Surface Reactions of Amines and Hydrogen/Silicon Substrates

Surface reactions

SPECIAL SECTION
DOI: 10.1002/smll.200600103

Sequential Reactions with Amine-Terminated

Monolayers and Isolated Molecules on H/SiACHTUNGRE(111)
Brian J. Eves, Chaoyang Fan, and Gregory P. Lopinski*

A simple method for preparing monolayers with terminal amine func-

tionality is demonstrated. A gas-phase photochemical reaction of 1,3-di- Keywords:
· amines
ACHTUNGREaminopropane with a H-terminated SiACHTUNGRE(111) surface results in the · electron energy loss
molecules covalently attaching to the surface, primarily through the spectroscopy
formation of a Si N bond. These monolayers are characterized by · monolayers
scanning tunneling microscopy (STM) and high-resolution electron · scanning tunneling
microscopy
energy loss spectroscopy (HREELS). The reactivity of the terminal
amine is confirmed by exposing the monolayer to benzaldehyde, resulting
in the formation of an imine link and the grafting of phenyl rings onto
the surface. For short irradiation times, this reaction leads to the
formation of isolated amine groups on an otherwise pristine H-terminated
surface. STM and HREELS studies of the benzaldehyde reaction on
these low-coverage surfaces (less than 0.005 monolayers) indicate that the
reaction is restricted to the reactive amine groups, leaving the remainder
of the surface unaffected. This simple approach for a sequential coupling
reaction is expected to facilitate attachment of more complex molecules
(molecular switches, biomolecules) for single-molecule STM studies.

1. Introduction

There has been considerable activity and progress in the
development of methods for the controlled attachment of
organic molecules to silicon surfaces, largely motivated by
the promise of fabricating hybrid devices and sensors.[1–5] A
major challenge in this area is the coupling of complex func-
tional molecules such as molecular switches or biomolecules
to the surface while retaining their functionality and pre-
serving the chemical and electronic integrity of the surface.
[*] Dr. B. J. Eves, Dr. C. Fan, Dr. G. P. Lopinski
Steacie Institute for Molecular Sciences
National Research Council
100 Sussex Drive, Ottawa, K1A 0R6 (Canada)
Fax: (+ 1) 613-991-4278
E-mail: Gregory.Lopinski@nrc-cnrc.gc.ca
Dr. B. J. Eves
Institute for National Measurement Standards
National Research Council, Ottawa (Canada)
While in some cases the attachment of reactive tethers facil-
itates direct reaction of such molecules with the surface,[6, 7]
this approach has significant limitations. A more general
and flexible strategy involves the formation of a functional
monolayer, followed by a coupling reaction. Several such se-
quential reaction schemes have been reported for molecular
monolayers on silicon surfaces.[8–13] However, these studies
were carried out using macroscopic surface science probes,
precluding the examination of the quality of the resulting
surfaces at the molecular scale.
Recently we have developed a new method for forming
molecular monolayers on H-terminated Si surfaces using
photochemical reactions in the gas phase.[14] This approach
involves the generation of gas-phase radicals that abstract H
atoms from the surface, creating Si dangling bonds. These
reactive sites can lead to monolayer formation via two
mechanisms: a propagating radical chain reaction, leading
to the formation of molecular islands, or direct reaction of
radicals with the dangling bonds, resulting in the formation

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of isolated molecules attached to the surface. In an attempt
to form surfaces with terminal amine functionality, the bi-
functional molecule allylamine (C3H5NH2) was reacted
using the gas-phase method. However, it was found that the
majority of the molecules reacted with the surface via the
NH2 group rather than the alkene end, resulting in attach-
ment through a Si N bond and loss of the amine functional-
ity.[14]
In this paper we demonstrate that monolayers with ter-
minal amine functionality can be formed via gas-phase pho-
tochemical reactions of 1,3-diaminopropane with the
H/SiACHTUNGRE(111) surface. These monolayers are characterized by
scanning tunneling microscopy (STM) and high-resolution
electron energy loss spectroscopy (HREELS). The reactivity
of the terminal amines is confirmed by following their reac-
tion with benzaldehyde. Furthermore, we show that this
method can also be used to create isolated amine groups on
the H/SiACHTUNGRE(111) surface. The sequential reaction is also fol-
lowed at these very low coverages (  0.005 monolayers),
where it is found to proceed selectively at the reactive sites
with no degradation of the surrounding surface. This simple
approach is expected to enable the attachment of isolated
molecular switches or biomolecules for single-molecule
studies using STM. This contrasts with previously reported
solution-phase methods for forming amine monolayers,
which require the use of protecting groups.[10–11] The addi-
tional proACHTUNGREcessing steps required to recover the amine func-
tionality are expected to degrade the surface quality.
2. Results and Discussion
Hydrogen-terminated SiACHTUNGRE(111) surfaces were prepared by
etching clean 1–5 W cm n-type Si wafers in 40 % NH4F for
15 min.[15] The prepared surfaces were quickly placed into
an ultrahigh vacuum (UHV) chamber to reduce degradation
of the surface via oxidation, and were subsequently heated
to less than 200 8C to remove any physisorbed species. 1,3-
Diaminopropane (Aldrich, 99 %), and benzaldehyde (Al-
drich, + 99.5 %) were both freeze-pump-thawed with liquid
N2 to remove dissolved oxygen prior to use. The H/SiACHTUNGRE(111)
surfaces were exposed to 1,3-diaminopropane (1 Torr) in
the load lock of the UHV system. The load lock was fitted
with a sapphire window for transmission of UV radiation.
Photochemical excitation was provided by a Hg vapor pen
lamp (Oriel Model 6035). An irradiance of approximately
2 B 10 4 W cm 2 has been measured[16] for the pen lamp at a
distance of 10 cm. The ultraviolet radiation produced by the
lamp was dominated by the 254 nm line (  95 %), but also
found to contain a weaker 185 nm line (  5 %). Based on
our previous work, which showed that direct illumination of
the sample was not necessary for the gas-phase reaction to
proceed,[14] the sample face was kept parallel to the UV
beam during the irradiation so as to minimize potential
damage of the monolayer. After the photochemical reaction
the sample was again heated gently (< 200 8C) to remove
any physisorbed 1,3-diaminopropane.
The samples were characterized without subsequent ex-
posure to atmospheric conditions in a UHV chamber
1380 www.small-journal.com < 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
ACHTUNGREequipped with both STM and HREELS. An G.LK3000 P. Lopinski et al.
spec-
trometer (LK Technologies, Bloomington, IN) was em-
ployed for the HREELS measurements. Spectra were ac-
quired in the specular geometry (608 with respect to the sur-
face normal) at an incident beam energy of 6 eV and a nom-
inal resolution of 6 meV. The STM used for the experiments
was a UHV1 from Omicron. Images were acquired in the
constant-current mode at currents in the range of 30–
100 pA and sample biases of 2–3 V.
Figure 1 shows a sequence of HREELS spectra follow-
ing the reaction of 1,3-diaminopropane with the H/SiACHTUNGRE(111)
Figure 1. HREELS spectra for a) a clean H/SiACHTUNGRE(111) surface and
b–d) after a UV photochemical reaction with 1,3-diaminopropane
(1 Torr) for b) 6 s, c) 18 s, and d) 72 s. The elastic and loss peak
intensities for the clean H/SiACHTUNGRE(111) surface have been reduced by a
factor of two.
surface. The spectrum for the initial H-terminated surface is
dominated by characteristic peaks at 630 and 2095 cm 1, cor-
responding to the Si H bend and stretch modes, respective-
ly.[17] The peak at 510 cm 1 can be assigned to a Si substrate
phonon, while the weak peaks in the 750–1200 cm 1 region
are indicative of a small amount of oxidation. No discern-
able peak is apparent at the C H stretch frequency of
2920 cm 1, indicating negligible hydrocarbon contamination.
Upon exposure to diaminopropane in the absence of UV
light this spectrum remains unchanged. However, under
photochemical excitation the reaction is seen to proceed
quite rapidly. Even after six seconds of irradiation signifi-
cant changes are observed in the HREELS spectra, most
notably a decrease in the elastic peak and Si H mode inten-
sities, as well as the growth of new modes at 1120 and
2920 cm 1. As the irradiation time was increased these new
peaks continue to grow in intensity along with peaks at 850,
1390, and 3370 cm 1. The elastic peak is also seen to contin-
ue to decrease in intensity and broaden; the full width at
half-maximum (FWHM) increases from 65 cm 1 on the H-
terminated surface to 120 cm 1 after the reaction has pro-
ceeded for 72 s. The most significant of these peaks is that
at 3370 cm 1, which can be assigned to the N H stretch and
indicates the presence of terminal amine groups. The peaks
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Surface Reactions of Amines and Hydrogen/Silicon Substrates
at 2920 cm 1 and 1390 cm 1 are attributed to the stretch and
bending modes associated with the three CH2 groups in the
molecule, whereas the 1120 cm 1 peak is a combination of
C C and C N stretching modes. The weak peak at 850 cm 1
likely contains contributions from both the NH2 wag
mode[18] and also the Si N stretch[19] (ob-
served at  810 cm 1 for allylACHTUNGREamine, which
reacts by forming a Si N bond[14]). In
summary, the observed vibrational spec-
trum is consistent with diaminopropane
bonding to the surface through one of its
amine groups, resulting in the formation
of a Si N bond, and leaving its remaining
amine group free for further reaction.
The formation of the amine-terminat-
ed surface upon UV photochemical reac-
tion can be explained on the basis of our
previous work on gas-phase photochemi-
cal reactions with H/SiACHTUNGRE(111) and an under-
standing of the photodissociation products
of diaminopropane. Although photodisso-
ciation data for 1,3-diaminopropane are
Figure 2. Constant-current occupied-state STM images ( 2.5 V, 30 pA, 18 1 18 nm) of a
not available, we note that methylamine H/SiACHTUNGRE(111) surface after a UV photochemical reaction with 1,3-diaminopropane (1 Torr) for
has four main dissociation pathways when a) 72 s and b) 144 s.
irradiated with 194–244 nm photons: H +
CH3NH, H + CH2NH2, CH3 + NH2, H2 +
CH3N.[20] The majority (75 %) dissociates
into CH3NH and H radicals. The cleavage of the N H bond
has also been reported as the main dissociation route for n-
butylACHTUNGREamine, n-amylamine, and n-hexylamine irradiated by a
mercury arc lamp.[21] Therefore, it is likely that the main
photodissociation product for diaminopropane
NH2C3H6NH and H. The amine and H atom radicals pro-
duced by photolysis of the reactant gas can abstract H
atoms from the silicon surface, creating reactive Si radicals
(dangling bonds). The amine radicals can then add directly
at these reactive sites, via formation of a Si N bond. It is
important to note that this mechanism makes it highly un-
likely that both amine groups on the molecule will react
with the surface. The amines only react after losing a hydro-
gen and becoming a radical and then only with dangling
bonds on the surface.
The significant broadening of the HREELS elastic peak
upon addition of the amine suggests that the reaction has al-
tered the free-carrier density in the near-surface region of
the silicon substrate. HREELS is sensitive to changes in the
electron density at the surface of semiconductors due to
coupling to the free-carrier plasmon mode, the energy of
which depends on the carrier density.[22, 23] For carrier densi-
ties in the range of 1016–1018 cm 2, losses associated with
coupling to the plasmon mode show up as a broadening of
the elastic peak.[23, 24] The increase in carrier density suggest-
ed by the broadening of the elastic peak can be attributed
to band-bending induced by amine functionalization of the
surface. As the amine group is expected to be an electron
donor this would result in bending the bands into accumula-
tion (on the n-type samples used here). We note that allyl-
ACHTUNGREamine, which binds through a Si N bond, does not show
this broadening effect,[14] which indicates that the effect is
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SPECIAL SECTION
due to the free terminal amine rather than the formation of
a Si N bond.
Figure 2 shows STM images illustrating the evolution of
the surface morphology with increasing reaction time. The
image in Figure 2 a shows the typical state of the surface
after reaction for 72 s. A single monoatomic height step
edge is seen to run through the image. The terraces are cov-
ered with numerous protrusions (2–3 F in height) that
appear to cover  50 % of the surface. The image is consis-
is tent with the HREELS spectrum of the same sample in Fig-
ure 1 d, which indicates a substantial amount of diaminopro-
pane on the surface. The observation of a fairly strong Si H
mode in the spectrum is in line with the significant area of
the surface that appears to remain unreacted. Many of the
protrusions are isolated and the remainder do not appear to
be correlated with one another. This is in contrast to images
observed for surfaces partially reacted with alkenes where
the monolayer growth proceeds via formation of irregularly
shaped island structures due to a propagating radical-chain
reaction mechanism.[25] Rather the absence of islands is ex-
pected for the direct addition of amine radicals at isolated
Si dangling bonds.
Upon doubling the reaction time to 144 s (Figure 2 b),
the surface appears to be mostly covered with only relative-
ly small unreacted regions remaining. It is difficult to re-
solve the individual molecular features within the reacted
regions, which appear rather flat and have a height variation
of < 1 F. The HREELS spectrum corresponding to this re-
action duration (Figure 3 a) shows that the Si H bend and
stretch modes are substantially reduced, with the bend
mode barely observable above background. Further expo-
sure of the surface to diaminopropane results in only a
small amount of additional molecules being added to the
surface, with little change observed in the HREELS spec-
trum. The image in Figure 2 b also allows us to address the
possibility of multilayer formation. Since photodissociation
of diaminopropane leads to the formation of gas-phase radi-
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Figure 3. HREELS spectra for a H/SiACHTUNGRE(111) surface reacted with 1,3-
diaminopropane under UV irradiation for 144 s before (a) and after
(b) exposure to benzaldehyde (1 Torr). The arrows highlight the addi-
tional features appearing after reaction with benzaldehyde.
cals, it is possible that these radicals could abstract H atoms
from the terminal amine groups, creating reactive sites on
the monolayer and leading to multilayer growth. This would
lead to increasing roughness of the monolayer. However,
the observation of a flat surface with only a very small
number of additional protrusions indicates that attachment
of additional molecules to the monolayer is rare. Ellipsome-
try measurements on surfaces reacted for up to 10 min indi-
cate that the film thickness remains 4–5 F as expected for a
monolayer of diaminopropane bonded to the surface via a
Si N bond.
The reactivity of the terminal amine groups was con-
firmed by studying their reaction with benzaldehyde. The
terminal amine groups were reacted by exposure of the sur-
face to benzaldehyde (1 Torr) for 5 min in the load lock of
the UHV system. An addition–elimination reaction of the
aldehyde to form an imine (C=N link) and devolve water is
expected to occur. Since the reaction is carried out under
vacuum with an extremely low concentration of water, the
reaction is expected to proceed to completion. Figure 3
shows HREELS spectra of a surface reacted with diamino-
propane for 144 s (corresponding to the STM image shown
in Figure 2 b) before and after exposure to benzaldehyde.
The initial surface exhibits the characteristic modes at 830,
1120, 1400, 2920, and 3380 cm 1 associated with the grafting
of the terminal amine groups via a Si N link. As observed
in Figure 1, this surface exhibits a rather broad elastic peak,
attributed to accumulation of majority carriers induced by
the electron-donating character of the terminal amine
group. Upon exposure to benzaldehyde the N H stretch at
3380 cm 1 is reduced in intensity and three new features (in-
dicated by arrows in Figure 3) are observed in the HREELS
spectrum. In particular, new peaks at 730 and 3050 cm 1 can
be associated with the attachment of phenyl rings to the sur-
face. A shoulder appearing at 1630 cm 1 is assigned to the
C=N stretch arising from the grafting reaction.[18] These
changes in the vibrational spectra definitively show that the
addition–elimination reaction of the aldehyde has occurred.
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G. P. Lopinski et al.
In solution this imine formation reaction requires an acid
catalyst, obviously not present in the gas-phase reaction re-
ported here. However, the reaction of aldehyde vapor with
levitated droplets containing diaminonaphthalene (in the
absence of acid catalyst) has been observed to result in
imine formation,[26] suggesting that the catalyst is not re-
quired for the gas-phase reaction to proceed.
Also notable in Figure 3 is the narrowing of the elastic
peak upon reaction. The FWHM of the elastic peak is re-
duced from 135 to 75 cm 1 and the peak intensity increases
from 9 to 17 kHz (the spectrometer settings were main-
tained constant during this experiment). The total intensity
of the quasi-elastic peak is seen to be conserved to within
5 %. The narrowing of the elastic peak upon reaction (to a
value similar to that observed on the H-terminated surface)
is consistent with the suggestion that the initial broadening
is due to the accumulation of majority carriers (band-bend-
ing) as discussed above. Once the amine groups are con-
sumed by the reaction this band-bending effect is expected
to be lifted, as observed.
Having established that the gas-phase photochemical re-
action approach is a simple method to form amine-terminat-
ed monolayers for further reaction, the methodology was
used to form isolated reactive groups on a surface. The mo-
tivation for creating isolated reactive groups on an other-
wise H-terminated surface is the prospect of coupling com-
plex molecules (such as biomolecules or molecular switches)
to the surface via sequential reactions in order to facilitate
single-molecule studies with STM. HREELS spectra follow-
ing the progress of the reaction sequence discussed above,
but in the low-coverage limit, are presented in Figure 4. The
Figure 4. HREELS spectra for a) a clean H/SiACHTUNGRE(111) surface, b) after a
UV photochemical reaction with 1,3-diaminopropane for 6 s, and
c) exposure to benzaldehyde (1 Torr) for 5 min. The dotted lines mark
the positions of the C=N stretch (1630 cm 1), the C H stretch for
sp3-bonded carbon (2920 cm 1), and the N H stretch (3375 cm 1).
spectrum for the clean H/SiACHTUNGRE(111) surface is virtually identi-
cal to that in Figure 2 a, indicating a high-quality H-termi-
nated surface with negligible hydrocarbon contamination.
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Surface Reactions of Amines and Hydrogen/Silicon Substrates

SPECIAL SECTION
After reaction with 1,3-diaminopropane for 6 s, the ble to image the same area over the course of the experi-
HREELS spectrum (Figure 4 b) reveals weak (note the mul- ment, however, the images represent typical areas on the
tiplication factor of 12 000 relative to the elastic peak) but surface at each stage. The clean H/SiACHTUNGRE(111) surface (Fig-
clearly observable peaks associated with the C H methyl- ure 5 a) has few defects and is indicative of the quality of
ene stretches and the N H stretch of the terminal amine. surfaces that can be routinely achieved. After reaction with
These new features are consistent with the reaction of di- 1,3-diaminopropane, a number of bright isolated features
ACHTUNGREaminopropane with the surface and the formation of termi- are observed (Figure 5 b). Large areas of clean H/SiACHTUNGRE(111)
nal amine groups on the surface. The peaks due to Si H are visible, consistent with the HREELS data in Figure 4,
remain largely unchanged, suggesting that only a small which shows only a slight decrease in the Si H peak intensi-
number of molecules have been attached and that the re- ty after reaction for 6 s. In fact, by counting the number of
mainder of the surface has not been adversely affected by observed features the coverage is determined to correspond
the reaction. In fact, STM images of this surface (shown in to only 0.5 % of a monolayer. There is no indication of Si
Figure 5 b) indicate that the coverage of adsorbed species is dangling bonds being present on the surface. A close exami-
nation of the image shows
that there are at least two
different features with dif-
ferent apparent heights on
the surface. This is made
clear by plotting a histo-
gram of the apparent
height of these features
(Figure 5 d). Approximate-
ly 65 % of the features ex-
hibit an apparent height of
 3 F with the remainder
appearing somewhat small-
er ACHTUNGRE(2 F). Therefore the
STM imaging at low cover-
age reveals that the photo-
chemical reaction of 1,3-di-
ACHTUNGREaminopropane is likely
more complicated than
suggested above from the
analysis of higher coverage
HREELS spectra. The ma-
jority features are likely
due to molecules that have
reacted by losing a H atom
from one of the amine
groups and reacting with a
Figure 5. STM images (25 1 25 nm ) of H/SiACHTUNGRE(111) at various stages of the sequential reaction: a) clean
2

H/SiACHTUNGRE(111), b) exposed to 1,3-diaminopropane (1 Torr) and UV radiation for 6 s, c) exposed to benzaldehyde

(1 Torr) for 5 min. d) A histogram of the apparent molecule height created using data from Figure 2 b. e) A
histogram of the apparent molecule height created using data from Figure 2 c.
only  0.5 % and that these species are isolated on an other-
wise pristine H-terminated surface. Upon exposing this sur-
face to benzaldehyde, the HREELS spectrum (Figure 4 c)
shows the disappearance of the N H stretch at 3380 cm 1 as
well as the appearance of the C=N stretch[18] at 1630 cm 1
and the C H stretch of sp2-bonded carbon found at
3050 cm 1. These changes are the same as those observed
for the reactions with the amine-terminated monolayer and
definitively show that the addition–elimination reaction
with the aldehyde has occurred.
Figure 5 shows STM images corresponding to the
HREELS spectra of Figure 4. As the reactions to form the
reactive amine groups and couple the benzaldehyde are car-
ried out in the load lock of the UHV system, it is not possi-
dangling bond on the sur-
face via formation of a Si
N bond, as discussed
above. However, also as
discussed above, breakage
of a C N bond to form CH3 radicals has been observed as a
minority photodissociation channel of methylamine.[20] It is
therefore plausible that the “shorter” minority species is
due to molecular fragments bound to the surface via Si C
bonds. No direct evidence for Si C bond formation (the Si
C stretch mode is expected at  670 cm 1) is observed in the
vibrational spectra due to the small coverage and the close
proximity of the Si H bending mode. The absence of a sig-
nificant Si C peak in the high-coverage HREELS spectrum
(Figure 3 a) suggests that this is indeed a minority species.
After exposure of the isolated 1,3-diaminopropane-ter-
minated surface to benzaldehyde the STM images of the
surface do not look substantially different (Figure 5 c). The
density of features has not increased, indicating that the re-

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 full papers
SPECIAL SECTION
action has only occurred at the sites with the attached
amine groups. In the absence of dangling bonds, benzalde-
hyde is not expected to react directly with the H/SiACHTUNGRE(111) sur-
face as has been confirmed in a separate control experiment
(not shown). Somewhat surprisingly, there is no observation
of a significant increase in the apparent height of the molec-
ular features after reaction. In fact, the histogram of the ob-
served heights actually shows that features have decreased
in height (Figure 5 e). It is important to note that in addition
to reflecting the conformation and electronic states of the
adsorbed molecules, the apparent height in these systems
has been found to strongly depend on the state of the tip,
complicating quantitative interpretation of height changes
in different images. In addition, the electronic changes ob-
served in the HREELS spectra in the case of the initial for-
mation of the amine-terminated surfaces and their subse-
quent reaction with benzaldehyde may offer a potential ex-
planation for this observation. These observations serve to
highlight the difficulty in studying these types of sequential
reaction by STM. Based on the STM data alone, without
the corresponding HREELS data (which clearly indicate a
reaction has occurred), one may have concluded that the ex-
pected coupling reaction did not occur.
3. Conclusions
In summary, a simple method for the formation of
amine-terminated silicon surfaces has been presented. This
method makes use of gas-phase photochemical reactions of
1,3-diaminopropane with H/SiACHTUNGRE(111). The reactivity of the
surfaces has been confirmed by demonstrating a sequential
reaction with benzaldehyde. The production of these func-
tional monolayers is straightforward and requires very little
processing, in direct contrast to existing methods requiring
protection/deprotection approaches,[10, 11] which may ad-
versely affect the surface quality. Broadening of the elastic
peak in the HREELS spectra upon the formation of amine-
terminated monolayers, and the subsequent narrowing upon
coupling the benzaldehyde suggests that the amine function-
alization is altering the electronic states of the silicon sub-
strate, an effect warranting further investigation. We have
also succeeded in generating isolated amine groups on an
otherwise clean H/SiACHTUNGRE(111) surface and have successfully re-
acted these groups with an aldehyde. The sequential reac-
tion proceeded without degrading the surface quality, an es-
sential requirement for STM studies of isolated molecules.
The amine-terminated surfaces produced here have also
been used for solution-phase sequential reactions with vari-
ous aldehydes (work currently in progress). While the Si N
bond remains intact and the aldehydes are successfully cou-
pled to the surface, some oxidation of the silicon substrate
is noted, particularly for incomplete monolayers. This work
is expected to enable future studies of single photoactive,
electroactive, or biomolecular species on silicon substrates.
1384 www.small-journal.com < 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
G. P. Lopinski et al.
Acknowledgements
The authors acknowledge N. Branda, T. Mischki, and D. D. M.
Wayner for helpful discussions. This work was partially sup-
ported by funding from the NRCs Genomics and Health Initia-
tive.
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Received: March 1, 2006
Revised: May 26, 2006
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