Molecular Dynamic Simulations of Self-Assembled Alkylthiolate

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Molecular Dynamic Simulations of Self-Assembled Alkylthiolate Monolayers on an Au(111) Surface Beena Rai,† Sathish P.,† Chetan P. Malhotra,† Pradip,*,† and K. G. Ayappa‡ Tata Research Development and Design Centre, 54B, Hadapsar Industrial Estate, Pune 411013, India, and Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India Received September 15, 2003. In Final Form: January 26, 2004 Molecular dynamics simulations incorporating explicit gold atoms in the simulations have been carried out for alkanethiol self-assembled monolayers chemisorbed on the Au(111) surface. The structural properties of the monolayer are evaluated for two force fields: one in which the Au-S-C bond is fixed (FF I), and the other in which it is flexible (FF II). The influence of these force fields on the structural properties of HS(CH2)14CH3 on the structured Au surface is compared at different temperatures. FF I yields greater tilt angles and a smaller film thickness when compared with FF II. Both of the force fields predict that the tilt angles do not follow a monotonic decrease with temperature but show minima around 200 K. Simulations carried out at different chain lengths at 300 K reveal that FF II predicts a greater film thickness than FF I; however, the difference is within 1 Å.

Introduction Self-assembled monolayers (SAMs) have been a focus of research for a decade or so because of their potential use in technological applications.1 Some of these areas are adhesion promotion/resistance,2,3 novel biomaterials,4-7 corrosion resistance,8,9 lithographic patterning,10,11 and microelectronics.12,13 The most well studied SAMs are those prepared by the adsorption of alkanethiols on gold.14-17 When adsorbed from the solution onto the Au(111) surface, alkanethiols form well-ordered monolayers possessing a (x3 × x3)R30° structure, wherein the sulfur atoms are bound to the 3-fold hollow sites of the Au(111) surface.18,19 The thermal stability and structural properties of SAMs are governed by both the substrate-thiol interactions and chain-chain interactions in the chemisorbed layer. Al* Author to whom correspondence should be addressed. Email: [email protected]. † Tata Research Development and Design Centre. ‡ Indian Institute of Science. (1) Whitesides, G. M. Sci. Am. 1995, 9, 146. (2) Lopez, G. P.; Albers, M. W.; Schreiber, S. L.; Caroll, R.; Peralta, E.; Whitesides, G. M. J. Am. Chem. Soc. 1993, 115, 5877. (3) Wasserman, S. R.; Biebuyck, H. A.; Whitesides, G. M. J. Mater. Res. 1989, 4, 886. (4) Prime, K. L.; Whitesides, G. M. Science 1991, 252, 1164. (5) Singhvi, R.; Kumar, A.; Lopez, G. P.; Stephanopoulos, G. N.; Wang, D. I. C.; Whitesides, G. M.; Inber, D. E. Science 1994, 264, 696. (6) DiMilla, P. A.; Folkers, J. P.; Biebuyck, H. A.; Harter, R.; Lopez, G. P.; Whitesides, G. M. J. Am. Chem. Soc. 1994, 116, 2225. (7) Deng, L.; Mrksich, M.; Whitesides, G. M. J. Am. Chem. Soc. 1996, 118, 5136. (8) Jennings, G. K.; Laibinis, P. E. J. Am. Chem. Soc. 1997, 119, 5208. (9) Zamborini, F. P.; Campbell, J. K.; Crooks, R. M. Langmuir 1998, 14, 640. (10) Calvert, J. M. J. Vac. Sci. Technol., B 1993, 11, 2155. (11) Kumar, A.; Whitesides, G. M. Science 1994, 263, 60. (12) Xia, Y.; Zhao, X.-M.; Whitesides, G. M. Microelectron. Eng. 1996, 32, 255. (13) Huang, Z.; Wang, P.-C.; MacDiarmid, A. G.; Xia, Y.; Whitesides, G. M. Langmuir 1997, 13, 6480. (14) Ulman, A. An Introduction to Ultrathin Organic Films; Academic: Boston, MA, 1991. (15) Bain, C. D.; Whitesides, G. M. Angew. Chem., Int. Ed. 1989, 28, 506. (16) Dubois, L. H.; Nuzzo, R. G. Annu. Rev. Phys. Chem. 1992, 43, 437. (17) Ulman, A. Chem. Rev. 1996, 96, 1533.

kanethiols bind to the 3-fold hollow site of the gold atoms to maximize the gold-sulfur interactions, and chains tilt to ∼30° to maximize the chain-chain interactions.20,21 The structural features of these SAMs have been studied in detail by several experimental techniques such as optical ellipsometry,22 IR spectroscopy,22-25 X-ray diffraction,26-28 electron diffraction,29,30 electrochemistry,22,31 He diffraction,18,28 and scanning tunneling microscopy.32 These experimental studies reveal that the ordered or crystalline nature of the SAMs is a function of the temperature and chain length. At room temperature, SAMs with longer chain lengths prefer next-nearestneighbor (NNN) tilt conformation as compared to shorter chains, which show no preferred tilt direction. Below 300 K, the chains undergo a bulk-phase transformation from one ordered phase (nearest-neighbor (NN) tilt) to another ordered phase (NNN tilt). At higher temperatures, the chains gradually untilt and form a disordered liquidlike phase (melting of the chains). The melting temperature is chain-length-dependent and ranges from 325 to 350 K. (18) Chidsey, C. E. D.; Liu, G.-Y.; Rowntree, P.; Scoles, G. J. Chem. Phys. 1989, 91, 4421. (19) Widrig, C. A.; Alves, C. A.; Porter, M. D. J. Am. Chem. Soc. 1991, 113, 2805. (20) Laibinis, P. E.; Whitesides, G. M.; Allara, D. L.; Tao. Y.-T.; Parikh. A. N.; Nuzzo, R. G. J. Am. Chem. Soc. 1991, 113, 7152. (21) Jaschke, M.; Scho¨nherr, H.; Wolf, H.; Butt, H.-J.; Bamberg, E.; Besocke, M. K.; Ringsdorf, H. J. Phys. Chem. 1996, 100, 2290. (22) Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359. (23) Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93, 767. (24) Bensebaa, F.; Ellis, T. H.; Badia, A.; Lennox, R. B. J. Vac. Sci. Technol., A 1995, 13, 1331. (25) Bensebaa, F.; Ellis, T. H.; Badia, A.; Lennox, R. B. Langmuir 1998, 14, 2361. (26) Samant, M. G.; Charles, A. B.; Gordon, J. G., II Langmuir 1991, 7 (3), 437. (27) Fenter, P.; Eisenberger, P.; Liang, K. S. Phys. Rev. Lett. 1993, 70, 2447. (28) Camillone, N., III; Chidsey, C. E. D.; Fenter, P.; Li, J.; Liang, K. S.; Liu, G.-Y.; Scoles, G. J. Chem. Phys. 1993, 99 (1), 744. (29) Strong, L.; Whitesides, G. M. Langmuir 1988, 4, 546. (30) Dubois, L. H.; Zegarski, B. R.; Nuzzo, R. G. J. Chem. Phys. 1993, 98 (1), 678. (31) Badia, A.; Back, R.; Lennox, R. B. Angew. Chem., Int. Ed. Engl. 1994, 33, 2332. (32) Noh, J.; Hara, M. Langmuir 2001, 17, 7280.

10.1021/la0357256 CCC: $27.50 © 2004 American Chemical Society Published on Web 03/12/2004

Self-Assembled Alkylthiolate Monolayers

Besides several experimental studies, the molecular simulations, namely, Monte Carlo and molecular dynamics (MD), have also been applied as complementary theoretical techniques for studying the structural and dynamical properties of adsorbed SAMs on the Au(111) surface.33-42 In most of these simulations, the gold surface is considered as a flat rigid substrate with the sulfur atoms effectively constrained in the (x3 × x3)R30° positions. The alkanethiol chains are considered rigid or semiflexible (C-C bonds are always constrained). Both the united-atom33-37,40 and all-atom models34,38,39 are used to model the methyl and methylene groups in the alkanethiols. In all of the above molecular simulation studies, the gold substrate is considered structureless and the interactions between the alkanethiol and the substrate are treated using a 12-3 potential, which is only a function of the normal distance of the atom from the substrate. Models that include the gold atoms explicitly in the simulation attempt to provide a more realistic description in the region of the sulfur headgroups. A more detailed description of the substrate39,40,43,44 is expected to be important while attempting to elucidate the possible low-temperature packing arrangement that can exist in SAMs. The differences between the low-temperature structures, which all correspond to the underlying hexagonal (x3 × x3)R30° lattice, arise from one, two, and four chains per unit cell.44 These differences result from the different relative orientation of the hydrocarbon backbones. The force fields used for molecular simulations are able to capture much of the observed experimental trends for alkanethiols on gold and, with perhaps the exception of the low-temperature phases, have proven to be very successful in illustrating the interplay between the various interactions that lead to the melting of SAMs. The first MD study that investigates the influence of the Au-S-C bond on the properties of the SAMs was by Hautman and Klein.33 In this study, the model studies were carried out with the Au-S-C bond left unconstrained and with the bond constrained at an angle of 100°. The study revealed that the differences between the two models were small, with the main difference in the reorientational relaxation. The model that kept the Au-S-C bond free was found to have a relaxation time similar to that observed for bulk alkanes, and when the bond was kept fixed, the relaxation time was significantly slower. We note that the early study by Mar and Klein38 was carried out on a smooth substrate, and it is reasonable to expect that the differences in the structural and dynamic properties observed for both of the models of the Au-S-C bond would be influenced by the corrugation of the gold substrate. In subsequent molecular simulations with the exception of the Pertsin and Grunze study,39 the Au-S-C bond has always been left free. With the motivation to develop a more accurate description of the chemisorbed species in the Au-S region for alkanethiols on gold, ab initio quantum chemical (33) Hautman, J.; Klein, M. L. J. Chem. Phys. 1989, 91 (8), 4994. (34) Bareman, J. P.; Klein, M. L. J. Chem. Phys. 1990, 94, 5202. (35) Hautman, J.; Klein, M. L. J. Chem. Phys. 1990, 93 (10), 7483. (36) Klein, M. L.; Mar, W.; Bareman, J. P.; Hautman, J. J. Chem. Soc., Faraday Trans. 1991, 87 (13), 2031. (37) Siepmann, J. I.; McDonald, I. R. Mol. Phys. 1993, 79 (3), 457. (38) Klein, M. L.; Mar, W. Langmuir 1994, 10, 188. (39) Pertsin, J. A.; Grunze, M. Langmuir 1994, 10, 3668. (40) Garrison, B. J.; Bhatia, R. Langmuir 1997, 13, 765. (41) Jung, H. H.; Won, Y. D.; Shin, S.; Kim, K. Langmuir 1999, 15, 1147. (42) Pertsin, J. A.; Grunze, M. Langmuir 2000, 16, 8829. (43) Bhatia, R.; Garrison, B. J. Langmuir 1997, 13, 4038. (44) Zhang, L.; Goddard, W. A., III; Jiang S. J. Chem. Phys. 2002, 117, 7342.

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calculations have been carried out for small thiol molecules on gold. The studies focus on determining the nature of the adsorption site, the Au-S and Au-S-C bond angles. Density functional calculations45 with methylthiolate [CH3-S] molecules on the Au(111) surface reveal that the S-C bond is tilted at an angle to the surface normal of the gold surface at around 43.2° with the sulfur atom position in a bridged-face-centered cubic (fcc) site and not directly above the fcc site on the Au(111) surface. The Au-S-C angle was found to lie between 108° and 116°. This geometric picture was found to be true for longer chains [CH3(CH2)2-S] as well. On the other hand, the ab initio quantum chemical calculations with the CH3-S molecule indicate that the 3-fold fcc site is preferred over the other sites. However, both of the models are able to capture the experimentally observed four chains per unit cell structures. The directional nature of the S-Au bond and its influence on the Au-S-C bond angle have been verified by the ab initio calculations,46,47 which reveal that the Au-S-C angle for CH3-S on both the gold clusters and the Au(111) surface lies in the range of 108-116°. These ab initio studies indicate that developing a force field with a fixed Au-S-C angle might provide a more accurate description for the interaction of alkanethiols at the gold substrate, provided the gold atoms are treated explicitly. In this paper, we focus on the nature of the Au-S-C bond and its influence on the structure and stability of the SAMs. We report that the MD simulations of alkanethiol SAMs on the Au(111) surface were made from five atomic layers. The S atoms in alkanethiols are covalently attached to the surface gold atoms. In one model, the Au-S-C bond is assumed to be fixed and the results are compared with the model where the Au-S-C bond is left unrestrained. Our study reveals that the explicit representation of the gold atoms introduces significant structural differences between the two models. The CH3 and CH2 groups in the fully flexible alkanethiol chains are treated in the united-atom approximation. In addition, we report a study of the tilt angles, gauche defects, and other film properties as a function of the chain length. Simulation Methodology Molecular Model. A 2D periodic unit cell comprised of five atomic layers was created at the Au(111) Miller plane. The initial configuration consisted of all trans chains placed in a herringbone configuration. The area per alkanethiol chain was 21.6 Å2. The unit cell was extended in x and y directions to create a rectangular simulation box (43.26 × 51.91 Å2), periodic in the plane parallel to the surface and nonperiodic in the plane normal to the surface. The sulfur atoms in the alkanethiol chains were covalently bonded to a gold atom using a harmonic potential with an Au-S bond length of 2.4 Å, and the Au-S-C angle was fixed at 100° (FF I). This method of attachment restricts the position of the S atom to a position directly above the Au atom to which it is attached. Although the Au-S-C bond angle is slightly lower than that observed from the ab intio calculations for small chain thiols, it enables us to compare our results with those reported by Hautman and Klein.33 In addition, there is as expected some variation in the Au-S-C angle for fully covered long chain SAMs compared with the values reported from the ab initio studies on small chain segments. We compare and contrast the structural properties of SAMs using FF I, where the Au-S-C bond angle is fixed with the model, where the Au-S-C bond is unconstrained (FF II). Force Fields. The force field parameters used in this study were taken from the literature.33,49 FF I is comprised of the functional forms and parameters listed in Table 1. (45) Yourdshahyan, Y.; Rappe, A. M. J. Chem. Phys. 2002, 117, 825. (46) Majumdar, C.; Mizuseki, H.; Kawazoe, Y. J. Chem. Phys. 2003, 118, 9809. (47) Majumdar, C.; Briere, T.; Mizuseki, H.; Kawazoe, Y. J. Chem. Phys. 2002, 117, 2819.

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Table 1. FF I Functional Forms and Parametersa Bond Stretch, Ebond ) 0.5Kr (r -

r0)2

bond

r0 (Å)

Kr [kcal/(mol/Å2)]

C-C C-S Au-S

1.54 1.82 2.40

900.58 1000 1000

Angle Bend, Eangle ) 0.5Kθ (θ - θ0)2 angle

θ0 (deg)

Kθ [kcal/(mol/rad2)]

C-C-C S-C-C Au-S-C

114 114 100

124.28 124.28 124.28

Torsions, Etorsions ) 0.5a1 (1 + cos φ) + 0.5a2 (1 - cos 2φ) + 0.5a3 (1 + cos 3φ) dihedral

a1 (kcal/mol)

a2 (kcal/mol)

a3 (kcal/mol)

C-C-C-C S-C-C-C Au-S-C-C

1.411 931 8 1.411 931 8 0

-0.271 187 31 -0.271 187 31 0

3.147 029 5 3.147 029 5 0

van der Waals, Evdw ) D0 [(R0/R)12 - 2(R0/R)6], R0 ) 21/6 σ and D0 )  On-Diagonal Parameters atom C1 (CH3 group) C2 (CH2 group) S Au

D0 (kcal/mol)

R0 (Å)

0.226 685 39 0.093 458 011 0.250 547 01 0.039 000 001

4.411 275 8 4.411 275 8 3.987 440 3 3.293 000 0

Off-Diagonal Parameters (Mixing Rule: Dij ) (Di Dj)1/2 and Rij ) (Ri + Rj)/2) atoms C1-C1 C2-C2 C1-C2 C1-S C1-Au C2-S C2-Au S-Au S-S Au-Au

D0 (kcal/mol)

R0 (Å)

0.226 685 39 0.093 458 011 0.145 552 5 0.238 317 6 0.094 025 1 0.153 021 6 0.060 372 6 0.098 850 0 0.250 547 01 0.039 000 001

4.411 275 8 4.411 275 8 4.411 275 8 4.198 008 1 3.852 137 9 4.198 008 1 3.852 137 9 3.638 870 2 4.602 094 4 3.293 000 0

a FF II has all of the functional forms and parameters similar to FF I, except that the angle-bend term was absent for the AuS-C angle.

MD Conditions. We have used the molecular modeling program CERIUS2 (Accelrys Inc., San Diego, CA)48 to carry out our MD simulations. The customized force fields were created using the force field editor module in CERIUS2. Microcanonical MD simulations were performed using a time step of 3.0 fs. The temperature of the system during the equilibration was controlled by scaling the velocities in the usual fashion. A direct cutoff at 21.5 Å was used for the nonbonded van der Waal interactions. The gold atoms were kept fixed during the entire simulation. The system was allowed to equilibrate at a particular temperature for about 200 ps, and then the averages of various structural features of interest such as the tilt angle, layer density profile, and distribution of gauche defects within the monolayer were collected over the next 150 ps.

Results and Discussion Density Distributions. We shall first discuss the results for SH(CH2)14CH3(C15) SAMs. The density distributions at different temperatures of the united-atom methylene and methyl units normal to the Au surface are illustrated in Figure 1 for FF I, where the Au-S-C bond angle is restrained. Two distinct characteristics are (48) CERIUS2, version 4.0; Molecular Simulations Inc.: San Diego, CA, 2001. (49) Balasubramanian, S.; Siepmann, J. I.; Klein, M. L. J. Chem. Phys. 1997, 103, 3184.

observed for the temperatures above and below 250 K. Above 250 K, the density distributions reveal the formation of doublets corresponding to pairs of carbon atoms after the first S-C bond. If the numbering of the carbon atoms begins from the S-C bond, then the first peak of each doublet is associated with the even-numbered C atoms, which at 250 K is smaller than the second peak of the doublet, implying that there is a greater out-of-plane motion of the even-numbered C atoms at this temperature. These relative heights in the doublet persist up to 350 K, above which, the second peak in the doublet has the lower intensity. Above 350 K, there is a significant untilting of the chains (Figure 3) and peaks in the density distribution are well-defined only near the Au surface. Previous studies with this model,33 albeit on a smooth gold surface, reveal the higher degree of gauche defects in the first dihedral angle formed with the S-C-C-C unit at the base of the monolayer. The propensity to retain the energetically favored trans configuration leads to a steplike configuration of the carbon atoms and hence the formation of the doublets in the density distributions. Below around 200 K, we observe some interesting features in the density distributions. The first peak of each doublet starts to split around 200 K, where a weak shoulder appears. The splitting is clearly observed at lower temperatures of 100 and 50 K. The reason for this change in the structure below 200 K will be discussed later in the text. It is interesting to note that the normal position of the first C atom remains unchanged over the entire range of temperatures. Figure 2 illustrates the density distributions for the C15 thiol using FF II. The doublets that appeared in the density distribution for FF I are absent, and the peak intensities alternate as one moves up the chain from the substrate.33 The first peak is broad and relatively weak in intensity, indicating that the flexibility of the Au-S-C bond allows a greater out-of-plane mobility of the first carbon atom. Because this feature has not been observed on a structureless gold substrate, this effect is due to the explicit representation of the gold atoms in the Au surface. Figure 3 illustrates the tilt angles for C15 SAMs for both FF I and FF II. The tilt angles for each chain were computed as the angle formed between the surface normal and the line passing through the S atom and the centeroid of each chain. At low temperatures, the tilt angle for FF I is larger than that predicted by FF II with a difference of about 3°. The constraint on the Au-S-C bond creates a nearly parallel configuration for the S-C bond relative to the gold surface, leading to a larger tilt angle for the monolayer. As the temperature is increased, the interesting feature that is common to both of the force fields is the initial untilting of the chains until 150 K; thereafter, the chains begin to tilt once again before the thermal disorder leads to the untilting of the chains at higher temperatures. As the temperature is increased from 50 K, the tilt angle for FF I initially decreases by about 2.5°, achieving a minimum value of 27.5° between 150 and 200 K. A further increase in the temperature results in an increase in the tilt angle to 31.7° at 300 K, after which there is a continuous decrease in the tilt angle above 300 K. We note that this small decrease in the tilt angle observed between 50 and 200 K occurs around the same temperatures that the additional splitting was observed in the first peak of the doublets in the density distributions shown in Figure 1. The increased tilting around 250-300 K for FF I (Figure 3) is accompanied by a small increase in the intensities of the peaks in the density distribution (Figure 1), indicating an increased order normal to the Au substrate at these intermediate temperatures. The variation in the

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Figure 1. Density distributions of the terminal CH3 and CH2 groups in alkanethiol chains normal to the gold surface for FF I at different simulation temperatures.

tilt angle for the monolayer with FF II indicates that the tilt angles are smaller than those obtained for FF I and untilting occurs more rapidly as the temperature is raised. At 400 K, the tilt angle obtained from FF I is 24.4° and from FF II is 13.2°. For illustration, the snapshots of C15 SAMs obtained using FF I at two different temperatures, namely, 300 and 400 K, are presented in Figure 4. As can be seen in the figure as compared to 400 K, the chains are more ordered with less gauche defects at 300 K, as anticipated. We next compare the tilt angles for C15 SAMs, obtained in our study, with that reported at 300 K in the Hautman and Klein33 study. The calculated average tilt angle of the chains from the surface normal was 32.1° for FF I and 27.8° for FF II, which yield a film thickness of 20.3 and

20.9 Å, respectively. In contrast, the tilt angles predicted by Hautman and Klein,33 albeit for C16 SAMs, are 19.6° and 28.0° for the corresponding force fields on a structureless gold surface. The presence of the gold atoms creates a significant change in the tilt angles when the Au-S-C bond is constrained. Interestingly, the large difference in the tilt angles, between the two force fields, observed in the Hautman and Klein33 study was not observed in our study. The tilt angles predicted by both force fields in our study are consistent with the experimental values27,28 of 30.3 ( 0.5° and 32.0 ( 1.5°. Azimuthal Tilt Angle (χ). To rationalize the trends in the tilt angles as a function of the temperature, we calculated the azimuthal tilt angle χ of the chains.50 The angle χ is defined as the angle formed by the projection

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Figure 2. Density distributions of the terminal CH3 and CH2 groups in alkanethiol chains normal to the gold surface for FF II at different simulation temperatures.

Figure 3. Variation of the tilt angle θ for SH(CH2)14CH3 SAMs at different simulation temperatures calculated for both FF I and FF II.

on the x-y plane (substrate) of the line passing through the S atom and the centeroid of alkanethiol and the nearest-neighbor sulfur atom. The choice of the NN S atom

is chosen such that 0 < χ < 90°. If the angle is 0 or 60°, it corresponds to a NN tilt, if it is 30 or 90°, it points to a NNN tilt, and if 15, 45, or 75°, it shows a NNNN tilt. The values plotted in Figure 5 represent the plot of the averaged χ (taken for every chain over a trajectory) as a function of the temperature for both of the force fields. Though in principle there can be multiple possible azimuthal angles for the NN, NNN, and NNNN tilts, we do not observe a significant variation in the values throughout the entire simulation run of 300 ps. For example, at 100 and 300 K, for FF I, the values for χ are 59 ( 1.3° and 58 ( 2.6°, respectively. At lower temperatures, the chains adopt a NN tilt for FF I. As the temperature is raised, the χ angles drop to around 50° at 150 K and the angle increases back to the NN tilt at higher temperatures. For FF II, the situation at low temperatures is significantly different with the chains showing a NNNN tilt for temperatures below 150 K. There is a sharp change in the tilt direction at temperatures above 150 K to the more(50) McTague, J. P.; Frenkel, D.; Allen. M. P. Ordering in two Dimensions; Elsevier/North Holland: New York, 1980; p 147.

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Figure 5. Variation of the azimuthal angle χ for SH(CH2)14CH3 SAMs at different simulation temperatures calculated for both FF I and FF II.

Figure 4. Snapshots of SH(CH2)14CH3 SAMs obtained using FF I showing variation in the tilt angles and gauche defects at (a) 300 K and (b) 400 K.

favored NN direction (χ ) 60°). This change is reflected in the increase in the tilt angle for the monolayer observed in Figure 3. We also calculated χ by considering the S and the first C atoms for both FF I and FF II. At low temperatures (