Bonding thiol-substrate

Among the factors crucial for a SAM structure, the thiol-substrate bond has been a subject of particular controversy over more than 15 years. It is worth discussing the SAM/substrate interface in some detail since it is important not only for understanding SAM structures in general but also for electrochemical metal deposition when metal is intercalated at the SAM/Au interface (Section 5.4.3). As indicated above we limit the discussion to SAMs on Au(l 11) as this is the interface where theoretical and experimental work is sufficiently detailed to allow for a discussion at the atomic level. 

Metal UPD at the SAM/substrate interface is of interest for several reasons. Firstly, from an application point of view as the intercalation of another metal alters the thiol-substrate bond and, thus, the stability of a SAM that can be exploited to generate heterogeneous and patterned SAMs, a point we will return to later. Secondly, the intercalation and alteration of the thiol-substrate bond changes the morphology of a... 

GaAs has been coated with thiols with a view to modifying devices [123]. For these films, S-As bonds are presumed to be present. An ordering of the chains for = 18 has been reported. However, this system has generally been much less investigated than those involving metal substrates. 

Wet preparation of metal nanoparticles and their covalent immobilization onto silicon surface has been surveyed in this manuscript. Thiol-metal interaction can be widely used in order to functionalize the surface of metal nanoparticles by SAM formation. Various thiol molecules have been used for this purpose. The obtained functionalized particles can be purified to avoid the effect of unbounded molecules. On the other hand, hydrogen-terminated silicon surface is a good substrate to be covered by Si-C covalently bonded monolayer and can be functionalized readily by this link formation. Nanomaterials, such as biomolecules or nanoparticles, can be immobilized onto silicon surface by applying this monolayer formation system. 

Two examples from literature illustrate this approach nicely. Moore et al.114 assembled thiol-terminated long-chain S204-crown TTF onto Au and Pt surfaces by thiolato-metal bonds (see Figure 12). In the presence of various cations, most successfully Ag+, small differences were observed in the first oxidation potential (typically 60-80 mV). Similar responses were observed in solution state experiments with the same materials. The SAMs were stable when electrochemically cycled over the first oxidation wave but unstable when scanned beyond this point. Liu et al.115,116 prepared SAMs of 45 and 46 on Au substrate. Anchored to the solid surface by four Au S bonds per molecule, these SAMs were stable for hundreds of cycles over the full oxidation range. In response to the presence of Na+ both the TTF oxidation waves were shifted anodically by 55-60 mV. This observation was ascribed to either surface aggregation or cooperativity of neighbouring crown rings. 

Fig. 5.1. The ubiquitin-conjugation pathway. Steps in ubiquitin activation and substrate modification. El, ubiquitin activating enzyme E2, ubiquitin-conjugating enzyme E3, ubiquitin-protein ligase. Atoms involved in the thiol ester and amide bonds are shown.

Fig. 5.8. Model for catalytic role of E2 active-site asparagine. The side chain of the asparagine in the conserved HPN" motif (Figure 5.2) stabilizes the oxyanion that forms when the substrate s lysine attacks the E2/ubiquitin thiol ester bond. N79 is numbering for Ubcl (Figure 5.2).

Ylide formation, and hence X-H bond insertion, generally proceeds faster than C-H bond insertion or cyclopropanation [1176], 1,2-C-H insertion can, however, compete efficiently with X-H bond insertion [1177]. One problem occasionally encountered in transition metal-catalyzed X-H bond insertion is the deactivation of the (electrophilic) catalyst L M by the substrate RXH. The formation of the intermediate carbene complex requires nucleophilic addition of a carbene precursor (e.g. a diazocarbonyl compound) to the complex Lj,M. Other nucleophiles present in the reaction mixture can compete efficiently with the carbene precursor, or even lead to stable, catalytically inactive adducts L M-XR. For this reason carbene X-H bond insertion with substrates which might form a stable complex with the catalyst (e.g. amines, imidazole derivatives, thiols) often require larger amounts of catalyst and high reaction temperatures. 

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