Thermal Healing of a Mixed-Thiol Monolayer at the Nanoscale - The

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Thermal Healing of a Mixed-Thiol Monolayer at the Nanoscale Zhengqing Zhang, Manho Lim, Yoonho Ahn, and Joonkyung Jang J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b03012 • Publication Date (Web): 17 May 2018 Downloaded from http://pubs.acs.org on May 17, 2018

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The Journal of Physical Chemistry

Zhang et al. Page 1

Thermal Healing of a Mixed-Thiol Monolayer at the Nanoscale Zhengqing Zhang,1 Manho Lim,2 Yoonho Ahn3,* and Joonkyung Jang1,* 1

Department of Nanoenergy Engineering and 2Department of Chemistry, Pusan National

University, Busan 46241, Republic of Korea 3

School of Liberal Arts, Korea University of Technology and Education, Cheonan 31253,

Republic of Korea *Corresponding authors. E-mail: [email protected], [email protected]

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Zhang et al. Page 2

ABSTRACT

Using molecular dynamics simulation, we study the thermal healing of a mixed-thiol monolayer grown by contact printing. By simulating the monolayers with various compositions of octadecanethiol and decanethiol molecules, we show that a mixed-thiol monolayer grown by contact printing contains a significant portion of unbound molecules which fail to bind their sulfur atoms to the underlying gold surface. A subsequent thermal annealing (300-370K) however removes the unbound thiol molecules and gives an ordered and compact monolayer. We uncover the molecular pathways behind the removal of the unbound molecules during the thermal annealing.

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Zhang et al. Page 3 INTRODUCTION

Alkanethiol molecules spontaneously form a monolayer on a gold surface, because the sulfur atoms chemisorbs to the surface and the alkyl chains pack and align together through the van der Waals forces. Such a thiol monolayer is therefore ordered, thermally stable, and compact in molecular packing. Owing to these structural features, a thiol monolayer is now extensively used for modification, functionalization, or protection of a surface. The applications of a thiol monolayer are diverse, including catalysis,1 control of a surface wettability,2,3 corrosion resistance,4 molecular recognition5,6 and organic electronics.7,8 More recently, a mixed-thiol monolayer containing molecules with different lengths or functional groups are used as well. Such a mixed-thiol monolayer is used for selective immobilization of proteins and cells,9-12 fabrication of biosensor,13,14 multifunctional switching for killing bacteria,15 and thermal transport in a molecular junction,7 just to name a few. Presently, the fundamental properties of thiol monolayers are well known. Various experimental and theoretical studies elucidate the molecular orientation,16-20 adsorption kinetics,21-23 thermal stabilities,3,24,25 alkyl chain length effects,20,26-28 packing structures,29-31 defects,17,30-32 and phase transitions.29,33 Relatively less studied however are the properties of the thiol-monolayers with nanometer sizes. Such a nanoscale monolayer is typically grown by contact with a nanoscale tip or a stamp coated with thiol molecules.12,34 This contact printing however gives rise to a monolayer containing a significant portion of unbound molecules which fail to bind their sulfur atoms to the underlying surface.17,32 For example, a nm-sized monolayer of 1-octadecanethiol (ODT) contains up to 20 % of unbound molecules when grown by contact printing.17 The unbound molecules arise from the tumbling and diffusion of molecules during the contact printing. Two types of unbound thiol molecules are found: first, an unbound molecule 3 ACS Paragon Plus Environment


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Zhang et al. Page 4 can be piled on top of the monolayer through a van der Waals interaction. Or, an unbound molecule is inverted with its methyl tail group, instead of its sulfur atom, touching the substrate. Obviously, the unbound molecules undermine the stability and order and therefore applications of thiol monolayers. Previously, we have shown that the unbound molecules can be efficiently removed by a mild (300-400 K) thermal annealing. In the annealing, a thiol monolayer partially melts due to heating, so that the unbound molecules piled on top of the monolayer penetrates down to contact the surface, and the inverted molecules flip to achieve upright adsorption. With subsequent cooling, the packing of sulfur atoms and the alignment of alkyl chains of the monolayer are recovered. A mixed thiol monolayer with a nanoscale size can be grown by contact printing. Such a mixed-thiol monolayer is expected to contain unbound thiol molecules, just as a monolayer of a single chemical species. The rising question is whether and how thermal annealing cures the unbound molecules. Herein, we study the growth and subsequent thermal annealing (300-370K) of a mixed-thiol monolayer of 1-octadecanethiol (C18H37SH, ODT) and 1-decanethiol (C10H21SH, DT) molecules. By performing molecular dynamics (MD) simulation for various compositions of ODT and DT, we show the annealing indeed cures the unbound molecules in a mixed-thiol monolayer grown by contact printing. We uncover the molecular pathways in removing the unbound molecules via thermal annealing. Moreover, we investigate how the thermal annealing is affected by the composition of the mixed-thiol monolayer.

MOLECULAR DYNAMICS SIMULATION METHODS We treat the CH3, CH2, and SH groups of both ODT and DT molecules as united atoms,35,36 in order to save simulation time without losing the accuracy of an all-atom simulation.37,38 The 4 ACS Paragon Plus Environment

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Zhang et al. Page 5 orientation of each molecule is calculated by selecting the even-numbered carbon atoms (see

r th Figure 1 for the numbering). The tilt direction vector of the i molecule, u i , is defined as the th average of the vectors from the S atom to these selected carbon atoms. The tilt angle of the i

r molecule, θ i , is given by the polar angle of u i measured from the surface normal. The order parameter of the molecular orientation is defined as39 r r Ou = 0 .5[( u i ⋅ u j ) 2 − 1]

where

i≠ j

i≠ j

,

represents the average over all the intermolecular pairs.

We model the bond stretching and bending angle interactions between atoms as the harmonic potentials.40 The four-atom torsion potential (C−C−C−C or C−C−C−S) is taken to be a triple cosine function of the dihedral angle.41 We model the non-bonded interactions between united atoms by using the Lennard-Jones potential,36,42 All the potential parameters are taken from our previous work.16,17,32,43 We run a series of constant number, volume, and temperature (NVT) MD simulations using the Berendsen thermostat.44 We integrate the equation of motion by using the velocity Verlet algorithm with a time step of 1.0 fs. We apply the periodic boundary conditions in the direction parallel to the gold surface made of two rigid layers (12800 gold atoms). As the initial condition of MD simulation, we prepare a droplet of a mixture of ODT and DT molecules using the PACKMOL package.45 The droplet is equilibrated by running an NVT simulation at 300 K for 1.0 ns. The equilibrated droplet is placed 1.1 nm above the gold (111) surface. We further run an MD simulation for 60 ns to grow a mixed-thiol monolayer (see Figure 2 for example). The resulting monolayer has unbound thiol molecules which fail to bind their sulfur atoms to the gold surface. We simulate the subsequent thermal annealing by heating (from 300 to 370 K) and



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Zhang et al. Page 6 cooling (back to 300 K) the mixed-thiol monolayer. We increase or decrease temperature by 10 K and run a10ns- long MD simulation at each temperature. Therefore, the heating and cooling rates are identically set to 0.9 K/ns. We simulate the mixed-thiol monolayers having the mole fractions of ODT xODT s of 0.125, 0.375, 0.500, 0.625, and 0.875. We use the DLPOLY package to implement the MD simulation methods described above.

RESULTS AND DISCUSSION We investigate the growth of a mixed-thiol monolayer by spreading a droplet over the gold surface. As shown in Figure 2, a mixed-thiol droplet spreads over the gold surface and forms a circular monolayer at the nanoscale (Figure 2). Owing to the tumbling and diffusion of molecules, the resulting monolayer contains a significant portion of unbound thiol molecules (4.25% of total molecules in this case). The unbound molecules are either sitting on top of the monolayer or standing up with their methyl groups, instead of sulfur atoms, contacting the surface. The unbound molecules of the latter type are called inverted molecules and are found among both ODT and DT molecules. By contrast, the former type is found for ODT molecules only. This presumably arises from the fact that the DT molecules, having relatively short alkyl chains, move quickly on top of the monolayer to reach the periphery and slide down to the bare surface.17,46,47 We study the time variations of the structural parameters of a mixed-thiol monolayer grown by contact printing. As shown in Figure 3a, the average tilt angle of alkyl chain, θ , decreases with time from 90° (corresponding to a random orientation) to a smaller value after 20 ns. The converged θ increases from 27.8 to 43.1 ° with increasing xODT . The converged θ for


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xODT = 0.875 (=43.1°) is close to that found for a monolayer of ODT.43 The previous simulation using the same model as in the present work16 reports that a tilt angle of the bulk DT monolayer is 24°, agreeing with the experimental values (20-30°).48 With increasing xODT , the overall length of the thiol molecules in the monolayer increases, and the average tilt angle also increases as shown in Figure 3a. This trend accords with the previous studies.20,49 Figure 3b shows the portion of the trans conformations of alkyl chains vs. time. The percentage of trans conformation increases with time, leveling off after 20ns to 93.1%, 91.1%, 93.1%, 91.8%, and 93.5%, respectively, for xODT = 0.125 , 0.375, 0.5, 0.625 to 0.875. These percentages manifest the stabilities of the mixed-thiol monolayers but are slightly lower than found for a monolayer of ODT (96%). Figure 3c shows the order parameter of molecular orientation, Ou , vs. time. With increasing time, Ou increases from zero and converges to 0.78, 0.77, 0.77, 0.72, and 0.68 for

xODT = 0.125 , 0.375, 0.5, 0.625, and 0.875, respectively. This indicates a substantial ordering in the molecular orientation in the monolayer, regardless of the composition. We study the subsequent thermal annealing (300-370 K) of the mixed-thiol monolayers. As shown in Figure 4, upon heating from 300 to 370 K, the mixed-thiol monolayer with

xODT = 0.125 slightly disperses without desorption of any molecule: the monolayer expands laterally, and the sulfur atoms, which are initially closely packed, disperse slightly. At the same time, the alkyl chains become curly and disordered. At 340 K, all of the unbound molecules that piled on top of the monolayer move down and directly contact the surface, either upright or inverted. When temperature reaches 370 K, all of the inverted molecules flip to stand upright. Upon subsequent cooling to 300 K, the monolayer recovers the compact packing of sulfur atoms. Moreover, the alkyl chains straighten and align with each other, resulting in an ordered and 7 ACS Paragon Plus Environment


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Zhang et al. Page 8 compact monolayer. The pinholes remain in the final monolayer however, due to three ODT molecules with their alkyl chains folded. The pinholes arising from the folded alkyl chains are reported for the bulk thiol monolayers as well.31,47,50 The present annealing is determined by the interplay between the intermolecular cohesion and molecule-surface interaction. Therefore, the dynamics of annealing depends on the composition of the mixed-thiol monolayer. As shown in Figure S1, with a high fraction of ODT molecules ( xODT = 0.875 ), the monolayer melts only at its periphery with heating to 370 K, due to the increased intermolecular cohesion between ODT molecules. Consequently, a substantial portion of inverted ODT molecules remains after the annealing. We point out that the present simulated annealing is done much faster than in experiment, owing to the limited timescale of MD simulation. The previous experiments show that a reduced annealing rate decreases the number of unbound thiol molecules in the bulk thiol monolayers.51 Presumably, an experimental annealing obviates the pinholes and therefore gives a more ordered monolayer. We observe three pathways in the adsorption of an unbound molecule in the annealing: in the first, an unbound molecule piled on top of the monolayer migrates to the periphery and hops down to the bare gold surface. In the second, a molecule on top of the monolayer pushes away the molecules below it and contacts the surface. In the third, the sulfur atom of an inverted molecule pushes its way down to the surface and adsorbs to the surface while raising its methyl tail group. These pathways are in agreement with those found for a nanoscale monolayer of ODT.17 In addition to the pathways above, we find two new pathways in the present annealing. In the first pathway (Figure 5a), an inverted ODT molecule, surrounded by other molecules, rises to the


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Zhang et al. Page 9 top of the monolayer. The same molecule later moves on top of the monolayer and reaches the periphery. The molecule finally hops down and adsorbs to the bare surface. In the other pathway shown in Figure 5b, an inverted ODT molecule rises to the top of the monolayer. Later, the ODT molecule pushes away molecules below it and penetrates down into the monolayer. The sulfur atom of the ODT molecule eventually contacts the gold surface to be adsorbed. These two pathways are also found for inverted DT molecules (Figure S2). In these new pathways, an inverted ODT or DT molecule, upon reaching the top of the monolayer, randomly moves for 0.06 to 1.19 ns (an ODT molecule spends more time than a DT molecule does) before it finally adsorbs to the surface. These pathways for ODT molecules are found at temperature higher than that found for DT molecules (Figure 5 and Figure S2), due to the enhanced cohesion between ODT molecules. The two-step healing processes shown in Figure 5 are quite different from those previously found for healing of inverted molecules (where inverted molecules only flip to adsorb). Figure 6 illustrates the monolayers after annealing for five different compositions. Regardless of composition, the mixed-thiol monolayer improves its order and compactness with the annealing. One can see that the unbound molecules on top of the monolayers are completely removed after annealing. There exist however inverted molecules in the monolayers, especially for the highest xODT . Unlike for the bulk counterpart,52-54 a pronounced segregation into two domains with long (ODT) and short (DT) thiol molecules are not seen for the present monolayers at the nanoscale. Figure 7 shows the percentage of the defects in the mixed-thiol monolayer vs. xODT . Here the defects include both unbound molecules and the molecules giving the pinholes in the monolayers. With or without annealing, the defects increase in portion with rising xODT . Before 9 ACS Paragon Plus Environment


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Zhang et al. Page 10 annealing, the percentage of defects increases from 4.25 to 21.25% by rising xODT . This can be attributed to the fact that ODT molecules, bigger than DT molecules, are slower in binding their sulfur atoms in the growth of the monolayer by contact printing. Therefore, ODT molecules tend to be kinetically trapped to become inverted, piled on top of the monolayer, or folded. With the annealing however, the defects almost vanish, constituting less than 5 %. The increased defects for the highest xODT originates from the fact that the ODT molecules are more cohesive than DT molecules. Consequently, an annealing slightly disturbs the mixed-thiol monolayer (the highest temperature is 370 K). Such a slight melting of the monolayer cannot provide enough space for an inverted ODT molecule to tumble and for an ODT molecule on top of the monolayer to squeeze down into the monolayer and contact the bare surface. By varying the composition xODT , we quantitatively study the effects of annealing on the structural parameters of the mixed-thiol monolayers (Figure 8). The average tilt angle of alkyl chain, θ , is plotted vs. xODT in Figure 8a. θ increases with increasing xODT from 0.125 to 0.875, regardless of the presence of thermal annealing. Upon thermal annealing, θ decreases by 3.3~11.4°depending on the composition. The θ values after annealing range from 23.0 to 31.7° which are close to those found for the monolayers of single chemical species (20~30°).48 Figure 8b shows the percentage of trans conformations of alkyl chains for various xODT s. Overall, the trans conformation increases in percentage by 0.6-2.6 % with the annealing, ranging from 92.0 to 95.8%. Figure 8c presents the order parameter of molecular orientation, Ou , vs. xODT . Regardless of the composition, the annealing increases Ou , signifying the enhanced order in the molecular orientation. Overall, the molecular orientation is more ordered with increasing the mole fraction of ODT. These results quantitatively illustrate the enhanced stability and orientatioal order of a 10 ACS Paragon Plus Environment

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Zhang et al. Page 11 mixed-thiol monolayer with the help of thermal annealing, regardless of the composition of the monolayer.

CONCLUSION We investigate the structural and thermal properties of a monolayer in which ODT and DT molecules are mixed together. We observe such a mixed-thiol monolayer grown by contact printing has a significant amount of unbound thiol molecules. A subsequent thermal annealing efficiently removes the unbound thiol molecules, giving an ordered and compact monolayer. We uncover the molecular pathways in the thermal healing of the mixed-thiol monolayer. At the outset, it is not clear how thermal annealing works out for the present monolayers with various compositions of ODT and DT molecules. Indeed, thermal annealing gives a nearly defect-free monolayer if it is mainly composed of short DT molecules, but a substantial portion of inverted ODT molecules exists for the monolayers with high fractions of ODT molecules. The quantitative variation in the structural parameters of the monolayers with varying composition is another novel insight provided by this work. In short, the present results provide molecular insights for improving the quality of a mixed-thiol at the nanoscale.

ASSOCIATED CONTENT Supporting Information Thermal annealing of the mixed-thiol monolayer with xODT = 0.875 (Figure S1). Molecular pathways for the adsorption of an inverted DT molecule (Figure S2). The Supporting Information is available free of charge on the ACS Publications website at DOI:xxxxx.



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Zhang et al. Page 12 AUTHOR INFORMATION Corresponding author *E-mail:[email protected], Tel.: +82-51-510-3928 Notes The authors declare no competing financial interests ACKNOWLEDGMENTS This study was supported by National Research Foundation Grants funded by the Korean Government (MSIP, NRF-2014R1A4A1001690 and NRF-2015R1A2A2A01004208).

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Zhang et al. Page 20

th

Figure 1. Molecular orientation of the i molecule (ODT or DT). By selecting even-numbered

r carbon atoms, excluding three methyl groups at the tail, we define the tilt direction vector u i as the average of the direction vectors from the S atom to these selected carbon atoms. The tilt

r angle, θ i , is the polar angle of u i measured from the surface normal (Z direction).


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Figure 2. Contact printing of a mixed-thiol monolayer. (a) A spherical droplet of mixed thiol molecules initially placed 1.1 nm above a gold (111) surface. (b) Droplet contacting the surface after 40 ps. (c) A hemispherical droplet and (d) the monolayer formed after 1.0 and 60ns, respectively. The droplet is made of 50 ODT and 350 DT molecules ( xODT =0.125). The alkyl chains (sulfur atoms) of ODT and DT are drawn in cyan (yellow) and red (blue), respectively. Gold atoms are drawn as dots.



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Figure 3. Structural parameters vs. time for the mixed-thiol monolayers with different xODT s. Drawn are the time variations of the (a) tilt angle θ , (b) percentage of trans conformations, %trans , and (c) the order parameter of the tilt direction of the alkyl chain, Ou .


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Figure 4. Thermal annealing of a mixed-thiol monolayer (clockwise starting from the upper left). Shown in each panel are the snapshot of the monolayer and the sulfur atoms of the monolayer with xODT = 0.125 .The alkyl chains of ODT and DT molecules are drawn in cyan and red, respectively. The sulfur atoms of ODT and DT molecules appear in yellow and blue, respectively. Both the heating and cooling rates are 0.9 K/ns. The gold (111) surface is drawn as dots.



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Figure 5. Two pathways for the thermal healing of an inverted ODT molecule in a mixed-thiol monolayer. An inverted molecule, sandwiched among upright molecules, crawls up to the top of the monolayer. After that, the molecule either moves to the periphery and hops down to the bare surface (a) or pushes its way down to the surface (b). The first (a) and second (b) pathways are observed at 360 K ( xODT = 0.125 ) and 370 K ( xODT = 0.5 ), respectively.


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Figure 6. Snapshots of the mixed-thiol monolayers with various xODT s during thermal annealing. Each panel shows top and side views of the mixed-thiol monolayers at 370 K for (a)

xODT = 0.125 , (b) xODT = 0.375 , (c) xODT = 0.500 , (d) xODT = 0.625 , and (e) xODT = 0.875 . The gold (111) surface is drawn as dots. 25 ACS Paragon Plus Environment


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Figure 7. Percentage of defect molecules as a function of xODT . Plotted are the percentages of defect molecules with and without thermal annealing at 300 K (final snapshot). The defects include the molecules piled on the top of the monolayers, inverted molecules, and unfolded molecules.


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Figure 8. Structural parameters of the mixed-thiol monolayers with various xODT s. Plotted are the average tilt angles of alkyl chains θ s (a), the percentages of trans conformations % trans (b), and the orientational order parameters Ous. The results with and without the annealing are shown together. Shown as error bars are the standard deviations.



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Thermal Healing of a Mixed-Thiol Monolayer at the Nanoscale - The

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