Temperature-Programmed Desorption (TPD) and Density Functional

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Temperature-Programmed Desorption (TPD) and Density Functional Theory (DFT) Study Comparing the Adsorption of Ethyl Halides on the Si(100) Surface Jing Zhao, Benjamin W. Noffke, Krishnan Raghavachari, and Andrew V. Teplyakov J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b12184 • Publication Date (Web): 17 Mar 2017 Downloaded from http://pubs.acs.org on March 25, 2017

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The Journal of Physical Chemistry

Temperature-Programmed Desorption (TPD) and Density Functional Theory (DFT) Study Comparing the Adsorption of Ethyl Halides on the Si(100) Surface Jing Zhao1, Benjamin W. Noffke2, Krishnan Raghavachari2, and Andrew V. Teplyakov1* 1

Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 2

Department of Chemistry, Indiana University, Bloomington, IN 47405

Abstract: In this work, the differences between the dissociative adsorption of chloroethane-d5 (C2D5Cl) and iodoethane-d5 (C2D5I) on a Si(100)-2x1 surface are compared by analyzing the results of density functional theory (DFT) calculations and temperature programmed desorption (TPD) experiments. The adsorption mechanism for both chloroethane-d5 and iodoethane-d5 on a clean Si(100)-2x1 surface is based on a dissociative chemisorption following halogen-carbon bond cleavage. Further surface transformations upon heating cause hydrogen elimination by ethyl groups followed by ethylene and hydrogen desorption. The key difference between iodoand chloro-derivatives is that the corresponding sticking probabilities of chloroethane-d5 and iodoethane-d5 in the same reaction system are extremely different. The experimental study reveals that the exposure for the monolayer saturation of chloroethane-d5 is twenty times higher than that for iodoethane-d5. These differences are attributed to the stability of surface-mediated molecular adsorbates rather than to the differences in the dissociation barriers based on the DFT investigation.

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Author to whom the correspondence should be addressed: 112 Lammot DuPont Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716. Tel.: (302) 831-1969; e-mail: [email protected]. 1 ACS Paragon Plus Environment


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I.

Introduction: Organic modification of semiconductor surfaces has attracted substantial interest for

many years because of advances in a number of applications including microelectronics, catalysis, and bio-sensing.1 Among organic modification schemes, the reactions of alkyl halides with elemental semiconductor surfaces including porous silicon2 as well as silicon and germanium single crystals3 have been investigated as a means to introduce model simple functional groups, alkyls, to the surface. For example, the dissociation of methyl halides (CH3Cl, CH3Br, CH3I) on Si(100)4-14 can lead to a controlled formation of mixed methyl and halogen monolayers. Although similar species can be formed by a direct dissociative adsorption of molecular halogens (Cl2, Br2, I2) or hydrogen halogenides (HCl, HBr, HI),15-17 the reactions of these species are often complicated by additional pathways. These chemicals are also relatively difficult to handle. Thus, dissociation of methyl halides seems to provide a much more controlled method for semiconductor surface modification with halogens. However, if the target is a specific halogen pattern on a single crystalline surface or carbon-free interface, methyl halides may not be the optimal choice, as the heating of the silicon surface produced by methyl halide dissociation leads to carbon contamination. With this in mind, a number of researchers turned towards ethyl derivatives, where β-hydrogen elimination is a facile and clean process on elemental semiconductor surfaces,18, 19 and ethylene desorption following this process leaves the surface essentially carbon-free. Over the past years, the experimental and computational studies of ethyl iodide and ethyl bromide adsorption on Si(100)-2×1 surface18-21 targeted the pathways of their dissociative attachment. The focus has largely been on the differences in energy barriers required to dissociate different carbon-halogen bonds. Much less research has been directed towards evaluating the differences in precursor states for different alkyl halides on clean semiconductor surfaces. A study of CH3Cl adsorption mechanism on Si(100)-2×1 surface has investigated the 2 ACS Paragon Plus Environment

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role of the formation of “precursor state” in determining the sticking probability.9 The competition between the desorption from precursor state into the gas phase and the chemisorption from precursor state to dissociated state was considered as the key point to determine the reaction efficiency. In the corresponding discussion, the surface coverage dependence on the sticking probability is determined largely by the nonactivated precursor mediated chemisorption. The chemisorption of CH3Cl on Si(100) was also specifically studied by DFT calculations to compare the different dissociation reaction pathways on silicon dimers of this surface.5 One of the conclusions of this work was the observation that the calculated energy barriers for desorption and chemisorption from precursor state depend dramatically on different computational approaches. An important takeaway from this work is that in evaluating the adsorption mechanisms for alkyl halides on Si(100)-2x1 surface it is imperative to compare the experimentally observed changes in sticking probabilities with exposure and evaluate the impact of surface-mediated molecularly adsorbed states on the dissociation process. Alkyl chlorides have definitely received more attention in computational studies than the alkyl derivatives with heavier halogens. However, there is definitely sufficient amount of experimental data available for several bromo- and iododerivatives. For example, the chemistry of C2H5I on Si(100)-2×1 surface has been reported.18, 19 It was proven that a low iodoethane exposure is sufficient to form a saturated monolayer on a clean Si(100) surface, thus suggesting very high sticking probability and simple dissociation mechanism for this compound. In fact, the surface produced by iodoethane dissociation on Si(100)-2x1 could be further transformed by βhydrogen elimination/ethylene desorption leading to a specific arrangement of surface iodine atoms and hydrogen atoms resulting from the elimination process. Overall, the mechanism of CHalogen dissociation would be expected to be similar for different halogens. The previously reported work on chloroethane dissociation suggested overall similar mechanism for iodoethane

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and chloroethane reactions with the Si(100)-2x1 surface.22 However, a substantial difference in the exposure required to complete a chemisorbed monolayer was also reported. If the previous computational mechanism to explain the CH3Cl reaction on Si(100) could be summarized as a precursor-mediated chemisorption,9 a similar approach can also be used to describe the reactions of more complex alkyl halides. Except that for these compounds the experimental measurements have to be supported by more advanced computational analysis. This paper presents a detailed study of C2H5Cl-d5 and C2H5I-d5 adsorption on a clean Si(100)-2x1 surface analyzed experimentally with thermal desorption and theoretically with DFT methods. The work compares the dissociation processes for these two molecules with the primary target to differentiate the role of the carbon-halogen dissociation barrier and the stability of the surface-mediated precursor state. II.

Experimental and Computational Methods: For temperature-programmed desorption studies, an ultra-high vacuum chamber with

base pressure below 1×10-9 Torr was used. This chamber is equipped with a differentially pumped mass spectrometer (Hiden Analytical) for confirming the purity of the gases dosed into the chamber and for thermal desorption studies, an Auger electron spectrometer, and a lowenergy electron diffraction set-up. A standard preparation procedure to obtain a clean and wellordered Si(100)-2×1 surface was applied before the exposure to alkyl halides. Briefly, the surface was cleaned by ion sputtering with argon (99.9999%, Matheson) and 20-minute annealing above 1000 K.18 Following this preparation procedure, the structure and cleanliness of the surface was confirmed by low-energy electron diffraction (LEED) and Auger electron spectroscopy (AES), respectively. In order to obtain the most reliable and quantifiable results for evaluation of adsorption of alkyl halides, isotopically labeled C2D5Cl and C2D5I were utilized instead of C2H5Cl or C2H5I to follow the desorption of D2 as a result of surface reaction. This 4 ACS Paragon Plus Environment

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approach avoids the possible effects of electron-stimulated processes (from AES) or interference of background gases with the mass spectrometry pattern of the desorbing species. Iodoethane-d5 (99%, Sigma-Aldrich) used in the experiment was purified by three freeze-pumpthaw cycles before being introduced into the chamber via a leak valve. The chloroethane-d5 gas (99%, Sigma-Aldrich) was used without additional purification and also introduced via a leak valve. All exposures are reported in Langmuirs (1L=10-6 Torr·s) without additional corrections to the ion gauge sensitivity. The heating rate of 2 K/s was used throughout all the temperature programmed desorption experiments reported. Density functional theory (DFT) calculations were conducted using the Gaussian 09 suite of programs.23 Calculations were performed using the B3LYP24,

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and M0626 density

functionals with Grimme’s D3 dispersion corrections.27 The M06 functional has previously been shown to perform well for characterizing surface chemistry reactions.28 The 6-311+G(3df,p) basis set29-31 was used for geometry optimizations and frequency calculations. Transition state guesses were obtained by performing relaxed internal coordinate scans for the ethyl halide bond dissociation. The transition state structure is then optimized and verified to have one imaginary frequency. The aug-cc-pVTZ basis set32, 33 was used for hydrogen, carbon, silicon, and chlorine atoms and the aug-cc-pVTZ-PP basis set34 was used for iodine atoms in single point energy calculations, to which the zero point energy from the frequency calculations is added. The basis set superposition error was evaluated for the aug-cc-pVTZ basis set and counterpoise corrections were applied to the complexation energies of the interaction complexes. The resulting counterpoise corrections are quite small (~3 kJ/mol). Full details on the counterpoise corrections can be found in the Supporting Information section. A Si9H12 model cluster representing a single silicon surface dimer was used without additional geometric constraints. As has been shown previously, this model is sufficient to investigate direct adsorption on a single Si–Si dimer.19 Overall, there are a number of dissociation mechanisms



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suggested for alkyl halides on a Si(100)-2x1 surface. Some of these mechanisms involve multiple dimers and multiple dimer rows, as has been explored for alkyl chlorides,5 these mechanisms can be coverage-dependent; however, it is largely agreed upon that the most stable final structure for alkyl halide dissociation consists of alkyl and Cl fragments, which are bound to the two silicon atoms of the same surface silicon dimer.6 We have included selected investigations of the double dimer surface cluster in the SI and show that dissociation on the single dimer is the preferred mechanism. Thus, rather than explore all the possible mechanisms of dissociation, this work will target similar dissociation pathways leading to the same type of stable surface-dissociated structure but focus on the role of the adsorbed precursor state for comparing the efficiency of a reaction for iodoethane and chloroethane. III.

Results and Discussion: The overall mechanism for haloethanes adsorption and dissociation on a clean Si(100)-

2x1 surface is summarized in Figure 1. The gas phase molecule of C2H5X (X=Cl, I) is first proposed to molecularly adsorb on a surface forming a mediated state, which can either release the molecule back to gas phase or lead to carbon-halogen dissociation. The efficiency of both processes depends upon their respective energy barriers.


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Figure 1: Schematic representation of chloroethane-d5 and iodoethane-d5 adsorption, dissociation, and thermal chemistry on Si(100) surface.

III.1. Experimental Results. . According to this mechanism, the dissociation of C2H5X on a bare Si(100) surface ultimately releases ethylene and hydrogen into the gas phase as the surface temperature is increased. Therefore, temperature-programmed desorption can be used to obtain quantitative information on ethylene and hydrogen desorption at approximately 600 K and 800 K, respectively, thus providing quantitative information about the amount of C2H5X dissociated. As noted above in the experimental section, this approach avoids the possible effects of electronstimulated processes (from AES) or interference of background gases with the mass spectrometry pattern of the desorbing species. This work will mainly use hydrogen desorption 7 ACS Paragon Plus Environment


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data as the reference for comparing the amount of EtCl and EtI dissociated as a function of the molecular exposure. In order to differentiate between hydrogen present in small amounts on the background of the ultra-high vacuum chamber, deuterated derivatives of alkyl halides, EtCl-d5 and EtI-d5 were used and the thermal evolution of deuterium, D2 (m/z=4), was followed as a function of surface temperature. Temperature-programmed desorption results are summarized in Figure 2. In the experiments with EtCl-d5, the exposure of 2000 L was required for the desorption peak corresponding to D2 to reach the maximum peak intensity. This is the saturation exposure for this haloalkane. For EtI-d5 adsorption, the saturation exposure was determined to be 100 L in this experimental setup, 20 times lower than the saturation exposure in EtCl-d5. Thus, the sticking probability differences seem to be consistent with the precursor mediated process.35,36 We also monitored ethylene desorption in the TPD experiments. However, due to the reduced signal to noise and interference of the background gases trapped in the shield of the differentially pumped mass spectrometer, the D2 desorption was chosen as the most reliable method to quantify the adsorption of ethyl halides on a clean Si(100)-2x1 surface. According to the previous studies of CH3Cl,9 the independence of sticking probability of surface coverage observed here for iodoethane identifies the adsorption process as nonactivated, which is determined by the fact that the activation barrier height from the precursor state to chemisorption is lower than into the gas phase. However, the question is whether the stability of this surface-mediated precursor state plays substantial role in determining the ratio of desorption and dissociation for the adsorbed iodoethane and chloroethane. Previous computational work on CH3Cl adsorption on Si(100) dimers5 cautioned that computationally predicted barrier heights varied substantially with the computational method used. In fact, even geometrical structures of the adsorbed species are expected to be influenced by different computational methods. Thus, the DFT investigations presented below have to rely on


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comparing the computational results with known structural parameters to establish the appropriate computational strategy and then to evaluate the barriers for the proposed surface transformations of iodoethane and chloroethane. In order for these predictions to be compared with reliable experimental results and to avoid the effects of different possible surface structures affecting the adsorption processes at high coverages, the initial reaction rates will be used as the comparators.

Figure 2: Surface coverage as a function of exposure for ehtylchloride-d5 and ethyliodide-d5 adsorption on a clean and reconstructed Si(100)-2x1 surface following m/z=4 evolution during temperature-programmed desorption experiments. Temperature-programmed desorption spectra for ethylchloride-d5 and ethyliodide-d5 are provided as insets. The surface coverage of 1 ML was considered as a saturated monolayer when the peak intensity of m/z=4 reached the maximum, since no molecular physisorption in multilayers is possible for either one of the compounds studied at room temperature. 9 ACS Paragon Plus Environment


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III.2. DFT results. Zero point corrected energies at the B3LYP-D3/aug-cc-pVTZ and M06-D3/aug-cc-pVTZ levels of theory are used to construct reaction profiles for both EtCl and EtI adsorption on the Si(100)-2x1 surface represented by cluster models described earlier. In addition to the diagram shown in Figure 3, the Supporting Information section presents the summaries of the investigations with other methods and basis sets.


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Figure 3: DFT-predicted reaction energy profile for B3LYP-D3/aug-cc-pVTZ (blue numbers) and M06-D3/aug-cc-pVTZ (red numbers) for EtCl and EtI adsorption on a Si9H12 dimer cluster model. Optimized structures for single molecule, adsorbed precursor state, transition state and final dissociation product are presented. All energies are given in kJ/mol and are relative to the ethylhalide and silicon cluster at infinite separation. White: hydrogen atom; Gray: carbon atom; Dark Green: silicon atom; Bright Green: chlorine atom; Purple: iodine atom.



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Since the stability of the final dissociated state is considerably exothermic in both cases, the energy barriers leading from the surface-mediated precursor state to either desorption or dissociation should be carefully compared. The energy barriers from precursor state to chemisorption are higher than those to desorption. This observation is in complete agreement with the previous studies of chloromethane adsorption on Si(100).5 Since the observed sticking probability (based on the dissociation followed by hydrogen desorption) for EtI-d5 is much higher than that for EtCl-d5, one might expect a substantially lower energy barrier from weakly bound species to chemisorption for EtI than that for EtCl. However, according to all the DFT calculations summarized in this work, that is not the case. Figure 3 shows that for the B3LYPD3 functional (blue lines and numbers), the relative barrier height (with respect to gas phase reactants) for EtI dissociation is lower than that of EtCl dissociation by a mere 3.6 kJ/mol, while for the M06-D3 functional (red lines and numbers), the relative barrier for EtCl dissociation is less than 5 kJ/mol lower than that of EtI. The M06-D3 results are taken to be more accurate by previous calibrations.28,

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Nevertheless, the difference in relative barriers for EtCl and EtI

dissociation is not significant enough to explain the kinetic differences observed experimentally. Thus, it becomes important to focus on the influence of adsorption precursor state on the dissociation process and on differences between molecular adsorption of EtCl and EtI. The complexation energy for EtI is more than 14 kJ/mol greater than that of EtCl, supporting the sticking probability as the prime factor in the experimentally observed differences. It is expected that EtI should have a larger complexation energy than EtCl, given the trends in the polarizability of the halogens. The results for the complexation energies are qualitatively the same between the B3LYP-D3 and M06-D3 functionals, with M06-D3 exhibiting stronger complexation energies of approximately 10 kJ/mol.


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Figure 4: DFT-predicted reaction energy profile for B3LYP-D3/aug-cc-pVTZ (blue lines and numbers) and B3LYP/aug-cc-pVTZ (red lines and numbers) for EtCl and EtI adsorption on a Si9H12 dimer cluster model. Optimized structures for single molecule, adsorption precursor state, transition state and final dissociation product are presented. All energies are given in kJ/mol and are relative to the ethylhalide and silicon cluster at infinite separation. White: hydrogen atom; Gray: carbon atom; Dark Green: silicon atom; Bright Green: chlorine atom; Purple: iodine atom.



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The most important factor to accurately capture the non-covalent interactions of EtCl and EtI with the Si(100) dimer cluster is an adequate description of dispersion interactions. As shown in Figure 4, the B3LYP-D3 results experience a three-fold increase for EtCl and more than a two-fold increase for EtI in the molecular adsorption energies to form the interaction complex when dispersion is taken into consideration (i.e., relative to B3LYP). The larger change for EtI molecular adsorption is expected because of the polarizability trends in the halogen series. The barriers for EtCl and EtI dissociation see a minor decrease on the order of 4 kJ/mol with the inclusion of dispersion. Though the absolute barrier is not impacted significantly, the effective barrier is much lower with dispersion given the larger molecular adsorption energy. This suggests that dispersion corrections are vital when using B3LYP to model surface adsorption phenomena. The effect of including D3 dispersion corrections does not change the M06 results significantly because dispersion is already included in the parameterization of the functional. Explicit comparisons on the effect of dispersion can be found in the SI. Table 1: Summary of bond lengths for EtCl Si(100) dimer cluster complex and dissociation transition state for the B3LYP, B3LYP-D3, and M06-D3 functionals.

Bond Si–C Si–X

B3LYP 3.868 2.679

EtX Interaction Complex Geometry Bond Lengths (Å) EtCl EtI B3LYP-D3 M06-D3 B3LYP B3LYP-D3 3.769 3.678 3.837 3.762 2.550 2.597 2.913 2.830

M06-D3 3.660 2.775

Considering the drastic impacts of dispersion, we detail the bond lengths for dispersion and functional dependence. Table 1 summarizes the bond lengths that participate in the interaction complex of the ethyl halides on the Si(100) surface dimer. The interaction complex is quite sensitive to the presence of dispersion corrections for B3LYP, exhibiting significant changes on the order of 0.1 Å for the Si–C and Si–X bonds. The M06-D3 functional exhibits a shorter Si–C bond length, but a comparable Si–X bond length. As for halogen dependence, the


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chloride geometries experience slightly larger changes in bond length than the iodide geometries. All of these differences are reflected in the relative complexation energies for forming the interaction complex, with the shorter bond lengths in the interaction complex giving rise to stronger complexation energies for the B3LYP-D3 and M06-D3 functionals. The larger complexation energy for the M06-D3 functional compared to the B3LYP-D3 functional is reflected in the Si–C bond lengths. It should be emphasized that having a functional which includes dispersion is vital to describing the stability of the surface-mediated precursor state, which dictates the surface sticking probability. Given that B3LYP is the most widely used functional, its lack of dispersion effects may lead to erroneous conclusions when a non-covalent interaction intermediate is present.

IV.

Conclusions: The comparison of EtCl-d5 and EtI-d5 adsorption on a clean Si(100)-2x1 surface has

been performed by analyzing the results of thermal desorption data that follow the formation of hydrogen following β-hydrogen elimination and ethylene desorption for the ethyl groups formed as a consequence of the dissociation. Both reactions were determined to be typical precursor mediated processes by comparing experimental results with the DFT-predicted dissociation processes for both compounds. EtI-d5 was discovered to be much more efficient in dissociating on surface than EtCl-d5. DFT studies with dispersion corrected B3LYP and M06 functionals in conjunction with the aug-cc-pVTZ basis sets were conducted to reveal the reason why these two reaction processes are so different. The DFT results provided the results fully consistent with the experimental observation and supported the hypothesis that the stability of the surfacemediated precursor state determined the efficiency of haloethane dissociation. 15 ACS Paragon Plus Environment


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Supporting Information The Supporting Information is available: Computational details and geometric parameters of the interaction complexes and transition states, basis set effect studies, Iodine 6-311+G(3df,p) basis set information, complete reference 23.

Acknowledgements: Acknowledgment is made to the donors of the Petroleum Research Fund, administered by the American Chemical Society, for partial support of this research. This work at University of Delaware was also supported by the National Science Foundation grant (CHE1057374). The work at Indiana University was supported by the National Science Foundation grant (CHE-1266154).

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Temperature-Programmed Desorption (TPD) and Density Functional

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