Article pubs.acs.org/JPCC
Thermal Healing of the Nanometer-Wide Lines of Self-Assembled Monolayer Zhengqing Zhang,† Yoonho Ahn,‡ Jong Yeog Son,‡ and Joonkyung Jang*,† †
Department of Nanoenergy Engineering, Pusan National University, Busan 609-735, South Korea Department of Applied Physics, Kyung Hee University, Yongin 446-701, South Korea
‡
S Supporting Information *
ABSTRACT: The structural and thermal properties of the nanometer-wide lines of a self-assembled monolayer (SAM) were investigated using molecular dynamics simulations. When grown by contact printing, a linear SAM contained a significant portion (8%) of unbound molecules that are inverted among upright molecules. This paper proposes thermal annealing (300−400 K) as an efficient method to remove the unbound molecules and improve the quality of the linear SAM. The partial melting of the SAM during heating enabled the unbound molecules to flip and adsorb. With subsequent cooling, the linear SAM recovered its compact ordered structure. The molecular mechanisms and activation energies involved in the thermal annealing were elucidated.
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INTRODUCTION Self-assembled monolayers (SAMs) of alkanethiol are used widely to control the physical and chemical properties of surfaces. For example, the SAMs are used to adjust the wetting properties of surfaces1,2 and protect various surfaces from corrosion and wear.3−5 With the help of various lithographic techniques, SAMs are patterned routinely with a nanometer spatial resolution. These nanoscale SAMs are used to construct biosensors6−8 and molecular electronic devices9,10 as well as many other nanostructures. These applications essentially rely on the notion that nanoscale SAMs retain their ordered and stable structures, as in their bulk states: the sulfur atoms adsorb strongly and are closely packed, and the alkyl chains are aligned and packed together, slightly (∼30°) tilted from the surface normal.11,12 A nanometer-wide SAM of alkanethiol is commonly grown by contact with a stamp12 or an atomic force microscope tip13 coated with molecules. The alkanethiol molecules initially deposited from such a source are temporarily piled up on the surface with their alkyl chains tangled up. The majority of molecules then self-assemble into an ordered SAM. On the other hand, there can be unbound molecules whose sulfur atoms fail to adsorb to the surface, being kinetically trapped among the upright molecules. In the case of a bulk SAM, these unbound thiol molecules can be detected by X-ray photoelectron spectroscopy.14−17 Observing the unbound molecules in the nanoscale SAMs experimentally is quite difficult due primarily to their small sizes. Only the molecular dynamics (MD) simulation18,19 can uncover two types of unbound molecules: the unbound molecules are piled above other molecules already adsorbed, or the unbound molecules are © 2016 American Chemical Society
inverted with their terminal methyl groups instead of sulfur atoms in contact with the underlying surface. These unbound molecules will deteriorate the order and stability of the nanoscale SAMs and therefore limit their applications. Therefore, it is important to devise a method to remove these unbound molecules. In the case of a circular SAM, a prior MD simulation showed that such unbound molecules can be removed by thermal annealing.19 One of the most common motifs of nanoscale SAMs is the line. In the present study, MD simulations were performed to examine the growth and subsequent thermal annealing of a linear SAM on the nanoscale. In the case of a linear SAM of 1-octadecanethiol (ODT) grown on a gold surface, the simulations show that thermal annealing efficiently cures these unbound molecules. The molecular mechanisms and activation energies involved in the thermal healing process are elucidated.
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MOLECULAR DYNAMICS SIMULATION METHODS The CH3, CH2, and SH groups of ODT are treated as united atoms20,21 because this implicit hydrogen model successfully reproduced the results of the all-atom simulations.22,23 The bond stretching and bending angle interactions between the united atoms were modeled as the harmonic potentials.24 The four-atom torsion potential (C−C−C−C or C−C−C−S) was taken to be a triple cosine function of the dihedral angle.25 Nonbonded interatomic interactions were described using the Lennard-Jones (LJ) potentials.20 The chemisorption of a sulfur Received: May 19, 2016 Revised: June 25, 2016 Published: July 5, 2016 15509
DOI: 10.1021/acs.jpcc.6b05078 J. Phys. Chem. C 2016, 120, 15509−15513
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The Journal of Physical Chemistry C atom was described by the Morse potential.26 The LJ and Morse parameters were taken from previous simulation studies.18−20,27,28 The gold surface was made of two layers and 6728 atoms and were held rigid. The MD trajectories were propagated using the velocity Verlet algorithm with a time step of 1.0 fs. Prior to annealing, a droplet of 346 ODT molecules in contact with a gold (111) surface was formed. A constant force of 0.2 nN was then applied to drag the droplet across the surface (Figure 1) for 4 ns. An 80 ns long MD trajectory was
temperature, an NVT MD simulation was run for 4 ns (the heating and cooling rates were identical, 4.2 K/ns). The DLPOLY package29 was used to implement the MD methods described above. The free energy profile of the adsorption of an inverted molecule was constructed by calculating the potential of mean force (PMF) vs the height of the sulfur atom, ξ, the height of the terminal methyl group, ω, or both ξ and ω (see Figures S1 and S2 in the Supporting Information). Using umbrella sampling,30 these variables were restrained to their target values by imposing the harmonic potentials. Typically, 39 windows were used to achieve sufficient overlap between the neighboring histograms. In each window of the PMF calculation, a 6.0 ns MD simulation was run, and the initial 0.5 ns part was discarded for equilibration. The free energy was extracted using the weighted histogram analysis method.31−33 All restrained MD simulations were run using the DLPOLY combined with the PLUMED package.34 The molecular orientation was examined by selecting nine CH3 or CH2 groups, which have odd (1−17) numbers of intervening CH2 groups between them and a S atom. The tilt direction vector of the ith molecule, u⃗i, was defined as the average over the vectors from the S atom to these united atoms (Figure S4).20,35 The tilt angle of the ith molecule, θi, was given by the polar angle of ui⃗ measured from the surface normal. The surface projection of ui⃗ was designated by vi⃗ . The ui⃗ s were normalized as unit vectors, and three methyl groups at the tail of the chain were excluded. The order parameter of the molecular orientation was defined as36 Ou = ⟨0.5[(u⃗i·u⃗j)2 − 1]⟩i≠j, where ⟨ ⟩i≠j represents the average over all the intermolecular pairs.
Figure 1. Growth of a linear SAM on a gold (111) surface. Dragging an ODT droplet across the surface gives a linear SAM containing unbound molecules that are inverted among upright molecules.
further run by switching off the external force. The resulting SAM line was heated to 400 K in 20 K increments and then cooled to 300 K in 20 K decrements. At each annealing
Figure 2. Structural changes in the linear SAM during heating from 300 to 400 K and cooling from 400 to 300 K (clockwise). Each panel also shows a snapshot of the sulfur atoms only (middle) and the projections of the tilt direction vectors of alkyl chains (bottom). 15510
DOI: 10.1021/acs.jpcc.6b05078 J. Phys. Chem. C 2016, 120, 15509−15513
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RESULTS AND DISCUSSION
A nanoscale SAM line was grown by contacting a droplet of ODT and subsequently dragging the droplet across the surface (Figure 1a). A linear SAM, 4.53 and 15.31 nm in width and length, respectively, was formed as a result. This type of spreading and self-assembly of a droplet into a monolayer is essential in the contact printing of a nanoscale SAM. The majority of ODT molecules assembled into a monolayer, where their sulfur atoms are adsorbed to the gold surface and their alkyl chains aligned together (Figure 1d). Some molecules (27 out of 346 molecules), however, were inverted and trapped among the upright molecules, failing to bind to gold via their sulfur atoms. No molecule was observed sitting on top of other molecules, presumably because the present linear SAM is narrow in width. Therefore, the molecules on top promptly reach the periphery of the SAM line and hop down to the bare surface. Next, the linear SAM with the unbound molecules was annealed thermally (300−400 K). Upon heating from 300 to 400 K in 20 K increments (clockwise in Figure 2), the linear SAM expanded laterally, and the sulfur atoms, which were initially closely packed, dispersed slightly (shown in the middle of each panel in Figure 2). At the same time, the alkyl chains became disordered and wavy, which is in contrast to the initially straight and aligned chains. None of the inverted molecules escaped into the vacuum because their alkyl chains were entangled with the alkyl chains of the neighboring molecules. When the temperature reached 340 K, one molecule near the periphery of the linear SAM flipped and adsorbed. When the linear SAM was heated further to 380 K, 18 inverted molecules flipped. At 400 K, all the remaining (8) inverted molecules flipped to stand upright. Upon subsequent cooling to 300 K, the sulfur atoms were densely packed again. The alkyl chains also aligned with each other, resulting in an ordered compact SAM. The linear SAM after annealing clearly shows the (√3 × √3)R30° packing of sulfur atoms and the alignment of the alkyl chains (Figure 2). In addition, both ends of the linear SAM were rounded after annealing. Various structural parameters corroborate the structural order in the linear SAM. The S−S distance, dss (=5.00 Å), tilt angle of the alkyl chains, θ (=25.2°), percentage of trans conformations (=97.5%), and the order parameter of the tilt orientation, Ou (=0.95), were all close to the corresponding values of a defectfree SAM in the bulk (Table S1 in Supporting Information). A further insight into the linear SAM is provided by the tilt direction vectors of alkyl chains projected onto the surface, vi⃗ s (see the Simulation Methods section). In each panel of Figure 2, vi⃗ s are drawn as arrows in the bottom. Before annealing, the alkyl chains tilt preferentially toward the right end of the SAM line. After annealing, the alkyl chains tilt toward the left end of the SAM line. This preferential tilting of the alkyl chains toward either end of the SAM line contrasts with the random isotropic tilting of the alkyl chains in circular SAMs. At elevated temperatures of 380 and 400 K, however, the alkyl chains tilt randomly. An inverted molecule flipped by moving its sulfur atom down and terminal methyl group up either sequentially (Figure 3, top) or simultaneously (Figure 3, bottom). In the sequential flip (top), the sulfur atom of an inverted molecule penetrated down without moving its methyl tail group. After the sulfur atom was bound to the surface, the methyl group moved up to
Figure 3. Mechanism of the flip of an inverted molecule at 380 K. An inverted molecule was flipped by lowering its sulfur atom and raising terminal methyl group either sequentially (top) or simultaneously (bottom). Four consecutive snapshots are drawn for each mechanism.
provide an upright molecule. In the simultaneous flip (bottom), the sulfur atom of an inverted molecule was lowered with its terminal methyl group raised simultaneously. The majority (70%) of the inverted molecules followed the simultaneous flip mechanism. The molecular flip events were facilitated by partial melting of the SAM line in heating. On the other hand, it is unclear if any flip event is possible without the help of thermal annealing. To address this, the activation energy required for the molecular flip at room temperature was estimated by constructing the free energy profile. Depending on whether the flip is sequential or simultaneous, the free energy (PMF) was calculated by varying the height of the methyl tail group ω and sulfur atom ξ separately and sequentially or simultaneously (Figures S1 and S2). As the first step of a sequential flip event requires lowering of the sulfur atom of an inverted molecule without moving its methyl tail group, the PMF was calculated by decreasing ξ only, as displayed in the top of Figure S1. As ξ decreased from 23.0 to 4.0 Å, the PMF increased, reaching a maximum with a height of 33.0 kBT at ξ = 10 Å, followed by a decrease. In the second step, the methyl tail group was raised above the surface by tethering the sulfur atom to the surface (by fixing ξ = 4.0 Å). The PMF was then plotted by increasing ω only. With increasing ω from 4.0 to 23.0 Å, the PMF increased to another maximum of 14.4 kBT at ω = 16.8 Å, followed by a decrease (bottom, Figure S1). On the other hand, for the simultaneous flip event, the PMF was calculated by decreasing ξ and increasing ω simultaneously. The PMF surface was plotted as a function of both ξ and ω, by decreasing ξ from 23.0 to 4.0 Å and increasing ω from 4.0 to 23.0 Å, as shown in Figure S2. Only the diagonal portion of the PMF surface was calculated because ξ and ω vary simultaneously in the opposite direction. The PMF increased and reached a maximum of 30.2 15511
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Figure 4. Domain boundaries (highlighted as red ellipses) in the linear SAMs when using the annealing rates 4 (16.7 K/ns) (a) and 2 (8.3 K/ns) (b) times faster than the default one. The snapshots and projected tilt direction vectors, v⃗is, are shown.
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kBT at (ξ, ω) = (14.9 Å, 13.2 Å), followed by a decrease. A sequential flip event corresponds to an off-diagonal path in the two-dimensional plot of the PMF surface in Figure S2. In principle, the PMF for other off-diagonal paths can be calculated as well. Qualitatively, any off-diagonal path will face at least one local maximum in the free energy due to the activation energy required for any flip event. As seen above, however, an off-diagonal path, except the path for the sequential flip, was not observed in the present thermal annealing of the nanoscale SAM lines. In summary, the activation energies derived from the barriers of the PMF curves or surface were at least 14 times the thermal energy. Therefore, flip events are not feasible without thermal annealing. The linear SAMs were checked by annealing 2 and 4 times faster than above (the default annealing rate was 4.2 K/ns). The resulting SAMs had the domain boundaries, where alkyl chains with almost opposite tilt directions confront each other (Figure 4). These domain boundary defects37 were reported in bulk SAMs, but to the best of the authors’ knowledge, there are no reports of these in nanoscale SAMs. The structural parameters, dss, θ, percentage of trans conformations, and Ou (Table S1), indicate that the structural order in the linear SAM increases with decreasing annealing rate. Therefore, typical experimental annealing, which is much slower than the present simulated annealing, is expected to yield a highly ordered linear SAM without any domain boundaries. Above, a linear SAM was simulated with a finite length and a length-to-width aspect ratio of 3.4. Sometimes, linear SAMs with high aspect ratios are constructed experimentally. In this regard, infinitely long SAM lines were simulated by applying the periodic boundary conditions at the both ends of the SAM lines. The same percentage of inverted molecules (7.8%) found in the SAM line with a finite length was introduced. The positions of the inverted molecules in the linear SAM were chosen randomly. The SAMs were simulated with four different line widths. As in the linear SAM with a finite length, thermal annealing healed all the inverted molecules, resulting in a dense and ordered SAM structure. Regardless of the line width, the structural parameters of the infinite SAM lines were close to the corresponding values of an ordered SAM in the bulk (Table S2). On the other hand, linear SAMs less than 4.5 nm in width had a nonuniform width after annealing (Figure S3). The previous MD simulation showed that the linear SAM eventually becomes disconnected when the line width is less than 1.7 nm.38
CONCLUSIONS A linear nanoscale SAM grown by contact printing contains a significant amount of unbound molecules, which are inverted among the upright molecules. Thermal annealing triggered partial melting of the linear SAM, which in turn enabled the inverted molecules to flip. The activation energies for the flip events of inverted molecules were too high (>14 times thermal energy) without annealing. Therefore, this paper proposes thermal annealing as an efficient way to heal the nanometerwide line of SAM containing inverted molecules.
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ASSOCIATED CONTENT
* Supporting Information S
The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcc.6b05078. Free energy profiles for the sequential (Figure S1) and simultaneous (Figure S2) flip events; thermal annealing of the infinitely long SAM lines with different line widths (Figure S3); schematics of the molecular orientation of ODT (Figure S4); structural parameters of the linear SAM, the bulk SAM, and the linear SAMs annealed 2 and 4 times faster (Table S1); structural parameters of the infinitely long SAM lines with four different line widths (Table S2) (PDF)
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]; Tel: +82-51-510-7348 (J.J.). Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (NRF2015R1A2A2A01004208 and NRF-2014R1A4A1001690).
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