Naked molecule exposed

Posted: Thursday, August 27, 2009 8:10 PM by Alan Boyle

IBM Research - Zurich

Click for video: This graphic shows how scientists
used a carbon monoxide molecule on the end of a
metal tip to map a pentacene molecule. Click on the
image to watch a video from NBC's "Nightly News."

Scientists have traced the structure of a complete molecule in all its glory, using the sharpest pen ever devised: an atomic force microscope tipped with a single molecule of carbon monoxide.

The experiment, detailed in Friday's issue of the journal Science, could help open up a new frontier for molecular-scale circuitry and construction.

Researchers have been imaging molecules and their constituent atoms in crystals for decades, but the trick is to get a fine-resolution fix on the structure and behavior of an entire, self-contained molecule as it sits on a surface.

If you have the wrong stuff at the very tip of your probe, the very act of mapping the molecule can spoil the picture.

Leo Gross and his colleagues at IBM's Zurich Research Laboratory found that a carbon monoxide molecule (with its oxygen atom sticking straight out from the tip) produced "spectacular" images of the pentacene molecule. That's a well-studied type of hydrocarbon composed of five benzene rings interlocked in a row (C₂₂H₁₄).

Science / IBM

Several pentacene molecules are imaged using non-contact atomic force microscopy.

The benzene rings showed up brightly in the atomic-scale images, just as predicted by theory. One of the images published in Science even showed several of the five-ring molecules scattered around a surface like nano-caterpillars.

The researchers said their results were so good because the carbon monoxide molecule could get incredibly close to the pentacene molecule without picking it up or moving it around. When they tried probes that were tipped in metals, such as gold or silver or copper, the pentacene molecule would move around before the tip came close enough to map the chemical forces holding the molecule together.

The IBM team concluded that non-contact atomic force microscopy can be a great way to see how molecules are put together, but only if the microscope's probe is tipped with the right stuff.

The next step is to probe differently constructed molecules to see how they react with various types of tips - and see which kinds of surfaces work best as a molecular-scale lab bench. The goal of all this is to devise a molecular construction toolkit, as well as methods for watching how the tools in the kit work together.

"Eventually we want to investigate using molecules for molecular electronics," Gross told Chemistry World. "We want to use molecules as wires or logic switches or elements."

Experts in nanotechnology have long dreamed of creating molecular-scale circuitry that could revolutionize the computer world. But Gross told EETimes that the revolution is still far off. "It will take at least 15 years to see molecular electronic applications," he said, "and it is by no means certain that we will succeed."

That sounds like a refreshingly realistic assessment to me - but what do you think? Feel free to add your comments below.

Update for 10 p.m. ET Aug. 31: I've added a link to the video from NBC's "Nightly News" in which anchor Brian Williams discusses the magnificent molecule imagery.

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Comments

Wow. Just Wow. this is fabulous technology and fascinating look at a world we have heretofore only guessed at and imagined! Thanks for this glimpse of the possible!

Betina Krahn (Sent Thursday, August 27, 2009 9:11 PM)

Great writeup of a fascinating result, Alan.

john doe (Sent Thursday, August 27, 2009 9:27 PM)

This is great from a biotech systems point
of view -- i.e. Can you say Nanites that
clean the blood or clean the kitchen all
by themselves!

However this does seem one step closer to
that Liquid Metal T1000 Terminator
from Terminator-2 Judgement Day which is
a scary thought for me.

And since I have a background in
Computer Science and some minor knowledge
of using biotechnology processes for making
computation engines, I must emphasize that
humanity must be careful of stuffing an
enormous amount of computing horsepower
into a mobile system that can theoretically
outperform the human mind by many thousands
of times...Maybe NOT such good an idea!!!

We will have to evolve some well-defined
ethical considerations when using molecular
technology to build intelligent computing
systems or Borg-like nanites that could
possible run amok and out of our control!

Any other thoughts on my points?

Henry A. Eckstein (Sent Thursday, August 27, 2009 9:29 PM)

If that is a 'picture' of molecules, what is the surface they are resting on made of?

[ALAN ADDS: Good question. The surface consists of two atomic layers of sodium chloride (as an insulator) on top of a copper substrate. You may actually be asking, "Why can't we see the atomic structure of the surface the molecules are resting on?" The answer, I think, is that the scanning tip was doing the measurements on the atoms sticking up from the surface, and that the surface itself is therefore basically "out of focus." I realize it looks as if there is a shadow being cast by those nano-caterpillars in the picture, and here's how it's explained in the paper: "The asymmetry in the molecular imaging ... (showing a 'shadow' only on the left side of the molecules) is probably caused by asymmetric adsorption geometry of the CO molecule at the tip apex." So how far down the rabbit hole do you want to go? ;-) ]

Geronimo509 (Sent Thursday, August 27, 2009 9:29 PM)

This is incredible. It won't be too long off before we're able to see all molecules that make up the atomic structure of other molecules. Then science will be able to study the art of assembling and dissabling molecules at the atomic level, which will not only be applicable in electronics but health care, imaging, and so forth. Imagine if you could disasemble a disease like cancer at the atomic level.

Rob, Kansas City, MO (Sent Thursday, August 27, 2009 9:44 PM)

Who would've thought that atomic-specific microscopy would have been the answer to assay the organization of larger molecules. VERY COOL!!!!

Scott Renart, Huntington, NY (Sent Thursday, August 27, 2009 9:46 PM)

I thank God for the engineers and scientist, we can see marvels and take another step forward. I wonder about the atoms electron clouds, they show here almost as lines like the conceptual molecule. I had always expected these images would not be so detailed, always thought the day we saw this would be more fuzzy and no so defined, I believe this, but looks handmade.

Felix Cuevas, Miami, Florida (Sent Thursday, August 27, 2009 9:51 PM)

I've been so caught up in reading about the subatomic work scientists have been doing that I forgot all about the molecular level. It's almost the less famous step-child of nano-tech, but likely far more useful and practical.

I'm going to have to go read up on molecular "machines" now. Thanks for directing my curiosity in a new direction.

Very cool.

Jared Nielsen, Jacksonville, Florida (Sent Thursday, August 27, 2009 9:51 PM)

Very cool, but leaves questions. What was the substrate or sensor used? Did the CO molecule emit electrons, or was something else used in the non contact tracing process? And when can we expect tracing of this sort at the quantum level?

[ALAN ADDS: I was hoping I wouldn't have to get into this, but here goes. The researchers measured slight frequency shifts in a tuning fork as they passed the scanning tip over the molecule at a constant height. These shifts are caused by short-range chemical forces, but there are lots of other forces involved on that scale, so a lot of the research paper was devoted to explaining how those other forces were separated out. The ideal distance between the tip and the pentacene molecule turned out to be 1.2 angstroms, for what that's worth. To make sense out of all this, a bit of knowledge about atomic force microscopy may be helpful, more knowledge that I have, but this Wikipedia article tells you more about how AFM works: http://en.wikipedia.org/wiki/Atomic_force_microscope ...]

Ray Mosely, Tucson, AZ (Sent Thursday, August 27, 2009 10:10 PM)

This is a great tool in the quest for the ever-shrinking size of the circuits. What an accomplishment.

David Fong, Sunnyvale, CA (Sent Thursday, August 27, 2009 10:12 PM)

God's Design is truly amazin! Wow!

Christen Odom, Arkansas (Sent Thursday, August 27, 2009 10:19 PM)

Nanotechnology is a facinating area of development. Now once the technology occurs and manufacturing facilities are built to produces goods that rely upon the nanotechnology, the educational system is going to have to become involved to educate the individuals on the production and manufacturing processes.

J. M. Weikle (Sent Thursday, August 27, 2009 10:25 PM)

Awesome! Let's get it going! Where can I invest? LoL

John (Sent Thursday, August 27, 2009 10:26 PM)

This is very exciting technology. IBM is traditionally, in top of the patent filings. The patent system allows for them to make these advances and instead of keeping them secret disclose them to the public.

John C. Thomas III, Pittsburgh PA (Sent Thursday, August 27, 2009 10:29 PM)

The tools are being developed to herald in the next great era of technology.

First, we had the Industrial Revolution, then the Atomic Age. The Space Race began, then came the Information Age, followed by the mapping of the Human Genome. We work to reclaim our planet from the brink, while we are discovering new solar systems in deep space, possibly harboring a planet like our own. One day, we will no longer be alone. While we accelerate particles to nearly the speed of light to discover how our universe works, we are on the verge of creating artificial life. While knowledge is exploding and is being shared all around us through the world wide, the nanotech era has begun.

What an amazing time to be alive.

R.R., Columbus, OH (Sent Thursday, August 27, 2009 10:29 PM)

This will definitely accelerate Nanotech. And man as an engineer I want that scope!

FrankH, San Diego, CA (Sent Thursday, August 27, 2009 10:30 PM)

Fifteen years seems like a long time from experimental technique validation to production. Maybe they are thinking universal, pervasive technology? Does anyone know what Ray Kurzweil thinks about this?

Dariel, Santa Cruz, California (Sent Thursday, August 27, 2009 10:33 PM)

Pretty cool article. I am not a scientist but have had the chance to work with some dealing with atomic force microscopes from a mechanical engineering standpoint. It never ceases to amaze me at the things GOD created.

Michael R. Ft. Worth, Texas (Sent Thursday, August 27, 2009 10:38 PM)

This is the stuff the government should be funding, not cash for clunkers.

Rob Blakey, Basehor, KS (Sent Thursday, August 27, 2009 10:38 PM)

The money would be better spent on health care for everyone!

Joe (Sent Thursday, August 27, 2009 10:45 PM)

What will it take to speed up the process?

Roger Sikes,Gastonia, NC (Sent Thursday, August 27, 2009 10:46 PM)

What an image. Too see a moment on that scale of reality and the basic geometries of atoms/molecules interacting is very exciting.

JohannesNova, Newport, RI (Sent Thursday, August 27, 2009 10:50 PM)

Great technological break through. However,I can't help but wonder if the Defense Department is considering weaponizing this technology through DARPA or a Black Program. Let's hope not.

Robert, Upstate, NY (Sent Thursday, August 27, 2009 11:02 PM)

I dont get it...are these nude photos?

Zapperman (Sent Thursday, August 27, 2009 11:13 PM)

and yet they cant make a toothpaste that doesnt taste like ass when you drink orange juice...

rob atall, ann arbor, MI (Sent Thursday, August 27, 2009 11:23 PM)

Over 35 years ago I dreamt of this sort of thing. It occurred to me during a class in semiconductors that there might be organic semiconductors. There were but they were not very developed.
So now we have organic light emitting diode displays (in camera viewers and elsewhere). We might get to: Molecule scale transistors and gates, caged active molecules shuttled around by other molecules and oriented for structuring that would help an electronic circuit self assemble similar to the way the body self assembles, way way strong and advanced materials with amazing characteristics, systems of useful molecules that might store the total information of the library of congress in a few cubic centimeters.
Looking closer at just one of these concepts, consider semiconductor technology which can pattern the two dimensional silicon surface of a memory device to yield over ten billion devices in a square centimeter. If the promise of the nanoscale devices holds true then approximately 100,000 devices per each of three dimensions could yield one million billion devices per cubic centimeter. That is the promise of self assembly as is presently routinely done in biological systems. Easy, no, but the payoff is huge.
To organize and design at this level would yield incredible advances that would dwarf the electronics revolution and enable so many other advances.

Bob, Hendersonville, NC (Sent Friday, August 28, 2009 12:00 AM)

It appears as if the ends of the molecule are brighter in the image. I wonder if this is an artifact of the imaging technique or if it could be due to resonance or the aromatic nature of the terminal benzene rings.

Someone, Somewhere (Sent Friday, August 28, 2009 12:00 AM)

What a bunch of garbage. Just a liberal attempt to wastes more tax payer dollars.......

Donald R. May, MD, Lubbock, Texas (Sent Friday, August 28, 2009 12:01 AM)

Does the weirdness of quantum physics enter into this development? Was the structure of the molecule fixed by by our preconceived notion at the time of viewing it? These are interesting times.

William, Shelby, Ohio (Sent Friday, August 28, 2009 12:04 AM)

This was invisioned more than 10 years ago. It has taken this long to improve this technique. It's quite an accomplishment.

R.B.A., Los Angeles, California (Sent Friday, August 28, 2009 12:13 AM)

Can anyone explain in laymen terms what implications this discovery has for the common man?

Joe Doe (Sent Friday, August 28, 2009 12:59 AM)

This is a great step forward in our discovery of the sublime intricacy right in front of us- too bad there are only a handful of people who can work on this and understand it. Our general lack of scientific understanding, as a society, keeps us from truly unlocking all the benefits technology offers- but these images are a nice step to see in my lifetime.

I wonder how much these researchers get paid for these contributions. Odds are it isn't anything near what Andres Hill (Citigroup) makes in bonuses alone. Yeah, we really need more hedge fund managers.

Nonplussed (Sent Friday, August 28, 2009 1:19 AM)

Alan -- Great story! You're dead-on regarding the decades that scientists have been imaging molecules. To see just how far the technology has come, check out the first image of a benzene molecule, done in 1988 by scientists at IBM's Almaden Research Center in San Jose. The only web copy I could find is Fig 17 of this pdf: http://www.nanoinfo.net/images_workshop/papers/frommer1.pdf . At the time, it was big news, too, as evidenced by this New York Times article: http://www.nytimes.com/1988/08/16/science/a-pervasive-molecule-is-captured-in-a-photograph.html?pagewanted=all .

It may prove to be impractical to hand-built macroscopic structures atom-by-atom, but these scanning probe microscopes give scientists unprecedented -- and constantly improving -- ability to explore and understand molecules and their properties ... which has to be a big assist in all sorts of chemical and biological achievements.

Mike (Sent Friday, August 28, 2009 1:56 AM)

i'm glad there are smart people in the world who can figure out the world and explain it to me. kudos on the discovery, and the article.

julius willis (Sent Friday, August 28, 2009 2:35 AM)

if you like this article you would also like reading about molecule cascade http://almaden.ibm.com/st/past_projects/molecule_cascades/ and a gallery of atomic-level images http://almaden.ibm.com/vis/stm/gallery.html

Arnon, San Jose (Sent Friday, August 28, 2009 4:37 AM)

This sounds really cool. I wish I was smart enough to understand these discoveries. I hope it benefits humans.

NimrodWildfire (Sent Friday, August 28, 2009 7:37 AM)

I am amazed and thankful. Keep up the good work.

Ginn Wild, Dix Hills, N.Y. (Sent Friday, August 28, 2009 9:23 AM)

Donald R. May, MD wrote:
"What a bunch of garbage. Just a liberal attempt to wastes more tax payer dollars....... "

WHAT?@!#!# The last time I checked, tax dollars weren't funding IBM's Zurich Research Laboratory. [...]

Scott M. (Sent Friday, August 28, 2009 9:30 AM)

Thanks for the Naked Truth about this amazing new atomic microscopy technology Alan! Truly amazing how the scientists have done electron microscopes one better. So cool that now we can really see molecules and hopefully someday we'll be able to see individual atoms and their components moving about.

Could an even more powerful atomic microscope finally put to rest Heisenberg's Uncertainty Principle by being able to see and pinpoint individual electrons and particles so that we finally can tell where one is and where it's headed and at what speed? I doubt I'll live to see it but hopefully my Daughter or Granddaughters will.

Eric, Salinas, CA (Sent Friday, August 28, 2009 9:37 AM)

Thank you for the detailed information you gave in response to questions. I have bookmarked the wikipedia site about AFM and am looking forward to reading it. And my thanks also for many of the contributed comments.

Sue Atkins, Honolulu, Hawaii (Sent Friday, August 28, 2009 10:16 AM)

Amazement and thanks to Alan for responding to comments.

Bill, Proctorville, OH (Sent Friday, August 28, 2009 11:04 AM)

Seems to me that we are sort of going back in the 17/18 centry of hand building intricate mechonisms and clocks hand made one at a time.

A big difference though is at this level quantum effects dominate and "machines" will not be intuitive for the macro-mechanic to build, power or operate. but a fasinating new field to get into.

Gary Camp near LA, CA (Sent Friday, August 28, 2009 11:09 AM)

Alan,
Wonderful inversion of the telescope! I can remember being taught long, long ago that we would never "see" atoms or molecules. Depends on how you define "seeing", I guess.

To Dr. D.R. May.
Get your head out of your prejudices. The work was done at the IBM Lab. [ALAN ADDS: The work did not receive funding from the U.S. government, but it did receive funding from a European Community initiative as well as the Swiss "Nanoscale Science" initiative. One of Gross' collaborators, Peter Liljeroth, received Dutch research funding.]
2. The biggest waste of taxpayer dollars in history was by your fellow texas citizen, Bushie. Remember, he started with a "Liberal" surplus.

And before you say anything, I was a Goldwater Republican who couldn't stomach Bushie in 1990 and I'm a former Marine.

Wade Whitlock, Aberdeen, MD (Sent Friday, August 28, 2009 11:17 AM)

Alan,
Non Sequitor! Have you seen the news item about production of butanol with mutated bacteria and polyester? Question: What if the bacteria are released? Would that force a change to natural fibers?

Wade Whitlock, Aberdeen, MD (Sent Friday, August 28, 2009 11:36 AM)

Others have said it: WOW.
Remember Stanley's masterpiece, 2001 A Space Odyssey?
Remember the star of the show? His name was HAL 9000. He'd never made a mistake. Vast power, as the post earlier discusses. This discovery just might let us make a HAL 9000. Oh, what are the letters in the alphabet before each letter in HAL? Hmmmm. And we know who did this brilliant work and who they work for. Stanley, I wish you were still with us.

Fred Ficarra, Seabeck Wash (Sent Friday, August 28, 2009 12:30 PM)

I wish I had this instrument in my research. I study the assembly of amyloid peptides in diseases such as Alzheimer's and Parkinson's. We use atomic force microscopy, but the resloution is extremely limited when compared to these images. I can't wait to see instruments such as these being applied in the field in the future. I also hope I get one!

For all those who need a better understanding of what this means: This resolution opens up a window to view molecular interactions that cause disease, the inner workings of the cell, or drug interactions with biomolecules. It means that money and time need not be wasted doing countless expensive experiments that still leave us groping in the dark for answers. Molecules can now be "seen" instead of only inferred. Molecules are like tiny machine parts and if we can see them better we can manipulate them better. This will have repercussions across many fields from materials manufacturing to biomedicine.

Mike, Long Island, NY (Sent Friday, August 28, 2009 12:48 PM)

This is excellent science that will lead to 'real world' applications quickly - I have no doubt of this.

David Lincoln, Gaithersburg, Maryland (Sent Friday, August 28, 2009 12:49 PM)

This will pretty soon prove there is no existence of a so called "God". Religion will fall off the grid while science and technology will lead us forward. You can't believe in fairy tale-superstition religions. Nobody can live past the age 900 years old such as Noah and get a boat with every species on it. It's completely ridiculous and you are all brain washed if you believe in religion period. Humans are just another animal on this planet that have evolved and adapted to our surroundings. Humans along with everything else will not be able to fully understand the real concept of life. Yes, it’s scary; but technology has gotten us this far to understand religions are old fairy tale with fictional characters. People need to look more into a book Physics instead of a book of garbage written over 2,000 years ago with no science at all. Science is everything.

Ron Sochacki, Crystal Lake, IL (Sent Friday, August 28, 2009 1:33 PM)

I think this is a really significant accomplishment but I am a bit dismayed to see how few women have picked up on it. I counted 2 female respondents out of (approx) 50 comments. It is my belief that only science and technology will save us and I think the world is going to be seriously hobbled if we don't get more women engaged in those disciplines.

Jim Christensen, El Cajon, Ca (Sent Friday, August 28, 2009 2:09 PM)

I have a different take on the whole "terminator" theory that so many people freak out about. I think we will see robotics more and more in the future, just not in the doomsday scenario. We will see robotics become intertwined with our organic bodies. Implements, prosthetics, things of that nature. We will meld the best of both worlds and that will be the next evolutionary step for man we will become bio-mechanical organisms. Provided, we don't blow ourselves up first, of course.

Bill Brasky (Sent Friday, August 28, 2009 2:17 PM)

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