Patterned monolayer self-assembly programmed by side chain shape: Four-component gratings

Article abstract of DOI:10.1021/ja2115019

A molecular recognition strategy based on alkadiyne side chain shape is used to self-assemble a four-component, 1D-patterned monolayer at the solution-HOPG interface. The designed monolayer unit cell contains six molecules and spans 23 nm × 1 nm. The unit cell's internal structure and packing are driven by complementary shapes and lengths of six different alkadiyne side chains. A solution of the four compounds on HOPG self-assembles monolayers (i) comprised, almost entirely, of the intended unit cell, (ii) exhibiting patterned domains spanning 10⁴ nm², and (iii) which are sufficiently robust that patterned domains survive solvent rinsing and drying. The patterned monolayer affords 1D-feature spacings ranging from 3.3 to 23 nm. The results demonstrate the remarkable selectivity afforded by molecular recognition based on alkadiyne side chain shape and the ability to program highly complex 1D-patterns in self-assembled monolayers.

Full text of DOI:10.1021/ja2115019

Communication
pubs.acs.org/JACS
Patterned Monolayer Self-Assembly Programmed by Side Chain
Shape: Four-Component Gratings
Yi Xue and Matthew B. Zimmt*
Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
*
S Supporting Information
9
10
dinate covalent or hydrogen bonding has been used to direct
monolayer self-assembly. The geometric constraints of a planar
substrate and monolayer prompted this effort to use aliphatic
side chains with “Tetris-like” shapes (Chart 1) to realize
ABSTRACT: A molecular recognition strategy based on
alkadiyne side chain shape is used to self-assemble a four-
component, 1D-patterned monolayer at the solution−
HOPG interface. The designed monolayer unit cell
contains six molecules and spans 23 nm × 1 nm. The
unit cell’s internal structure and packing are driven by
complementary shapes and lengths of six different
alkadiyne side chains. A solution of the four compounds
on HOPG self-assembles monolayers (i) comprised,
almost entirely, of the intended unit cell, (ii) exhibiting
Chart 1. Self-Incommensurate (top) and Pairwise
a
Complementary (bottom) Alka-n,n+2-diyne Side Chains
4
2
patterned domains spanning 10 nm , and (iii) which are
sufficiently robust that patterned domains survive solvent
rinsing and drying. The patterned monolayer affords 1D-
feature spacings ranging from 3.3 to 23 nm. The results
demonstrate the remarkable selectivity afforded by
molecular recognition based on alkadiyne side chain
shape and the ability to program highly complex 1D-
patterns in self-assembled monolayers.
a
elf-assembled monolayers with designed supramolecular
Side chains are characterized (X/Y) by length (X = number of C + O
1
S
structure continue to be of great interest. Such composi-
tionally patterned monolayers have potential as templates to
atoms) and the side chain position (Y) of the first alkyne carbon. Black
ovals indicate regions lacking chain−chain van der Waals contact.
2
direct multilayer assembly or as tools to probe nm-length scale
phenomena in chemistry, biology, and physics. While there are
molecular recognition and supramolecular assembly in
monolayers formed from mixtures of 1,5-(side chain)-
substituted anthracenes. Optimized van der Waals interactions
from close packing of specific pairs of shape complementary
side chains is the anticipated energetic basis for molecular
recognition. Monolayers assembled by these substituted
anthracene derivatives exhibit alternating aryl and aliphatic
columns. The aliphatic columns contain interdigitated side
chains attached, alternately, to anthracenes in the flanking aryl
columns. This morphology promotes assembly of adjacent
3
4
many examples of two- and three-component monolayers,
few of these exhibit supramolecular features spanning 10 nm or
3
e,f
more.
Tailoring the monolayer structure on these length
5
scales requires bigger molecules and/or larger sets of
molecular components that scrupulously select neighboring
molecules in the monolayer. As examples of four-component
11
6
self-assembled monolayers are rare, development of robust
strategies for engineering supramolecular structure in multi-
component monolayers remains an important and unsolved
challenge. Here we demonstrate the potency of molecular
anthracene columns bearing identical length side chains; i.e. the
7
3f,12
shape selection by alkadiyne side chains to program supra-
aliphatic columns segregate side chains by length.
However,
molecular structure in multicomponent monolayers; the
designed four-component monolayer exhibits supramolecular
structure (i) assembled, almost exclusively, from one out of
length alone cannot differentiate multiple molecules bearing the
12
same length side chain. Additional structural differences and
interactions are needed to implement such selection. This study
uses the kinked shape of alka-n,n+2-diynes to select among
identical length chains. Each internal diyne group creates a 0.3
nm offset between two parallel, terminal alkyl groups. Diyne
“kinks” located near the aryl core or near the chain terminus
reduce van der Waals contacts between identical, interdigitated
4
more than 6 × 10 possible, six-molecule building blocks, (ii)
built on a 1D-pattern repeat that spans 23 nm, and (iii) that
retains pattern registration for hundreds of nanometers. The
monolayer survives solvent rinsing and drying and exhibits
uninterrupted supramolecular structure across areas as large as
4
2
1
0 nm .
Supramolecular assembly requires molecular recognition
among components. Molecular recognition based on coor-
Received: December 19, 2011
Published: February 28, 2012
8
©
2012 American Chemical Society
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Journal of the American Chemical Society
Communication
a
Chart 2. Structures, Intended Neighbor Selection, and Half the Designed Unit Cell of Diyne Bearing Anthracenes
a
Side chains are characterized (X/Y) by length (X = the number of non-hydrogen atoms) and the side chain position (Y) of the first alkyne carbon.
side chains (Chart 1, top); the chains are shape “self-
incommensurate”. By contrast, interdigitation of side chains
with complementary kink locations yields optimal contacts and
van der Waals stabilization (Chart 1, bottom). Pairwise “shape
complementarity” affords molecular recognition and selection
parallel (horizontal in Figure 1), indicating adsorption to
HOPG via the same enantiotopic face. The center to center
spacings of the four anthracene columns crossing the green
rectangle in Figure 1 are 3.8, 3.3, and 4.4 nm. These distances
are in good agreement with anthracene column spacings
obtained from a monolayer simulation on graphene (Table 1):
13
from among identical length diyne side chains.
In this study, four anthracenes bearing a total of six different
diyne side chains were prepared and their self-assembly on
graphite was studied. Side chain shape was modulated using
both chain length (23, 27, and 31 heavy atoms) and diyne
Table 1. Measured and Simulated Spacings (nm) of Nearest
Anthracene and Diyne Columns
14a
14c
“kink” location to produce two “self-incommensurate”, but pair
wise complementary, diyne side chains of each length. A unit
cell comprised of six molecules was designed to contain one
copy of two molecules with C symmetry (S1 and S2) and two
2
h
copies of two molecules with C symmetry (D1 and D2). Chart
h
2
displays the intended, shape-based neighbor selection of the
four molecules and half the designed, C2h symmetric unit cell.
15
3.92 nm for S2-D2, 3.35 nm for D2-D1, and 4.48 nm for D1-
With six side chains and two enantiotopic faces per molecule,
14c
4
14b
S1.
Diffuse, lower-tunneling diyne columns (red arrows,
>
6 × 10 enantiomeric pairs of six-molecule units
might
Figure 1) run parallel to the anthracene columns. The close
packing and linearity of the diyne columns, along with the
measured anthracene−diyne spacings (Table 1), is consistent
with the shape based molecular recognition proposed in Chart
assemble on HOPG, but the designed unit cell dominates.
Figure 1 displays a monolayer section self-assembled on
HOPG from a phenyloctane solution of the four compounds
(0.4 mM S1, S2; 0.8 mM D1, D2). The anthracene cores
2
and confirms the anthracene column compositions as S2, D2,
appear as 3 × 2 dot, high-tunneling patterns (yellow) and
assemble as columns via close approach of adjacent
anthracenes' corners. The long axes of all anthracenes are
D1, and S1 from top to bottom along the unit cell asymmetric
unit (green rectangle).
The complete unit cell of the 1D patterned monolayer is
visible in larger monolayer sections (Figure 2). At this length
scale, the anthracene columns are visible, but the anthracene 3
×
2 dot patterns are not. The stacked diyne column edges
exhibit STM contrast, appearing as “train tracks” within the
aliphatic columns (red arrows). Once again, the anthracene and
diyne spacings identify the column compositions and confirm
the 1D patterned monolayer unit cell contains six molecules in
the order S1-D1-D2-S2-D2-D1. The image in Figure 2 was
recorded at the air−HOPG interface. After a 3 μL drop of the
phenyloctane solution was applied to HOPG and annealed at
4
0 °C for 2 h, the sample was rinsed with 2 mL of cold ethanol
to remove the phenyloctane solution and then air-dried for 1 h.
Figure 2 demonstrates that monolayer physisorption to the
HOPG is sufficient to resist the forces active during solvent
16
washing and drying. A defect near the bottom of the left D2
column consists of two D2 molecules with improperly directed
14d
side chains.
scan.
This defect was absent from the next STM
1
4d
A 140 nm × 140 nm STM scan of a similarly prepared “dry”
sample characterizes the spatial persistence of the monolayer
pattern (Figure 3). Diyne column locations are not discernible
at this image scale, so the sequence of anthracene column
spacings serves to identify column compositions. In the
direction perpendicular to the anthracene columns (red line),
the designed anthracene spacing pattern persists for at least 160
nm (>7 unit cells). In the direction parallel to the anthracene
Figure 1. Constant current image (0.85 V, 0.1 nA, 20 nm × 20 nm) of
the monolayer assembled from a phenyloctane solution of S1, D1, D2,
and S2. Red arrows mark diyne columns. The asymmetric unit (green
rectangle) parameters are a = 11.5 ± 0.4 nm, b = 0.93 ± 0.05 nm, α =
9
1 ± 3°.
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Communication
2
000 molecules that assemble and pack using the intended
shape-based selection.
The sequence of column spacings in the region below the
dashed white line confirms assembly of the intended monolayer
pattern. However, the registration of the unit cells below the
dashed line is shifted left by ∼7.5 nm relative to the unit cells
14f
above the dashed line. Upon close inspection, anthracene
columns assigned as D2 (yellow bar) or S1 (red bar) exhibit
unbroken lines of dots (anthracenes) crossing the dashed line.
By contrast, columns assigned as D1 (green bar) or S2 (blue
bar) exhibit broken lines of dots (anthracene) in crossing the
dashed white line. As the unit cells on opposite sides of the
dashed line are out of registration, by two columns, every
column must contain at least one defect, i.e., a change in
orientation or identity of adjacent anthracenes. The packing of
these defects must be characterized and understood in order to
increase pattern persistence parallel to the anthracene columns.
The presence of all four compounds is sufficient to direct self-
assembly of patterned monolayers, but is it necessary? For this
control and to check the fidelity of side chain molecular
recognition, phenyloctane solutions lacking one of the four
14g
Figure 2. Constant height STM image (0.85 V, 0.04 nA, 43 nm × 43
nm) of the monolayer assembled from a solution of S1, D1, D2, and
S2. This image was recorded at the air-HOPG interface after ethanol
rinsing. Cyan (red) arrows mark anthracene (diyne) columns. The
unit cell (green rectangle) parameters are a = 23.0 ± 0.9 nm, b = 0.95
compounds were applied to HOPG.
No STM detectable
monolayers are observed when S1, D1, or D2 is excluded from
solutions of the other three compounds. The three molecules in
each of these solutions are not adequate to substitute for the
missing compound and assemble a monolayer. Exclusion of S2
from the mixture of compounds did produce monolayers
comprised of small domains (<35 nm in both directions)
exhibiting various spacing patterns between anthracene
±
0.06 nm, α = 90 ± 5°. The anthracene column spacings are ∼3.8 nm
for S2/D2, ∼3.3 nm for D1/D2, and ∼4.4 nm for D1/S1.
14g
columns.
The most common of these column spacing
patterns, a (4.4 nm-3.3 nm-4.4 nm) repeat, can be rationalized
X
as substitution of S1 for the missing S2; i.e. (S1-D1-D2) . The
X
3
1
1
1 atom side chain of S1 can pack its diyne carbons and outer
5 CH units in registration with the diyne carbons and inner
2
14h
6 CH /O units of D2.
Although S1 can fill in for the
2
absence of S2 in three-component monolayers, the lack of any
4.4 nm-3.3 nm-4.4 nm) repeat in monolayers formed from all
(
X
four compounds suggests greater stability (selectivity) of the
D2-S2 contact compared to the D2-S1 contact. Although the
S1, D1, D2 mixture does assemble monolayers, the domains'
limited spatial extents and frequent 1D pattern disruption
indicate reduced stability and robustness compared to the large
domains and pattern coherence in the monolayer assembled by
all four components.
In conclusion, the self-assembly of complex, supramolecular
structure in monolayers can be programmed using shape
complementarity of alkadiyne side chains. The four molecular
shapes used here afford excellent, albeit imperfect, molecular
recognition. In addition, the two, long alkadiyne side chains on
each molecule and the assembly of dense-packed domains
produce robustly physisorbed monolayers that survive solvent
rinsing and drying. This strategy for side chain shape based
patterning of monolayers should be scalable to unit cells of
sufficient length (∼50 nm) that a single repeat can be
Figure 3. Constant current image (0.85 V, 0.040 nA, 140 nm × 140
nm) of the monolayer assembled from a solution of S1, D1, D2, and
S2. This image was recorded at the air−HOPG interface after ethanol
rinsing and drying. The long red line spans 165 nm. Solid white lines
separate enantiomeric domains. The colored bars mark columns of S1
(
red), D1 (green), D2 (yellow), and S2 (blue).
17
interfaced with top-down assembly tools. Efforts to improve
molecular recognition fidelity, to increase unit cell size and
complexity, and to use monolayers as templates are ongoing.
columns, the pattern’s persistence length is shortened by
various defects including (i) interfaces between enantiomeric
1
4e,15
domains
(solid white lines), (ii) interfaces between
ASSOCIATED CONTENT
Supporting Information
■
domains related by graphite’s 3-fold symmetry (black line),
and (iii) single and clusters of improperly aligned/adsorbed
molecules. A domain in the center of Figure 3 (between the
upper solid white and dashed white lines) contains more than
*
S
Syntheses and spectral data, STM sample preparation and
acquisition procedures, adsorption orientations and estimated
count of unique unit cells, STM images of three-component
4
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Journal of the American Chemical Society
Communication
monolayers, Figure 3 zoomed views, molecular mechanics
simulation and chain energetics, defect models. This material is
available free of charge via the Internet at http://pubs.acs.org.
(8) Lehn, J.-M. Science 1993, 260, 1762−1763.
9) (a) Semenov, A.; Spatz, J. P.; Moller, M.; Lehn, J. M.; Sell, B.;
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1
AUTHOR INFORMATION
Corresponding Author
mbz@brown.edu
■
(
Schmittel, M.; Lackinger, M. Langmuir 2010, 26, 10708−10716.
(b) Ivasenko, O.; Perepichka, D F. Chem. Soc. Rev. 2011, 40, 191−206.
(11) (a) Dickerson, P. N.; Hibberd, A. M.; Oncel, N.; Bernasek, S. L.
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c) Tahara, K.; Johnson, C. A. II; Fujita, T.; Sonoda, M.; De Schryver,
The authors declare no competing financial interest.
̈
(
ACKNOWLEDGMENTS
We gratefully acknowledge computational assistance from Dr.
Wenjun Tong, data collection assistance from Tereza Pask
and financial support from the National Science Foundation
■
F. C.; De Feyter, S.; Haley, M. M.; Tobe, Y. Langmuir 2007, 23,
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CHE1058241).
monolayer, preparations, and characterization, (b) the 12 possible
adsorption orientations and estimate of the number of unique unit
cells, (c) a molecular mechanics minimized monolayer section (CPK
models) and key spacings, (d) a model of the D2 defect (in Fig. 2)
and the next STM scan, (e) an STM image of the interface between
enantiomeric domains, (f) a magnified image centered around the
dashed white line in Figure 3, (g) conditions and STM images of the
three-component control experiments, and (h) a model of the (S1-
D1-D2)X three-component repeat and molecular mechanics energy
estimates of various side chain (and defect) packings.
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