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Charge-Transfer in Silicon Governs the Pattern of Dissociative Attachment of Hydrogen Halides; HCl, HBr, HI. Si Yue Guo, Maryam Ebrahimi, Iain Ross McNab, and John C. Polanyi J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b07062 • Publication Date (Web): 12 Sep 2016 Downloaded from http://pubs.acs.org on September 17, 2016

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The Journal of Physical Chemistry

Charge-Transfer in Silicon Governs the Pattern of Dissociative Attachment of Hydrogen Halides; HCl, HBr, HI. Si Yue Guo, Maryam Ebrahimi†, Iain R. McNab‡, and John C. Polanyi* Lash Miller Chemical Laboratories, Department of Chemistry and Institute of Optical Science, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada †

Current Address: Centre Énergie, Matériaux et Télécommunications, Institut National de la Recherche

Scientifique, Université du Québec, 1650 boulevard Lionel-Boulet, Varennes, Québec J3X 1S2, Canada ‡

Current Address: Faculty of Applied Science and Technology, Sheridan College-Trafalgar Road

Campus, 1430 Trafalgar Road, Oakville, Ontario, L6H 2L1, Canada *

Corresponding author: tel.: (416) 978-3580, fax: (416) 978-7580, email: [email protected].

Article for J Phys Chem C C2 Surfaces, Interfaces, Porous Materials, and Catalysis

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Abstract (169/200 words) The dissociative attachment of hydrogen halides, HCl, HBr and HI, on Si(100) were studied by Scanning Tunneling Microscopy, and modeled by Molecular Dynamics computations based on density functional theory. The relative yields of on-dimer (OD), inter-dimer (ID), and inter-row (IR) products, reported here for the first time, were unaltered by temperature change, indicative of barrier-free reaction. Inter-dimer reaction was found experimentally to be overwhelmingly the favoured reaction path at all temperatures, 175-300 K. This is a preference that theory accounts for by a combination of kinematics favoring the initial approach of H, and subsequent charge-displacement directing the halogen atom to an inter-dimer site. Molecular dynamics, with statistical sampling of the initial collision-geometry at the surface, showed that the light H-atom invariably was the first to engage with the surface, forming H-Si. This bond-formation resulted in directional charge-transfer to a neighbouring Si dimer-pair of the same dimer-row. As a consequence this neighbouring Si became attractive to the incoming electrophilic halogen-atom, accounting for the observed strong preference for the inter-dimer outcome.

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1. Introduction There is interest in understanding the factors governing the pattern of reaction at ordered, semiconductor surfaces.1,2 Dissociative attachment (DA), in which an existing bond breaks and two new bonds form yielding chemisorbed reaction products, is one of the most common surface reactions, with applications to heterogeneous catalysis. Anisotropic crystal surfaces such as Si(100) with surface reconstructions (2×1) or c(4×2) offer incoming molecules multiple pathways for DA, namely reaction with different pairs of Si-atoms, the most common pairs being on-dimer (OD), inter-dimer (ID), and inter-row (IR). The choice of reaction site is most often ascribed to physisorbed precursor states leading over differing energy-barriers to distinct product states. Here the choice of pathway will be shown to be governed by a combination of kinematics and charge-displacement at the surface. In the following paragraphs we review earlier work on the DA of other molecules on Si(100). Scanning tunneling microscopy (STM) experiments by Lyubinetsky et al. showed that Cl2 dissociatively attached on Si(100) to give preferentially 52% IR products, with the remaining products 33% ID and 15% OD.3 Density functional theory (DFT) calculations explained this by an increase in energy barrier in going from IR to ID and OD.4 Relative barrier heights in the approach co-ordinate were also employed to explain the observation of H2 forming exclusively ID products on Si(100), the barriers being 0.2 eV for ID and 0.3 eV for OD.5,6,7 In these studies barrier heights were computed starting at the site of adsorption. The surface atoms of the clean Si(100) surface form buckled dimers in which the 'down' Si transfers charge to the 'up'. Hence ammonia and water were found to adsorb at Si(100) via a precursor state in which the lone pair on N or O formed a dative bond with a 'down' Si.8,9,10,11,12 Dissociative attachment resulted thereafter from the transfer of an H-atom to give OD and ID products with differing activation energies. More recently, STM studies of alkyl halides (CH3Br, CH3Cl, and R-Br, R=C2H5, C3H7, C4H9) reacting at Si(100) have shown that the computed energy barriers favoured inter-row, IR, reaction.13,14,15,16 The present study is of DA in the family of hydrogen halides HX (X=Br, Cl, I) at Si(100). To our knowledge, HBr, HCl, and HI have not previously been examined at the single-molecule level. We find that in this series of reactions the observed marked site-selectivity favouring the ID outcome was unaffected by temperature change. It was not therefore due to differing energy-barriers for the three reaction paths, as in the previous examples cited. No physisorbed precursor states were observable by 3 ACS Paragon Plus Environment


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STM at any of the temperatures employed. These observations accord with our ab initio calculations, reported here, which predicted unstable precursors that reacted without an appreciable barrier for all three chemisorbed outcomes, OD, ID, and IR. To compute the relative yields of these three products from barrier-less reaction we have employed a statistical model, applying molecular dynamics (MD) to a representative sample of HBr plus surface collisions in the field of an ab initio potential representing the Si(100) surface. This method was introduced by Tuckerman and coworkers to study rapid cycloaddition reactions, also at Si(100).17,18 We expanded it to a greater range of initial states and applied it, here, for the first time to dissociative attachment (DA). Our MD simulations revealed that the DA of the hydrogen halide family proceeded sequentially, starting with the formation of H-Si, exclusively with an 'up' Si19,20, followed thereafter by X-Si bonding preferably to a 'down' Si. We shall show that charge-flow along the dimer-row from the 'up' Si steered the electrophilic X-atom to the neighbouring Si of the same row, i.e. to the observed preferred inter-dimer (ID) outcome. This preference was clearly evident in ab initio studies, performed here. The novelty of the dissociative attachment dynamics found in the present work is two-fold; first, it takes place in two discernible stages – H-attachment followed femtoseconds later by halogen-atom attachment – and secondly it is governed in its direction by charge-flow along the dimer-rows of the surface. Earlier experiments of HCl and HBr on Si(100) were performed – in contrast to the present work – at saturation coverage21,22,23,24 or on a hydrogenated surface25. While dissociative attachment was found to be a major pathway, previous authors found evidence of the abstraction of single atoms, H or Cl, by the surface. Adsorbate-adsorbate interactions were investigated to explain the pattern of long-range ordering of Cl at high coverage. Charge-transfer through the surface has been studied extensively for various reactions on metal and on semiconductor surfaces.14,19,20,26,27,28,29,30,31 For single H-atoms at Si(100), Radny et al. found, as here, that the charge in the adjacent dangling bond was transferred along the dimer row rather than across.19 Charge flow along dimer-rows has also previously been noted in theoretical studies of adsorption of Oand N-containing molecules on the surface studied here; Si(100).27,28,29


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2. Methods 2.1 Experiment The experiments were carried out on an Omicron VT-STM. Si(100) samples were cut from n-type, phosphorus-doped single crystal wafers (Virginia Semiconductors, 0.02 Ω · cm) and prepared by repeated flashes to 1400 K using the procedure described in Ref. [32]. For experiments at 265 K, the sample was cooled by passing cold nitrogen gas through the STM cryostat. The gas was cooled in a copper tube immersed in LAr, which has a higher boiling point than nitrogen thereby ensuring that N2(g) does not condense. Lower temperatures were achieved using LN2. In both cases the temperature of the sample was stabilized by counter-heating the cryostat, using a Lakeshore 331 temperature-controller. Before dosing, we checked the surface for defects and found less than 0.2%. Adsorbates were introduced from a lecture bottle by background dosing via a leak valve on the preparation chamber. The doses were monitored using an ion gauge in the STM chamber and reported as duration × pressure, in Langmuirs (1 L = 1 × 10-6 torr × s).The ion gauge in the preparation chamber was turned off during dosing (average 0.01 L) to avoid pyrolising the dosed molecule. Hydrogen chloride and hydrogen bromide were purchased from Linde Canada, and hydrogen iodide from MEGS Specialty Gases Inc. All products were rated > 99% pure. HI, being prone to disproportionation, was degassed by freeze-pump-thaw cycles using an acetone-dry-ice mixture.

2.2 Computation Ab initio calculations were performed to elucidate the mechanism of dissociative attachment. They included computed minimum-energy pathways and classical trajectories using density functional theory (DFT) as implemented in the Vienna Ab initio Simulation Package (VASP)33,34 to obtain the potentialenergy surface. The crystal surface was modeled on the Si(100)-c(4×2) reconstruction. The slab, Si112H32 (15.36Å × 15.36Å × 25 Å), embodied seven layers with a 15 Å vacuum layer, terminated below by hydrogen atoms. The bottom two layers and the H-atoms were fixed during all calculations. The Perdew-Burke-Ernzerhof (PBE) functional35 generalized-gradient approximation (GGA) approach was



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used with the projector augmented wave (PAW)36 and an energy cutoff of 450 eV. Calculations included the semi-empirical DFT-D237 van der Waals correction. Since the physisorption geometries were unstable with respect to product formation, they were obtained by systematically exploring a grid of positions above the Si(100)-c(4×2) surface. At each point, the atomic coordinates were fixed in place for a single-energy calculation. Configurations whose energies were local minima in the potential-energy surface were then subjected to a full relaxation calculation, with geometry optimization. The chemisorption geometries were obtained by geometry optimizations. Since the Si(100)-c(4×2) surface consisted of buckled dimers with one up-Si and one down-Si atom, there were two possible configurations of H and X for each outcome. The most stable configuration was found to be one where H reacted by movement to an up Si. The Climbing-Image Nudged Elastic Band (CI-NEB) method was used to map out the minimum energy pathways for OD, ID, and IR, and to locate the small energy-barriers to reaction.38,39 Trajectories were produced by ab initio molecular dynamics (AIMD) using VASP40. To obtain the initial conditions we sampled the phase-space for a molecule impinging at the surface. The molecule was placed in varied configurations above the surface, and given varied initial velocities. A complete study was performed for the main exemplar of HBr, encompassing 342 trajectories distributed over the many initial-state parameters. In addition, we calculated a small sample of 12 trajectories for HCl and 8 for HI. All trajectories were computed employing a time step of 0.5 fs for a total trajectory duration of 3 ps. In the dynamical calculation each reagent parameter (molecular geometry and initial velocity) was tested for sensitivity to establish the sample size. The calculations were initiated with the molecule 5 Å above the surface, sampling every point of a spatial grid systematically, and thereafter calculating a weighted average.


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Figure 1 – Starting positions, A-I, for the MD calculations sampling the Si(100) surface c(4×2) unit cell (7.68 Å × 3.84 Å). The 'D' and 'U' on the right label the 'down' and 'up' Si atoms.

In Figure 1 we divided the unit cell into a (x, y) grid with a 1.92 Å spacing. The crosses in the figure label the starting positions for the center of HX. Due to the symmetry of the surface, the points F and J were redundant, so were not calculated. In addition to these positions, we considered eight in-plane orientations for the molecule uniformly distributed at π/4 intervals. Taking into account the symmetry of the system, we employed 38 unique positions and orientations, each weighted according to their probability of occurrence in the unit cell of Figure 1. Since the out-of-plane orientation of the molecule at 5 Å above the surface had no detectable effect on the outcome, all calculations began with the H-X bond parallel to the surface. The three velocity magnitudes employed were the energy per degree of freedom, ½ kBT, the most probable velocity, kBT, and the root mean square velocity, 3/2 kBT. The outcomes were then weighted according to the Maxwell-Boltzmann distribution at 300 K. In addition to the velocity magnitudes, we varied the in-plane, ϕ, and out-of-plane, θ, directions of the velocity vector. The in-plane angles were weighted equally, the out-of-plane angles by a cosθ distribution, reflecting the probabilities of angles of impingement.41 The velocity directions could also be simplified due to symmetry so that only four combinations were needed, in radians: (ϕv, θv) = (0, 0), (0, π/4), (π /4, π /4), (π /2, π /4) [these being normal to the surface, along the row, across the rows, and diagonally]. Additionally we compared two crystal surfaces. The first was a buckled surface at zero K, with all atoms at their equilibrium position. The second was equilibrated at 300 K for 2 ps to obtain an approximation to a 300 K thermal surface. A small but representative sample of calculations on both surfaces gave indistinguishable results, so the zero K surface was used.



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The Si(100)-c(4×2) surface was employed since its asymmetric dimers yielded the charge landscape in which the down-Si transferred charge to the up-Si. At 300 K, the dimers had a rocking period of 200300 fs and complete inversion-flipping period of ~1 ps18,42,43,44,45 both times being encompassed in the 13 ps duration of our trajectories.

3. Experimental Results 3.1 Identification of products Dosing HX on Si(100) gave only pairs of chemisorbed H and X on neighbouring Si-atoms in the STM images (i.e. no single-atom abstraction). The absence of intact physisorbed species and single-atom features indicated that HX had reacted thermally at all temperatures employed, by dissociative attachment (DA). In DA, the H-X bond was broken and the fragments, H and X were covalently bound to Si-atoms at the surface. The STM images of the products were similar for the three hydrogen halides. Figure 2 shows the three types of H + Br products, for the principle example of HBr adsorbed on-dimer (OD), inter-dimer (ID), and inter-row (IR), at Si-Si separations 2.2 Å, 3.8 Å, and 5.2 Å. For OD products, H and Br attached to the two silicon atoms of one dimer. For ID and IR the fragments reacted with silicon atoms on adjacent dimers in a dimer row and at adjacent dimer rows. In these last two cases, ID and IR, the reaction involved opening two Si-Si double-bonds. For all three configurations of the products, both H and Br imaged as “dark” depressions at ~ +/- 1 Vs. The adjacent dangling bonds could be identified as “bright” protrusions in the filled-state (negative surface) STM images.


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Figure 2 – STM Images at 300 K. of the main HBr products; on-dimer (OD), inter-dimer (ID), and interrow (IR), taken at three biases.

Imaging at different bias voltages, as shown in Figure 2, was instructive for discriminating the products from defects. Most notably we observed the brightening of the Br-atom at biases above +1.5 Vs, due to a localized increase in density of states in the Br-Si bonds.46 The same increase in brightness was observed above +2 Vs for Cl-Si46 and above +1.3 Vs for I-Si. As a result, the OD product appeared asymmetric with one side of the dimer brighter at + 2 Vs, as in Figure 2. Typical OD contaminants included dimer vacancies, nickel, and reacted water, all of which imaged as symmetric dark depressions on the surface which, in contrast to OD HBr, remained dark at +1.5 Vs. Thermal and STM tip-induced hopping of halogen atoms assisted in identifying the halogen products.13,47,48 Specifically, Br exhibited thermal hopping at temperatures above 270 K. To obviate this hopping, experiments were generally performed below this temperature. Since the main ID contaminants were "C-shaped" water defects, halogen atom hopping also helped to distinguish HX from water.

3.2 Product distribution Product ratios were measured at 265 K, 210 K, and 175 K, to obtain the temperature dependence. Table 1 gives the relative yield of OD, ID, and IR products for HBr dosed on Si(100). At all temperatures the reaction was overwhelming ID, with some OD and negligible amounts of IR. Since the product distribution remained constant over this substantial range of absolute temperatures, energy barriers do 9 ACS Paragon Plus Environment


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not explain the site-preference. Additionally, the similarity of the results above and below 200 K49 suggest that surface buckling does not play a significant role in site-selection. Table 1 – HBr product distribution for on-dimer (OD), inter-dimer (ID), and inter-row (IR), measured at three temperatures

Temperature

265 K

210 K

175 K

OD

21% ± 3%

16% ± 3%

25% ± 3%

ID

79% ± 6%

84% ± 6%

73% ± 5%

IR

0%

0%

~ 2%

N (total counts)

195

367

638

Similar experiments were performed for HCl and HI. In Table 2 we compare the room-temperature product yields for the three molecules. The outcomes were identical to HBr, indicating that the pattern of reaction was not sensitively affected by changes in bond length (1.27 Å for HCl, 1.41 Å for HBr, and 1.61 Å for HI) or gaseous bond-energy (4.47 eV, 3.79 eV, and 3.09 eV).50 Table 2 – Comparison of product distribution for HCl, HBr, and HI at 300 K

300 K

HCl

HBr

HI

OD

26% ± 4%

32% ± 5%

34% ± 5%

ID

74% ± 7%

68% ± 7%

66% ± 7%

IR

0%

0%

0%

N (total counts)

127

140

131

4. Theoretical Results 4.1 Activation energies The three minimum-energy pathways leading to OD, ID, and IR were obtained by ab initio computation. They gave negligible activation barriers, Eb, for all three hydrogen halides, the barriers being below the integration and wrap-around errors in VASP, ~0.005 eV51, for OD and ID, and ~10 meV for IR. In Table 3 we report the energies for the initial, physisorption states (IS), barrier-crest (Eb), and final, chemisorption state (FS) for HBr. These states were obtained using the method described in Section 2.2. (See Supporting Information for HCl and HI, and for a representative minimum-energy pathway for HBr reacting IR.)


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Table 3 – Energy of the initial state (IS), activation barrier (Eb), and final state (FS) relative to the gas phase for the three reaction pathways for HBr

(eV)

IS

Eb

FS

-∆Hrxn

OD

-0.42a

< 0.005

-3.11

2.69

ID

-0.47a

< 0.005

-2.80

2.33

IR

-0.67

0.010

-2.95

2.29

If the observed site-selectivity were to be explained by the energy barriers, they would need to differ by ~30 meV between OD and ID and at least 125 meV between IR and ID. The computed barriers of ≤ 10 meV clearly do not account for the observed strong preference for ID.

4.2 Molecular dynamics Since both observation and calculation gave barrier-less reaction, we employed ab initio molecular dynamics to calculate the relative reaction probabilities at the three sites, OD, ID, and IR. For HBr, a total of 342 trajectories were computed systematically, and thereafter subjected to appropriate weighting as described in the methods section. In the overwhelming majority of cases (97%) the dissociative attachment of HBr at the Si slab occurred within 3 ps of the start of the trajectory. The trajectory was considered complete when both H and Br atoms had reached the equilibrium bond separations; 1.5 Å for H-Si and 2.26 Å for Br-Si (2.09 Å for Cl-Si and 2.48 Å for I-Si). Since the top five layers of the slab were allowed to move, the 2.29-2.69 eV energy released in the reaction (Table 3) was dissipated into the surface, the computed products remaining adsorbed.

a

approx. minimum energy.



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Figure 3 – Result of MD calculation sampling initial approach conditions for HBr impacting Si(100)c(4×2),with trajectories grouped according to reaction outcome. The pie chart of (a) shows the overall, weighted percentages, and (b) shows the distribution of products for each starting position, A to I, labeled in Figure 1. The computed inter-dimer (ID) product in solid red dominates, in agreement with the observations. (Due to the symmetry of the surface, positions F and J are omitted in (b), being equivalent to B and I.)

The pie chart in Figure 3 (a) above gives the weighted average for each product pair; OD, ID, IR, totaling 92%. The MD gave a majority of ID reaction (54%, compared to the observed 75%), with some OD (24%, compared with 25% observed) and IR (14%, compared with 0%). 'Other' reactions (Figure 3) were rare (5%) and included non-adjacent products and Br insertion into the surface by reacting with a Si atom of the second layer. The remaining 3% were the abortive reactions in which the reagent molecule returned to the gas-phase. All three incoming velocity magnitudes gave a preference for ID (see Supporting Information for details).


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Figure 3 (b) gives the breakdown of outcomes for all starting positions. The bar chart shows that a majority of (x, y) impact points led to ID. The ID outcome was achieved from many initial geometries whereas OD and IR came largely from starting points directly above the silicon atom that reacted. The small computed amount of IR reaction (14%), despite its absence from the experiments, was found to be connected with over-counting of starting point, C, directly above the IR position.

4.3 Discussion of Dynamics Figure 4 exemplifies the delay between the attachment of H and of X (Cl, Br or I) in a typical DA event. The figure plots as a function of time the distances between H and X and the Si-atoms to which they eventually bond. These trajectories are for the major ID pathway, but the sequence of events is characteristic of all the reactive events (314 for HBr, 12 for HCl and 8 for HI). The incoming molecule was considered to have reacted when it first reached the equilibrium bond length, indicated by the horizontal lines in Figure 4. For all HX we observed a kinematic (mass-ratio) effect, where the H-atom reacted tens of femtoseconds ahead of the X. On average H reacted 20 fs before Cl, 87 fs before Br, and ~200 fs before I. For HBr, which was subjected to a comprehensive statistical study, 90% of the reacted trajectories gave a delay between H-attachment and Br-attachment between 20 and 160 fs. The second reacting specie, Br, can be seen to have experienced an attraction to the surface once the H had reacted, evidenced by the change in slope in the Br-Si curve in Figure 4 (b). Attachment of H followed by Br involved a delay of 73 fs in the case illustrated in Figure 4 (b). The two-step dynamics were found to be characteristic of HX dissociative-attachment involving a light and a heavy atom in the reagent.

Figure 4 –Distance plots for a representative trajectories giving ID product, for (a) HCl, (b) HBr, and (c) HI, showing the separation as a function of time for the faster H-atom and the subsequent slower X-



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atom approaching the Si-atoms with which they react. In these examples the halogen atoms reached their equilibrium position 40, 73, and 94 fs after the H (as indicated by the dotted lines). (See supporting information for additional details: the H-X separation as a function of time, the out-of-plane angle as a function of time, and images from the trajectory.)

Examination of the trajectories showed that the two-step dissociative attachment of HBr was initiated by the attraction of the H-atom by an up Si-atom. H was found to react exclusively with the negative up-Si, and can be seen to be repelled by the down Si. Once a partial H-Si bond is formed, the slow-moving Br radical reacts preferentially with a down Si. The predominance of ID products was in part due to the symmetry of the surface: once an H had reacted, there were two possible ID sites for Br. By contrast there was only one choice for OD and one for IR. However, if the reaction depended on combinatorics alone, we would expect 25% OD, 50% ID and 25% IR, whereas the observed ID significantly exceeds this percentage (~75% ID). The source of this extra bias toward ID is discussed below. The site-selectivity of the reaction can be explained by the fact that the Br-atom approaches a hydrogenated surface. To examine the effect of H-attachment on the surface-charge, we calculated the charge density difference between a clean surface and one with a chemisorbed H. Figure 5 (a) and (b) gives the isocharge surfaces showing electron gain and loss. The H can be seen to withdraw charge from the adjacent silicon in the same silicon dimer-pair, and transferred it to the silicon atoms along the dimer row in the adjacent silicon dimers. In Figure 5 (c) we have summed the valence charge on each surface Si-atom contained within the sphere of van der Waals radius, 2.1 Å. We calculated the substantial difference of 0.5 electrons between the OD site and the ID site. Since Br radicals are known to prefer an electron-rich environment31,52,53, the increased charge adjacent to a reacted H favoured ID reaction by the Br-atom.


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Figure 5 – (a)-(b) Isosurfaces of charge-density differences between a clean surface and a silicon surface following chemisorption of an H-atom. The contours are drawn in (a) at +3.6 × 10-4 e/Å3 showing electron gain (cyan), and in (b) at -1.2 × 10-4 e/Å3 showing electron loss (magenta). The site for an incoming X-atom to react 'on-dimer' (OD) and 'inter-dimer' (ID) are indicated. (c) Valence charge (in units of e) contained within each surface Si-atom within its van der Waals radius (2.1 Å).

V. Conclusions The dissociative attachment of hydrogen halides at Si(100) has been studied by STM showing that interdimer (ID) dissociation was consistently favoured over on-dimer (OD) and inter-row (IR), leading to ~75% ID, ~25% OD, 0% IR. This site-selectivity was maintained throughout the series of HX= HCl, HBr and HI. The absence of detectable temperature-dependence in the case of HBr, from 175-265 K, indicated that the reaction rates were not governed by differing activation energies. Theory confirmed that the three pathways were barrierless: Eb ~ 0 eV (

HCl, HBr, and HI - ACS Publications - American Chemical Society

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