Name: hand controlled manipulation of single molecules via a scanning probe microscope with a 3d virtual reality interface
Uploaded: 2016-10-02T14:00:00
Description: Watch this Scientific Journal Video about Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface at JoVE.com

The authors have no acknowledgements.

Caution: PTCDA can be irritating to the skin or eyes and should therefore be handled with care using appropriate gloves. Please consult appropriate safety brochures. Cryogenic liquids can produce effects on the skin similar to a thermal burn or can cause frostbite on prolonged exposure. Always wear safety glasses and appropriate cryogenic gloves when handling cryogenic liquids. The gas formed by cryogenic liquids is very cold and usually heavier than air and can accumulate near the floor displacing air. When there is not enough air or oxygen...

<ol>
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Nanotechnol. 6, 2148-2153 (2015).</li><li>Wagner, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scanning+Quantum+Dot+Microscopy.">Scanning Quantum Dot Microscopy.</a> Phys. Rev. Lett. 115 (2), 026101 (2015).</li><li>Mura, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Experimental+and+theoretical+analysis+of+H-bonded+supramolecular+assemblies+of+PTCDA+molecules.">Experimental and theoretical analysis of H-bonded supramolecular assemblies of PTCDA molecules.</a> Phys. Rev. B. 81 (19), 195412 (2010).</li><li>Besocke, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+easily+operable+scanning+tunneling+microscope.">An easily operable scanning tunneling microscope.</a> Surf. Sci. Lett. (1-2), 145-153 (1987).</li><li>Giessibl, F. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+atomic+force+microscopy.">Advances in atomic force microscopy.</a> Rev. Mod. Phys. 75 (3), 949-983 (2003).</li><li>Albrecht, T. R., Gru&#776;tter, P., Horne, D., Rugar, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frequency+modulation+detection+using+high-Q+cantilevers+for+enhanced+force+microscope+sensitivity.">Frequency modulation detection using high-Q cantilevers for enhanced force microscope sensitivity.</a> J. Appl. Phys. 69 (2), 668-673 (1991).</li><li>Temirov, R., Lassise, A., Anders, F. B., Tautz, F. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kondo+effect+by+controlled+cleavage+of+a+single-molecule+contact.">Kondo effect by controlled cleavage of a single-molecule contact.</a> Nanotechnology. 19 (6), 065401 (2008).</li><li>Gl&#246;ckler, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+ordered+structures+and+submolecular+scanning+tunnelling+microscopy+contrast+of+PTCDA+and+DM-PBDCI+monolayers+on+Ag(111)+and+Ag(110).">Highly ordered structures and submolecular scanning tunnelling microscopy contrast of PTCDA and DM-PBDCI monolayers on Ag(111) and Ag(110).</a> Surf. Sci. 405 (1), 1-20 (1998).</li><li>Simon, G. H., Heyde, M., Rust, H. -. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recipes+for+cantilever+parameter+determination+in+dynamic+force+spectroscopy:+spring+constant+and+amplitude.">Recipes for cantilever parameter determination in dynamic force spectroscopy: spring constant and amplitude.</a> Nanotechnology. 18 (25), 255503 (2007).</li><li>Rohlfing, M., Temirov, R., Tautz, F. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adsorption+structure+and+scanning+tunneling+data+of+a+prototype+organic-inorganic+interface+PTCDA+on+Ag+(111).">Adsorption structure and scanning tunneling data of a prototype organic-inorganic interface PTCDA on Ag (111).</a> Phys. Rev. B. 76 (11), 115421 (2007).</li><li>Guthold, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlled+Manipulation+of+Molecular+Samples+with+the+nanoManipulator.">Controlled Manipulation of Molecular Samples with the nanoManipulator.</a> IEEE/ASME Trans. Mechatronics. 5 (2), 189-198 (2000).</li></ol>

Like other SPM-based methods, the molecular manipulation experiments described in this paper also depend to some extent on the properties of the SPM tip. The tip apex structure (which cannot be fully controlled) determines the strength of the tip-molecule bond. Hence the strength of the tip-molecule contact may vary considerably and thus sometimes may be too low. Hence within the protocol we refer to some basic tests of tip quality and tip treatment procedures. However, a more severe tip treatment might be required in so...

The low-temperature non-contact atomic force/scanning tunneling microscope (LT NC-AFM/STM, in the following simply termed SPM) is the tool of choice for atomically precise manipulation of individual atoms or molecules1-3. SPM-based manipulation is typically limited to two dimensions and consists of a series of abrupt and often stochastic manipulation events (jumps). This essentially limits the control over the process. Contacting the molecule in question by a single chemical bond at a well-defined atomic position leads to an approach that can overcome these limitations4-9. Throughout its manipulation the contacted molecule is connected to the SPM tip so that moving the molecule in all three dimensions by appropriate displacements of the tip becomes possible. This creates the possibility for various complex manipulation procedures performed in 3D space. However the contacting manipulation may be hindered by interactions of the manipulated molecule with the surface or/and other molecules in its surroundings, which may create forces that are large enough to rupture the tip-molecule contact. Therefore a particular 3D trajectory of the SPM tip may or may not result in a successful manipulation event. A question thus arises how to define protocols that lead to successful completion of manipulation in the circumstances when the tip-molecule bond has a limited strength, while the interactions of the manipulated molecule with its environment are not a-priori well characterized.
Here this question is approached in the most intuitive manner imaginable. The experimenter is allowed to control the displacements of the SPM tip simply by moving their hand7. This is achieved by coupling the SPM to a commercial motion capture system, some of the specifications of which are provided below. The advantage of &#34;hand controlled manipulation&#34; (HCM) is in the experimenter&#39;s ability to try out different manipulation trajectories quickly and learn from their failure or success.
The HCM setup has been used to conduct a proof-of-principle experiment in which a word (&#34;J&#220;LICH&#34;) was stenciled in a closed layer of perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) molecules on Ag(111), removing 48 molecules, one by one, with HCM7. Lifting a molecule from the surface cleaves its intermolecular hydrogen bonds which bind the molecules in the monolayer10. Typically the total strength of the present intermolecular bonds exceeds the strength of the single chemical bond between the outermost atom of the tip and a carboxylic oxygen atom of PTCDA by which the molecule is contacted (see Figure 1). That may lead to the rupture of the tip-molecule contact and the following failure of the manipulation attempt. The experimenter&#39;s task is thus to determine a tip trajectory that breaks the resisting intermolecular bonds sequentially rather than simultaneously, so that the total force applied to the tip-molecule contact never exceeds its strength.
Although the desired trajectory may in principle be simulated, due to the size and complexity of the system involved the necessary simulations would take a prohibitively large amount of time. In contrast to that, using HCM it was possible to remove the first molecule after 40 minutes. Towards the end of the experiment the extraction took already much less time which confirms the effectiveness of the learning procedure. Additionally, the accuracy and versatility of the HCM method was evidenced in the act of reverse manipulation when a molecule extracted from the neighboring location was used to close the void left after the erroneous removal of another molecule from the monolayer.
Motion capture approach, while being fast and intuitive, is limited to the generation of tip-trajectory data. For further systematic development of new molecular manipulation protocols it is equally important to be able to view the tip trajectory data in real time as well as to analyze previously generated data. Therefore, the functionality of the HCM setup is enhanced substantially by adding virtual reality goggles which allow the experimentalist to see the data plotted in the 3D virtual scene where the tip trajectory is augmented by the current (I) and frequency shift (&#916;f) values measured by the SPM in real-time8 (see below). In addition to that, the virtual reality scene shows a model of the manipulated molecule that serves as a visual scale reference. Thus the HCM setup complimented by the virtual reality interface is suitable for systematic mapping of the manipulation trajectory space and successive refinement of the promising manipulation protocols. Besides that the system also facilitates the knowledge transfer between different experiments. The following paragraphs give a description of the setup and some of its specifications that are relevant for manipulation experiments.
The experiments are performed in ultra-high vacuum (UHV) at a base pressure of 1 x 10-10 mbar with a commercial SPM consisting of a preparation chamber and an analysis chamber. The preparation chamber is equipped with: Ar+ source used for sample sputtering, sample transfer via manipulator (allows heating and cooling of a sample), low-energy electron diffraction (LEED), a customized Knudsen cell (K-cell) containing PTCDA powder purified by sublimation. The analysis chamber is equipped with: LN2 bath cryostat with a volume of 12 L and a holding time of 46 hr, LHe bath cryostat (5 L, 72 hr), Besocke11 beetle-type SPM equipped with a tuning fork sensor12 (TFS) consisting of a quartz tuning fork with an electrically connected PtIr tip (for STM operation), which is cut and sharpened by a focused ion beam (FIB) (Figure 2).
<img alt="Figure 1" src="/files/ftp_upload/54506/54506fig2.jpg" /> 
Figure 2. Tuning fork sensor. (a) Image of a commercial tuning fork sensor with attached PtIr tip. (b) SEM image of the PtIr tip apex cut with FIB. <a href="https://www.jove.com/files/ftp_upload/54506/54506fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The AFM is operated in the frequency-modulated (FM) mode13 where the TFS is excited at the resonance (f0 &#8776; 31,080 Hz) with a dither piezo. The piezoelectric signal of the oscillating tuning fork is amplified and used by a phase locked loop (PLL), which keeps the amplitude of the TFS&#39;s oscillation constant and tracks changes of its resonance frequency, &#916;f = f - f0, that originates from the gradient of the force acting on the tip. As shown in Figure 3 the SPM tip position is controlled by voltages (ux, uy, uz) applied to a set of x-, y-, z-piezos (piezo constants at 5 K: x=15, y=16, z=6 &#197;/V). The ux, uy, uz-voltages (&#177;10 V at 20 bit resolution) are generated at the SPM electronics outputs. They are further amplified by a high voltage (HV) amplifier that has a maximum output voltage of &#177;200 V.
<img alt="Figure 1" src="/files/ftp_upload/54506/54506fig3.jpg" /> 
Figure 3. Schematics of the HCM setup. The position of (tracked object) TO that has multiple (infrared) IR sources installed on its surface is tracked by two infrared cameras of the motion capture system (MCS). TipControl software obtains the TO coordinates (x,y,z) from MCS and passes it to the remote voltage source (RVS) which generates a set of voltages (vx,vy,vz) that are summed with the voltages (ux,uy,uz) produced by the SPM electronics for control of the SPM tip position. The added voltage passes through a high-voltage (HV) amplifier and is further applied to the piezo-positioning system of the SPM tip. The setup allows manual control of the tip positioning when the SPM feedback (FB) loop is open. The (x,y,z) position of the tip as well as I(x,y,z) and &#916;f(x,y,z) are passed to the VRinterface software that plots it in the 3D virtual scene seen by the operator wearing the head-mounted display (HMD). <a href="https://www.jove.com/files/ftp_upload/54506/54506fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The tunneling current that flows between the SPM tip and the surface is measured by a transimpedance amplifier with a variable gain that ranges from 1 x 103 to 1 x 109 V/A (bandwidth at gain 1 x 109 V/A is 1 kHz). The output of the amplifier is fed into the STM feedback (FB) loop to regulate the tip height above the surface in constant current scanning mode. The stability of the junction (with the TFS oscillation turned off) is 1-3 pm. The piezoelectric oscillation signal of the TFS is amplified in two stages: (1) preamplifier fixed to the LN2&#160;shield (gain 1 x 108 V/A, bandwidth 20 kHz), and (2) external voltage amplifier with variable gain from 1 x 101 to 5 x 104 and a bandwidth of 1 MHz.
For HCM experiments, the SPM setup is extended with: motion capture system (MCS), remotely controllable multichannel voltage source (RVS), summing amplifier and virtual reality head mounted display (HMD). All of the listed devices except the summing amplifier were acquired commercially.
MSC is an infrared (IR) marker-tracking system that allows millimeter resolution of spatial displacements at a rate of 100 Hz. The system consists of two IR cameras, a trackable object (TO) and the control software. The MCS software obtains the x-, y-, z-coordinates of the TO in 3D space by analyzing its images obtained by the two cameras. MCS provides a programming library that allows use of the coordinates of TO in a separate software program.
The coordinates of TO (xTO, yTO, zTO) are passed to a custom-developed software program &#34;TipControl&#34;. Figure 4 shows a screenshot of the graphical user interface. The software is activated by the &#34;start&#34; button in the window. After activation (&#964;=0) the software sets all vx-, vy-, vz-voltages on RVS (voltage range &#177;10 V at 16 bit resolution, 50 msec latency per voltage step) according to the following expression <img alt="Equation 1" src="/files/ftp_upload/54506/54506eq1.jpg" />etc., where cx, cy, cz are the factors that convert 5 cm of the displacement of TO into 1 &#197; displacement of the SPM tip. The factors px(t), py(t), pz(t) have values defined by the status of the x-, y-, z-checkboxes in the software window. If the box is checked then the corresponding p(t) is set to 1. All p(t) are set to 0 at the moment when the &#34;pause&#34; button is pressed in the software window. That allows the operator to temporarily &#34;freeze&#34; the position of the tip. Pressing the &#34;reset all&#34; button in the software window sets vx-, vy-, vz-voltages to zero which returns the tip to its initial position defined by the SPM software. The text field &#34;manual command to RVS&#34; in the software window can be used to set any of the vx-, vy-, vz-voltages to any value in the allowed range of &#177;10 V. The vx-, vy-, vz-voltages generated by RVS are added to the ux-, uy-, uz-output voltage signals of SPM electronics via a summing amplifier (gain 1, bandwidth 50 kHz, output range &#177;10 V).
<img alt="Figure 1" src="/files/ftp_upload/54506/54506fig4.jpg" /> 
Figure 4. Screenshot of the interface window. Two indicators exhibit the status of connection with MCS and RVS systems. Checkboxes are used to activate hand-control along selected spatial axes. The button &#8220;Start&#8221; initiates data flow between MCS, TipControl and RVS according to the scheme shown in Figure 3. Button &#8220;Pause&#8221; stops the data flow. Button &#8220;Reset All&#8221; sets all RVS voltages to zero. <a href="https://www.jove.com/files/ftp_upload/54506/54506fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
For visualization of the experimental data (tip trajectory, I, &#916;f) a head mounted display (HMD) is used. The HMD provides a stereoscopic view (split HD display &#8212; one half for each eye, 1,920 x 1,080 pixels at 75 Hz). A dedicated IR camera tracks the position and orientation of HMD in 3D space using IR-LEDs fixed on the surface of HMD. The HMD tracking system allows the operator to change the view inside the 3D virtual reality scene by a turn of their head or simply moving their body.
The custom-written software &#34;VRinterface&#34; collects the data both from SPM and MCS, renders it in the 3D scene using OpenGL and displays it in the HMD with the help of the HMDs software development kit (SDK). VRinterface retrieves the actual x-, y-, z-coordinates of the tip directly from the tip software (few millisecond latency) while I and &#916;f signals are read directly from the outputs of the SPM electronics (latency &#8776; 250 msec). Figure 5 shows a screenshot of the 3D virtual scene as seen by the operator wearing HMD during HCM. Inside the 3D virtual scene the tip apex is rendered as a white sphere. The coloring of the recorded tip trajectories reflects values of either log(I(x,y,z)) or &#916;f(x,y,z). Switching between log(I(x,y,z)) or &#916;f(x,y,z) color modes is done by the press of a button. Another button initiates the recording (and displaying) of experimental tip trajectory data. When pressed again the button stops the recording. The virtual scene also shows a static PTCDA molecule which is used as a visual aid during manipulation. The operator aligns its orientation manually to fit the orientation of the real molecule on the surface by using buttons on a keyboard.
Caution: Because the head tracking of HMD relies on IR-LEDs, it may interfere with the MCS since it also uses IR light to track the position of TO. Therefore TO has to have a unique shape recognized by the MCS. This helps MCS to discriminate between the signals that come from TO and those coming from IR-LEDs of HMD.
<img alt="Figure 1" src="/files/ftp_upload/54506/54506fig5.jpg" /> 
Figure 5. Screenshot of the 3D virtual scene displayed to the operator in HMD during HCM. A set of white spheres forms a model Ag(111) surface. Orientation of the model surface may not necessarily coincide with the orientation of the sample. A model of the PTCDA molecule is placed above the model surface. C, O, H atoms of PTCDA are shown in black, red and white respectively. For the purpose of convenience azimuthal orientation of the model molecule can be adjusted to fit the orientation of the real molecule chosen for manipulation. The tip position is marked by a single white sphere representing the outermost tip apex atom. The real-time I(x,y,z) and &#916;f(x,y,z) data are displayed as bar indicators placed next to the tip. Previously recorded as well as the currently executed manipulations are displayed as 3D trajectories whose color represents either log(I(x,y,z)) or &#916;f(x,y,z) values measured at corresponding positions of the trajectory. The figure shows trajectories that are colored with log(I(x,y,z)) signal. The color contrast can be switched between log(I(x,y,z)) and &#916;f(x,y,z) modes by press of a button. <a href="https://www.jove.com/files/ftp_upload/54506/54506fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>LN2</td>
			<td></td>
			<td></td>
			<td>caution: cryogenic liquid</td>
		</tr>
		<tr>
			<td>LHe</td>
			<td></td>
			<td></td>
			<td>caution: cryogenic liquid</td>
		</tr>
		<tr>
			<td>PTCDA</td>
			<td></td>
			<td></td>
			<td>caution: irritating substance</td>
		</tr>
		<tr>
			<td>Knudsen cell (K-cell)</td>
			<td></td>
			<td></td>
			<td>custom</td>
		</tr>
		<tr>
			<td>ErLEED</td>
			<td>Specs</td>
			<td></td>
			<td>used with power supply ErLEED 1000A</td>
		</tr>
		<tr>
			<td>combient LT NC-AFM/STM</td>
			<td>Createc</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>qPlus sensor</td>
			<td>Createc</td>
			<td></td>
			<td>TFS</td>
		</tr>
		<tr>
			<td>preamplifier&#160;</td>
			<td>Createc</td>
			<td></td>
			<td>amplifier for tuning forc signal fixed to LN2 shield (stage 1)</td>
		</tr>
		<tr>
			<td>Low-Noise Voltage Preamplifier</td>
			<td>Standford Research System</td>
			<td>SR560</td>
			<td>external amplifier for tuning forc signal (stage 2)</td>
		</tr>
		<tr>
			<td>Variable Gain Low Noise Current Amplifier</td>
			<td>Femto</td>
			<td>DLPCA-200</td>
			<td>amplifier for tunneling current</td>
		</tr>
		<tr>
			<td>Bonita</td>
			<td>Vicon</td>
			<td>B10, SN: MXBN-0B10-3658</td>
			<td>MCS IR camera</td>
		</tr>
		<tr>
			<td>Apex Interaction Device</td>
			<td>Vicon</td>
			<td>SN: AP0062</td>
			<td>MCS trackable object (TO)</td>
		</tr>
		<tr>
			<td>MX Calibration Wand</td>
			<td>Vicon</td>
			<td></td>
			<td>MCS calibration object</td>
		</tr>
		<tr>
			<td>Tracker</td>
			<td>Vicon</td>
			<td></td>
			<td>MCS software</td>
		</tr>
		<tr>
			<td>BS series voltage supply</td>
			<td>stahl-electronics</td>
			<td>BS 1-4</td>
			<td>RVS</td>
		</tr>
		<tr>
			<td>summing amplifier&#160;</td>
			<td></td>
			<td></td>
			<td>custom, gain 1, based on operational amplifier TL072</td>
		</tr>
		<tr>
			<td>Oculus Rrift Development Kit 2</td>
			<td>Oculus VR</td>
			<td></td>
			<td>HMD</td>
		</tr>
		<tr>
			<td>TipControl</td>
			<td></td>
			<td></td>
			<td>custom-written software</td>
		</tr>
		<tr>
			<td>VRinterface</td>
			<td></td>
			<td></td>
			<td>custom-written software</td>
		</tr>
	</tbody>
</table>

hand controlled manipulation of single molecules via a scanning probe microscope with a 3d virtual reality interface

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building blocks in a bottom-up approach is still open. The scanning probe microscope (SPM) could be a tool of choice; however, SPM-based manipulation was until recently limited to two dimensions (2D). Binding the SPM tip to a molecule at a well-defined position opens an opportunity of controlled manipulation in 3D space. Unfortunately, 3D manipulation is largely incompatible with the typical 2D-paradigm of viewing and generating SPM data on a computer. For intuitive and efficient manipulation we therefore couple a low-temperature non-contact atomic force/scanning tunneling microscope (LT NC-AFM/STM) to a motion capture system and fully immersive virtual reality goggles. This setup permits &#34;hand controlled manipulation&#34; (HCM), in which the SPM tip is moved according to the motion of the experimenter&#39;s hand, while the tip trajectories as well as the response of the SPM junction are visualized in 3D. HCM paves the way to the development of complex manipulation protocols, potentially leading to a better fundamental understanding of nanoscale interactions acting between molecules on surfaces. Here we describe the setup and the steps needed to achieve successful hand-controlled molecular manipulation within the virtual reality environment.

Note: This part shows work published in7,8.
Applying HCM to the problem of lifting PTCDA/Ag(111) out of a layer, we were able to write a pattern by sequentially removing individual molecules (Figure 9). In total 48 molecules were removed, 40 of which could be redeposited to the clean Ag(111), showing that the molecules stay intact during the manipulation process. This allows using HCM...

Watch this Scientific Journal Video about Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface at JoVE.com

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

We demonstrate the precise manipulation of individual organic molecules on a metal surface with the tip of a scanning probe microscope driven in 3D by the experimenter's hand using a motion capture system and fully immersive virtual reality goggles.

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building ...

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.

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