Self-assembled

monolayer

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.[1][2] 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[3] of e.g.
Perylenetetracarboxylic dianhydride
(PTCDA) on gold[4] or of e.g. porphyrins on
highly oriented pyrolitic graphite (HOPG).[5]
In other cases the molecules possess a
head group that has a strong affinity to the
substrate and anchors the molecule to it.[1]
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.
Figure 1. Representation of a SAM structure

SAMs are created by the chemisorption of

"head groups" onto a substrate from either
the vapor or liquid phase[6][7] followed by a
slow organization of "tail groups".[8]
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",[6] 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.[9] 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[1] 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.[10][11] 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.[9] The monolayer
packs tightly due to van der Waals
interactions,[1][11] thereby reducing its own
free energy.[1] 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.[9]
Types
Selecting the type of head group depends
on the application of the SAM.[1] Typically,
head groups are connected to a molecular
chain in which the terminal end can be
functionalized (i.e. adding –OH, –NH2, –
COOH, or –SH groups) to vary the wetting
and interfacial properties.[10][12] 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.[13]
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 45kcal/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).[1] Additionally, it can
withstand harsh chemical cleaning
treatments.[9] Recently other chalcogenide
SAMs: selenides and tellurides have
attracted attention[14][15] 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;[1] however monolayers formed
from covalent bonds between silicon and
carbon or oxygen cannot be considered
self assembled because they do not form
reversibly. Self-assembled monolayers of
thiolates on noble metals are a special
case because the metal-metal bonds
become reversible after the formation of
the thiolate-metal complex.[16] 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.[17]

Preparation
Metal substrates for use in SAMs can be
produced through physical vapor
deposition techniques, electrodeposition
or electroless deposition.[1] Thiol or
selenium SAMs produced by adsorption
from solution are typically made by
immersing a substrate into a dilute
solution of alkane thiol in ethanol, though
many different solvents can be used[1]
besides use of pure liquids.[15] While SAMs
are often allowed to form over 12 to 72
hours at room temperature,[9][18] SAMs of
alkanethiolates form within minutes.[19][20]
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.[21][22] In this case
appropriate choice of solvents, their
degassing by inert gasses and preparation
in the absence of light is crucial[21][22] and
allows formation of "standing up" SAMs
with free –SH groups. Self-assembled
monolayers can also be adsorbed from the
vapor phase.[7][23] 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.[17][24]

Characterization
The thicknesses of SAMs can be
measured using ellipsometry and X-ray
photoelectron spectroscopy (XPS), which
also give information on interfacial
properties.[21][25] 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)[19][22]
studies. Numerous other spectroscopic
techniques are used[7] such as Second-
harmonic generation (SHG), Sum-
frequency generation (SFG), Surface-
enhanced Raman scattering (SERS), as
well as[26] 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.[27] More recently, however,
diffractive methods have also been
used.[1] The structure can be used to
characterize the kinetics and defects
found on the monolayer surface. These
techniques have also shown physical
differences between SAMs with planar
substrates and nanoparticle substrates.
An alternative characterisation instrument
for measuring the self-assembly in real
time is dual polarisation interferometry
where the refractive index, thickness,
mass and birefringence of the self
assembled layer are quantified at high
resolution. Contact angle measurements
can be used to determine the surface free-
energy which reflects the average
composition of the surface of the SAM
and can be used to probe the kinetics and
thermodynamics of the formation of
SAMs.[19][20] The kinetics of adsorption
and temperature induced desorption as
well as information on structure can also
be obtained in real time by ion scattering
techniques such as low energy ion
scattering (LEIS) and time of flight direct
recoil spectroscopy (TOFDRS).[23]

Defects

Defects due to both external and intrinsic

factors may appear. External factors
include the cleanliness of the substrate,
method of preparation, and purity of the
adsorbates.[1][9] SAMs intrinsically form
defects due to the thermodynamics of
formation, e.g. thiol SAMs on gold typically
exhibit etch pits (monatomic vacancy
islands) likely due to extraction of
adatoms from the substrate and formation
of adatom-adsorbate moieties. Recently, a
new type of fluorosurfactants have found
that can form nearly perfect monolayer on
gold substrate due to the increase of
mobility of gold surface atoms.[28][29][30]

Nanoparticle properties

The structure of SAMs is also dependent

on the curvature of the substrate. SAMs on
nanoparticles, including colloids and
nanocrystals, "stabilize the reactive
surface of the particle and present organic
functional groups at the particle-solvent
interface".[1] These organic functional
groups are useful for applications, such as
immunoassays or sensors, that are
dependent on chemical composition of the
surface.[1]

Kinetics
There is evidence that SAM formation
occurs in two steps: an initial fast step of
adsorption and a second slower step of
monolayer organization. Adsorption
occurs at the liquid–liquid, liquid–vapor,
and liquid-solid interfaces. The transport
of molecules to the surface occurs due to
a combination of diffusion and convective
transport. According to the Langmuir or
Avrami kinetic model the rate of
deposition onto the surface is proportional
to the free space of the surface.[6]

Where θ is the proportional amount of

area deposited and k is the rate constant.
Although this model is robust it is only
used for approximations because it fails to
take into account intermediate
processes.[6] Dual polarisation
interferometry being a real time technique
with ~10 Hz resolution can measure the
kinetics of monolayer self-assembly
directly.

Once the molecules are at the surface the

self-organization occurs in three phases:[6]

1. A low-density phase with random

dispersion of molecules on the surface.
2. An intermediate-density phase with
conformational disordered molecules or
molecules lying flat on the surface.
3. A high-density phase with close-
packed order and molecules standing
normal to the substrate's surface.
The phase transitions in which a SAM
forms depends on the temperature of the
environment relative to the triple point
temperature, the temperature in which the
tip of the low-density phase intersects with
the intermediate-phase region. At
temperatures below the triple point the
growth goes from phase 1 to phase 2
where many islands form with the final
SAM structure, but are surrounded by
random molecules. Similar to nucleation in
metals, as these islands grow larger they
intersect forming boundaries until they
end up in phase 3, as seen below.[6]
At temperatures above the triple point the
growth is more complex and can take two
paths. In the first path the heads of the
SAM organize to their near final locations
with the tail groups loosely formed on top.
Then as they transit to phase 3, the tail
groups become ordered and straighten
out. In the second path the molecules start
in a lying down position along the surface.
These then form into islands of ordered
SAMs, where they grow into phase 3, as
seen below.[6]

The nature in which the tail groups

organize themselves into a straight
ordered monolayer is dependent on the
inter-molecular attraction, or van der
Waals forces, between the tail groups. To
minimize the free energy of the organic
layer the molecules adopt conformations
that allow high degree of Van der Waals
forces with some hydrogen bonding. The
small size of the SAM molecules are
important here because Van der Waals
forces arise from the dipoles of molecules
and are thus much weaker than the
surrounding surface forces at larger
scales. The assembly process begins with
a small group of molecules, usually two,
getting close enough that the Van der
Waals forces overcome the surrounding
force. The forces between the molecules
orient them so they are in their straight,
optimal, configuration. Then as other
molecules come close by they interact
with these already organized molecules in
the same fashion and become a part of
the conformed group. When this occurs
across a large area the molecules support
each other into forming their SAM shape
seen in Figure 1. The orientation of the
molecules can be described with two
parameters: α and β. α is the angle of tilt
of the backbone from the surface normal.
In typical applications α varies from 0 to
60 degrees depending on the substrate
and type of SAM molecule. β is the angle
of rotation along the long axis of tee
molecule. β is usually between 30 and 40
degrees.[1] In some cases existence of
kinetic traps hindering the final ordered
orientation has been pointed out.[7] Thus in
case of dithiols formation of a "lying down"
phase[7] was considered an impediment to
formation of "standing up" phase, however
various recent studies indicate this is not
the case.[21][22]

Many of the SAM properties, such as

thickness, are determined in the first few
minutes. However, it may take hours for
defects to be eliminated via annealing and
for final SAM properties to be
determined.[6][9] The exact kinetics of SAM
formation depends on the adsorbate,
solvent and substrate properties. In
general, however, the kinetics are
dependent on both preparations
conditions and material properties of the
solvent, adsorbate and substrate.[6]
Specifically, kinetics for adsorption from a
liquid solution are dependent on:[1]

Temperature – room-temperature
preparation improves kinetics and
reduces defects.
Concentration of adsorbate in the
solution – low concentrations require
longer immersion times[1][9] and often
create highly crystalline domains.[9]
 Purity of the adsorbate – impurities can
affect the final physical properties of the
SAM
Dirt or contamination on the substrate –
imperfections can cause defects in the
SAM

The final structure of the SAM is also

dependent on the chain length and the
structure of both the adsorbate and the
substrate. Steric hindrance and metal
substrate properties, for example, can
affect the packing density of the film,[1][9]
while chain length affects SAM
thickness.[11] Longer chain length also
increases the thermodynamic stability.[1]
Patterning
1. Locally attract

This first strategy involves locally

depositing self-assembled monolayers on
the surface only where the nanostructure
will later be located. This strategy is
advantageous because it involves high
throughput methods that generally involve
fewer steps than the other two strategies.
The major techniques that use this
strategy are:[31]

Micro-contact printing
Micro-contact printing or soft
lithography is analogous to printing ink
with a rubber stamp. The SAM
molecules are inked onto a pre-shaped
elastomeric stamp with a solvent and
transferred to the substrate surface by
stamping. The SAM solution is applied
to the entire stamp but only areas that
make contact with the surface allow
transfer of the SAMs. The transfer of the
SAMs is a complex diffusion process
that depends on the type of molecule,
concentration, duration of contact, and
pressure applied. Typical stamps use
PDMS because its elastomeric
properties, E = 1.8 MPa, allow it to fit the
countour of micro surfaces and its low
surface energy, γ = 21.6 dyn/cm². This is
a parallel process and can thus place
nanoscale objects over a large area in a
short time.[1]
Dip-pen nanolithography
Dip-pen nanolithography is a process
that uses an atomic force microscope to
transfer molecules on the tip to a
substrate. Initially the tip is dipped into a
reservoir with an ink. The ink on the tip
evaporates and leaves the desired
molecules attached to the tip. When the
tip is brought into contact with the
surface a water meniscus forms
between the tip and the surface
 resulting in the diffusion of molecules
from the tip to the surface. These tips
can have radii in the tens of nanometers,
and thus SAM molecules can be very
precisely deposited onto a specific
location of the surface. This process
was discovered by Chad Mirkin and co-
workers at Northwestern University.[32]

2. Locally remove

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 end 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:[31]

Scanning tunneling microscope

The scanning tunneling microscope can
remove SAM molecules in many
different ways. The first is to remove
them mechanically by dragging the tip
across the substrate surface. This is not
the most desired technique as these
tips are expensive and dragging them
causes a lot of wear and reduction of
the tip quality. The second way is to
degrade or desorb the SAM molecules
by shooting them with an electron
beam. The scanning tunneling
microscope can also remove SAMs by
field desorption and field enhanced
surface diffusion.[31]
Atomic force microscope
The most common use of this technique
is to remove the SAM molecules in a
process called shaving, where the
atomic force microscope tip is dragged
along the surface mechanically
removing the molecules. An atomic
force microscope can also remove SAM
molecules by local oxidation
nanolithography.[31]
Ultraviolet irradiation
 In this process, UV light is projected
onto the surface with a SAM through a
pattern of apperatures in a chromium
film. This leads to photo oxidation of the
SAM molecules. These can then be
washed away in a polar solvent. This
process has 100 nm resolutions and
requires exposure time of 15–
20 minutes.[1]

3. Modify tail groups

The final strategy focuses not on the

deposition or removal of SAMS, but the
modification of terminal groups. In the first
case the terminal group can be modified to
remove functionality so that SAM
molecule will be inert. In the same regards
the terminal group can be modified to add
functionality[33] so it can accept different
materials or have different properties than
the original SAM terminal group. The
major techniques that use this strategy
are:[31]

Focused electron beam and ultraviolet

irradiation
Exposure to electron beams and UV light
changes the terminal group chemistry.
Some of the changes that can occur
include the cleavage of bonds, the
forming of double carbon bonds, cross-
linking of adjacent molecules,
 fragmentation of molecules, and
confromational disorder.[1]
Atomic force microscope
A conductive AFM tip can create an
electrochemical reaction that can
change the terminal group.[31]

Applications
Thin-film SAMs

SAMs are an inexpensive and versatile

surface coating for applications including
control of wetting and adhesion,[34]
chemical resistance, bio compatibility,
sensitization, and molecular recognition
for sensors[35] and nano fabrication.[6]
Areas of application for SAMs include
biology, electrochemistry and electronics,
nanoelectromechanical systems (NEMS)
and microelectromechanical systems
(MEMS), and everyday household goods.
SAMs can serve as models for studying
membrane properties of cells and
organelles and cell attachment on
surfaces.[1] SAMs can also be used to
modify the surface properties of
electrodes for electrochemistry, general
electronics, and various NEMS and
MEMS.[1] For example, the properties of
SAMs can be used to control electron
transfer in electrochemistry.[36] 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.[37]

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.[38]

Patterned 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 a 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.[31][39]
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.[27]

Metal organic superlattices

There has been considerable interest in
use of SAMs for new materials e.g. via
formation of two- or three-dimensional
metal organic superlattices by assembly
of SAM capped nanoparticles[40] or layer
by layer SAM-nanoparticle arrays using
dithiols.[41]

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Further reading
Sagiv, J.; Polymeropoulos, E.E. (1978).
"Adsorbed monolayers - molecular-
organization and electrical-properties".
BERICHTE DER BUNSEN-GESELLSCHAFT-
PHYSICAL CHEMISTRY CHEMICAL
PHYSICS. 82 (9): 883–883.
doi:10.1002/bbpc.19780820917 .
I. Rubinstein, E. Sabatani, R. Maoz and J.
Sagiv, Organized Monolayers on Gold
Electrodes, in Electrochemical Sensors
for Biomedical Applications, C.K.N. Li
(Ed.), The Electrochemical Society 1986:
175.
Faucheux, N.; Schweiss, R.; Lützow, K.;
Werner, C.; Groth, T. (2004). "Self-
assembled monolayers with different
terminating groups as model substrates
for cell adhesion studies". Biomaterials.
25: 2721–2730.
doi:10.1016/j.biomaterials.2003.09.069
. PMID 14962551 .
Wasserman, S. R.; Tao, Y. T.; Whitesides,
G. M. (1989). "Structure and Reactivity
of Alkylsiloxane Monolayers Formed by
Reaction of Alkyltrichlorosilanes on
 Silicon Substrates". Langmuir. 5: 1074–
1087. doi:10.1021/la00088a035 .
Hoster, H.E.; Roos, M.; Breitruck, A.;
Meier, C.; Tonigold, K.; Waldmann, T.;
Ziener, U.; Landfester, K.; Behm, R.J.
(2007). "Structure Formation in
Bis(terpyridine)Derivative Adlayers –
Molecule-Substrate vs. Molecule-
Molecule Interactions". Langmuir. 23:
11570–11579. doi:10.1021/la701382n .
Sigma-Aldrich "Material Matters",
Molecular Self-Assembly

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