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A way to measure the bonds that hold together a single molecule is developed by Cornell physicists

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Ordinary STM images of an acetylene molecule
Cornell University
Ordinary STM images of an acetylene molecule adsorbed (bonded) to a copper surface. (A) shows the molecule, which consists of two carbon atoms, each with a hydrogen atom attached. The two light areas represent the hydrogen atoms, whose bonds are tipped slightly up from the surface when the molecule is bonded to copper. The dark area represents the cloud of electrons around the carbon atoms, which is squeezed out to the sides of the space between the nuclei. In (B), the STM is adjusted to show the copper atoms on the surface, arranged in a crystal lattice. In (C), a diagram of the lattice is superimposed over the image of the molecule. (D) is a schematic diagram showing how the molecule appears when bonded to the copper surface. In the top view, the dashed line represents the dark area in the STM image.

Ever since the invention in 1982 of the scanning tunneling microscope (STM), which can see single atoms, scientists have been trying to use the instrument to examine the bonds that hold atoms together in molecules.

In a significant advance, a team of Cornell University physicists has successfully made a measurement of the frequency at which atoms in a bond are vibrating against each other in a single molecule of acetylene. The research for the first time provides a way to identify single molecules by their vibrational signatures and to study how their bonds change during chemical processes. It could lead to better understanding of how catalysts work and a new way to study biological molecules like DNA.

The experiment by Cornell physics graduate students Barry Stipe and Mohammad Rezaei and Wilson Ho, professor of physics, is described in the June 12, issue of Science.

Vibrational spectroscopy is the study of the energy (which for scientists identifies the frequency) of vibration of molecular bonds. Atoms are held together in molecules because the negatively charged electrons in one atom are pulled toward the positively charged nucleus of another and vice versa. But at the same time, the electrons in one atom repel those in the other, and the protons in the nuclei do the same.

This constant push-pull can create a vibration, as if the atoms were connected by tiny springs in constant motion. The vibration is unique for each possible arrangement of atoms in a molecule, and in the language of quantum mechanics, each vibration has a characteristic "energy level." An electron whose energy matches or exceeds that of a vibrational energy level in a molecule can pass through the molecule more easily.

By measuring current flow through molecules over a wide range of energies, scientists can create a "vibrational spectrum" that provides a fingerprint of the bonds in a molecule and thus is a powerful analytical method for identification of unknown chemicals.

For years the only useful way to do this type of vibrational spectroscopy was to pass a current through a thin film of a substance and vary the voltage, and therefore the energy of the electrons in the current. This method, called "inelastic electron tunneling spectroscopy," only gives an average reading on billions of molecules. Since the invention of the STM, scientists have searched for a way to do the same measurements on one molecule at a time.

vibrational microscopy, with computer-generated 3-dimensional images
Cornell University
An example of vibrational microscopy, with computer-generated 3-dimensional images of an ordinary acetylene molecule (C2H2) and an acetylene molecule in which hydrogen has been replaced by deuterium (C2D2). (A) shows an ordinary STM scan of the surface. Both molecules appear as depressions because the tip moves closer to the surface when the tip scans over them; the depressions appear circular because the molecules are rotating between two possible positions on the copper surface. (B) shows a scan of the surface with the STM voltage set at 358 mV, with a peak identifying the C2H2 molecule. (C) is a scan at 266 mV, with a peak identifying the C2D2 molecule. (D) is a scan at an intermediate voltage of 312 mV, which barely responds to either molecule.

Stipe, Rezaei and Ho succeeded by using a specially made STM cooled to 8 degrees Kelvin (minus 265 degrees Celsius, minus 445 degrees Fahrenheit) to minimize molecular motion, and working with acetylene (C2H2) molecules bonded to a copper surface.

An STM consists of a needle so sharp that its tip can narrow to just one atom, suspended less than a billionth of a meter above the surface to be scanned. When a voltage is applied between the needle and the surface a tiny electric current, called a "tunneling current," flows between the two. To form an image, the tip is moved back and forth across the surface and its height is adjusted so that the current remains constant. A computer converts these movements into an image that shows individual atoms as "bumps" or "dips."

For these experiments the tip was held still at a constant height above a molecule of acetylene, and the voltage was varied between 0 and 500 millivolts (mV). A peak was seen at 358 mV, representing a point at which the energy of the electrons matched that of the vibration of the bond between a carbon atom and a hydrogen atom in the acetylene molecule.

Previous researchers had not been able to obtain such a clear result, the Cornell researchers say, because the change in current at the peak was less than variations caused by unsteadiness of the STM needle. The instrument the Cornell researchers built in their laboratory is capable of holding steady the height of its needle tip to better than 0.01 Angstroms, or less than 1 percent of the diameter of an atom. The precision is obtained by a combination of careful design and special electronics and software to control the instrument.

The ability to identify molecular bonds in a single molecule opens a new way of using the STM that the Cornell researchers call "vibrational microscopy." If a surface is scanned with the STM tip held at a constant current while the voltage is set to detect a particular molecular bond, molecules with that bond will be highlighted on the scan while other molecules will remain invisible.

The Cornell researchers demonstrated this by comparing the images of an ordinary acetylene molecule with that of a molecule in which both hydrogen atoms are replaced with deuterium, or "heavy hydrogen." At 358 mV the scan shows only the ordinary acetylene molecule, while at 266 mV it shows only the molecule of deuterated acetylene. By increasing the resolution, the researchers say, the technique they have developed can, in principle, be used to image the positions of each of the chemical bonds within a single molecule.

The title of the paper in Science is "Single Molecule Vibrational Spectroscopy and Microscopy." The research was supported by a grant from the National Science Foundation.