Amphiphile self-assembly dynamics at the solution-solid interface reveal asymmetry in head/tail desorption

Article abstract of DOI:10.1039/c8cc04465a

Amphiphilic alkoxybenzonitriles (ABNs) of varying chain length are studied at the solution/graphite interface to analyze dynamics of assembly. Competitive self-assembly between ABNs and alkanoic acid solvent is shown by scanning tunneling microscopy (STM)

Full text of DOI:10.1039/c8cc04465a

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M. Espinosa-Duran, J. R. Dobscha, D. Ashley, S. Debnath, B. Hirsch, S. R. Schrecke, M. Baik, P. Ortoleva, K.
Raghavachari, A. H. Flood and S. L. Tait, Chem. Commun., 2018, DOI: 10.1039/C8CC04465A.
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Amphiphile Self-Assembly Dynamics at the Solution-Solid
Interface Reveal Asymmetry in Head/Tail Desorption
Henry D. Castilloa†, John M. Espinosa-Durana†, James R. Dobschaa, Daniel C. Ashleya,b, Sibali
Debnatha, Brandon E. Hirscha,c, Samantha R. Schreckea,d, Mu-Hyun Baika,e, Peter J. Ortolevaa,
Krishnan Raghavacharia, Amar H. Flooda, Steven L. Taita*
Received 00th January 20xx,
Accepted 00th January 20xx
DOI: 10.1039/x0xx00000x
www.rsc.org/
Amphiphilic alkoxybenzonitriles of varying chain length are studied surfaces, it is limited to those 2D structures that are stable for
at the solution / graphite interface to analyze dynamics of many seconds. The atomic-level subtleties of picosecond to
assembly. Competitive self-assembly between alkoxybenzonitriles nanosecond motions remain elusive when using microscopic
and alkanoic acid solvent is shown by scanning tunneling techniques. Thus, a full understanding of the fundamental steps
microscopy (STM) to be controlled by concentration and molecular and molecular design rules governing self-assembly require
size. Molecular dynamics (MD) simulations reveal key roles of the integrated study by experiment, theory, and computation.
sub-nanosecond fundamental steps of desorption, adsorption, and
MD simulations offer a means to elucidate how atomistic
on-surface motion. We discovered asymmetry in desorption- interactions dictate the sub-nanosecond molecular motions
adsorption steps. Desorption starting from alkyl chain detachment leading to molecular organization during self-assembly on the
from the surface is favored due to dynamic occlusion by surface and in solution. MD has been used to understand and
neighboring chains. Even though the nitrile head has a strong design biomolecular systems and synthetic polymers,10-12 as
solvent affinity, it more frequently readsorbs following
detachment event.
a
well as synthetic molecular materials .13-15 Previous works with
STM and MD have shown the power of combining these
techniques to understand self-assembly at the interface of
solution with highly oriented pyrolytic graphite (HOPG). 16, 17
Molecular self-assembly at interfaces provides a means to
develop highly ordered nanomaterials using bottom-up
strategies with applications in electronics, photovoltaics,
sensors, and separations.1-3 Bottom-up strategies rely on
precise control over geometry and organization of self-
assembled structures, which is only possible through a full
understanding of the complex interplay of the intermolecular
interactions. Since the advent of STM and pioneering work at
liquid-solid interfaces,4, 5 much has been learned about the roles
of supramolecular interactions, chemical potential, and other
physical parameters on 2D self-assembly.2, 6-9 While STM allows
sub-molecular resolution of assemblies on flat conductive
Fig. 1 Possible motions of ABN-C8 (inset) on graphite. Top: Fully desorbed. Bottom: fully
adsorbed. Left: desorption of alkyl chain. Right: desorption of benzonitrile group.
a.Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue,
Bloomington, Indiana 47405, USA
We present a nanoscale analysis of self-assembly at the
solution-solid interface using a synergistic experiment-theory
approach. Large scale (>300 nm2 substrate) atomistic MD
simulations for hundreds of ns (2 fs time steps) were conducted
in conjunction with STM imaging to study self-assembly of the
prototypical molecule alkoxybenzonitrile (ABN) on HOPG in
octanoic acid (OA) solvent. Alkoxybenzonitriles are easily
synthesized and were designed for their amphiphilic character:
to examine strong electrostatic (ES) interactions at the polar
benzonitrile head group (4.97 D18) and van der Waals (vdW)
b.Current address: Department of Chemistry, North Carolina State University,
Raleigh, North Carolina 27695, USA
c. Current address: Division of Molecular Imaging and Photonics, Department of
Chemistry, KU Leuven–University of Leuven Celestijnenlaan 200F, 3001 Leuven,
Belgium
d.Current address: Department of Chemistry, Texas A&M University, College
Station, Texas 77840, USA
e. Current address: Department of Chemistry, Korea Advanced Institute of Science
and Technology 291 Daehak-ro, Yuseong-gu Daejeon, 34141, Republic of Korea
† These authors contributed equally to this work.
* Corresponding author: tait@indiana.edu, Tel.: +1-812-855-1302.
Electronic Supplementary Information (ESI) available: Details of experimental and
computational methods. Supplementary data. See DOI: 10.1039/x0xx00000x
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21
interactions of the alkyl chain. The alkyl chain length was ideal alkyl spacing of 4.9 ± 0.3 Å (ideal = 4.4 Å) results in a
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DOI: 10.1039/C8CC04465A
modified from 4 to 18 carbons to test the dependence of moiré pattern along lamellar rows (Fig. 2b). Alkoxybenzonitrile
interdigitation from vdW interactions in alkoxybenzonitrile self- assembly involves several interactions: (a) C-H•••N-C hydrogen
assembly: ABN-C4
,
ABN-C8
,
ABN-C12
,
ABN-C16, and ABN-C18
.
(H-) bonding between aryl hydrogens and cyano nitrogens of
Concentration was varied from neat alkoxybenzonitrile (~8 M) the head group, (b) nitrile-nitrile dipolar coupling, and (c) vdW
to neat solvent to provide insights into the effect of altering the interdigitation of alkyl chains (Fig. 2b).
chemical potential of the alkoxybenzonitrile/octanoic
Octanoic acid self-assemblies, by comparison, are
acid/HOPG system. Our analysis also reveals that OA is surface characterized by a single row of bright features, attributed to H-
active. We present novel observations of the atomistic and sub- bonded carboxylic acids, alternating with lamellar alkyl rows
nanosecond motions during assembly and make progress
toward computer aided design strategies for molecular self- dimerized carboxylic acid heads and alkyl chains interdigitating
assembly at interfaces (Fig. 1). to produce lamellar rows. The unit cell is consistent with the size
(Fig. S4). STM images are consistent with models featuring
Surface structures were characterized by STM. The of the octanoic acid dimers and is independent of ABN chain
adsorbed structures seen after equilibration at room length. Dodecanoic acid was also tested as solvent and adsorbs
temperature for various concentrations and chain lengths are in the same structures as OA but with wider rows (Fig. S5).
summarized in a phase diagram (Fig. 2a). STM of high
MD simulations (1800 nm3, 2 700 molecules, 120 000
concentrations (≥ 100 mM ABN-C8, ≥ 25 mM ABN-C12, > 10 mM atoms) were undertaken to investigate (1) dynamics of self-
ABN-C16, ≥ 1.5 mM ABN-C18) produce a tightly packed assembly starting from an initially disordered state and (2)
alkoxybenzonitrile monolayer with interdigitated alkyl chains stability of 2D assemblies starting from the experimentally
(Fig. 2b); lower concentrations only show self-assembly of determined packing structure. Simulations were performed
solvent (Fig. S4). The phase boundary between OA and with a constant number of atoms (fixed concentration), volume,
alkoxybenzonitrile assemblies depends on alkyl chain length. and temperature (NVT ensemble).
Assemblies of alkoxybenzonitriles with longer chains are more
Simulations starting from an initially ordered state still show
stable on the surface than those with shorter chains, as interdigitated packing after hundreds of nanoseconds (Fig. 3a
expected based on the interaction enthalpy and the entropy of and 3b) with unit cells that match experiment to within one
solvent displaced by the adsorbed alkoxybenzonitriles.19, 20
standard deviation (Table S1). Starting from an ordered state,
The competition between alkoxybenzonitrile vs. OA 22% of ABN-C8 molecules desorb (Fig. 3c), while ABN-C4 retains
adsorption is also observed in MD simulations. ABN-C18 (233 an ordered interdigitated structure at 444 mM despite ca. 30%
mM) and ABN-C12 (286 mM) are found to preferentially adsorb, desorption (Fig. 3c and Fig. S6d). Both ABN-C12 and ABN-C18 also
as seen by STM. However, ABN-C8 (414 mM) is displaced by OA, retain the ordered structure, but with almost no desorption. On
even at much higher concentration than for self-assembly in areas of HOPG not filled with alkoxybenzonitriles, OA assembles
experiment. ABN-C4 did not adsorb in MD (444 mM) or in as carboxylic acid dimers in an anti-parallel fashion producing
experiment (100 uM – 1 M).
lamellae (Fig. 3), matching solvent structures observed at low
alkoxybenzonitrile concentrations (Fig. S4).
Of the simulations starting from the disordered state, only
ABN-C18 and ABN-C12 yield interdigitated ABN domains (Fig. 3d
and Fig. S6f); initially disordered simulations of ABN-C8 and
ABN-C4 exhibit desorption and replacement with octanoic acid
(Fig. 3e, 3f and Fig. S6h). Increased desorption and on-surface
lateral movement with shorter alkyl chain length point to the
importance of vdW contacts in stabilizing ABN layers.
MD simulations reveal that assembly relies more on vdW
interactions between alkyls than H-bonding between
benzonitrile dimers. With few exceptions (ABN-C8 and ABN-C4
simulations starting from disordered initial states) an anti-
parallel orientation of alkoxybenzonitriles is always adopted in
ordered domains (Fig. 3 and Fig. S6), consistent with STM.
Although the anti-parallel orientation allows for CH•••NC H-
bonding between head groups, alkoxybenzonitriles were
observed in MD to shift along the direction of the alkyl chains,
disrupting this H-bonding, which is not consistent with the
ordered domains in STM images. The dynamics hint that vdW
interactions are more influential in the early stages of domain
formation in MD. The non-directionality of vdW interactions
allows movement of molecules without breaking interactions.
That is, the vdW interdigitation offers some structural flexibility
Fig. 2 High resolution STM images and packing models of alkoxybenzonitriles and
octanoic acid at the solution/HOPG interface. (a) Phase diagram of alkoxybenzonitriles
in octanoic acid as function of alkyl chain length and mole fraction. Blue: octanoic acid
self-assembly. Red: alkoxybenzonitrile self-assembly. (b) ABN-C18. Conditions: 10 mM,
It= 0.40 nA, Vsample= -1.2 V. Refer to Fig. S4 for STM images of octanoic acid.
The packing density of alkoxybenzonitriles with different
alkyl groups scales with the alkyl chain length, indicating full
adsorption of the alkyls (Table S1). The most notable feature in
the STM images is the distinct contrast between two types of
rows: the double row of bright round features is attributed to
head-to-head packing of aromatic benzonitrile groups6 and
lower contrast rows are assigned to interdigitated alkyl chains.
Alkyl chains are aligned with the primary axes of HOPG. A non-
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along the direction parallel to the alkyl axis, though this is not might be due to an imbalance in vdW vs. electrostatic
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DOI: 10.1039/C8CC04465A
favourable for the H-bonding.
interaction strengths in the simulation, but a systematic
variation of both of those did not significantly improve the
structural match (specifically, the row to molecule axis angle)
between experiment and simulation.
Fig. 4 H-bond angle vs. distance between nitrile nitrogen and aryl hydrogen of paired
alkoxybenzonitriles. Plotted alkoxybenzonitriles are the final state of MD simulations
from ordered initial states. Right: Benzonitrile model with angle being measured. n=98
ABN-C18, n=160 ABN-C12, n=152 ABN-C8, n=223 ABN-C4. Measurements taken at 368 ns
(ABN-C18), 285 ns (ABN-C12), 354 ns (ABN-C8), 326 ns (ABN-C4).
Fig. 3 (a-b) MD simulations of alkoxybenzonitriles in OA (adsorbed OA in green) on HOPG
from initially ordered alkoxybenzonitrile state with varying chain length at 280 ns. (d-e)
MD simulations from initially disordered alkoxybenzonitrile state with varying chain
length at 215 ns. Desorbed alkoxybenzonitrile and octanoic acid molecules have been
omitted for clarity. (c and f) Percentage of desorbed alkoxybenzonitriles as a function of
time based on analysis of molecular dynamics simulations starting from initially (c)
ordered and (f) disordered states. Note that zero desorption is observed for ABN-C18 for
both initial states and ABN-C12 for the ordered initial states. For images of all
alkoxybenzonitrile MD simulations, see Fig. S6.
We examined the MD simulation results for insight into the
fundamental steps of partial detachment, molecular
desorption, re-adsorption, and on-surface diffusion that are
essential steps in surface self-assembly. Partial detachment of
alkoxybenzonitriles is initiated at either end of the molecule,
but most often occurs at the benzonitrile head (Fig. S10a). As a
portion of the molecule detaches from the surface, the free
surface area is immediately taken (within several ps) by
neighbouring adsorbed molecules. With no open surface
available for re-adsorption, molecules may be trapped in a
partially desorbed state for over 100 ns until an open area
becomes available and re-adsorption becomes possible.
MD simulations that led to alkoxybenzonitrile domains show
that alkoxybenzonitriles align with the primary axis of graphite
(Fig. S8), consistent with experimental results. ABN alkyl chains
in MD simulations pack at the most stable density (4.4 Å),21
which contradicts the observation of the moiré pattern in STM
(4.9 Å, Fig. 2b). This indicates that the HOPG lattice acts to
template the 2D orientation of these organic molecules.
The expected CH•••NC distance (weak H-bond) is 2.75 Å.22
MD simulations show bond distances clustered near this value,
Full desorption of the entire alkoxybenzonitrile occurs by
initial partial detachment, followed by peeling off the surface
and inhibition of re-adsorption by neighbouring molecules
(Figs. 5a-b). The timescale of full desorption varies from several
ps to hundreds of ns. Unlike partial desorption, full desorption
is more often initiated from the alkyl chain than the benzonitrile
head (Fig. S10b). This is surprising as the benzonitrile should
have a greater affinity for the OA solution. The alkyl flexibility
contributes to more frequent desorption. As an alkyl chain
begins to peel away from the surface, neighbouring molecules
fill in the open surface. When this happens, the detached alkyl
is prevented from re-adsorbing and further desorption is
possible. Unlike the stepwise detachment of flexible alkyls, the
rigid benzonitrile detaches completely and re-adsorbs back to
its original π-stacked conformation, but usually via edge-on
perpendicular interactions with the surface (Fig. 5c). The open
surface area created by a detached head is wider than an alkyl.
Neighbouring adsorbed heads are constrained in their motion
by their attachment to the interdigitated alkyls. C–O bond
rotations of the detached head groups allow initial re-
adsorption in a perpendicular conformation, then the head
rotates to a flat-lying orientation.
but with a significant spread to even longer H-N lengths (Fig. 4
,
Fig. S9c, and Table S2). The ideal alignment angle for a single
CH•••NC bond is 180°,22 but the ideal CH•••NC bond angle for
a benzonitrile dimer with two CH•••NC bonds is 120° (Fig. 4
inset), which is consistent with MD simulations (Fig. 4, Fig. S9b,
and Table S2). The long CH•••NC distance is consistent with the
relatively weak character of this non-traditional hydrogen
bond.22 It seems that assembly is primarily directed by the alkyl
interdigitation, with the head group sterics and nitrile H-
bonding being secondary interactions in the ordering hierarchy.
Although the CH•••NC bond angles and distances did not
change during progression of the simulations from the initially
ordered state, we observed a change in angle between the row
direction and molecule axis; the final result of each simulation
does not match corresponding experimental results (69° vs.
84°). This angle change occurs within the first 60 ns for each of
the molecules studied. We considered that this discrepancy
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This work was supported by the National Science
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Foundation (NSF), Designing MaterialsDtOoI: R10e.1v0o3l9u/tCio8CnCiz0e44a6n5dA
Engineer the Future program (DMR-1533988). MD calculations
were conducted on Indiana University’s Big Red II
supercomputer supported in part by Lilly Endowment, Inc.,
Indiana University’s Pervasive Technology Institute, and by the
Indiana METACyt Initiative. JMED acknowledges support from
the Colombian Administrative Department of Science,
Technology and Innovation. SRS was supported by the IU
Chemistry NSF REU program (CHE-1460720).
Conflicts of interest
There are no conflicts of interest to declare.
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Fig. 5 (a and b) Top down and side view snapshots showing desorption of ABN-C8 (pink)
starting from the head (a) and chain (b). From left to right, the alkoxybenzonitrile is fully
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