Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface

The overall goal of hand controlled manipulation of individual molecules with the scanning probe microscope is the systematic and intuitive exploration of manipulation protocols in three dimensions. This method expands our capabilities in the field of molecular nanotechnology. For example, enabling us to systematically refine manipulation protocols for molecules and study inter-molecular directions or even to manufacture complex super-molecular structures.

The main advantage of this technique is its intuitive nature. The experimenter breaks the mold of programming automatically executed tip trajectories. And engages directly in the manipulation process.

Extending molecule manipulation to the third dimension and detaching from the surface opens up many new opportunities, but at the same time the requirement for 3D visualization control inevitably emerges. Set up the low temperature scanning probe microscope driven in 3D by the experimenter's hand, using a motion capture system as described in the text protocol. Also prepare a sample by depositing PTCDA on silver one one one, as described in the text protocol.

Set the scanning tunneling microscope or STM in constant current mode with the parameters that facilitate LUMO contrast for PTCDA. This allows one to determine the molecular orientation. In the SPM software, enter the parameters for the scan, including the area to be scanned, set points for the feedback loop, and the scanning speed.

Click the start button in the SPM software to image the PTCDA. After finding the surface area suitable for manipulation as described in the text protocol, create an overview window and adjust the area to be scanned and the scan speed. In order to record a detailed STM of a small region.

Next, test the ability of the tip to bind to the PTCDA molecule. Then prepare to record a current distance spectrum in which the tip is moved vertically towards carboxylic oxygen atoms of PTCDA by three to five angstroms. I as a function of Z is recorded by setting a constant bias voltage and defining a ramp of tip height to approach and to retract the tip from the surface.

Then click on the button single spectrum in the SPM software, and select a position on the most recently-recorded STM image above the carboxylic oxygen atoms of the PTCDA molecule selected for manipulation. Where the current distance spectrum should be recorded. To check whether the tip is in the proper condition, verify that the recorded current distance curve exhibits contact formation between the tip and the molecule in the form of a sharp increase of the current.

Typically the contact is strong enough for 0.5 to three angstroms lifting through vertical tip retraction after which the current drops abruptly when the bond ruptures. After re-scanning the PTCDA molecule selected for manipulation, position the tip over the carboxylic oxygen atom chosen for the manipulation by selecting set X, Y offset top, and then clicking in the respective image. Use the correct contact point as was verified earlier.

Activate the phase-locked loop and set the amplitude control mode. Set the oscillation amplitude as low as possible but high enough such that delta-F detection is possible with acceptable noise conditions and detection speed. Open the feedback loop and enter zero for the integrator value in the SPM software parameter window.

Then, set the junction bias to a few millivolts in the SPM software parameter window. Finally, set the current amplifier gain to one times 10 to the 7th volts per ampere in the SPM software value parameter window. Put on the head mounted display or HMD then take the trackable object.

If needed, re-position the HMD on the user's head while performing the following steps to either view the virtual reality scene or the lab environment, keyboard, and computer monitor. The next step is to mark the contact point in the 3D virtual scene. This anchor helps to find the contact easily for further manipulation attempts using hand controlled manipulation without the need to reset the remotely controllable multichannel voltage source.

To do so, activate the hand control along the z-axis only by checking the corresponding check box in the tip software, while keeping the X and Y checkboxes unchecked. Move the trackable object down while watching the current and delta-f realtime signals displayed in green and pink in the virtual scene. Stop moving the trackable object when the current and delta-f signals show a simultaneous sharp jump.

The signature of a contact formation. Start the trajectory recording in the VR interface by clicking the corresponding button and moving the trackable object up. Stop the trajectory recording in the VR interface by clicking the corresponding button as soon as the contact between the molecule and the tip ruptures.

The signature is a simultaneous sharp drop of the current and the delta-f signals. Click the pause button in the tip software to deactivate hand control. Activate the hand control of the tip movement along all spatial axes by checking the X, Y, and Z checkboxes in the software and clicking the start button in the tip software.

Try to find a successful lifting trajectory where the contacted molecule is completely detached from the surface at the end of the trajectory. To do so, approach the point where the anchor exhibited formation of the tip molecule contact by moving the trackable object while following the movement of the sphere representing the current tip position in the virtual scene. As soon as the contact is formed, start recording a new trajectory in the VR interface.

Pull the molecule in a direction suitable for lifting by moving the trackable object accordingly. If a rupture of the tip molecule contact is detected, stop recording the trajectory. Return to the contact point, start trajectory recording on contact formation, and execute a different manipulation.

Repeat this sequence until the lifting was successful. If the tip molecule contact is still stable at Z is greater than 10 angstroms, this is the signature for successful lifting of the molecule. To ensure that the molecule is on the tip, approach the surface again.

A smooth increase of delta-f occurring during the approach while the tip is still far from the surface indicates that the molecule is attached to the tip and oriented perpendicular to the surface. After a successful lifting, move the trackable object up to retract the tip an additional 10 to 20 angstroms from the surface. This reduces any interaction of the lifted molecule with the surface.

Fix the tip height by unchecking the Z checkbox and move the tip back to the initial X, Y coordinates using hand control. Uncheck the X or Y checkbox once the respective coordinate has come close to zero. Click on the pause button in the tip software to fix the current tip position and to deactivate hand control.

Without turning the feedback loop on, select set X Y offset top, and then click in the respective image to position the tip over the clean silver one one one surface 50 to 100 angstroms away from the island where the molecule was extracted. Then set the current amplifier gain to one times 10 to the 9th volts per ampere. Uncheck the X and Y checkboxes in the tip software, and click the start button.

Move the trackable object to approach the surface until a measurable current appears. Click on the pause button in the tip software to deactivate hand control. Step wise, increase the bias voltage by using a mouse-controlled slider in the SPM software until there is a simultaneous jump in current and delta-f which indicates that the molecule dropped to the surface.

Scan the area in constant current mode and check whether the molecule was indeed deposited back onto the surface. Finally, scan the area in the region where the molecule was extracted to examine the created vacancy. Shown here is an example for the nanostructuring of a molecular layer by hand controlled manipulation.

The series of STM images shows the sequential creation of 47 vacancies by consecutive removal of individual PTCDA molecules from a closed layer. This animation shows 34 manipulation trajectories that all led to the successful removal of PTCDA from the mono layer. Here is an animation of 3D tip trajectories demonstrating trajectory refinement and reproducability will hand controlled manipulation.

The gray curve represents an initial reference obtained from averaging the trajectories shown in the previous animation. The colored curves are seven manipulation attempts following the reference trajectory that were all unsuccessful, and seven successful attempts along a newly found kinked trajectory. Our method of hand controlled manipulation can be easily applied to new manipulation tasks or to new molecules.

Without the necessity to involve costly simulations. Once mastered, hand controlled manipulation can be used to study single molecules in configurations that are otherwise inaccessible. Performing such experiments may considerably widen our understanding of the fundamental processes that take place in such metal molecule metal junctions.

When doing hand controlled manipulation, the experimenter is subject to learning process. Later we intend to formalize that learning and finally delegate it to a computer.