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J. Phys. Chem. B 2005, 109, 13656-13662
A Theoretical Study of Biotin Chemisorption on Si-SiC(001) Surfaces Yosuke Kanai,*,† Giancarlo Cicero,§ Annabella Selloni,† Roberto Car,†,‡ and Giulia Galli§ Department of Chemistry, Princeton UniVersity, Princeton, New Jersey 08544, Princeton Institute for the Science and Technology of Materials (PRISM), Princeton UniVersity, Princeton, New Jersey 08544, and Lawrence LiVermore National Laboratory, Post Office Box 808, LiVermore, California 94550 ReceiVed: March 15, 2005; In Final Form: May 10, 2005
Biotin is a promising candidate for functionalization of semiconducting surfaces, given its strong, unmatched affinity to specific proteins such as streptavidin and avidin. Using density functional theory, we have carried out a theoretical investigation of the structural and electronic properties of biotin chemisorbed on a biocompatible substrate; in particular we have considered the clean and hydroxylated Si-SiC(001) surfaces. Our calculations show that, upon chemisorption, biotin retains the electronic properties responsible for its strong affinity to proteins. While the electronic states of the hydroxylated surface undergo negligible changes in the presence of the molecule, those of the clean surface are considerably affected.
I. Introduction In recent years, substantial experimental efforts have been devoted to achieving functionalization of semiconductor surfaces for protein immobilization. Most of these studies have been motivated by the search for promising biosensing platforms to be integrated in nanoscale electronic devices. A promising technique to functionalize semiconducting and gold surfaces involve biotin chemisorption: the ability of this molecule to form strong, selective complexes with streptavidin and avidin makes it an ideal candidate for protein immobilization. In addition, it has been proposed that the biotin/streptavidin system could be used for bioaffinity sensors and drug delivery.1 Several experimental groups have already succeeded to directly chemisorb biotin on solid surfaces such as diamond and gold, and the experiments were conducted using hydroxylated surfaces in wet ambient conditions.2,3 However, experimental studies may also be possible on clean surfaces, if conducted under ultrahigh vacuum (UHV) condition. Another promising substrate for functionalization study is silicon carbide, and outstanding progress has been recently reported in both SiC fabrication4 and characterization.5,6 In addition to its high electrical conductivity, which permits its integration in electronic devices, SiC is particularly attractive for its high mechanical, thermal, and chemical stability. Very recent experimental and theoretical studies have been able to characterize water-exposed SiC surfaces, which may be used in functionalization experiments. Spectroscopic measurements on the Si-rich (3 × 2)-reconstructed SiC(001) surface7 indicated that dissociation of water molecules leads to perfect passivation of the outermost excess Si layer. These results are consistent with those of ab initio simulations of water molecules on SiC(001) surfaces.8,9 In particular, the theoretical studies predicted that the hydrophilic/-phobic character of the SiC(001) surfaces depends on its silicon or carbon terminations, and proposed a model for the hydroxylated surface. In this paper, using first principles calculations, we studied the adsorption of biotin molecules onto clean and hydroxylated †
Department of Chemistry, Princeton University. Princeton Institute for the Science and Technology of Materials (PRISM), Princeton University. § Lawrence Livermore National Laboratory. ‡
silicon carbide (SiC) surfaces, with the aim of understanding the structural and electronic modifications mutually induced at the surface, and on the molecule, upon chemisorption. Understanding these changes is an essential prerequisite to control and use functionalized surfaces for selective binding to desired agents. Our results show that on the clean surface the biotin acid group spontaneously releases its hydrogen, chemisorbing to the surface. On the hydroxylated surface an esterification reaction involving the surface -OH groups appears to be an activated process. In both cases we found that stable surface functionalization can be achieved. Particular attention was devoted to the analysis of the electronic structure modifications of the surface and the molecule upon adsorption, aimed at assessing if the binding affinity of biotin to proteins could be altered by the surface. The remainder of the paper is organized as follows. In section II we briefly describe the theoretical method used here. We then discuss both the clean and hydroxylated Si-SiC(001) surfaces in sections III.A. Section III.B is devoted to the studies of isolated biotin molecule. We finally discuss the biotin chemisorption process in section III.C. II. Theoretical Methods We carried out ab initio calculations using density functional theory (DFT) within the generalized gradient approximation (GGA) for the exchange-correlation functional, as parametrized by Perdew et al. (PBE).10 Single-particle Kohn-Sham wave functions were expanded in planewaves with kinetic energy up to 80 Ry. We used norm-conserving psudopotentials11 derived within PBE. The integration over the Brillouin zone was performed using only the Γ point of our supercell.12 In our calculations, Si-SiC(001) surfaces were modeled by a slab periodically repeated along the [001] direction and with a p(4 × 4) surface supercell. The slab consists of 8 Si/C layers, and each layer contains 16 atoms (total of 144 atoms). The bottommost carbon atom layer was saturated with hydrogen atoms. In geometry optimizations, all atoms were relaxed until the forces were smaller than 1 × 10-4 au with the exception of the bottommost carbon atom layer which was held fixed at the theoretical equilibrium geometry.13 A vacuum region of 17 Å was taken in the direction perpendicular to the slab. This relatively large
10.1021/jp051360h CCC: $30.25 © 2005 American Chemical Society Published on Web 06/23/2005
Biotin Chemisorption on Si-SiC(001) Surfaces
Figure 1. Side views (along the [11h0] direction) of the clean and hydroxylated p(1 × 2) reconstructed silicon terminated SiC(001) surfaces are shown in (a) and (c), respectively. Top views are also shown in (b) and (d). Purple (Green) spheres in the substrate represent silicon (carbon) atoms; red (white) spheres represent oxygen (hydrogen) atoms.
vacuum region was found to be necessary since the biotin molecule possesses a long alkyl chain (about 7 Å) and a rather extended electrostatic potential. Calculations were carried out using the GP code14 in the context of the Car-Parrinello approach,15 with postprocessing analysis performed using the PWscf package.16 III. Results and Discussions We first describe our results for the Si-SiC(001) surface and the biotin molecule separately in sections III.A and III.B, respectively, and present our calculations for chemisorption in section C. III. A. Clean and Hydroxylated Si-SiC(001) Surfaces. The reconstructed Si-terminated SiC(001) surface forms rows of Si dimers (Figure 1a and b) in a p(2 × 1) arrangement similar to the case of the reconstructed Si(001) surface.17 However, these dimers are weakly bound and symmetric, unlike those on Si(001).13 The lattice constant of the cubic β-SiC is about 20% smaller than that of silicon, and the interrow spacing of the dimers is only 3.55 Å, compared to the Si dimer intrabond length of 2.65 Å. This rather small spacing is responsible for the interaction between dangling bonds (DBs) of neighboring Si dimers. To characterize the bonding properties of the Si-SiC(001) reconstructed surface, we calculated maximally localized Wannier functions (MLWFs), which are a unitary transform of Kohn-Sham orbitals maximally localized in space.18,19 We found that the MLWFs centered on surface atoms have large spreads (2.5-3.5 Å2) while those of the SiC bulk region have spreads of about 2.0 Å2. In addition these functions reside both within a Si dimer (intradimer) as well as between adjacent Si dimers (interrow). The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are surface states mainly deriving from the topmost silicon atoms. The surface presents an electrostatic potential which smoothly decreases to a plateau value20 at approximately 9 Å away from
J. Phys. Chem. B, Vol. 109, No. 28, 2005 13657 the topmost surface atoms. We note that there is an increase in the negative electrostatic potential between adjacent Si dimer rows (left panel of Figure 2), where pronounced reactivity was observed when studying interactions with water molecules.9 As discussed in a recent paper by some of us,8,9 the Si-terminated SiC(001) surface spontaneously becomes hydroxylated upon interactions with water molecules. Upon water dissociative adsorption, which was found to be barrierless, dangling bonds of surface Si atoms are saturated with either hydrogen atoms or hydroxyl radicals, and consequently Si dimer bond lengths are shortened to about 2.37 Å. Polarity induced on the surface dimers by the attached -H and -OH fragments is responsible for the bond-length shorteninig.8,9 Once adsorbed, the hydroxyl group orient so as to form a periodic network of hydrogen bonds which lowers the total energy of the system (Figure 1, c and d).21 Upon water molecule adsorption, the electronic structure of the surface is considerably altered as shown in the density of states (DOS) in Figure 3. The most noticeable feature is the drastic increase of the band gap to 1.6 eV,22 which arises from elimination of surface states due the saturation of Si dangling bonds (DBs). Moreover, the MLWFs localized between adjacent Si dimers (interrow) are no longer present. The electrostatic potential close to the surface is plotted in the right panel of Figure 2: the lone pair electrons of the oxygen atoms are responsible for potential wells above one of the Si dimer atoms. Compared to the clean surface, the electrostatic potential of the hydroxylated surface appears to be more confined, going to a plateau value around 5 Å away from the surface atoms. III. B. Biotin Molecule. Before studying the chemisorption of biotin on Si-SiC(001), we analyzed the physical and chemical properties of the isolated molecule. The biotin molecule consists of the following three main parts: a bicyclo ring system, a carboxyl group, and a bridging alkyl chain (Figure 4). The bicyclo ring contains a ureido group which plays an important role when the molecule binds to proteins. The ureido group can establish up to five hydrogen bonds and is responsible for the strong affinity to proteins such as streptavidin and avidin.23 In general, organic and biological molecules may assume several conformations characterized by small energy differences. In case of the biotin molecule, this possibility is mainly related to the rotational freedom of the alkyl chain. Previous ab initio calculations24 performed using MP2 (Moller-Plesset pertubation theory) showed that the lowest total-energy conformation of biotin in the gas phase has a curled shape, characterized by an intramolecular hydrogen bond stabilizing the molecule. However, as pointed out in ref 24, such a conformation is unlikely in the presence of water molecules. Since studying the energy landscape of the biotin molecule is beyond the scope of our work, we chose in our investigation the biotin conformer found in the streptavidin-biotin complex, as characterized by Salemme et al.25 and reported in the Protein Data Bank (PDB).26 This structure is of interest for our study in assessing how the surface could influence the biotin properties determining protein binding. Starting from this biotin conformer, we performed a structural relaxation within the DFT-GGA framework, allowing all the atoms to move (Figure 4). At the equilibrium geometry the O-H bond of the carboxyl functional group is 0.98 Å, the C-OH and CdO bond lengths are 1.39 and 1.23 Å, respectively. The CdO and N-H bond lengths of the ureido group are 1.24 and 1.02 Å, respectively. The two C-S bonds in the etherocyclic ring are 1.84 and 1.82 Å. The C-S with the alkyl chain attached is slightly longer by 0.02 Å. The biotin relaxed structure
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Kanai et al.
Figure 2. Comparison of electrostatic potential generated by (a) the clean and (b) hydroxylated Si-SiC(001) surface. The plot plane is perpendicular to the [11h0] direction and contains surface silicon dimer atoms. The Si dimer atoms are shown as gray filled circles. For the clean surface, (a), a well of negative [repulsive for electrons] potential is evident between the adjacent Si dimer rows. There exists a well of negative potential above the oxygen atom of the hydroxyl group in the case of the hydroxylated surface (b). The x and y axes of the plot are given in Å. The contour lines are given from -0.10 atomic units (au) to 0.10 au (0.01 au spacing).
Figure 3. Density of states (DOS) of the clean (dashed line) and hydroxylated (solid line) Si-SiC(001) surface calculated at the Γ point. DOS of the isolated biotin molecule is also shown in filled spectrum for comparison. The reference E ) 0.0 eV is taken to be HOMO of the clean Si-SiC(001) surface. Gaussian broadening was used with the width of 0.2 eV.
compared well with the experimental one observed when bound to streptavidin,25,26 and differences in the bond distances were less than 0.05 Å. For the isolated molecule, we found the HOMO-LUMO gap to be 3.96 eV. The HOMO state is highly localized on the sulfur atom, while the LUMO is localized around the carboxyl group. The HOMO-1 state, which lies 0.33 eV lower in energy than the HOMO, is highly localized around the ureido group. In the context of density functional theory, the local reactivity (Fukui function) is approximately given by the charge density of Kohn-Sham frontier orbitals.27 Therefore, this indicates that in the biotin molecule, the sulfur atom and carboxyl group are the two most probable local sites of chemisorption, which is consistent with chemical intuition. To gain insight into the role played by the ureido group in protein binding we analyzed its polar CdO group. The electrostatic potential due to the polar CdO group is largely responsible for extensive hydrogen-bond formation in protein complexes (see Figure 5, where the electrostatic potential around the water oxygen atom is also shown for comparison). It is important that this electrostatic potential is not strongly modified when biotin is attached to a surface, so that the molecule retains specific binding to the proteins.
Figure 4. Ball and stick representation of the optimized biotin structure. Charge density isosurfaces (0.01 au) of the HOMO, HOMO-1 and LUMO states are also shown.
In general, the solvation by water molecules could have a pronounced effect on the structure and electronic properties of polar molecules, such as biotin. To assess solvation effect on the biotin conformer, we used the continuum solvation model by Fattebert and Gygi.29,30 This model consists of altering the Hartree term in the DFT functional by introducing an additional charge density dependent potential in the Poisson equation for the dielectric water medium. The solvation effects of the water medium have been shown to be well reproduced by this scheme in previous studies.31 The structural differences of the analyzed biotin conformer with and without the solvation model were found to be negligible. The most noticeable change was observed within the carboxyl group; the distance between the hydrogen atom and the double-bonded oxygen atom was increased by approximately 2%.
Biotin Chemisorption on Si-SiC(001) Surfaces
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Figure 5. Comparison of the electrostatic potential generated by (a) ureido group of biotin molecule and (b) water molecule in vicinity of its oxygen atom. The plot plane contains the oxygen atom and the two maximally localized Wannier functions (MLWF) centers which correspond to the oxygen atom’s lone pair electrons. x and y axes of the plot are given in Å. The contour lines are given from -0.15 au to 0.15 au (0.015 au spacing).
Figure 6. Ball and stick representation of biotin chemisorbed on the clean Si-SiC(001) surface. (a) Charge density isosurfaces of chemisorbed system’s HOMO (0.007 au) and the states corresponding to biotin’s HOMO and HOMO-1 (0.01 au) are shown. The eigenvalues for the biotin’s HOMO and HOMO-1 states are also shown in parentheses with respect to the system’s HOMO state. (b) Charge density isosurfaces of LUMO (0.002 au) are shown.
III. C. Chemisorption of Biotin on Si-SiC(001) Surfaces. In this section, we report our results on biotin chemisorption on both the clean and hydroxylated Si-SiC(001) surfaces. III. C.1. Chemisorption on Clean Surface. From previous studies on interaction of water molecules with the Si-SiC(001) surface and the preceding discussion on biotin reactivity, one could reasonably expect dissociative chemisorption of the biotin carboxyl group at the surface. In case of water dissociation, the formation of HO-SiC(001) and H-SiC(001) bonds is observed with no energy barrier. Depending on the water chemisorption site on the surface, a reaction energy ranging from -3.2 to -3.5 eV was found.9 We first relaxed the biotin molecule with the carboxyl group intact, placed 2.0 Å above the surface between Si dimer rows. Similar to the water case, the dissociative chemisorption of biotin
via the carboxyl group was found to be highly exothermic (∆E ) -3.2 eV), and no energy barrier was observed. The resulting biotin chemisorbed on the surface is shown in Figure 6. The change in the alkyl chain length of the biotin is negligible upon chemisorption (less than 0.1 Å increase), and the Si-OR/Si-H bond lengths are 1.69 and 1.49 Å, respectively. Upon biotin attachment, a minor widening of the surface band gap to 0.36 eV takes place, which is attributed to modifications of surface states due to the saturation of two Si DBs. This saturation effect can be seen by examining the changes in projected DOS (PDOS) on the Si 2pz orbitals, which yield the most significant contribution to surface states. Graphs a and b of Figure 7 show the PDOS for the Si atoms at which the DBs become saturated with H atom and biotin, respectively. Figure 7c shows the PDOS averaged over all other Si top surface
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Kanai et al. potential from the surface to the biotin ureido group is likely to be responsible for this shift. Biotin adsorption may also take place through a dative bond formation via the lone pair electrons (HOMO) of the sulfur atom. To assess the interaction energy of the sulfur atom with the surface in the absence of the repulsion due to the rest of the biotin, we considered another conformal isomer (with the alkyl chain rotated at the carbon atom of the etherocyclic ring), which lies approximately 0.01 eV higher in energy. For this reaction we found a binding energy of approximately 1.2 eV. This result indicates that there is a strong preferential equilibrium distribution for biotin chemisorbed via the carboxyl group rather than via formation of a dative bond through the sulfur atom. III.C.2. Chemisorption on the Hydroxylated Surface. Chemically, the most straightforward procedure to attach biotin to a hydroxylated surface is through an esterification reaction via the carboxyl group of the molecule. Indeed, some experimental studies achieved this functionalization on both hydroxylated gold and diamond surfaces.2,3 In the esterification process, the -OH group of the surface reacts with the carboxyl group of the biotin molecule (R-COOH), and a single water molecule is produced as a byproduct:
R-COOH + Sisurf-OH f R-COO-Sisurf + H2O
Figure 7. Projected density of states (PDOS) on the 2pz orbitals of the topmost silicon surface atoms for the clean Si-SiC(001) surface, before and after the biotin chemisorption. The reference E ) 0.0 eV is taken to be HOMO state of the clean Si-SiC(001) surface. The solid line and dashed line are for the DOS after and before the chemisorption, respectively. Gaussian broadening was used with the width of 0.2 eV. (a) Si surface atom reacted with hydrogen atom. (b) Si surface atom reacted with the biotin via carboxyl group. (c) Averaged over all other topmost Si surface atoms which are not saturated in chemisorption.
atoms. There is an evident shift of the PDOS spectra of the two Si atoms that become saturated upon chemisorption, while other surface Si atoms show essentially the same features in the PDOS as on the clean surface. Analyzing the PDOS, we find that the features of the biotin LUMO state are no longer present due to the dissociative adsorption via the carboxyl group. On the other hand, HOMO and HOMO-1 states of the isolated biotin can still be identified, being decoupled from the surface. The eigenvalue difference between these two states, however, widens considerably, to 0.79 eV, from the value of 0.32 eV found in the isolated molecule. The extended electrostatic
Esterification reactions are generally complex activated processes, which could involve sequential transition states. It is beyond our scope to study such a reaction process; therefore, we restrict ourselves to investigating the final chemisorption state, rather than studying its mechanism. We found that, after an esterification reaction occurs, the fully relaxed biotin extends vertically from the surface (Figure 8), being still accessible for protein binding. The reaction is endothermic (∆E ) 0.55 eV) as oberved for many esterification processes. Chemisorption of biotin disrupts the network of hydrogen bonds of hydroxyl groups on the surface; thus, it is expected that ∆E may differ by the energy of a single hydrogen bond, depending on biotin’s orientation on the surface. The endothermicity of the reaction suggests that biotin esterification at the hydroxylated SiC surface is indeed an activated process. Consequently, to achieve efficient functionalization, one must activate biotin molecules with chemical auxiliary, as discussed in ref 2. Changes in the DOS of the surface caused by biotin chemisorption are minor, and the band gap remains the same, unlike the case of the clean surface. In fact, both HOMO and LUMO of the surface are almost unchanged with respect to the unreacted surface: the HOMO is a surface state localized within the top few layers, and the LUMO is localized more deeply into the SiC bulk region. These minor changes are consistent with the fact that the Si atom’s chemical environment does not change dramatically upon esterification: a Si-OH bond (1.66 Å) is replaced by the Si-OR bond (1.71 Å). Characteristics of HOMO and HOMO-1 states of the biotin (occupied states with the two highest energy, belonging to biotin molecule) are closely retained and decoupled from the surface, while the features of biotin LUMO state are no longer present as in the case of adsorption on the clean surface. The difference in eigenvalues of these HOMO and HOMO-1 states of the isolated molecule widens to 0.50 eV from 0.32 eV. This shift is smaller than in the case of the clean Si-SiC(001) surface because of the more confined electrostatic potential of the hydroxylated surface. Interestingly, we find that the characteristic feature and the magnitude of the electrostatic potential around the ureido group of the biotin are retained closely upon chemisorption (Figure
Biotin Chemisorption on Si-SiC(001) Surfaces
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Figure 8. Ball and stick representation of biotin chemisorbed on the hydroxylated Si-SiC(001) surface. (a) Charge density isosurfaces of the chemisorbed system’s HOMO (0.007 au) and the states corresponding to biotin’s HOMO and HOMO-1 (0.01 au) are shown. The eigenvalues for the biotin’s HOMO and HOMO-1 states are also shown in parentheses with respect to the system’s HOMO state. (b) Charge density isosurfaces of LUMO (0.002 au) are shown.
Figure 9. Comparison of the electrostatic potential of the biotin molecule chemisorbed (a) on the clean surface and (b) on the hydroxylated surface. The plot plane contains the ureido oxygen atom and two nitrogen atoms of the ureido group. x and y axes of the plot are given in Å. The contour lines are given from -0.15 atomic units (au) to 0.15 au (0.015 au spacing).
9). The comparison of the PDOS on 2p orbitals of the ureido oxygen atom, averaged over the magnetic quantum number (m ) -1, 0, 1), is shown in Figure 10. The ureido oxygen atom in the isolated biotin gives a strong contribution to the HOMO-1 state and another state about 4 eV lower in energy, which is highly localized on the OdC of the ureido group. When adsorbed on either surface, the PDOS of the biotin’s ureido oxygen is essentially unchanged without any noticeable broadening due to the presence of the surface. The electronic structure of the hydroxylated surface is almost unaffected by the biotin presence. These results suggest that the capacity of biotin to bind proteins is very likely to be retained upon chemisorption. IV. Conclusions Using accurate first principles DFT calculations, we studied biotin chemisorption on the clean and hydroxylated siliconterminated SiC(001) surfaces. Similar to the case of water-
molecule adsorption, the biotin adsorption on the clean surface is barrierless and highly exothermic. In the case of the hydroxylated surface, the reaction appears to be an activated process. Upon chemisorption, the electronic structure of the clean surface is significantly altered because of the saturation of Si dangling bonds, whereas for the hydroxylated surface, we found essentially no changes. Interestingly, on both clean and hydroxylated surfaces, the qualitative features of the electrostatic potential generated by the ureido group is retained. However, the more extended potential of the clean surface appears to have a larger influence on the ureido group than the more confined potential of the hydroxylated surface. The electronic structure surrounding the ureido oxygen atom also does not change appreciatebly in both cases. The spacial separation of biotin’s highly localized LUMO state from the ureido group by the long alkyl chain appears to be important in retaining characteristic features of potential around the ureido group. Our findings gain
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Figure 10. Projected density of states (DOS) on the ureido oxygen atom’s 2p orbitals in isolated biotin, on the clean surface, and on the hydroxylated surface. The PDOS is the average of all the magnetic quantum numbers (m ) -1,0,1) for the 2p orbitals. The reference (E ) 0.0 eV) is taken to be HOMO of the isolated biotin molecule. The PDOSs are aligned using the oxygen atom’s 2s orbital.
preliminary insight into the understanding of experimental observations showing that biotin molecules directly adsorbed on the hydroxylated surfaces bind strongly to streptavidin.2,3 Further studies are needed to understand how proteins such as streptavidin bind to the biotin molecule in the presence of the surface. Further interesting work could involve the analysis of the electrical conductance through the biotin molecule; this is of interest in biosensing applications when electrical transducers are used. The use of electrical transducers is particularly desirable because of direct integration with semiconductor circuitry. It may be interesting to further investigate if it is possible to replace the insulating alkyl chain with a conjugated chain without modifying the electronic properties of the biotin ureido group. Acknowledgment. Use of the computing facilities at the University of California, Lawrence Livermore National Laboratory (LLNL) is gratefully acknowledged. Part of this work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48. Y.K. is grateful to the CCMS Summer Institute and LLNL for hospitality and financial support. Y.K., A.S., and R.C. thank the NSF (Grant No. CHE-0121432). We also thank David Prendergast, JeanLuc Fattebert, and Felice Lightstone for fruitful scientific discussions. References and Notes (1) Wilchek, M.; Bayer, E. A. Anal. Biochem. 1988, 171, 1.
Kanai et al. (2) Delabouglise, D.; Marcus, B.; Mermoux, M.; Bouvier, P.; ChaneTune, J.; Peit, J.; Mailley, P.; Livache, T. Chem. Commun. 2003, 21, 2698. (3) Taylor, D. M.; Morgan, H.; D’Silva, C. J. Phys. D. 1991, 24, 1443. (4) Nakamura, D.; Gunjishima, I.; Yamaguchi, S.; Ito, T.; Okamoto, A.; Kondo, H.; Onda, S.; Takatori, K. Nature 2004, 430, 1009. (5) Ocelic, N.; Hillenbrand, R. Nat. Mater. 2004, 3, 606. (6) Derycke, V.; Soukiassian, P. G.; Amy, F.; Chabal, J.; D’angelo, M. D.; Enriquez, H. B.; Silly, M. G. Nat. Mater. 2003, 2, 253. (7) Amy, F.; Chabal, Y. J. J. Chem. Phys. 2003, 119, 6201. (8) Cicero, G.; Catellani, A.; Galli, G. Phys. ReV. Lett. 2004, 93, 016102. (9) Cicero, G.; Galli, G.; Catellani, J. Phys. Chem. B. 2004, 108, 16518. (10) Perdew, J.; Burke, K.; Ernzerhof, M. Phys. ReV. Lett. 1996, 77, 3865. (11) Hamann, D. Phys. ReV. B: Condens. Mater. Phys. 1989, 40, 2980. (12) This is equivalent to including 6k points in the irreducible BZ of the p(2 × 1) unit cell. (13) Catellani, A.; Galli, G. Prog. Surf. Sci. 2002, 69, 101. (14) GP code (F. Gygi, LLNL 1998-2003). (15) Car, R.; Parrinello, M. Phys. ReV. Lett. 1985, 55, 2471. (16) Baroni, S.; Dal Corso, A.; de Gironcoli, S.; Giannozzi, P. http:// www.pwscf.org/. (17) The model that is most agreed upon for the ground state of SiSiC(001) is a c(4 × 2) structure with alternate up and down dimers (AUDD model). This reconstruction, although having a primitive cell different from the p(2 × 1), has Si-Si and Si-C bonding configurations that differ very little from the one considered here. In both cases one has rows of weakly bound Si dimers, which have alternate up and down z coordinates (z being the direction perpendicular to the surface) in the AUDD model, and the same z coordinate in the p(2 × 1) reconstruction. Furthermore, in ab initio simulations (both at the LDA and GGA level) the energy difference between c(4 × 2) and p(2 × 1) is of the order of room temperature. In the present work we have chosen the p(2 × 1) reconstruction for consistency with SiSiC(001) hydroxylation studies previously reported (see refs 8 and 9), being confident that the surface reactivity with biotin would not be affected. (18) Marzari, N.; Vanderbilt, D. Phys. ReV. B: Condens. Mater. Phys. 1997, 56, 12847. (19) Gygi F.; Fattebert JL.; Schwegler E. Comput. Phys. Commun. 2003, 155, 1. (20) The potential was considered to reach plateau when its gradient becomes smaller than 0.001 au. (21) In our studies we have chosen the configuration which was determined to be the one with lowest energy in previous work (see ref 9). (22) This value was calculated by using a symmetric slab of 11 SiC layers. Since the LUMO of the slab system is a bulk SiC state, a number of layers larger than eight was needed to obtain a converged value. (23) Weber, P. C.; Wendoloski, J. J.; Pantoliano, M. W.; Salemme, F. R. J. Am. Chem. Soc. 1992, 114, 3197. (24) Strzelczyk, A. A.; Dobrowolski, J. Cz.; Mazurek, A. P. Theor. Chem. 2001, 541, 283. (25) Weber, P. C.; Ohlendorf, D. H.; Wendoloski J. J.; Salemme, F. R. Science 1989, 243, 85. (26) (a) Sussman, J. L.; Lin, D.; Jiang, J.; Manning, N. O.; Prilusky, J.; Ritter, O.; Abola, E. E. Protein Data Bank (PDB), Acta Crystallogr. 1998. D54, 1078. (b) Abola, E. E.; Sussman, J. L.; Prilusky, J.; Manning, N. O. In Methods in Enzymology; Carter, C. W., Jr., Sweet, R. M., Eds.; Academic Press: San Diego, 1997; Vol. 277, p 556. (27) Parr, R. G.; Yang, W. J. Am. Chem. Soc. 1984, 106, 4049. (28) Galvan, M.; Pino, A. D., Jr.; Joannopoulos, J. D. Phys. ReV. Lett. 1993, 70, 21. (29) Fattebert, J. L.; Gygi, F. Int. J. Quantum. Chem. 2003, 93, 139. (30) Fattebert, J. L.; Gygi, F. J. Comput. Chem. 2002, 23, 662. (31) Fattebert, J. L. Unpublished work.
