovered by the fact that the crystal structure must be physically sound, i.e. no negative electron density and sharp peaks which are not too close. (There are some freak structures where the diffraction image is not unambiguous, a fact which is known since the dawn of X-ray diffraction. But this is not your common boring organic molecule.)

Quote: Originally posted by franklyn  
Because they are set unusually far apart , atoms of uranium in its oxide have been imaged by electron microscopy many years ago.

The difference between TEM/SEM/AFM of bulk and single molecules has already been discussed above. All these methods measure different things. Read the thread.

psychokinetic - 3-9-2009 at 23:41

Feeling around in the dark makes sense, but then the same could be said for many forms of imaging...not only in chemistry I suppose.

franklyn - 4-9-2009 at 15:38

@ turd
My "shadow" metaphor if taken literally is not descriptive of the methodology as
you have detailed somewhat. You are welcome to provide a more accurate descriptor.
At large scale , computer axial tomography ( CAT ) scanning unlike optical polaroids
similarly displays images produced as interpretations from the gathered data.
" Seeing " unless it is itself just an abstract reference such as "viewing " " picturing "
" imaging " or " resolving " is just as misrepresentive of what is in essence remote sensing
of nano scale objects and their depiction as a graph - what prompted my comment.

" All these methods measure different things " ,
- gee I hope not , Robin Williams said it best " reality , what a concept "
and Lilly Tomlin " what's reality anyway , nothing but a collective hunch "

.

thaflyemcee - 5-9-2009 at 10:31

There are images of orbitals in W and Si observed by AFM a few years back. It relies on some neat tricks, like getting the sample to image the tip, but it's totally valid. I'll post the paper once I find it again.

Before anyone jumps on me for "orbitals are mathematical constructs", let me remind you that on the timescale on which AFM image is acquired, we are ultimately looking at a map of where the tip was repelled by the surface on average, which allows the geometry of allowed electron positions (i.e., an orbital) to be imaged.

Ozone - 6-9-2009 at 07:31

"Fractal molecule bacteria!"

I have attached a shot of the other picture (on ~60A scale) which shows many pentacene molecules. Note that they all exhibit greater electron density at the ends.

It verifies theoretical predictions and it does so with very nice "science fair appeal".


Now, I want to see anti-aromaticity;).

Cheers,

O3


Pentacene 20A from Gross et al 2009.jpg - 29kB

JohnWW - 6-9-2009 at 08:13

Quote: Originally posted by Ozone  
I have attached a shot of the other picture (on ~60A scale) which shows many pentacene molecules. Note that they all exhibit greater electron density at the ends. It verifies theoretical predictions and it does so with very nice "science fair appeal".
Now, I want to see anti-aromaticity.

The greater electron density observed in the pi orbitals at the ends of pentacene molecules would be explainable by their mutual electrostatic repulsion.
"Anti-aromaticity"? Perhaps someone could write to that AFM micrographer, to suggest that he tries the same technique on molecules of cyclooctatetraene, and on suitably stable derivatives of cyclobutadiene.

psychokinetic - 6-9-2009 at 13:21

Now that's a more interesting picture :)

franklyn - 31-10-2009 at 14:24

http://www.bnl.gov/bnlweb/pubaf/pr/PR_display.asp?prID=1008

Ramiel - 1-11-2009 at 01:33

Interesting, I've been doing a lot of reading on pentacene crystallisation, the last picture is very interesting. I wonder what surface they used? pMMA?

In any event, it's an incredible picture. The "image" of the electrons says a lot which the models could never really confirm. Interesting to see some allignment there, unless I'm imagining it - this is reminiscent of the slip dislocated herringbone arrangement pentacene adopts in bulk.

Sorry, I'm rambling, but I've just spent the last few months studying among other things the crystal packing of pentacene derivatives and this picture is very exiting.

franklyn - 11-3-2010 at 16:16

UPDATE

Near Field Microscopy - Nanoscale imaging using light
http://www.azom.com/news.asp?NewsID=20626

Celebrating the 50 th birthday of the laser
http://www.laserfest.org/lasers/video-lasers.cfm

.

smaerd - 12-3-2010 at 06:54

That's so awesome! I wish I had more to add to the discussion but it's just so cool to see a molecule.

edit -Why does the outside shine brighter than the inside?

[Edited on 12-3-2010 by smaerd]

chief - 12-3-2010 at 16:14

Whats beeing seen is the electron density distribution; same counts for crytallography, bu there it's 3D (though not for single molecules)

The picture is more a stunt than an appliable new method ...

franklyn - 4-6-2010 at 15:44

http://www.sciencedaily.com/releases/2010/03/100324162621.ht...

.

DNA strand - you can kind of see it

franklyn - 30-11-2012 at 17:41

http://pubs.acs.org/doi/abs/10.1021/nl3039162

sparkgap - 30-11-2012 at 19:29

Quote:
Direct Imaging of DNA Fibers: The Visage of Double Helix
Francesco Gentile, Manola Moretti, Tania Limongi, Andrea Falqui, Giovanni Bertoni, Alice Scarpellini, Stefania Santoriello, Luca Maragliano, Remo Proietti Zaccaria, and Enzo di Fabrizio
Nano Letters (Article ASAP), November 22, 2012
DOI:10.1021/nl3039162

Abstract
Direct imaging becomes important when the knowledge at few/single molecule level is requested and where the diffraction does not allow to get structural and functional information. Here we report on the direct imaging of double stranded (ds) λ-DNA in the A conformation, obtained by combining a novel sample preparation method based on super hydrophobic DNA molecules self-aggregation process with transmission electron microscopy (TEM). The experimental breakthrough is the production of robust and highly ordered paired DNA nanofibers that allowed its direct TEM imaging and the double helix structure revealing.


Get it here.