Applications and Properties of Organic Binding
Molecules to Inorganic Substrates
By
Lindsey Kato
ChemE 554
March 2, 2006
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Applications and Properties of Organic Binding
Molecules to Inorganic Substrates
Lindsey Kato
Abstract:
The interfacial properties between organic compounds and a substrate are very important
to understand, so that they can be applied to other areas of science. Once the properties of
the interface are understood, there are a wide array of applications where this information
could be applied. These applications can be in the area of semiconductors and electronics,
food processing, biomimetrics, and many more. There are still many challenges in this
area, including the recognition of the compounds on a substrate, the structured assembly
of molecules on the surface, and the functionality of these molecules once they are
assembled. Many groups have written journal articles on how these molecular chains are
binding, whether it is through covalent bonds, physisorption, or electrostatic interactions.
Once these binding forces are understood the production and assembly of the chains can
be improved and applied more efficiently to many different areas for use.
Introduction:
Organic molecules are in and around us; they are a part of everything that is living.
Inorganic substrates are also in many things that we use in our every day lives like
electronics, cars, medical equipment, among other things. Nature has shown us that
organic molecules and inorganic particles will function together, like in the controlled
growth of crystals for a mollusk shell [1]. Understanding of these organic molecules work
and function can lead to other applications in many areas that will benefit our life. Brown
et al. has found that this can be applied to the formation of gold crystals on a surface from
polypeptides binding to a {111} gold surface. This may be caused from the preference of
the peptide binding to the {111} face of the gold over any other configuration [2]. This
paper will give an overview of the work that has been done in the last several years on
inorganic-organic interactions, mainly on substrate to chain interactions, but also
interactions with nanoparticles. First the many different and potential uses of these
substrates and molecule interactions in the area of semiconductors and electronics, food
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processing, biomimetrics, and particle assembly will be discussed. Then the research that
has been done to determine the mechanisms behind these binding interactions will be
covered.
Uses of Organic Molecules on Inorganic Substrates:
There are several areas in science were the binding of organic molecules to inorganic
substrates can be applied. Research in many areas has been done and the application of
these interfaces can be seen. In other areas the potential for these interfaces is known, but
breakthroughs in there actual use has yet to be accomplished. Some of the areas for use of
these surfaces are in semiconductors and electronics, food processing, and biomimetrics.
There have also been several developments for using these peptides for particle assembly
and substrate formation.
Semiconductors and Electronics:
Circuits and chips are mass produced and new advancements in these areas are constantly
being sought. Finding more efficient ways that these devices can be made, or cheaper
materials that can be used are all investigated. Electronic devices are also continually
being made smaller. As the size of these devices decreases, the methods of production
must be refined so that the circuit connections are made properly. Research in organic
binding molecules to inorganic substrates has allowed for the possibility of the selfassembly of substrates layers on the silicon chips. This type of technology would allow
for the precise production of chips using organic materials. Several groups have
documented and written papers about experiments that have identified specific molecular
sequences that have a binding affinity to only certain substrates and/or certain crystal
structures. This will allow only certain molecules to assemble on a surface.
The self-assembly of molecules to a substrate is the natural linkage of molecular chains to
a surface. Self assembly monolayers (SAMs) have been studied in great depth, and
certain chain sequences have been found to assemble and pack together well on a surface.
One example of a self assembly molecules are thiols. Thiols (CH3(CH2)nSH) have been
shown to bind well to a gold surface. AFM scanning on the nanoscale has been done to
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reveal the lattice structure of the molecules and the spacing that is observed between the
chains. [3]
Mirkin et al. did a review of the work that has been completed to link semiconductors
with advances in the area of biology[4]. Mirkin discusses the option of molecule-based
electronics, which uses the self-assembly approach for the placement of materials. Using
self-assembly would allow the deposition of materials onto a surface to be more accurate,
so that smaller structures and connections can be formed. By being able to find chains of
organic molecules that will bind to a specific surface, a substrate could be evenly covered
by molecules and the only limiting factor would be the accuracy of the substrate design.
Molecular chains that have a specified binding affinity to certain substrates have been
identified by Whaley et al. By using phage libraries (sequences of amino acids that have
shown an affinity to different materials), peptide chains were found that would bind to
only certain substrate surfaces. One experiment performed by their group showed how a
specific peptide sequence would bind to the GaAs surface, but would not bind to the SiO2
surface of the substrate[5]. Figure 1a shows a surface where none of the peptides were
present in the solution. Figure 1b shows the surface where the peptide (fluoresced to be
red) is only bound to certain areas of the substrate.
Figure 1: GaAs and SiO2 surface; (a) no peptide present in solution and no
binding occuring; (b) peptide is present in solution and shows a binding affinity
only for the GaAs surface, but not he SiO2 surface. [5]
The use of this technology for the formation of nanowires has also been investigated.
Mao et al. used a viral sequence of amino acids that had a binding affinity to ZnS and
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CdS[6]. A long chain of the virus was used and through a chemical scheme another
peptide chain, with a known strong binding affinity to ZnS, was attached to the virus.
Then when the peptide chain was put into a solution of ZnS or CdS an interaction of the
metal with the peptide chains would occur and a nanowire would be formed. The
nanowires were imaging using STEM and the results can be seen in Figure 2. Figure 2a
shows a single nanowire that was formed and Figure 2b shows a close up view of the
nanowire and the close packing of the ZnS. There work showed that nanowires can be
successfully formed and there is great potential for there use in device fabrication[6].
Figure 2: Nanowires; (a) single nanowire of ZnS; (b) high resolution
image of the nanowire showing the close packing of the ZnS. [6]
Food Processing:
The use of organic and inorganic interfaces can be used in other areas like for food
processing. Binding of peptide sequence to metals is good for conductive substrates, but
is also useful for other metals as well. Zuo et al. found specific peptides that had a high
binding affinity to aluminum and steel[7]. This characteristic is valuable because of its
use in the food processing industry. Damage to the pipes could be reduced by coating the
pipes with something that would prevent corrosion. This corrosion is caused by bacteria
and oxygen in the fluids. Specific peptides were chosen from a phage library and
experiments performed to see how well it bonded to the surface. Unfortunately Zuo et al.
was not able to determine the cause of this strong binding affinity that the peptides
exhibited [7].
Biomimetrics and the use as Linkers:
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Biomimetrics is a combination of two different disciplines that has brought together,
nature or biology and engineering. This is different from biological engineering in that
biomimetrics is taking the ideas that we observe in nature and applying them to
engineering. Ideas such as seashell formation and the production of tooth enamel have all
been studied [8]. This phenomena allows scientists to use these properties of known
proteins and combine them to form specific structures or to have specific functions. In a
review article from Nature Materials, Sarikaya et al. talks about the possibility of using
biomimetrics to produce proteins with specific functions that will act as linkers [8]. These
proteins would be attached to some type of inorganic substrate on one end of the chain
and the other end would be free to attach to something else. Figure 3 is a diagram that
shows how we can combine the information that we know on materials and surfaces with
biology to form many new structures.
Figure 3: Figure showing the links between combining Materials science and Biology to
molecular biomimetics and the formation of linkers [8].
Zin et al. looked at combining biomimetrics and microcontact printing (μCP) as a way to
pattern peptides onto a surface [9]. They used both a known sequences of binding
peptides and cell-surface display, for development of repeating peptides, to genetically
engineer peptides that would recognize certain metals. Zin et al. observed the difference
in binding between a bare gold sample and a SAMs surface with a genetically
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engineering protein. They found that the proteins would bind better to the SAMs surface
over the bare gold substrate [9].
Particle Assembly:
Specific organics have been found that will bind and pack closely to certain substrates,
and these peptides have also been found to pack closely around nanoparticles. Research
has been done by several groups that have found peptides that will bind with a specificity
to a certain particle and pack very densely around it. One group is Dai et al. who found a
peptide sequence that would bind only to Cu2O [10]. This peptide would pack closely
around the particles and then the peptides would link together to form a ring. Figure 4
shows the formation and structure of these rings. It was also found that the peptides could
cause the formation of these rings even when the conditions of the solution may have
been unfavorable. With this discovery it could be possible for other sequences to be
found that would cause the formation of other structures[10]. Other peptides have been
found that can bind to two nanoparticles. Xu et al. found a peptide that would bind to
gold particles and then bind together[11]. They found that by using a condensation
reaction the chains would bind together and link two gold nano particles. The spacing
between the two nanoparticles can be controlled by the length of the sequences, and this
would help with the direct assembly of the nanoparticles[11].
Figure 4: Formation of a Cu2O ring, at a scale
of 100 nm [10].
Surface Interactions and Bonding Forces:
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The bonding forces between the peptides and the substrate can be hard to determine along
with the exact mechanism that causes the attraction. Understanding how the atoms will
bind to each other helps to determine what types of sequences to use and how strong the
chains will be bound to the surface. Several groups have done research to determine what
the binding interactions are between the molecules and substrate. Other groups have
performed molecular simulations to confirm the arrangement of the atoms and how they
will bond.
One of the most studied and documented organic-inorganic binding pairs are alkanethiols
and gold substrates. As was mentioned earlier, Alves et al. [3] performed high resolution
imaging on alkanethiols. This interaction is very strong between the thiol chain and the
gold surface. Zhang et al. found that this strong bond is caused from a covalent bond
between the sulfur molecule on the thiol and the metal surface [12]. They also found that
there are several other forces occurring simultaneously to help with the bonds, including
interchain, intrachain, and surface-chain interactions. Molecular simulations were
performed to determine how the chains interacted and what were the effects, depending
on the hybridization of the orbital [12]. From the simulations it was concluded that the
surface atom is sp hybridized, because if it was sp3 hybridized the tilt angle of the chains
would differ from the experimental results. They were also able to conclude that the
chains do not rotate much because of the interactions between the neighboring chains,
which also accounts for the tight packing structure and the slight tilt angle that is
observed [12]. In contradiction to this interaction Fenter et al. states that there is no
covalent bond between the gold molecules and thiol, but between the sulfur molecules
[13]. They came to this conclusion because of the spacing of the lattice using x-ray
diffraction. The spacing of the chains is the same size as would be a sulfur-sulfur bond.
They found that this opposing theory to be true because of the results they have found
and simulations that were performed that showed no possible configurations that would
give an ideal gold-sulfur bond packing structure [13].
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Understanding the different forces that cause the binding of peptide sequences are much
more difficult. Peptide chains are generally long chains containing 10-15 or more amino
acids. With these long chains the close packing of these molecules for assembly on a
substrate can be harder to obtain. Research and molecular simulations have been
performed on these molecules to determine what type of forces cause them to bind to the
surface and the type of configuration they are in. Braun et al. researched gold binding
peptides and found that sequences containing serine and threonine bond well to gold
substrates, which was also mentioned by others [2,7]. From these observations they
proposed that this was caused by the physisorption of the polar side-chains onto the gold
surface [2]. The molecular simulations performed showed that the main contributions to
the binding energy were caused from the polar amino acids on the chains; previously it
was thought to be caused from the hydrophobic amino acids. They also found that the
polar residues had little deviation from there original positions than the non-polar
residues, which was an indication of greater stability with the fixed gold lattice [2]. In
these simulations two different surface configurations were observed, {111} and {211}, it
was found that water hinders the absorption of the peptides to the surface of the {211}
plane because the H2O molecules diffuse into the corrugations in the surface. Figure 5 is
a picture of a peptide binding to a {111} plane (a) and a {211} plane (b). Notice that the
peptide chains lay parallel with the surface as opposed to perpendicular, like the thiols.
This may present a problem for the close packing of the chains. [2]
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Figure 5: Gold Binding Peptides on {111} (a) and {211} (b) gold surfaces; show a view
form above (top) and form the edge (bottom). Atoms are shown for those near the surface.
Blue: polar residues; Green: charges residues; Red: hydrophobic residues [2].
Molecular simulations have also been performed using other substrates. Kantarci et al.
performed simulations using peptides with a binding affinity to platinum. They looked at
the interaction of threonine-serine-threonine (T-S-T) sequences with the surface [14]. It
was found that chains with this sequence had more interaction with the surface and it was
found to bind better to metal surfaces. The T-S-T sequence also has greater flexibility
that allows for better binding with the surface. There analysis is just the beginning to a
more in-depth study on the sequence, structure, and binding process for peptides binding
to metals [14]. Simulations have also been done for large molecules and there orientation
on the substrate surface. Qian et al. performed simulations for large molecules and looked
at there binding affinity to a surface; these simulations provide a good basis for the
orientation of other large molecules [15].
In order to find good peptide sequences that will work for semiconductors, an
understanding of how all the amino acids interact with a surface must be understood. A
study on the interactions of several different amino acids to different surfaces was
investigated by Willett et al. They looked at 20 different amino acids and how they
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interacted with metals, semiconductors, and insulators[16]. From their study they
discovered which amino acids would bind to a surface and which had the highest
adhesion. Table 1 shows all the amino acid that were observed and the material substrates
used for testing [16]. The values in the table show the adhesion for several amino acids to
nine different substrates. Willett et al. then examined the mechanism for adhesion with
fluorescence output and looked at the concentration and pH dependence of the amino
acids. They found that the mechanisms for adhesion varied depending on the amino acid
and the state of the solution and substrate [16].
Table 1: Adhesion values ofr 20 amino acids were found for several different substrates. The
highest adhesion values are colored darker [16].
Other experiments have been done without the use of molecular simulations to determine
what may be the cause of the binding forces of the peptide sequences. Imamura et al. did
a study of the binding effects of peptides to stainless steel [17]. This is very important for
its use in the food processing industry, as was mentioned earlier. There study looked at
the effects of pH and ionic strength on the absorption isotherms. They suggest that the
acidic and basic amino acids absorb to the stainless steel surface through two electrostatic
interactions of the ionized groups on the amino acids [17].
Conclusion:
There is still much to learn about substrates and the mechanisms that cause different
organic sequences to bind to them. Unfortunately there hasn’t been much success in the
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actual application of these substrates. The potential is there and can been seen, but journal
articles have not been written on how they have been applied. The next step is to find a
way to successfully use these peptides to an area. Also, more needs to be done to figure
out exactly how the peptides are bonding with the surface. Many groups have done
research and found several possibilities and proposed many different ideas for the reason
these molecules cleave to a surface, but more tests need to be done. This paper is just a
brief overview of some of the applications that are available for these bio-inorganic
interfaces, and their mechanisms for binding.
References:
1. Brown S, Sarikaya M, Johnson E: A genetic analysis of crystal growth. Journal of
Molecular Biology 2000, 299:725-735.
2. Braun R, Sarikaya M, Schulten K: Genetically engineered gold-binding
polypeptides: structure prediction and molecular dynamics. Journal of
Biomaterials Science-Polymer Edition 2002, 13:747-757.
3. Alves CA, Smith EL, Porter MD: Atomic Scale Imaging of Alkanethiolate
Monolayers at Gold Surfaces with Atomic Force Microscopy. Journal of the
American Chemical Society 1992, 114:1222-1227.
4. Mirkin CA, Taton TA: Materials chemistry - Semiconductors meet biology. Nature
2000, 405:626-627.
5. Whaley SR, English DS, Hu EL, Barbara PF, Belcher AM: Selection of peptides with
semiconductor binding specificity for directed nanocrystal assembly. Nature
2000, 405:665-668.
6. Mao CB, Flynn CE, Hayhurst A, Sweeney R, Qi JF, Georgiou G, Iverson B, Belcher
AM: Viral assembly of oriented quantum dot nanowires. Proceedings of the
National Academy of Sciences of the United States of America 2003, 100:69466951.
7. Zuo RJ, Ornek D, Wood TK: Aluminum- and mild steel-binding peptides from
phage display. Applied Microbiology and Biotechnology 2005, 68:505-509.
8. Sarikaya M, Tamerler C, Jen AKY, Schulten K, Baneyx F: Molecular biomimetics:
nanotechnology through biology. Nature Materials 2003, 2:577-585.
9. Zin MT, Ma H, Sarikaya M, Jen AKY: Assembly of gold nanoparticles using
genetically engineered polypeptides. Small 2005, 1:698-702.
10. Dai HX, Choe WS, Thai CK, Sarikaya M, Traxler BA, Baneyx F, Schwartz DT:
Nonequilibrium synthesis and assembly of hybrid inorganic-protein
nanostructures using an engineered DNA binding protein. Journal of the
American Chemical Society 2005, 127:15637-15643.
11. Xu L, Guo Y, Xie RG, Zhuang JQ, Yang WS, Li TJ: Three-dimensional assembly
of Au nanoparticles using dipeptides. Nanotechnology 2002, 13:725-728.
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12. Zhang Z, Beck TL, Young JT, Boerio FJ: Molecular structure of monolayers from
thiol-terminated polyimide model compounds on gold .2. Molecular
dynamics simulations. Langmuir 1996, 12:1227-1234.
13. Fenter P, Eberhardt A, Eisenberger P: Self-Assembly of N-Alkyl Thiols as
Disulfides on Au(111). Science 1994, 266:1216-1218.
14. Kantarci N, Tamerler C, Sarikaya M, Haliloglu T, Doruker P: Molecular dynamics
simulations on constraint metal binding peptides. Polymer 2005, 46:43074313.
15. Qian J, Hentschke R, Knoll W: Superstructures of cyclodextrin derivatives on
Au(111): A combined random planting molecular dynamics approach.
Langmuir 1997, 13:7092-7098.
16. Willett RL, Baldwin KW, West KW, Pfeiffer LN: Differential adhesion of amino
acids to inorganic surfaces. Proceedings of the National Academy of Sciences of
the United States of America 2005, 102:7817-7822.
17. Imamura K, Mimura T, Okamoto M, Sakiyama T, Nakanishi K: Adsorption
behavior of amino acids on a stainless steel surface. Journal of Colloid and
Interface Science 2000, 229:237-246.
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