Inter- and intramolecular temperature-dependent vibrational perturbations of alkanethiol self-assembled monolayers

Article abstract of DOI:10.1021/jp031273u

The infrared spectra of octanethiol, dodecanethiol, and hexadecanethiol (C₈, C₁₂, and C₁₆, respectively) monolayers adsorbed on Au(111) textured surfaces have been explored in the 25-300 K regime. The C-H stretching modes typically shift by several wavenumbers to lower frequencies and the intensities increase by as much as 75% as the temperature is decreased, providing evidence of, among other effects, the coupling of these stretching modes with lower energy vibrational modes. In contrast, for all temperatures below 300 K, the positions of the C-H bands of fully hydrogenated C₁₆, shift by several wavenumbers to higher frequencies as the hydrogenated adsorbates are increasingly diluted in a matrix of fully deuterated C₁₆, showing that all bands are subject to intermolecular couplings. The analysis of the behavior of the C-H stretching bands suggests that the temperature dependence of the vibrational frequencies associated with the methylene stretching modes is principally due to intermolecular couplings, whereas the temperature dependence of the vibrations associated with the methyl terminations is largely due to intramolecular couplings. It is suggested that the highly constrained geometry of the isotopically diluted monolayer may provide an environment that is less sensitive to intramolecular couplings with low-frequency modes than that of urea-clathrate-isolated species.

Full text of DOI:10.1021/jp031273u

8182
J. Phys. Chem. B 2004, 108, 8182-8189
Inter- and Intramolecular Temperature-Dependent Vibrational Perturbations of Alkanethiol
Self-Assembled Monolayers
EÄ tienne Garand, Jean-Franc¸ois Picard, and Paul Rowntree*
De´partement de chimie, UniVersite´ de Sherbrooke, Sherbrooke, Que´bec, Canada J1K 2R1
ReceiVed: NoVember 26, 2003
The infrared spectra of octanethiol, dodecanethiol, and hexadecanethiol (C8, C12, and C16, respectively)
monolayers adsorbed on Au(111) textured surfaces have been explored in the 25-300 K regime. The C-H
stretching modes typically shift by several wavenumbers to lower frequencies and the intensities increase by
as much as 75% as the temperature is decreased, providing evidence of, among other effects, the coupling of
these stretching modes with lower energy vibrational modes. In contrast, for all temperatures below 300 K,
the positions of the C-H bands of fully hydrogenated C16 shift by several wavenumbers to higher frequencies
as the hydrogenated adsorbates are increasingly diluted in a matrix of fully deuterated C16, showing that all
bands are subject to intermolecular couplings. The analysis of the behavior of the C-H stretching bands
suggests that the temperature dependence of the vibrational frequencies associated with the methylene stretching
modes is principally due to intermolecular couplings, whereas the temperature dependence of the vibrations
associated with the methyl terminations is largely due to intramolecular couplings. It is suggested that the
highly constrained geometry of the isotopically diluted monolayer may provide an environment that is less
sensitive to intramolecular couplings with low-frequency modes than that of urea-clathrate-isolated species.
Introduction
Au(111) surfaces, Parikh and Allara’s2 formalism to study thin
films is commonly applied. It is based on the decomposition of
an appropriate reference spectrum (usually taken to be the
isolated molecule or microcrystal in an inert host matrix) into
individual bands with known orientations of the individual
transition dipole moments relative to the molecular axis, and
then the optical equations for these optical properties and those
of the substrate for various model structures are resolved. The
parameters that define this structural model (e.g., molecular tilt
and twist, which define the projection the individual transition
dipole moments onto the incident radiation field) are systemati-
cally varied to optimize the agreement with the experimental
IR-RAS data. Clearly, the appropriate reference spectrum is the
key ingredient for this approach, and the authors caution that
there can be “no significant difference with regard to inter- and
intramolecular interactions, electronic structure and packing
density between the reference and film phase”.2 In the case of
the bulk polymethylene chains, these interactions have been
characterized in great detail by Snyder et al. and MacPhail et
al.;4-6 intramolecular couplings take the form of Fermi reso-
nances between the fundamental stretching modes and combina-
tions of the chain bending modes. Intermolecular couplings can
be evidenced by comparing the bulk n-alkane spectra with those
of the same species isolated within the 5.25 Å diameter
cylindrical pores of urea-clathrates;7 these intermolecular
interactions are caused by the resonant interaction of oriented
and identical oscillators among adjacent molecules and have
been explored in detail for simple adsorbates such as CO
adsorbed on crystalline copper surfaces.8-10 To our knowledge,
however, there is little information available in the literature
concerning these effects in SAM systems, and as such, the
structural parameters extracted from these measurements and
analyses may include systematic errors. This lack of information
is due, in part, to the much lower signal-to-noise ratio in the
monolayer films as compared to the bulk samples.
Quantitative infrared spectroscopy of the C-H stretching
bands is widely used for the characterization of condensed acyl
chains including polymers, lipid membranes, and self-assembled
monolayers. Ideally, such a characterization would include
information on both the molecular conformations and the
orientation of the molecular system within the macroscopic
sample under investigation. For relatively simple film constitu-
ents containing extended hydrocarbon chains, the position and
the width of C-H stretching bands are often used to probe chain
order and identify structural phase transitions; for these com-
ponents, it is commonly presumed that the spectroscopic
signature of a highly ordered film is the observation of the
dominant methylene stretching bands at relatively low frequen-
cies. The origin of this is the presumed reduced density of
conformational (gauche) defects in such films, because gauche
defects tend to have vibrational frequencies several wavenum-
bers higher than the all-trans conformations.1 In the special case
of highly organized films on planar surfaces, the intensities can
be analyzed in terms of average molecular orientations relative
to the polarization vector of the incident radiation field,
according to standard dipole selection rules.2,3 Although the
computational implementation of these principles may be
complex (according to the sophistication of the treatment of
the substrate’s optical response), the conceptual simplicity of
these principles makes the use of quantitative infrared spec-
troscopy very appealing in surface science.
Self-assembled monolayers (SAMs) of simple organic species
chemically bound to noble metal surfaces have been explored
extensively using this approach, and many of the structural
models were initially developed on the basis of these spectral
studies. In the case of the organothiol monolayers adsorbed on
* Corresponding author (e-mail Paul.Rowntree@USherbrooke.ca).
10.1021/jp031273u CCC: $27.50 © 2004 American Chemical Society
Published on Web 05/22/2004

Temperature-Dependent Vibrational Perturbations
J. Phys. Chem. B, Vol. 108, No. 24, 2004 8183
The interpretation of the spectral properties of these films is
becoming increasingly important as the study of SAMs extends
into new regimes of temperature and molecular environments,
and notwithstanding the experimental challenges, it is increas-
ingly important to understand the underlying factors that
determine the band positions and intensities for the monolayer
systems. Infrared spectroscopy has been used by Nuzzo et al.11
to characterize the temperature-dependent behavior of long-chain
alkanethiol monolayers on gold. They concluded that most of
the important changes observed in the low-temperature infrared
spectra reflected an intrinsic dependence of the C-H stretching
modes and the elimination of gauche defects near the chain
terminations; large scale reorientation of the molecules was not
deemed to be a significant factor, due to the already optimized
geometry of the two-dimensional SAM system. This was
supported by qualitatively similar observations on crystalline
n-alkanes by Snyder and co-workers.6 Bensebaa et al.1 have
confirmed that the increased band intensities that are observed
upon heating of n-alkanethiol SAMs above 300 K are due to
the introduction of such defects, thus supporting the inter-
pretation of the cryogenic results. However, recent molecular
dynamics simulations suggest that alkanethiol SAMs can
undergo temperature-dependent structural transitions by the
variation of tilt angles12,13 or orientation angles.14 Experimental
validation of these theoretical works by infrared spectroscopy
requires a quantitative understanding of the intrinsic behavior
of the C-H stretching bands as a function of both the
temperature and chemical environment.
dependent spectra can only underestimate the actual degree of
intermolecular couplings.
This study shows that the spectral positions and intensities
of the h33-C16 components of the SAM provide evidence of inter-
and intramolecular couplings, and we have isolated the relative
magnitudes of these effects; we also make preliminary sugges-
tions as to the fundamental nature of these couplings. This work
shows that the direct use of CH2-derived band positions to assess
the density of gauche molecular defects in SAMs confounds
the spectroscopic influence of local gauche effects with long-
range compositional disorder, as both tend to broaden the
observed band envelopes and displace them to higher frequen-
cies. Similar conclusions were obtained by Kodati et al.16 for
condensed phase acyl chains, but as will be shown, the
environment and behavior of the two-dimensional SAM vary
considerably from those of the three-dimensional condensed
phases. We feel that the demonstration of these effects may have
a significant impact on the use of quantitative infrared spec-
troscopy to elucidate the structural characteristics of these Cn
SAMs. It has been noted2 that this structure-only approach
cannot simultaneously fit the intensities of the observed CH3
and CH2 associated bands, and local film defects were suggested
to be the underlying cause. Parikh and Allara’s initial work2
applied the protocol to the case of C18 SAM bound to a
polycrystalline Au(111) substrate, using the spectrum of C19H39-
CO2Na as a reference; in their optimized geometry it was found
that the bands associated with the methyl terminations could
not be satisfactorily explained on the basis of an all-trans
molecular model, and structural disorder near these groups was
proposed to be the fundamental cause.
One of the objectives of the present work is to explore inter-
and intramolecular interactions in SAMs, to better understand
the nature of the IR-RAS results for alkanethiol SAMs. Isotopic
dilution is a very simple method to isolate intramolecular and
resonant intermolecular coupling contributions in vibrationnal
spectra without significant structural perturbations. To clarify
the temperature-dependent vibrational behavior of alkanethiol
SAMs on gold, we have monitored the band intensities and
positions as a function of temperature for pure and isotopically
diluted hexadecanethiol SAMs. The type of analysis employed
herein is predicated upon the assumption that there is no
preferential aggregation of one isotopic species within the
chemisorbed film (i.e., that the h33-C16 and d33-C16 film
constituents are perfectly miscible in the two-dimensional
adsorbed state). Indeed, it has been suggested that mixed
Langmuir-Blodgett films may show compressive behavior that
is distinguishable from that of the isotopically pure films, but
the origins of these differences were not elaborated. Although
it is difficult to directly probe this issue, Buckingham et al.15
have shown that the onset for isotope-based segregation in melts
of linear Cn molecules is expected only for chains containing
at least 100 methylene repeat units; above this threshold, the
nonequivalent chain folding dynamics may lead to phase
separation, depending on the temperature. Segregation was
presumed to be negligible in the work on three-dimensional
mixtures of hydrogenated and deuterated C32, and ideal mixing
behavior was considered to be operant. According to Bucking-
ham’s analysis, phase separation of three-dimensional h33-C16
and d33-C16 may be possible for temperatures below 2 K, and
as such, we conclude that this process is not relevant to the
present study. Furthermore, it should be noted that if two-
dimensional segregation of the h33-C16 and d33-C16 components
of the film occurred, the local environment of each component
would more closely resemble a pure film and would mask any
composition-dependent effects; the observed composition-
As mentioned above, this approach to the structural analysis
of the film using grazing incidence reflection-absorption
spectroscopy2,3,17 presumes that the reflectivity of the monolayer/
substrate system is determined by the absorption band strengths
of the isolated molecules (as measured in an inert host matrix
such as KBr), subject to the structural perturbations imposed
by the highly oriented film system and the projection of the
transition dipole moments of the C-H oscillators onto the
surface normal (plus the optical perturbation introduced by the
substrate and the index of refraction of the film). This structural
model explains, for example, the high absorption of the
symmetric methyl stretch bands (r+, 2875 cm-1) in the two-
dimensional environment of the film, where the transition dipole
moment is almost parallel to the surface normal) as compared
to the isotropic melt5,16 and in the case of alkanethiol-coated
gold nanoparticles.18,19 However, the neglect of intermolecular
effects when considering the band strengths and band positions
may lead to systematic errors in the structural parameters
extracted from these measurements. The present work provides
an alternative basis to understand these discrepancies in terms
of differing intermolecular couplings related to the various
vibrational modes of the alkanethiol SAM.
Experimental Section
The Au films were evaporated on freshly cleaved mica
surfaces following a modification of DeRose’s protocol,20 which
is known to prepare high-quality films with a strongly Au(111)
texture. Mica substrates (Proscience-Techniglass ASTM-V2)
were degassed at 300 °C for 12-20 h in a turbomolecularly
pumped system (∼1 × 10-7 Torr) prior to deposition. Following
evaporative deposition of ∼150 nm of gold, the samples were
annealed at 300 °C for 2 h under vacuum prior to removal from
the system. When possible, the gold substrates were immediately
exposed to the thiol solutions; otherwise, they were stored in
sealed polycarbonate vials under an argon atmosphere until use.

8184 J. Phys. Chem. B, Vol. 108, No. 24, 2004
Garand et al.
TABLE 1: Observed Bands for Pure h33-C16 and d33-C16
Octanethiol, dodecanethiol, and hexadecanethiol (h17-C8,
h25-C12, and h33-C16, respectively) were used as received
(Aldrich, 95%). Deuterated hexadecanethiol (d33-C16) was
synthesized from palmitic-d31 acid (Cambridge Isotope Labo-
ratories, 98%) following a slight modification of Badia’s
protocol.19 d31-Palmitic acid (0.5 g, 1.7 mmol) was reduced with
LiAlD4 (Aldrich) (0.47 g, 14 mmol) in freshly distilled
tetrahydrofuran to the corresponding alcohol (0.46 g, 98% yield).
d33-Hexadecanol was then treated under reflux with 30 mL of
48% HBr, giving the d33-bromohexadecane (0.47 g, 83% yield).
Finally, the d33-bromohexadecane was treated with Na2S2O3
(0.37 g, 1.5 mmol) in ethanol under reflux, and the resulting
Bunte salt was hydrolyzed with 4 mL of concentrated HCl to
give the desired d33-hexadecanethiol (0.37 g, 94% yield) after
purification by flash chromatography. The overall yield of the
synthesis is 75%, and the purity of the final product was >99%
as found by GC-MS. Film deposition onto the Au/mica
substrates was by immersion in 1.0 mM thiol/methanol solutions
for at least 24 h. For the (h,d) mixed monolayers, the deposition
solutions were prepared from appropriate volumes of the pure
1.0 mM h33-C16 and d33-C16 solutions. Individual 10 × 25 mm
SAM/Au/mica samples were secured to 3 mm thick copper
carrier plates using copper straps to provide thermal contact to
the front-surface gold film. These carrier plates had a 10 × 5
mm tab extension in the plane of the sample to provide a thermal
contact to the sample manipulator and cryostat assembly. With
the carrier plates and the attached samples lying in the vertical
plane, and mechanically supported on two rearward-facing
protrusions, this tab loosely fit into a Ga-filled “well” on the
copper sample support block that was permanently attached to
an XYZ-tilt-rotation manipulator (Thermionics). A 25 W heater
is integrated into the sample support block as well. OFHC
copper braids connected the sample support to the tip of a
closed-cycle He cryostat head (APD Cryogenics model 21-B)
to permit sample movement. This sample support block was
electrically and thermally isolated from the 300 K manipulator
support using glass beads as the tilt pivot points; electrical
insulation from the grounded cryostat was via a sapphire plate
sandwiched between OFHC plates. When the sample was cooled
to below the freezing point of Ga (27 °C), the Ga provided a
rigid link between the sample carrier plate and the manipulator
system, as well as an excellent thermal link to the cryostat; the
vapor pressure of Ga is always below 10-11 Torr in the
temperature range employed herein.21 Temperatures were
measured and stabilized using a 0.07% Fe/Au thermocouple
attached to the sample support and a commercial controller
system (Omega Engineering CYC-3000). Due to the relatively
large thermal mass of the carrier plate plus sample support
assembly, the maximum heating and cooling rates were 10 and
1.4 K/min, respectively; at such slow rates of temperature
variations, there is no evidence that the SAM is out of thermal
equilibrium or that a significant temperature gradient exists
between the thermocouple and the organic film. No spectro-
scopic evidence of contamination by adsorbed species was found
upon cooling or during the multihour experiments.
SAMs
C-H position
(cm-1
25 K 300 K
C-D position
(cm-1
)
)
transition dipole
orientation
band
d+
25 K
2093
300 K
2097
in C-C-C plane to
molecular axis
to C-C-C plane
| to terminal C-C
in C-C-C plane to
terminal C-C
2848
2851
d-
r+
2921
2876
2962
2921
2197
2198
2878 ∼2078 ∼2078
r -
2962
2217a 2217a
a
r -
to C-C-C plane to 2955 ∼2957
b
terminal C-C
-
a r
for d33-C16 are unresolved at all temperatures studied.
a,b
beam using an ellipsoidal mirror configured with one focus at
the sample and the other at the 1.0 mm2 InSb detector element.
The incident angle is ∼85° from the surface normal.3,17 Light
was transferred into and from the vacuum system via differen-
tially pumped NaCl windows.22 For reasons not related to the
work presented herein, the optical path is folded within the
vacuum system using two plane-mirrors that can be indepen-
dently adjusted. These data are collected without the use of a
polarizer, such that the overall intensities are systematically a
factor of 2 lower than in works that include the polarizer. Data
were collected with a stated resolution of 2 cm-1 (post-FFT
data point spacing of 1.0 cm-1) with a 3 cm/s moving mirror
velocity, Happ-Ganzel apodization, and no zero-filling. “Ab-
sorption spectra” present the reflectivity of a SAM referenced
to that of a pristine Au/mica surface, whereas “∆ absorbance
spectra” present the reflectivity referenced to the same film
measured at 300 K. With the exception of baseline correction
at 2800 and 3000 cm-1 (2050 and 2250 cm-1 for the d33-C16
results), no data editing or filtering has been performed on the
data used in this study. All measurements were repeated at least
in triplicate using different samples; the error bars reflect the
sample-to-sample variations. Peak heights and positions are
determined using in-house LabVIEW-based software.
Spectroscopic Background
The nomenclature used in this work to identify the C-H and
C-D stretching modes follows that commonly used in spec-
troscopic studies of Cn films. Table 1 shows the band assign-
ments for these bands, along with the description of the transition
dipole vector direction (presuming an all-trans Cn chain
conformation) and the band positions measured for a pure h33-
C16 and a pure d33-C16 film at 300 and 25 K. The projections of
these transition dipole moments onto the surface normal (and
therefore to a first approximation the observed intensities) as a
function of molecular tilt and twist angles have been elaborated
elsewhere.23 In the following text we will identify the samples
using the notation x%-Cn, where Cn identifies the chain length
and x identifies the percentage of the fully hydrogenated Cn
chains in the film.
Results
Samples were transferred via a turbopumped load-lock into
our in-house-designed vacuum system (240 L/s TNB-X ion
pump, base pressure of 2 × 10-10 Torr at ambient temperature,
5 × 10-11 Torr with cryostat operating) and mounted onto the
sample stage using a UHV-wobble-stick.
Figure 1 shows the effect of sample temperature on the C-H
stretching vibrations of a 100% h33-C16 monolayer; the top panel
(A) presents the absorption spectra of the films, whereas the
lower panel (B) presents the ∆ absorbance spectra, the latter
focusing on the details of the temperature-related changes. The
most evident temperature effect on the spectra is the progressive
intensity increase of the principal absorption bands upon cooling,
along with a shift of the peaks to lower frequency. Large
Spectra were recorded by focusing the modulated infrared
radiation from a Nicolet Magna-IR 560 bench (ThermoInstru-
ments) onto the surface using an external parabolic mirror
assembly and planar steering optics and collecting the reflected

Temperature-Dependent Vibrational Perturbations
J. Phys. Chem. B, Vol. 108, No. 24, 2004 8185
Figure 1. Temperature-dependent direct absorbance spectra (A) and
∆ absorbance spectra (B) of 100% h33-C16 SAMs; sample temperatures
are 300, 250, 200, 150, 100, 50, and 25 K. The ∆ absorbance spectra
are obtained using the 300 K reflectivity as a reference.
Figure 2. Temperature-dependent direct absorbance spectra (A) and
∆ absorbance spectra (B) of 100% d33-C16 SAMs; sample temperatures
are 300, 250, 200, 150, 100, 50, and 25 K. The ∆ absorbance spectra
are obtained using the 300 K reflectivity as a reference.
intensity increases and spectral shifts have also been observed
by Nuzzo et al.11 and by Bensebaa et al.1 for h45-C22 films cooled
to 80 and 155 K, respectively. These changes are fully reversible
on heating from 25 to 300 K and upon subsequent thermal
cycles. There is no evidence of discontinuous spectral tendencies
that could be indicative of first-order phase transitions within
the film. It is noteworthy that in all cases there remain significant
spectral changes as the temperature is cooled to below 200 K,
at which temperature molecular dynamics simulations indicate
that the population of structural gauche defects in the film is
below 0.3%.24 Thus, structural changes are most likely restricted
to minor changes in molecular orientations rather than chain
conformations. Indeed, tilt-angle changes of 2-4° have been
predicted for the sub-200 K regime,24 as have azimuthal rotations
of molecular domains with respect to the substrate.14 Figure 2
presents the absorption and ∆ absorption spectra for pure d33-
C16 films in the 25-300 K regime, using the same scales as
Figure 1 for pure h33-C16; to the best of our knowledge these
are the first published spectra of d33-C16 SAMs and their
temperature dependencies. The C-D stretching bands are of
significantly lower intensity than their C-H counterparts, and
their evolution with temperature is less pronounced. This has
been reported previously for bulk n-alkane samples and for
n-alkanes trapped within urea-clathrates.7,16 Like their hydro-
genated analogues, the dominant C-D stretches shift by several
wavenumbers to lower frequencies and increase in intensity as
the temperature is reduced to 25 K. However, the relatively poor
signal-to-noise ratio of the C-D monolayer spectra makes the
quantitiative analysis less certain; instead, this work will
concentrate on the behavior of the d+ and r+ C-H bands as
the film composition is changed.
Figure 3. Peak position (A) and peak absorbance (B) for the symmetric
methylene stretching vibration (d+) of 100% h33-C16 and h25-C12 samples
as a function of sample temperature. The straight lines of (A) and the
curves of (B) are provided to guide the eye through the data.
perature in the T ) 25-300 K regime for all chain lengths,
with the magnitude of the increases being systematically greater
for the longer chain systems. The d+ peak approaches an
asymptotic intensity of ∼1.1 mAbs for h33-C16. The integrated
intensity grows (relative to that at 300 K) by 75%. The r+ bands
shows similar behavior (Figure 4): increased absorptions at
progressively lower frequencies than the peak position at 300
K cause the peaks to shift almost linearly from 2877.5 to 2876
cm-1 (5.5 × 10-3 cm-1/K). The r+ intensity increases sublin-
early as the temperature is reduced to 25 K, with integrated
intensity changes of ∼30% relative to that at 300 K. The
behavior of the r+ peak is relatively insensitive to the chain
length. There is some evidence of a net loss of intensity of the
background near the r+ peak (Figure 1B), but the integrated
area of this loss is significantly less than the net growth of the
vibrational band; as such, the observed increase is not simply
the redistribution of oscillator strength. The temperature-
dependent evolutions of the asymmetric bands (i.e., d- and r-)
are more difficult to establish. The methylene-derived d- peak
Figure 1 shows that the growth of the d+ band (∼2850 cm-1
)
is caused by increased optical absorbance at progressively lower
frequencies, such that the overall envelope is subject to a
systematic red shift. In our measurements of h17-C8, h25-C12,
and h33-C16, the d+ band presents the strongest increase of peak
absorbance, whereas previous work on h45-C22 films1,11 showed
more pronounced changes on the d- structure (∼2929 cm-1).
Figure 3A shows that the d+ band shifts linearly from ∼2851
to 2848.5 cm-1 as the temperature is reduced from 300 to 25 K
(9.1 × 10-3 cm-1/K); h25-C12 presents similar trends. The d+
intensity (Figure 3B) increases sublinearly with reduced tem-

8186 J. Phys. Chem. B, Vol. 108, No. 24, 2004
Garand et al.
Figure 4. Peak position (A) and peak absorbance (B) for the symmetric
methyl stretching vibration (r+) of 100% h33-C16 and h25-C12 samples
as a function of sample temperature. The lines are provided to guide
the eye through the data.
Figure 5. Peak position (A) and peak absorbance (B) for the symmetric
methylene stretching vibration (d+) of h33-C16 samples as a function of
the SAM composition, for sample temperatures of 25 and 300 K. The
curved lines are provided to guide the eye through the data.
converges toward 2852.5 ( 0.3 cm-1 in the limit of the isolated
h33-C16 molecule, regardless of the sample temperature; ex-
pressed in a slightly different manner, the position of the
symmetric methylene band of an isolated h33-C16 impurity in a
d33-C16 film is essentially independent of temperature below 300
K. Under these conditions any intramolecular interactions that
influence the d+ band position have no significant temperature
dependence. Given that intramolecular interactions are expected
to be largely independent of film composition, we anticipate
that the intramolecular interactions within a 100% h33-C16 SAM
should also be subject to negligible temperature-induced d+ band
shifts. This strongly suggests that essentially all of the 3 cm-1
downward shift of this band for the full SAM that is seen upon
cooling (Figure 3A) is due to changes in the intermolecular
couplings, with very little intramolecular contributions. We stress
that all evidence indicates that the physical environment of this
impurity molecule is identical to that of the 100% h33-C16 film.
Figure 5B shows that the intensity of the d+ peak is a linear
function of the quantity of adsorbed h33-C16; as required, the
optical absorbance of the film tends toward zero as the number
of absorbers is decreased, and the optical absorbance per
molecule (at a given temperature) is independent of film
composition, showing that intermolecular effects are minimal.
The apparent optical absorbance of the d+ band increases at
lower temperatures, as anticipated from Figures 1 and 3, with
a d+(300 K)/d+(25 K) ratio of 0.6-0.7 for all film compositions.
Whereas the d+ band position is influenced by changes in the
intermolecular interactions with temperature, the variation of
the d+ band intensity with temperature is determined almost
exclusively by changes in the intramolecular couplings.
shows a rather uniform growth across the entire absorption
feature (Figure 1B) down to 200 K. At lower temperatures, the
difference spectra show a distinct splitting into a peak at 2919
cm-1 and a smaller, sharper component at 2922 cm-1, indicating
the presence of two overlapping spectral bands. The resolution
of this splitting is highly dependent upon the quality of the SAM;
surfaces that exhibit broader than usual CH2 bands do not exhibit
this splitting. The integrated intensity of the d- band (2910-
2930 cm-1) grows by ∼45% in the 300-25 K regime. As
reported by Nuzzo et al.,11 the r- bands show a complex
behavior with temperature. The out-of-plane stretch r-b becomes
a resolved peak at ∼250 K, then increases in intensity and shifts
by -2.0 cm-1 with lower temperatures. At low temperatures
-
the rb band is dominant; the results of Nuzzo et al. for 100%
h45-C22 show similar trends, although the resolution of the two
antisymmetric components is less evident in their data. These
workers attributed the evolution of the CH2- and CH3-derived
bands to the reduction in the number of gauche defects near
the chain terminations and the stabilization of a structural unit
cell containing more than one molecule at low temperatures;11
it was also proposed that the intensity increases may reflect
intrinsic changes of the vibrational modes, rather than changes
to the structural characteristics of the film. This is supported
by the similarity to the spectroscopy of crystalline polymethylene
samples.6 To distinguish the structural from the spectral proper-
ties of these films, we have repeated the thermal cycling
experiments with mixed monolayers containing controlled
proportions of h33-C16 and d33-C16. With the increasing isotopic
dilution of the SAMS, these bands suffer shifts to higher
frequencies and are subject to intensity changes; the magnitudes,
but not the direction of the spectral shifts, are influenced by
the temperature. Panels A and B of Figure 5 show the position
and the intensity, respectively, of the d+ band for T ) 300 and
25 K for the five film compositions considered; the shifts and
intensity changes are monotonic functions of temperature in the
sub-300 K regime. In addition to the ∼3 cm-1 downward shift
that has been described upon cooling for pure films, the
symmetric methylene band can shift as much as 4 cm-1 to
higher frequencies as the h33-C16 molecules are increasingly
diluted in a d33-C16 film; the effect of this dilution is more
significant at lower temperatures. Remarkably, the peak position
The behavior of the r+ bands with changing composition is
fundamentally different from that of the d+ band. Figure 6A
shows that the r+ band shifts by ∼2 cm-1 to higher frequencies
as the hydrogenated fraction of the film is reduced from 100 to
0%, revealing the influence of changing intermolecular interac-
tions. The magnitude of this shift is, to our experimental
precision, insensitive to the sample temperature; equivalently,
the 2.0 cm-1 temperature-induced downward shift of the r+ band
is independent of the film composition. For the reasons discussed
above in the context of the d+ band, we anticipate that the
intramolecular contributions are largely independent of film

Temperature-Dependent Vibrational Perturbations
J. Phys. Chem. B, Vol. 108, No. 24, 2004 8187
Discussion
The results presented herein demonstrate clearly that although
temperature-dependent structural changes are certainly expected
in Cn/Au SAMs,24 the infrared spectroscopic signatures of these
films are also strongly affected by the molecular environment
of the film for any given structural motif. The magnitude of
these intermolecular effects can exceed that of the structure-
induced effects, and as such, it is important to understand the
physical basis for the various perturbations that are imposed
upon the vibrational spectra of the films as the microscopic and
macroscopic environments of the SAM are modified.
The key conclusions that are derived from this study are as
follows:
(1) The d+ band position is strongly influenced by both
temperature and film composition; the temperature dependence
is largely of intermolecular origin.
(2) The r+ band position is influenced by both temperature
and composition to similar degrees; the temperature dependence
is largely of intramolecular origin.
Figure 6. Peak position (A) and peak absorbance (B) for the symmetric
methyl stretching vibration (r+) of h33-C16 samples as a function of the
SAM composition, for sample temperatures of 25 and 300 K. The
curved lines are provided to guide the eye through the data, whereas
the straight lines are obtained by linear regression fits to the most dilute
data available in this study.
(3) The d+ band intensity (per molecule) is insensitive to the
composition of the film; the temperature dependence is due to
intramolecular interactions.
(4) The r+ band intensity (per molecule) is strongly influenced
by intermolecular interactions; the temperature dependence is
largely of intramolecular origin.
composition and, therefore, virtually all of the 2.0 cm-1
temperature-induced shift seen for the r+ band in the 100% h33-
C16 SAM (Figure 3A) is due to changes in the intramolecular
couplings, with very little that can be attributed to changes in
the intermolecular couplings. Although the r+ band position is
affected by both composition and temperature (changing inter-
molecular and intramolecular couplings, respectively) to similar
degrees, these two influences are completely uncoupled. We
note that the observed linear trends of the peak position provide
confirmation that there is no significant isotopic segregation in
the film, because segregation would tend to maintain the peak
frequency to be that of the pure h33-C16 film, regardless of
composition. Figure 6B demonstrates that the intensity of the
C-H r+ band varies nonlinearly with the h33-C16 content of
the film; as expected, the intensity tends to zero at low h33-C16
compositions, but films that are rich in the hydrogenated com-
ponent have greater intensities than would be predicted on the
basis of the isolated molecule spectrum. Note that these data
were obtained with the same samples as the d+ bands of Figure
5, which displayed linear intensity-composition trends; the
observed nonlinearity of Figure 6B cannot be due to surface
compositions that do not reflect that of the prepared thiol/
methanol deposition solutions or manipulation errors. It is clear
that the nonlinearity of Figure 6B will have important conse-
quences for attempts to interpret the intensity of the r+ band of
a two-dimensional SAM on the basis of the optical properties
of isolated molecules or attempts to correlate depletions of this
band to changes in the film composition upon reaction or
substitution at random sites.25 The dotted lines of Figure 6B
shows the extrapolated r+ intensities based on the most dilute
samples used in this study at 25 and 300 K. For the 100%
h33-C16 SAM, we estimate that the intermolecular interactions
can increase the r+ intensity by as much as 40-50%. It is
interesting to note that the r+(300 K)/r+(25 K) ratio is a constant
0.6 for all samples. The insensitivity of this ratio to the film
composition (and its close correspondence to the ratio calculated
for the d+ band above) indicates that the temperature-induced
variations of the r+ band intensity are largely due to changes
among the intramolecular interactions.
The tendencies of the methylene stretching bands (d+, d-)
toward isotopic dilution and temperature have been previously
addressed for crystalline polymethylene chains5,6 and for con-
densed phase hexadecane and decane.16 They too observe a sys-
tematic shift of the d+ band to higher frequencies as the fraction
of hydrogenated molecules is reduced; this was attributed to
the perturbation of the intermolecular Fermi resonance,5 which
couples the fundamental symmetric CH2 stretching mode with
lower frequency modes of the solid. Although this resonance
affects the distribution of intensity among the various sub-bands
related to methylene vibrations of the extended chains, it is not
expected to significantly change the total integrated intensity
of the fundamentals themselves.5 Because the d+ band at ∼2850
cm-1 is mostly constituted of the fundamental symmetric
stretching of the CH2 group and the secondary bands (2890 and
2853 cm-1 5) are weak, the intensity of the principal d+ band
(per molecule) should not be strongly affected by isotopic
dilution. This is as observed in our study.
The d+ intensity loss with the increasing temperature has been
also observed in the polymethylene chains in crystalline state,6
and it has been pointed out that density, refractive index, and
conformational effects are too small to account for the large
intensity changes. They proposed that most of the intensity
changes are associated with the low-frequency large-amplitude
“lattice-like” modes, especially the torsional modes of the carbon
skeleton. These modes affect the transition dipole moment
through higher order dipole-derivative terms. This explanation
is highly consistent with our observations. First, this is a strong
intramolecular effect, and the amplitudes of these low-frequency
modes are temperature dependent, with higher temperatures
leading to increased molecular flex, thus changing the coupling
to the fundamental stretching mode. Although not considered
in detail herein, this also explains the difference of intensity
change among h17-C8, h25-C12, and h33-C16 because this disrup-
tion is more important in longer chains that can have larger
amplitude low-frequency motions.
Low-frequency modes could also be a part the observed
frequency shift of the d+ band, because they induce a loss of
symmetry required for the intermolecular Fermi resonance. Thus,

8188 J. Phys. Chem. B, Vol. 108, No. 24, 2004
Garand et al.
increased temperatures lower the intermolecular coupling,
leading to a shift in frequency similar to isotopic dilution.
Finally, the participation of low-frequency modes can explain
the observation that the amplitudes of changes in both intensity
and frequency with temperature are significantly lower in d33-
induced shifts, whereas the d+ band position was more affected
by intermolecular couplings. We suggest that the intramolecular
nature of the r+ shifts is likely caused by the less constrained
movement and flex of the methyl chain terminations in the SAM
environment. Elimination of gauche defects near this site may
have a role at elevated temperatures, but it is unlikely that there
are sufficient numbers of such defects at lower temperatures
that can still be removed; permanently trapped defect configura-
tions cannot contribute to the observed temperature-induced
shifts. It is interesting to note that intramolecular effects (related
to the temperature-dependent fluctuations of the angular orienta-
tion of the methyl groups) have been invoked by MacPhail et
al.29 to explain the splitting of the antisymmetric methyl stretches
in n-alkane crystals. Although we have not explored this band
in detail, it is interesting to note that this supports our conclusion
that the spectral profile relating to the methyl terminations is
largely affected by intramolecular interactions.
C16 SAMs as shown in Figure 2. Amplitudes of low-frequency
modes are mass dependent and decrease in going to the
perdeuterated chains.
It is interesting to compare the “isolated” molecule behavior
obtained at infinite dilution in the SAM with that obtained by
embedding similar length n-alkane chains in urea-clathrates.7,16
The cavities formed in these solids are ∼5.25 Å in diameter
and are therefore considerably larger than the ∼4.5 Å cylindrical
“diameter” of the all-trans conformation. In both cases it is
presumed that intermolecular interactions have negligible
importance due to the relatively large separation between
identical molecules. Kodati et al.16 have shown that the d+ and
d- bands of C16 in this environment shift to lower frequency
with reduced temperature at a rate of 1.5 × 10-2 cm-1/K and
ascribed this to the intramolecular effects of chain vibrations
as discussed above. In the present study, the d+ band shifts at
infinite dilution (Figure 5A) are too small to be reliably
measured, but they are certainly below 3 × 10-3 cm-1/K (i.e.,
at least 4-fold lower). We suggest that this remarkable reduction
in the sensitivity to low-frequency chain motion is due to the
highly constrained environment of the C16 SAM, as compared
to the extended pore structure of the clathrate. Snyder et al.7
have estimated that the expectation value of the torsional “flex”
of C16 in urea-clathrates is ∼0.58 rad2. It is not possible for
individual molecules that are chemisorbed to the Au(111)
substrate to deform to this degree, and although the collective
motion of large numbers of adjacent molecules may allow such
distortions, this would be energetically prohibitive. By structur-
ally confining the C16 molecules in the two-dimensional SAM,
low-frequency vibrations are sharply reduced, even at 300 K,
such that the temperature dependence is less pronounced. This
is consistent with recent STM26 and molecular dynamics
simulations12 that indicate that even short-chain SAMs are
essentially crystalline in nature, even at 300 K, contrary to
previous reports.27 One possible origin for the intermolecular-
based shifts of the d+ peak with temperature seen in hydrogen-
rich films is dipolar coupling among adsorbates. This effect is
most commonly observed as a repulsive interaction between
transition dipole moments that are aligned perpendicular to the
surface plane8-10,28 that leads to positive peak shifts, but
attractive interactions have been reported due to transition dipole
moments lying closer to the surface plane. We have confirmed
that simple lattice sums of the transition dipole-transition dipole
interaction of the d+ and d- modes within the organic layer
provide attractive interactions for highly organized SAMs with
tilt and twist angles of ∼30° and (45°, although we are unable
at this point to estimate the amplitude of this interaction or how
it varies with temperature. We presume that as the dynamic
motion of the chains is reduced, this attractive interaction causes
the progressive shift of the d+ band to lower frequencies as
shown herein.
The nonlinearity of the r+ intensity as a function of film
composition is an issue that requires further work. Previous work
has indicated that the IR-RAS intensity of the methyl modes is
more difficult to reconcile with crystalline models of SAM
structure2, and it is important to determine if domain size effects
are important.
Conclusions
This study has determined that both intra- and intermolecular
factors have strong influences on the IR-RAS spectra of
n-alkanethiol SAMs adsorbed on Au(111) surfaces. The relative
contributions of these factors have been assessed using both
temperature-dependent and composition-dependent IR-RAS
spectroscopy. Although the temperature-dependent changes in
the r+ and d+ band intensities are shown to be universally due
to the changes in intramolecular couplings, the position of the
d+ band evolves more profoundly with temperature due to
changing intermolecular interactions. We propose that this may
be due to intermolecular coupling of the transition dipole
moments, which becomes more pronounced as the sample
temperature is reduced and the h33-C16 content of the film
increases. The temperature-related shift of the d+ bands at
infinite dilution is significantly less than that of h33-C16
molecules trapped within urea-clathrate pores, indicating that
the amplitude of the molecular distortions within these pores is
larger than in the highly constrained two-dimensional SAM
structure. Finally, we note that although the varying effects of
inter- and intramolecular couplings on the spectra are quantifi-
able, their molecular interpretation requires more study; this
would provide a more solid basis for the routine application of
infrared spectroscopy to the structural study of these films.
Acknowledgment. We gratefully acknowledge financial
support from NSERC (Canada) and FCAR (Que´bec). We thank
Prof. A. Badia (Universite´ de Montre´al) for providing details
of her synthetic methods for the preparation of the perdeuterated
thiols.
References and Notes
To our knowledge, this is the first report of the r+ band
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obscured in the spectra of solid polymethylene by the d+ bands
and is poorly resolved in h33-C16/d33-C16 mixtures.16 Our results
show that the r+ and d+ bands show similar shifts to higher
frequency with isotopic dilution. However, in the case of the
r+ band the results presented herein indicate that changes of
intramolecular couplings are the origin of the temperature-
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