Low-energy ion-surface reactions of pyrazine with two classes of self- assembled monolayers: Influence of alkyl chain orientation

Article abstract of DOI:10.1021/ac0001028

Collisions of pyrazine with two classes of serf-assembled monolayer (SAM) films are employed to determine whether surface confinement and the resulting alkyl chain orientation, influences low-energy ion-surface reactions. SAM films formed from n-alkanethiols (CH₃(CH₂)(n)-S-Au, n = 14- 17) and 4-(4-alkoxyphenylbenzenethiols (4-(4-CH₃(CH₂)(m)OC₆H₄)-C₆H₄-S- Au, m = 14-17) chemisorbed onto Au (111) substrates are known to exhibit a chain-length-dependent odd-even effect that places the terminal C-C bond into different orientations. Ion-surface collisions (20 eV) of pyrazine molecular ion (M = m/z 80) with these surfaces yield reaction product ions corresponding to the addition of hydrogen atoms ([M + H]⁺ = m/z 81) and methyl groups ([M + CH₃]⁺ = m/z 95) from the surface to the probe ion. Differences in the relative abundance of the reaction product ions are measured as a function of chain length for both classes of SAM film. SAM films with odd chain lengths (n, m = 14 and 16) have a consistently higher abundance of H addition product ions than SAM films with even chain lengths (n, m = 15 and 17). Alternating reactivity is also observed for the addition of CH₃, with methyl addition occurring more readily on even-chain-length films. The variations are consistent with the well-characterized orientation differences known to exist for films of this type. Specifically, odd-chain- length films are oriented such that the last C-C bond is more parallel to the plane of the surface than it is for even-chain-length films. The critical element of the parallel orientation is that it leaves, on average, one hydrogen atom on the terminal methyl and both hydrogen atoms on the first underlying methylene in more reactive positions compared to even chain lengths. Conversely, the trend in the relative abundance of CH₃ addition indicates that the orientation produced by an even-chain-length film, with the last C-C bond more perpendicular to the surface, allows the probe ion better access to the methyl carbon. Reflection absorption IR spectroscopy (RAIRS) data independently confirm the orientational disposition of the films. The RAIRS data show that the odd-even effect is less dramatic for the n-alkanethiols when compared to 4-(4-alkoxyphenyl)-benzenethiols. A smaller difference in ion-surface reactivity is measured for n-alkanethiols, demonstrating that ion-surface reactions can distinguish subtle differences in average orientation. In short, we report that the extent of ion-surface reactions of pyrazine ion with two classes of SAM films is directed by the spatial orientation of the surface-confined species that participate in the reaction.

Full text of DOI:10.1021/ac0001028

Anal. Chem. 2000, 72, 2603-2608
Low-Energy Ion-Surface Reactions of Pyrazine
with Two Classes of Self-Assembled Monolayers:
Influence of Alkyl Chain Orientation
Vincent J. Angelico, Scott A. Mitchell,† and Vicki H. Wysocki*
Department of Chemistry, University of Arizona, Tucson, Arizona 85721
Collisions of pyrazine with two classes of self-assembled
monolayer (SAM) films are employed to determine whether
surface confinement and the resulting alkyl chain orienta-
tion, influences low-energy ion-surface reactions. SAM
films formed from n -alkanethiols (CH3 (CH2 )n -S-Au,
n ) 1 4 -1 7 ) and 4 -(4 -alkoxyphenylbenzenethiols (4 -(4 -
CH3 (CH2 )m OC6 H4 )-C6 H4 -S-Au, m ) 1 4 -1 7 ) chemi-
sorbed onto Au (1 1 1 ) substrates are known to exhibit a
chain-length-dependent odd-even effect that places the
terminal C-C bond into different orientations. Ion-
surface collisions (2 0 eV) of pyrazine molecular ion (M )
m / z 8 0 ) with these surfaces yield reaction product ions
corresponding to the addition of hydrogen atoms ([M +
H]+ ) m / z 8 1 ) and methyl groups ([M + CH3 ]+ ) m / z
9 5 ) from the surface to the probe ion. Differences in the
relative abundance of the reaction product ions are
measured as a function of chain length for both classes
of SAM film. SAM films with odd chain lengths (n , m )
1 4 and 1 6 ) have a consistently higher abundance of H
addition product ions than SAM films with even chain
lengths (n , m ) 1 5 and 1 7 ). Alternating reactivity is also
observed for the addition of CH3 , with methyl addition
occurring more readily on even-chain-length films. The
variations are consistent with the well-characterized ori-
entation differences known to exist for films of this type.
Specifically, odd-chain-length films are oriented such that
the last C-C bond is more parallel to the plane of the
surface than it is for even-chain-length films. The critical
element of the parallel orientation is that it leaves, on
average, one hydrogen atom on the terminal methyl and
both hydrogen atoms on the first underlying methylene
in more reactive positions compared to even chain lengths.
Conversely, the trend in the relative abundance of CH3
addition indicates that the orientation produced by an
even-chain-length film, with the last C-C bond more
perpendicular to the surface, allows the probe ion better
access to the methyl carbon. Reflection absorption IR
spectroscopy (RAIRS) data independently confirm the
orientational disposition of the films. The RAIRS data
show that the odd-even effect is less dramatic for the
n -alkanethiols when compared to 4 -(4 -alkoxyphenyl)-
benzenethiols. A smaller difference in ion-surface reac-
tivity is measured for n -alkanethiols, demonstrating that
ion-surface reactions can distinguish subtle differences
in average orientation. In short, we report that the extent
of ion-surface reactions of pyrazine ion with two classes
of SAM films is directed by the spatial orientation of the
surface-confined species that participate in the reaction.
Proposed uses of self-assembled organic thin films range from
molecular-based electronic and optical devices to biorecognition
sensors.1-6 There are a variety of self-assembling systems, but
some of the most extensively studied are the thiol-based self-
assembled monolayers (SAMs) on gold.7-10 Various techniques,
including FT-IR, Raman spectroscopy, XPS, contact angle mea-
surements, ellipsometry, STM, FFM, and AFM, have been used
to describe the chemistry and molecular architecture of these
films.11-16 These techniques are often used in a complementary
fashion to characterize a given thin film.17-19 Accelerating the
development of applications based on thin films will depend on
† Present address: Pharm-eco Laboratories, 128 Spring St., Lexington, MA
02421.
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Films 1 9 9 8 , 329, 150-155.
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10.1021/ac0001028 CCC: $19.00 © 2000 American Chemical Society
Published on Web 04/26/2000
Analytical Chemistry, Vol. 72, No. 11, June 1, 2000 2603

the ability of researchers to more accurately characterize the
physical and chemical properties of these systems.
In 1991, the use of SAM films on gold as targets for low-energy
(10-200 eV) ion-surface collisions in a tandem mass spectrom-
eter was first reported.20,21 In these experiments, ions are mass-
selected by the first mass analyzer and potentials are adjusted to
cause the selected ions to collide into the thin film. The products
of the collision are then focused into and analyzed by the second
mass analyzer of the tandem system. When polyatomic ions are
collided into the films at low energy (<100 eV), the product ions
that are observed in the spectra can arise from fragmentation of
the projectile (surface-induced dissociation (SID)) or a chemical
reaction between the projectile and the film. A considerable
amount of work has been reported in the literature that illustrates
the use of SID to investigate the energetic requirements and
mechanisms for fragmentation of protonated peptide ions pro-
duced by electrospray ionization.22-28 In these studies, the surface
functions primarily as a collision target to facilitate fragmentation.
However, early studies focused on using ion-surface reaction
products as a means of characterizing the surface rather than the
projectile.20,21,29 An initial rationale for using SAM films in SID
studies was to increase signal throughput by providing a barrier
to neutralization of the ion beam, often a dominant pathway when
the target is bare metal. In later experiments, the films were
exploited as model systems that provided a highly organized target
surface to investigate the fundamental processes that occurred
during low-energy ion-surface collisions.30-40 It was noted that
certain projectiles react with films to provide spectral peaks
Figure 1. SAM films composed of (a) n-alkanethiol and (b) 4-(4-
alkoxyphenyl)benzenethiol bound to polycrystalline gold (111) sub-
strate.
characteristic of film quality. For example, a damaged or con-
taminated fluorocarbon film can be readily identified by detection
of product ions corresponding to H or CnHx additions to projectile
ions such as acetone or dimethyl sulfoxide.31 A report by Cooks
and coauthors investigated the abstraction of multiple surface
atoms from unlabeled and perdeuterated n-alkanethiol SAM films
by pyrazine and pyrene projectile ions. In that work, they
concluded that when reaction product ions are formed that contain
more than one atom or group from the surface those atoms or
groups originated from the same chain and not adjacent chains.41
Recent work with labeled Langmuir-Blodgett (LB) films at
low collision energies has shown that the interactions of the
projectile ion are predominately with the terminal groups or atoms
of a target surface.42,43 Of particular relevance to the present study
is work using LB films formed from stearic acid where the
terminal methyl groups are labeled with deuterium or 13C. A key
finding made in this study was that when small organic projectiles
(e.g., benzene, pyrazine) react with atoms and groups native to
the film, the products formed originate predominately, but not
exclusively, from the upper portion of the film and not the
underlying methylenes.43 This was observed as a one mass unit
shift in the hydrogen addition (H f D) or formal methyl addition
(CH3 f 13CH3) when the target was changed from an unlabeled
to a labeled film.
(19) Walczak, M. M.; Chung, C. K.; Stole, S. M.; Widrig, C. A.; Porter, M. D. J
Am. Chem. Soc. 1 9 9 1 , 113, 2370-2378.
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Soc. 1 9 9 1 , 113, 8967-8969.
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8970.
(22) McCormack, A. L.; Jones, J. L.; Wysocki, V. H. J Am. Soc. Mass Spectrom.
1 9 9 2 , 3, 859-862.
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1 9 9 4 , 116, 8368-8369.
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1 9 9 6 , 118, 8365-8374.
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339-350.
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Acta 1 9 9 9 , 397, 247-256.
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H.; Summerfield, S. G.; Gaskell, S. J., J. Am. Chem. Soc. 1 9 9 9 , 121, 5142-
5154.
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H.; Summerfield, S. G.; Gaskell, S. J. J. Am. Chem. Soc. 1 9 9 9 , 121, 5142-
5154.
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C. E. D. Int. J. Mass Spectrom. Ion Process. 1 9 9 2 , 122, 181-217.
(30) Somogyi, A.; Kane, T. E.; Ding, J. M.; Wysocki, V. H. J. Am. Chem. Soc.
1 9 9 3 , 115, 5275-5283.
The goal of the present study is to take advantage of the
sensitivity and shallow depth of penetration provided by low-
energy ion-surface collisions to investigate the influence of alkyl
chain orientation on ion-surface reactions. Two model SAM
systems were selected for this study. The first system is a series
of simple n-alkanethiols of the form CH3(CH2)nSH (n ) 14-17)
(Figure 1a). SAM films of this type have a well-documented
orientation difference for the terminal methyl groups.10,44,45 Dif-
(31) Kane, T. E.; Somogyi, A.; Wysocki, V. H. Org. Mass Spectrom. 1 9 9 3 , 28,
1665-1673.
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Spectrom. 1 9 9 3 , 28, 1021-1033.
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6706-6715.
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241-246.
1 9 9 3 , 4, 938-942.
(42) Gu, C. G.; Wysocki, V. H.; Harada, A.; Takaya, H.; Kumadaki, I. J Am. Chem.
(36) Pradeep, T.; Ast, T.; Cooks, R. G.; Feng, B. J. Phys. Chem. 1 9 9 4 , 98, 9301-
9311.
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Soc. 1 9 9 9 , 121, 10554-10562.
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558-569.
R. J. Am. Chem. Soc. 1 9 9 4 , 116, 8658-8665.
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2604 Analytical Chemistry, Vol. 72, No. 11, June 1, 2000

(Ithaca, NY). The surfaces are 17 mm × 13 mm (0.5-mm silica
base) and have a 5-nm underlayer of titanium that is covered with
100 nm of vapor-deposited gold. Before immersion in the thiol
solution, the surfaces were UV cleaned for 10 min (Boekel UV
cleaner model 135500, Boekel Industries Inc.).
Monolayer P reparation. Alkanethiolate surfaces were pre-
pared by immersing freshly cleaned gold substrates into a ∼20
mM ethanol solution of a given thiol and allowing them to react
for 72 h. The films were then rinsed 4-6 times by sonication in
ethanol, dried, immediately inserted into the fast entry lock on
the mass spectrometer, and put under vacuum or into the dry
air-purged FT-IR chamber. The 4-(4-alkoxyphenyl)benzenethiolate
surfaces were prepared in a similar fashion in ∼20 mM THF/
EtOH (1:1 v/ v) solution of a given 4-(4-alkoxyphenyl)benzenethiol.
RAIRS Measurements. Reflection absorption IR measure-
ments were collected on a Nicolet Magna 550. The spectrometer
was equipped with a Spectra Tech FT-80 grazing angle accessory
(80° incident angle). p-Polarization was used for all measurements.
A freshly UV cleaned gold surface was used as the background
for all spectra. The spectrometer was set up to collect 400 scans
Figure 2. Idealized structure for n-alkanethiols with an odd (right)
number of carbons and even (left) number of carbons. The odd alkyl
chain length positions the terminal C-C bound more parallel to the
plane of the surface compared to the even alkyl chain length. The
parallel orientation places the terminal hydrogen atoms in a more
favorable position to react with impinging ion beam while hindering
access to the terminal carbon.
ferences in orientation of the terminal groups have been reported
experimentally by FT-IR, Raman, and wetting studies and most
recently by friction force microscopy.12,44-46 This so-called “odd-
even” effect arises from a tilt angle (θ) of ∼24° with respect to
the surface normal for the all-trans alkyl chains, resulting in
different cant angles versus the surface normal for the terminal
methyl group of odd versus even chain length films (Figure 2).45
The second system of thiols investigated is composed of a rigid
biphenyl mercaptan headgroup with a long-chain alkoxy substitu-
ent (4-(4-(CH2)mOC6H4)-C6H4-SH, m ) 14-17) (Figure 1b). The
odd-even effect reported for these compounds measured by FT-
IR and contact angle is enhanced47,48 over that of simple n-
alkanethiols due to steric constraints imposed by the aromatic
headgroups that limit chain twisting. Pyrazine is used as the probe
ion in all experiments. This compound is selected because at low
collision energies (e100 eV) with hydrocarbon-containing films
the molecular ion is moderately reactive, with a little over half
the detected ions reacting with the film.
at a resolution of 4 cm-1
.
Mass Spectrometric Measurements. The tandem MS sys-
tem consists of two Extrel 2000 u quadrupoles arranged in a 90°
geometry with a surface intersecting the ion optical path. Experi-
ments are carried out with the surface at a 45° angle relative to
the ion beam exiting from the first quadrupole. The collision
energy is determined by the potential difference between the ion
source and the surface (for singly charged ions). Increasing the
ion source potential relative to the surface potential varies the
collision energy. A detailed description of the basic tandem system
is published elsewhere,49 and only new design features are
described below. A multiple surface holder has been constructed
which allows up to four surfaces to be positioned in the vacuum
chamber. The holder is an 18 mm × 140 mm Kel-f strip connected
to the end of a magnetically coupled movable rod that allows
precise linear movement of the surface holder in the z direction
and full rotation in the x, y plane. The holder is positioned
perpendicular to the ion beam exiting the first quadrupole,
allowing any of the four surfaces to be positioned into the path of
the ion beam. Surfaces are inserted into the instrument through
a fast-entry apparatus constructed from a stainless steel cube that
can be isolated from the main vacuum system via a gate valve.
The surfaces are electrically linked via the back of the holder,
and a single power supply is used to apply an equivalent potential
to each of the surfaces. The base pressure in the main chamber
is e2 × 10-7 Torr with a sample pressure of ∼6 × 10-7 Torr.
Results indicate that the pressure and general instrument condi-
tions do not change significantly from surface to surface or sample
set to sample set. All data points represent the average of at least
three independent measurements.
EXPERIMENTAL SECTION
Materials. Four alkanethiols, CH3(CH2)nSH (n ) 14-17) were
used in these experiments. CH3(CH2)15SH and CH3(CH2)17SH
were used as purchased from Aldrich (99%). CH3(CH2)14SH and
CH3(CH2)16SH were synthesized, as previously described,30 from
the corresponding alkyl iodides (CH3(CH2)14I, Aldrich (98%) and
CH3(CH2)16I, Fluka (97%)). The 4-(4-alkoxyphenyl)benzenethiols,
4-(4-CH3(CH2)mOC6H4)-C6H4SH (m ) 14-17), were prepared by
the synthetic route outlined in Scheme 1 , and a more detailed
description of the synthesis is provided as Supporting Information.
Scheme 1
RESULTS AND DISCUSSION
Ion-Surface Reactions. Figure 3 shows the tandem mass
spectrum for a 20-eV collision of pyrazine molecular ion M•+ (m/ z
(46) Tao, Y.-T. J Am. Chem. Soc. 1 9 9 3 , 115, 4350-4358.
(47) Tao, Y. T.; Lee, M. T.; Chang, S. C. J Am. Chem. Soc. 1 9 9 3 , 115, 9547-
9555.
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Soc. Mass Spectrom. 1 9 9 2 , 3, 27-32.
Substrate P reparation. All SAM films were formed on vapor-
deposited gold surfaces obtained from Evaporated Metal Films
Analytical Chemistry, Vol. 72, No. 11, June 1, 2000 2605

Figure 3. The 20 eV collision of pyrazine ion M•+ (m/z 80) with a
CH3(CH2)17-S-Au SAM film. The base peak in the spectrum MH+
(m/z 81) represents a reaction of the probe ion and a hydrogen atom
from the SAM film. The peak at m/z 95 is the formal addition of methyl
to the M•+ ion. The two most abundent fragment ions at m/z 53 and
54 represent [M - HCN]•+ and [MH - HCN]+.
Figure 5. Percentage of the total ion current that corresponds to
methyl addition plotted versus total number of alkyl carbons.
observed for both systems with the odd-chain-length analogues
leading to a greater abundance of H addition product ions. Each
point represents an average of the measurements taken on three
different SAM films. The variation in reaction quotient for each
point reflected by the error bars is likely due to small changes in
instrument conditions and the reproducibility of substrate and film
quality. A similar plot for methyl addition is presented in Figure
5 for the 4-(4-alkoxyphenyl)benzenethiols. In this case, the y axis
represents percentage of the total ion current that corresponds
to methyl addition. An alternating reactivity is again observed,
however, in contrast to hydrogen addition results, methyl addition
occurs more readily on even chain length films.
The variations in reactivity for odd versus even chain lengths
are consistent with chain-length-dependent differences in terminal
group orientation.10,44,45 Specifically, the difference in cant of the
terminal methyl groups produced by the chain tilt (θ) (Figure 1)
results in subtle differences in the position of the terminal C-C
bond with respect to the surface normal.50 When the chain length
is odd, the terminal C-C bond is more parallel to the surface
than when the chain length is even. These orientations present
the incoming ion with two spatially distinct environments each
with a different set of steric requirements that must be met for
an ion-surface reaction to take place. The parallel orientation
adopted by the final C-C bond of the odd-chain-length films places
one terminal hydrogen atom, on average, slightly above the plane
of the chain termini and also allows the impinging ion more ready
access to the hydrogen atoms bound to the first underlying
methylene (Figure 2). The exposed hydrogen atoms are not only
likely to be more reactive but they also inhibit access to the
terminal carbon. Conversely, the perpendicular orientation adopted
by the even chain lengths exposes the terminal carbon, places
the terminal hydrogen atoms in equivalent but less exposed
orientations, and hinders access to the first underlying methylene.
n -Alkanethiols versus 4 -(4 -Alkoxyphenyl)benzenethiols.
A comparison of the plots in Figure 4 shows that the 4-(4-
alkoxyphenyl)benzenethiols have a larger variation in reactivity
quotient than do the n-alkanethiols. Parts a and b of Figure 6 show
Figure 4. Reaction peak intensities presented as a ratio of (MH+
+ [MH - HCN]+)/(M•+ + [M - HCN]•+) plotted versus chain length
for n-alkanethiols and 4-(4-alkoxyphenyl)benzenethiols. Larger values
for the quotient indicate more H addition.
80) with a CH3(CH2)17-S-Au surface. Two reaction products can
be observed in the spectrum. The peak at m/ z 81 labeled MH+
represents a reaction between the M•+ ion and the SAM film
resulting in the addition of a hydrogen atom to the projectile. The
peak at m/ z 95 corresponds to the addition of CH3 to the M•+
ion. At this collision energy, the M•+ and MH+ ions acquire
adequate internal energy to fragment. Two dominant fragment
ions corresponding to loss of a neutral HCN appear at m/ z 53 [M
- HCN]•+ and m/ z 54 [MH - HCN]+. The integration of the
normalized peak areas followed by the summation of the contribu-
tions from unreacted pyrazine, H addition, and CH3 addition ions
provides a means to plot and track changes in the abundance of
these species for a series of films.
Figure 4 is a plot tracking the relative H addition where the y
axis is the quotient (MH+ + [MH - HCN]+)/ (M•+ + [M -
HCN]+) and is plotted versus the total number of alkyl carbons.
The solid line represents the data collected for the n-alkanethiol
system and the dashed line represents the data collected for the
4-(4-alkoxyphenyl)benzenethiols. A clear odd-even effect can be
(50) Parikh, A. N.; Allara, D. L. J. Chem. Phys. 1 9 9 2 , 96, 927-945.
2606 Analytical Chemistry, Vol. 72, No. 11, June 1, 2000

is the different conformational constraints imposed on the alkyl
moiety by the aromatic headgroup versus the n-alkanethiols.48 The
maximum effect is observed in RAIR spectra for an odd-even
pair when the chain twist angle (φ) is minimized (Figure 1). As a
consequence of the available stable packing arrangements and
the decrease in rotational freedom, films formed from 4-(4-
alkoxyphenyl)benzenethiols have a larger portion of the terminal
methyl group population in the optimum position (small twist
angle) versus n-alkanethiols.48 The increased degree of variation
of the reactivity quotient for odd versus even for the 4-(4-
alkoxyphenyl)benzenethiols (Figure 4) is consistent with this
explanation. The significant new result presented here is that small
differences in the average orientation of the film can be detected
by ion-surface reactions.
Effects of Film Order and Substrate Topography. Another
general observation that can be made when comparing the data
plots in Figure 4 is an overall decrease in the H-addition intensity
for the 4-(4-alkoxyphenyl)benzenethiols. The reaction quotient
values for the n-alkanethiols vary from 1.82 to 2.08 and those for
the 4-(4-alkoxyphenyl)benzenethiols range from 1.65 to 2.05. We
speculate that differences in film order and the effects of using a
polycrystalline gold substrate are influencing the degree of
hydrogen addition. It has been shown that the 4-(4-alkoxyphenyl)-
benzenethiols tend to form more ordered films than the n-
alkanethiols primarily due to constraints imposed by the rigid
aromatic headgroup.48 Another possible contributing factor is the
increased thickness of 4-(4-alkoxyphenyl)benzenethiols. The
aromatic headgroups add ∼12 Å to the thickness of each SAM
film. The added film thickness could compensate for edge effects
and other heterogeneities in the polycrystalline Au substrate by
bridging the defect sites and allowing more chain-chain interac-
tions to occur. Earlier work published by this group highlighted
the potential effects of film order on reaction intensity by compar-
ing short- (1-butanethiol) and long- (1-octadecanethiol) chain
n-alkanethiols.30 The short-chain films were consistently better
hydrogen donors. The conclusion drawn in that research was that
the short-chain film was less ordered, leaving more of the
underlying methylenes exposed and/ or more susceptible to
adsorption or insertion of hydrocarbon contaminants.30 In separate
but related work that is part of an ongoing study, results for CH3-
(CH2)19-S-Au, CD3(CD2)19-S-Au, and CD3(CH2)19-S-Au SAM
films are used to evaluate and separate the contribution of all
possible sources of hydrogen to the total hydrogen addition ion
current. During a 20 eV collision of pyrazine with the hydrocarbon
SAM films, ∼65% of the total ion current measured at the detector
is observed as H addition ions. We have calculated that of the
total ion population that reacts to form hydrogen adducts, ∼70%
originate from the terminal methyl group, 21% from the underlying
methylenes, and 9% from hydrocarbon contaminants. Clearly,
these numbers are controlled by a combination of the quality of
the film that can be formed from a particular compound and the
topography of the substrate onto which it is deposited. The
substrate used in these experiments is a silica slide with a 5 nm
underlayer of titanium onto which 100 nm of gold is deposited.
The morphology of the gold is not consistently smooth at the
atomic level but is known to have a “hill-like” landscape with
crystalline-like features ∼0.01 µm2 and an average height variation
in the 5-10 nm range (unpublished result). We acknowledge that
Figure 6. Methyl and methylene stretching region of the reflection
absorption IR spectra of (a) 4-(4-alkoxyphenyl)benzenethiols and (b)
n-alkanethiols.
the RAIR spectra for films composed of 4-(4-CH3(CH2)mOC6H4)-
C6H4SH (m ) 14-17) and CH3(CH2)SH (n ) 14-17), respectively.
The RAIRS data are shown here as an independent measure of
our monolayer structures. The peaks of interest occur at 2878
and 2965 cm-1 corresponding to the νs(CH3) and νa(CH3, ip)
stretches respectively, with the methylene stretching modes
νs(CH2) and νa(CH2) appearing at 2850 and 2919 cm-1 10
. For 4-(4-
alkoxyphenyl)benzenethiols films with R groups containing an
even number of carbons (m ) 15, 17), the intensity of the νs-
(CH3) stretching mode for the terminal methyl group is enhanced
and the intensity of the νa(CH3, ip) stretching mode is diminished
while the reverse is observed for films with R groups containing
an odd number of carbons (m ) 14, 16). Figure 6b is the same
spectral region for the series of n-alkanethiols. When compared
to that for the 4-(4-alkoxyphenyl)benzenethiols, the odd-even
effect for the n-alkanethiol system is diminished.51 The reactivity
data in Figure 4 are clearly mirroring the same trend seen in
Figures 6, both in odd-even effect and in the intensity of the
effect.
The basis for the enhanced odd-even effect in the RAIRS data
for the SAM films composed of 4-(4-alkoxyphenyl)benzenethiols
(51) Chang, S. C.; Chao, I.; Tao, Y. T. J Am. Chem. Soc. 1 9 9 4 , 116, 6792-6805.
Analytical Chemistry, Vol. 72, No. 11, June 1, 2000 2607

the topography of the gold can introduce a degree of nonunifor-
mity to the film orientation and order that is sufficient to expose
some underlying methylenes to the colliding projectile. However,
the results indicate that the size of the ion beam used in these
experiments (∼6 × 8 mm)52 is sufficient to ensure a valid average
sampling of the film. Despite irregularities in the film and
substrate, it is still possible to observe that the orientation of these
surface-confined species influences the extent of ion-surface
reaction.
distinguish small differences in the average orientation. The
difference in reactivity of surface-confined alkyl chains with
different numbers of carbons seems somewhat remarkable, at first
consideration, because polycrystalline vapor-deposited gold and
a standard SAM surface preparation is used with no annealing of
the gold or the SAM film. However, if one considers that each
probe of the surface is a single ionized molecule, the results are
reasonable since even relatively small ordered domains on the
surface present a relatively large ordered domain to the ionic
probe molecule and provide an average result that is consistently
different for odd versus even chain lengths.
CONCLUSIONS
We report that low-energy (20 eV) ion-surface reactions of
pyrazine ions are remarkably sensitive to small differences in the
orientation of alkyl-based SAM films. The intensity of hydrogen
and methyl addition ions is shown to vary for odd versus even
chain lengths for two different SAM systems. The variation of the
intensity of the reaction product ions is attributed to subtle
differences in the position of the terminal C-C bond. The
orientation of the odd-chain-length films allows better access to a
terminal hydrogen atom while hindering access to the terminal
carbon. The even-chain-length orientation limits access to the
hydrogen atoms but better exposes the terminal carbon. The
sensitivity of the process is underscored by comparing the data
collected for the n-alkanethiol system and the 4-(4-alkoxyphenyl)-
benzenethiol system where reactions of pyrazine ion with hydro-
gen atoms native to the films are discriminating enough to
ACKNOWLEDGMENT
Funding was provided by the National Science Foundation
(Grant CHE-9224719). We also thank Dr. Jeanne Pemberton and
members of her group of the University of Arizona for the use of
the Nicolet FT-IR instrument and the helpful instruction on the
use of the instrument and interpretation of the spectra.
SUPPORTING INFORMATION AVAILABLE
Detailed procedures for the synthesis of 4-(4-alkoxyphenyl)-
benzenethiols, including summaries of NMR and mass spectral
data. This material is available free of charge via the Internet at
http:/ / pubs.acs.org.
Received for review February 2, 2000. Accepted February
28, 2000.
(52) Kane, T. E.; Angelico, V. J.; Wysocki, V. H. Anal. Chem. 1 9 9 4 , 66, 3733-
3736.
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2608 Analytical Chemistry, Vol. 72, No. 11, June 1, 2000