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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", 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 A trichlorosilane based "head group", for example in a FDTS molecule, reacts with a 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. An appropriate substrate is chosen to react with the head group. Substrates can be planar surfaces, such as silicon and metals, or curved surfaces, such as nanoparticles. Alkanethiols are the most commonly used molecules for SAMs. Alkanethiols are molecules with an alkyl chain, (C C)ⁿ chain, as the back bone, a tail group, and a S H head group. Other types of interesting molecules include aromatic thiols, of interest in molecular electronics, in which the alkane chain is (partly) replaced by aromatic rings. An example is the dithiol 1,4 Benzenedimethanethiol (SHCH2C6H4CH2SH)). Interest in such dithiols stems from the possibility of linking the two sulfur ends to metallic contacts, which was first used in molecular conduction measurements. Thiols are frequently used on noble metal substrates because of the strong affinity of sulfur for these metals. The sulfur gold interaction is semi covalent and has a strength of approximately 45 kcal/mol. In addition, gold is an inert and biocompatible material that is easy to acquire. It is also easy to pattern via lithography, a useful feature for applications in nanoelectromechanical systems (NEMS). in a search for different bonding characteristics to substrates affecting the SAM characteristics and which could be of interest in some applications such as molecular electronics. Silanes are generally used on nonmetallic oxide surfaces; This reversibility is what gives rise to vacancy islands and it is why SAMs of alkanethiolates can be thermally desorbed and undergo exchange with free thiols.

Metal substrates for use in SAMs can be produced through physical vapor deposition techniques, electrodeposition or electroless deposition. SAMs of alkanethiolates form within minutes. Special attention is essential in some cases, such as that of dithiol SAMs to avoid problems due to oxidation or photoinduced processes, which can affect terminal groups and lead to disorder and multilayer formation. In this case appropriate choice of solvents, their degassing by inert gasses and preparation in the absence of light is crucial In some cases when obtaining an ordered assembly is difficult or when different density phases need to be obtained substitutional self assembly is used. Here one first forms the SAM of a given type of molecules, which give rise to ordered assembly and then a second assembly phase is performed (e. g. by immersion into a different solution). This method has also been used to give information on relative binding strengths of SAMs with different head groups and more generally on self assembly characteristics.

The thicknesses of SAMs can be measured using ellipsometry and X ray photoelectron spectroscopy (XPS), which also give information on interfacial properties. The order in the SAM and orientation of molecules can be probed by Near Edge Xray Absorption Fine Structure (NEXAFS) and Fourier Transform Infrared Spectroscopy in Reflection Absorption Infrared Spectroscopy (RAIRS) High resolution electron energy loss spectroscopy (HREELS). The structures of SAMs are commonly determined using scanning probe microscopy techniques such as atomic force microscopy (AFM) and scanning tunneling microscopy (STM). STM has been able to help understand the mechanisms of SAM formation as well as determine the important structural features that lend SAMs their integrity as surface stable entities. In particular STM can image the shape, spatial distribution, terminal groups and their packing structure. AFM offers an equally powerful tool without the requirement of the SAM being conducting or semi conducting. AFM has been used to determine chemical functionality, conductance, magnetic properties, surface charge, and frictional forces of SAMs. The scanning vibrating electrode technique (SVET) is a further scanning probe microscopy which has been used to characterize SAMs, with defect free SAMs showing homogeneous activity in SVET. More recently, however, diffractive methods have also been used.

The locally remove strategy begins with covering the entire surface with a SAM. Then individual SAM molecules are removed from locations where the deposition of nanostructures is not desired. The result is the same as in the locally attract strategy, the difference being in the way this is achieved. The major techniques that use this strategy are: so it can accept different materials or have different properties than the original SAM terminal group. The major techniques that use this strategy are: chemical resistance, bio compatibility, sensitization, and molecular recognition for sensors and nano fabrication. They can serve to protect metals from harsh chemicals and etchants. SAMs can also reduce sticking of NEMS and MEMS components in humid environments. In the same way, SAMs can alter the properties of glass. A common household product, Rain X, utilizes SAMs to create a hydrophobic monolayer on car windshields to keep them clear of rain. Another application is an anti adhesion coating on nanoimprint lithography (NIL) tools and stamps. One can also coat injection molding tools for polymer replication with a Perfluordecyltrichlorosilane SAM. Thin film SAMs can also be placed on nanostructures. In this way they functionalize the nanostructure. This is advantageous because the nanostructure can now selectively attach itself to other molecules or SAMs. This technique is useful in biosensors or other MEMS devices that need to separate one type of molecule from its environment. One example is the use of magnetic nanoparticles to remove a fungus from a blood stream. The nanoparticle is coated with a SAM that binds to the fungus. As the contaminated blood is filtered through a MEMS device the magnetic nanoparticles are inserted into the blood where they bind to the fungus and are then magnetically driven out of the blood stream into a nearby laminar waste stream.

Photolithographic methods are useful in patterning SAMs. SAMs are also useful in depositing nanostructures, because each adsorbate molecule can be tailored to attract two different materials. Current techniques utilize the head to attract to a surface, like a plate of gold. The terminal group is then modified to attract a specific material like a particular nanoparticle, wire, ribbon, or other nanostructure. In this way, wherever the SAM is patterned to a surface there will be nanostructures attached to the tail groups. One example is the use of two types of SAMs to align single wall carbon nanotubes, SWNTs. Dip pen nanolithography was used to pattern a 16 mercaptohexadecanoic acid (MHA)SAM and the rest of the surface was passivated with 1 octadecanethiol (ODT) SAM. The polar solvent that is carrying the SWNTs is attracted to the hydrophilic MHA; as the solvent evaporates, the SWNTs are close enough to the MHA SAM to attach to it due to Van der Waals forces. The nanotubes thus line up with the MHA ODT boundary. Using this technique Chad Mirkin, Schatz and their co workers were able to make complex two dimensional shapes, a representation of a shape created is shown to the right. Another application of patterned SAMs is the functionalization of biosensors. The tail groups can be modified so they have an affinity for cells, proteins, or molecules. The SAM can then be placed onto a biosensor so that binding of these molecules can be detected. The ability to pattern these SAMs allows them to be placed in configurations that increase sensitivity and do not damage or interfere with other components of the biosensor. or layer by layer SAM nanoparticle arrays using dithiols. A detailed review on this subject using dithiols is given by Hamoudi and Esaulov