none

Inspired by Poirier’s mechanism of self-assembled monolayers (SAMs) formation, we realized that observation of the change of molecular orientation relative to the surface using a suitable spectroscopic method might be able to reveal the self – assemblied processes. We mimicked the SAMs formation under UHV conditions, the Reflection Absorption Infrared Spectroscopy (RAIRS) and Temperature-Programmed Desorption / Reaction Spectrometry (TPD/R) were utilized to understand the adsorption, self-assembling and thermal stability after vapor desorption of 1H, 1H, 2H, 2H-perfluorodecanethiol on Cu(111). At 100K, the adsorption of 1H, 1H, 2H, 2H-perfluorodecanethiol was entirely molecular. As the surface was annealed above 220K, the cleavage of the S – H bonds occurred to afford chemisorbed thiolates. By comparisons of spectra to the SAMs / Au(111) and the bulk compound, forming of an orderly and densely packed monolayer on Cu(111) was inferred. Focusing on room temperature deposition experiments, We found that the increase in ratios of Iν(CF2 ∥ chain) (bands in 1300cm-1 ~ 1400 cm-1) to Iν(CF2 ⊥ chain) (bands in 1100cm-1 ~ 1300 cm-1) as a function of exposure implicates a transition from that the lying – down geometry to the more upright orientation relative to the surface as we anticipated, the phase transformation concomitant with the SAMs formation could be identified by RAIRS. By TPD/R measurements, the molecular desorption occurred at 220K and 290K, corresponding to the condensed multilayer and a physisorbed layer on top of the chemisorbed monolayer, respectively. Furthermore, the monolayer would undergo the S – C bond dissociation to sender surface – bound semifluorinated alkyl groups and sulfur atoms. The semifluorinated decene and decane were evolved above 360K as results of β – hydride elimination and hydrogen addition.

Table of Contents

1. Introduction
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
2. Experimental
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
3. Results
3.1 Low Temperature Vapor Deposition and Film Characterization by RAIRS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
3.2 Room Temperature Vapor Deposition and Film Characterization by RAIRS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
3.3 Thermal Behaviors of the Monolayer Probed by TPD/R
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
4. Discussions
4.1 Effect of Substrate Materials on Orientation of 1H, 1H, 2H, 2H-perfluorodecanethiolSAMs
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
4.2 Implication for Phase Transformation and Self-Assembly
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
4.3 Vertical (Substrate-Sulfur) Interaction and Molecular Sticking Probabilty
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
5. Conclusions
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
References
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .I



List of Figures

Figure 1. RAIR spectra of 1H, 1H, 2H, 2H-perfluorodecanethiol deposited on the Cu(111) surface at 100K with the indicated exposures.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure.2. RAIR spectra after depositing 20L multiplayer 1H, 1H, 2H, 2H- perfluorodecanethiol on the Cu(111) surface at 100K, followed by annealing the surface to various elevated temperatures.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Figure. 3. IR spectrum of bulk 1H, 1H, 2H, 2H-perfluorodecanethiol and 1H, 1H, 2H, 2H-perfluorodecanethiol SAMs on Au (111) compare with that were obtained in this experiment
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Figure 4. Schematic diagram indicating the direction of the various vibration transition dipole moments (TDM) for CF2 of 1H, 1H, 2H, 2H-perfluorodecanethiol and the (νCF2 ?? chains) / (νCF2 ⊥ chains) intensity ratios are plotted as a function of the indicated annealing temperature
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 5. RAIR spectra obtained by depositing 1H, 1H, 2H, 2H-perfluorodecanethiol at the indicated exposures on Cu (111) at 300K
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 6. The monolayer RAIR spectrum as a function of temperature
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 7. TPD/R measurements of molecular desorption monitored by CH2SH+ (m/e 47) at the indicated exposures of 1H, 1H, 2H, 2H-perfluorodecanethiol. the inset is the residual gas analysis of 1H, 1H, 2H, 2H-perfluorodecanethiol. RAIR spectra in the low frequency region (670cm-1 ~ 750 cm-1) illustrating the change of surface species before and after each desorption feature.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Figure 8. Mutiplex TPR spectra collected after dosing 4.0L 1H, 1H, 2H, 2H-perfluorodecanethiol on Cu(111) at 300K
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Figure 9. The RAIR spectra at 0.1L, 0.3L, 0.5L, 4.0L of 1H, 1H, 2H, 2H-perfluorodecanethiol deposited on Cu(111) at room temperature and followed by annealing to 380K. and schematic diagram of phase transformation
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35



List of Schemes

Scheme 1. The phase transformation in the mechanism of SAMs growth
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Scheme 2. Schematic diagram indicates the proposed orientation of individual 1H, 1H, 2H, 2H-perfluorodecanethiolate on Au (111) and Cu (111)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32



List of Table

Table 1. The assignment of vibration mode of the transition dipole moment for 1H, 1H, 2H, 2H-perfluorodecanethiol SAMs
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Table of Contents

1. Introduction
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
2. Experimental
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
3. Results
3.1 Low Temperature Vapor Deposition and Film Characterization by RAIRS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
3.2 Room Temperature Vapor Deposition and Film Characterization by RAIRS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
3.3 Thermal Behaviors of the Monolayer Probed by TPD/R
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
4. Discussions
4.1 Effect of Substrate Materials on Orientation of 1H, 1H, 2H, 2H-perfluorodecanethiolSAMs
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
4.2 Implication for Phase Transformation and Self-Assembly
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
4.3 Vertical (Substrate-Sulfur) Interaction and Molecular Sticking Probabilty
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
5. Conclusions
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
References
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .I




List of Figures

Figure 1. RAIR spectra of 1H, 1H, 2H, 2H-perfluorodecanethiol deposited on the Cu(111) surface at 100K with the indicated exposures.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure.2. RAIR spectra after depositing 20L multiplayer 1H, 1H, 2H, 2H- perfluorodecanethiol on the Cu(111) surface at 100K, followed by annealing the surface to various elevated temperatures.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Figure. 3. IR spectrum of bulk 1H, 1H, 2H, 2H-perfluorodecanethiol and 1H, 1H, 2H, 2H-perfluorodecanethiol SAMs on Au (111) compare with that were obtained in this experiment
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Figure 4. Schematic diagram indicating the direction of the various vibration transition dipole moments (TDM) for CF2 of 1H, 1H, 2H, 2H-perfluorodecanethiol and the (νCF2 ?? chains) / (νCF2 ⊥ chains) intensity ratios are plotted as a function of the indicated annealing temperature
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 5. RAIR spectra obtained by depositing 1H, 1H, 2H, 2H-perfluorodecanethiol at the indicated exposures on Cu (111) at 300K
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 6. The monolayer RAIR spectrum as a function of temperature
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 7. TPD/R measurements of molecular desorption monitored by CH2SH+ (m/e 47) at the indicated exposures of 1H, 1H, 2H, 2H-perfluorodecanethiol. the inset is the residual gas analysis of 1H, 1H, 2H, 2H-perfluorodecanethiol. RAIR spectra in the low frequency region (670cm-1 ~ 750 cm-1) illustrating the change of surface species before and after each desorption feature.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Figure 8. Mutiplex TPR spectra collected after dosing 4.0L 1H, 1H, 2H, 2H-perfluorodecanethiol on Cu(111) at 300K
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Figure 9. The RAIR spectra at 0.1L, 0.3L, 0.5L, 4.0L of 1H, 1H, 2H, 2H-perfluorodecanethiol deposited on Cu(111) at room temperature and followed by annealing to 380K. and schematic diagram of phase transformation
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35





List of Schemes

Scheme 1. The phase transformation in the mechanism of SAMs growth
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Scheme 2. Schematic diagram indicates the proposed orientation of individual 1H, 1H, 2H, 2H-perfluorodecanethiolate on Au (111) and Cu (111)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32



List of Table

Table 1. The assignment of vibration mode of the transition dipole moment for 1H, 1H, 2H, 2H-perfluorodecanethiol SAMs
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12