LETTER pubs.acs.org/JPCL
On the Use of the SiC(100)-c(22) Surface as a Substrate for the Creation of Ordered OrganicSemiconductor Interfaces Yanli Zhang† and Mark E. Tuckerman*,‡ †
Department of Chemistry and ‡Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York
bS Supporting Information ABSTRACT: The creation of ordered organicsemiconductor interfaces on many commonly used semiconductor surfaces poses a significant challenge due to the large number of reaction products that can be formed with small conjugated molecules on these surfaces. In this Letter, we employ ab initio molecular dynamics simulations to investigate the reaction between the SiC(100)-c(22) surface and 1,3-cyclohexadiene. By generating detailed freeenergy profiles for different possible reaction channels, we find that one of the products, a [4+2] intradimer adduct, is thermodynamically highly favored over other adducts that could potentially form on this surface, suggesting that this product state could form the basis of an ordered interfacial structure. Further investigation of an example of such an ordered structure, again using ab initio molecular dynamics, reveals that this structure is stable at room temperature. SECTION: Surfaces, Interfaces, Catalysis
T
he chemistry of hybrid structures composed of organic molecules and semiconductor surfaces is opening up new areas of technological development.1,2 The creation of ordered organicsemiconductor interfaces through covalent attachment of organic molecules to the surface has received considerable attention because of the applicability of such structures in nanolithography,3 molecular electronics,410 and biological and other nanoscale sensing devices.1113 Experimental techniques for creating ordered nanostructures include self-directed growth,1418 electrografting,19 and templating.20,21 To date, there has been some success in obtaining locally ordered structures on the hydrogen-terminated Si(100) surface.14,2225 These methods require a dangling Si bond without a hydrogen to initialize the self-replicating reaction. Another approach eliminates the initialization step by exploiting the reactivity between surface dimers on certain reconstructed surfaces with the π bonds in many organic molecules. The challenge with this approach lies in engineering the surface and/or the molecule so as to eliminate all but one desired reaction channel. The need to restrict the product distribution between the molecule and surface means that the popular Si(100)-21 surface is not a suitable choice. This surface consists of rows of closely spaced buckled SiSi dimers that serve as reactive sites for cycloadition reactions with conjugated dienes such as 1,3-butadiene or 1,3-cyclohexadiene.2639 However, the charge asymmetries on this surface caused by the dimer buckling lead to a violation of the usual WoodwardHoffmann selection rules, which govern many purely organic reactions, thereby allowing a variety of possible [4+2] and [2+2] surface adducts.2639 Silicon carbide (SiC), which is often the material of choice for sensor r 2011 American Chemical Society
applications under extreme conditions4042 or subject to biocompatibility constraints,43 offers a potentially attractive alternative to its more popular cousin Si because individual reactive sites are farther apart, thereby reducing the number of reaction channels at each site. Even with SiC, however, the choice of the surface reconstruction is critical. The 3C-SiC(001)-3 2 surface contains alternating layers of Si and C in the same zinc blend structure as Si(001) with widely spaced SiSi dimers in the top layer, suggesting that a restricted product distribution with a conjugated diene might result. A recent theoretical study44 suggests that, while fewer cycloaddition products compared to Si(100)-21 do, indeed, result, it is not possible to restrict the distribution to a single reaction product on this surface. In this Letter, we employ ab initio molecular dynamics (AIMD), in which the finite-temperature nuclear motion of a system is driven by forces generated “on the fly” from densityfunctional-based electronic structure calculations, to explore the cycloaddition reaction of 1,3-cyclohexadiene with a different SiC surface reconstruction, specifically, SiC(100)-c(22). This surface exhibits a crucial difference from the 3C-SiC(001)-3 2 in that it is characterized by CtC triple-bonded dimers in the surface layer, which bridge SiSi single bonds. These triple bonds are well separated and reactive, suggesting that this particular surface reconstruction of SiC could lead to a restricted product distribution for the cycloaddition reaction. In this study, AIMD calculations are employed to generate thermodynamic (free-energy or Received: June 3, 2011 Accepted: July 2, 2011 Published: July 02, 2011 1814
dx.doi.org/10.1021/jz200750b | J. Phys. Chem. Lett. 2011, 2, 1814–1819
The Journal of Physical Chemistry Letters
LETTER
Figure 1. Snapshot of the 1,3-cyclohexadiene + SiC(100)-c(22) system used in this study.
thermal energy) profiles for seven possible reaction products, and it is found that, among these, one product, a [4+2]-intradimer DielsAlder type product, is highly favored thermodynamically over the remaining products, suggesting that this reaction channel could be used to create an ordered interface on this surface. The system setup used in our calculations, which is shown in Figure 1, together with the electronic structure protocol employed and explicit treatment of surface periodicity (see Computational Methods), is capable of reproducing the experimentally observed CtC surface dimer buckling45 that static ab initio calculations using cluster models are unable to describe.46 The calculated buckling angle is approximately 9 on average. At a temperature of 300 K, employed in these calculations, the dimers are observed to undergo a “rocking” motion about their equilibrium position. Consequently, they rarely tilt in the same direction, as is seen in zerotemperature STM images.45,47 The average distance between dimers in a row is 4.39 Å, and the distance between neighboring rows is 4.97 Å, both of which agree well with other calculated results. Other structural parameters are given in the Supporting Information. In order to monitor the progress of the cycloaddition reactions of the surface with 1,3-cyclohexadiene, we employ a reaction coordinate given by 1 ξðrÞ ¼ jðrCma þ rCmb Þ ðrXcs þ rXds Þj 2
ð1Þ
where rCma and rCmb are the positions of two carbon atoms of the 1,3-cyclohexadiene molecule and rXsc and rXsd are two surface or sublayer atoms (either C or Si) with which the two carbon atoms in the molecule will form covalent bonds in the reaction. For the reactions studied here, a = 1 and b = 2 or 4, corresponding to [2 +2] and [4+2] adducts, respectively. The coordinate ξ was shown previously to correctly predict the reaction path of 1,3butadiene with the Si(100)-21 surface.37 By generating freeenergy profiles as functions of ξ and comparing these profiles, we can readily determine if a particular reaction product is thermodynamically favored over others. Because large barriers along the reaction path are expected, the blue moon ensemble method48,49 is employed to generate these free-energy profiles. In the blue moon
Figure 2. Labeled atoms on the first two layers for the constrained simulations.
approach, the value of ξ is fixed at a set of discrete values along the reaction path, and the free-energy derivative dG/dξ is computed from a conditional average of the generalized force Fξ = ∂H/∂ξ over an ensemble at each value of ξ. The full free-energy profile is then computed by integrating the average force according to Z ΔGðξÞ ¼
ξ
ξ0
ÆFξ0 æðcondÞ dξ0
ð2Þ
where the average ÆFξ0 æ(cond) indicates that the condition ξ(r) = ξ0 is imposed and, in practice, the integral is performed numerically at the chosen values of ξ(r) starting from a chosen reference point ξ0. Complete free-energy profiles are necessary in order to establish any initial barriers to the reaction and to identify potential stable intermediate states. The free-energy profiles also provide information about reaction mechanisms. Free-energy profiles for the following reaction products were determined (see Figure 2 for the atom labeling scheme and ref 52 for a clarification of the terminology employed): (1) a [4+2] intradimer DielsAlder type adduct, (2) a [2+2] intradimer adduct, (3) a [4+2] interdimer, interrow adduct with carbons C8 and C9 (denoted [4+2]8,9(inter)), (4) a [4+2] interdimer, intrarow adduct with carbons C8 and C12 (denoted [4+2]8,12(inter)), and (5) a [2+2] sublayer adduct with silicon atoms Si1 and Si2. We also computed average energetics of two additional products related 1815
dx.doi.org/10.1021/jz200750b |J. Phys. Chem. Lett. 2011, 2, 1814–1819
The Journal of Physical Chemistry Letters
LETTER
Table 1. Energies (ΔEb in kcal/mol) and locations along the ξ coordinate (in Å) of the initial barriers to the formation of different adducts quantity
Figure 3. Free-energy profiles for the formation of the [4+2] intradimer adduct (A), [4+2]8,9 interdimer adduct (B), and [4+2]8,12 interdimer adduct (C). The snapshots include configurations along the reaction path. White, blue, and yellow spheres denote H, C, and Si atoms, repectively, and red spheres indicate the location of centers of maximally localized Wannier orbitals (see text).
Figure 4. Free-energy profiles for the formation of the [2+2] intradimer adduct (A) and [2+2] sublayer adduct (B). The snapshots include configurations along the reaction path. White, blue, and yellow spheres denote H, C, and Si atoms, repectively, and red spheres indicate the location of centers of maximally localized Wannier orbitals (see text).
to (4), namely, a [4+2] interdimer, intrarow adduct with carbons C8 and C11 (denoted [4+2]8,11 (inter)) and a [2+2] interdimer, intrarow adduct with carbons C8 and C11 (denoted [2+2]8,11 (inter)). Adducts in which the molecule forms one covalent bond to a surface Si and one covalent bond to a surface C were considered and found to be unstable; hence, free-energy profiles for such adducts were not explicitly computed. Free-energy profiles (FEPs) for the [4+2] adducts are shown in Figure 3, while those for the [2 +2] adducts are shown in Figure 4. With the exception of the [4+2] intradimer adduct, it is clear that each of the remaining reaction products has a substantial initial free-energy barrier. These barriers are compiled in Table 1 together with their location along the ξ path. While the barrier for the formation of the [4+2] intradimer DielsAlder type adduct is less than 10 kcal/mol, those for the remaining products all
[4+2]
[4+2]8,9
[4+2]8,12
[2+2]
[2+2]
(intra)
(inter)
(inter)
(intra)
(sublayer)
ξ
2.42
1.84
2.32
2.32
2.38
ΔEb
8.11
26.04
18.13
24.83
44.48
exceed 18 kcal/mol. The largest barrier (∼44 kcal/mol) is associated with the [2+2] sublayer adduct. Such large barriers indicate that in an initial approach of the molecule to the surface, the [4+2] intradimer adduct would be overwhelmingly favored, even though some of the other products are thermodynamically favored once the initial barrier is surmounted. This is in accord with static ab initio calculations of the reaction between the SiC(100)-c(22) and the electronically similar 1,3-butadiene using either cluster models46 or periodic slabs.53 For clarity, in Figure 5, we show a closer snapshot view of the [4+2] intradimer adduct. Products such as the [4+2] interdimer adduct with carbons C8 and C12 and the sublayer adduct are only metastable compared to the unbound state. For the [4+2] and [2+2] interdimer products with carbons C8 and C11, although we do not have full free-energy profiles for these, we see from the average energetics plotted in Figure 6 that the process is significantly uphill before the final product forms, indicating that, as with the [4+2] adduct with C8 and C12, these adducts are also very unlikely to form. The FEPs in Figures 3 and 4 provide important insights into the underlying reaction mechanism. In refs 3739, it was shown that the reaction of 1,3-butadiene or 1,3-cyclohexadiene with the Si(100)-21 surface proceeds via an asymmetric, nonconcerted mechanism that begins with a nucleophilic attack of the CdC double bond on the positively charged member of a buckled surface dimer and passes through a well-defined carbocation intermediate state. This is true for all adducts formed on Si(100)21, including the [4+2] intradimer product. By contrast, on the SiC(100)-c(22) surface, the [4+2] intradimer adduct proceeds via an asymmetric, concerted mechanism, as evidenced by the lack of a stable intermediate after the initial barrier. The asymmetric nature of the reaction is a result of the dimer buckling on the surface, which gives rise to a slight charge asymmetry between the two carbons in the dimer, with the lower carbon carrying a small positive charge and the upper carbon compensating for it with an equal negative charge. As with the Si(100)-21 surface, each reaction begins with a nucleophilic attack on the positively charge carbon in the buckled dimer. The change in the bonding pattern as a function of ξ can be visualized using the centers of maximally localized electronic orbitals (also called Wannier functions),54 shown as red spheres in Figure 3 (see, also, Figure 4). These show that at the putative transition state of the FEP, one of the CC bonds forms, but just past this state, the Wannier center moves into he second CC bond, so that at ξ ≈ 1.89 Å, this second bond is essentially in place, and the cycloaddition process is strongly downhill from there to the formation of the final adduct at the free energy minimum where ξ = 1.43 Å. Although most of the reaction channels also appear to be governed by asymmetric, concerted mechanisms, as judged from their free energy profiles, at least one of them (the [4+2]8,12 interdimer adduct in Figure 3C) shows a metastable intermediate complex, which bears some similarity to an [4+2]8,11 adduct. Further insight into the reaction mechanisms of the different adducts, including potential intermediate states, can be 1816
dx.doi.org/10.1021/jz200750b |J. Phys. Chem. Lett. 2011, 2, 1814–1819
The Journal of Physical Chemistry Letters
LETTER
Figure 5. Closeup snapshot of the [4+2] intradimer adduct corresponding to the final product in Figure 3A. Figure 7. Single-point energy differences (kcal/mol) between triplet SU and singlet SU for different adducts. Representative configurations taken along the reaction path at 300 K.
Figure 6. Average energy at 300 K from 1 ps equilibration runs for the [4+2]8,11(inter) and [2+2]8,11(inter) adducts.
gleaned from the average carboncarbon and carbonsilicon bond lengths as functions of the ξ coordinate along the reaction path plotted in the Supporting Information, together with snapshots of representative configurations. Finally, we consider the possibility of a radical mechanism in the reactions studied. As the AIMD calculations performed here do not allow for surface hopping between a singlet and a triplet state, we cannot probe such a mechanism directly but can only estimate its potential importance from single-point energy calculations. To this end, we performed two sets of spin-unrestricted (SU) calculations at various points along the reaction paths for several of the reaction channels; specifically, one set contained an equal number of spin-up and spin-down electrons while the other contained two more spin-up than spin-down electrons. This approximation was employed by us in a previous study to estimate the importance of a radical mechanism in the cycloaddition of 1,3-cyclohexadiene to the Si(100)-2139 and 3C-SiC(001)-3 244 surfaces. The energy difference between these two electronic configurations as a function of ξ for SiC(100)-c(22) is shown in Figure 7. At most of the points considered, the difference in energy between the triplet and singlet states is sufficiently large that a radical mechanism, although clearly not impossible, would not be energetically favored. The clear exceptions occur along the path of the [4+2] interdimer product with surface carbons C8 and C9 and the [2+2] intradimer product. For the former, however, it is also clear that this energy difference becomes small only after a barrier of roughly 26 kcal/mol is surmounted, suggesting that the reaction is unlikely to reach this possible curve-crossing point in the first place. In the latter, the small energy difference occurs only when the molecule is far from the surface and is likely a consequence of the chosen initial configuration.
In order to test the stability of an ordered interfacial structure constructed based on our findings, we set up a nanoline by placing a 1,3-cyclohexadiene molecule in the [4+2] intradimer adduct configuration on each of the CtC dimers in one (diagonal) row, annealed the system to 300 K, and ran the system under constant-temperature conditions for 4 ps. A snapshot from this run is shown in Figure 8 (left), and a plot of the evolution of the ξ coordinate averaged over all of the adducts is shown in Figure 8 (right). From the latter, we clearly see that the nanoline is stable on this time scale. The average value of ξ oscillates very close to its value at the free-energy minimum of Figure 3A, suggesting that each of the adducts remains tightly bonded to the surface, maintaining the ordered nanoline structure. In summary, ab initio molecular dynamics calculations combined with enhanced free-energy sampling has been used to show that the product distribution for the cycloaddition reaction of 1,3-cyclohexadiene with the SiC(100)-c(22) surface can be restricted likely to a single product state due to the specific choice of the surface. It is worth noting that the initial barrier (
