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Molecule’s ’Anatomy’ Imaged
Aug 2009
ZURICH, Switzerland, Aug. 31, 2009 -- The "anatomy," or chemical structure, inside a molecule has been imaged with unprecedented resolution through the use of noncontact atomic force microscopy (AFM).

Imaging individual atoms within a molecule has been a long-standing goal of surface microscopy. The results by IBM scientists in Zurich push the exploration of using molecules and atoms at the smallest scale and could greatly impact the field of nanotechnology, which seeks to understand and control some of the smallest objects known to mankind.

A 3-D rendered view of the "anatomy" of a pentacene molecule. By using an atomically sharp metal tip terminated with a carbon monoxide molecule, IBM scientists were able to measure in the short-range regime of forces which allowed them to obtain an image of the inner structure of the molecule. The colored surface represents experimental data. The model below shows the position of the atoms within the molecule. (Images courtesy of IBM Research - Zurich)

"Though not an exact comparison, if you think about how a doctor uses an x-ray to image bones and organs inside the human body, we are using the atomic force microscope to image the atomic structures that are the backbones of individual molecules," said IBM Researcher Gerhard Meyer. "Scanning probe techniques offer amazing potential for prototyping complex functional structures and for tailoring and studying their electronic and chemical properties on the atomic scale."

As reported in the Aug. 28 issue of Science, IBM Research -- Zurich scientists Leo Gross, Fabian Mohn, Nikolaj Moll and Gerhard Meyer, in collaboration with Peter Liljeroth of Utrecht University -- used an AFM operated in an ultrahigh vacuum and at very low temperatures ( -268 °C or - 451 °F) to image the chemical structure of individual pentacene molecules.

With their AFM, the scientists, for the first time ever, were able to look through the electron cloud and see the atomic backbone of an individual molecule (View the video). While not a direct technological comparison, this is reminiscent of x-rays that pass through soft tissue to enable clear images of bones.

The team's current publication follows on the heels of another experiment published two months ago in the June 12 issue of Science, where IBM scientists measured the charge states of atoms using an AFM (See AFM Gauges Atom Charge State). These breakthroughs will open new possibilities for investigating how charge transmits through molecules or molecular networks. Understanding the charge distribution at the atomic scale is essential for building smaller, faster and more energy-efficient computing components than today's processors and memory devices.

The delicate inner structure of a pentacene molecule imaged with an atomic force microscope. For the first time, scientists achieved a resolution that revealed the chemical structure of a molecule. The hexagonal shapes of the five carbon rings in the pentacene molecule are clearly resolved. Even the positions of the hydrogen atoms around the carbon rings can be deduced from the image. (Pixels correspond to actual data points)

The AFM uses a sharp metal tip to measure the tiny forces between the tip and the sample, such as a molecule, to create an image. In the present experiments, the molecule investigated was pentacene.

Pentacene is an oblong organic molecule consisting of 22 carbon atoms and 14 hydrogen atoms measuring 1.4 nm in length. The spacing between neighboring carbon atoms is only 0.14 nm – roughly 1 million times smaller then the diameter of a grain of sand. In the experimental image, the hexagonal shapes of the five carbon rings as well as the carbon atoms in the molecule are clearly resolved. Even the positions of the hydrogen atoms of the molecule can be deduced from the image.

"The key to achieving atomic resolution was an atomically sharp and defined tip apex as well as the very high stability of the system," said IBM scientist Leo Gross.

To image the chemical structure of a molecule with an AFM, it is necessary to operate in very close proximity to the molecule. The range, where chemical interactions give significant contributions to the forces, is less than a nanometer. To achieve this, the IBM scientists were required to increase the sensitivity of the tip and overcome a major limitation: Similar to the way two magnets would attract or repel each other when getting close, the molecules would easily be displaced by or attach to the tip when the tip was approached too closely – rendering further measurements impossible.

"We prepared our tip by deliberately picking up single atoms and molecules and showed that it is the foremost tip atom or molecule that governs the contrast and resolution of our AFM measurements," Gross said.

A tip terminated with a carbon monoxide (CO) molecule yielded the optimum contrast at a tip height of approximately 0.5 nm above the molecule being imaged and – acting like a powerful magnifying glass – resolved the individual atoms within the pentacene molecule, revealing its exact atomic-scale chemical structure.

IBM Research - Zurich scientists (l-r) Nikolaj Moll, Reto Schlittler, Gerhard Meyer, Fabian Mohn and Leo Gross stand behind an scanning tunneling/atomic force microscope similar to the one they used to image the "anatomy" of the pentacene molecule at an atomic resolution. (Photo by Michael Lowry)

Furthermore, the scientists were able to derive a complete 3-D force map of the molecule investigated. “To obtain a complete force map, the microscope needed to be highly stable, both mechanically and thermally, to ensure that both the tip of the AFM and the molecule remained unaltered during the more than 20 hours of data acquisition,” said Fabian Mohn, who is working on his PhD thesis at IBM Research - Zurich.

To corroborate the experimental findings and gain further insight into the exact nature of the imaging mechanism, IBM scientist Nikolaj Moll performed first-principles density functional theory calculations of the system investigated.

“The calculations helped us understand what caused the atomic contrast. In fact, we found that its source was Pauli repulsion between the CO and the pentacene molecule,” he said. 

This repulsive force stems from a quantum mechanical effect called the Pauli exclusion principle. It states that two identical electrons cannot approach each other too closely.

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The use of atoms, molecules and molecular-scale structures to enhance existing technology and develop new materials and devices. The goal of this technology is to manipulate atomic and molecular particles to create devices that are thousands of times smaller and faster than those of the current microtechnologies.
The technology of generating and harnessing light and other forms of radiant energy whose quantum unit is the photon. The science includes light emission, transmission, deflection, amplification and detection by optical components and instruments, lasers and other light sources, fiber optics, electro-optical instrumentation, related hardware and electronics, and sophisticated systems. The range of applications of photonics extends from energy generation to detection to communications and...
1. In optics, the ability of a lens system to reproduce the points, lines and surfaces in an object as separate entities in the image. 2. The minimum adjustment increment effectively achievable by a positioning mechanism. 3. In image processing, the accuracy with which brightness, spatial parameters and frame rate are divided into discrete levels.
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