Imaging the Molecular Orbitals of Pentacene

eparker05 writes "Researchers at University of Liverpool have used a scanning tunneling microscope to image the aromatic molecule pentacene (Abstract). Not unexpectedly, the resulting images showed an astonishingly close correlation to the theoretically predicted molecular orbitals. This incredible set of images reminds me of the group that imaged a single carbon atom in 2009."

Comments

Re:Oxidizers == Death

[el_jake]

Okay, i'll stop breathing then...

Re:Oxidizers == Death

[GameboyRMH]

There are a few of your posts that are so over-the-top ridiculous, including this one, that they reveal you're actually a very dedicated troll and not a real chiropractic voodoo doctor who actually believes this stuff.

Not to discourage you, I find this hilarious, keep it up XD

Re:Oxidizers == Death

[interkin3tic]

The big message: AVOID ALL OXIDIZING MATERIALS! If you cannot and must work around it, be SURE to visit a reputable Chiropractor and explain that you work around oxidizers. The Doctor will be able to focus his treatments accordingly.

Fact: Chiropractors are funded by the shadowy oxidizing lobby. When they give you an expensive massage, doing nothing to treat your ailments, they are secretly rubbing in oxidizing agents.

Re:Oxidizers == Death

[Anonymous Coward]

Canned reply gets paid score of two? Last day of that!

Re:Oxidizers == Death

[el_jake]

What you actually write between the lines is that you skipped chem classes and confused muscular science with nutrition...

real imaginary numbers

[condition-label-red]

Did anyone else notice that the article with the images has an incorrect definition of imaginary numbers (i.e. says i=sqrt(1) instead of i=sqrt(-1) ).

Re:real imaginary numbers

[ericloewe]

They're keepin' it a bit too real

Re:real imaginary numbers

[Bob the Super Hamste]

Why would you RTFA. When you read it you always get let down.

I noticed that as well. I mostly wanted to look at the pictures and wonder why the model images have such nice right angles as I would have thought they would been more similar to the actual pictures. Then again I am a software guy, not a physics or nanotech guy.

Re:real imaginary numbers

[Amouth]

you are thinking of i they are using i

Re:real imaginary numbers

[Anonymous Coward]

can't expect much from writers who thought algebra1 was hard math

Re:real imaginary numbers

[Anonymous Coward]

I prefer i^2 = -1

Re:real imaginary numbers

[idontgno]

think you're just imagining things.

I mean, really, is it that complex?

Re:real imaginary numbers

[Mitchell314]

I find the whole matter irrational.

Re:real imaginary numbers

[Anonymous Coward]

Clearly this is more evidence of tampering by those who believe in AGW.

Re:Oxidizers == Death

[GameboyRMH]

I feel the need to post this here. Minutes ago I received this email from Dr. Bob himself:

Sorry for writing you like this but I cannot post any more replies (thanks to all the voting down of my posts by the Big Pharmacy shills)

I'd like to let you know that I'm completely serious. If you'd like to follow me on FaceBook, I'm at:
http://www.facebook.com/profile.php?id=100002475387056

We offer advice for patients and others interested in their health.

Either this guy is real or he is the best troll in Internet history. Even if he is a troll, I think this performance deserves a serious reply, so I will send him this:

If this is true then why do you post on Slashdot? You do realize that site is caters to and is full of people who are...extremely skeptical of the basis of your profession, to put it mildly. You've become a laughing stock to most users there.

Can't wait to see his reply.

Electron Density

[Anonymous Coward]

These methods do not image orbitals themselves - it is generally regarded as impossible to do this. These instead image electron density, which is separate but related (square of the wavefunction)

Re:Electron Density

[eparker05]

True, but the shape of the isodensity surface is so closely related (the square of the wave function) that imaging one can pretty much validate the other. Also, while in the journal article they show the MO, the actual comparison between the image and MO theory is on the basis of electron density.

Re:Electron Density

[scheme]

According to the article, they actually do image the orbitals because they're looking at the interaction of the orbitals of CO and the target orbitals. This way they can calculate phase information and get the actual orbitals themselves instead of just electron density.

Re:Electron Density

[Anonymous Coward]

These methods do not image orbitals themselves - it is generally regarded as impossible to do this.

...impossible to do this because there's no such thing as an orbital (as they and eveyone else here is using it) except for one-electron systems, like H or He+.
An orbital is a fictitious effective one-electron wavefunction.
The are used to approximate a function of many variables as a product of functions of single variables.
The function of many variables is the wavefunction. Thefunctions of single variables are orbitals... and the "variables" are electrons; e.g., the position and spin of electron 1, electron 2, electron 3... etc...

They can probe things and talk about how the net many-electron Napthalene + CO wavefunction changes as the CO is moved around, but they can't say anything about "orbitals" (using the description given in the article and used by other commenters here).

Re:Oxidizers == Death

[Samantha Wright]

Trivia time for anyone who's never taken organic chemistry: What's the opposite of oxidation and why do they have such obscure names?

First correct answer wins a free olfactory impression of CmdrTaco's old foof chair.

Re:Oxidizers == Death

[JonySuede]

what about good old bleach ?
Strongest oxidizing agent in my home, man made but useful as hell for sanitation... It helped saved the western civilization from cholera in the 18th century....

Re:Oxidizers == Death

[NatasRevol]

Chiropractic medicine?

Re:Oxidizers == Death

[TrisexualPuppy]

Reduction. This was taught in my HS chemistry courses.

Re:Oxidizers == Death

[Anonymous Coward]

A proper diet, preferably vegan and organic is something to consider as well.

OK Dr. Quack! A proper diet for modern homo sapien is mostly animal protein and fat, with small portions of plant matter for supplemental vitamins and fiber. Enough of this bullshit save-the-cute-fuzzy-animals lie. It's a high grain diet that makes people fat/stupid by starving the brain of the essential acids that are not found in 'a proper diet, preferably vegan and organic' (aka, grain diet), and by filling the bloodstream with glucose and fructose. Fat is healthier source of carbohydrate gram for gram than grains/pasta/breads, as fat breaks down to glycerol and essential acids, and your liver metabolizes glycerol into glucose which can be used by every cell in your body. Grains, pastas, and breads also fill your blood stream with fructose, which is basically worse for your liver than alcohol, and also causes cirrhosis.

We simply did not evolve to run on massive amounts of glucose, and fructose has extremely limited uses (like sperm). It's sad that people don't even know that animal fat breaks down to glucose, but it's sadder that people buy into bullshit like this Dr.Bob and end up less healthy and a lot dumber.

-1 for the "organic" food comment bullshit too

Re:Oxidizers == Death

[Samantha Wright]

I'm sorry, that's incorrect! You'll have to try harder if you want a whiff of Slashdot history!

Re:Oxidizers == Death

[Anonymous Coward]

The control factor ignores the general hint in the word control.

Hole without donut

[Anonymous Coward]

How can something be unexpected yet astonishing at the same time. Is this like holding tea and no tea?

Re:Hole without donut

[Anonymous Coward]

Sorry, I meant not unexpected.

Re:Oxidizers == Death

[GameboyRMH]

Oh! Oh! Here it is:

Thank you for replying, that demonstrates an open mind!

I post as I've been a 'tech lover' for a while and am always looking at ways to use technology in the best and safest means to help my patients. I've had some people from here "Friend" me on FaceBook, in fact someone bought me a Subscription to the blog. I posted about it in my Slashdot Journal.

If just one person takes my advice and helps their health it's all been worth it. And I have a thick skin, I've been called all sorts of horrible things. :)

Now I'm thinking he's a real chiropractic guy who honestly believes this stuff. I feel a little bad about hurting his feelings. But if he is a troll, he must be rolling on the ground and pissing himself right now. And he would deserve those lulz. But he's really swaying me back towards thinking he's not a troll.

He later pointed out that it is bad Internet etiquette to post private emails. Well yes, but I did at least make sure nothing personal was in there, but Internet etiquette goes right out the window out in these here parts, sorry. If this was 4chan he'd be getting death threats over the phone and his children would be getting pics of strange men's penises in their email by now, so, consider it a lesson.

Old hat

[Anonymous Coward]

Atomic resolution of atoms and molecules with SPM have been around for a while. Pentacene was imaged back in 2009 and atomic resolution of surfaces goes back to the 90s . The only thing that is new about this article is a slightly different flavor of STM. Not what the authors are imaging with it.

Re:Old hat

[black soap]

Was that imaging the molecule, or the electron orbitals? There is a difference.

Re:Old hat

[TeethWhitener]

The only thing that is new about this article is a slightly different flavor of STM

Now that's just plain wrong. First off, the pentacene molecule imaged by the group at IBM was imaged using atomic force microscopy (AFM), which uses a nanoscale piezoelectric cantilever to measure the force between the tip of the microscope and the substrate. The IBM team realized that picking up a single CO molecule with the tip allowed them to have an atomically sharp tip, thus giving them the drastically increased resolution apparent in that paper. This paper presents an STM method, which uses the current caused by electron tunneling between a tip and substrate (which dies off exponentially with distance between the two). The major breakthrough is this: scientists working in this field have known for quite some time that the electron tunneling was a function of both the starting state (tip state) and the ending state (substrate) of the electron. The problem with this is that the tip state up until now has only been known very vaguely. At the atomic level, the tip of the STM is in general a poorly defined blob of metal. What the researchers in this paper have done is pick up a CO molecule to act as the tip of the probe, just like the researchers on the pentacene paper before. The advantage now is that we can model CO quite well quantum mechanically, so that we have a much better idea of the starting state of the electrons. Of course, there will be some interaction of the CO with the metal in the tip, but nonetheless, this method provides us with a much clearer picture of what the electrons are actually doing when they tunnel from the tip to the substrate below. This is the reason that the researchers were able to get so much more information out of these experiments than previous researchers. /rant

Re:Old hat

[MagusSlurpy]

It's actually the same group from IBM, expanding upon their earlier work.

Re:Oxidizers == Death

[Anonymous Coward]

this is so true : proper diet for modern homo sapien is mostly animal protein and fat, with small portions of plant matter for supplemental vitamins and fiber.

I told my doctor, some years ago, that my diet consist of almost exclusively of reasonably sized portions of*1 red meat, fish, fruit and white meat, he is always amazed at the excellent quality of my pressure, LDL and HDL readings.

1- ordered by mass eaten per week

Benzene, anyone?

[Anonymous Coward]

Remember this 2009 article? http://physicsworld.com/cws/article/news/40250

Not-Unexpectedly Astonishingly Close?

[Anonymous Coward]

That's a bit of an oxymoron, I think.

Re:Oxidizers == Death

[Anonymous Coward]

Bitcoins found in /./.

Image authentication is the dog-complex./b/-complex.

Re:Oxidizers == Death

[NatasRevol]

Chiropractic quackery?

Re:Oxidizers == Death

[Anonymous Coward]

You're loosing your touch. Many of your earlier posts sounded like something you might actually believe. However this one is far to insane.

Yrore trying to hard to use the word "Frankenstein molecule" for one, and also talking about subluxation as if they are a physical thing " wrapped around nerves, almost like cancers" while also claiming they can't be removed and studied.

What happened to you Bob? you used to be cool.

Re:Oxidizers == Death

[black soap]

So, you are against hydrocarbons in general, and that leads you to a rant against oxidizers? Are there any chemical compounds you endorse, or does exposure to anything at all require a quick trip to the chiropractist?

Obligatory XKCD

[Anonymous Coward]

http://xkcd.com/865/

Re:Oxidizers == Death

[Samantha Wright]

Keep trying! You're only one answer away from an experience your nostrils will never forget!

Measured cloud is "fuzzier"

[GodfatherofSoul]

Does that mean there's some slight difference from the theoretical model or just an artifact of how the cloud was imaged?

Re:Measured cloud is "fuzzier"

[Anonymous Coward]

"I'm uncertain of that." -- Heisenberg.

Re:Measured cloud is "fuzzier"

[mapkinase]

Looks like I am the only one who is not impressed by the comparison pictures. Pictures basically match in "shape", but not exactly in density distribution.

It seems to me that it's not very difficult to figure out the shape, that is where the minimums and maximums are without any computations.

Re:Oxidizers == Death

[Samantha Wright]

Bingo. The terms come from smelting, where most ores came in oxides, and had to be reduced to their oxygenless forms. Most people start glazing over when you explain what they actually mean.

Re:Oxidizers == Death

[NatasRevol]

Come on!

Homeopathy?

Atomic and Electronic Structure

[structural_biologist]

The same group of researchers published a paper in 2009 in the journal Science using a technique called atomic force microscopy (AFM) rather than the scanning tunneling microscopy (STM) approached used here. This technique allowed them to resolve the atomic structure of pentacene, showing the classic ring structure as one might see drawn on a chalk board in their chemistry class. Combined with their means of imaging molecular orbitals by STM, these researchers have developed some really nice tools for studying molecules. Here's the citation for the AFM paper:

Gross et al. (2009) The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy. Science, 325: 1110. doi:10.1126/science.1176210

Re:Oxidizers == Death

[sjames]

He's super serial!

Re:Oxidizers == Death

[Samantha Wright]

I'm sorry, someone else already claimed the correct answer to the first part of the question, which was "reduction." We remind you that quiz show hosts rarely have worthwhile senses of humour, and encourage you to try your best at the second part.

Re:Oxidizers == Death

[Sarten-X]

...a committed Chiropractor.

I think all chiropractors should be committed. They're all crazy.

Dupe!

[munozdj]

I remember having seen this very same picture a year ago or so posted here... It's still in my pictures folder because it really impressed me that time. Guess it shows that chemistry isn't alchemy after all. Link to the original article

Re:Dupe!

[munozdj]

My mistake. As always, I didn't RTFA before posting. Now I realize that they're talking about the molecuar orbitals (who would've guessed!) and not the picture taken by IBM before. It's actually pretty nice. Again, apologies.

Re:Oxidizers == Death

[NatasRevol]

Ahh, I see my problem: Funny != good answer.

Re:Oxidizers == Death

[NatasRevol]

My answers were still better, if less correct.

Re:Oxidizers == Death

[Sulphur]

You're loosing your touch. Many of your earlier posts sounded like something you might actually believe. However this one is far to insane.

Yrore trying to hard to use the word "Frankenstein molecule" for one, and also talking about subluxation as if they are a physical thing " wrapped around nerves, almost like cancers" while also claiming they can't be removed and studied.

What happened to you Bob? you used to be cool.

Global uncooling.

Re:Oxidizers == Death

[SleazyRidr]

OIL RIG FTW!

Re:Oxidizers == Death

[Samantha Wright]

Only on Slashdot.

...seriously, I've tried it on 4chan and they totally miss it.

Ummm... Not surprising?

[Anonymous Coward]

Hey Subbie... If the results are "unsurprising" then why is the accuracy of the data when compared to the model "astonishing"?

Re:Oxidizers == Death

[mangu]

Tell him to go to Reddit. He could start posting in http://www.reddit.com/r/chiropractic

Re:Oxidizers == Death

[Anonymous Coward]

So, did you spend 1300$ yet to make inferior useless copies of LEGO?

Difference between theory and practise.

[rew]

Of course some differences between theory and practice can be expected. For example, some experimental noise is expected. And at these scales, some fuzziness is also weird if it wouldn't happen.

However the topology should be correct. Now in the top image on the right there is a "white" area at the top. Whereas on the left (the real data) the white area at the top has a dent in it. As if there is a black area on the top with two white areas on the corners.

In short: From this experiment I'd say: The theoretical model is seriously flawed.

Re:Difference between theory and practise.

[cnettel]

I think there is a dent even in the simulated one. Remember that these 2D visualizations are only representations of the 3D densities. Where you put your cutoff for surfaces, or in this case, where you put the steepest slope in your grayscale definition, can influence the perceived shape a lot more than what is actually the case.

Isn't that

[jimmydevice]

The square root of -1?

Obligatory

[frenchbedroom]

Science : it works, bitches.

In other news...

[Anonymous Coward]

Baseball thrown in a vacuum shows astonishingly close correlation to the prediction of Newtonian physics.

Re:Oxidizers == Death

[GameboyRMH]

Take a look around this site Mr. Troll:

http://www.shapeways.com/gallery?mg%5Bsearch%5D%5Bcategories%5D=21&mg%5Bsearch%5D%5Bclear%5D

Impressed yet?

Re:Oxidizers == Death

[FredFredrickson]

Global uncooling.

That's just a myth. The evidence was faked. The earth has always gone through these cycles. What was once Cool will be Retro cool soon in the future.

Buy my book: Hipster Science