Competitive Chemisorption of Bifunctional Carboxylic Acids on H:Si

Jun 14, 2008 - CNR-INFM National Center on nanoStructures and bioSystems at ... on fully hydrogenated H:Si(100), using first-principles density functi...
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J. Phys. Chem. C 2008, 112, 10167–10175

10167

Competitive Chemisorption of Bifunctional Carboxylic Acids on H:Si(100): A First-Principles Study Clotilde S. Cucinotta,* Alice Ruini, and Elisa Molinari CNR-INFM National Center on nanoStructures and bioSystems at Surfaces (S3), and Dipartimento di Fisica, UniVersita di Modena e Reggio Emilia, Via Campi 213a, 41100 Modena, Italy

Carlo A. Pignedoli† IBM Research, Zurich Research Laboratory, CH-8803 Rueschlikon, Switzerland

Alessandra Catellani CNR-IMEM, Parco Area delle Scienze 37a, 43010 Parma, and S3, Italy

Marilia J. Caldas Instituto de Fı´sica, UniVersidade de Sa˜o Paulo, Cidade UniVersita´ria, 05508-900 Sa˜o Paulo, Brazil ReceiVed: NoVember 29, 2007; ReVised Manuscript ReceiVed: April 07, 2008

We investigate competitive chemisorption processes of bifunctional R-carboxy ω-alkenes and ω-alkynes on fully hydrogenated H:Si(100), using first-principles density functional theory, in extended surface simulations. We study the structural properties and quantify the energetics and activation barriers, analyzing the reaction paths. Our results reveal that, if the plain, unactivated chemisorption reaction is always achieved through high barriers, once realized the configurations are very stable, ensuring robustness and reliability of the functionalized interface. We identify the conditions where disordered configurations are more likely to arise, with both functionalities offered at the free surface. For all stable configurations, a thorough analysis of the electronic properties and the extent of hybridization in the functionalized interface allows us to identify promising candidates for applications in molecular electronics. I. Introduction Organic functionalization of silicon substrates is a promising development toward semiconductor-based hybrid molecular devices. For molecular electronics, e.g., for memory and logic applications, it would be interesting to obtain stable nanostructuring of the surface through spontaneous and self-directed chemisorption; in other directions, the covalent attachment of organic molecules could impart new characteristics to the inorganic electronic substrate, such as nanopatterning, and recognition or sensing capabilities.1–8 One important goal is the design of specific monolayers over the Si surface that present reasonable stability at working temperatures: the molecule should anchor to the Si surface through a very stable covalent bond with sufficiently high desorption barriers. At the same time, the adsorbed monolayer should exhibit the desired functional group at the free surface; thus, the molecule itself should have head-and-tail functionality. This would lead to possible competing grafting mechanisms that may give rise to disordered interfaces. Indeed, the interface structure is in many cases not clearly known, and a reliable and quantitative characterization of the possible stable configurations and the microscopic understanding of the anchoring mechanism is highly desirable. * Corresponding author. E-mail: [email protected]. Present address: Department of Chemistry and Applied Biosciences, ETHZ, Lugano, Switzerland. † Present address: EMPA, Materials Science and Technology, Duebendorf, Switzerland.

Exposing a carboxy-headgroup at the outside of the functionalized Si surface offers several advantages for patterning or further processing.9–11 Si-organic interfaces are often characterized by Si-C anchorage, obtained through reacting unsaturated alkene-12–15 or alkyne-terminated16–18 molecules (RsCHdCH2 and RsCtCH). If such molecules also contain a carboxylic (COOH) functional group, the strong affinity between oxygen and silicon atoms may alternatively lead to Si-O-C bond formation.1,7,19,20 Indeed, the attempt21 to prepare COOH-terminated layers on the H:Si(100) surface, at 200 °C starting from R-functionalized alkenes, led to very poorly ordered or even disordered monolayers: no conclusive proof about the presence of the reactive carboxylic group at the free surface was obtained. More recently, an experimental study of competition between alkene and carboxylic functionalities was carried out also for the H:Si(111) surface, and it was concluded that under UV illumination alkene-grafting proceeds faster,22 and leads to more ordered monolayers. Proposed alternative ways toward ordered COOH-terminated monolayers starting from alkene hydrosilation involve more complicated two-step procedures.10,21 COOH-terminated monolayers on H:Si surfaces have also been recently prepared through chemical electrografting16 of bifunctional alkynes, with no protection of the COOH group. However, the alkyne grafting through hydrosilation results temperature, reconstruction, and technique dependent,23 and no conclusive interpretation has been provided for the structure of the resulting interface layer, even when the same H:Si(100) flat surface and the same thermal method are used.18

10.1021/jp711303j CCC: $40.75  2008 American Chemical Society Published on Web 06/14/2008

10168 J. Phys. Chem. C, Vol. 112, No. 27, 2008 In particular, the presence of a structure with 2 Si-C bonds at the interface (following the opening of the residual double bond) was strongly debated.18,23 The Si-O-C anchorage may be very helpful for designing molecular electronics devices, in stabilizing the interface and substituting for the need of previous oxidation of the Si surface,24 which leads to poorly defined interfaces, and at the same time it can be convenient to have an unsaturated molecular group at the outer surface, due to the convenient energy location of these moieties compared to the Si valence band. Si-C and Si-O-C bonded monolayers are generally characterized by different properties,25,26 not only in terms of stability and coverage but also of structural and electronic properties. Theoretical simulations can be very helpful to explore such issues, as confirmed by the growing number of related studies.10,13,14,18,23,27–33 Extended surface models were used to study geometrical properties, through empirical molecular mechanics methods,23,28,33 while a self-consistent semiempirical tight-binding approach was used to investigate the electronic properties of these systems.10 Ab initio calculations focusing on reaction mechanisms for radical hydrosilation have been performedforH:Si(100)andH:Si(111)throughbothcluster14,18,27,32,33 and extended surface models;13,29,30 also the radical reaction of aldehydes on H:Si(111) has been simulated via first principles methods.31,33 Studies for the reaction on the fully hydrogenated surface, involving a concerted mechanism, have not been considered so far to the same extent;34,35 in particular, to our knowledge, no systematic investigations were yet performed on the competition between the two potentially reactive groups and on the comparison between the different properties that would arise for the resulting systems. In previous papers36–38 alkyl monolayers on the same H:Si(100)1 × 1 surface were investigated through extended surface ab initio density functional theory (DFT) calculations. We proposed that controlled oxidation of the Si-organic interface could be achieved through a double Si-O-C anchorage. We here study bifunctional molecules, focusing on unsaturated carboxylic acids reacting on the same Si surface: we investigate from first-principles the different bonding configurations for functionalization via molecular tail- and head-groups, along with the interface electronic properties. We explore the reaction kinetics and evaluate the energy barriers for the uncatalyzed chemisorption reactions leading to the formation of the Si-O-C and Si-C bonds, with specific attention toward molecular electronic applications. II. Methodology Ab initio theoretical approaches based on DFT are very useful for the analysis and understanding of processes involving organic molecules at surfaces; for these studies, DFT can be implemented with periodic-boundary-conditions and planewave39 basis sets, or in molecular cluster approaches using local basis sets (e.g., Gaussian33 functions). We adopt the former scheme, which allows us to study different coverage regimes and at the same time takes into account the extended nature of the surface states. The electronic structure of the surface states can critically affect the reaction mechanisms via charge transfer and rearrangement; also the different lateral steric hindrances can be better gauged in a periodic surface environment,28,33 that eliminates edge-effects. Furthermore, from purely numerical considerations, the supercell plane-waves approach is a reliable procedure, allowing for stringent convergence tests. For our studies we simulate the H:Si(100)1 × 1 surface40 with slabs of 6 Si layers, fully H-saturated (dihydride) on both

Cucinotta et al.

Figure 1. Schematic representation of the reacting systems studied here: the alkane- (A), alkene- (E), alkyne-tailde (Y) carboxylic acids and the dihydride terminated Si surface.

sides, and with an intervening vacuum layer of 15 Å. One side of the slab is then reacted with the molecule, and the cell is made large enough so that the interaction between molecule replicas is negligible. For the simulations of chemisorption through the COOH head, the supercell has 4 Si atoms per layer in a 2 × 1 configuration in terms of the conventional cubic unit cell, while for the study of the chemisorption mechanism through the unsaturated tails we use 8 Si atoms per layer in order to avoid lateral interactions through the “large” exposed carboxylic heads. The initial configurations are obtained using the PCFF empirical force field,33,41,42 and ab initio DFT structural relaxations are then performed, without symmetry constraints, until the forces on all atoms vanish within 0.005 eV/Å. For the DFT calculations, we use the parallel version of the ESPRESSO package43 with the PW9144 generalized gradient approximation for the exchange and correlation functional and consistent “ultrasoft” pseudopotentials.45 The wave functions are expanded in plane waves up to an energy cutoff of 25 Ry (200 Ry for electronic density) and the Monkhorst-Pack special k-points46 sampling of the Brillouin Zone was employed. Reaction pathways and activation energies for the chemisorption are evaluated within the nudged elastic band (NEB) approach in the “climbing image” implementation.47,48 The analysis of the electronic charge distributions of both the isolated molecule and the H:Si(100)1 × 1 surface gives useful hints for the individuation of an optimal starting configuration: as a general rule, in selecting the initial configurations for evaluating the intermediate images in the NEB procedure, we considered the geometries where the molecule exposes the active site and possible charge protrusions to the underlying surface charge depletion; we then let the path relax toward its nearest minimum. During path optimization, only the end points of the minimum energy path (MEP) are kept fixed, while the specific features of the intermediate configurations are not a priori defined. The accuracy of the path minimization was determined by the maximum force in the direction perpendicular to the path (set to 0.09 eV/ Å). We used up to 21 replicas, depending on the particular path, which corresponds to a small (below 1.8 Å) averaged distance between the images composing the path. We have chosen prototypical molecules taken as representatives of alkane-, alkene-, and alkyne-tailed carboxylic acids: we focus in this work on the butanoic acid CH3-(CH2)2-COOH, the 3-butenoic acid CH2dCHsCH2sCOOH, and the 3-butynoic acid CHtCsCH2sCOOH at the H:Si(100) surface (see Figure 1 and Table 1). We consider here the 1 × 1 reconstruction for the H-saturated surface, corresponding to dihydride terminations for the surface Si atoms; this substrate is well characterized,40 technologically relevant, and environmentally robust.17 The absolute value of the activation barriers is expected to be high due to the use of this fully passivated substrate; on the other hand, this condition should impart a superior stability to the functionalized surface.

Chemisorption of Carboxylic Acids on H:Si(100)

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TABLE 1: Interatomic Distances (in Å) for the Initial Configurations, Free Molecules, and Clean Dihydride H:Si(100) Surfacea system

A

E

Y

CdO CsOH CωsCζ C-C C-H Sis-Siss Sis1-Sis2 Si-H

1.23 1.37 1.52 1.51 1.10

1.23 1.36 1.34 1.50 1.09

1.23 1.35 1.21 1.45 1.07

H:Si(100)

2.34 3.87 1.50

a Only relevant atoms involved in the molecule-surface reactions are included. The surface Si atom is labeled Sis, the nearest subsurface neighbor is labeled Siss; Sis1 and Sis2 are nearest-neighbor surface atoms.

We simulate all chemically feasible chemisorbed structures for the chosen molecules and calculate binding energies as the difference between the total energy of the reaction products (functionalized surface and residue, if any) and the total energy of the reagents (hydrogenated surface and carboxylic acid), all with fully optimized geometries. Binding energies are given in eV per molecule. Reaction pathways and activation barriers are directly obtained from the potential energy variation as a function of the image position along the MEP, that comes out from the NEB calculation. Energy spectra and band alignments are analyzed through the density of states for each system, and charge density plots are studied for relevant states. For each molecule, we compare anchoring through the head (carboxyl) and tail groups, in order to obtain a thermodynamic and kinetic estimate of the degree of disorder to be found in actual experiments of surface functionalization. In the following we first briefly describe the simulation results for energetics and structure of the chemisorption reactions; we then discuss possible competitions arising from reaction through head (COOH) and tail (CωtCζ or CωdCζ) groups, before passing to the analysis of the electronic structure. III. Results: Structure, Energetics and Reaction Pathways A. Oxygen Grafting. For the propionic acid (CH3-CH2-COOH), we recently showed36,38 that the reaction through the oxygen atoms in the carboxylic group is conducive to a densely covered monolayer (50% coverage):49 each molecule may bond to the surface through a double Si-O-C bridge (we will refer to this configuration as OO system), with a binding energy of 1.23 eV per molecule. The functionalization has a very local character, so that the difference in binding energy for coverages49 of 0.125, 0.25, and 0.5 ML is small (lower than 0.05 eV per molecule). To address reaction kinetics, we perform our calculations for the propionic acid, which helps to eliminate the effect of the vibrational degrees of freedom. Two intermediate configurations may be obtained by reacting the COOH group with the surface through a single O atom. If the O atom involved in the bond comes from the carbonyl group CdO, no residue is released, while a hydrogen molecule is released if the O atom comes from the hydroxyl OH group. We set up two guess-paths leading to the intermediate chemisorbed configurations characterized by only one Si-O-C carbon bridge. We then complete each path to obtain the second Si-O bond. We describe first the process starting from the reaction through the carbonyl group, which we will label as OO-1,

Figure 2. Representation of the chemisorption reactions OO-1, starting from the opening of the carbonyl group CdO. Top: Change in the potential energy relative to noninteracting molecule and substrate Superimposed dashed line in the first path is the similar curve for adsorption of the alkyne-tailed molecule CHtCsCH2sCOOH. Bottom, from left to right: Ball-and-stick snapshot for the first transition, intermediate, second transition states and final stable configuration A-OO; in dark gray Si, in green C, in red O, and IN white H atoms, respectively.

represented50 in Figure 2. Along this path we first detect a physisorbed configuration, at ∆E ) -0.14 eV from the reference energy of the isolated reagents; the molecule still presents its trans-gauche51,52 configuration (bond lengths dCdO ) 1.23 Å and dC-OH ) 1.36 Å, to be compared to the distances for the isolated molecule in Table 1); from this physisorbed state the reaction faces a barrier of ∆E ) 1.62 eV over the first transition state (Figure 2), characterized by overcoordination of the Si atom, and under-coordination of the C atom, the double CdO bond is disrupted while a stretched bond O-Si is already established (see Table 2). From this configuration, one of the H atoms bound to the Si atom involved in the reaction leaves the surface to saturate the carboxyl C atom, and the system relaxes to a (meta)stable intermediate configuration (Figure 2 and Table 2) with binding energy of EB )0.84 eV. Up to here there is no reaction residue. To establish the second bond, the reaction would proceed through nucleophilic attack of the O atom of the OH group to a neighboring Si surface atom; in this step a hydrogen molecule must be released, as clearly visible in our representation of the transition state (Figure 2), and the barrier is thus higher ∆E ) 1.96 eV, with a final energy lowering53 of additional ∆E ) -0.33 eV to the doubly bonded configuration (Figure 2). The second process, which we label OO-2, starts from the hydroxyl insertion on a surface Si-H group and is summarized in Figure 3; also in this mode of approach we observed a physisorbed configuration at ∆E ) -0.10 eV, and the molecule is also trans-gauche. In this process the first barrier to be faced involves already the release of the hydrogen molecule, as represented in Figure 3, and is actually higher (∆E ) 2.30 eV) than in the case where the first bond had already been established; the molecule is very distorted, we have quasiovercoordination of both O and Si atoms, with quasi-undercoordination of the C atom (see Table 2). It should be noted that the intermediate chemisorbed state (Figure 3) with a single Si-O-C bond is now hardly favored with respect to the physisorbed configuration, with EB ∼ 0.26 eV; the molecular segment is distorted, the methylene group having lost the staggered symmetry with respect to the methyl group, and the

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TABLE 2: Interatomic Distances (in Å) at Transition (TS), Intermediate (int), and Final States for the Most Relevant Atoms Involved in the Reactionsa reaction C-O C-OH Si-O Cω-Cζ C-H Cω-Sis C-Sis Sis-Siss Sis1-Sis2 Si-H

OO-1 TS 1.33 1.34 A:1.89 Y:1.95

2.38 4.04 1.65

int

OO-2 TS

int

OO final

1.41 1.41 1.67

1.23 1.38 2.09

1.23 1.37 1.72

1.43 1.41 1.68

2.35 3.88 1.50

2.35 4.08 1.50

2.35 3.89 1.72

2.35 4.08 1.50

E-C TS

final

Y-C TS

1.40 1.09 2.16

1.54 1.10 1.91

1.34 (ζ) 1.16

1.35 1.10 1.88

2.45

2.36

2.34

2.37

1.62

1.50

2.02

1.50

final

Y-SiCSi final

Y-SiCCSi final

1.55 1.11 1.90 (ω) 1.91 2.36 3.29 1.50

1.53 1.11 1.89 (ζ) 1.95 2.34 3.77 1.50

a

The step reactions leading to A-OO are labeled OO-1 (first grafting through the carbonyl group) and OO-2 (first grafting through the hydroxyl group) as described in text. Labeling as in Table 1 and in Figure 4.

Figure 3. Representation of the chemisorption reactions OO-2, starting from the reaction through the hydroxyl group OH. Top: Change in the potential energy relative to noninteracting molecule and substrate. Bottom, from left to right: Ball-and-stick snapshot for the first transition, intermediate, second transition states and final stable configuration A-OO; color code as in Figure 2.

surface is also stressed. To complete the reaction the system has now to overcome the second barrier, of ∆E ) 1.19 eV, where again we have overcoordination of the Si and undercoordination of the C atom to arrive at the final configuration with a large partial gain of ∆E ) -0.91 eV. In the final configuration, we have a molecular moiety with the alkyl all-trans symmetry completely restored. The configuration at the interface reflects a similarity to silica networks, in that the distance between the involved Si surface atoms has increased, and the distances Si-O are also close to those found in silica; at the Si side of the interface, already at the second layer, the configuration of the normal hydrogenated surface is recovered. Due to the local character of the chemical bond, these mechanisms can be easily transposed to other situations, such as the alkanoic acid, where again the molecular tail is nonreactive. Indeed, the results obtained for the alkanoic acid are very similar to our previous study, with a binding energy of 1.26 eV for the double Si-O-C bonded structure, revealing a negligible dependence on the chain length. The same occurs also for bifunctional molecules, such as the alkyne-tailed acid CHtCsCH2sCOOH: to verify this point, we have performed reaction-path calculations for the first path of process OO-1 (through the carbonyl group). We include the results in Figure 2 and Table 2: it can be seen that absorption occurs via the

same reaction mechanism and leads to very similar interface structure, electronic charge distribution at the interface and energy barriers (within 0.1 eV). The final interfacial configurations obtained for the alkane-, alkene-, and alkyne-tailed acids respectively are labeled as A-OO, E-OO, and Y-OO: the resulting functionalized structures are schematized in Figure 4a-c, with geometric details in Table 1 and 2. B. Carbon Grafting. A completely different situation occurs when studying functionalization through Si-C bond formation. In this case, while the alkane-tailed acid cannot bind to the surface, the other bifunctional molecules lead to possible competing events; furthermore, completely different energetics, and electronic properties pertain to the interface when anchoring through alkene tails (thus breaking a C double bond) or alkynes (via triple bond breaking). 1. Alkenes. The concerted reaction leading to the opening of the alkene double bond4,5,29 leads to a Si-C linkage (Si-Cω), whereas a surface H atom saturates the next C atom (Cζ) of the molecule; no hydrogen molecule is expected as reaction residue. We find that this reaction is exothermic; a stable (EB ) 1.16 eV) covalent Si-C bond is formed (system E-C, see Figure 4d). The results for the reaction process are shown in Figure 5 where we see that a rather high energy barrier of ∆E ) 2.15 eV is predicted for the chemisorption. The transition state is also represented in Figure 5 with structural data in Table 2. In this case, the surface is much distorted: the involved Si atom is placed in an almost planar hybridization structure (sp2-like) bonding to the two H saturators and one of the two subsurface Si neighbors, while two more “bonds” extend to the other Si sub-surface neighbor and the approaching Cω atom (almost in line, internal angle Cω-Sis-Siss of ∼160°). Our simulations indicate a severe stretching of the surface Si-Si bonds well before the concerted bonds Si-Cω and H-Cζ take place: in the transition state still the distance Cω-Cζ is small while the distance Si-Cω is too large. At the end of the reaction, in the stable final state (Figure 5 and Table 2), the surface is relaxed almost back to normal distances of the di-hydrogenated surface; the molecule reflects plain alkyl structure and the Si-C bondlength is rather close to the calculated distance in the regular SiC crystal structures54 of 1.89Å. 2. Alkynes. Although with similar reaction mechanism and barrier heights (see Figure 2), the competing configuration arising from the reaction through the unsaturated termination is energetically favored for the 3-butyneic acid: indeed, it leads to a very stable configuration (Y-C, see Figures 1 and 4e)

Chemisorption of Carboxylic Acids on H:Si(100)

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Figure 4. Schematic representation of the most favorable chemisorbed structures. Configurations type OO (a-c) correspond to the dissociative chemisorption of the carboxylic acids through the COOH group, leading to stable double-O bonded structures and to the release of a H2 molecule as reaction residue. Configurations type C (d and e) anchor through singly Si-C bonded hydrosilated structures. The two different doubly Si-C bonded hydrosilated configurations for the alkyne-tailed system (f and g) are labeled Y-SiCSi and Y-SiCCSi.

Figure 5. Representation of the chemisorption reactions leading to the E-C configuration. Left: Change in the potential energy relative to noninteracting molecule and substrate. Right, from top to bottom: Balland-stick snapshot for the transition state and final stable configuration E-C; color code as in Figure 2.

grafted by a Si-C bond, with a binding energy of EB )1.90 eV. No reaction residue is present in this case. Moreover, the reaction still leaves a residual double bond at the unsaturated tail of the molecule, opening the possibility for one additional Si-C bond.18,27 As depicted in Figure 4, we investigated two possible configurations. In the first, a second bond connects the same Cω atom to the nearest Si surface atom: the bond can thus bridge over an underlying empty or filled site, giving rise to differently strained metastable geometries, among which the most stable is at EB ) 3.17 eV (Y-SiCSi, Figure 4f).55 In the alternative configuration (Y-SiCCSi, Figure 4g, EB ) 2.54 eV) the second bond is established between the Cζ atom and that same neighbor surface Si. No residue is released in either case, the ejected surface H atom is found saturating the Cζ or Cω atom, respectively. In the more stable SiCSi configuration, a five-member ring is established at the interface, and the structure turns out to be stabilized by a second “easy” bond per molecule, as in the OO cases; the distances for the final relaxed configuration are indicative of the structural stability: the bonded molecule shows plain alkyl structure (see Table 2). The interface (see Figure 6) is very interesting, with Sis-Siss and Si-Cω distances very close to the respective Si and SiC bulk bond lengths, whereas the distance between the 2 Si surface atoms is shortened to 3.29Å, close to the distance in the dimers formed on the mono-hydride H:Si(100).40 In the SiCCSi case, we observe a smaller distortion, with Si-C bond lengths affected by the non-symmetric “hindrance” caused by the molecule; the Sis-Siss bond is completely relaxed. Indeed both the SiCSi and SiCCSi configurations are very stable, with an increase in binding energy of more than

Figure 6. Representation of the chemisorption reactions leading to the Y-C and Y-SiCSi configurations. Top: Change in the potential energy relative to noninteracting molecule and substrate. Bottom, from left to right: Ball-and-stick snapshot for the first transition, intermediate Y-C, second transition states and final stable configuration Y-SiCSi, respectively; color code as in Figure 2.

1.2 and 0.6 eV, respectively, compared to the singly-bonded Y-C configuration, and more than 1.7 and 1.1 eV, respectively, compared to the Y-OO system. The MEP for the chemisorption reaction leading to the SiCSi configuration is represented in Figure 6; the first part of the path (Y-C configuration in Figure 6) is the same for both final doubly Si-C bonded structures. We do not find any physisorbed configuration, and the first bond-opening is characterized by a relatively high energy barrier of ∆E ) 1.81 eV, as seen in Figure 6. In the transition state the molecule rotates to expose the Cζ atom involved in the triple bond to the surface, to capture a passivating hydrogen that helps reduction of the C-C bond; here the surface Si atom is under-coordinated, and the Cζ atom overcoordinated (see Table 2). From the transition state the reaction proceeds toward the first chemisorbed stable configuration Y-C (Figure 6). The process next faces a double-bond opening, with a barrier similar to that of the alkene E-C bond opening, this time even slightly higher due to the additional hindrances. C. Discussion. We can now comment on the possible competition between the different mechanisms, with a complete assessment of the energetics involved. We summarize in Table 3 the binding energies for all stable bonded configurations and in Table 4 the energy barriers through the different transition states. We include also in Table 3 binding energies for the radical hydrosilation reactions from refs 29 and 31.

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TABLE 3: Binding Energies EB (in eV) of the Most Exothermic Chemisorption Reactionsa system

A-O

E-C

Y-C

A-OO

E-OO

Y-OO

Y-SiCSi

Y-SiCCSi

H:Si(100) H:Si(111)

0.84/0.26 1.31b/

1.16 1.30c

1.90 1.97c

1.26

1.33

1.41

3.17

2.54

a Labeling as in Figure 4. (The first A-O grafting is given for both paths, namely bonding through the carbonyl or the hydroxyl oxygen.) Results are compared to previously published radical hydrosylation reactions of propanaldehyde, ethene and ethyne molecules on H:Si(111). b Reference 31. c Reference 29.

TABLE 4: Energy Barriers (in eV) for the Chemisorption Reactions Described in the Texta reaction

OO-1

OO-2

E-C

Y-SiCSi

Y-SiCCSi

first step second step

1.62 1.96

2.30 1.19

2.15

1.81 2.30

1.81 2.50

a Labeling as in Figure 4. In the case of multistep reactions, all of the different barriers are indicated.

Focusing first on plain energetics for the reactions through the unsaturated tails, we can see that the dominant effect is molecular energetics, in that the gain in reducing the triple to double bond is larger than the one for double to single bond; also, the gain in the second bond-opening of the alkyne-tailed molecule is roughly the same as opening the initial double bond of the alkene-tailed molecule. This is consistent with results concerning reactions on a different surface, in this case H:Si(111), with an activated site: the energies are very similar for E-C and Y-C (the dangling bond in the activated case exists at the surface before and after the reaction, on a different site, so the plain energetic comparison can be made). On the other hand, we find a relevant difference in binding energy for reactions through the carbonyl group on the different surfaces: This effect must thus be ascribed to the difference in the molecular head and points to steric hindrances related to the additional OH group of the carboxylic acid. The energetics of the stable configurations would point at Si-C bonded interfaces as most favored, since they are much more exothermic, with no indication of real competition: this is particularly true for the Y-C structures, which present superior stability and energy gain. Passing to the comparison of energy barriers needed for the reactions (Table 4), we find a very different picture. Again focusing on the first grafting mechanism, we argue that there will be a good advantage for carbonyl grafting against alkene reduction, while there could be competition between carbonyl grafting and alkyne reduction. As already pointed out, the alkyne grafting through a single Si-C bond can also be considered as the intermediate step for reaching different structural configurations of the molecule on this surface, namely the SiCSi and SiCCSi configurations. However, despite the prominent stability of both doubly bonded structures, our calculation of the reaction pathways suggest that they are not easily accessible from a kinetic point of view. The barrier faced by the reaction to the double-O bridge is again smaller (but non-negligible, and also here we should find a good proportion of singly bonded molecules). Our results suggest that the E-OO configuration should be preferred to the E-C one, at least for what concerns the first Si-O bond formation. The complexity of this scenario requires that reaction kinetics is taken into account in the interpretation of the experiments that may depend on the preparation conditions. Indeed, experimental results on thermally activated chemisorption of carboxylicfunctionalized alkenes (ω-undecenoic acids) on hydrogenated silicon substrates suggest the presence of poorly ordered monolayers.21 The degree of disorder of the monolayer can be

controlled by means of head-protection or catalyzed techniques that are the most reliable approaches in order to obtain the chosen overlayers in an ordered configuration. In what follows, we discuss the electronic properties of the final configurations, so as to provide more data to determine that choice. IV. Results: Electronic Properties The electronic features of the molecule-substrate interfaces are investigated through a detailed analysis of relevant electronic states, total density of states (DOS) and projected DOS (PDOS). We show in Figure 7 the DOS of the functionalized surfaces resulting from reactions of the R-carboxy-ω-alkene (top panels) and R-carboxy-ω-alkyne (bottom panels) molecule; the discrete molecular levels of the corresponding reacting molecule (vertical lines) and the DOS of the unreacted dihydride-terminated (100) silicon surface (shaded area) are also shown. The origin of the energy scale Ev ) 0 corresponds to the top valence state of the clean hydrogenated surface. The alignment of the functionalized with respect to hydrogenated surfaces is always performed through the unperturbed surface state of the H peak at the back surface: we can see that the top valence states of both systems naturally coincide, even though we did not directly impose this constraint. As expected the gap is completely free of states. In every DOS of the functionalized surfaces, four semicore molecular levels are found below the H:Si valence-band (VB) energy region. The energy levels of the isolated molecules were aligned with the DOS of the hydrogenated surfaces through a clean molecular state of the functionalized system, namely the fourth peak for all systems (at ∼EV- 13 eV, see Figure 7). The electronic states corresponding to the two lowest semicore levels always carry a major contribution from the s-type molecular states of the carboxylic group. When the bond is formed through the carboxylic group, we see that the two lowest peaks interestingly experience a large energy shift, registered in Table 5. This shift can be attributed to the hybridization of the s orbitals centered on O and C atoms of the carboxylic termination: after chemisorption, the C atom assumes a tetrahedral coordination and both O atoms strongly modify their bonding geometry. This general phenomenon of structure modification is present to a smaller extent also in singly O-bonded configurations.36 In the case of surface grafting through hydrosilation the carboxylic moiety remains mostly unperturbed, exposed at the outside of the functionalized surface: in this case none of the four semicore levels shift (Figure 7, right), since the relevant s-type orbitals are not strongly involved in the formation of the Si-Cω bond. Our results thus indicate that semicore energies can provide useful insight for the experimental discrimination between Si-C and Si-O-C bonded monolayers. In order to get a more detailed analysis of the electronic charge distribution, in energy and in space, we calculate the PDOS on both oxygen and carbon atomic states for some relevant configurations (Figure 7, solid red and dashed lines respectively). We first consider the OO bonded systems, for which we find the oxygen molecular states spread to an extended

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Figure 7. Total density of states of carboxylic acids chemisorbed on H:Si(100) for the E-OO, E-C (top panels), Y-OO, and Y-C (bottom panels) configurations. The comparison to the clean hydrogenated surface (shaded region) and the isolated molecule (lines) is also shown, together with projected DOS over the O atoms (red lines) and C atoms other than the CR of the carboxyl head (dashed lines).

Figure 8. Isosurface of charge density for the highest occupied molecular orbital HOMO of the molecules considered here: (a) 3-butanoic acid CH3s(CH2)2sCOOH; (b) 3-butenoic acid CH2dCHsCH2sCOOH; (c) 3-butynoic acid CHtCsCH2sCOOH.

TABLE 5: Semi-Core Level Shift (in eV) for the First Two Energy Peaks of the the Most Relevant Configurations Following the Chemisorption Reactions Described in the Text (See Figures 4 and 7) system A-OO E-OO Y-OO ∆E1 ∆E2

0.99 0.74

0.95 0.69

1.03 0.79

E-C

Y-C Y-SiCSi Y-SiCCSi

0.00 0.00 0.07 0.03

0.00 0.04

0.00 0.03

band, which covers the full width of the Si VB, up to the VB top. The large width of the resulting oxygen band is related to the very large energy distribution of the O states of the molecular carboxylic group, that allows for extended hybridization between substrate and adsorbate. It is interesting to note (see Figure 8) that the HOMO of the isolated COOH-terminated molecules always carry a strong contribution from the carboxylic head,

bearing however also a relevant contribution from the tail in the case of the unsaturated molecules; the head is directly involved in the bonding to the surface for all OO configurations, thus this state turns out to be disrupted and the HOMO-related peak in the PDOS of O-states disappears; the C-bands for the E-OO and Y-OO functionalized systems still show a peak coinciding with the molecular HOMO (see Figure 7). For the Si-C bonded systems, in the topmost part of the valence band, we see two O-related strong peaks at Ev ≈ -1.8 and -3.0 eV, slightly displaced compared to the corresponding molecular energies. As for the C-derived states, for the Y-C configuration seen in Figure 7 a broader C-related band can still be seen below the valence band top, extending up to -3.5 eV, originating by modifications of the double bond CωdCζ. The existence of this residual C bond can also provide an extension to the outside carboxylic moiety, for short molecules, as can be gauged from comparison of Figure 8, panels b and c, and from the slight displacement of relevant O-related peaks compared to the molecular energies seen also in Figure 7. Remarkable differences occur when the residual C double bond is cleaved, as in the special E-C case: for this particular hybrid interface, the states close to the top of the valence band are completely free from molecular contributions and the onset of the molecular band occurs below -1 eV thus creating a welldefined tunneling barrier (Figure 7). The DOS of the Si-O and Si-C bonded configurations present a few common features. First, a sharp molecule-related peak always appears at ∼1.5 eV below Ev: it is concentrated however on the chemical group exposed at the free surface of

10174 J. Phys. Chem. C, Vol. 112, No. 27, 2008 the overlayer, and represents the interface molecular state that could be mainly involved in the tunneling between a metallic electrode (at positive bias) and the silicon substrate. This same general feature has also been detected by Lenfant and coworkers10 in their tight-binding calculation of the hydrosilated H:Si(100), linked through longer (6 and 12 CH2 groups) alkyl chains to a phenyl termination. Second, an energy superposition between head- and tail-centered states is found for the systems considered here consistently with the resonant nature of the molecular HOMO states. V. Summary and Conclusions We presented a systematic study of the stability, reaction pathways and electronic properties of the uncatalyzed functionalization of dihydride H:Si(100) surfaces, resulting from the different possible mechanisms for chemisorption of bifunctional R-carboxy-ω-alkenes and alkynes. Our study was conducted with first-principles calculations within DFT, for several chemisorbed configurations, obtaining electronic structures and energy barriers for the concerted reaction mechanism. Concerning the electronic structure of these systems, we find that in all cases when the chemisorption occurs through the carboxylic head, the O-derived states develop into a band that covers the full valence bandwidth, reaching the valence band top. The alkyl-related states are found to develop a band at lower energies, with a reasonable energy-overlap with the strongest O-related bands at Ev ≈ -3 and -5 eV. The transition from Si-surface states to the molecular chain involves the Si-O-C hybridization and can be used either to define the tunneling barrier or, if the chain is built to have resonant HOMO states, to provide a channel for holes as in the case of the alkyneic acid studied here: the link through the carboxylic group results in optimal contact to the Si substrate, as required for electronic probing. When the chemisorption occurs through the tail the C-derived states develop into a broadband; however, in particular for the E-C systems, it is possible to define a tunneling barrier, which would be appealing for molecular electronics applications. The Y-C configuration presents very special electronic properties for the short chains investigated here, since it provides a channel for molecular electronics besides leaving the carboxylic moiety undisturbed at the outmost surface, which can be desirable in view of subsequent layering chemistry; also, our analysis of reaction barriers indicates that the probablity for a second Si-C bond to form (leading to the SiCSi or to the SiCCSi configuration) is very low. Our data for the energy barriers suggest that molecules with R-carboxy-ω-alkene bifunctionality will preferentially anchor through the carboxylic group, due to a markedly higher energy barrier for the reaction through the alkene group. In the case of R-carboxy-ω-alkyne bifunctionality, reaction barriers are similar for the first step of each configuration; however, the grafting through the carbonyl group still is kinetically favored. Finally, the high desorption barriers and the totally relaxed character of the final structures indicate that the obtained monolayers would be very robust and reliable. The electronic structure for both the double O-bridge and the single C-bonding of R-carboxyω-alkynes bifunctional molecules show promising characteristics for molecular electronics and further patterning of the Si substrate: we thus suggest that once the choice of overlayer has been made, the competition problem may be solved by moietyprotection or catalyzed processes. Acknowledgment. We are grateful to E. Chang, G. Cicero, S. Corni, R. Di Felice, and A. Migliore for fruitful discussions.

Cucinotta et al. Computer time was partly provided by CINECA through INFM Parallel Computing Projects. We acknowledge support by the RTN EU Contract “EXCITING” No. HPRN-CT-2002-00317 and by FIRB “NOMADE” and “Latemar”; M.J.C. also thanks INFM-S 3, Italy, FAPESP and CNPq, Brazil. References and Notes (1) Ulman, A. Chem. ReV. 1996, 96, 1533. (2) Lopinski, G. P.; Wayner, D. D. M.; Wolkow, R. A. Nature 2000, 406, 48. (3) Wieringa, R. H.; Siesling, E. A.; Werkman, P. J.; Vorenkamp, E. J.; Schouten, A. J. Langmuir 2001, 17, 6491. (4) Buriak, J. M. Chem. ReV. 2002, 102, 1271. (5) Bent, S. F. Surf. Sci. 2002, 500, 879. (6) Filler, M. A.; Bent, S. F. Prog. Surf. Sci. 2003, 73, 1. (7) Liu, Z.; et al. J. Org. Chem. 2004, 69, 5568. (8) Langner, A.; Panarello, A.; Rivillon, S.; Vassylyev, O.; Khinast, J. G.; Chabal, Y. J. J. Am. Chem. Soc. 2005, 127, 12798. (9) Hoeppener, S.; Maoz, R.; Sagiv, J. Nano Lett. 2003, 3, 761. (10) Lenfant, S.; Krzeminski, C.; Delrue, C.; Allan, G.; Vuillaume, D. Nano Lett. 2003, 3, 741. (11) Cerofolini, G. F.; Arena, G.; Camalleri, C. M.; Galati, C.; Reina, S.; Renna, L. Nanotechnology 2005, 16, 1040. (12) Mischki, T. K.; Donkers, R. L.; Eves, B. J.; Lopinski, G. P.; Wayner, D. D. M. Langmuir 2006, 22, 8359. (13) Cho, J.-H.; Oh, D.-H.; Kleinman, L. Phys. ReV. B 2002, 65, 081310. (14) Kang, J. K.; Musgrave, C. B. J. Chem. Phys. 2002, 116, 9907. (15) Kruse, P.; Johnson, E. R.; DiLabio, G. A.; Wolkow, R. A. Nano Lett. 2002, 2, 807. (16) Cattaruzza, F.; Cricenti, A.; Flamini, A.; Girasole, M.; Longo, G.; Mezzi, A.; Prosperi, T. J. Mater. Chem. 2004, 14, 1461. (17) Cerofolini, G. F.; Galati, C.; Reina, S.; Renna, L. Semicond. Sci. Technol. 2003, 18, 423. (18) Cerofolini, G. F.; Galati, C.; Reina, S.; Renna, L.; Condorelli, G. C.; Fragala´, I. L.; Giorgi, G.; Sgamellotti, A.; Re, N. Appl. Surf. Sci. 2005, 246, 52. (19) Boukherroub, R.; Morin, S.; Sharpe, P.; Wayner, D. D. M. Langmuir 2000, 16, 7429. (20) Liu, Y. -J.; Navasero, N. M.; Yu, H.-Z. Langmuir 2004, 20, 4039. (21) Sieval, A. B.; Demirel, A. L.; Nissink, J. W. M.; Linford, M. R.; van der Mass, J. H.; de Jeu, W. H.; Zuilhof, H.; Sudhoelter, E. J. R. Langmuir 1998, 14, 1759. (22) Asanuma, H.; Lopinski, G. P.; Yu, H.-Z. Langmuir 2005, 21, 5013. (23) Sieval, A. B.; van den Hout, B.; Zuilhof, H.; Sudhoelter, E. J. R. Langmuir 2000, 16, 2987. (24) Aswal, D. K.; Lenfant, S.; Guerin, D.; Yakhmi, J. V.; Vuillaume, D. Anal. Chim. Acta 2006, 568, 84108. (25) Lee, E. J.; Bitner, T. W.; Ha, J. S.; Shane, M. J.; Sailor, M. J. J. Am. Chem. Soc. 1996, 118, 5375. (26) Linford, M. R.; Fenter, P.; Eisenberger, P. M.; Chidsey, C. E. D. J. Am. Chem. Soc. 1995, 117, 3145. (27) Sieval, A. B.; Opitz, R.; Maas, H. P. A.; Schoeman, M. G.; Meijer, G.; J.Vergeldt, F.; Zuilho, H.; Sudho¨lte, E. J. R. Langmuir 2000, 16, 10359. (28) Sieval, A. B.; van den Hout, B.; Zuilhof, H.; Sudhoelter, E. J. R. Langmuir 2001, 17, 2172. (29) Takeuchi, N.; Kanai, Y.; Selloni, A. J. Am. Chem. Soc. 2004, 126, 15890. (30) Takeuchi, N.; Selloni, A. J. Phys. Chem. B 2005, 109, 11967. (31) Kanai, Y.; Takeuchi, N.; Car, R.; Selloni, A. J. Phys. Chem. B 2005, 109, 18889. (32) Bateman, J. E.; Eagling, R. D.; Horrocks, B. R.; Houlton, A. J. Phys. Chem. B 2000, 104, 5557. (33) Pei, Y.; Ma, J.; Jiang, Y. Langmuir 2003, 19, 7652. (34) Coletti, C.; Marrone, A.; Giorgi, G.; Sgamellotti, A.; Cerofolini, G.; Re, N. Langmuir 2006, 22, 9949. (35) Boukherroub, R.; Morin, S.; Wayner, D. D. M.; Bensebaa, F.; Sproule, G. I.; Baribeau, J. M.; Lockwood, D. J. Chem. Mater. 2002, 13, 2002. (36) Cucinotta, C. S.; Ruini, A.; Caldas, M. J.; Molinari, E. J. Phys. Chem. B 2004, 108, 17278. (37) Cucinotta, C. S.; Bonferroni, B.; Ferretti, A.; Ruini, A.; Caldas, M. J.; Molinari, E. Surf. Sci. 2006, 600, 3892. (38) Caldas, M. J.; Calzolari, A.; Cucinotta, C. S. J. Appl. Phys. 2007, 101, 081719. (39) Di Felice, R.; Selloni, A.; Molinari, E. J. Phys. Chem. B 2003, 107, 1151. (40) Northrup, J. E. Phys. ReV. B 1991, 44, 1419. (41) Sun, H. J. Comput. Chem. 1994, 15, 752. (42) Hwang, M. J.; Stockfisch, T. P.; Hagler, A. T. J. Am. Chem. Soc. 1994, 116, 2515.

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(49) We here adopt the standard definition for the coverage, in terms of number of molecules per surface Si atoms.

evaluated separately. However, the zero of ∆E in the potential energy plots of MEPs is obtained for non-interacting systems, thus the curves can be compared. (51) Mac¸oas, E.; Khriachtchev, L.; Pettersson, M.; Fausto, R.; Rasanen, M. J. Phys. Chem. A 2005, 109, 3617. (52) Stiefvater, O. L. J. Chem. Phys. 1975, 62, 244. (53) The difference with respect to the value calculated in ref 36 is due here to the presence in the simulation cell of the residual H2 molecule, close to the functionalized surface. (54) Catellani, A.; Galli, G. Prog. Surf. Sci. 2002, 9, 101, and refs. therein. (55) In ref 37, we investigated a SiCSi configuration, bridging over an underlying filled site: the resulting geometrical structure was found to be characterized by drastic structural changes and lower stability.

(50) The two paths, from the initial configuration to the singly-O-bonded metastable state, and from the metastable to final configuration, have been

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