Single-Hydrogen Dissociation Paths for Upright and Flat

Sep 22, 2014 - molecule on a Si(001) surface and their follow-up proton transfer processes. We examine two possible types of dative-adsorption...
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Single-Hydrogen Dissociation Paths for Upright and Flat Acetophenone Adsorbates on the Si(001) Surface Hamid Mehdipour* Centre for Quantum Computation and Communication Technology, School of Physics, The University of Sydney, Sydney, NSW 2006, Australia Department of Physics, Sharif University of Technology, Tehran 11155-9161, Iran

ABSTRACT: Using cluster-based density functional theory we investigate adsorption configurations of an acetophenone molecule on a Si(001) surface and their follow-up proton transfer processes. We examine two possible types of dative-adsorption configurations, up-right standing and flat, as well as compute their follow-up kinetically preferable on-dimer, interdimer, and inter-row proton transfers. Energetics of possible conversions between the achieved adsorption configurations are computed as well. Using all the data obtained, we theoretically illustrate reaction pathways leading to detached hydrogen positions captured in STM imaging of a Si(001) surface exposed to acetophenone vapor at room temperature.

1. INTRODUCTION Owing to possible manipulation of organic molecules adsorbed on semiconductor surfaces1,2 and fabrication of organic molecules-based electronic devices in nanoscale dimensions,3−5 silicon surface organic chemistry has drawn great attention in recent years.1,6−8 Among organic molecules acetophenone has shown intriguing reaction properties when landing on the free2 and H-terminated Si(001)9 surfaces. The molecule can be manipulated on the surface through its phenyl ring2 and it can acquire a completely decoupled electronic state from that of the Si(001) surface when a molecular line is assembled on the surface.10 These all make the acetophenone an attractive option for STM/semiconductor-based molecular conductance measurement2 as well as fabrication of π-conjugated-molecule-based nanodevices. Dative adsorption followed by a proton-shift is a common reaction pattern observed for gas-phase molecules reacting with the silicon (001) surface. This pattern is followed by many organic molecules, such as acetophenone and acetone,2 as well as inorganic molecules (water, phosphine, etc.).11−13 This reaction pattern comprises two distinct steps in which some common features are followed by a variety of molecules, but each step is completed slightly differently by molecules of different sizes. In the first step, the gas phase molecule first approaches with a lone-pair orbital (of electron rich constituent atom) to a down-buckled, positively polarized atom of a silicon dimer on the Si(001) surface. This leads to a dative chemisorption of the landing molecule and thus a positive © 2014 American Chemical Society

charge transfer from the surface to the molecule, which is common among molecules. This step also can be accompanied by formation of more (covalent) bonds depending on the size of the adsorbate molecule.2,8 In the second step, the charge imbalance is offset by detachment of a proton (H+) from the adsorbate, which acquired a positive charge, and the detached H+ is transferred to a negatively polarized, up-buckled silicon atom. Thus, the molecular adsorbate is turned to a molecular fragment which is covalently bond to the surface. Each step results in a substantial gain of energy and thus more stabilized stage of the system, which provides the thermodynamical driving force for this reaction pattern. Depending on electronic size of the adsorbate molecule, the detached H+ is transferred to up-buckled Si atoms of the same Si dimer (where the molecule datively bound), the adjacent dimer, or the nearest Si dimer on the adjacent row, which are referred to as Si sites for on-dimer (OD), interdimer (ID), and inter-row (IR) H shift processes. The ID and IR H shift processes are also called growth processes parallel and perpendicular to the Si dimer row, respectively. For a molecule of small (electronic) size, like water, STM imaging (of Si(001) surface exposed to water vapor) supported with first-principle investigations suggests that the OD and ID H shifts are the most dominant reactions that take place when a water molecule Received: May 19, 2014 Revised: September 15, 2014 Published: September 22, 2014 23682

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adsorbs and dissociates on the Si(001) surface at room temperature.11,12 For large molecules like acetophenone, however, as Schofield et al. reported,2 the inter-row H shift (perpendicular to the Si dimer row) and attachment can occasionally take place as well, which results in an emergence of a hemihydride protrusion on the adjacent Si dimer row in a typical STM image.2 More details, obtained from counting the appeared features on the typical STM images suggest that OD H shift takes place occasionally as well, but it comes second in terms of occurrence and therefore presents a slightly lower (much larger) energy barrier than the IR (ID) H shift process. Here, we present a detailed density functional theory-based investigation of the acetophenone adsorption and singledehydrogenation (H detachment and transfer) processes. Two types of adsorption onto Si(001), namely upright and flat standing, are proposed and possible relaxed configurations are obtained for each and, also, the energetics of conversion between achieved sets of adsorption configurations are obtained. On-dimer, interdimer (parallel to the Si dimer row), and inter-row (perpendicular to the row) proton transfers originating from each (upright or flat) adsorption configuration are modeled and the corresponding activation energies are calculated. The kinetically and thermodynamically preferred adsorption and reaction scenarios are discerned and designated by comparing the formation and activation barriers of the possible configuration and activations barriers of their connecting pathways. Then, the preferred adsorption and H shift scenarios are compared with results of a very relevant recent experimental work.2

Figure 1. Top and side views of the small ((a) and (c)) and large ((b) and (d)) Si(001) model clusters used in the computations of acetophenone adsorption and single-hydrogen shift. The topmost Si dimer atoms are shown in black. Also, the darkness of constituent cluster Si atoms fades away, going deeper in the model cluster.

all the involved atoms and additional ++ diffuse functions have been added for the interacting atoms. The combination of single-point energy calculation and small and large geometry optimizations (plus zero-point energy correction) presented as the composite model in eq 1 aims to provide an accurate estimation of high-level functional (B3LYP) adsorption energies for a large cluster size at considerably low computational costs. The composite model, in another words, enables us to effectively minimize the effects of low level of theory and small cluster size and thus efficiently avoid prohibitively expensive all-in-one calculations of adsorption energy at the high-level theory and the large cluster size. The first term in eq 1 accounts for a single-point formation energy calculation at the higher level of theory (hybrid functional, B3LYP) and larger basis set (BS2) for the geometry obtained at the low-level functional (PW91) and small basis set (BS1). It should be noted here that in eq 1 we have used the conventional quantum chemical notation B3LYP/BS2// PW91/BS1 which denotes a single-point energy calculation at a high-level of theory and a larger basis set (here B3LYP and BS2, respectively) for an optimized geometry obtained at lowlevel of theory (here PW91/BS1). The combination of the second and third terms provides a size (thickness)-correction from a small cluster, Si49H40, to a larger cluster, Si75H56, at a low-level of theory and small basis set (PW91/BS1). Lastly, the fourth term accounts for the zero-point energy correction (ZPC) which is obtained through a harmonic vibrational frequency calculation for the small cluster/molecule system at the PW91 level of theory and BS1 basis set. After obtaining a pair of local reactant and product minima, their connecting transition state was optimized using Quadratic Synchronous Transit method,18 using which a first-order saddle point (true transition state) is obtained through searching for a maximum along a parabola (or circle) path, and for all minima along directions perpendicular to the parabola. In this method, the reactant and product points are assumed to be on a curve path,

2. THEORETICAL METHOD Studying the dehydrogenation (H shift) reaction competitions upon acetophenone adsorption onto Si(001) surface is conducted with employing the finite-size-cluster models of the surface-molecule interaction within the framework of a widely accepted composite model.8,14,15 The use of the composite model minimizes the effect of finite cluster size and finite basis set as well as the approximate exchangecorrelation theory. The Gaussian 09 software16 has been used to carry out the geometry optimization and frequency calculations. Based on the composite model used, the formation energy of every involved (intermediate and transition) state is expressed as E = E(B3LYP/BS2//PW91/BS1, Si49H40)+ E(PW91/BS1, Si 75H56) − E(PW91/BS1, Si49H40)+ EZPC(PW91/BS1, Si49H40)

(1)

where BS1 and BS2 stand for small and large basis sets, respectively, and PW9117 and B3LYP denote two types of (generalized-gradient approximation and hybrid, respectively) exchange-correlation functionals used in this work. Also, Si49H40 and Si75H56 are small and large model clusters, which both comprise two rows of three surface Si dimers, see Figure 1a,b, and are four and five layer deep, respectively (see Figure 1c,d). The small basis set (BS1) consists of 6-311++G(d,p) atomic basis sets for the atoms of the molecule and topmost Si layer (called interacting atoms here), 6-311G(d,p) for the atoms of the second layer, and LANL2DZ for the rest of Si atoms as well as the terminating hydrogen atoms. In the BS2 basis set, 6-311G(2df,2pd) atomic basis set is used to describe 23683

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pathways in terms of the competitiveness of the activation energy. Also, upright-to-flat (and reverse) dative adsorption conversions are computed and the possibilities of these interactions are discussed as to kinetics of the adsorption conversions versus H shift process. The numerical results obtained are then compared with the available STM imaging data, and relevant discussions are provided accordingly.

on which the calculation gets closer to the quadratic region around the transition state point. Then eigenvector-following steps (using Quasi-Newtown algorithm) are taken to complete the optimization. In order to climb (in a number of steps) to the quadratic region around the transition structure point, a tangent vector at each point X is calculated (from the corresponding reaction and product vectors, R and P, respectively), which is read (P − X) (R − X) T∝ − 2 |P − X| |R − X|2

3. RESULTS AND DISCUSSION 3.1. Upright Standing-Led H Shift. Each row in Figure 2 shows side and top views (left and right panels, respectively) of

(2)

Each step size along the path is determined according to eigenvector-following procedure by calculating the gradient (g) and Hessian (H), which are then used to obtain the displacement

ΔX = −gH −1

(3)

Climbing toward the quadratic region is continued until the displacement falls below a specific threshold value. Also, in the eigenvector-following step, the overlap between the tangent vector and the Hessian eigenvectors is computed, and the eigenvector with greatest overlap with the tangent vector is chosen to guide the optimization along the right path. Having chosen the right eigenvector, subsequently, the structure optimization is completed when some standard convergence criteria (on the gradient and the displacement) are met.18 All possible vibrational modes associated with every obtained transition state are calculated to see if the set of vibration modes satisfy true-transition state requirements (except one imaginary frequency all frequencies are real). In a typical frequency calculation, all possible Vineyard attempt vibrational modes are calculated and then used to verify the optimized geometries as true minima or transition states. In our cluster model, where the surface is modeled using a finite-size representation and truncated bonds (between the cluster and its remainder) are terminated, the finite size imposes a limit on the degree to which the surface−molecule system relaxes and the Si surface responds to the strains induced by the adsorption/H shift processes. These introduce errors in the calculations of binding energy: the smaller the model cluster is chosen, the greater underestimation of the binding would be.15 A similar trend is observed for a typical periodic slab model. However, in the slab model calculations, the sources of errors come from a periodic repeat from one cell into the next, which this introduces not only constraints that limit the degree the system relaxes to, but also unwanted electrostatic and steric interactions (between adsorbate and its periodic images). These sources of errors both energetically destabilize the systems and thus make large underestimation when a small unit cell is used to model a reaction, etc.15 Further underestimation errors can also be made in DFT calculations by using less-expensive simpler exchange-correlation functionals and smaller basis sets in both cluster and slab model. The use of composite models in both cluster model (employed in the present work) and periodic slab model, however, indirectly reduce these errors within the energy calculations.15 In the present work, we searched for all possible on-dimer, interdimer, and inter-row pathways of the H-shift for all possible upright and flat standing dative-adsorption configurations of a single acetophenone molecule. A set of energetically preferable H-shifts for each dative-adsorption configurations is achieved by selecting among several obtained

Figure 2. Side and top views of the three possible up-right adsorption configurations. Red arrows in the top views indicate possible proton transfer reactions leading to H-shifted configurations (B1 to B3). Calculated formation energies of the adsorbates are given in eV relative to a gas phase molecule and the free surface.

a stable upright (standing) configuration for an acetophenone molecule which has datively adsorbed onto the Si(001) surface. The notable negative values of the formation energy for acetophenone/Si(001) systems indicate the high level of stability of the dative adsorption which is triggered by interaction between nucleophilic element of the acetophenone tethering group, oxygen, and electrophilic constitutes of the Si(001) surface, down-buckled Si atoms. This is in agreement with the broad consensus in the literature,8,19 where similar highly stable dative adsorptions are reported for the molecules containing electron-rich elements. A single-, dative-bond formation gives rise to upright standing of the molecule, and also renders an up-buckled negatively charged Si site (at the other end of the Si dimer), which then along with the similar neighboring site (up-buckled Si atoms on the adjacent dimer and the nearest dimer on the adjacent row) could act as Lewis base sites (which are indicated by the red arrows pointing toward them in Figure 2). These Lewis base Si atoms can accept a proton from α-CH3 group in the course of a follow-up H-shift reaction. Due to dative-bond attachment of the 23684

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acetophenone molecule at the down-buckled Si dimer end, the molecule becomes partially positively charged, while the Si dimer end opposite to the adsorbed molecule is up-buckled and thus becomes a negative donor site.20 The up-buckled Si atom thus cannot only act as a donor site for a detached proton (H+) but also react with the molecule body pre-H shift process, through formation of bond with (central) chiral C atom of the adsorbed acetophenone.20 The formed adsorption configuration is called [2 × 2]-cycloaddition product and is more stable than the upright standing dative adsorption configuration.20 This shows that up-buckled Si dimer end can act as a reactive site in the acetophenone adsorption process prior to the followup dissociation processes. Our calculations suggest that the least stable (upright standing) conformation (A1c) can almost barrierlessly convert to more stable (A1b) and then the most stable (A1a) conformations by two consecutive small-angle rotations. As can be seen in the top views (right column in Figure 2), the conformation A1a can give rise to on-dimer and interdimer H shifts, the conformation A1b to interdimer and inter-row H shifts, and, finally, the conformation A1c to only an inter-row H shift (see red arrows in Figure 2b, d, and f). Correspondingly, there are five H-shift products (so-called enolates) of which only three have been shown in Figure 3. The

Figure 4. Potential energy profiles of on-dimer (solid), interdimer (dotted), and inter-row (dashed) H-shift reactions. Activation barriers leading to on-dimer, interdimer, and inter-row enolates are 0.25, 0.38, and 1052 eV, respectively.

corresponding adsorption and (H-shift) product states and then subtracting the adsorption state formation energy from the transition state energy. Since there are two H shifts for interdimer and inter-row processes, the lower activation energy is taken to be the kinetically preferred activation energy for the H shift process. The obtained set of activation energies is a clear indication of the prevalence of the on-dimer reaction over the interdimer and inter-row reactions (see calculated reaction rate constant for each reaction in Table 1). However, although, Table 1. Normalized Reaction Rate Constants (A exp(−Ea/ KT)) of the H-Shift Processes Resulted from Upright Standing- and Flat-Dative Adsorption Configurationsa adsorption/H shift process upright standing flat

on-dimer 1 4.8 × 10−5

interdimer −3

5.8 × 10 1

inter-row 2.4 × 10−5 1.1 × 10−6

a

The attempt frequency A is assumed to be 1012 Hz. The normalization factor for each (upright or flat) set is the maximum reaction rate constant obtained for the set.

the activation energy order for interdimer and inter-row reaction agrees well with the reported STM imaging findings,2 the quantified on-dimer reaction prevalence largely contradicts with the relatively smaller number of on-dimer dissociated-H positions counted in the typical STM image of the Si(001) surface dosed with acetophenone at room temperature.21 The predicted kinetically preferred on-dimer reaction commences from the most-stable upright conformation, A1a, and ends at the enolate B1 with an energy gain of 0.9 eV (see Figure 3a,b). As mentioned above, the reaction presents a facile barrier (0.25 eV), suggesting a relatively high rate of on-dimer enolate production at the room temperature. The conformation A1a as well stands as the precursor for the preferred interdimer reaction which will ends at the enolate conformation B2 (see Figure 3c,d). Unlike the first two reactions, the (kinetically preferred) inter-row H-shift is triggered by an acetophenone assuming the least stable conformation, A1c, and presents a mild barrier, which is well reachable at room temperature and finally results

Figure 3. Side and top views of the enolates produced due to on-dimer ((a) and (b)), interdimer ((c) and (d)), and inter-row ((e) and (f)) H-shift reactions.

energy gain for the on-dimer enolate is over 0.1 eV larger than those of interdimer and inter-row enolates. This reflects the fact that a singlet state (of molecule/surface) always acquires lower energy than a triplet state does. As shown in Figure 4, the calculated smallest (preferred) activation energies for on-dimer, interdimer, and inter-row H shifts are 0.25, 0.38, and 0.52 eV, respectively. The activation energies for each H shift process are calculated by finding the transition state between its 23685

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in the enolate conformation B3 (Figure 3e,f) with the energy gain of 0.8 eV. These all indicate that, in spite of an existing seemingly large inter-row distance, the inter-row H shift is possible for the acetophenone/Si(001) surface system, and also, the final enolate product should have a long lifetime and, thus, is observable in a typical STM imaging run of minutes time scale. This is in good agreement with STM observations of Schofield et al.,2 who reported coexistence of interdimer and inter-row enolate features in STM images of an acetophenonevapor-exposed Si(001) surface. However, the theoretically predicated dominance of on-dimer enolates points out the incompleteness/deficiency of the upright standing-adsorption model for an acetophenone/Si(001) system with respect to competition of different single first-deprotonation paths for an acetophenone molecule on the Si(001) surface at room temperature. This incompleteness of the model will be addressed and resolved (by a complementary model) in the next sections. 3.2. Flat Standing, Dative-Led H Shift. Given that upright set of H-shift activation barriers can only partially explain the relative abundance of the H shift products on a typical STM image,2 other possible adsorption configurations (and their follow-up H shift reactions) should be investigated in order to obtain a complete or (at least) better agreement with results of the STM experiments.21 Among numerous possible adsorption configurations is the flat, datively bonded adsorption configuration of the acetophenone molecule (on Si(001) surface) in which not only the molecule is still datively bonded via its (nucleophilic) oxygen atom, but also its phenyl ring is double-bonded to the Si dimers. This configuration is assumed when the acetophenone phenyl ring bridges two ends of either a single Si dimer or two neighboring dimers on the same row or two dimers of two neighboring rows (see first, second and third rows, respectively, in Figure 5), which we hereafter refer to them as on-dimer, interdimer, and inter-row attachments of the phenyl ring, respectively. As a result, the acetophenone phenyl ring assumes a flat configuration (while the molecule is still datively bonded to the surface) and the acetophenone α-CH3 group assumes an up-pointed or flat orientation with respect to the Si surface. This three-bond adsorption configuration of the acetophenone molecule can resulted by either two step conversion of an upright standing adsorption configuration or direct tumbling of the gas molecule onto the Si(001) surface; in the former the two extra σ-bond formations can take place in two steps (i. e., consecutive formations of two C−Si bonds), whereas in the latter all three bonds are formed at once when an acetophenone molecule tumbles onto the Si(001) surface. Figure 5 shows six possible flat adsorption configurations, which (as stated above) differ from each other in the attachment orientation of the acetophenone phenyl ring and the α-CH3 group. As the binding energy calculations suggest, on-dimer orientations (designated with C1a and C1b) of phenyl ring result in more stable configurations (regardless of the α-CH3 orientation) owing to the singlet form associated with the on-dimer phenyl (dimer bridge) attachment. It should be noted that for the same two phenyl configurations, and differently oriented methyl groups, a flat α-CH3 orientation (−CH3 closer to the surface) appears to render a more stable overall configuration. We should also note here that not all obtained flat configurations, particularly the highly stable ondimer configurations (C1a and C1b), can give rise to competitively low-barrier H shift reactions.

Figure 5. Top views of six possible flat-dative adsorption configurations in which a phenyl ring can connect two silicon atoms of a single dimer ((a) and (b)), two silicon dimers on a single row ((c) and (d)), and two dimers of neighboring rows ((e) and (f)). Adsorption configurations with the same phenyl ring attachments are differentiated by upward and (almost) flat orientation of the α-methyl part with respect to the surface. Small red arrows indicate possible H shift directions for each adsorption configuration.

The preferred interdimer H shift reaction is started off from interdimer oriented phenyl configuration C2b (flat α-CH3 with the binding energy −0.91) and it converts to the less stable interdimer configuration (C2a) and then the H transfer process happens. The interdimer H shift results in the product configuration D2 with a thermodynamic energy gain of 0.89 eV. The calculated overall effective activation energy turns out to be 0.35 eV, which is again low, see Figure 7. Unlike the interdimer H shift, the preferable on-dimer and inter-row reactions commence from inter-row (oriented) phenyl configuration C3b (see Figures 5f and 7) and results in final products by overcoming overall (effective) energy barriers of 0.61 and 0.71 eV, respectively. It should be noted that, as Figure 7 displays, the on-dimer H shift is completed in two steps: (1) upward rotation of the α-CH3, turning the C3b configuration to a less stable configuration, C3a, and (2) a relatively low barrier H shift which results in an energy gain of over 1.2 eV. The obtained new set of preferable H shift barriers suggest that the interdimer H shift is orders of magnitude faster than on-dimer and inter-row reactions (see their corresponding reaction rate constants in Table 1), which points out the fact that the interdimer product would be the most prominent feature in a typical image that is recorded in an STM experiment. This appears to be in good agreement with the work of Schofield et al.2 where much more abundance of the interdimer feature was reported. Also, the obtained order of activation energies for on-dimer and inter-row reactions 23686

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possibility of either the flat-configuration-initiated H shift model or the upright H shift model presented so far. We will address the possibility of such interactions (between the acetophenone molecule and Si(001) surface) by thoroughly exploring all possible steps and presenting the associated energetics in conversions from the upright configurations to flat configurations and vice versa. 3.3. Upright-Dative to Flat-Dative Adsorption Conversion versus H-Shift Reaction. As noted in the previous section, the phenyl ring of an upright acetophenone adsorbate can form two single-bonds with the Si atoms via two of its C atoms. This tendency can trigger an upright to flat adsorption conversion, which normally takes places in two consecutive steps, namely the formation of a C−Si bond between one phenyl C atom and the nearest Si atom on an adjacent dimer, and then formation of a second C−Si bond on the adjacent Si dimer or the nearest Si dimer of the neighboring Si dimer row. The initial dative bond between a down-buckled Si atom and the oxygen of the tethering carbonyl group is preserved throughout the configuration transition. However, the total electronic configuration of the acetophenone/Si(001) surface system could undergo changes and turn to an open shell configuration during the geometry transition process; when the first C−Si bond is formed between the phenyl ring C atom and an up-buckled end of adjacent Si dimer, the free ends of the two Si dimers have singly occupied dangling bonds, which renders a less stable configuration (see energy states for a half-flat adsorption configurations in Figure 7). In the second step, the total closed shell electronic configuration is again obtained when another phenyl ring C atom forms the second bond with an end of an adjacent Si dimer (see Figure 5). We have calculated energetics of two-step conversion processes (from upright geometries) leading to all obtained six flat geometries (in Figure 5). Potential energy profiles for most important upright-to-flat configuration conversion have been displayed in Figure 7. In fact, the (energy) profiles have been depicted for the conversions that lead to suitable flat configurations which give rise to (energetically) preferable H

Figure 6. Product configurations of one-dimer (a), interdimer (b), and inter-row (c) H shifts initiated from flat-dative adsorption configurations C3a, C2a, and C3b, respectively.

qualitatively confirms the number of on-dimer and inter-row H shift positions observed and counted in the STM experiments.21 However, here one could raise some arguments that concern the occurrence of energetically possible conversions between the upright and flat standing adsorption configurations. These adsorption conversions could compete with the H shift reactions at room temperature and thus phase out the

Figure 7. Potential energy profiles of energetically preferable on-dimer (solid), interdimer (dotted), and inter-row (dashed) H shift reactions. Also, dotted and dashed lines profile conversions from the up-right standing configuration A1a to most suitable flat adsorption configurations (C2b and C3b) as well as from flat to upward-methyl orientations (C2b to C2a and C3b to C3a). 23687

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shift reactions. It can be seen that upright-to-flat-conversion activation energies (EA = 0.71 and 0.81 eV) are larger than those of the H shift processes initiated by the upright standing dative conformations (EA = 0.24, 0.35, and 0.52 eV for ondimer, interdimer, and inter-row H shifts, respectively). This indicates that the deprotonation processes are more likely to happen before adsorption conversion when the molecule only datively adsorbs on the Si(001) surface. Therefore, the process of upright to flat configuration transition followed by H shift at room temperature is in fact inconsequential, and its occurrence can be ruled out. Likewise, we see that the activation barriers for the reverse process (i.e., the flat to upright configuration transition; for example C2b to A1a configuration transition) are so large (EA = 0.77 and 0.86 eV) that a flat, datively adsorbed molecule is very unlikely to detach from its phenyl side and assume an upright standing configuration. Arriving at all these facts, we can come to the conclusion that once the molecule tumbles and flat-datively binds to the Si(001) surface it is more likely to undergo dehydrogenation process than detachment from its phenyl ring side and assume an upright standing dative configuration instead. Here it should be noted that since the occurrence of a H shift process depends on the availability of the (up-buckled) donor sites adjacent to the adsorption site and the fact that an acetophenone molecule preferably react (from its carbonyl oxygen) with a down-buckled Si dimer end, it could be speculated that the second molecule adsorption cannot affect (presumably restrict) the H shift processes started off the first adsorbate. However, this is the case only when the molecule uprightly binds to the surface, and thus a more-stable [2 × 2]cycloaddition adsorption of the second molecule on the same row (or the nearest Si dimer on the next row) could make the interdimer (inter-row) donor site unavailable for an interdimer H shift.20 Besides, the [2 × 2]-cycloaddition adsorption of the first molecule itself can phase out not only the on-dimer H shift process but also a possible inter-row H shift process since the methyl group will be disposed far from a nearest donor site on the next dimer row.

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AUTHOR INFORMATION

Corresponding Author

* E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS H.M. would like to thank Dr. Oliver Warschkow for sharing his useful and constructive views to this study. H.M. also acknowledges the courtesy of Adam Rahnejat from the University College London for providing unreported details of their published STM results.2

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REFERENCES

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4. CONCLUSION In this work, we have used density functional theory in the framework of a cluster composite model to study on-dimer, interdimer, and inter-row H shift processes for an acetophenone molecule upon landing on the Si(001) surface. Possible upright and flat adsorption configurations and their inter conversions have been studied as well. Using the composite model, we have shown that the activation energy for inter-row H shift is relatively small suggesting that the inter-row process can easily take place at room temperature which is in good agreement with the findings of the STM experiments.2 Besides, the provided composite model calculates very low activation barriers for interdimer H shift, which confirms the reported largest number of interdimer dissociation product captured in a typical STM imaging run.2 It, moreover, rules out any prominency for on-dimer reaction again in good agreement with the rare emergence of on-dimer H shift positions in the STM images recorded from the Si(001) surface exposed to acetophenone vapor at room temperature.21 More DFT data obtained fades out any possibility of competitiveness for adsorption configuration interconversions versus H shift reactions and, therefore, suggests that H shifts are the more likely processes that can occur to the acetophenone molecule when it adsorbs onto the Si(001) surface. 23688

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and Surfaces: Applications of the Generalized Gradient Approximation for Exchange and Correlation. Phys. Rev. B 1992, 46, 6671−6687. (18) Peng, C.; Ayala, P. Y.; Schlegel, H. B.; Frisch, M. J. Using Redundant Internal Coordinates to Optimize Equilibrium Geometries and Transition States. J. Comput. Chem. 1996, 17, 49−56. (19) Schofield, S. R.; Saraireh, S. A.; Smith, P. V.; Radny, M. W.; King, B. V. Organic Bonding to Silicon via a Carbonyl Group: New Insights from Atomic-Scale Images. J. Am. Chem. Soc. 2007, 129, 11402−11407. (20) Huang, H. G.; Huang, J. Y.; Cai, Y. H.; Xu, G. Q. Vibrational Studies of the Reactions of Acetophenone with Si(100)−2 × 1. Chem. Phys. Lett. 2005, 414, 143−147. (21) Out of 752 dissociation features (of which 135 were unidentifiable) in a typical STM image, which was taken from an As-doped Si(001) sample pre-exposed to acetophenone vapor,2 76 (10.1%), 528 (70.3%), and 12 (1.6%) features were counted for ondimer, interdimer, and inter-row H shift positions, respectively.

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