Effects of Molecular Geometry on the STM Image Contrast of Methyl- and Bromo-Substituted Alkanes and Alkanols on Graphite

Article abstract of DOI:10.1021/jp992257t

Scanning tunneling microscopy (STM) images have been collected for a series of substituted alkanes and alkanols that form ordered overlayers at room temperature on highly ordered pyrolytic graphite surfaces. Molecules that have been imaged possess an internal bromide, with or without terminal alcohol groups (HO-(CH₂)₉CHBr(CH₂)₁₀OH and H₃C(CH₂)₁₆CHBr(CH₂) ₁₆CH₃), an internal -OH group (H₃C(CH₂)₁₆CHOH(CH₂) ₁₆-CH₃), and an internal methyl group (H₃C(CH₂)₁₆CHCH₃(CH ₂)₁₆CH₃). These data allow comparison to the STM image contrast reported previously for molecules in which -OH, -Br, and -CH₃ groups were located in terminal positions of alkane chains adsorbed onto graphite surfaces. When the functional groups were in gauche positions relative to the alkyl chain, and thus produced molecular features that protruded toward the tip, the functional groups were observed to produce bright regions in a constant current STM image, regardless of the STM contrast behavior observed for these same functional groups when they were in terminal positions of adsorbed alkyl chains. These observations are in excellent agreement with theoretical predictions of the STM behavior of such systems. Additionally, several interesting packing structures have been observed that have yielded insight into the intermolecular forces that control the packing displayed by these overlayers.

Full text of DOI:10.1021/jp992257t

9690
J. Phys. Chem. B 1999, 103, 9690-9699
Effects of Molecular Geometry on the STM Image Contrast of Methyl- and
Bromo-Substituted Alkanes and Alkanols on Graphite
Christopher L. Claypool, Francesco Faglioni, Adam J. Matzger, William A. Goddard III,* and
Nathan S. Lewis*
DiVision of Chemistry and Chemical Engineering, California Institute of Technology,
Pasadena, California 91125
ReceiVed: July 1, 1999; In Final Form: August 27, 1999
Scanning tunneling microscopy (STM) images have been collected for a series of substituted alkanes and
alkanols that form ordered overlayers at room temperature on highly ordered pyrolytic graphite surfaces.
Molecules that have been imaged possess an internal bromide, with or without terminal alcohol groups (HO-
(
CH
CH
STM image contrast reported previously for molecules in which -OH, -Br, and -CH
2
)
9
CHBr(CH
2
)
10OH and H
3
C(CH
2
)
16CHBr(CH
2
)
16CH
3
), an internal -OH group (H
(CH ). These data allow comparison to the
groups were located
3 2 2 16
C(CH )16CHOH(CH ) -
3
), and an internal methyl group (H
3
C(CH 16CHCH
2
)
3
2 3
)16CH
3
in terminal positions of alkane chains adsorbed onto graphite surfaces. When the functional groups were in
gauche positions relative to the alkyl chain, and thus produced molecular features that protruded toward the
tip, the functional groups were observed to produce bright regions in a constant current STM image, regardless
of the STM contrast behavior observed for these same functional groups when they were in terminal positions
of adsorbed alkyl chains. These observations are in excellent agreement with theoretical predictions of the
STM behavior of such systems. Additionally, several interesting packing structures have been observed that
have yielded insight into the intermolecular forces that control the packing displayed by these overlayers.
I. Introduction
Various laboratories have now reported scanning tunneling
microscopy (STM) images that appear to reveal the internal
structure of molecules.1-20 Unlike optical microscopy, where
knowledge of the spatial variation in the values of the real and
imaginary components of the refractive index allows computa-
tion of the image contrast between adjacent regions of an
interfacial layer, the fundamental mechanisms that produce the
2
1-25
contrast in a STM image remain to be fully elucidated.
In
general, variations in both topographic and electronic properties
of a molecular overlayer will influence the contrast of an STM
image. To date, the relative role of these factors remains largely
unexplored experimentally.
A particularly attractive system for the investigation of these
questions involves imaging alkanes or alkanols that are adsorbed
2
1-35
onto highly ordered pyrolytic graphite (HOPG) surfaces.
These species produce ordered overlayers that allow resolution
21-35
of various atomic and functional group features using STM.
In addition, systematic changes in the topographic and electronic
structure of these molecules can be correlated with changes in
the observed STM images.21-35
In prior work, the interplay between topographic and elec-
tronic considerations was seen to be critical to determining the
local contrast of STM images of various functional groups in
alkane and alkanol overlayers on graphite. For example, relative
to a “reference” methylene region of the molecule, the larger
but poorer-coupling -CF3 groups were dark in STM images,
whereas double and triple bonds, with their π systems, produced
locally bright regions in STM images.25 In some cases, changes
in the topographic parameters were predicted to change the sign
of the image contrast of a given functional group. For example,
a terminal -Br group in straight-chain R,ω alkanol bromides
was observed to be dark relative to the alkyl chain.26 This was
believed to be due to poorer electronic coupling of the -Br
3 2 2 3
Figure 1. STM image of H C(CH )16CHOH(CH )16CH molecules on
graphite (V ) 1.210 V, I ) 200 pA). The bright region in the middle
of the molecular rows is assigned to the hydroxyl functionality (white
arrows).
group relative to the alkyl chain when the -Br is in the trans
conformation and when the alkyl chain is oriented such that its
carbon-carbon skeleton is parallel to the graphite surface plane.
Theoretical calculations, however, predict that because of the
dominant influence of topography, if the terminal -Br were in
a gauche position and all other factors were constant, the -Br
25
group would produce a bright region in the STM image.
Similarly, terminal -OH groups in straight-chain alkanol
1
0.1021/jp992257t CCC: $18.00 © 1999 American Chemical Society
Published on Web 10/15/1999

STM of Alkanes and Alkanols on Graphite
J. Phys. Chem. B, Vol. 103, No. 44, 1999 9691
Figure 2. (A) Calculated constant-current STM image for an alcohol molecule laid flat on the graphite surface with the terminal OH group in a
position trans to the alkyl chain (flat on the graphite) and (B) gauche to the alkyl chain (pointing away from the graphite). Molecular modeling of
CH (CH ) CHOH(CH ) CH indicated that the -OH group was 0.9 Å higher than the methylene portion of the molecule, while the STM simulation
3 2 5 2 5 3
in part B produced a 0.06 Å protrusion over the region of the -OH group.
overlayers were observed to be dark relative to the reference
methylene chain regions, but such terminal -OH groups are
predicted computationally to be bright if they are instead located
prepared by placing a 6 µL droplet of a concentrated solution
of the organic compound in phenyloctane onto a freshly cleaved
highly ordered pyrolytic graphite (HOPG, Union Carbide)
surface. A mechanically formed Pt-Ir tip was then immersed
in the liquid droplet, and the imaging was performed at the
liquid-graphite interface. Images were obtained using a Digital
Instruments (Santa Barbara, CA) Nanoscope III STM. All of
the images presented herein were obtained at constant current
in the variable height mode. Bright portions of the images
correspond to points at which the tip retracted from the surface
in order to maintain a constant current.
25
in gauche conformations relative to the carbon-carbon chain.
This work describes the results of a series of experiments
that have been designed to address further the interplay between
topographic and electronic factors in an STM image. Bromide,
-
OH, and -CH3 groups have been placed at internal positions
in an alkane chain; in addition, a -Br group has been located
internally on a long-chain R,ω diol. STM images of overlayers
of these molecules on HOPG have revealed the location of, and
the image contrast displayed by, all of these functional groups.
In addition, several interesting packing arrangements have been
identified for these molecules, and the variation in packing has
yielded insight into the intermolecular forces that determine the
packing arrangements exhibited by two-dimensional ordered
overlayers.
The lattice spacing of graphite (2.46 Å) was used as the
calibration standard for the x and y piezo dimensions. Step edges
36
observed on an oxidized graphite surface (3.35 Å) were used
as a calibration standard for the z piezo dimension. Distances
and angles were determined using Nanoscope III software, and
the apparent heights of heteroatoms and functional groups are
reported with respect to the average height of the image over
the methylene portion of the adsorbed molecule. Errors in the
distances quoted in this manuscript include estimates of the
measurement errors associated with determining the metrics
II. Experimental Section
A. Methods. Sample preparation and imaging conditions were
similar to those reported previously.24 Briefly, samples were

9692 J. Phys. Chem. B, Vol. 103, No. 44, 1999
Claypool et al.
geometry was estimated using the DreidingII force field37 by
placing one molecular monolayer on graphite. The position of
the adsorbed molecules was optimized on the original graphite
plane using a DreidingII force field. Since there are no explicit
bonds between graphite and the adsorbates, the position of the
adsorbate is determined mainly by van der Waals interactions.
This results in the adsorbate’s carbon backbone being as
staggered as possible with respect to the graphite carbons and
with the hydrogens of the absorbate resting on top of the surface
hexagons. Then one molecule from the monolayer was selected
and the alkyl chains were truncated three or four carbon atoms
away from the functional group of interest. The dangling bonds
of the fragment were saturated with hydrogen atoms, but the
geometry of the fragment was otherwise preserved. Then a gas-
phase Hartree-Fock computation was performed on the frag-
38
ment using the commercial Gaussian package. The force field
geometry and Hartree-Fock wave function were then used to
estimate the perturbative coupling of the tip and the graphite
states. In the STM simulation the graphite was replaced with a
finer rectangular grid of orbitals in order to minimize the effect
of lateral displacements of the adsorbates that may occur in the
real system. As a consequence, different arrangements of the
molecules with respect to the graphite lattice have very little
effect on the simulated STM images as long as the molecular
geometry is not changed significantly (e.g., going from a flat
to a vertical orientation). The coupling, which is related to the
tunneling current, was computed using a simple model that
3 2 3 2 3
Figure 3. STM image of H C(CH )16CHCH (CH )16CH molecules
on graphite (V ) 1.351 V, I ) 200 pA). The bright regions are assigned
to the internal methyl groups.
from the images as well as variation in the metrics over various
experiments. To reduce noise, the images were filtered using
Nanoscope III software. The filtering was primarily performed
to enhance the visual presentation of the printed images, but
the filtering was performed in such a way that it did not distort
any of the primary metrics evident in the original data. The
filtering procedure also did not introduce any new spot patterns
or new topographic features into an image.
Images similar to those reported in this work were obtained
many times in several different imaging sessions. In all cases,
similar images were observed at many different locations on a
sample. Nearly every sample yielded evidence of the adsorbed
monolayer in the STM image; however, several different tips
were usually necessary to achieve the high-resolution images
reported in this work.
2
5
contained only one adjustable parameter. The value of this
parameter was fixed to be the same as that used previously.25
The vertical position of the model tip was then adjusted to
maintain a constant current at every point on a rectangular grid
that covered the adsorbed fragment. The optimal tip height was
recorded and used to produce simulated constant-current images.
The data from the simulations are reported both as three-
dimensional surfaces, representing the vertical tip displacement
with respect to an arbitrary zero, and as contour plots. The
1
2
3
4
5
contour levels are /6, /6, /6, /6, and /6, respectively, of the
maximum peak of each plot.
Numerical simulations of the STM images of adsorbates were
B. Materials. Stearone (TCI) and phenyloctane (Aldrich) are
commercially available and were used as received. The proce-
performed as described previously.25 First, the adsorbate
Figure 4. Calculated constant-current STM image for a methyl alkane molecule laid flat on the graphite surface with the internal methyl group in
a position pointing away from the graphite surface. Molecular modeling of H C(CH 16CHCH (CH indicated that the internal methyl group
3
2
)
3
2 3
)16CH
is 1.7 Å higher than the methylene backbone of the molecule, while the STM simulation shown in the figure produces a 1.58 Å peak over the region
of the internal methyl group.

STM of Alkanes and Alkanols on Graphite
J. Phys. Chem. B, Vol. 103, No. 44, 1999 9693
a
mL) and cooled in an ice bath. Diisobutylaluminum hydride
(7.0 mL of a 1.0 M solution in THF) was added to this solution
dropwise over 10 min. After 4.5 h, the reaction was quenched
by slow addition of methanol (3.0 mL) and 10 min of stirring
followed by the addition of 1 M HCl (10 mL). The solution
was warmed to room temperature, and more 1 M HCl (30 mL)
was added. The organic layer was separated, washed with brine
(
50 mL), and dried over anhydrous Na2SO4. Removal of the
solvent yielded an oil that solidified upon standing (0.314 g,
1% for two steps). Further purification was achieved by
7
crystallization from CH2Cl2-hexanes at -6 °C to give a white
powder. Anal. Calcd for C20H41BrO2: C, 61.06; H, 10.50.
Found: C, 61.51; H, 10.19.
Synthesis of CH3(CH2)16CHOH(CH2)16CH3. Stearone (3.00
g, 5.92 mmol) and LiAlH4 (0.339 g, 8.93 mmol) were dissolved
in THF (200 mL) and stirred for 3 days. Excess reducing agent
was quenched by sequential addition of water (0.30 mL), 10%
NaOH solution (0.45 mL), and water (0.90 mL). The resulting
salts were filtered off on a fritted funnel and the product
recovered from the filtrate by evaporation (0.612 g, 20%), mp
1
7
7.5-80.0 °C. H NMR (CDCl3): δ 0.88 (t, 6 H), 1.25 (s, 60
H), 1.55 (br s, 4H), 3.58 (br s, 1 H). Anal. Calcd for C35H72O:
C, 82.60; H, 14.26. Found: C, 82.85; H, 14.13.
Synthesis of CH3(CH2)16CHBr(CH2)16CH3. PPh3 (1.29 g, 4.94
mmol) and Br2 (250 µL, 4.85 mmol) were added to 18-
pentatriacontanol (0.528 g, 1.04 mmol) suspended in dry THF
b
(75 mL). After 20 h, methanol (0.75 mL) was added and the
solvent was removed under reduced pressure. Purification by
column chromatography on silica gel with hexanes as eluent
provided a colorless oil that solidified upon standing. Further
purification was achieved by crystallization from ethanol/CH2-
Cl2 (3:1) to afford a white powder (0.3875 g, 65%), mp 44-
1
4
1
7
5.5 °C. H NMR (CDCl3): δ 0.88 (t, 6 H), 1.25 (s, 60 H),
.79 (m, 4 H), 4.03 (q, 1 H). Anal. Calcd for C35H71Br: C,
3.51; H, 12.51. Found: C, 74.45; H, 12.52.
2 9 2
Figure 5. (a) STM image of HO(CH ) CHBr(CH )10OH molecules
Synthesis of CH3(CH2)16(CCH2)(CH2)16CH3. Butyllithium
on graphite (V ) 1.061 V, I ) 200 pA). The black arrows indicate the
dark troughs associated with the terminal hydroxyl groups, and the
bright regions (white arrows) are assigned to the internal bromine atoms.
(
5.60 mL of a 1.6 M solution in hexanes, 8.96 mmol) was added
to a solution of methyltriphenylphosphonium bromide (3.67 g,
0.3 mmol) in THF (100 mL). After 5 min, stearone (1.50 g,
1
(b) Single line scan along the length of a molecule. Note the asymmetric
location of the peak assigned to the bromine atom relative to the location
of the troughs assigned to the terminal hydroxyl groups.
2.96 mmol) was added and the solution was stirred for 3 days.
Excess reagent was quenched by addition of acetone (1.5 mL),
and the solvent was removed under reduced pressure. Pure
product was obtained after chromatography on silica gel eluting
dures used to prepare and purify the other compounds imaged
in this work are described below.
with hexanes followed by evaporation of the solvent (1.13 g,
Synthesis of H3CO2C(CH2)9CHdCH(CH2)9CO2CH3. Methyl
undecylenate (2.58 g, 13.0 mmol) was treated with (PCy3)2-
Cl2RudCHPh (108 mg, 0.132 mmol) (Cy ) cyclohexyl) and
vigorously stirred under vacuum for 5 h. Filtration of the crude
reaction mixture through silica gel eluting with 25% EtOAc
in hexanes afforded 2.33 g (97%) of dimethyl eicos-10-ene-
1
7
1
6%), mp 53.5-55 °C. H NMR (CDCl3): δ 0.88 (t, 6 H),
.25 (s, 60 H), 2.01 (t, 4 H), 5.45 (br s, 2 H). Anal. Calcd for
C36H72: C, 85.63; H, 14.37. Found: C, 85.68; H, 14.45.
Synthesis of CH3(CH2)16CHCH3(CH2)16CH3. The alkene
(0.190 g, 0.375 mmol) and 10% Pd-C (20.5 mg) were
suspended in THF (50 mL) and kept under a hydrogen
atmosphere for 1 day. The product was recovered after filtration
through silica gel eluting with hexanes and concentration of
1
,20-dicarboxalate as a mixture of isomers. Further purification
1
was achieved by recrystallization from methanol. H NMR
(
2
CDCl3): δ 1.27 (s, 20 H), 1.61 (t, 4 H), 1.91-1.98 (m, 4 H),
1
the resulting filtrate, mp 48.5-49 °C. H NMR (CDCl3): δ
.30 (t, 4 H), 3.66 (s, 6 H), 5.37 (t, 2 H).
0
.83 (d, 3 H), 0.88 (t, 6 H), 1.25 (s, 65 H). Anal. Calcd for
Synthesis of H3CO2C(CH2)9CHBr(CH2)10CO2CH3. Dimethyl
C36H74: C, 85.29; H, 14.71. Found: C, 85.68; H, 14.45.
eicos-10-ene-1,20-dicarboxylate (0.415 g, 1.13 mmol) was
dissolved in acetic acid (10 mL) and treated with HBr in acetic
acid (4.0 mL of a 30% solution). The product was isolated by
pouring the solution into water after 6 h. The oil formed was
recovered from the aqueous layer by extraction with ether/
hexanes (1:1) and was then dried over anhydrous Na2SO4.
Concentration afforded an oil (0.320 g) that was used crude in
the next step.
III. Results
1. STM Images of H3C(CH2)16CHOH(CH2)16CH3. Figure
1 presents an STM image of an alkane having an internal
hydroxyl functionality, 18-hydroxy-pentatriacontane, H3C(CH2)16-
CHOH(CH2)16CH3. The mean molecular length in the image is
46.7 ( 0.5 Å, compared to molecular modeling predictions of
a molecular length of 45.5 Å for the all-trans conformation of
H3C(CH2)16CHOH(CH2)16CH3. Features that are assigned to
hydroxyl groups (white arrows) appear bright relative to the
Synthesis of HO(CH2)9CHBr(CH2)10OH. Dimethyl 10-bro-
moeicosane-1,20-dicarboxylate was dissolved in dry CH2Cl2 (20

9694 J. Phys. Chem. B, Vol. 103, No. 44, 1999
Claypool et al.
Figure 6. (A) Calculated constant-current STM image for a terminal bromine atom in a position trans to the alkyl chain (flat on the graphite) and
B) gauche to the alkyl chain (pointing away from the graphite).
(
methylene units and have an average length of 9.0 ( 0.5 Å
and an average height of 0.30 ( 0.05 Å. The molecules are
ordered in a parallel arrangement, with the packing angle θ
defined as the angle between the vector parallel to an alkyl chain
and the vector perpendicular to the propagation direction of a
lamella, equal to 0°. Adjacent molecules in abutting lamellae
observations for H3C(CH2)16CHOH(CH2)16CH3 (Figure 1),
whose internal -OH group must obviously be in a gauche
conformation relative to the alkyl chain.
2. STM Images of H3C(CH2)16CHCH3(CH2)16CH3. The
STM image of an alkane having an internal methyl functionality,
18-methylpentatriacontane, H3C(CH2)16CHCH3(CH2)16CH3, is
shown in Figure 3. The average length of the molecules is 46.3
( 0.5 Å, which is in good agreement with the expected length
of 45.6 Å that is obtained from molecular modeling of the all-
trans comformation of H3C(CH2)16CHCH3(CH2)16CH3. The
packing angle is the same as that observed for other alkanes,
with θ ) 0°. However, in contrast to the behavior observed for
alkane overlayers on HOPG and in contrast to the packing of
H3C(CH2)16CHOH(CH2)16CH3 (Figure 1), the H3C(CH2)16-
CHCH3(CH2)16CH3 molecules do not stagger perpendicular to
1
stagger by /2 a molecular width.
The STM image contrast displayed by the -OH group clearly
depends on its geometric orientation in the molecule. Terminal
alcohols in C10H21OH, C12H25OH, C14H29OH, 1,12-dodecane-
diol, 1,14-tetradecanediol, CF3(CH2)11OH, CF3(CF2)3(CH2)10-
OH, Br(CH2)11OH, Br(CH2)12OH, Cl(CH2)12OH, I(CH2)12OH,
H3C(CH2)7CtC(CH2)6OH, and HO(CH2)12CtN overlayers on
graphite2
1-24
have been observed to produce dark -OH regions
relative to the methylene regions of these molecules. In contrast,
the calculated images for the situation in which the -OH group
points away from the graphite (gauche to the alkyl chain)
indicate that the -OH group should be slightly brighter in an
STM image than the surrounding methylene units (Figure 2).
This prediction is in excellent agreement with the experimental
1
the propagation direction of a lamella by /2 a molecular width.
Instead, within observational accuracy, adjacent molecules in
abutting lamellae are collinear.
The bright features in the image have a mean length of 10.9
( 0.5 Å and a mean height of 0.74 ( 0.05 Å. These features

STM of Alkanes and Alkanols on Graphite
J. Phys. Chem. B, Vol. 103, No. 44, 1999 9695
bright feature that is centered 14.7 Å from one end of the
molecule and 13.5 Å from the other (Figure 5) is assigned to
the Br- functionality. This bright feature has an average length
of 8.8 ( 0.2 Å and a mean height of 3.11 ( 0.05 Å. For
comparison, molecular modeling of an all-trans conformation
of HO(CH2)9CHBr(CH2)10OH predicts that the bromine atom
is located 14.8 Å from one end of the molecule and 13.5 Å
from the other end of the molecule. In Figure 5, the position of
the Br- functionality appears to alternate by 1.2 Å, consistent
with its asymmetric location in the molecule and with disorder
in the position of the bromine group within individual lamellae.
The bright STM region exhibited by the internal -Br group
stands in contrast to the behavior previously reported for
overlayers of 12-bromododecanol on HOPG, in which the region
containing the -Br was observed to be dark relative to the
methylene groups (the Br region had a mean length of 4.1 (
2
4
0
.1 Å and a mean height of -0.41 ( 0.05 Å). Calculations
suggest that this difference in image contrast between the
terminal and internal -Br group is a consequence of topographic
differences in the location of the functionality relative to the
Figure 7. STM image of H
graphite (V ) 1.304 V, I ) 200 pA). The bright regions correspond to
the bromine heteroatoms.
3
C(CH
2
)
16CHBr(CH
2
)
16CH
3
molecules on
25
STM tip. Parts A and B of Figure 6 show the simulated STM
images for a terminal bromine in the trans and gauche
conformations, respectively. For the trans conformation, the
bromine atom is dark, but for the gauche conformation, the
bromine atom is bright. These results are in excellent agreement
with the experimental data reported herein.
are attributed to the internal methyl groups. Calculations indicate
that topographical effects should make the methyl group bright
relative to the surrounding methylene units (Figure 4), and this
prediction is in excellent agreement with the experimental
results.
4
. STM Images of H3C(CH2)16CHBr(CH2)16CH3. Figure
7
presents the STM image of an alkane having an internal
3
. STM Images of HO(CH2)9CHBr(CH2)10OH. An STM
bromide functionality, 18-bromopentatriacontane, H3C(CH2)16-
CHBr(CH2)16CH3. The average molecular length is 48.8 ( 0.5
Å, compared to the expected length of 45.5 Å obtained from
molecular modeling of the all-trans conformation of H3C(CH2)16-
CHBr(CH2)16CH3. The bright features in the image are attributed
to the internal -Br groups and have a mean length of 10.6 (
0.1 Å and a mean height of 2.86 ( 0.05 Å. As with the internal
bromoalkanediol, the theoretical calculations are in excellent
agreement with the experimental results (Figure 8), with the
calculations predicting that regions around internal -Br groups
are bright in STM images.
image of 10-bromo-1,20-eicosanediol, HO(CH2)9CHBr(CH2)10-
OH, is shown in Figure 5a. The average length of the molecules
is 28.4 ( 0.2 Å, which is in excellent agreement with the length
of 28.3 Å obtained from molecular modeling for the all-trans
conformation of HO(CH2)9CHBr(CH2)10OH. The molecules
display a molecular packing angle of θ ) 23° and thus appear
to be ordered in the herringbone fashion exhibited by unsub-
stituted alkanols.
The terminal -OH groups are identifiable as troughs of length
.5 ( 0.1 Å and depth -0.61 ( 0.05 Å (black arrows). The
3
Figure 8. Calculated constant-current STM image for an internally substituted bromoalkane molecule laid flat on the graphite surface with the
bromine heteroatom in a position pointing away from the graphite surface. Molecular modeling of H C(CH 16CHBr(CH indicated that the
Br group is 1.1 Å higher than the methylene backbone of the molecule, while the STM simulation shown produces a 1.26 Å peak over the region
of the methyl group.
3
2
)
2 3
)16CH
-

9696 J. Phys. Chem. B, Vol. 103, No. 44, 1999
Claypool et al.
Figure 9. Schematic diagram of the proposed packing of the methylalkane molecules; H
clarity. Note that the packing angle θ is 0° in this configuration.
3
C(CH
2
)
4
CHCH
3
(CH
2
)
4
CH
3
molecules are shown for
Despite the steric similarities between -CH3 and -Br groups,
the H3C(CH2)16CHBr(CH2)16CH3 overlayers exhibit a different
molecular packing arrangement than that displayed by H3C-
CH3(CH2)17NH2,22 even though the amine group is sterically
smaller than the methylene regions of these molecules.
The results described herein demonstrate an even more subtle
interplay between the topographic and electronic features of
various functional groups. Bromide and -OH groups were
bright in STM images when these groups were located in
internal positions on alkane chains (Figures 1, 3, 5, 7), whereas
when these groups were placed in terminal positions on alkanol
(CH2)16CHCH3(CH2)16CH3 (cf. Figures 3 and 7). As observed
for H3C(CH2)16CHCH3(CH2)16CH3, H3C(CH2)16CHBr(CH2)16-
CH3 molecules in adjacent rows of abutting lamellae are aligned
collinearly. However, for H3C(CH2)16CHBr(CH2)16CH3, the
packing angle θ is observed to be 8° rather than the angle of 0°
that is observed for overlayers of H3C(CH2)16CHCH3(CH2)16-
CH3 and for overlayers of alkanes on graphite.
24
chains, they produced dark regions in the STM images. The
calculations and experimental results presented here for -Br
groups are in agreement with the image-contrast reversal that
has been reported for terminal -Br groups after sustained
imaging of n-alkyl bromide overlayers on graphite.23 These
topographic and electronic effects can be understood, and in
fact correctly predicted, from electronic structure calculations
of the molecules studied to date. In this respect, the agreement
between theory and experimental data on these systems is very
encouraging. Thus, certain functional groups, such as thiols or
thioethers, can potentially be used as markers to probe molecular
topography in a variety of complex systems, including possibly
oligonucleotides and other large molecules. However, the
changes in sign, as well as in magnitude, of the STM image
contrast of the -OH and -Br functional groups observed herein
imply that, in these cases at least, identification of the composi-
tion and geometric arrangement of an unknown molecule from
its STM image will be difficult without the use of supplemental
information.
IV. Discussion
1
. Relative Importance of Molecular Geometry and
Topography on STM Image Contrast. The STM data de-
scribed herein underscore the interplay between the topographic
and electronic coupling factors that determine the local contrast
observed in a STM image. The locations of bright spots in STM
images of alkane and alkanol overlayers have been shown
previously to be strongly correlated with the positions of the
upward-pointing hydrogen atoms in the methylene units of these
2
4,25,34
molecules.
Thus, topography plays an important role in
determining the image contrast of such systems. However, for
24
some of the functional groups observed previously, electronic
coupling factors appear to dominate the image contrast. For
example, even though -CF3 groups are large relative to methyl
groups, they appear dark relative to methylene units in STM
images of CF3(CH2)11OH or CF3(CF2)3(CH2)10OH. Similarly,
the amine functionality appears bright relative to internal
2. Intermolecular Interactions in the Substituted Alkane
and Alkanol Overlayers. The STM images discussed above
2
4
methylene groups in dioctadecylamine, (C18H37)2NH and in

STM of Alkanes and Alkanols on Graphite
J. Phys. Chem. B, Vol. 103, No. 44, 1999 9697
Figure 10. Schematic diagram of the proposed packing of the bromoalkane molecules; H
Note that the packing angle θ is 8° in this configuration.
3 2 4 2 4 3
C(CH ) CHBr(CH ) CH molecules are shown for clarity.
reveal several different packing structures of the molecules both
within and between the lamellae of the various overlayers. The
intermolecular angle θ and the locations of the internal
functional group markers in the molecules studied in this work
provide useful metrics that allow investigation of these packing
interactions.
can be driven by a favorable hydrogen-bonding interaction
between functional groups at the other terminus of the alkane
chains, as evidenced by the observation that θ ) 26° for alkanols
2
4
on HOPG, or can be driven by the tendency to avoid
unfavorable interactions between functional groups in the centers
of such chains, as presumably reflected in the value of θ ) 26°
that is exhibited by overlayers of (C16H33)2O on HOPG.24 The
diol having an internal Br group, HO(CH2)9CHBr(CH2)10OH,
was observed in this work (Figure 5) to pack in a fashion similar
to that of other substituted and unsubstituted alkanols and
displayed θ ) 23°. This packing therefore presumably reflects
the strong tendency to obtain favorable hydrogen-bonding
interactions at the termini of the molecules in the overlayer,
and these interactions dominate any steric interactions within a
lamella that might arise because of the presence of the internal
-Br groups.
Other molecules studied in this work, however, exhibited
different packing angles and different molecular arrangements
within a lamella from those displayed by n-alkanes or n-alkanols.
The H3C(CH2)16CHCH3(CH2)16CH3 overlayer is one such
system of interest. Figure 9 depicts a proposed packing scheme
for this system that is consistent with the STM images of Figure
3. In this structure, adjacent molecules within a lamella form
pairs, with molecules in each pair having their methyl groups
staggered and pointing away from each other. Additionally, the
methyl groups occupy troughs formed by the ends of similar
molecules that are packed in an identical structure but that are
located in abutting, adjacent lamellae. Finally, adjacent pairs
of molecules in a given lamella are in translational registry with
each other relative to the propagation direction of a lamella.
The simplest packing arrangements can be readily understood
from steric considerations. Alkane overlayers on graphite exhibit
θ ) 0°, which is consistent with the tendency to maximize van
der Waals interactions between neighboring molecules within
2
4
a lamella. This packing arrangement also minimizes steric
repulsions between methylene hydrogen atoms on adjacent
alkane chains. Additionally, repulsions between adjacent mol-
ecules in abutting lamellae are minimized by having these
1
molecules stagger by /2 a molecular width, and this feature is
2
4
clearly observed in the STM images of such systems. The
internal -OH group in the molecule H3C(CH2)16CHOH(CH2)16-
CH3 studied in this work apparently did not induce sufficient
steric repulsion between adjacent molecules in a lamella or offer
the opportunity for sufficient hydrogen-bonding interactions
within a lamella to perturb this basic packing structure; thus,
the packing arrangement exhibited by H3C(CH2)16CHOH-
(
CH2)16CH3 (Figure 1) is, within experimental error, identical
2
4
to that exhibited by simple n-alkane overlayers on graphite.
The next simplest packing arrangement has θ ≈ 26°. In this
situation, adjacent molecules within a lamella sacrifice a van
der Waals interaction and stagger by two full methylene units
such that internal hydrogens on one chain fill hollows in the
structure of the adjacent chain in a lamella.24 The loss of the
van der Waals interactions at one end of the alkyl chain either

9698 J. Phys. Chem. B, Vol. 103, No. 44, 1999
Claypool et al.
Figure 11. Schematic diagram showing the conversion between the proposed packing of H
CHBr(CH (right) on graphite. For clarity, the molecules have been shortened in the figure to 11 carbon chains to allow the viewer to focus
on the packing around the functional group regions. In addition, the diagram on the left has placed Br functional groups in positions that would be
3 2 3 2 3 3 2 16
C(CH )16CHCH (CH )16CH (left) and H C(CH ) -
2 3
)16CH
occupied by internal methyl groups in the H
3
C(CH
C(CH
overlayer into that of the H
2
)
16CHCH
3
(CH
2
)
16CH
3
structure so that the interconversion between the packing of the H
can be seen by comparison of the two diagrams. Conversion of the
C(CH 16CHBr(CH layer can be achieved by translation of the
-CH - distance normal to the vector that lies parallel
to the propagation direction of the lamella, as indicated by the arrows in the diagram on the left.
3 2 16
C(CH ) -
CHCH
3
(CH
2
)
16CH
3
overlayer and that of the H
3
2
)16CHBr(CH
2
)16CH
3
packing of the H
3
C(CH
2
)16CHCH
3
(CH
2
)
16CH
3
3
2
)
2 3
)16CH
2
outermost two molecules that form adjacent molecular pairs within a lamella by one -CH
2
This overlayer structure is consistent with the observations of
a packing angle of θ ) 0° (Figure 3).
packing arrangement of the molecules both within a lamella
and across abutting lamellae. One method to visualize the
conversion of the packing of the H3C(CH2)16CHCH3(CH2)16-
CH3 overlayer into that of the H3C(CH2)16CHBr(CH2)16CH3
layer involves translation of the outermost two molecules that
form adjacent molecular pairs within a lamella. The translation
occurs by one -CH2-CH2- distance normal to the vector that
lies parallel to the propagation direction of the lamella (Figure
11). This translation retains a staggered interaction between
adjacent molecules that form pairs in the packing structure, but
it also translationally offsets adjacent pairs of molecules in a
lamella relative to the propagation vector of a lamella. Consis-
tently, the packing of Figure 11 predicts an angle θ of 8°, in
accord with the experimental observations for this system
An alternative structure for this system, in which the methyl
groups of a given pair of molecules are directed toward one
another rather than away from each other, with otherwise
identical interlamellar packing parameters, can be ruled out from
the STM data. The observed distance of 11.7 ( 0.3 Å between
the pairs of bright spots in Figure 3 is in excellent agreement
with the expected distance of 11.8 Å obtained from the packing
arrangement of Figure 9, whereas if the methyl groups pointed
toward each other, a much smaller methyl-methyl distance
would be observed.
The differences in packing observed for this overlayer relative
to the packing of simple alkane chains presumably arise because
of steric interactions imposed by the presence of the internal
methyl functionality. Although a search of the Cambridge
structural database did not readily yield analogies to this
structure in available crystal structures of internally substituted
alkanes, the pairing motif revealed by the STM images of the
system is clearly a low-energy packing arrangement for two-
dimensional systems that have significant steric interactions
arising from a functional group being located at an internal
position on a trans conformation alkyl chain.
(Figure 7). Furthermore, such a packing arrangement results in
a chiral overlayer domain because the mirror image of this
structure exhibits θ ) -8° relative to the propagation direction
of a lamella.
The difference between the packing in the Br and Me cases
is very subtle. The electrostatic energy difference between
H3C(CH2)16CHBr(CH2)16CH3 molecules arranged in the packing
arrangement of Figure 11 vs H3C(CH2)16CHBr(CH2)16CH3
molecules arranged in the H3C(CH2)16CHCH3(CH2)16CH3 pack-
ing structure of Figure 10 is <1 kcal/mol. Additionally, Br and
Me are conventionally thought to be sterically nearly identical.
Investigations of the analogous compounds that contain -Cl
or -F instead of -Br, as well as temperature-dependent
experiments to evaluate the energetic differences between the
two packing structures, would be especially interesting to
address the subtleties that control these packing force issues
in detail. In addition to elucidating features that control the
image contrast of functional groups, STM studies of these
systems thus offer an opportunity to examine, both theoretically
and experimentally, the intermolecular interactions that dic-
tate crystalline packing arrangements in two-dimensional over-
layers.
The substitution of an internal -Br group for the internal
CH3 group results in yet another molecular packing arrange-
-
ment. Figure 10 displays a packing scheme that is consistent
with the STM data for H3C(CH2)16CHBr(CH2)16CH3 overlayers
on graphite (Figure 7). The pairing motif of adjacent molecules
in a lamella displayed by H3C(CH2)16CHCH3(CH2)16CH3 (cf.
Figure 9) is also evident in this packing structure. As is the
case for H3C(CH2)16CHCH3(CH2)16CH3, the functional groups
(-Br in this case) for a given pair of molecules can be assigned
to be directed away from one another because the measured
distance of 7.8 ( 0.3 Å is in excellent agreement with the
expected distance of 7.6 Å.
Interestingly, the packing structure for H3C(CH2)16CHBr-
(
CH2)16CH3 differs from that of H3C(CH2)16CHCH3(CH2)16CH3
V. Conclusions
with respect to the arrangement of the functional groups relative
to each other at the level of second- and third-nearest-neighbor
functional group interactions. This results in a distinctly different
STM images have revealed the interplay between the
topographic and electronic coupling factors that determine the

STM of Alkanes and Alkanols on Graphite
J. Phys. Chem. B, Vol. 103, No. 44, 1999 9699
local contrast of a functional group in an STM image. Bromide
and -OH groups were bright in STM images when these groups
were located in internal positions on alkane chains, whereas
when these groups were placed in terminal positions on alkane
chains, locally dark regions were observed in the STM images
of such systems. These topographic and electronic effects can
be understood, and in fact correctly predicted, from electronic
structure calculations of the molecules studied to date. However,
the changes in sign, as well as in magnitude, of the STM image
contrast of the -OH and -Br functional groups observed herein
imply that, in these cases at least, identification of the composi-
tion and geometric arrangement of an unknown molecule from
its STM image will be difficult without the use of supplemental
information. Additionally, STM has been shown to be a useful
tool to investigate the different packing arrangements of
adsorbates on a surface in equilibrium with the adsorbed
molecules dissolved in solution phase.
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