3.3 Molecule Deposition
The molecules to be investigated must be attached to the gold leads in some way.
This is achieved by the high chemical affinity of the molecules’ thiol ends to the gold leads, as described in section3.3.1. Nevertheless, a carrier must first be found that lets the molecules float around the leads freely until they finally attach. This carrier is nothing but a fluid chemical solvent, in this experiment tetrahydrofuran (THF) and toluene, respectively. During this thesis, a method was developed by the author which facilitates the molecule deposition. A pipet is utilized to apply the molecules in solution onto the leads, as seen in Figure 3.10. It surrounds both electrodes at the same instance. The opening of the pipet is coated with a ring of PDMS2, a transparent, elastic material which is highly resistant against the solvent THF. A special device was designed by the author to adjust the size of the PDMS gasket to the diameter of the opening. The PDMS easily adapts to the substrate surface so the solution does not flow out of the pipet. At the same time, the soft PDMS prevents the delicate gold conductors from being scratched or destroyed by the glass pipet. This simple liquid cell facilitates measurements in solvents without the solution being evaporated.
Figure 3.10: Photography of the PDMS-coated pipet approaching the sample.
Also visible are the pushing rod, the counter supports and the electrical contact clamps (blurred in the foreground).
A specially designed pipet holder is integrated into the mechanical setup. The holder is mounted on a stage which can be moved in a horizontal plane. This permits accurate positioning of the pipet over the break junction. The pipet holder itself is connected to a vertical manipulator that allows the pipet to be carefully lowered onto the break junction.
2Polydimethylsiloxan, a silicon elastomer.
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3.3.1 Molecule Preparation
The molecules investigated have been designed at Columbia University with special respect to good electrical conductivity realized by conjugated bonds throughout the molecules [41]. Figure3.11 shows the base structure for all molecules investigated.
The end groups, denoted as X and Y in figure3.11, are connected by a continuous chain of conjugated bonds. Three different compounds have been designed by different choices for X and Y, as follows:
• The first type of molecules has one SBoc end (protected sulfur)3 and one CHO end (aldehyde).
• In the second type of molecules, X and Y both represent NHBoc, a protected NH group.
• The third type of molecules contains one SBoc end group and one CHCH2 (vinyl) end group.
OC12H25
OC12H25 O
N O
N
X Y
Figure 3.11: General structure formula of the molecules investigated, with X and Y denoting different end groups as described in the bullets above.
All molecules investigated have long lateral spacer groups in common. The dodecane chains at each side of the structure ensure that the molecules do not interfere with one another when forming a monolayer.
The first subject of research is provided by a combination of both the first and the second compound: The first molecule forms a monolayer on each gold lead due to its SH end groups (thiols), which have a strong affinity to gold. The free floating CHO ends of these anchor molecules can then connect to the second type of molecules, which provide a bridging link. Only through this reaction step is the gap between the gold leads finally crossed by a stable connection. The trimer-linkage process is illustrated in figure3.12.
3‘Boc’ denotes a commonly used protection group that is to prevent oxidation of stored molecules and reactions among them. It can easily be removed without damaging the molecule.
3.3 Molecule Deposition
Figure 3.12: Final formation of the trimer-molecule bridge (an imine) between the gold leads by two identical anchor parts and a single central group.
The third type of molecules provides a separate subject of investigation. Two molecules together form a dimer, which bridges the gap between the gold leads, as shown in figure 3.13.
Before the anchor molecules can form a monolayer, the protection groups must be removed. The deprotection is the same for all compounds. Exactly 1 mg of the compound is dissolved in 1 ml CH2Cl2 (methylene chloride) and 1 mg TFA (trifluoroacetic acid) and stirred at room temperature for 2-4 hours. The solvent is then removed in vacuo or by heating. The solution must remain under vacuum for a few hours for any remaining acid to be removed.
Monolayer formation is the same for both the vinyl and the aldehyde compound, i.e. the dimer anchors and the trimer anchors. The molecules are dissolved in 0.1 mM solutions of inhibitor-free THF. The sample sits in this solution for a few hours. This time is not enough to achieve ordered coverage of the monolayer, but it is sufficient for the measurements. A well ordered monolayer is not needed, rather only one molecule strand between the tips of the gold leads is sufficient.
Once the anchor molecules of the monolayers have finished assembling, the final linking process is started. This is obviously different for the trimer and the dimer.
To form the imines, which means to insert the center part of the trimer, a 0.6 mM
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OC12H25
Figure 3.13: The dimer formed by two molecules with vinyl ends.
solution in toluene is used. Again the sample sits in the solution for a few hours and is maintained at 60◦C during this time. It is important not to go above 60◦C because the monolayer will degrade above this temperature [41].
To form the dimer, the so-called metathesis reaction must be used, because the vinyl only dimerizes in the presence of Grubb’s catalyst 2nd generation. A 1 mM solution in methylene chloride is maintained at 50◦C.