Chapter 3

Design and Synthesis of Organic Molecules for Molecular Electronics

Karsten Jennum and Mogens Brøndsted Nielsen

3.1 Introduction

Innovative developments within electronic device fabrication have turned millimeter transistors into micrometer-integrated circuit systems throughout the last half of the former century. This technological advance has given us faster, smaller, and more advanced computer systems. If this miniaturization trend continues to push the size boundaries for integrated circuits to meet the growing demands of society, some limitations in the classical silicon-based devices will occur. The present technology might encounter some inherent limitations that would lead to a dead end within the next few years because of some major challenges: for example, the micropatterning techniques to produce circuitry on the silicon wafers in the nanometer regime or the fact that, when silicon layers are just a few atoms thick, the band structure disappears [1]. To secure further advances within this field, it is crucial to develop novel manufacturing procedures for future nanoscale electronics. For this purpose, organic materials could be the right alternative to obtain the desired electronic capabilities for a given molecular-based device. π-Conjugated molecules are particularly attractive as wires and electronic components, with their size in the range of nanometers, delocalized electrons, and small highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO–LUMO) gaps, which can be tuned by suitable functionalization. The aim of this multidisciplinary research field is to mimic key electronic components such as wires, rectifiers, switches, and memory devices [2].

Device fabrication on the molecular scale and controlled assembly of molecules are still major issues to overcome if computers are to be equipped with “molecular” circuits. Nevertheless, much knowledge has been added to this field in the last decades, and several new techniques have been developed. For instance, today's microscope techniques allow measurements on single molecules both in solid state and in solution [3], and this provides a golden opportunity to test and measure the intrinsic properties of molecular systems. This chapter, however, will instead focus on the actual design of organic molecules as components for molecular electronics and, in particular, on their synthesis.

3.2 Organic Molecular Wires

3.2.1 Terminal Connectivity: The “Alligator Clip Principle”

A molecular wire has to be bound to metal-based electrodes via suitable anchoring groups. Considering these anchoring groups in a macro perspective, one could imagine them as being alligator clips on metal wires used for simple test circuits. Figure 3.1 shows a selection of such molecular anchoring groups [2–17]. The thiol (SH) anchoring group was the first to be exploited in charge transport experiments through single organic wires, and it is still the most widely used anchoring group. This is due to the strong binding of sulfur to metals such as silver, copper, and gold [4]. In a recent study by Wandlowski and coworkers [5], four tolane derivatives with –SH (thiol), –NH2 (amino), –CN (cyano), and –PY (pyridine) end groups were compared in regard to anchoring to gold electrodes in single-molecular conductance experiments using mechanically controlled microscopy break junctions (MCBJs) and scanning tunneling microscopy break junctions (STM-BJs). The following sequence for junction formation probability and stability was obtained: PY > SH > NH2 > CN. Charge transport through SH/NH2-bound molecular junctions is dominated by hole transport via the HOMO, since the HOMO energy levels are here closest to the metal Fermi level [6]. On the other hand, charge transport through a nitrile (CN) or a pyridine (PY) linker is expected to go through the LUMO [7]. In addition to the above-mentioned anchoring groups, the isonitrile (NC) group has also been used as a linker in single-molecular junction measurements [8] and is among a group of alternative alligator clips counting carboxylic acid (COOH) [9], nitro (NO2) [10], dimethylphosphine (PMe2) [11], and methylsulfide (SMe) [11]. Recently, Venkataraman and coworkers [12] investigated molecules (Me3Sn–CH2-π-system-CH2–SnMe3) terminated with trimethyltin end groups that were cleaved off in situ. This gave rise to a direct σ-bond between the carbon backbone (methylene unit) and the gold metal electrodes and, in consequence, a direct coupling between the neighboring π-system and the electrodes, which resulted in a 100-fold enhancement in the conductivity compared with junctions with conventional linkers.

Figure 3.1. Anchoring groups that can act as connecting link between the molecular wire and the metal electrodes.

It is essential for reliable molecular junctions that the anchoring group is either covalently bound or well adsorbed to the electrode surface. A study of the adsorption of Buckminsterfullerene (C60) on gold surfaces has revealed that C60 hybridizes strongly with gold [13], leading to a high single-molecular conductance [14]. In the case of 1,4-dithiobenzene, 1,4-diaminobenzene, and a fullerene diaminobenzene dumbbell molecule, MCBJ experiments showed that the C60 dumbbell exhibited an increasing stretching length before breaking compared with the others, indicating that fullerenes form stable molecular junctions and are suitable as anchoring groups [15]. Yao and Tour [16] have also reported a tripod structure containing three protected thiolate groups, which when standing on its three legs should create a more well-defined wire-to-metal surface interface. In a recent example, three pyridine units were also arranged in a tripod structure (Figure 3.1) that was found to be very suitable as an anchoring group in single-molecular junctions [17].

The thiophenol anchoring group has found the most widespread usage. A toolbox for synthesizing thiophenols is presented in Scheme 3.1. The thiophenols are normally converted into the S-acetyl-protected derivatives because of their air instability. Nevertheless, this S-acetyl-protecting group is very labile and can easily be cleaved under various conditions [18].

Scheme 3.1. Synthesis of thiophenols.

Alternatively, it can be an advantage to protect the thiophenols with more persistent groups. This could be either the tert-butyl protecting group, which is resistant to both strongly basic and acidic conditions but is easily removed with BBr3 [19], or the cyanoethyl group, which is suitable when nonalkaline conditions are used; NaOMe/HOMe removes this protecting group readily [20].

A particularly interesting compound is the S-acetyl-4-iodothiophenole 1, which is a key compound for thiol end-capped molecular wires, since the iodine functionality is a precursor for C–C bond formations to aromatics [21], double [22], and triple [23] bonds in various metal-mediated coupling reactions. The synthetic approach toward compound 1 has evolved into a handful of different pathways, which are shown in Scheme 3.2, Scheme 3.3, Scheme 3.4, and Scheme 3.5. Pearson and Tour [24] synthesized alligator clip 1 from diiodide 2, which was treated with t-BuLi to form the monolithiated phenyliodide that was then treated with elemental sulfur, and SAc was finally formed upon quenching with AcCl. Subjecting compound 1 to a Sonogashira palladium-catalyzed cross-coupling reaction with trimethylsilylacetylene gave compound 3, which ultimately was converted into ethynylbenzene 4 after removal of the trimethylsilyl group. Compound 4 can subsequently be coupled with other halide scaffolds for further expansions of the π-conjugated wire.

Scheme 3.2. Synthesis of acetyl-protected thiol end-capped building block.

Scheme 3.3. Alternative synthesis of building block 1.

Scheme 3.4. Alternative synthesis of building block 1.

Scheme 3.5. Alternative synthesis of building block 1.

In the route toward compound 1, it is crucial to form only the monolithiated iodobenzene, a reaction that is not always easy to reproduce. To solve this problem, Bryce and coworkers [25] developed a four-step high-yielding synthetic procedure shown in Scheme 3.3. N,N-Dimethylthiocarbamoyl chloride was treated with 4-iodophenol 5 forming compound 6, which at high temperatures underwent a Newman–Kwart rearrangement affording product 7. Hydrolysis of 7 yielded iodothiophenol 8 that finally was converted into 1 by treatment with AcCl.

A shorter pathway to 1 is by reduction of commercially available pipsyl chloride (4-iodobenzenesulfonyl chloride) 9 with triphenylphosphine (Scheme 3.4), giving in one step iodothiophenol 8, which was then subjected to S-acylation [26]. Alternatively, pipsyl chloride 9 can be reduced by zinc powder and dichlorodimethylsilane in N,N-dimethylacetamide (DMA) and 1,2-dichloroethane, followed by the addition of acetyl chloride to form 1 in a one-pot reaction (Scheme 3.4) [27].

Reaction between sodium thioacetate and stable iododiazonium salt 10 in a nucleophilic aromatic substitution gave 1 in high yield (Scheme 3.5). This procedure could also be extended to a variety of...