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Self-assembled monolayers (SAM) of organic molecules are molecular assemblies formed spontaneously on surfaces by adsorption and are organized into more or less large ordered domains. In some cases molecules that form the monolayer do not interact strongly with the substrate. This is the case for instance of the two-dimensional supramolecular networks of e.g. Perylenetetracarboxylic dianhydride (PTCDA) on gold or of e.g. porphyrins on highly oriented pyrolitic graphite (HOPG). In other cases the molecules possess a head group that has a strong affinity to the substrate and anchors the molecule to it. Such a SAM consisting of a head group, tail and functional end group is depicted in Figure 1. Common head groups include thiols, silanes, phosphonates, etc.

SAMs are created by the chemisorption of "head groups" onto a substrate from either the vapor or liquid phase followed by a slow organization of "tail groups". Initially, at small molecular density on the surface, adsorbate molecules form either a disordered mass of molecules or form an ordered two-dimensional "lying down phase", and at higher molecular coverage, over a period of minutes to hours, begin to form three-dimensional crystalline or semicrystalline structures on the substrate surface. The "head groups" assemble together on the substrate, while the tail groups assemble far from the substrate. Areas of close-packed molecules nucleate and grow until the surface of the substrate is covered in a single monolayer.
Adsorbate molecules adsorb readily because they lower the surface free-energy of the substrate and are stable due to the strong chemisorption of the "head groups." These bonds create monolayers that are more stable than the physisorbed bonds of Langmuir–Blodgett films. A Trichlorosilane based "head group", for example in a FDTS molecule, reacts with an hydroxyl group on a substrate, and forms very stable, covalent bond [R-Si-O-substrate] with an energy of 452 kJ/mol. Thiol-metal bonds are on the order of 100 kJ/mol, making them fairly stable in a variety of temperatures, solvents, and potentials. The monolayer packs tightly due to van der Waals interactions, thereby reducing its own free energy. The adsorption can be described by the Langmuir adsorption isotherm if lateral interactions are neglected. If they cannot be neglected, the adsorption is better described by the Frumkin isotherm.

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