The binding of multi functional organic molecules on silicon surfaces 1

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 + 6 + 1, 12 arising from

Chapter 1 Introduction

1 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

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

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 9 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 + 6 + 1), 12 arising from the adatoms, 6 from the rest atoms, and one from the corner hole There are seven types of spatially-inequivalent dangling bonds in each unit cell: four from the adatoms (corner adatom or

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 filled-state 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

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

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

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 1 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 buckled-

up 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

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]

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

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 near-edge 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

HREELS studies [76, 77] In a separate theoretical investigation of a series of carbonyl containing compounds, Barriocanal et al identified a barrierless pathway that passes through a dative-bonded precursor state for the [2+2]-like C=O cycloaddition product of glyoxal [78] In contrast, Wang et al were not able to find a barrierless pathway for the reaction of acetone on Si(100)-2×1 [79] and they proposed that steric interactions of the methyl groups with the surface likely play a role in hindering the reaction of acetone

In summary, the majority of unsaturated organic molecules containing just one functional group chemisorbs on Si(100)-2×1 and Si(111)-7×7 to form a [2+2]-like cycloaddition product through a low symmetry transition state with a small activation barrier

1.3.1.2 [4+2]-like cycloaddition reactions

Konecny and Doren first proposed that more complex alkenes could also form cycloaddition products [80] They showed with DFT calculations of 1, 3-cyclohexadiene that the [4+2]-like cycloaddition should occur on Si(100)-2×1 A binding energy of 54 kcal /mol indicates that there is a substantial thermodynamic driving force for the formation of the [4+2]-like cycloaddition product Experimental investigations of 1, 3-butadiene on Si(100)-2×1 at room temperature with IR spectroscopy, TPD, and NEXAFS first confirmed the theoretical prediction of Konecny and Doren, showing that the major surface species is indeed the [4+2]-like cycloaddition product [81] On Si(111)-7×7, Lu

et al using the (U)B3LYP cluster model calculations suggested that 1,3-butadiene undergoes barrierlessly the [4+2]-like cycloaddition adsorption on an adatom-rest-atom pair by following a stepwise, diradical pathway [63] This is different from the adsorption

of conjugated dienes on the Si(100)-2×1 surface, for which ab initio cluster model calculations predicted barrierless and concerted pathways [82, 83]

Heteroaromatic molecules such as thiophene and furan have all been investigated experimentally and theoretically on Si(111)-7×7 and Si(100)-2×1 [63, 83-89] Several groups have investigated thiophene on Si(111)-7×7 and Si(100)-2×1 and are in general agreement that a [4+2]-like cycloaddition product comprises the major surface product at low temperature For thiophene adsorption on Si(111)-7×7, energy loss peaks near 2190

cm-1 in the HREELS spectrum for the chemisorbed 2,5-deuterated thiophene, consistent with alkane ν(-C-D) stretching modes, lead Cao et al conclude that thiophene looses its aromaticity through the α-positions in thiophene directly bonding to the surface reactive sites, forming a [4+2]-like cycloaddition adduct at low temperature [84, 85] A related investigation of thiophene on Si(100)-2×1 by Qiao et al.[86], employing XPS, UPS, and HREELS, also concluded that [4+2]-like cycloaddition product is the major surface adduct at low temperature Theoretical studies by Lu and coworkers [63, 83, 87] of several aromatic molecules further indicated that the [4+2]-like cycloaddition has no apparent activation barrier and gives the most stable surface product by nearly 36.0 and 34.3 kcal/mol on Si(111)-7×7 and Si(100)-2×1, respectively

Similar to the case of thiophene, the HREELS spectrum for furan on Si(100)-2×1 and Si(111)-7×7 [88, 89] suggests the coexistence of (sp3) C-H and (sp2) C-H stretching modes, indicating furan binding to silicon surfaces via the [4+2]-like cycloadditions at low temperature In addition to the [4+2]-like cycloaddition producing the 2,5-dihydrofuran-like surface species, the dimerization of furan mediated by the surface

dangling bonds was also evidenced [89], which was further confirmed by recent theoretical study by Lu et al [63]

1.3.2 Dative bonding and proton transfer

On Si(111)-7×7 or Si(100)-2×1, nucleophilic / electrophilic reactions are possible because of the different electronic densities of the reactive silicon sites Previous studies [90-108] showed that organic molecules with electron rich or deficient atoms can form a dative bond with Si(111)-7×7 and Si(100)-2×1 The dative-bonded state is the final surface species for some simple molecules In other cases, it acts as a precursor state for

formation of products which are thermodynamically more favorable

Ammonia, an excellent nitriding agent for the fabrication of oxidation masks, gate dielectrics, and diffusion barriers in microelectronic devices [109–112], with a lone pair, reacts with the Si(100)-2×1 and Si(111)-7×7 surfaces via cleavage of an N-H bond, producing chemisorbed H atoms and NH2 fragments [90-96] Computational studies suggested that this reaction proceeds through a mechanism in which the nitrogen lone-pair electrons interact at the edge of a Si=Si dimer via a kind of transient dative bonding, which in turn weakens the N-H bond and leads to dissociative adsorption [97, 98]

Several groups have investigated the bonding of organic amines on Si(100)-2×1 and Si(111)-7×7 in an effort to understand the reaction mechanisms on these surfaces [99-108] On Si(100)- 2×1, the most important factor influencing the final surface product is the presence of an N-H bond in the reacting molecule Primary and secondary amines, both of which contain at least one N-H bond, undergo proton transfer while tertiary amines do not [99-105], but forming dative-bond On Si(111)-7×7, trimethylamine and

pyridine also form a stable dative-bonded species at room temperature and low temperature, respectively; pyrrole undergoes proton transfer [101, 106, 107]

Cao and Hamers investigated the bonding of trimerthylamine (TMA) on 2×1 and Si(111)-7×7 with a combined experimental and theoretical approach [101] XPS spectra show that TMA forms stable dative-bonded adducts on both Si(001) and Si(111) surfaces, characterized by very high N(1s) binding energies of 402.2 eV on Si(100)-2×1 and 402.4 eV on Si(111)-7×7 The highly ionic nature of these adducts confirms the dative bonding of TMA on Si(100) and Si(111) surfaces [101] More recently, it was experimentally demonstrated that the nucleophilic dimer atom can also donate electrons

Si(100)-to the empty orbital of boron trifluoride (BF3) [103] When BF3 is exposed Si(100)-to a silicon surface pre-saturated with trimethylamine, it molecularly adsorbs to the nucleophilic dimer atom, forming a surface-mediated donor–acceptor complex (TMA–Si–Si–BF3) Pyrrole, as a aromatic cyclic amine, was initially studied on Si(100)-2×1 with HREELS and XPS at room temperature by Qiao et al [105] and the dominant surface species was found to be an N-H dissociated product, as opposed to the [4+2]-like cycloaddition products observed for thiophene and furan The reaction was presumed to take place via the dissociative adsorption of pyrrole by the interaction of the lone-pair electrons on the N atom with the unoccupied orbital in one of the surface Si-dimer atoms This surface reaction was confirmed by Cao et al [103] using FTIR spectroscopy studies and deuterated pyrrole Besides the predominant N-pyrrolyl adspecies, they also observed the presence of di-σ bonded adspecies presumably formed by further cleaving a C(α)-H bond of the N-pyrrolyl adspecies More recently, Pyrrole adsorption on Si(111)-7×7 has been investigated using HREELS, TDS, and DFT by Yuan et al [106] The observation

of N–Si and Si–H vibrational features, together with the absence of N–H stretching mode for chemisorption clearly demonstrates the dissociative nature of pyrrole chemically binding on Si(111)-7×7 through the breakage of N–H bond Moreover, the resulting fragments of pyrrolyl and H atom are proposed to bind with an adatom and an adjacent rest atom, respectively, based on the STM results

The stable dative-bonded species at low temperature can also be observed for aromatic amines binding on silicon surfaces Tao et al [107, 108] investigated the chemical binding of pyridine on Si(100)-2×1 and Si(111)-7×7 using XPS, HREELS, and DFT calculations A dative bonding between the electron-rich N-atom of pyridine and electron-deficient silicon atom was detected in addition to the di-σ binding configuration through the N-atom and its opposite C-atom at 110 K The two chemisorption states of pyridine on Si(100)-2×1 and Si(111)-7×7 was supported by the two N 1s binding energies at 398.8 and 401.8 eV in XPS studies and the coexistence of (sp2)C-H and (sp3) C-H stretching modes in vibrational studies The dative-bonded (Si←N) pyridine was

found to thermally convert to covalent di-σ bonded cycloadduct with the increase of

surface temperature

1.4 Multifunctional organic molecules to be explored

The formation of dative bond, [2+2]-like and [4+2]-like cycloaddition strategies can be employed as the typical methods for binding functional organic molecules to silicon surfaces Most of the previous works on organic modification of silicon surfaces focused on the initial layer growth through the formation of Si-C or Si-N or Si-O sigma linkages The attachment mechanism and adduct configurations of some simple