The binding of multi functional organic molecules on silicon surfaces 1

The Binding of Multi-functional Organic Molecules on Silicon Surfaces Chapter Introduction 1 Motivation Advances in micro-fabrication, which makes possible the manufacture of computer "chips," have launched us into a new age of technological innovation Devices such as the cellular phone and portable computers rely on semiconductor-based microelectronics to function The genesis of the innovations required for faster, more powerful computers and other futuristic applications depends on our ability to fabricate smaller, but more complex structures in an economically efficient manner The next challenge will be to create microelectronic devices that comprise of billion of components but are smaller than a fingernail [1] The formation of these intricate structures involves repeated steps of material deposition and selective removal As devices decrease in size but become more complex in terms of material requirements, a molecular understanding of basic chemical reactions is required [1] Recently, the marriage of organic molecules with silicon-based devices attracts much attention [2-6] It offers potential opportunities to combine high chemical, mechanical, and thermal stabilities with tailored electronic or optical properties into existing device technologies [7-10] However, the physical properties and chemical nature of these interfacial atoms or molecules are expected to play crucial roles in the functions and characteristics of devices [1] Thus, it is essential to understand the selectivity, configuration, and mechanism in covalent binding multifunctional organic molecules to silicon surfaces The Binding of Multi-functional Organic Molecules on Silicon Surfaces 1.2 The Si(111)-7×7 and Si(100)-2×1 surfaces Silicon crystals have the diamond-like structure, i.e the atoms are sp3 hybridized and bonded to four nearest neighbors in the tetrahedral coordination The covalent bonds are 2.35 Å long and each has the bond strength of 226 kJ / mol [11] When the crystal is cut or cleaved, bonds are broken, creating dangling bonds at the surface As a typical covalently bonded material, the clean silicon surfaces reconstruct in order to reduce the energy associated with the surface dangling bonds On Si(100), the surface atoms pair up as dimers to form a (2×1) reconstruction [12-14] On Si(111), equilibrium (7×7) reconstruction with a more complicated DAS (dimer-adatom-stacking) structure is formed upon thermal annealing [15, 16] It is worth noting that the dangling bonds are the origin of the chemical activity of silicon surfaces Thus, the reactivity of organic molecules on the silicon surface is intimately connected with the geometric and electronic structures of the surface silicon atoms 1.2.1 The structure of Si(111)-7×7 The (7×7) reconstructed silicon surface has been a subject of continued interest for more than a quarter of a century Since the first report of a (7×7) LEED pattern by Schlier and Farnsworth in 1959 [17], numerous structural models have been proposed to account for this observation over the following 25 years Ion-scattering experiments [18-19] provided evidence for a significant rearrangement of the atoms in the deeper layers of the surface, interpreted by Bennett et al [19] in terms of a surface stacking-fault In 1985, Takayanagi et al [15, 16] proposed a new structural model for the (7×7) reconstruction based on the results from transmission electron diffraction (TED) experiments This model, referred to as the DAS (dimer-adatom-stacking) model (Figure 1.1), further The Binding of Multi-functional Organic Molecules on Silicon Surfaces supported by numerous evidences from other surface techniques such as medium-energy ion scattering [20] and grazing x-ray diffraction [21], is now the most widely accepted model for Si(111)-7×7 The scanning tunneling microscopic (STM) study of the Si(111)7×7 surface by Binnig et al [22] gave the first real space image including 12 protrusions per unit cell and deep holes at the corners, strongly favoring the DAS model with adatoms and corner vacancies The dimer-adatom-stacking faulted (DAS) model is schematically presented in top and side views in Figure 1.1, a unit cell (a rhombohedral-like dimensions of 46.56 Ǻ for the long diagonal and 26.88 Ǻ for the short diagonal) covering a surface area equivalent to 49 atoms of the (111) plane A stacking fault is present in the second atomic layer, but it affects only one half of the cell (on the left of Figure 1.1) Therefore, the unit cell is further divided into two half, i.e the faulted part and the unfaulted [23] Figure 1.2 shows the layer-by-layer buildup of the Si(111)-7×7 structure The first layer contains 12 adatoms so that each one of them saturates three atoms of the second layer Six of the second layer atoms remain nevertheless unsaturated, we call them rest atoms At the third atomic layer, there are dimers along the edge of the (7×7) structure One atom is missing at the corner of the unit cell (i.e one missing atom per unit cell) which leaves a place for fourth layer atom, creating the “corner holes” The most important structural effect of the reconstruction is a dramatic reduction in the number of surface dangling bonds in the (7×7) unit cell from 49 to 19 (12 + + 1), 12 arising from the adatoms, from the rest atoms, and one from the corner hole There are seven types of spatiallyinequivalent dangling bonds in each unit cell: four from the adatoms (corner adatom or The Binding of Multi-functional Organic Molecules on Silicon Surfaces center adatom on the faulted or the unfaulted halves), two from the rest atoms in the faulted and unfaulted parts, and one from the corner hole 1.2.2 Electronic properties of Si(111)-7×7 The seven types of spatially-inequivalent atoms, namely, four adatoms including corner, center atoms on both faulted and unfaulted halves, faulted and unfaulted rest atoms, and the corner hole atom, are also electronically-inequivalent The inherent differences in the density of electronic states between these atoms are readily distinguishable in STM images [22] For example, when the occupied states of the sample are probed with negative sample bias, the STM images reveal a marked asymmetry between the two halves of the unit cell [24] The adatoms in the faulted half appear to have a higher intensity than those in the unfaulted half due to the difference in electronic structure caused by the stacking fault [25] Moreover, in each half of the unit cell, the three corner adatoms are brighter than the three center adatoms [14] This observation is attributed to the charge transfer between adatom and rest atom [26] Each center adatom has two neighboring rest atoms, but only one for each corner adatom The amount of charge for transferred from a center adatom to the rest atoms is roughly twice as much as that from the corner adatom Consequently, the corner adatom has a high density of occupied states, which accounts for its brighter appearance in the STM filledstate images It was shown experimentally and theoretically that each adatom dangling bond has an occupancy of approximately one-half an electron, whereas each rest atom dangling bond has two electrons It is generally accepted that the dangling bonds are the centers of chemisorption reactions As the Si(111)-7×7 surface presents seven types of such bonds, different The Binding of Multi-functional Organic Molecules on Silicon Surfaces chemical behaviors are expected One way of quantifying the reactivity of a site is to look at its capacity to give or receive electrons under the influence of an external potential created, for example, by an exterior atom Brommer et al [27] evaluated this capacity by the local softness The greater the density of the empty states (acceptor), or filled states (donor), around the Fermi level, the greater the softness The calculation of the softness on the dangling bonds of the Si(111)-7×7 gave the following results: For electrophilic reactants (absolute electronegativity greater than that of silicon), the sites apt to give electrons are, in decreasing order, the corner hole, the rest atoms and the adatoms The sites situated on the faulted side have a greater softness than those on the unfaulted For nucleophilic reactants (absolute electronegativity inferior to that of silicon), the adatoms have the greatest tendency for accepting electrons, followed by the corner hole and rest atoms 1.2.3 The structure of Si(100)-2×1 The commonly accepted model for the reconstructed Si(100) surface is the dimer model The first model of this kind was proposed by Schlier and Farnsworth on the basis of their observation of a (2×1) low-energy electron diffraction (LEED) pattern [17] and was confirmed by scanning tunneling microscopic (STM) studies [12-14] In this model the density of dangling bonds is decreased by 50% by creating rows of dimers, where each surface silicon atom bonds to a neighboring atom along the {110} direction using one of its dangling bonds, as shown in Figure 1.3 The original model was modified by Levine [28], and later by Chadi [29], who proposed that the dimers could be asymmetric (buckled, i.e one member atom is higher from the surface than the other) The discussion leading to the acceptance of the dimer model was reviewed by Haneman in 1987 [30] The Binding of Multi-functional Organic Molecules on Silicon Surfaces together with several other models Many experiments [31-34] and theoretical calculations [29, 35-39] have been devoted to resolve the question of whether the dimers are symmetric or asymmetric on perfect regions There is no consensus yet and though the majority of the results points toward the buckled dimers model, the symmetric dimers are favored in several works The compromise viewpoint expressed in a number of publications [40-43] implies that as the calculated energy difference between the symmetric and asymmetric dimers is very small (e.g only ∼ 0.02 eV according to Ref [40]), it is therefore quite possible that both kinds of dimers could coexist on the surface The STM observations [12-14] have clarified the situation only partially STM images show the presence of both buckled and non-buckled dimers in roughly equal amounts as well as a high density (∼ 10%) of vacancy type defects (missing dimers) In defect-free areas only symmetric dimers were observed while buckled dimers appeared to be stabilized near surface defects However, the authors [14] pointed out that they were unable to ascertain whether the symmetric-looking dimers are truly symmetric or whether the STM image is only sensitive to the time-average position of dimers which may flip dynamically on a time scale shorter than the STM measurement time The idea that buckled dimers may rapidly interconvert with symmetric dimers or simply flip found theoretical support in Refs (35, 36) Moreover, the results of several theoretical works [44-46] showed that biasing the surface, used in STM experiment, can visibly influence the resulting surface image In the case of the 2×1 reconstruction of the Si(100) surface this means that one can expect STM images to show symmetric dimers even if the dimers in the unbiased surface are buckled The Binding of Multi-functional Organic Molecules on Silicon Surfaces 1.2.4 Electronic properties of Si(100)-2×1 In the (2×1) reconstructed surface, adjacent Si atoms pair into dimers, shown in Figure 1.4a The bonding configuration within the surface dimers can be formally described in the terms of a Si-Si σ bond coupled with a π bond [13, 14, 47], analogous to the C=C double bond of alkenes since C and Si belongs to the same group (group IV), suggesting a possible similarity of chemical reactivity between them On the other hand, the π overlap of the Si surface dimers is poor This is particularly attributable to the strained geometry at the surface preventing good spatial overlap of the orbitals needed to achieve strong π bonding The pairing energy associated with the dimer π bond on a clean Si(100) has been estimated at values between and 31 kJ/mol, [47-51] with most estimates clustering between 20 and 30 kJ/mol; this value is much smaller than the typical Si bond strength of 226 kJ/mol for bulk Si and 250-310 kcal/mol for silicon hydrides [11] In fact, the Si=Si dimer might be regarded as a di-radical [48] as schematically presented in Figure 1.4(b) A great number of theoretical calculations [35-39] and experimental investigations [28-34] confirmed the existence of buckling Si=Si dimer The buckling dimer is accompanied by a charge transfer from the buckled-down atom to the buckledup The scheme of this unique surface structure is shown in Figure 1.4(c) Due to its asymmetry nature, the Si=Si dimer displays both electrophilic and nucleophilic 1.3 Reaction mechanisms of functional molecules with silicon surfaces Previous work in this field has been mainly focused on the binding of unsaturated organic molecules on silicon surfaces [2-6] Based on the reactive mechanisms, two The Binding of Multi-functional Organic Molecules on Silicon Surfaces broad areas of organic reaction will be highlighted, including cycloaddition reactions, and dative bonding and proton transfer 1.3.1 Cycloaddition reactions In organic chemistry, one of the most important and widely used reactions to extend molecular architecture is cycloaddition [52-54] Cycloaddition are reactions in which two π bonded molecules approach each other to form a new cyclic structure, losing two π bonds and producing two new σ bonds in the process Two typical cyclic addition reactions are [2+2] and [4+2] cycloadditions For [2+2] cycloaddition, two alkenes react to produce a new four-membered ring by the interaction of two π electrons in one of the alkenes with two π electrons of the other alkenes The [4+2] addition, also known as Diels-Alder reaction [52], was named in the memory of Otto Diels and Kurt Alder, who enjoyed the Nobel Prize honor for their discovery of this mechanism In this reaction, “4” represents the four π electrons of conjugated dienes (the simple example is butadiene) The conjugated diene interacts with alkene to form a new six-memebered ring In this cycloadduct, a new C=C double bond is produced in the resulting cyclohexene-like structure The difference in reactivity observed for the [2+2] and [4+2] cycloaddition reactions can be predicted by a symmetry analysis of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reacting molecules Such an analysis yields the Woodward–Hoffman selection rules [55] These rules dictate that the parity of the p orbital lobes involved in the creation of the new σ bonds must be identical for the reaction to proceed As demonstrated in Figure 1.5, [4+2] The Binding of Multi-functional Organic Molecules on Silicon Surfaces cycloaddition or Diels–Alder reactions are symmetry-allowed while [2+2] cycloaddition reactions are symmetry-forbidden If the analogy made between traditional alkenes and the dimers of Si(100)-2×1 and the adjacent adatom-rest-atom pairs of Si(111)-7×7 surfaces, then it would be expected that cycloaddition surface products may be observed as a surface reaction product The [2+2]-like and [4+2]-like cycloaddition reactions have indeed been observed on the Si(111)-7×7 and Si(100)-2×1 surfaces 1.3.1.1 [2+2]-like cylcoaddition reactions Alkenes, the simple unsaturated organic molecules, bond to Si(100)-2×1 and Si(111)-7×7 to form a [2+2]-like cycloaddition product On the basis of their IR experiments on the adsorption of cis- and trans-1,2-dideuterioethylene on Si(100), Liu et al believed that the interaction of ethylene with Si(100)-2×1 is stereospecific and would follow the low-symmetry pathway [56] In contrast, the recent scanning tunneling microscopy (STM) experiments revealed that for the adsorption of trans-2-butene on Si(100), the [2+2]-like reaction is not stereospecific with a stereoselectivity of 98% and a small degree of isomerization, implying a diradical mechanism for the gas-surface reaction [57] Lu et al by means of density functional cluster model calculations showed that the adsorption of ethylene on a Si(100) surface follows a diradical mechanism [58], proceeding via a σ-complex precursor and a singlet diradical intermediate, consistent with the STM observation [57] For ethylene on Si(111)-7×7, the formation of a [2+2]like cycloaddition product have been drawn from HREELS [59], photoemission [60, 61], and STM [62] data Theoretical studies reveal that the reactions of unsaturated The Binding of Multi-functional Organic Molecules on Silicon Surfaces hydrocarbons with Si(111)-7×7 through [2+2]-like cycloaddition, including ethylene and acetylene, along a diradical reaction pathway [63] Yoshinobu and coworkers [64] first proposed that acetylene is di-σ bonded to the adjacent adatom-rest-atom pair on Si(111)-7×7 through the [2+2]-like cycloaddition at room temperature Synchrotron radiation X-ray photoemission spectroscopy and nearedge X-ray adsorption fine structure spectroscopy data confirmed the di-σ configuration via the [2+2]-like cycloaddition [65] Similar to acetylene on Si(111)-7×7, several different experimental [66-68] and theoretical [69-71] investigations show that acetylene reacts with Si(100)-2×1 to form a [2+2]-like cycloaddition as the major surface species In part due to their large dipole moments, compounds containing nitrile (C≡N) and carbonyl (C=O) have attracted considerable attention recently and several studies have begun to elucidate their rich chemistry on Si(100)-2×1 and Si(111)-7×7 surfaces [72-79] Tao et al first concluded that acetonitrile formed a [2 + 2]-like cycloadduct through the C≡N group as the majority species at low temperature on Si(100)-2×1 [72] and Si(111)7×7 [73] Their conclusions were based on the presence of a ν(C=N) stretching mode near 1600 cm-1 A recent room temperature photoemission and NEXAFS study by Bournel et al.[74] identified a [2+2]-like C≡N cycloadduct, in agreement with Tao et al On the other hand, the calculations of Lu et al indicate a pathway for the [2+2]-like C≡N cycloaddition product that passes through a dative-bonded precursor state [75] The carbonyl group is another functionality which can potentially be exploited to attach organics to silicon surfaces, white and co-workers found that the majority surface adducts for acetone, acetaldehyde, and biacetyl at low temperature are [2+2]-like cycloaddition products through the C=O group using a combination of TPD, XPS, and 10 The Binding of Multi-functional Organic Molecules on Silicon Surfaces functionalization of silicon surfaces consists of two stages Above all, functional molecules are directly chemically attached to Si surfaces The second is to grow controllably the next-layer of organic molecules through the formation new chemical bonds between adjacent two layers (the first and second layers, the second and third layers, etc.) Clearly, in order to fabricate the multi-layer organic building through chemical linkages, the layer directly bonded to silicon surfaces must contain multifunctional groups Therefore, the imperative work is to explore the reactivity and selectivity of multifunctional molecules on silicon surfaces to provide scientific knowledge for the further organic modification and functionalization of Si-based microelectronic devices and materials Pyrazine, pyrimidine, s-triazine are six-membered heteroatomic aromatic compounds containing two or three N-atoms Their ring is an important functional constituent in a variety of natural and synthetic compounds, e.g monoucleotides [113] All C and N atoms take part in the large π bond formed by six conjugated 2p electrons (one from each of them) Expectably, each nitrogen atom has a lone-pair of electrons which does not directly participate in the formation of aromatic ring These electrons are localized at the nitrogen atoms, making them electron-rich Thus, on the surface, the Natoms of these molecules can possibly act as a donor to form dative bond with electrondeficient Si dangling bonds on adatoms, similar to the interaction of pyridine on Si(111)7×7 [107] On the other hand, the aromatic ring may also react with the adjacent adatomrest atom pair through [4+2] or [2+2]-like addition pathway to form a di-σ bonded surface adduct Thus, studying the reaction of these molecules will enable us to correlate 16 The Binding of Multi-functional Organic Molecules on Silicon Surfaces the electronic properties of the constituent atoms of the ring with their reactivity and selectivity on Si(111)-7×7 For acetylethyne [CH ≡ C-C (CH3) =O)], the reactive C≡C and C=O groups are able to interact through the conjugation Previous studies showed that acetylene and acetone can individually bind to silicon surface reactive sites through a [2+2]-like addition mechanism [64, 66, 76, 77] Due to acetylethyne displaying a combined chemical structure of acetylene and acetone, thus, acetylethyne can be chosen as a template to demonstrate the selectivity and reactivity of functional groups coexisting in a multifunctional molecule on Si(111)-7×7 and Si(100)-2×1 In addition, due to the different spatial and electronic structures between Si(111)-7×7 and Si(100)-2×1 surfaces, the different binding configurations may form for acetylethyne adsorption on these two surfaces, showing the selectivity on surface structures Cyanoacetylene (CH≡C-C≡N) and diacetylene (CH≡C-C≡CH) are two conjugated molecules made of a C≡C and C≡N(C) in the atmosphere of Titan Most recently, the interesting theoretical DFT calculation has demonstrated the feasibility of the formation of [3]-cumulenic adspecies in the reaction of diacetylene on Si(111)-7×7 [114] However, experimental evidence is still to be established Thus, investigating their interactions with Si surfaces will provide the correlation of reaction selectivity and binding configuration with the functional groups in the molecule, offering the necessary flexibility in the functionalization and modification of silicon surfaces Benzadehyde and acetophenone containing a conjugated phenyl ring and a carbonyl group may selectively bind to Si(100) through a typical 1,2-dipolar cycloaddition of the carbonyl group with a Si-dimer, leaving its phenyl ring skeleton 17 The Binding of Multi-functional Organic Molecules on Silicon Surfaces intact on Si(100) The other possibility is that they can bind to the Si surface through its phenyl ring Thus, for benzadehyde and acetophenone containing a conjugated carbonyl and phenyl ring, rich attachment chemistry on Si(100)-2×1 can be expected In this work, pyrazine, pyrimidine, s-triazine, acetylethyne, cyanoacetylene, diacetylene, benzadehyde and acetophenone were chosen as model systems to understand chemical attachment mechanisms of multi-functional organic molecules on silicon surfaces using high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), ultra-violet photoelectron spectroscopy (UPS), scanning tunneling microscopy (STM) and density functional theory calculation (DFT) Through these studies, we expect to obtain extensive and comprehensive knowledge of the reactivity and selectivity of multi-functional molecules on Si(100)-2×1 and Si(111)7×7 through covalent attachment schemes 18 The Binding of Multi-functional Organic Molecules on Silicon Surfaces Top view a1 a2 Dimer [110] Corner hole [112 ] Adatom Adatom-Rest atom pair Rest atom Dangling bonds Side view [111] Faulted 10 Unfaulted 20 30 40 50 Å Figure 1.1 Dimer-Adatom-Stacking (DAS) model (Refs 15, 16) of the atomic structure of the Si(111)-7×7 surface The faulted half of the unit-cell is at right and the unfaulted at left Only adatoms, rest atoms, and corner hole atoms have dangling bonds The adatoms are divided into the corner adatoms and the center adatoms 19 The Binding of Multi-functional Organic Molecules on Silicon Surfaces d) Adatom layer c) Restatom layer b) Dimer layer a) Base layer Figure 1.2 Layer-by-layer construction of the Si(111)-7×7 structure (Ref 23): (a) (1×1) unreconstructed surface (terminated by a double layer); (b) addition of the bottom layer of the reconstructed double layer, the dimer layer; (c) addition of the second layer of the reconstructed double layer, the restlayer; and (d) introduction of the Si adatoms The dashed lines show the outline of the (7×7) unit cell for each layer drawn in the plane of the underlying layer 20 The Binding of Multi-functional Organic Molecules on Silicon Surfaces TOP VIEW SIDE VIEW (a) Ideal TOP VIEW SIDE VIEW (b) Symmetric dimers Figure 1.3 Top and side views (Ref 28) of the ideal and reconstructed Si(100) surface 21 The Binding of Multi-functional Organic Molecules on Silicon Surfaces dimer Si Si Si Si Si Si π Si σ Si π Si Si di-radical Si Si Si Si Si Si Si Si Si σ Si (a) (b) electron-rich electron-deficient Si Si (c) Figure 1.4 Schematic presentation of Si(100) surface structure at low temperature and room temperature (a) (2×1) surface structure of Si(100) (b) Spatial and electronic structure of Si=Si dimer (c) Electronic structure of buckling Si=Si dimer at low temperature 22 The Binding of Multi-functional Organic Molecules on Silicon Surfaces HOMO HOMO Sy S ym me etr ric c ma ma tch ch tch tch ma ma [2+2] cycloaddition t i tric me Sy Sy m Symmetric un-match Symmetric match Symmetric match Symmetric match LUMO LUMO [4+2] cycloaddition Figure 1.5 Analysis of [2+2] and [4+2] cyclic additions with frontier orbital theory (Ref 55) The frontier orbiters referred here are the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) The symbols “+” and “-” show the mathematical signs of the molecular orbital Thus, “+” should combine“+” and “-” should combine “-” Unmatched combination leads to symmetry forbidden reaction as the [2+2] case 23 The Binding of Multi-functional Organic 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functionalization of silicon surfaces consists of two stages Above all, functional molecules are directly.. .The Binding of Multi- functional Organic Molecules on Silicon Surfaces 1. 2 The Si (11 1)-7×7 and Si (10 0)-2? ?1 surfaces Silicon crystals have the diamond-like structure, i.e the atoms are... knowledge of the reactivity and selectivity of multi- functional molecules on Si (10 0)-2? ?1 and Si (11 1)7×7 through covalent attachment schemes 18 The Binding of Multi- functional Organic Molecules on Silicon