Filler 2003

Progress in Surface Science 73 (2003) 1–56
www.elsevier.com/locate/progsurf
Review
The surface as molecular reagent:
organic chemistry at the semiconductor interface
Michael A. Filler, Stacey F. Bent *
Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA
Abstract
Methods for the incorporation of organic functionality onto semiconductor surfaces have
seen immense progress in recent years. Of the multiple methods developed, the direct, covalent
attachment of organic moieties is valuable because it allows for excellent control of the in-
terfacial properties. This review article will focus on a number of synthetic strategies that have
been developed to exploit the unique reactivity of group-IV surfaces under vacuum. A picture
of the semiconductor surface and its reactions will be developed within the standard frame-
work of organic chemistry with emphasis on the importance of combined experimental and
theoretical approaches. Three broad areas of organic chemistry will be highlighted, including
nucleophilic/electrophilic, pericyclic, and aromatic reactions. The concept of nucleophilicity
and electrophilicity will be discussed within the context of dative bonding and proton transfer
of amines and alcohols. Pericyclic reactions cover the [4 + 2] or Diels–Alder cycloaddition,
[2 + 2] cycloaddition, dipolar, and ene reactions. Examples include the reactions of alkenes,
dienes, ketones, nitriles, and related multifunctional molecules at the interface. Aromaticity
and the use of directing groups to influence the distribution of surface products will be il-
lustrated with benzene, xylene, and heteroaromatic compounds. Finally, multifunctional
molecules are used to describe the competition and selectively observed among different sur-
face reactions.
2003 Elsevier Ltd. All rights reserved.
Keywords: Organic; Semiconductor; Surface; Silicon; 100; Germanium; Pericyclic; Cycloaddition; Dative;
Aromatic
*
Corresponding author. Tel.: +1-6507230385; fax: +1-6507239780.
E-mail address: sbent@stanford.edu (S.F. Bent).
0079-6816/$ - see front matter 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/S0079-6816(03)00035-2
2 M.A. Filler, S.F. Bent / Progress in Surface Science 73 (2003) 1–56
Contents
1. Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 02
2. Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 03
3. Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 04
3.1. Group-IV semiconductor surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 05
3.2. Structural theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 07
3.3. Competition, selectivity, and reaction control . . . . . . . . . . . . . . . . . . . . . 08
4. Nucleophilic/electrophilic reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 09
4.1. Dative bonding and proton transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
4.2. Donor–acceptor complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.3. Non-local interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.4. Reactivity trends . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
5. Pericyclic reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
5.1. [2 + 2] cycloaddition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.2. [4 + 2] cycloaddition (Diels–Alder) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.3. Dipolar addition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.4. Group transfer (a-CH dissociation) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6. Aromatic reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
6.1. Benzene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
6.2. Substituents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
6.3. Heteroaromatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
6.4. Reactivity trends . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
7. Multifunctional compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
8. Future directions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
9. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Notes added during proof. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Acknowledgements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
1. Motivation
It was considered landmark in the 1960Õs if a single transistor could be patterned

onto a semiconductor wafer. In contrast, semiconductor manufacturing companies
are currently able to systematically fabricate over 100 million transistors on a single
crystalline silicon substrate. The transistor count is expected to follow MooreÕs law
M.A. Filler, S.F. Bent / Progress in Surface Science 73 (2003) 1–56 3
for several more generations; however, transistors will soon approach the size of
single molecules and atoms. As we approach this transition, the device scaling that
has been the foundation of fabricating ever-faster processors becomes increasingly
difficult. Interactions at the subnanometer length scale are now of paramount im-
portance and this has spurred the study of the atomic-level phenomena that govern
chemical reactions occurring directly at semiconductor interfaces.
In parallel to the development of the inorganic materials used extensively in the
semiconductor industry, considerable attention has been given to organic materials.
Organic materials are currently used in applications ranging from plastics [1] to
semiconductors [2]. The diverse range of properties that make organic materials so
appealing is exemplified by organic semiconducting polymers. This field began in
1977 with the discovery by Heeger, MacDiarmid, and Shirakawa that the conduc-
tivity of polyacetylene could be enhanced by nearly seven orders of magnitude by
doping with iodine [3]. A decade later Tang and VanSlyke pioneered organic elec-
troluminescence [4], and organic light emitting diodes (LEDs) based on this
phenomenon are now ready for mainstream applications [2]. Although inorganic
electroluminescence has been known for many years, the advantage of organic
materials lies in their tailorability. Since the first organic LED was fabricated, mo-
lecular engineering has allowed access to the entire visible color spectrum, a task
which proved significantly more difficult with traditional inorganic materials.
The explosive advancement in microelectronics technology and overall trend to-
ward molecular devices coupled with the tailorability inherent in organic systems has
sparked interest in combined inorganic/organic systems. As we move into the next
decade, technology from both arenas offers an unparalleled opportunity to create
hybrid devices that exploit the best properties of inorganic and organic compounds.
Already, applications in the areas of molecular electronics, biological recognition,
and chemical sensors have been proposed [5–7]. Previous reviews have summarized
the surface reactions that originally sparked interest in this field [8–12].
2. Overview
The overarching goal of this review is to illustrate the analogies between classic
organic chemistry and the growing field of organic functionalization of semicon-
ductor surfaces. The analogies provide a method of classifying and understanding
many of the surface reactions that have been observed on (1 0 0)-2 · 1 reconstructed
surfaces of group-IV semiconductors. The reactions reviewed are not intended to be
comprehensive, but are chosen to provide examples with which to demonstrate key
similarities. Moreover, it is important to realize that although many of the trends
observed on these surfaces parallel those from classic organic chemistry, other
analogies are only illustrative and will be treated as such.
We also endeavor to create a toolbox of reaction mechanisms. Many important
organic functional groups have already been studied individually and their reactivity on
group-IV semiconductor surfaces is becoming well understood. More recently, inves-
tigations have begun examining multifunctional compounds in an effort to elucidate the
fundamental principles that govern pathway competition and product selectivity. As

research in this field continues, we anticipate that the analogies and categories pre-
sented here will become helpful ‘‘tools’’ used to facilitate the selection, or design, of
organic molecules which bond to Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1 in a specific manner.
In this article, the interplay of experimental and theoretical approaches will be
highlighted. While a wide range of experimental techniques have been brought to
bear on these systems, relatively few publications have focused on the direct mea-
surement of kinetics and dynamics. However, as ab initio quantum chemical cal-
culations have obtained the level of accuracy needed to describe these reactions, they
have been employed increasingly in the identification and quantification of kinetic
barriers. Reaction dynamics continues to be the least studied aspect of this class of
surface reactions and hence will not be covered in this review.
The review is biased towards vacuum studies (dry functionalization) because the
precise structure and order observed with these characterized surfaces allows for
excellent, molecular-level control of interfacial properties, a requirement that is ex-
pected to be important for several applications including molecular electronics, non-
linear optics, and reagentless micropatterning [13–15]. In addition, integration with
silicon processing in a cluster tool environment is often desired, and thus vacuum-
based surface-modification methods are preferred. Due to their current technological
prevalence, the review only examines (1 0 0) surfaces.
Related solution chemistry techniques (wet functionalization) have also been
developed to covalently attach organics to group-IV semiconductor substrates.
Chidsey and coworkers originally showed that alkyl monolayers could be added to
hydrogen terminated Si(1 1 1) surfaces through a radical initiated mechanism [16–18]
and several groups have found success attaching organic monolayers to porous
substrates [19–29]. Wet functionalization with halogen terminated silicon substrates
has also shown promise [30–32]. Excellent discussions of these alternative attach-
ment methods are available in the literature [11,33,34].
The review is organized as follows. In Section 3 we detail the similarities and
differences of Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 surfaces. A brief summary of valence
bond theory and reaction control is also included in that section to provide the
foundation upon which several analogies are based. Three broad areas of organic
reactions will then be highlighted, including nucleophilic/electrophilic reactions
(Section 4), pericyclic reactions (Section 5), and aromatic surface reactions (Section
6). The concepts developed in Sections 4–6 are then applied to investigate compe-
tition and selectivity of multifunctional compounds (Section 7). We close with a look
at the prospects for the field of organic functionalization as well as the challenges
that need to be overcome if this surface chemistry is to become technologically viable
(Section 8).
3. Background
This section is intended to give a brief introduction to the key features of group-
IV semiconductor surfaces in addition to the classic organic chemistry that will be
used as the basis for the analogies to be presented in subsequent sections. In addi-
tion, we strive to bridge several key concepts from organic chemistry and surface
science to establish a common ground to describe the competition and selectivity
observed on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1.
3.1. Group-IV semiconductor surfaces
Silicon and germanium are group-IV semiconductors with a bulk crystal structure
that is face centered cubic with a two atom basis, also known as the diamond
structure, as shown in Fig. 1a [35]. When the (1 0 0) surface of silicon or germanium
is exposed by truncation of the bulk crystal, each surface atom contains two dangl-
ing bonds. Under suitable preparation conditions, which usually include argon ion
sputtering and annealing, the dangling bonds of adjacent surface atoms pair to
create surface dimers that are ordered in rows [36]. Fig. 1b illustrates the key features
of the surface, particularly the dimer rows and the trenches which separate each
dimer row. This rearrangement, known as a (1 0 0)-2 · 1 reconstruction, minimizes
the surface energy because the stability gained by creating a chemical bond out-
weighs that lost from strain. Although the number of dangling bonds is reduced by
the reconstruction, both Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 are still highly reactive and
sticking probabilities of many organic molecules are near unity at room temperature
[10].
The specific electronic characteristics of the Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1
surface dimers lead to two main classes of surface reactions that have analogies in
classic organic chemistry. The dimer bond is composed of a full r bond and a partial
Fig. 1. (a) Bulk diamond structure of crystalline silicon and germanium. Each atom is tetrahedrally
bonded to four nearest neighbors. (b) The dimer rows of the (1 0 0)-2 · 1 surface reconstruction, spaced by
trenches.
Fig. 2. The highest occupied molecular orbital of a Si9 H12 dimer cluster. The top two Si atoms comprise
the surface dimer and the remaining seven Si atoms comprise three subsurface layers which are hydrogen
terminated to preserve the sp3 hybridization of the bulk diamond lattice. The up atom is nucleophilic and
possesses the majority of electronic charge.
p bond [36]. Although the strength of this weak p bond interaction is still under
debate, reported values are approximately 2–8 kcal/mol [37–43], far less than the 64
kcal/mol of traditional alkenes [44]. Nonetheless, the partial p bond of the surface
dimer mimics that of an alkene from classic organic chemistry and leads to the reac-
tions that are classified as pericyclic. This class of reactions is discussed in Section 5.
Due to solid state electronic effects, the surface dimers tilt out of the surface plane
(Fig. 1b) [36]. The recessed atom, known as the ‘‘down atom,’’ donates significant
electronic charge to the protruding or ‘‘up atom,’’ as shown in Fig. 2 for a
Si(1 0 0)-2 · 1 dimer cluster model. Consequently, the down atom is electrophilic and
the up atom is nucleophilic [45]. The charge separation between the nucleophilic
and electrophilic dimer atoms gives rise to a zwitterionic character leading to
the observation of nucleophilic/electrophilic reactions, which will be examined in
Section 4.
Scanning tunneling microscopy (STM) measurements show that the silicon dimers
are asymmetrically buckled at low temperatures while measurements at room tem-
perature display symmetric dimers [46]. This suggests that silicon surface dimers
dynamically tilt when enough thermal energy is available. Molecular dynamics
simulations agree with this finding and demonstrate that silicon dimers should dy-
namically tilt on the picosecond timescale at room temperature [47]. Ge(1 0 0)-2 · 1,
on the other hand, exhibits statically tilted dimers at both low and room temperature
[48]. Although outside the scope of this review, the dynamic tilting observed at room
temperature for Si(1 0 0)-2 · 1 is expected to affect the dynamics of surface reactions.
The tilting is observed to alternate down the dimer row for both Si(1 0 0)-2 · 1 and
Ge(1 0 0)-2 · 1. A c(4 · 2) structure is observed if the tilting is staggered between
dimer rows and a p(2 · 2) structure is observed if the dimers are tilted in the same
direction between rows. Numerous studies have revealed a preference for the c(4 · 2)
structure and it is generally agreed that this is the ground state [36].
3.2. Structural theory
Due to the extreme diversity and sheer number of organic molecules and reac-
tions, a categorization method is necessary. One method of classifying the enormous
number of organic compounds into smaller, more tractable families is structural
theory. Structural theory is based upon the fact that molecules with similar ar-
rangements of atoms will react similarly. These atomic arrangements are known as
functional groups and Fig. 3 identifies the functional groups that will be important in
this review.
For comparison, we have separated these functional groups into two broad cat-
egories. The ‘‘bonding’’ functional groups include alkanes, alkenes, and alkynes.
Each of these functional groups have all of their valence electrons paired with
electrons from a neighboring atom to form single, double, and triple covalent bonds,
respectively. It will be shown that molecules with these functionalities form pericyclic
surface products (Section 5). The functional groups containing ‘‘non-bonding’’
Cyclic
Alkene Alkene Diene
Alkyne Benzene
(a) Bonding functional groups
N
OH N
Cyclic
Alcohol Amine
Amine
C O C N
Carbonyl Nitrile
(b) Functional groups with non-bonding electrons
Fig. 3. (a) Several bonding functional groups and (b) several non-bonding functional groups which will be
discussed in this review. The non-bonding groups contain valence electrons that are not paired with an
electron from another atom.
electrons, consisting of alcohols, amines, carbonyls, and nitriles, all contain valence
electrons that are not paired with an electron from an adjacent atom. These non-
bonding electrons are still spin coupled, according to the Pauli Exclusion Principle,
into a single orbital called a non-bonding orbital. Also known as a lone pair, these
orbitals have a significant cloud of electronic charge that can be donated during a
chemical reaction as will be observed for electrophilic/nucleophilic reactions (Sec-
tion 4).
3.3. Competition, selectivity, and reaction control
Initial work comparing the reactivity of Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 to-
wards unsaturated organic molecules revealed that similar products were formed
on each surface [49,50]. However, significant differences in surface reactivity be-
tween these two surfaces have recently been identified [51–53]. The concepts of ki-
netic and thermodynamic control provide a good starting point from which to
identify the reaction pathways that ultimately lead to the observed products on each
surface.
Organic chemists discuss a reaction as being controlled by the relative rates of
competing reactions (kinetics) or by the relative stabilities of the final products
(thermodynamics). At low temperatures, where little thermal energy is available, the
pathway with the lowest activation barrier will dominate, yielding the majority
product. For these conditions, the reaction is said to be under kinetic control. On the
other hand, enough thermal energy is available at higher temperatures such that
every activation barrier can be surmounted. In this case, the reaction is under
thermodynamic control and the product distribution is dictated by the relative
change in free energy of the final products, with the most exergonic reaction pathway
yielding the dominant surface product.
Similar concepts can be employed to understand the surface product distributions
on silicon and germanium. The observed pathways on Si(1 0 0)-2 · 1 have low acti-
vation barriers in the forward direction and tend to be highly (50–90 kcal/mol)
exothermic. Since the barriers for multiple reaction pathways of the same molecule
are low and can be overcome at room temperature, as schematically shown with
pathways PSi1 and PSi2 in Fig. 4, a distribution of several surface adducts is usually
observed. Because the product distribution is dictated by the kinetics of the surface
reactions, not the change in free energy, we can consider many reactions to be under
kinetic control on Si(1 0 0)-2 · 1. In solution chemistry, if the kinetically favored
products were not desired, one would likely employ thermodynamic control and
affect the final product distribution by increasing the temperature or changing the
solvent. However, the strong bonding observed for Si(1 0 0)-2 · 1 often leads to
product decomposition and surface carbide formation instead of conversion to a
more stable product [54], deterring the use of this strategy.
Recently, several distinct features of Ge(1 0 0)-2 · 1 have been identified which can
lead to a narrower, or more selective, product distribution. The Ge–C bond strength
is 7–9 kcal/mol less stable than its silicon analog, as calculated for 1,3-butadiene on
Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 [43], and this difference alters the thermodynamics
‡
‡
Relative Energy
1
PGe
STABLE at
PGe2
PSi1
300K
PSi2
Reaction Coordinate
Fig. 4. Schematic illustration of partial potential energy surfaces for competing pathways on Si(1 0 0)-2 · 1
and Ge(1 0 0)-2 · 1. The figure illustrates the more stable products and more closely spaced activation
barriers typically observed for reactions on Si(1 0 0)-2 · 1 compared to those on Ge(1 0 0)-2 · 1.
and kinetics of surface reactions on Ge(1 0 0)-2 · 1. In some sense, we can say that
many reactions on Ge(1 0 0)-2 · 1 are under thermodynamic control. The weaker
surface bonds lead to reduced binding energies and certain products will reversibly
desorb on a timescale shorter than that of many experimental techniques at room
temperature [55]. Thus, some products observed on Si(1 0 0)-2 · 1 will likely not be
observed on Ge(1 0 0)-2 · 1 (compare pathways PSi1 and PGe 1
in Fig. 4). A greater
separation of activation barriers is also found on Ge(1 0 0)-2 · 1 (compare the
1 2
transition states of pathways PGe and PGe , in Fig. 4), causing an increase in the
branching ratio that ultimately leads to another method of enhancing selectivity [52].
The concepts of competition, selectivity, and reaction control have been presented
here because they are central to the topic of this review. Many examples of these
principles will be presented throughout this review and the important reactivity
differences between the Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 interfaces will be illustrated.
4. Nucleophilic/electrophilic reactions
Nucleophilic/electrophilic reactions are frequently observed in solution phase

organic chemistry and have thus been subjected to detailed study [44]. In the ma-
jority of these reactions, each participating molecule shares one of its electrons to
form a new covalent bond. Dative bonding, also known as coordinate covalent
bonding, occurs when one molecule donates both of the electrons needed to form a
covalent bond. One of the best known examples of dative bonding in chemistry is the
H F H F
H N B F H N B F
H F H F
Fig. 5. Valence bond illustration of the formation of a NH3 /BF3 donor–acceptor complex as a result of
dative bonding.
addition of ammonia to boron trifluoride (BF3 ), shown in Fig. 5 [56]. Since boron
has three valence electrons, the valence shell of BF3 has only six electrons and is
electron deficient. However, ammonia can donate both of its lone pair electrons to
overcome this deficiency and create a filled valence shell with eight electrons. In this
reaction, BF3 is known as the electrophile and ammonia is the nucleophile.
On Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1, nucleophilic/electrophilic reactions are possi-
ble because of the zwitterionic nature of the buckled surface dimer. Since the down
atom is electron deficient, it is an electrophile and can react with an impinging nu-
cleophile to form a dative bond [51]. All of the functional groups with non-bonding
electrons discussed in Section 3 contain lone pairs and are capable of forming a
dative bond with the surface dimer as shown in the literature [45,51–53,57–64].
Recent experimental work has also shown that charge donation can occur the other
way, i.e. the nucleophilic dimer atom can donate its electron density to an impinging
molecule that is electron deficient [65].
According to previous studies, dative bonding is a phenomenon common to many
organic reactions on Si(1 0 0)-2 · 1 and Ge(1 0 0)-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. This
section begins by introducing the basic surface chemistry of ammonia and water on
Si(1 0 0)-2 · 1. Although not organic molecules, both are technologically relevant
[66,67] and are model examples of dative bond formation as well as proton transfer,
one type of subsequent surface reaction. The section continues with examples of both
non-cyclic and cyclic amines followed by a brief discussion of non-local interactions
and reactivity trends.
4.1. Dative bonding and proton transfer
Due to the importance of the initial stages of silicon oxidation in current tran-
sistor fabrication, there has been a great deal of interest in the reaction of water, an
oxidant, on the Si(1 0 0)-2 · 1 surface. Early ultraviolet photoelectron spectroscopy
(UPS) investigations of the reaction of water on Si(1 0 0)-2 · 1 were interpreted as
evidence for molecular adsorption [68,69]. However, subsequent electron energy loss
spectroscopy (EELS) [70,71], surface infrared (IR) spectroscopy [72,73], electron-
stimulated desorption ion angular distribution (ESDIAD) [74–76], secondary ion
mass spectrometry (SIMS) [77,78], and temperature programmed desorption (TPD)

[79] investigations resulted in general agreement that water instead adsorbs in a
dissociated state consisting of OH(a) and H(a) species adsorbed on the Si surface
dimer at room temperature.
A series of density functional theory calculations (DFT) calculations by Konecny
and Doren revealed that water first molecularly adsorbs through one of its lone pairs
in a weakly bound precursor state, although not explicitly called a dative bond, and
then undergoes proton transfer to form the experimentally observed OH(a) and H(a)
species on the surface dimer [45]. The pathway to proton transfer is found to be
unactivated with respect to the vacuum level which suggests that OH(a) and H(a) are
the dominant surface species at room temperature, in agreement with previous ex-
perimental work [70–79].
Chabal and coworkers reinvestigated this system with several IR spectroscopy
techniques including multiple internal reflection (MIR), external reflection, and ex-
ternal transmission that allowed high resolution access to the low energy spectral
region and enabled identification of Si–H bending modes, Si–O stretching modes,
and others that were invisible in previous studies [80–83]. Interestingly, they found
that upon heating to temperatures near 600 K, the oxygen of the surface-bound
hydroxyl group can insert into the silicon dimer bond to form a suboxide (Si–O–Si)
structure. DFT calculations indicated that the suboxide structure is approximately
50 kcal/mol more stable than the dissociated state, but the pathway consists of
multiple activation barriers in excess of 40 kcal/mol [83,84], explaining why oxygen
insertion is detected only at elevated temperatures.
Ammonia, an excellent nitriding agent for the fabrication of oxidation masks,
gate dielectrics, and diffusion barriers in microelectronic devices [85–88], is similar
to water in that it contains an atom with a lone pair bonded to hydrogen atoms and
is expected to react through an analogous pathway. A low energy electron dif-
fraction (LEED) investigation by Dresser et al. found that ammonia dissociatively
adsorbs on Si(1 0 0)-2 · 1 at room temperature, preserving the (1 0 0)-2 · 1 recon-
struction [89], a finding which was consistent with a STM study by Hamers et al.
[90]. Coadsorption TPD experiments by Dresser et al. determined that NH2 (a) and
H(a) were the adsorbed surface species at room temperature. Subsequent work with
high-resolution electron energy loss spectroscopy (HREELS) found, in agreement
with Dresser et al., absorption peaks corresponding to Si–NH2 stretching and
bending modes as well as a Si–H stretching mode [91]. These surface species de-
compose above 600–700 K but, unlike the dissociated state of water, nitrogen in-
sertion into the dimer bond or backbond has not been observed experimentally
[89,91–93]. At temperatures below 120 K, ammonia coexists in both the molecularly
adsorbed and dissociated forms, suggesting that between these two states exists a
barrier that not all molecules can traverse [94]. Recent TPD data reveals an am-
monia desorption channel at 400 K and suggests that ammonia may also exist in a
molecularly adsorbed state at room temperature [95]. Musgrave and coworkers
investigated the bonding of ammonia on Si(1 0 0)-2 · 1 with density functional
theory using a cluster approximation [96–98] and dative bonding was proposed as
the mechanism of molecular adsorption. On Ge(1 0 0)-2 · 1, ammonia does not
undergo proton transfer and is found to form a stable molecularly adsorbed species
[99–103].
The concepts of dative bonding and proton transfer previously developed for
water and ammonia on Si(1 0 0)-2 · 1 can easily be extended to their organic analogs.
Simple alcohols, such as methanol and ethanol, are found to undergo O–H disso-
ciation, in the same manner as water, to form alkoxy linkages on Si(1 0 0)-2 · 1 [104–
108]. Several groups have also investigated the bonding of organic amines on
Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 in an effort to understand the kinetic and thermo-
dynamic factors controlling reactions on these surfaces [51,57,59,65,108,109]. On
Si(1 0 0)-2 · 1, the most important factor influencing the final surface product was 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, underwent proton transfer while
tertiary amines did not. Non-aromatic cyclic amines [53,60,61,110,111] were found
to have a reactivity similar to that for non-cyclic amines. On Ge(1 0 0)-2 · 1, non-
aromatic amines form a stable dative-bonded species at room temperature and do
not undergo proton transfer [51,53].
Mui et al. investigated the bonding of methylamines on Si(1 0 0)-2 · 1 with a
combined experimental and theoretical approach [57]. They showed that the primary
and secondary amines in their study, methylamine and dimethylamine, adsorb in a
dative-bonded precursor state before undergoing proton transfer in a manner similar
to that observed for ammonia on Si(1 0 0)-2 · 1. As shown in Fig. 6b and d, the
presence of a m(Si–H) stretching mode near 2170 cm1 is strong evidence of the
dissociated state for methylamine and dimethylamine. In addition, strong m(–C–H)
stretching modes observed below 2800 cm1 indicate that a lone pair is present in the
surface product. Known as Bohlmann bands, these modes originate from the in-
teraction of the nitrogen lone pair with the C–H r-orbitals located trans periplanar
to the lone pair.
DFT calculations, displayed in Fig. 7 for dimethylamine, show that this system is
under kinetic control on Si(1 0 0)-2 · 1 [57]. Although the binding energy for the
methyl dissociated product is stronger than the hydrogen dissociated product, the
barrier for N–C bond cleavage is high, located 19.3 kcal/mol above the vacuum level.
In contrast, that for N–H cleavage is 9.3 kcal/mol below the vacuum level. The
barrier for N–C cleavage is difficult to surmount at room temperature, explaining the
experimental observation that monomethylamine and dimethylamine undergo only
proton transfer. Similar theoretical results are obtained by Cao et al. [59].
In comparison, Mui et al. find that trimethylamine does not exhibit a significant
peak in the m(Si–H) stretching region (Fig. 6f), indicating that the majority surface
species is adsorbed molecularly in a stable dative-bonded state at room temperature
[57] as shown in Fig. 8. Additional analysis of the infrared data for trimethylamine
reveals that some m(–C–H) modes are detectable below 2800 cm1 , indicative of a
nitrogen lone pair, and are possibly due to a minor N–C dissociated product. X-ray
photoelectron spectroscopy (XPS) data from Cao and Hamers has provided addi-
tional confirmation that the majority of trimethylamine does indeed bond molecu-
larly via a dative bond with a minority side product [59]. These data, displayed in
Fig. 9, show that two N(1s) photoelectron peaks are present near 402.2 and 398.9 eV
Fig. 6. Infrared spectra for the saturation coverage of methylamine, dimethylamine, and trimethylamine
on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 at room temperature. Figure reprinted with permission from Ref. [51].
Copyright 2002 American Chemical Society.
at room temperature. The high binding energy peak comprises 85% of the area and is
characteristic of an atom in an extremely electron deficient environment. In agree-
ment with the infrared and theoretical results of Mui et al., the authors assign this
feature to dative-bonded trimethylamine and believe that the low energy peak,
at 398.9 eV, is evidence for a minority surface species, possibly a N–C dissociated
product, which consumes the remaining 15% of the available surface sites. Inter-
estingly, when trimethylamine is adsorbed onto Si(1 0 0)-2 · 1 at 190 K, only one
N(1s) peak at 402.2 eV and one C(1s) peak at 286.9 eV are observed, providing
preliminary evidence that the minority peak corresponds to a product with a higher
activation barrier. A more recent survey, by the same authors, of alkylamines on
Si(1 0 0)-2 · 1 with IR spectroscopy, XPS, UPS, and STM makes similar conclusions
to those presented above [58].
Fig. 7. Theoretically calculated potential energy surfaces for (a) N–H dissociation and (b) N–C dissoci-
ation of dimethylamine on Si(1 0 0)-2 · 1. All energies are with respect to the vacuum level in kcal/mol.
Geometries were optimized at the B3LYP/6-31G(d) level and single point energies are from a split basis set
calculation at the B3LYP/6-311++G** level of theory for the surface dimer atoms and amine adsorbate
and B3LYP/6-31G(d) for all subsurface atoms and terminating H atoms. Figure adapted from Ref. [57]
with permission from the American Institute of Physics.
Fig. 8. Highest occupied molecular orbital for the formation of a dative bond by trimethylamine with the
electrophilic dimer atom of silicon.
Fig. 9. XPS data for the exposure of trimethylamine at Si(1 0 0)-2 · 1 at room temperature and after
annealing. Both spectra show two distinct binding energies for the N(1s) and C(1s) core electrons. Figure
reprinted with permission from Ref. [59]. Copyright 2001 American Chemical Society. The authors are
also thanked for permission to reprint this figure.
Mui et al. also studied the same series of methylamines on Ge(1 0 0)-2 · 1; how-
ever, on this surface neither N–H nor C–H cleavage was observed, and theoretical
calculations reveal that both pathways are activated with respect to the vacuum level
[51]. This finding is analogous to the observed molecular adsorption of ammonia on
Ge(1 0 0)-2 · 1 [99–103]. Investigation of the highest occupied molecular orbitals of
N–H cleavage transition states on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 revealed that the
proton transfer process is facilitated by electron donation from the nucleophilic
dimer atom [51]. Thus, the dimer atom with largest electron density will most easily
cleave the N–H bond. Since the nucleophilic Ge dimer atom has less electron density
than its Si counterpart, the N–H bond will need to be stretched further to acquire
enough electron density to form a Ge–H bond. The additional stretching would
induce additional strain resulting in an increased activation energy [51].
4.2. Donor–acceptor complexes
Evidence for the reverse process, donation of electron density from the nucleo-
philic dimer atom to an electron deficient molecule, also exists. Konecny and Doren
theoretically found that borane (BH3 ) will dissociatively adsorb on Si(1 0 0)-2 · 1
[112]. While much of the reaction is barrierless, they note an interaction between the
boron atom and nucleophilic dimer atom during the dissociation process.
More recently, Cao and Hamers have demonstrated experimentally that the
electron density of the nucleophilic dimer atom can be donated to the empty orbital
of boron trifluoride (BF3 ) [65]. XPS on a clean Si(1 0 0)-2 · 1 surface at 190 K reveals
two broad F(1s) peaks, near 688.1 and 686.5 eV, indicating that BF3 dissociates into
BF2 (a) and F(a) species similar to the amines and alcohols discussed previously.
However, when BF3 is exposed on a Si(1 0 0)-2 · 1 surface previously covered with a
saturation dose of trimethylamine, little B–F dissociation occurs, as evidenced by
single peaks near 686.7, 402.3, and 287.0 eV for the F(1s), N(1s), and C(1s) pho-
toelectrons, respectively. They conclude that BF3 molecularly adsorbs to the nu-
cleophilic dimer atom and DFT calculations indicate that the most energetically
favorable product is a surface-mediated donor–acceptor complex (TMA–Si–Si–BF3 )
as shown in Fig. 10.
4.3. Non-local interactions
Recent analyses have provided evidence that adsorption and dissociation of some
organics, particularly nucleophiles, are governed by non-local interactions involving
both bare and adsorbate-covered dimers [59,65,96–98,113]. Widjaja et al. thoroughly
investigated ammonia adsorption and dissociation with DFT calculations using a
cluster approximation [96–98]. With a three dimer silicon cluster model, their cal-
culations revealed that the donation of electronic charge from the ammonia lone pair
to the surface delocalizes across adjacent surface dimers in the same dimer row.
Additional calculations with a cluster that included two dimers separated by a trench
revealed that electron delocalization does not occur between rows. Electron delo-
Fig. 10. Schematic illustration of the formation of a donor–acceptor complex. Trimethylamine first ad-
sorbs molecularly to the electrophilic dimer atom to form a dative bond. Boron trifluoride is then exposed
to the surface and reacts with the nucleophilic dimer atom. Figure reprinted with permission from Ref.
[65]. Copyright 2002 American Chemical Society. The authors are also thanked for permission to reprint
this figure.
calization results in a binding energy for molecularly adsorbed ammonia of 26

kcal/mol, more favorable by 6 kcal/mol than the dative bonded binding energy
calculated with a single dimer cluster. Widjaja and Musgrave also calculated the
barrier to dissociation and the binding energy of the dissociated state and these are
found to be in accord with experimental results as well. In contrast to the dative
bonded state, the barrier and binding energy of the dissociated state are not strongly
influenced by choice of cluster size, suggesting minimal non-local interactions. It is
expected that this surface-mediated electron transfer plays a significant role in the
adsorption of nucleophiles on the Si(1 0 0)-2 · 1 surface.
Queeney et al. were the first to probe non-local interactions experimentally for
ammonia adsorption on Si(1 0 0)-2 · 1 [113]. Detailed IR spectroscopy coverage ex-
periments showed a redshift of the m(Si–H) stretching mode from 2078 cm1 at low
coverage to 2055 cm1 at high coverage. This coverage dependent shift occurs in the
opposite direction of what would be expected for dipole–dipole coupling and cannot
be explained by electronegativity arguments. DFT calculations on two dimer cluster
models were used to propose that the redshift is due to adsorbate-induced charge
polarization from opposed NH2 (a) and H(a) fragments on adjacent dimers. In ad-
dition, they also find that dissociation of NH3 on one dimer of the two dimer cluster,
stabilizes the buckling on an adjacent dimer by 1 kcal/mol, which has implications
for long range adsorbate ordering.
In their study of methylamines on Si(1 0 0)-2 · 1 [59], Cao et al. completed detailed
coverage dependence studies. They found that the quantity of minority product for
trimethylamine, likely an N–C dissociated product as evidenced by the N(1s) pho-
toelectron peak near 398.9 eV, increases with dose. No specific mechanism ex-
plaining this observation was presented. Furthermore, of the methylamines studied
on Si(1 0 0)-2 · 1, trimethylamine has the lowest surface coverage and a value near
0.25 ML has been reported [59,114]. It is, thus, interesting that no B–F dissociation
was observed upon dosing BF3 onto Si(1 0 0)-2 · 1 that has been saturated by
trimethylamine [65], a non-local effect that is likely due to geometric and/or elec-
tronic effects.
Non-local interactions, whether arising from surface- or adsorbate-medi-
ated electronic effects, dipole coupling, hydrogen bonding, or other mechanism, are
still under debate and will undoubtably vary with adsorption system. We foresee
that the identification and exploitation of interdimer interactions, for these and
other organic molecules, will likely be an important area of research in upcoming
years.
4.4. Reactivity trends
Several other functional groups, including carbonyls and nitriles, also form dative
bonds with the surface dimer. Molecules containing these functionalities participate
in subsequent reactions to form pericyclic products, and discussion of the experi-
mental results will be deferred until Sections 5 and 6. However, investigation of
theoretically-calculated binding energies for the dative bond formed by these mol-
ecules, in addition to those discussed in this section, reveal interesting trends that are
analogous to those observed for classic organic reactions.
The strength of a dative bond depends on two factors: the electronegativity of the
atom participating in the dative bond and its hybridization. Electronegativity is
defined as the ability for an atom to attract electrons [44] and depends on both the
effective nuclear charge and the distance of the outermost electrons from the nucleus.
Atoms at the far upper right corner of the periodic table are the most electronegative:
fluorine (Pauling electronegativity ¼ 4.0) is the most electronegative, followed by
oxygen (3.5), and then nitrogen (3.0). Since more electronegative atoms prefer to
attract charge rather than donate it, they tend to form weaker dative bonds with
Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. Fig. 11 shows the calculated dative-bonded binding
energies for methanol, trimethylamine, acetone, and acetonitrile on Si(1 0 0)-2 · 1
and Ge(1 0 0)-2 · 1. The energies for mono- and dimethylamine are similar to that of
trimethylamine. A comparison of methanol and trimethylamine, both of which have
a sp3 hybridized donor atom, shows that indeed oxygen forms a weaker dative bond
than nitrogen in agreement with their relative electronegativities. It is interesting to
note that the specific surface, silicon or germanium, does not significantly affect the
stability of the dative bonds formed by any of these molecules.
It is also known that decreasing the p-orbital character of a lone pair diminishes
the electron donor strength and leads to a weaker dative bond [115]. Thus, sp3 hy-
bridized atoms, which have 3/4 p-orbital character, can donate more charge to form
a more stable dative bond than sp hybridized atoms, which only have 1/2 p-orbital
character. It would then be expected that acetone and acetonitrile would have
weaker dative bonds than methanol and trimethylamine, respectively, a prediction
that is verified in Fig. 11.
A comparison of ammonia and phosphine, although not technically organic
compounds, can provide additional insight into dative bonding and the facility with
which a proton is transferred to the nucleophilic dimer atom. Proton affinity is de-
fined as a moleculeÕs tendency to attract protons while proton basicity is defined as a
moleculeÕs ability to donate protons. Said another way, proton affinity correlates
with a moleculeÕs ability to donate electronic charge. Thus, a molecule with a high
proton affinity will likely form a strong dative bond with the surface and a molecule
with a high proton basicity will most easily transfer a proton to the nucleophilic
CH3
H3C CH3
N
C
CH3 N
(a) Trimethylamine (b) Acetonitrile
Si – 23.4 Si – 14.0
Ge – 22.7 Ge – 12.1
H3C CH3
CH3
C
OH
O
(c) Methanol (d) Acetone
Si – 18.5 Si – 13.7
Ge n/a Ge – 12.3
Fig. 11. Theoretically predicted dative bond energies for (a) amines [51], (b) nitriles [63], (c) alcohols [105],
and (d) ketones [62] on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 (n/a indicates that no published data is available).
Note that reported values were calculated with different functionals and basis sets.
dimer atom. In fact, this is what is observed on Si(1 0 0)-2 · 1. Widjaja et al. and
Mysinger et al. have calculated the pathways for proton transfer on Si(1 0 0)-2 · 1 for
ammonia [97] and phosphine [116], respectively. Ammonia has a higher proton
affinity than phosphine and forms a dative bond with a binding energy of )26
kcal/mol, 10 kcal/mol more stable than that of phosphine. However, ammonia has a
lower basicity than phosphine. This correlates with the calculated barrier to proton
transfer for phosphine which is approximately 16 kcal/mol above the dative bonded
state as compared to 24 kcal/mol for ammonia.
5. Pericyclic reactions
Pericyclic reactions were originally proposed by Woodward and Hoffmann in

1965 to occur through cyclic transition states, with all bond breaking and bond
forming taking place in concert, without the formation of an intermediate, creating a
highly stereospecific product [117]. Although this is still thought to be the case for
many reactions, evidence currently exists that some thermally allowed pericyclic
reactions follow stepwise mechanisms with biradical intermediates [118]. Nonethe-
less, five broad categories of pericyclic reactions are identified: cycloadditions, group
transfer reactions, electrocyclic reactions, cheletropic reactions, and sigmatropic
rearrangements [117].
Of the different types of pericyclic reactions, cycloadditions are widely used in

organic synthesis and are characterized by the creation of new r bonds between at
least two component molecules to form a cyclic product. Two important cyclo-
addition reactions are the [2 + 2] cycloaddition and [4 + 2] cycloaddition, also known
as the Diels–Alder reaction. In a [2 + 2] cycloaddition, as illustrated in Fig. 12a, a
pair of p electrons from each alkene react to form a four-membered ring. This re-
action can only proceed after ultraviolet excitation, even at considerably elevated
temperatures [117]. In contrast to a [2 + 2] cycloaddition, a diene can readily react
with an alkene (the dieneophile) at room temperature in a [4 + 2] cycloaddition re-
action to form a six-membered ring shown in Fig. 12b.
The difference in reactivity observed for the [2 + 2] and [4 + 2] cycloaddition re-
actions 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 [119].
These rules dictate that the parity of the p orbital lobes involved in the creation of
the new r bonds must be identical for the reaction to proceed. As demonstrated in
Fig. 12, [4 + 2] cycloaddition or Diels–Alder reactions are symmetry-allowed while
[2 + 2] cycloaddition reactions are symmetry-forbidden.
Of the few reactions that fall under the category of group transfer, the ene re-
action is most well-known. Here, a compound with a double bond having an allylic
hydrogen (ene) adds to a compound with a p bond (enophile) with transfer of the
allylic hydrogen and a concomitant reorganization of the bonding as shown in Fig.
12c for the reaction of propylene and ethylene.
If the analogy made between traditional alkenes and the Si(1 0 0)-2 · 1 and
Ge(1 0 0)-2 · 1 surface dimers holds, then it would be expected that pericyclic surface
products may be observed as a surface reaction product. Many such examples have
indeed been observed on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. Examples of cycloaddi-
tion reactions that will be reviewed here include [2 + 2], [4 + 2], and dipolar
HOMO
H
H
LUMO
(a) (b) (c)

[2+2] [4+2] Group
Cycloaddition Cycloaddition Transfer
Fig. 12. Highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals
(LUMOs) for the (a) [2 + 2] cycloaddition reaction between two ethylene molecules without UV excitation,
(b) [4 + 2] cycloaddition reaction between 1,3-butadiene and ethylene, and (c) the group transfer reaction
between propylene and ethylene.
cycloadditions. Even though [2 + 2] cycloaddition reactions are classically symmetry

forbidden, these cycloadducts are observed on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 at
room temperature and below, as will be discussed in the following subsections. The
ene reaction, a type of group transfer, will also be discussed in this section. To date,
no electrocyclic, cheletropic, or sigmatropic reaction analogs have been identified on
Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1 and these classes are not included in this review.
It is important to note there has been little experimental or theoretical evidence
indicating that the creation of cycloaddition or group transfer products on
Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 occur via a concerted process through a cyclic
transition state. It is expected that many of the reactions occur in a non-concerted
process and pass through at least one short-lived intermediate state before arriving at
the final product. Thus, these reactions are not truly pericyclic as defined above;
however, the final surface species are identical to what would form via a concerted,
pericyclic reaction pathway. For this reason, the nomenclature still provides a
valuable method with which to classify the observed surface species, but we are
careful to use the term cycloaddition product, and not cycloaddition reaction, when
discussing the observed surface species.
5.1. [2 + 2] cycloaddition
Several authors have provided excellent reviews of the experimental and theo-
retical work leading to the determination of the surface structure of ethylene on
Si(1 0 0)-2 · 1 [120–123], but it is briefly presented here to lay the foundation for the
more complex chemistry to follow. Ethylene, the simplest unsaturated organic
molecule, bonds to Si(1 0 0)-2 · 1 to form a [2 + 2] cycloaddition product as shown in
the center of Fig. 13. This surface structure will hence be referred to as a [2 + 2] C@C
cycloaddition product to distinguish it from cycloadditions that occur with other
functional groups. STM images of ethylene on Si(1 0 0)-2 · 1 revealed that the
CH2
H2 C CH2
H2C Si
Si Si Si
X H2 C CH2
Si Si
Fig. 13. Reaction of ethylene with the Si(1 0 0)-2 · 1 surface to form a [2 + 2] C@C cycloaddition product.
The reaction that proceeds from the left, although analogous to solution phase chemistry, is not believed
to occur.
products are in registry with the underlying surface dimers and provide a well-
ordered monolayer [124]. The product has two strong Si–C bonds, and although the
four-membered ring is fairly strained, it has a binding energy near 40 kcal/mol [125].
Other small alkenes, such as propene and 2-butene, were investigated and found to
react in the same fashion as ethylene [126–129]. Propene and 2-butene differ from
ethylene, however, in that adsorption onto Si(1 0 0)-2 · 1 creates [2 + 2] C@C cyclo-
addition products with chiral centers [129].
Early investigators realized that although the formation of a [2 + 2] C@C cyclo-
addition product is symmetry forbidden in traditional organic chemistry [119], the
sticking probability of alkenes on Si(1 0 0)-2 · 1 is near unity at room temperature [8].
Liu et al. used IR spectroscopy to investigate the mechanism and stereoselectivity of
this reaction on Si(1 0 0)-2 · 1 [130]. By using cis- and trans-1,2-dideuteroethylene on
Si(1 0 0)-2 · 1 and comparing the splitting of ms (–C–H) and mas (–C–H) stretching
modes to those calculated theoretically, they showed that the reaction was, in fact,
stereoselective but does not proceed through the traditional symmetry-allowed
mechanism, shown on the left of Fig. 13. A subsequent STM study by Lopinski et al.
found that there is a small, but measurable, percentage (2–3%) of alkenes that have
isomerized during the adsorption to form a non-stereoselective [2 + 2] C@C cyclo-
addition product [129]. This result confirmed that [2 + 2] cycloaddition reactions,
unlike many of their solution phase analogs, are not concerted and likely occur
stepwise on the Si(1 0 0)-2 · 1 surface. It has been proposed that the tilting of the
dimers on Si(1 0 0)-2 · 1 allows the alkene to approach and bond to the surface
through an alternative low symmetry pathway with a small activation energy as il-
lustrated on the right of Fig. 13 [9,130–132].
Studies of larger, more complex alkenes have yielded similar results. Hamers et al.
first showed with IR spectroscopy that cyclic alkenes, such as cyclopentene [110] and
1,5-cyclooctadiene [133], also bond to the Si(1 0 0)-2 · 1 surface to give a [2 + 2] C@C
cycloaddition product. Furthermore, they demonstrated with STM that cyclopen-
tene and 1,5-cyclooctadiene form a well-ordered monolayer as shown in Fig. 14
[134]. 1,4-cyclohexadiene is also found to form [2 + 2] C@C cycloadducts [135,136].
Hovis et al. [137] and Abeln et al. [138] examined the bonding of 1,3,5,7-cyclo-
octatetraene and norbornadiene, respectively, on Si(1 0 0)-2 · 1 at room temperature
with STM. Both groups found that the majority of these molecules formed two
[2 + 2] C@C cycloaddition products that spanned two surface dimers (dual-[2 + 2]). A
reanalysis by Wolkow suggests that the majority species of 1,3,5,7-cyclooctatetraene
consisted of two [4 + 2] cycloaddition products (dual-[4 + 2]) [8]. However, a recent
combined photoemission and near-edge X-ray absorption fine structure (NEXAFS)
spectroscopy investigation confirmed the presence of the dual-[2 + 2] product and
reported that additional adducts with spectral features consistent with the dual-
[4 + 2] are also present [139]. In contrast to 1,3,5,7-cyclooctatetraene, which exhibits
local (2 · 2) and (4 · 2) order on Si(1 0 0)-2 · 1, antiphase domain boundaries are
characteristic of norbornadiene adsorption [138].
Reactions of simple alkenes on Ge(1 0 0)-2 · 1 are found to be similar to their
silicon analogs [50,140,141]. This is in stark contrast to the results of the nucleo-
philic/electrophilic reactions discussed in Section 4 in which different surface adducts
Fig. 14. STM images of the well-ordered monolayers formed from the reaction of (a) cyclopentene and (b)
1,5-cyclooctadiene with Si(1 0 0)-2 · 1. Notice that both molecules form well-ordered monolayers on
Si(1 0 0)-2 · 1. Figure adapted from Ref. [134] with permission from the Institute of Pure and Applied
Physics. The authors are also thanked for permission to reprint this figure.
are observed for the same molecule on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. By using IR
spectroscopy and TPD, Lal et al. provided the first experimental confirmation that
ethylene forms a [2 + 2] C@C cycloaddition product as the majority adduct on
Ge(1 0 0)-2 · 1 at room temperature [140], thus confirming a previous theoretical
prediction [142]. They also observed a complex coverage and time dependence for
ethylene on Ge(1 0 0)-2 · 1 in addition to molecular desorption at temperatures
greater than 365 K. Lee et al. [50] and Hamers et al. [141] report that cyclopentene
and cyclohexene also form a [2 + 2] C@C cycloaddition product on Ge(1 0 0)-2 · 1.
They note that the sticking probability on Ge(1 0 0)-2 · 1 is substantially less than
that on Si(1 0 0)-2 · 1 at room temperature. In addition, as mentioned above for
ethylene, many alkenes undergo reversible desorption on Ge(1 0 0)-2 · 1 when
heated, whereas most surface products decompose to form Si–C species on
Si(1 0 0)-2 · 1. These characteristics are likely a result of the weaker bonds formed
with the Ge(1 0 0)-2 · 1 surface.
The specific adsorption geometries of acetylene (H–CBC–H), the simplest triply
bonded molecule, on Si(1 0 0)-2 · 1 continue to be heavily debated [8,131,143–154].
Acetylene was first found experimentally to form a [2 + 2] CBC cycloaddition
product which exhibits a cyclobutene-like surface structure on Si(1 0 0)-2 · 1
[143,144]. Additional STM measurements revealed that at least two different surface
products were present [145]. From these images, it was argued that acetylene pre-
dominantly bonds between two dimers in a bridged structure (tetra-r) that com-
pletely saturates each carbon atom at low coverage, but as coverage increases, it
adopts a single dimer [2 + 2] CBC cycloaddition geometry. Several theoretical in-
vestigations of acetylene on Si(1 0 0)-2 · 1 have been performed and are in general
agreement that, although the bridge-bonded adduct was experimentally observed at
low coverage, it was not the most stable structure [131,146–150]. Kinetic arguments
were used to explain this difference. Two recent STM studies disagree on the pres-
ence of the tetra-r surface product, but both identify a product where acetylene
bridges two dimers to form a [2 + 2] CBC cycloaddition product that is oriented
perpendicularly to the dimer row [151,152]. Although acetylene has been thoroughly
investigated on Si(1 0 0)-2 · 1, only two theoretical studies, predicting a [2 + 2] CBC
cycloaddition product, for acetylene on Ge(1 0 0)-2 · 1 [155,156] are available. No
experimental studies have been published for this reaction on Ge(1 0 0)-2 · 1 and we
suspect that at room temperature, acetylene binds too weakly to be observed on an
experimental time scale.
Several research groups have studied related compounds that contain carbonyl
(C@O), nitrile (CBN), or azo (N@N) functional groups to provide insight into
pericyclic reactions of functional groups with polarized charge distributions. In
addition, these surface reactions will further underscore the importance of the da-
tive-bonded precursor state in the bonding of organic molecules on Si(1 0 0)-2 · 1 and
Ge(1 0 0)-2 · 1. The adsorption of carbonyl- and nitrile-containing compounds on
Ge(1 0 0)-2 · 1 usually involve group transfer reactions, thus discussion will be de-
ferred until Section 5.4.
Armstrong et al., using a combination of TPD, XPS, and HREELS report that
the majority surface adducts for acetone, acetaldehyde, and biacetyl at low tem-
perature are [2 + 2] C@O cycloaddition products as illustrated in Fig. 15a for the case
of acetone [157,158]. 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] C@O cycloaddition product
of glyoxal [159]. In contrast, Wang et al. were not able to find a barrierless pathway
for the reaction of acetone on Si(1 0 0)-2 · 1 [62] and they propose that steric inter-
actions of the methyl groups with the surface likely play a role in hindering the
reaction of acetone. Alternatively, the conjugated double bonds in glyoxal may
weaken the C@O bond and reduce or remove any activation barrier.
Two O(1s) photoelectron peaks near 532.5 and 531.5 eV led Armstrong et al. to
propose the existence of a C–O dissociated product in addition to the [2 + 2] C@O
cycloaddition product for acetone and acetaldehyde on Si(1 0 0)-2 · 1 [158]. An al-
ternative explanation for the presence of two O(1s) photoelectron peaks in the initial
study by Armstrong et al. is the existence of a dative-bonded species in addition to
the [2 + 2] C@O cycloadduct. IR spectroscopy results by Wang et al. [62] show
that acetone becomes trapped in the dative-bonded well at low temperatures on
Ge(1 0 0)-2 · 1, as evidenced by a 70–90 cm1 redshift of the observed m(C@O)
stretching mode. A more complete potential energy surface, including the kinetic
CH3
CH3
CH3
O CH3 O C
Si Si
Si
Si
(a) Si(100)-2x1: [2+2] C=O Cycloaddition
H 3C CH 3
H 3C
C CH 2
O O
H
Ge Ge Ge
Ge
(b) Ge(100)-2x1: α -CH Dissociation
Fig. 15. The majority product for the adsorption of acetone on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 is dif-
ferent. (a) A [2 + 2] C@O cycloaddition is the kinetically favored product and observed on Si(1 0 0)-2 · 1 at
low temperature. (b) An a-CH dissociation product is the thermodynamically favored product and ob-
served on Ge(1 0 0)-2 · 1 at room temperature.
barriers for molecular rearrangements on Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1, for this
and other related systems would be a valuable addition to the literature.
In part due to their large dipole moments, nitrile-containing compounds have
garnered considerable attention recently and several studies have begun to elucidate
their rich chemistry on group-IV semiconductor surfaces [160–165]. Tao et al. first
concluded that acetonitrile formed a [2 + 2] CBN cycloadduct as the majority species
at low temperature on Si(1 0 0)-2 · 1 [160]. Their-conclusions were based on the
presence of a m(C@N) stretching mode near 1600 cm1 . The calculations of Lu et al.
indicate a pathway for the [2 + 2] CBN cycloaddition product that passes through a
dative-bonded precursor state [161]. Tao et al. rule out tetra-coordinated bonding
between two dimers, which would completely saturate the nitrile functionality. A
recent room temperature photoemission and NEXAFS study by Bournel et al.
identifies a [2 + 2] CBN cycloadduct, in agreement with Tao et al., but also provides
evidence for two additional surface products [162]. Although these additional surface
products are not conclusively identified, the presence of an unpolarized C and N p
NEXAFS transition led Bournel et al. to postulate the possibility of a dative-bonded
product as well as surface species containing cyano or isocyano groups.
Ellison et al. used IR spectroscopy, XPS, STM, and DFT calculations to explore
the reaction of azo-tert-butane on Si(1 0 0)-2 · 1 [166]. Azo-tert-butane consists of a
N@N double bond with one tert-butyl group attached to each nitrogen. The authors
conclude that although some C–H or C–CH3 dissociation occurs at room temper-
ature (<3%), as evidenced by a m(Si–H) stretching mode at 2086 cm1 , this is an
activated process, so at lower temperatures the majority product is a [2 + 2] N@N
cycloaddition product through the azo group, analogous to the [2 + 2] C@C cyclo-
addition product observed for alkenes. It is currently unclear how the lone pair of
each nitrogen interacts with the surface in this system.
To review, results indicate that the majority surface species for unsaturated hy-
drocarbons on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 is a [2 + 2] cycloaddition product
occurring through a low symmetry transition state with a small activation barrier at
room temperature. Furthermore, some cyclic and non-cyclic alkenes are found to
create a highly ordered and anisotropic monolayer. The pathways for adsorption of
carbonyl- and nitrile-containing compounds are theoretically predicted to be unac-
tivated and pass through a dative-bonded precursor state. However, experimental
identification of final surface products for these species continues to be controversial
and additional work is necessary before definitive structures can be assigned.
5.2. [4 + 2] cycloaddition (Diels–Alder)
Konecny and Doren first proposed that more complex alkenes could also form
cycloaddition products [167]. They showed with DFT calculations of 1,3-cyclohex-
adiene that the [4 + 2] cycloaddition, or Diels–Alder reaction, should occur on
Si(1 0 0)-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] cycloaddition product.
Experimental investigations by Tepylakov et al. of 1,3-butadiene on Si(1 0 0)-2 · 1 at
room temperature with IR spectroscopy, TPD, and NEXAFS first confirmed the
theoretical prediction of Konecny and Doren, showing that the majority surface
species was indeed the [4 + 2] cycloaddition product [168].
Although we will discuss the effects of multifunctionality in Section 7, it is in-
structive to discuss the possibility of a competing [2 + 2] C@C cycloaddition product
for dienes because it provides another example of a kinetically controlled reaction on
Si(1 0 0)-2 · 1. In their pioneering study of 1,3-cyclohexadiene on Si(1 0 0)-2 · 1,
Konecny and Doren calculated a binding energy of 39 kcal/mol for the [2 + 2] C@C
cycloaddition product, a reduction of 15 kcal/mol when compared to the [4 + 2]
cycloaddition product, a difference that is attributed to strain in the four-membered
ring [167]. The authors expected that the [4 + 2] cycloaddition product should
dominate because it is a symmetry-allowed reaction while the [2 + 2] C@C cyclo-
addition is symmetry-forbidden on a symmetric surface dimer, a prediction that was
confirmed by Tepylakov et al [168]. A subsequent study of STM images suggested
that although the [4 + 2] cycloaddition product is predicted to be significantly more
stable due to a release of ring strain, only 80% of 2,3-dimethyl-l,3-butadiene form a
[4 + 2] cycloaddition adduct on Si(1 0 0)-2 · 1 while the remaining 20% form a [2 + 2]
C@C cycloaddition product [169]. However, theoretical analysis led Doren to pro-
pose that the [2 + 2] C@C cycloadduct observed by Hamers et al. is actually a [4 + 2]
cycloadduct that bridges two adjacent dimers [170]. While some studies have pro-
vided evidence for additional surface species at room temperature, identification of

specific products via filled-state and empty-state images is difficult and additional
techniques are needed.
Cyclic dienes such as 1,3-cyclohexadiene [171] and cyclopentadiene [172] were also
studied with IR spectroscopy and NEXAFS. In these studies, 1,3-cyclohexadiene
was found to exhibit features characteristic of both [4 + 2] and [2 + 2] cycloaddition
products, in agreement with STM work by Hovis et al. [169], while cyclopentadi-
ene primarily formed a [4 + 2] cycloaddition product. If these systems were under
thermodynamic control, one would expect the ratio of [2 + 2] to [4 + 2] cycloaddition
products to be approximately 1010 . Therefore, the presence of a quantifiable
amount of [2 + 2] side product suggests that these reactions are governed by the
difference in activation barriers and not relative product stabilities.
Dienes were also studied on Ge(1 0 0)-2 · 1 to probe the ability of this surface to
form [4 + 2] cycloaddition adducts. Following the determination of reversible
desorption of simple alkenes on Ge(1 0 0)-2 · 1 it was found that 1,3-butadiene and
2,3-dimethyl-1,3-butadiene undergo a retro-Diels–Alder reaction upon heating the
surface to 650 K [49]. That is, once adsorbed on Ge(1 0 0)-2 · 1, these molecules can
reversibly desorb upon heating, a result of the weaker Ge–C bonds that are formed
on Ge(1 0 0)-2 · 1. Lee et al. used UPS and HREELS to determine that 1,3-cyclo-
hexadiene forms a cycloaddition product on Ge(1 0 0)-2 · 1 although the specific
surface structure could not be identified [50,173].
In summary, several different experimental and theoretical techniques show that
cyclic and non-cyclic dienes react with Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 to form a
[4 + 2] cycloadduct as the major surface species at room temperature. There con-
tinues to be discussion over the presence of quantifiable amounts of other products.
Surface heating leads to product decomposition on Si(1 0 0)-2 · 1, while molecular
desorption is often observed on Ge(1 0 0)-2 · 1.
5.3. Dipolar addition
Dipolar addition products are also observed on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1.
The name dipolar is derived from the fact that one of the reactants consists of a
functional group with a dipole moment. Dipolar addition reactions are further de-
fined by the specific atoms that participate in the reaction. The reaction of nitro-
methane with ethylene, illustrated in Fig. 16, is considered a 1,3-dipolar addition
since the oxygens atom that participate in bonding are located in the 1 and 3 posi-
tions of the nitro functional group. Molecules that routinely participate in 1,3-di-
polar additions include ozone, nitro compounds, azides, and diazo compounds.
Although the carbonyl and nitrile functional groups also exhibit permanent dipoles
and could form 1,2-dipolar addition products, much of the literature refers to these
reactions as [2 + 2] cycloadditions, not 1,2-dipolar additions, and hence reactions of
these functional groups on Si(1 0 0)-2 · 1 were already discussed in Section 5.1. In
addition, Ellison and Hamers identified spectroscopically the 1,2-dipolar addition of
phenyl isothiocyanate to Si(1 0 0)-2 · 1, but discussion is deferred until Section 6.3
because of the aromatic system in this molecule [174].
CH3 CH3
N N
O O O O
H2 C CH2 H2 C CH2
Fig. 16. Schematic illustration of a 1,3-dipolar cycloaddition reaction between nitromethane and ethylene
to form a five-membered, cyclic product.
Two theoretical investigations by Barriocanal and Doren suggest that 1,3-dipoles

can undergo 1,3-dipolar addition reaction to form stable surface products on
Si(1 0 0)-2 · 1 with no significant activation barrier [175,176]. Both the Hamers [177]
and Bent research groups have attempted to experimentally detect 1,3-dipolar cy-
cloaddition products on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 but no conclusions have
been reported.
5.4. Group transfer (a-CH dissociation)
Of the reactions that fall under the category of group transfer, the ene reaction is
the most well known. An a-CH dissociation product, analogous to the ‘‘ene’’ from
classic organic chemistry, was first identified at a semiconductor surface by Wang
et al. in their study of acetone on Ge(1 0 0)-2 · 1 [62]. As shown in Fig. 17, their IR
spectroscopy investigation revealed absorption peaks near 1638 and 1967 cm1
corresponding to m(C@C) and m(Ge–H) stretching modes, respectively. Due to the
highly polarized carbonyl functional group, in the direction dþ C@Od , the hydrogen
atoms attached to the a-C are slightly acidic. As postulated by Wang et al., this
allows the nucleophilic dimer atom to more easily abstract a hydrogen once acetone
dative bonds through one of the oxygen lone pairs, forming the final product il-
lustrated in Fig. 15b.
The reaction of acetone was the first example of a system that formed a different
pericyclic product on Si(1 0 0)-2 · 1 than it did on Ge(1 0 0)-2 · 1 [62]. Moreover, it
serves as one of the best illustrations of reaction control on semiconductor surfaces
and clearly demonstrates that surface selection can significantly alter the final
product distribution. As discussed in Section 5.1, earlier work by Armstrong et al.
found that the reaction of acetone on Si(1 0 0)-2 · 1 produces primarily a [2 + 2] C@O
cycloaddition product at low temperature (Fig. 15a) [158]. In conjunction with their
infrared study of acetone, theoretical calculations by Wang et al. showed that the
a-CH dissociated product was 10 kcal/mol more stable than the [2 + 2] C@O cy-
cloaddition product on both Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 [62], but that its barrier
was higher. The activation barrier to the a-CH dissociation product is 14.6 kcal/mol
above the dative-bonded state while the barrier to the [2 + 2] C@O cycloaddition
product is only 10.5 kcal/mol above it. Investigation of the relative energetics and
activation barriers for these surface products ultimately led to the conclusion that the
Fig. 17. Infrared spectra of acetone adsorbed on the Ge(1 0 0)-2 · 1 surface: (a) 2000 L at 300 K, (b) 0.5 L
at 115 K, and (c) multilayers (scaled) at 115 K. Modes at 1967 cm1 and 1672/1638 cm1 are evidence of
m(Ge–H) and m(C@C) stretching modes, respectively, and are indicative of the a-CH dissociation product.
At low temperature, the presence of the redshifted m(C@O) mode at 1641 cm1 is indicative of a dative-
bond species. Figure reprinted with permission from Ref. [62]. Copyright 2001 American Chemical
Society.
reaction of acetone is under kinetic control on Si(1 0 0)-2 · 1 and thermodynamic

control on Ge(1 0 0)-2 · 1. The [2 + 2] C@O cycloaddition product, which has a lower
barrier to formation, is observed on Si(1 0 0)-2 · 1 because the final product is stable
at room temperature. However, the a-CH dissociation product, with a binding en-
ergy of 22.8 kcal/mol, is the majority species on Ge(1 0 0)-2 · 1 (Fig. 17b) because the
low barrier [2 + 2] C@O cycloaddition product has a binding energy of only 12.5
kcal/mol and reversibly desorbs.
6. Aromatic reactions
The adsorption of aromatic compounds on semiconductor surfaces has received

considerable attention not only because of the fundamental interest in these groups,
but also due to the possibility of forming p-conjugated molecular wires or arrays
through p-stacking interactions of the aromatic ring electrons [178,179]. Additional
interest has focused on the reaction of such compounds for use as highly ordered,
ultra-thin semiconducting polymer films [180].
A wide range of experimental and theoretical techniques have been applied to the
study of aromatic molecules on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. Fig. 18 briefly
H
O S
N
Benzene Pyrrole Furan Thiophene

CH3 CH3
CH3
Styrene Toluene Xylene

O
N
NH2
C
OH
Aniline Benzonitrile Benzoic Acid
Fig. 18. Examples of aromatic molecules that have been investigated on Si(1 0 0)-2 · 1 and/or
Ge(1 0 0)-2 · 1.
summarizes several aromatic molecules that have been studied on these surfaces.
After the identification of several surface species formed by adsorption of benzene at
room temperature on Si(1 0 0)-2 · 1 [8], subsequent studies have turned to the pos-
sibility of activating particular reaction pathways through the use of substitutents
and directing groups. Heteroaromatic compounds, where one or more ring carbons
are substituted with an electronegative atom such as nitrogen, oxygen, or sulfur,
have received some attention as of late, but more comprehensive studies are still
needed in order to fully appreciate possible adsorption mechanisms and pathways.
6.1. Benzene
Benzene was the first aromatic molecule for which extensive adsorption and re-
activity studies were performed on Si(1 0 0)-2 · 1 and the results have been reviewed
by Wolkow in detail [8]. Here we will only summarize the results briefly. A con-
siderable amount of controversy surrounded the identification of the surface species
[181–189], but many now agree that benzene forms three different surface adducts on
Si(1 0 0)-2 · 1 at room temperature [182,185,186,190]. The majority surface product is
a [4 + 2] cycloaddition structure as shown in Fig. 19c. Two additional surface
structures, shown in Fig. 19e and f, occupy two dimer sites, and conversion to the
tight-bridge structure of Fig. 19e, can occur from the [4 + 2] cycloaddition product
when adjacent surface sites are vacant. The conversion is found to take place on an
experimental time scale, indicating an activation energy of approximately 23
kcal/mol. The second two-dimer product only appears at two parallel buckled di-
mers, also known as a type C defect, which constitute approximately 1% of the
Fig. 19. (a) STM image of the three types of surface structures observed for the bonding of benzene to
Si(1 0 0)-2 · 1. (b)–(f) Schematic representations of possible surface products along with (g)–(k) calculated
charge density isosurfaces of occupied valence states for each geometry [8]. With permission, from the
Annual Review of Physical Chemistry, Volume 50 1999 by Annual Reviews (www.annualreviews.org).
The author is also thanked for permission to reprint this figure.
Si(1 0 0)-2 · 1 surface [8]. Several other works have considered additional char-
acteristics of benzene adsorption [191–194] including temperature dependences
[187] and dynamics [195]. Angle-resolved ultraviolet photoemission spectroscopy
(ARUPS) and TPD indicates that benzene forms similar products on Ge(1 0 0)-2 · 1
at low temperature [196].
On Si(1 0 0)-2 · 1 benzene reacts at room temperature to give a [4 + 2] cycload-
dition product, but no [2 + 2] C@C cycloaddition adduct is observed. This is in
contrast to systems like 1,3-butadiene [169,197] or 1,3-cyclohexadiene [125,171,198]
which have been reported to produce both [4 + 2] and [2 + 2] C@C cycloaddition
products at room temperature. The difference in reactivity lies in the resonance
stabilization energy of benzene. When benzene adsorbs onto Si(1 0 0)-2 · 1 to create
the [2 + 2] or [4 + 2] cycloaddition adduct depicted in Fig. 19b and c, respectively, two
new Si–C bonds are formed. In addition, the delocalized nature of the cyclic
p-electron wavefunctions must be broken for the molecule to bind with the surface.
This loss of resonance stabilization energy is approximately 30 kcal/mol in the case
of benzene, sufficient to destabilize the more weakly bound [2 + 2] C@C cycloaddi-
tion products.
6.2. Substituents
It is well-known that the addition of substituent groups on an aromatic molecule

can alter its reactivity [44]. Substituent groups located at specific locations on a
benzene ring can either activate or deactivate a particular ring-carbon in a chemical
reaction. Consequently, substituent groups can direct chemical reactions to take
place at certain atomic centers on an aromatic ring and several studies have begun to
probe their effects on Si(1 0 0)-2 · 1 [199,200].
Coulter et al. investigated whether methyl substituents on benzene could direct the
formation of a specific surface product on Si(1 0 0)-2 · 1 [199]. They studied xylenes,
which are relatives of benzene containing two methyl substituents on the ring, at
room temperature and low temperature with IR spectroscopy. The authors found
that benzene, toluene, and the xylenes all produce similar surface products at room
temperature, as evidenced by similar m(C–H) stretching modes directed parallel to the
surface plane, but specific bonding configurations could not be identified. Based on
isotopic labeling experiments, it was concluded that the presence of m(Si–H) growth
for each of the xylenes and toluene at room temperature results from substituent
methyl hydrogen dissociation and surface hydrogen coverages as high as 0.20
monolayers were reported. Because the bonding of benzene on Si(1 0 0)-2 · 1 has a
known temperature dependence [187], Coulter et al. also studied adsorption at low
temperature. Each of the xylenes formed the same surface products as at room
temperature, while benzene and toluene did not, and it was proposed that the sub-
stituent groups of the xylenes either reduce the barrier to product conversion by
stabilizing transient intermediates or prevent conversion by stabilizing the initial
surface adduct. These results are intriguing, and suggest future studies to determine
the specific surface species and fundamental reason for the differences in reactivity.
The known change in reactivity upon substitution spurred the investigation of
other benzene derivatives including styrene [178], aniline [201–203], phenyl isothio-
cyanate [174], benzonitrile [204], benzoic acid [201], and benzenethiol [205]. Al-
though unsubstituted benzene bonds directly through the aromatic ring, these other
molecules are observed to react with Si(1 0 0)-2 · 1 at room temperature through the
substituent group, leaving the ring intact. For example, as illustrated in Fig. 20,
aniline, benzenethiol, and benzoic acid undergo proton transfer while styrene, phenyl
isothiocyanate, and benzonitrile form cycloaddition products between the substitu-
ent and the surface.
6.3. Heteroaromatics
The concepts of aromaticity and resonance stabilization developed above for

benzene can easily be extended to the binding of heteroaromatic molecules on
Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1. Furan [180,206,207], thiophene [180,207–210], pyr-
role [53,61,211,212], pyridine [161,207], pyrazine [161,207], and s-triazene [12,213]
have all been investigated experimentally and/or theoretically on Si(1 0 0)-2 · 1. To
date, thiophene and pyrrole are the only molecules that have been studied on
Ge(1 0 0)-2 · 1 [53,210]. Beyond possessing a large resonance stabilization energy and
non-bonding electrons, many heteroaromatic molecules have significant dipole
moments, due to resonance and induction effects. This leads to an asymmetric charge
distribution in the cyclic p-system and can activate new reaction pathways and
produce new surface species not observed for benzene.
Several groups have investigated thiophene and furan on Si(1 0 0)-2 · 1 [180,206–
210,214] and are in general agreement that a [4 + 2] cycloaddition product com-
prises the majority of the surface at low temperature. For furan adsorption on
Si(1 0 0)-2 · 1, energy loss peaks near 2912 cm1 in the HREELS spectrum, consistent
with alkane m(–C–H) stretching modes, lead Qiao et al. to believe that furan looses its
aromaticity upon adsorption, forming a [4 + 2] cycloaddition adduct at low tem-
perature [206]. Two C(1s) XPS peaks at 284.7 and 285.5 eV, corresponding to a-C
C O
H NH H S
H O
Si Si Si Si
Si Si
(a) Proton Transfer Products
H2C CH C N N C
Si Si Si Si Si Si
(b) Cycloaddition Products
Fig. 20. (a) Proton transfer and (b) cycloaddition products observed for substituted benzenes on
Si(1 0 0)-2 · 1.
and b-C atoms, respectively, and one O(1s) photoelectron peak at 532.3 eV, are all
consistent with the formation of a [4 + 2] cycloaddition adduct. A related investi-
gation of thiophene on Si(1 0 0)-2 · 1 by Qiao et al. [208], employing XPS, UPS, and
HREELS, also concluded that [4 + 2] cycloaddition product is the major surface
adduct at low temperature.
Theoretical studies by Lin and coworkers [180,207,214] of several aromatic
molecules, including furan and thiophene, indicate that the [4 + 2] cycloaddition
adduct is likely the major surface adduct at low temperature because it has no ap-
parent activation barrier and is the most stable surface product by nearly 8.2 and
11.9 kcal/mol for furan and thiophene, respectively. A subsequent reaction pathway,
calculated on an unconstrained two-dimer cluster, is proposed where the oxygen or
sulfur of the [4 + 2] cycloaddition adduct can migrate to an adjacent dimer site with
an activation barrier of 19.8 and 16.0 kcal/mol for furan and thiophene, respectively.
This deoxygenation or desulfurization process, shown in Fig. 21, would create a
cyclic C2 H4 Si2 structure on one dimer and an epoxy-like structure on its neighbor.
These surface structures are also consistent with the experimental data of Qiao et al.,
and could provide an alternative explanation as to the origin of the alkane m(–C–H)
stretching modes present in the HREELS spectrum. However, the barrier to such a
process will likely be considerably greater on a cluster with constrained surfaces
Fig. 21. Theoretically calculated potential energy surface for thiophene (furan) chemisorption and de-
composition over an unconstrained, double-dimer Si15 H16 surface model. LM1_d and LM10 _d are [4 + 2]
cycloaddition products. LM10 _d can pass through transition state TS3_d to reach the sulfur (or oxygen)
dissociated state at LM4_d. Alternatively, LM1_d can proceed through transition state TS2_d to form a
[2 + 2] cycloaddition product with a neighboring dimer, LM3_d. All energies are with respect to the
vacuum level in kcal/mol at the B3LYP/6-31G(d) level of theory. Figure reprinted with permission from
Ref. [180]. Copyright 2001 American Chemical Society. The authors are also thanked for permission to
reprint this figure.
dimers and we hypothesize that such processes will be unlikely even at room tem-
perature.
Pyrrole has garnered considerable attention because of its complex reaction
mechanisms and close structural relationship to the heavily studied amine series
(Section 4.1). This system was initially studied on Si(1 0 0)-2 · 1 with HREELS and
XPS at low temperature by Qiao et al and the dominant surface species was found to
be an N–H dissociated product [211], as opposed to the [4 + 2] cycloaddition prod-
ucts observed for thiophene and furan. Their conclusions were supported by the
retention of aromatic m(C–H) stretching modes near 3100 cm1 and the growth of
m(Si–H) stretching modes at 2107 cm1 in their HREELS spectra as well as single
C(1s) and N(1s) XPS peaks with binding energies of 284.4 and 399.3 eV, respectively.
Later Cao et al. used IR spectroscopy studies and deuterated compounds to con-
clude that both C–H and N–H dissociation were possible at room temperature but
specific surface structures could not be assigned [61]. Based upon the arguments
made in Section 4, N–H dissociation would likely occur via a dative-bonded pre-
cursor state. However, a subsequent theoretical investigation found that this path-
way is activated and should not be observed at low temperatures [212]. They identify
an alternate pathway, shown in Fig. 22, that occurs via a ‘‘dative-bond’’ between an
a-C and the electrophilic dimer atom. This bonding is possible for pyrrole because of
Fig. 22. Theoretically calculated potential energy surface for the N–H dissociation reaction of pyrrole on
Si9 H12 dimer cluster. Two alternative pathways are depicted. In the higher energy pathway, pyrrole forms
a dative-bond through the nitrogen lone pair at Nads and then proceeds to the N–H dissociated product at
Prod. An alternative, lower energy pathway, begins with adsorption via a ring carbon, a-Cads , followed by
N–H dissociation to form a pyrrolyl radical, a-Cdis , and then isomerization to reach the N–H dissociated
state, Prod. All energies are with respect to the vacuum level in kcal/mol. Geometries were optimized at the
B3LYP/6-31G(d) level and single point energies are at the B3LYP/6-311++G(2df,2p) level of theory.
Figure reprinted from Ref. [12] with permission from Taylor & Francis Ltd (http://www.tandf.co.uk/
journals). The authors are also thanked for permission to reprint this figure.
resonance stabilization by the ring. This a-C dative-bonded surface product then
undergoes N–H dissociation and isomerizes so that the nitrogen is bonded to
the surface dimer, consistent with the experimental evidence of Qiao et al. and Cao
et al.
In the work by Cao et al., an adsorption peak near 3400 cm1 , corresponding to a
m(N–H) stretching mode, was observed. This observation led the authors to conclude
that a minor side product is formed during the adsorption of pyrrole on
Si(1 0 0)-2 · 1 by C–H dissociation, although a specific product or mechanism was
not identified [61]. Retention of an N–H bond in the surface product can be ex-
plained by considering the possibility of electrophilic aromatic substitution (EAS).
This reaction, specific to aromatic systems, occurs when an electrophile attacks a
ring carbon, cleaving an aromatic C–H bond, and creating a resonance stabilized
carbocation. EAS was recently identified by Wang et al. in their comprehensive IR
investigation of pyrrole and other cyclic aliphatic amines on Si(1 0 0)-2 · 1 and
Fig. 23. Infrared spectra of pyrrole on the Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 surfaces: (a) Saturation dose
(average of 5, 25, and 100 L doses) at 298 K on Si(1 0 0); (b) 100 L at 298 K on Ge(1 0 0); (c) 100 L pyrrole-
2,3,4,5-d4 on Ge(1 0 0) at 298 K on Ge(1 0 0); (d) multilayers (scaled) at 110 K. Figure reprinted with
permission from Ref. [53]. Copyright 2003 American Chemical Society.
Ge(1 0 0)-2 · 1 [53]. Similar to the findings of Cao et al. on Si(1 0 0)-2 · 1, the IR
spectrum for pyrrole (Fig. 23) on Ge(1 0 0)-2 · 1 measured by Wang et al. shows
adsorption peaks near 3400 and 3110 cm1 , indicative of m(N–H) and aromatic
m(C–H) stretching modes, respectively. In addition, Wang et al. observed that no
m(N–H) stretching modes remained after adsorption of the isotope pyrrole-2,3,4,5-d4
(in which all of the hydrogens attached to ring carbons have been replaced by
deuterium) on Ge(1 0 0)-2 · 1, indicating that virtually all of the deuterated pyrrole
reacted via N–H dissociation. This result was explained by the kinetic isotope effect,
in which the rate of C–D dissociation is significantly slower than the analogous C–H
dissociation and, in this case, prevents the formation of the EAS product. DFT
calculations of the partial potential energy surface for adsorption of pyrrole on
Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 suggest that both the N–H dissociation and EAS
reaction are feasible at room temperature.
After our discussion of dative bonding in Section 4, it would be expected that the
lone pair of the heteroatom should play a significant role in the bonding of all
heteroaromatics on Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1; however, this has not been found
experimentally or theoretically. The aromatic nature of pyrrole allows dative
bonding to occur at the ring carbons in addition to the nitrogen heteroatom. Wang
et al. used DFT to compare the stability of three different dative-bonded states of
pyrrole on Si(1 0 0)-2 · 1 [53]. They show that bonding at the a-C is most energeti-
cally favorable with a binding energy of 6.6 kcal/mol, followed by the b-C position
(4.1 kcal/mol). Perhaps surprisingly, dative bonding through the nitrogen lone pair is
the most unfavorable with a binding energy of 0.6 kcal/mol. By comparing this
value with the binding energy of dative-bonded pyrrolidine on Si(1 0 0)-2 · 1 (25.2
kcal/mol), Wang et al. conclude that pyrrole must sacrifice its aromaticity to dative
bond via the nitrogen lone pair. On the other hand, two lone pairs are located on the
oxygen and sulfur heteroatom of furan and thiophene, respectively, and an inter-
action between a heteroatom lone pair and the electrophilic dimer atom to form a
dative bond does not require removal of aromaticity.
In contrast to pyrrole, no EAS product has been reported for furan or thiophene.
Although the dipole moments of furan and thiophene point in the opposite direction
to that of pyrrole, which should weaken the a-C or b-C dative-bonded species
leading to the EAS product, we hypothesize that lack of experimental evidence for
the EAS product is more likely due to the experimental conditions under which these
reactions were studied. Currently published experimental data for furan and thi-
ophene were recorded at low temperature where barriers leading to products other
than the [4 + 2] cycloaddition adduct are insurmountable. Pyrrole, on the other hand,
was investigated at room temperature, where additional pathways (e.g. EAS) can
effectively compete with the [4 + 2] cycloaddition, leading to different surface product
distributions. Additional theoretical studies in this area could greatly improve our
understanding of the reaction pathways available to heteroaromatics on semicon-
ductor surfaces.
6.4. Reactivity trends
The rich and intensely studied chemistry of pyrrole on Si(1 0 0)-2 · 1 and
Ge(1 0 0)-2 · 1 provides an excellent opportunity to again evaluate how known so-
lution phase reactivity trends compare to those observed on semiconductor surfaces.
Dative bonding of pyrrole on Si(1 0 0)-2 · 1 is equivalent to the protonation of
pyrrole in solution, because both reactions involve electrophilic attack of the pyrrole
ring. Thus, we can compare the observed thermodynamic ordering of dative bonding
on Si(1 0 0)-2 · 1, a-C > b-C > N, with the protonation of pyrrole by Hþ in solution.
At equilibrium, in solution, protonation at the b-C and nitrogen is only 1% and
0.0001% that at the a-C, respectively, a trend that is consistent with the results for
dative bonding on Si(1 0 0)-2 · 1. Fig. 24 summarizes other observed reactivities of
pyrrole on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 and demonstrates that they are consis-
tent with several previously documented trends [53].
Molecular Reactivity Reactivity on Semiconductor Surfaces

Pyrrole less basic than aliphatic amines Dative bonding less favorable for pyrrole than for
aliphatic amines
Thermodynamic preference for protonation is: α -C Thermodynamic preference for dative bonding is:
> β -C > N α -C > β -C > N
Pyrrole more acidic than aliphatic amines N-H dissociation more facile on Ge for pyrrole than
for aliphatic amines
Pyrrole more reactive than benzene towards Electrophilic substitution observed for pyrrole on Si
electrophilic substitution reactions and Ge but not for benzene or derivatives
Proton transfer is 10-100 times faster at N than at N-H dissociation is faster than electrophilic
ring carbons substitution at ring carbons
Fig. 24. Comparison of the known reactivity of pyrrole in solution to that observed for pyrrole on
Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. Figure reprinted with permission from Ref. [53]. Copyright 2003
American Chemical Society.
7. Multifunctional compounds
Now that the basic principles of the reactions of organic molecules on

Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1 have been developed, it is possible to explore
multifunctional molecules. These molecules, which contain two or more reactive
moieties, provide valuable insight into the competition and selectively observed on
these surfaces. Since it is expected that many of the proposed applications of organic
functionalization will likely require the selective deposition of a monolayer with
known functionality followed by attachment of subsequent monolayers, knowledge
of the principles that govern competition and selectivity is essential [10].
The results of several recent studies keenly illustrate a major challenge that must
be overcome before vacuum-functionalization becomes viable for the stepwise
growth of ordered organic layers at the surface; namely, once more than one func-
tionality is present on the molecule, selectivity becomes a dominant issue [52]. Due to
the low barriers observed for many pathways on Si(1 0 0)-2 · 1, competition between
different available pathways is observed even for relatively simple multifunctional
compounds. Recall that molecules such as acetonitrile (Section 5.1) [162] and ben-
zene (Section 6.1) [8], for example, form multiple products at the surface. Even
alkenes (Section 5.1), which can produce a simple [2 + 2] product distribution and for
which well-ordered organic overlayers have been identified [9], encounter competi-
tive side reactions when combined with a second functionality. Here we present
several studies that have examined multifunctionality by combining alkenes with
other groups, including amines, carbonyls, and nitriles, and have shown that ki-
netically controlled surface reactions can lead to poor selectivity on semiconductor
surfaces, especially Si(1 0 0)-2 · 1.
3-Pyrroline, an unsaturated cyclic amine, was investigated by Liu et al. and Wang
et al. to determine whether the [2 + 2] C@C cycloaddition product was the majority
surface species on Si(1 0 0)-2 · 1 [53,111]. If this were the case, 3-pyrroline might form
well-ordered monolayers, similar to cyclopentene, and the amine would remain
available for second layer attachment. However, it was found that proton transfer
from the amine, an unactivated process, was favored over the formation of the [2 + 2]
C@C cycloaddition, an activated process. Similarly, on Ge(1 0 0)-2 · 1, the majority
of 3-pyrroline surface adducts populate the dative-bonded state and some proton
transfer is seen at higher coverage [53].
Richardson and coworkers have extensively studied maleic anhydride with STM,
HREELS, NEXAFS, and photoluminescence [215–218]. In contrast to the known
pathways for the reaction of 3-pyrroline on Si(1 0 0)-2 · 1 [60,111], maleic anhydride
preferentially forms a [2 + 2] C@C cycloaddition product at low coverage and CH
dissociated product at high coverage [216]. HREELS loss modes at 1619 and 1775
cm1 , which correspond to m(C@C) and m(C@O) stretches, respectively, are present
at coverages less than 2 L. As coverage is increased, growth of m(Si–H) modes at 2128
cm1 and alkene m( ¼ C–H) modes at 3147 cm1 become apparent. Although not
explicitly discussed by the authors, the high energy alkene m( ¼ C–H) modes observed
at high coverage are likely due to the remaining aromaticity in the ring after ad-
sorption. Further confirmation of the [2 + 2] C@C cycloadduct, comes from the
C(1s) NEXAFS spectra shown in Fig. 25 [219]. These data unambiguously show loss
of a p peak at 284.0 eV upon, assigned to transitions from C(1s) levels in the olefin
bond into the LUMO.
A recent study by Wang et al. investigating the reaction of ethylvinylketone
clearly demonstrates how kinetically controlled reactions on Si(1 0 0)-2 · 1 can lead
to poor selectivity on Si(1 0 0)-2 · 1 [52]. Using IR spectroscopy and DFT calcula-
tions, the authors found that the majority surface adduct for the conjugated ethyl-
vinylketone on Ge(1 0 0)-2 · 1 is a [4 + 2] cycloaddition product. This assignment was
based on the lack of intense m(C@O) stretching modes near 1675 cm1 and ap-
pearance of a m(C@C) stretch at 1620 cm1 . As evidenced by the absence of m(Ge–H)
stretching peaks near 1900–2000 cm1 , an a-CH dissociated product is not present.
Based on thermodynamic arguments, the dative-bonded state and [2 + 2] C@O
cycloaddition products were ruled out because of their weak binding energies.
In contrast to the selective formation of [4 + 2] cycloaddition products on
Ge(1 0 0)-2 · 1, the observed surface products on Si(1 0 0)-2 · 1 included the [4 + 2],
[2 + 2] C@O cycloadducts as well as a-CH dissociated products. The explanation
given by the authors was that all of the barriers to the formation of these products
are low enough on Si(1 0 0)-2 · 1 to be surmounted at room temperature, forming a
wide distribution of products on the surface. To probe the competing reactions of
ketones without the interference of the kinetically and thermodynamically favored
[4 + 2] cycloaddition product, the unconjugated probe molecule 5-hexen-2-one was
studied. On Ge(1 0 0)-2 · 1, the majority surface species is the a-CH dissociated
product, as evidenced by the m(Ge–H) peak at 1955 cm1 . A weak m(C@O) stretching
mode at 1720 cm1 indicates that a small quantity of the [2 + 2] C@C cycloadduct is
also present. On Si(1 0 0)-2 · 1, a [2 + 2] C@O cycloaddition product is predicted to
compete with the majority a-CH dissociated product on Si(1 0 0)-2 · 1, although its
presence could not be determined spectroscopically.
More recently, the investigation of multifunctional nitrile-containing compounds
has produced conflicting conclusions. Tao et al. studied the reaction of 2-propene-
nitrile on Si(1 0 0)-2 · 1 with HREELS, XPS, UPS, and DFT calculations [220].
Although 2-propenenitrile is a conjugated nitrile, analogous to ethylvinylketone, no
[4 + 2] cycloaddition product was observed and a [2 + 2] CBN cycloaddition product
Fig. 25. C1s NEXAFS spectra of (c) multilayers of maleic anhydride, and a 2 L dose on Si(1 0 0)-2 · 1 at
room temperature, recorded at (a) 30 and (b) 90 incidence angles. Figure reprinted and adapted from
Ref. [216] with permission from Elsevier Science B.V. The authors are also thanked for permission to
reprint this figure.
was found to be the majority surface species. Subsequent theoretical work by Choi
and Gordon [221] differs from the findings of Tao et al. and predicts that the [4 + 2]
cycloaddition product, creating a cyclic, six-membered ketenimine (C@C@N),
should be a significant surface product. Interestingly, cyclic ketenimines are highly
strained and have only been observed in solution in greater than eight-membered
rings. A combined IR spectroscopy and XPS [222] study followed by a NEXAFS
investigation [162] support the claim of Choi and Gordon, that the [4 + 2] cycload-
dition product is the dominant surface species. Although presence of a m(CBN)
stretching mode, at 2218 cm1 in the infrared data of Schwartz et al. suggests that a
[2 + 2] C@C cycloadduct is a minority product, observation of a m(N–H) mode near
3400 cm1 complicates this assignment [222].
Motivated by the possibility of increased selectivity on Ge(1 0 0)-2 · 1, as observed
by Wang et al. for ethylvinylketone, Filler et al. completed a study combining IR
spectroscopy and theory of several nitrile-containing compounds on Ge(1 0 0)-2 · 1
Fig. 26. Infrared spectra of 2-propenenitrile on Ge(1 0 0)-2 · 1: (a) 40 L at room temperature (b) multi-
layers (scaled) at 120 K.
[63]. On this surface, the [4 + 2] cycloaddition product through the conjugated

p-system is found to be the dominant surface adduct for 2-propenenitrile. A [2 + 2]
C@C cycloaddition product through the alkene comprises a minor side-product
(10%), and the [2 + 2] CBN cycloaddition product is not observed. The two surface
products are evidenced, respectively, by an extremely intense m(C@C@N) stretch at
1954 cm1 and the m(CBN) stretch near 2210 cm1 as shown in Fig. 26.
Despite the many pitfalls associated with the creation of selectively grown
monolayers on Si(1 0 0)-2 · 1, the bonding of extremely complex molecules are be-
ginning to be investigated. Richardson recently reported on the adsorption of uracil,
a component of ribonucleic acid (RNA), on Si(1 0 0)-2 · 1 [223]. Fig. 27 shows the
keto and enol tautomers of uracil. The energy loss spectra obtained for uracil are
difficult to interpret due to multiple tautomeric forms in addition to possible hy-
drogen bonding between molecules. However, it was proposed that the enol tau-
tomer of uracil bonds to Si(1 0 0)-2 · 1, via O–H cleavage (proton transfer). Analysis
of specular and off-specular vibrational data and STM images suggests that the
product is oriented perpendicular to the surface. Although various [4 + 2] and [2 + 2]
cycloaddition products are, in principle, possible for uracil, these surface species
were not discussed by the authors. These results clearly demonstrate that it is be-
coming possible to determine the adsorption configurations of complex molecules on
semiconductor surfaces; however, the continued investigation of simple probe mol-
ecules will be essential to enable a more complete understanding of the fundamental
kinetics and thermodynamics that govern functional group competition.
H H
H H H
N N
O N O HO N OH
H
(a) (b)
Fig. 27. (a) Keto and (b) enol tautomers of uracil.
8. Future directions
A number of challenges toward successful vacuum functionalization still exist and

remain an exciting topic for future study. These include selectivity, coverage and
order, and multilayer attachment. For most applications, one would like to deposit a
well-ordered layer with a single functional entity exposed outward. Most of the
vacuum-based attachment reactions examined to date, however, exhibit shortcom-
ings both in the degree of selectivity toward a single product, as discussed in
Section 7, and in the degree of order in the organic layer, resulting in a disordered
overlayer. In addition, once a bifunctional or polyfunctional organic molecule has
been selectively reacted as the initial layer, we must learn how to deposit multiple
organic layers in a controllable fashion.
In a sequence desired for multilayer deposition of organics, the first step is to
selectively deposit a closely-packed, well-ordered organic monolayer containing a
single reactive functional group extending from the surface as schematically illus-
trated in Fig. 28. One method to accomplish this task relies on the use of moieties
that react competitively over other functionalities in a molecule, although, as noted in
Section 7, controlling the competition with other functional groups has been espe-
cially challenging. With the present knowledge of individual group reactivity,
however, it is becoming possible to choose bifunctional molecules that are designed
to exhibit high selectivity at the surface. For example, previous studies have revealed
that the reaction leading to formation of an N–H dissociated and [2 + 2] C@O cy-
cloaddition product on silicon encounter activation barriers that differ by over 10
kcal/mol [51,62]; a difference of this magnitude corresponds to a reaction rate ratio of
approximately 107 at room temperature. An amide or a ketoamine, which combine
these two groups, is a model bifunctional compound for probing the competition
between attachment through the C@O (via [2 + 2] cycloaddition) and attachment
through the NH2 .
Richardson and coworkers reported on the selective adsorption of glycine [219],
an amino acid, and 4-aminobenzoic acid [224] on Si(1 0 0)-2 · 1. Each of these
molecules is multifunctional, containing a carboxylic acid and an amine functional
Fig. 28. Schematic illustration of an (a) ideal, anisotropic, selectively-bound monolayer and a (b) non-
ideal, randomly-oriented monolayer.
group. Glycine adsorbed on Si(1 0 0)-2 · 1 at room temperature results in HREELS

loss peaks at 2115 cm1 and 1750 cm1 corresponding to m(Si–H) and m(C@O)
stretching modes, respectively [219]. In addition, lack of a m(O–H) peak near 3600
cm1 led the authors to conclude that glycine binds selectively to Si(1 0 0)-2 · 1 via
proton transfer from the carboxylic acid group. Similar results and conclusions were
reported for the reaction of 4-aminobenzoic acid [224].
It has also been suggested that steric interactions can be employed to prevent
unwanted competing reactions and improve selectivity. In an attempt to prevent
pyrrolidine from reacting via N–H dissociation, and instead produce a [2 + 2] C@C
cycloaddition adduct, Wang et al. examined methylpyrrolidine on Si(1 0 0)-2 · 1 [60].
However, they found that the steric effects of the methyl substituent on the nitrogen
were not large enough to prevent dative bonding.
Long-range surface ordering remains a challenging aspect of organic function-
alization because of the high sticking probabilities and strong bonds formed with the
semiconductor surface, especially on Si(1 0 0)-2 · 1. As discussed in Section 4.3, some
work has investigated non-local interactions that affect bonding on adjacent dimer
sites. Although the mechanisms of non-local interactions are still under debate, an
understanding of these effects will likely facilitate the creation of highly ordered
monolayers. In addition, adsorption at different temperatures, a largely uninvesti-
gated aspect of organic adsorption, could enable ‘‘tuning’’ of the surface ordering or
product distribution. This is especially promising on Ge(1 0 0)-2 · 1 due to less
strongly bound surface products and reduced sticking probabilities.
Successful completion of second- and further-layer attachments under vacuum
conditions has been extremely limited. Historically, the creation of a [4 + 2] cyclo-
addition product for dienes, discussed in Section 5.2, was the one of the first reaction
classes where a reactive moiety was retained upon adsorption. It was originally
proposed that the remaining alkene in the cyclic surface product could undergo
additional cycloaddition reactions, resulting in molecular layering on the semicon-
ductor surface [167]. However, due to the low reactivity of the remaining alkene
when compared to the bare semiconductor surface, in addition to the low fluxes of
reactants to the surface, second layer attachment was not realized for that system.
Overall, the attachment of subsequent organic monolayers has proven difficult and,
to date, only simple hydrogenation [171], bromination [225], and imide coupling
[226] have been reported in vacuum.
Since the functional groups that are expected to be reactive in second layer re-
actions, such as amines and carbonyls, also react directly with the bare semicon-
ductor surface, the challenge is to protect these groups during the deposition of the
initial layer. Molecules can theoretically be designed with one of the groups pro-
tected, with the aim of directing the surface reaction toward the other end of the
molecule. At a later step, the protected group could be deprotected and subsequently
reacted. Protecting groups have a vast presence in the organic literature [227–229]
and have also been used successfully in solution-based functionalization [11,230].
However, protection/deprotection in vacuum functionalization is largely unexplored
and is expected to be significantly more challenging due to the constraints on the
reaction conditions. Three stringent requirements must be met in the selection of
vacuum-compatible protecting groups: (A) The group must satisfactorily protect the
functionality from reacting at the surface without itself reacting. (B) It must not be
so large that the protected molecule blocks multiple sites at the surface. (C) There
has to be a practicable strategy for deprotection. For vacuum deprotection, one must
devise non-traditional deprotection strategies using sources available in vacuum,
such as heat, light, electrons, or possibly radicals (e.g. H atoms). Recently, Filler et al.
identified the nitrile functional group as a good vehicle to introduce protected amines
[63]. Subsequent conversion of the remaining nitrile to an amine via in situ hydro-
genation may open the doorway to facile second layer attachment as illustrated in
Fig. 29. Beyond employing protecting group strategies, the use of symmetric mole-
cules, such as 1,4-phenylenediamine [202] could provide yet another method with
which to create an anisotropically adsorbed monolayer, ready for second layer at-
tachment.
Finally, molecular electronics have been widely anticipated and it is our opinion
that organic functionalization can help to create some of the nanoscale structures
necessary for such an application. The leading problem with the large scale inte-
gration of nanoscale devices or structures is the lack of an efficient patterning
technique; however, some intriguing methods have been proposed and demon-
strated. Several groups have employed hydrogen passivated Si(1 0 0)-2 · 1 surfaces
and created arrays of ‘‘active sites’’ by STM-induced desorption of hydrogen [231–
233]. Since traditional single tip probes cannot rapidly pattern large scale areas, some
research groups have developed multitipped probes in an attempt to overcome this
difficulty [234–236]. Lopinski et al. also demonstrated that removal of a single hy-
drogen atom from a monohydride covered Si(1 0 0)-2 · 1 surface dimer and sub-
sequent exposure with styrene can lead to a radical initiated polymerization of
O O
N N N N NH2 NH2 R
R
H2C CH2 NH HN
O
H2C CH2
C
H atoms R Cl
+ -HCl
Ge Ge Ge Ge Ge
Ge
Ge Ge
Fig. 29. Formation of an amine from a nitrile compound and subsequent creation of an amide on
Ge(1 0 0)-2 · 1.
styrene along a dimer row [13]. The same group recently extended this type of chem-
istry to include vinylferrocene, due to the potential for iron to catalyze carbon
nanotube growth [237]. In addition to these predominantly ‘‘serial’’ techniques, we
anticipate that exploitation of the newly discovered non-local interactions of dative-
bonded amines on Si(1 0 0)-2 · 1 [113] could lead to methods of self-assembly or
other ‘‘parallel’’ processing techniques for patterning large-scale areas. Although
some progress toward nanoscale architecture continues to be made, novel processes
for patterning must continue to be explored.
9. Conclusion
Significant strides have been taken in the effort to understand organic reactions on
group-IV semiconductor surfaces, particularly Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. The
majority of the scientific literature within this field has been surveyed and surface
reactions were categorized into three broad classes based on analogies from organic
chemistry. These categories include nucleophilic/electrophilic, pericyclic, as well as
aromatic surface reactions.
Nucleophilic/electrophilic and pericyclic surface products are possible because of
the unique nature of the surface dimer. The nucleophilic/electrophilic reactions
studied to date have been found to pass through a dative-bonded precursor state
where an impinging molecule has either donated its electronic charge to the electr-
ophilic dimer atom or accepted charge from the nucleophilic dimer atom. Although
subsequent pathways which lead to more thermodynamically-favorable surface
species have been identified, dative-bonded precursor states are a fundamental
property of many organic reactions on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1. Pericyclic
surface products, on the other hand, are possible due to an interaction of an alkene
or diene with the weak p bond of the surface dimer. Aromatic reactions were treated
separately because of the delocalized nature of the p-system electrons and resonance
stabilization which plays a role in their surface reactions.
As a result of the combination of experimental and theoretical approaches, many
of the fundamental thermodynamic and kinetic principles that govern these reactions
have been determined. Diverse spectroscopy and microscopy techniques have en-
abled the detection of complex surface products, intermediates, and some reaction
barriers. In addition, ab initio quantum chemical methods have proved invaluable in
the study of reaction potential energy surfaces and identification of surface products
in many studies.
We have constructed a substantial set of basic rules and trends for organic
functionalization and it is now plausible that novel molecules can be designed to
produce a desired surface product on the Si(1 0 0)-2 · 1 or Ge(1 0 0)-2 · 1 surface.
Once the challenges of competition, selectivity, order, and multilayer attachment are
overcome, vacuum-based functionalization of semiconductor surfaces will be poised
to contribute significantly to the emerging fields of molecular electronics, chemical
recognition, and nanoscience.
Notes added during proof
Since the submission of this article, the following publications have emerged
which are relevant to two of the systems discussed in this review:
[A] S. Bocharov, A.T. Mathauser, A.V. Teplyakov, Adsorption and thermal
chemistry of nitroethane on Si(1 0 0)-2 · 1, J. Phys. Chem. B, in press.
The authors use IR, TPD, and AES to argue that the barrier to adsorption of
nitroethane on Si(1 0 0)-2 · 1 is not barrierless as originally proposed theoretically by
Barriocanal and Doren [175,176].
[B] L.C. Teague, J.J. Boland, STM study of multiple bonding configurations and
mechanism of 1,3-cyclohexadiene attachment on Si(1 0 0)-2 · 1, J. Phys. Chem. B 107
(2003) 3820.
High resolution filled and empty state STM images of 1,3-cyclohexadiene ad-
sorbed on Si(1 0 0)-2 · 1 enable Teague et al. to identify several different surface
products. Similar to the previous results of Hovis et al. [169], both [4+2] and [2+2]
intradimer cycloaddition products were identified.
In addition, two different [2+2] cycloaddition conformers as well as [4+2] inter-
dimer cycloaddition products were observed. Most interestingly, product distribu-
tions are found to favor interdimer [4+2] bonding although intradimer bonding is
thermodynamically more favorable, indicating that these reactions are kinetically
controlled.
Acknowledgements
M.A.F. would like to acknowledge the National Science Foundation for financial
support in the form of a Graduate Research Fellowship. S.F.B. acknowledges fi-
nancial support from the National Science Foundation (CHE 9900041) and the
Stanford University Center for Integrated Systems for making this review possible.
S.F.B. is a Camille Dreyfus Teacher-Scholar. In addition, we greatly appreciate the
contributions made by Collin Mui, George T. Wang, Yuniarto Widjaja, James A.
Van Deventer, and Charles B. Musgrave as well as the following researchers who
graciously provided permission to reprint their figures: Prof. Robert J. Hamers, Prof.
M. C. Lin, Prof. Charles B. Musgrave, Prof. Neville V. Richardson, and Dr. Robert
A. Wolkow.
References
[1] M. Seiler, Dendritic polymers: interdisciplinary research and emerging applications from unique
structural properties, Chem. Eng. Technol. 25 (2002) 237.
[2] R.H. Friend, R.W. Gymer, A.B. Holmes, J.H. Burroughes, R.N. Marks, C. Taliani, D.D.C.
Bradley, D.A. Dos Santos, J.L. Bredas, M. Logdlund, W.R. Salaneck, Electroluminescence in
conjugated polymers, Nature 397 (1999) 121.
[3] C.K. Chiang, C.R. Fincher, Y.W. Park, A.J. Heeger, H. Shirakawa, E.J. Louis, S.C. Gau, A.G.
MacDiarmid, Electrical conductivity in doped polyacetylene, Phys. Rev. Lett. 39 (1977) 1098.
[4] C.W. Tang, S.A. VanSlyke, Organic electroluminescent diodes, Appl. Phys. Lett. 51 (1987) 913.
[5] J.T. Yates Jr, A new opportunity in silicon-based microelectronics, Science 279 (1998) 335.
[6] Z. Lin, T. Strother, W. Cai, X.P. Cao, L.M. Smith, R.J. Hamers, DNA attachment and
hybridization at the silicon (1 0 0) surface, Langmuir 18 (2002) 788.
[7] M.P. Stewart, J.M. Buriak, Chemical and biological applications of porous silicon technology, Adv.
Mater. 12 (2000) 859.
[8] R.A. Wolkow, Controlled molecular adsorption on silicon: laying a foundation for molecular
devices, Ann. Rev. Phys. Chem. 50 (1999) 413.
[9] R.J. Hamers, S.K. Coulter, M.D. Ellison, J.S. Hovis, D.F. Padowitz, M.P. Schwartz, C.M.
Greenlief, J.N. Russell, Cycloaddition chemistry of organic molecules with semiconductor surfaces,
Acc. Chem. Res. 33 (2000) 617.
[10] S.F. Bent, Organic functionalization of group-IV semiconductor surfaces: principles, examples,
applications, and prospects, Surf. Sci. 500 (2002) 879.
[11] J.M. Buriak, Organometallic chemistry on silicon and germanium surfaces, Chem. Rev. 102 (2002)
1271.
[12] X. Lu, M.C. Lin, Reactions of some [C, N, O]-containing molecules with Si surfaces: experimental
and theoretical studies, Int. Rev. Phys. Chem. 21 (2002) 137.
[13] G.P. Lopinski, D.D.M. Wayner, R.A. Wolkow, Self-directed growth of molecular nanostructures on
silicon, Nature 406 (2000) 48.
[14] R.J. Hamers, J.S. Hovis, S. Lee, H.B. Liu, J. Shan, Formation of ordered anisotropic organic
monolayers on the Si(0 0 1) surface, J. Phys. Chem. B 101 (1997) 1489.
[15] J.T.C. Wojtyk, M. Tomietto, R. Boukherroub, D.D.M. Wayner, Reagentless micropatterning of
organics on silicon surfaces: control of hydrophobic/hydrophilic domains, J. Am. Chem. Soc. 123
(2001) 1535.
[16] M.R. Linford, C.E.D. Chidsey, Alkyl monolayers covalently bonded to silicon surfaces, J. Am.
Chem. Soc. 115 (1993) 12631.
[17] M.R. Linford, P. Fenter, P.M. Eisenberger, C.E.D. Chidsey, Alkyl monolayers on silicon prepared
from 1-alkenes and hydrogen terminated silicon, J. Am. Chem. Soc. 117 (1995) 3145.
[18] J. Terry, M.R. Linford, C. Wigren, R.Y. Cao, P. Pianetta, C.E.D. Chidsey, Determination of the
bonding of alkyl monolayers to the Si(1 1 1) surface using chemical-shift, scanned-energy
photoelectron diffraction, Appl. Phys. Lett. 71 (1997) 1056.
[19] M.P. Stewart, J.M. Buriak, Photopatterned hydrosilylation on porous silicon, Angew. Chem. Int.
Ed. 37 (1998) 3257.
[20] J.M. Schmeltzer, L.A. Porter, M.P. Stewart, J.M. Buriak, Hydride abstraction initiated hydro-
silylation of terminal alkenes and alkynes on porous silicon, Langmuir 18 (2002) 2971.
[21] J.M. Buriak, M.J. Alien, Photoluminescence of porous silicon surfaces stabilized through Lewis acid
mediated hydrosilylation, J. Lumin. 80 (1998) 29.
[22] M.P. Stewart, E.G. Robins, T.W. Geders, M.J. Allen, H.C. Choi, J.M. Buriak, Three methods for
stabilization and functionalization of porous silicon surfaces via hydrosilylation and electrografting
reactions, Phys. Status Solid. A 182 (2000) 109.
[23] J.M. Buriak, M.P. Stewart, T.W. Geders, M.J. Allen, H.C. Choi, J. Smith, D. Raftery, L.T.
Canham, Lewis acid mediated hydrosilylation on porous silicon surfaces, J. Am. Chem. Soc. 121
(1999) 11491.
[24] J.M. Buriak, M.J. Allen, Lewis acid mediated functionalization of porous silicon with substituted
alkenes and alkynes, J. Am. Chem. Soc. 120 (1998) 1339.
[25] J.T.C. Wojtyk, K.A. Morin, R. Boukherroub, D.D.M. Wayner, Modification of porous silicon
surfaces with activated ester monolayers, Langmuir 18 (2002) 6081.
[26] N.Y. Kim, P.E. Laibinis, Thermal derivatization of porous silicon with alcohols, J. Am. Chem. Soc.
119 (1997) 2297.
[27] N.Y. Kim, P.E. Laibinis, Derivatization of porous silicon by Grignard reagents at room
temperature, J. Am. Chem. Soc. 120 (1998) 4516.
[28] J.H. Song, M.J. Sailor, Functionalization of nanocrystalline porous silicon surfaces with aryllithium
reagents: formation of silicon–carbon bonds by cleavage of silicon–silicon bonds, J. Am. Chem. Soc.
120 (1998) 2376.
[29] J.H. Song, M.J. Sailor, Reaction of photoluminescent porous silicon surfaces with lithium reagents
to form silicon–carbon bound surface species, Inorg. Chem. 38 (1999) 1498.
[30] A. Bansal, X.L. Li, I. Lauermann, N.S. Lewis, S.I. Yi, W.H. Weinberg, Alkylation of Si surfaces
using a two-step halogenation Grignard route, J. Am. Chem. Soc. 118 (1996) 7225.
[31] A. Bansal, X.L. Li, S.I. Yi, W.H. Weinberg, N.S. Lewis, Spectroscopic studies of the modification of
crystalline Si(1 1 1) surfaces with covalently-attached alkyl chains using a chlorination/alkylation
method, J. Phys. Chem. B 105 (2001) 10266.
[32] W. Cai, Z. Lin, T. Strother, L.M. Smith, R.J. Hamers, Chemical modification and patterning of
iodine-terminated silicon surfaces using visible light, J. Phys. Chem. B 106 (2002) 2656.
[33] J.M. Buriak, Organometallic chemistry on silicon surfaces: formation of functional monolayers
bound through Si–C bonds, Chem. Commun. (1999) 1051.
[34] D.D.M. Wayner, R.A. Wolkow, Organic modification of hydrogen terminated silicon surfaces,
J. Chem. Soc. Perk.T. 2 (2002) 23.
[35] N.W. Ashcroft, N.D. Mermin, Solid State Physics, Harcourt Brace College Publishers, Fort Worth,
1976.
[36] C.B. Duke, Semiconductor surface reconstruction: the structural chemistry of 2-dimensional surface
compounds, Chem. Rev. 96 (1996) 1237.
[37] C.J. Wu, E.A. Carter, Adsorption of hydrogen atoms on the Si(1 0 0)-2 · 1 surface: implications for
the H2 desorption mechanism, Chem. Phys. Lett. 185 (1991) 172.
[38] M.P. DÕEvelyn, Y.M.L. Yang, L.F. Sutcu, p-bonded dimers, preferential pairing, and 1st-order
desorption kinetics of hydrogen on Si(1 0 0)-2 · 1, J. Chem. Phys. 96 (1992) 852.
[39] U. H€ ofer, L.P. Li, T.F. Heinz, Desorption of hydrogen from Si(1 0 0)-2 · 1 at low coverages: the
influence of p-bonded dimers on the kinetics, Phys. Rev. B 45 (1992) 9485.
[40] P. Nachtigall, K.D. Jordan, C. Sosa, Ab initio calculation of the energy of recombinative hydrogen
desorption from the monohydride phase of Si(1 0 0), J. Phys. Chem. 97 (1993) 11666.
[41] M.P. DÕEvelyn, S.M. Cohen, E. Rouchouze, Y.L. Yang, Surface p bonding and the near 1st-order
desorption kinetics of hydrogen from Ge(1 0 0)-2 · 1, J. Chem. Phys. 98 (1993) 3560.
[42] M.C. Flowers, N.B.H. Jonathan, Y. Liu, A. Morris, Temperature programmed desorption of
molecular hydrogen from a Si(1 0 0)-2 · 1 surface: theory and experiment, J. Chem. Phys. 99 (1993)
7038.
[43] C. Mui, S.F. Bent, C.B. Musgrave, A theoretical study of the structure and thermochemistry of
1,3-butadiene on the Ge/Si(1 0 0)-2 · 1 surface, J. Phys. Chem. A 104 (2000) 2457.
[44] F.A. Carey, R.J. Sundberg, Advanced Organic Chemistry, Plenum Publishing Corporation, 2001.
[45] R. Konecny, D.J. Doren, Adsorption of water on Si(1 0 0)-2 · 1: a study with density functional
theory, J. Chem. Phys. 106 (1997) 2426.
[46] R.A. Wolkow, Direct observation of an increase in buckled dimers on Si(0 0 1) at low temperature,
Phys. Rev. Lett. 68 (1992) 2636.
[47] P.C. Weakliem, E.A. Carter, Constant temperature molecular dynamics simulations of Si(1 0 0) and
Ge(1 0 0): equilibrium structure and short time behavior, J. Chem. Phys. 96 (1992) 3240.
[48] J.A. Kubby, J.E. Griffith, R.S. Becker, J.S. Vickers, Tunneling microscopy of Ge(0 0 1), Phys. Rev. B
36 (1987) 6079.
[49] A.V. Teplyakov, P. Lal, Y.A. Noah, S.F. Bent, Evidence for a retro-Diels–Alder reaction on a
single-crystalline surface: butadienes on Ge(1 0 0), J. Am. Chem. Soc. 120 (1998) 7377.
[50] S.W. Lee, J.S. Hovis, S.K. Coulter, R.J. Hamers, C.M. Greenlief, Cycloaddition chemistry on
germanium (0 0 1) surfaces: the adsorption and reaction of cyclopentene and cyclohexene, Surf. Sci.
462 (2000) 6.
[51] C. Mui, J.H. Han, G.T. Wang, C.B. Musgrave, S.F. Bent, Proton transfer reactions on
semiconductor surfaces, J. Am. Chem. Soc. 124 (2002) 4027.
[52] G.T. Wang, C. Mui, C.B. Musgrave, S.F. Bent, Competition and selectivity of organic reactions on
semiconductor surfaces: reaction of unsaturated ketones on Si(1 0 0)-2 · 1 and Ge(1 0 0)-2 · 1, J. Am.
Chem. Soc. 124 (2002) 8990.
[53] G.T. Wang, C. Mui, J.F. Tannaci, M.A. Filler, C.B. Musgrave, S.F. Bent, Reaction of cyclic
aliphatic and aromatic amines on Ge(1 0 0)-2 · 1 and Si(1 0 0)-2 · 1, J. Phys. Chem. B 107 (2003)
4982.
[54] S.F. Bent, Attaching organic layers to semiconductor surfaces, J. Phys. Chem. B 106 (2002) 2830.
[55] Z. Wang, E.G. Seebauer, Estimating pre-exponential factors for desorption from semiconductors:
consequences for a priori process modeling, Appl. Surf. Sci. 181 (2001) 111.
[56] D.A. McQuarrie, P.A. Rock, General Chemistry, W.H. Freeman and Company, New York, 1987.
[57] C. Mui, G.T. Wang, S.F. Bent, C.B. Musgrave, Reactions of methylamines at the Si(1 0 0)-2 · 1
surface, J. Chem. Phys. 114 (2001) 10170.
[58] X.P. Cao, R.J. Hamers, Interactions of alkylamines with the silicon (0 0 1) surface, J. Vac. Sci.
Technol. B 20 (2002) 1614.
[59] X.P. Cao, R.J. Hamers, Silicon surfaces as electron acceptors: dative bonding of amines with
Si(0 0 1) and Si(1 1 1) surfaces, J. Am. Chem. Soc. 123 (2001) 10988.
[60] G.T. Wang, C. Mui, C.B. Musgrave, S.F. Bent, The effect of a methyl protecting group on the
adsorption of pyrrolidine on Si(1 0 0)-2 · 1, J. Phys. Chem. B 105 (2001) 3295.
[61] X. Cao, S.K. Coulter, M.D. Ellison, H. Liu, J. Liu, R.J. Hamers, Bonding of nitrogen-containing
organic molecules to the silicon (0 0 1) surface: the role of aromaticity, J. Phys. Chem. B 105 (2001)
3759.
[62] G.T. Wang, C. Mui, C.B. Musgrave, S.F. Bent, Example of a thermodynamically controlled reaction
on a semiconductor surface: acetone on Ge(1 0 0)-2 · 1, J. Phys. Chem. B 105 (2001) 12559.
[63] M.A. Filler, C. Mui, C.B. Musgrave, S.F. Bent, Competition and selectivity in the reaction of nitriles
on Ge(1 0 0)-2 · 1, J. Am. Chem. Soc. 125 (2003) 4928.
[64] C. Mui, M.A. Filler, S.F. Bent, C.B. Musgrave, Reactions of nitriles at semiconductor surfaces,
J. Phys. Chem. B, submitted for publication.
[65] X.P. Cao, R.J. Hamers, Formation of a surface-mediated donor–acceptor complex: coadsorption
of trimethylamine and boron trifluoride on the silicon (0 0 1) surface, J. Phys. Chem. B 106 (2002)
1840.
[66] R.E. Hummel, Electronic properties of materials, Springer-Verlag, Inc., New York, 2001.
[67] J.D. Plummer, P.B. Griffin, M.D. Deal, Silicon VLSI technology: fundamentals, practice, and
modeling, Prentice Hall, Upper Saddle River, 2000.
[68] K. Fujiwara, Localized bond model for H2 O chemisorption on silicon surfaces, Surf. Sci. 108 (1981)
124.
[69] D. Schmeisser, F.J. Himpsel, G. Hollinger, Chemisorption of H2 O on Si(1 0 0), Phys. Rev. B 27
(1983) 7813.
[70] H. Ibach, H. Wagner, D. Bruchmann, Dissociative chemisorption of H2 O on Si(1 0 0) and Si(1 1 1):
a vibrational study, Solid State Commun. 42 (1982) 457.
[71] F. Stucki, J. Anderson, G.J. Lapeyre, H.H. Farrell, Multiple vibrational excitations of H2 O and
D2 O on Si(1 0 0)-2 · 1: a HREELS study, Surf. Sci. 143 (1984) 84.
[72] Y.J. Chabal, Hydride formation on the Si(1 0 0)-H2 O surface, Phys. Rev. B 29 (1984) 3677.
[73] Y.J. Chabal, S.B. Christman, Evidence of dissociation of water on theSi(1 0 0)-2 · 1 surface, Phys.
Rev. B 29 (1984) 6974.
[74] C.U.S. Larsson, A.L. Johnson, A. Flodstrom, T.E. Madey, Adsorption of H2 O on planar and
stepped Si(1 0 0): structural aspects, J. Vac. Sci. Technol. A 5 (1987) 842.
[75] A.L. Johnson, M.M. Walczak, T.E. Madey, ESDIAD of 1st-row protic hydrides adsorbed on
Si(1 0 0): structure and reactivity, Langmuir 4 (1988) 277.
[76] Q. Gao, Z. Dohnalek, C.C. Cheng, W.J. Choyke, J.T. Yates Jr, Direct images of isotropic and
anisotropic vibrations in the Cl–Si and H–O–Si chemisorption bonds on Si(1 0 0), Surf. Sci. 312
(1994) 261.
[77] X.L. Zhou, C.R. Flores, J.M. White, Adsorption and decomposition of water on Si(1 0 0): a TPD
and SSIMS study, Appl. Surf. Sci. 62 (1992) 223.
[78] R.K. Schulze, J.F. Evans, Room temperature water adsorption on the Si(1 0 0) surface examined by
UPS, XPS, and static SIMS, Appl. Surf. Sci. 81 (1994) 449.
[79] M.C. Flowers, N.B.H. Jonathan, A. Morris, S. Wright, The adsorption and reactions of water on
Si(1 0 0)-2 · 1 and Si(1 1 1)-7 · 7 surfaces, Surf. Sci. 351 (1996) 87.
[80] M.K. Weldon, K.T. Queeney, A.B. Gurevich, B.B. Stefanov, Y.J. Chabal, K. Raghavachari, Si-H
bending modes as a probe of local chemical structure: thermal and chemical routes to decomposition
of H2 O on Si(1 0 0)-2 · 1, J. Chem. Phys. 113 (2000) 2440.
[81] M.K. Weldon, K.T. Queeney, Y.J. Chabal, B.B. Stefanov, K. Raghavachari, Mechanistic studies of
silicon oxidation, J. Vac. Sci. Technol. B 17 (1999) 1795.
[82] M.K. Weldon, B.B. Stefanov, K. Raghavachari, Y.J. Chabal, Initial H2 O-induced oxidation of
Si(1 0 0)-2 · 1, Phys. Rev. Lett. 79 (1997) 2851.
[83] B.B. Stefanov, A.B. Gurevich, M.K. Weldon, K. Raghavachari, Y.J. Chabal, Silicon epoxide:
unexpected intermediate during silicon oxide formation, Phys. Rev. Lett. 81 (1998) 3908.
[84] B.B. Stefanov, K. Raghavachari, Pathways for initial water-induced oxidation of Si(1 0 0), Appl.
Phys. Lett. 73 (1998) 824.
[85] E. Kooi, J.G. Vanlierop, J.A. Appels, Formation of silicon nitride at a Si–SiO2 interface during local
oxidation of silicon and during heat treatment of oxidized silicon in NH3 gas, J. Electrochem. Soc.
123 (1976) 1117.
[86] A. Hashimoto, M. Kobayashi, T. Kamijoh, H. Takano, M. Sakuta, Properties of PECVD SiOx Ny
films as selective diffusion barrier, J. Electrochem. Soc. 133 (1986) 1464.
[87] J.W. Osenbach, Sodium diffusion in plasma-deposited amorphous oxygen-doped silicon nitride
(a-SiON–H) films, J. Appl. Phys. 63 (1988) 4494.
[88] Y. Ma, T. Yasuda, G. Lucovsky, Fixed and trapped charges at oxide–nitride–oxide heterostructure
interfaces formed by remote plasma enhanced chemical vapor deposition, J. Vac. Sci. Technol. B 11
(1993) 1533.
[89] M.J. Dresser, P.A. Taylor, R.M. Wallace, W.J. Choyke, J.T. Yates Jr, The adsorption and
decomposition of NH3 on Si(1 0 0): detection of the NH2 (a) species, Surf. Sci. 218 (1989) 75.
[90] R.J. Hamers, P. Avouris, F. Bozso, A scanning tunneling microscopy study of the reaction of
Si(0 0 1)-2 · 1 with NH3 , J. Vac. Sci. Technol. A 6 (1988) 508.
[91] M. Fujisawa, Y. Taguchi, Y. Kuwahara, M. Onchi, M. Nishijima, Electron energy loss spectra of the
Si(1 0 0)-2 · 1 surface exposed to NH3 , Phys. Rev. B 39 (1989) 12918.
[92] F. Bozso, P. Avouris, Photoemission studies of the reactions of ammonia and N-atoms with
Si(1 0 0)-2 · 1 and Si(1 1 1)-7 · 7 surfaces, Phys. Rev. B 38 (1988) 3937.
[93] P.J. Chen, M.L. Colaianni, J.T. Yates Jr, Silicon backbond strain effects on NH3 surface chemistry:
Si(1 1 1)-7 · 7 compared to Si(1 0 0)-2 · 1, Surf. Sci. 274 (1992) L605.
[94] J.L. Bischoff, F. Lutz, D. Bolmont, L. Kubler, UPS differentiation between molecular NH3 and
partially dissociated NH2 fragments adsorbed at low temperature on Si(0 0 1) surfaces, Surf. Sci. 248
(1991) L240.
[95] L. Zhang, A.J. Carman, S.M. Casey, Observation of direct desorption from the ammonia dative-
bond well on Si(1 0 0), submitted for publication.
[96] Y. Widjaja, M.M. Mysinger, C.B. Musgrave, Ab initio study of adsorption and decomposition of
NH3 on Si(1 0 0)-2 · 1, J. Phys. Chem. B 104 (2000) 2527.
[97] Y. Widjaja, C.B. Musgrave, A density functional theory study of the nonlocal effects of NH3
adsorption and dissociation on Si(1 0 0)-2 · 1, Surf. Sci. 469 (2000) 9.
[98] Y. Widjaja, C.B. Musgrave, Ab initio study of the initial growth mechanism of silicon nitride on
Si(1 0 0)-2 · 1 using NH3 , Phys. Rev. B 64 (2001) 205303.
[99] W. Ranke, Equilibrium adsorption of NH3 on Ge(0 0 1), Ge(1 1 3), and Ge(1 1 1), Surf. Sci. 342
(1995) 281.
[100] W. Ranke, J. Platen, NH3 -induced c(4 · 2) to (2 · 2) transition on the Ge(0 0 1) surface by a domino-
like dimer flip, Surf. Sci. 349 (1996) L159.
[101] W. Ranke, J. Platen, Electronic and geometric structure of NH3 on Ge(0 0 1) under equilibrium
adsorption conditions, Phys. Rev. B 54 (1996) 2873.
[102] C. Bater, M. Sanders, J.H. Craig, Electron-stimulated dissociation of ammonia adsorbed on
Ge(1 0 0), Surf. Sci. 451 (2000) 226.
[103] M. Sanders, J.H. Craig, HREELS study of electron irradiation effects on ammonia adsorbed on the
Ge (1 0 0) surface, Appl. Surf. Sci. 171 (2001) 283.
[104] J. Eng, K. Raghavachari, L.M. Struck, Y.J. Chabal, B.E. Bent, G.W. Flynn, S.B. Christman, E.E.
Chaban, G.P. Williams, K. Radermacher, S. Manti, A vibrational study of ethanol adsorption on
Si(1 0 0), J. Chem. Phys. 106 (1997) 9889.
[105] X. Lu, Q. Zhang, M.C. Lin, Adsorption of methanol, formaldehyde, and formic acid on the
Si(1 0 0)-2 · 1 surface: a computational study, Phys. Chem. Chem. Phys. 3 (2001) 2156.
[106] M.P. Casaletto, R. Zanoni, M. Carbone, M.N. Piancastelli, L. Aballe, K. Weiss, K. Horn, High-
resolution photoemission study of ethanol on Si(1 0 0)-2 · 1, Surf. Sci. 447 (2000) 237.
[107] M.P. Casaletto, R. Zanoni, M. Carbone, M.N. Piancastelli, L. Aballe, K. Weiss, K. Horn, Metha-
nol adsorption on Si(1 0 0)-2 · 1 investigated by high-resolution photoemission, Surf. Sci. 505 (2002)
251.
[108] T. Kato, S.Y. Kang, X. Xu, T. Yamabe, Possible dissociative adsorption of CH3 OH and CH3 NH2
on Si(1 0 0)-2 · 1 surface, J. Phys. Chem. B 105 (2001) 10340.
[109] C.P.A. Mulcahy, A.J. Carman, S.M. Casey, The adsorption and thermal decomposition of
dimethylamine on Si(1 0 0), Surf. Sci. 459 (2000) 1.
[110] J.S. Hovis, S. Lee, H.B. Liu, R.J. Hamers, Controlled formation of organic layers on semiconductor
surfaces, J. Vac. Sci. Technol. B 15 (1997) 1153.
[111] H.B. Liu, R.J. Hamers, An X-ray photoelectron spectroscopy study of the bonding of unsaturated
organic molecules to the Si(0 0 1) surface, Surf. Sci. 416 (1998) 354.
[112] R. Konecny, D.J. Doren, Adsorption of BH3 on Si(1 0 0)-2 · 1, J. Phys. Chem. B 101 (1997) 10983.
[113] K.T. Queeney, Y.J. Chabal, K. Raghavachari, Role of interdimer interactions in NH3 dissociation
on Si(1 0 0)-2 · 1, Phys. Rev. Lett. 86 (2001) 1046.
[114] A.J. Carman, L. Zhang, J.L. Liswood, S.M. Casey, Methylamine adsorption on and desorption
from Si(1 0 0), J. Phys. Chem. B 107 (2003) 5491.
[115] H.A. Bent, An appraisal of valence-bond structures and hybridization in compounds of the first-row
elements, Chem. Rev. 61 (1961) 275.
[116] M. Mysinger, J. Han, C.M. Musgrave, First principles study of phosphine adsorption and
decomposition on Si(1 0 0)-2 · 1, in preparation.
[117] I. Fleming, Pericyclic Reactions, Oxford University Press, Oxford, 1999.
[118] K.N. Houk, Y. Li, J.D. Evanseck, Transition structures of hydrocarbon pericyclic reactions, Angew.
Chem. Int. Ed. 31 (1992) 682.
[119] R.B. Woodward, R. Hoffmann, The Conservation of Orbital Symmetry, Academic Press, New
York, 1970.
[120] M.P. Casaletto, R. Zanoni, M. Carbone, M.N. Piancastelli, L. Aballe, K. Weiss, K. Horn, Ethylene
adsorption on Si(1 0 0)-2 · 1: a high-resolution photoemission study, Phys. Rev. B 62 (2000)
17128.
[121] L. Clemen, R.M. Wallace, P.A. Taylor, M.J. Dresser, W.J. Choyke, W.H. Weinberg, J.T. Yates Jr,
Adsorption and thermal behavior of ethylene on Si(1 0 0)-2 · 1, Surf. Sci. 268 (1992) 205.
[122] C. Huang, W. Widdra, W.H. Weinberg, Adsorption of ethylene on the Si(1 0 0)-2 · 1 surface, Surf.
Sci. 315 (1994) L953.
[123] W. Widdra, C. Huang, W.H. Weinberg, Adsorption of ethylene on the Si(1 0 0)-2 · 1 surface: reply,
Surf. Sci. 329 (1995) 295.
[124] A.J. Mayne, A.R. Avery, J. Knall, T.S. Jones, G.A.D. Briggs, W.H. Weinberg, An STM study of the
chemisorption of C2 H4 on Si(0 0 1)-2 · 1, Surf. Sci. 284 (1993) 247.
[125] R. Konecny, D.J. Doren, Cycloaddition reactions of unsaturated hydrocarbons on the Si(1 0 0)-2 · 1
surface: theoretical predictions, Surf. Sci. 417 (1998) 169.
[126] M.J. Bozack, W.J. Choyke, L. Muehlhoff, J.T. Yates Jr, Defect-enhanced and electron-enhanced
chemistry at silicon surfaces: reactivity and thermal desorption of propylene on Si(1 0 0)-2 · 1, Surf.
Sci. 176 (1986) 547.
[127] B.I. Craig, A theoretical study of the structures of propylene adsorbed on the Si(1 0 0)-2 · 1 surface,
Surf. Sci. 298 (1993) 87.
[128] M. Kiskinova, J.T. Yates Jr, Observation of steric conformational effects in hydrocarbon adsorption
and decomposition: cis-butene-2 and trans-butene-2 on Si(1 0 0)-2 · 1, Surf. Sci. 325 (1995) 1.
[129] G.P. Lopinski, D.J. Moffatt, D.D. Wayner, R.A. Wolkow, Determination of the absolute chirality
of individual adsorbed molecules using the scanning tunneling microscope, Nature 392 (1998) 909.
[130] H.B. Liu, R.J. Hamers, Stereoselectivity in molecule-surface reactions: adsorption of ethylene on the
silicon(0 0 1) surface, J. Am. Chem. Soc. 119 (1997) 7593.
[131] Q. Liu, R. Hoffmann, The bare and acetylene chemisorbed Si(0 0 1) surface and the mechanism of
acetylene chemisorption, J. Am. Chem. Soc. 117 (1995) 4082.
[132] G.P. Lopinski, D.J. Moffatt, D.D.M. Wayner, R.A. Wolkow, How stereoselective are alkene
addition reactions on Si(1 0 0)?, J. Am. Chem. Soc. 122 (2000) 3548.
[133] J.S. Hovis, R.J. Hamers, Structure and bonding of ordered organic monolayers of 1,5-cyclooct-
adiene on the silicon(0 0 1) surface, J. Phys. Chem. B 101 (1997) 9581.
[134] J.S. Hovis, H. Liu, R.J. Hamers, Scanning tunneling microscopy of cyclic unsaturated organic
molecules on Si(0 0 1), Appl. Phys. A 66 (1998) S553.
[135] K. Hamaguchi, S. Machida, K. Mukai, Y. Yamashita, J. Yoshinobu, Adsorption state of 1,4-
cyclohexadiene on Si(1 0 0)-2 · 1, Phys. Rev. B 62 (2000) 7576.
[136] J.H. Cho, D.H. Oh, K.S. Kim, L. Kleinman, Adsorption structure of 1,4-cyclohexadiene on Si(0 0 1),
J. Chem. Phys. 116 (2002) 3800.
[137] J.S. Hovis, R.J. Hamers, Structure and bonding of ordered organic monolayers of 1,3,5,7-
cyclooctatetraene on the Si(0 0 1) surface: surface cycloaddition chemistry of an antiaromatic
molecule, J. Phys. Chem. B 102 (1998) 687.
[138] G.C. Abeln, S.Y. Lee, J.W. Lyding, D.S. Thompson, J.S. Moore, Nanopatterning organic mono-
layers on Si(1 0 0) by selective chemisorption of norbornadiene, Appl. Phys. Lett. 70 (1997) 2747.
[139] F. Rochet, F. Bournel, J.J. Gallet, G. Dufour, L. Lozzi, F. Sirotti, Electronic structure of 1,3,5,7-
cyclooctatetraene chemisorbed on Si(0 0 1)-2 · 1 at 300 K studied by PES, NEXAFS, and resonant
valence band spectroscopy, J. Phys. Chem. B 106 (2002) 4967.
[140] P. Lal, A.V. Teplyakov, Y. Noah, M.J. Kong, G.T. Wang, S.F. Bent, Adsorption of ethylene on the
Ge(1 0 0)-2 · 1 surface: coverage and time dependent behavior, J. Chem. Phys. 110 (1999) 10545.
[141] R.J. Hamers, J.S. Hovis, C.M. Greenlief, D.F. Padowitz, Scanning tunneling microscopy of organic
molecules and monolayers on silicon and germanium (0 0 1) surfaces, Jpn. J. Appl. Phys. 38 (1999)
3879.
[142] M. Toscano, Theoretical study of molecular and dissociative adsorption of ethylene on silicon and
germanium(1 0 0) surfaces, Surf. Sci. 251 (1991) 894.
[143] M. Nishijima, J. Yoshinobu, H. Tsuda, M. Onchi, The adsorption and thermal decomposition of
acetylene on Si(1 0 0) and vicinal Si(1 0 0) 9-degrees, Surf. Sci. 192 (1987) 383.
[144] C. Huang, W. Widdra, X.S. Wang, W.H. Weinberg, Adsorption of acetylene on the Si(1 0 0)-2 · 1
surface, J. Vac. Sci. Technol. A 11 (1993) 2250.
[145] L. Li, C. Tindall, O. Takaoka, Y. Hasegawa, T. Sakurai, STM study of C2 H2 adsorption on Si(0 0 1),
Phys. Rev. B 56 (1997) 4648.
[146] J.H. Cho, L. Kleinman, C.T. Chan, K.S. Kim, First principles study of the adsorption of C2 H2 and
C2 H4 on Si(1 0 0), Phys. Rev. B 6307 (2001) 3306.
[147] A.J. Dyson, P.V. Smith, A molecular dynamics study of the chemisorption of C2 H2 and CH3 on the
Si(0 0 1)-2 · 1 surface, Surf. Sci. 375 (1997) 45.
[148] X. Lu, M.C. Lin, Bonding configurations of acetylene adsorbed on the Si(1 0 0)-2 · 1 surface
predicted by density functional cluster model calculations, Phys. Chem. Chem. Phys. 2 (2000) 4213.
[149] W.A. Hofer, A.J. Fisher, R.A. Wolkow, Adsorption sites and STM images of C2 H2 on Si(1 0 0): a
first principles study, Surf. Sci. 475 (2001) 83.
[150] R. Miotto, A.C. Ferraz, G.P. Srivastava, Acetylene adsorption on the Si(0 0 1) surface, Phys. Rev. B
6507 (2002) 5401.
[151] W. Kim, H. Kim, G. Lee, J. Chung, S.Y. You, Y.K. Hong, J.Y. Koo, Acetylene molecules on the
Si(0 0 1) surface: room temperature adsorption and structural modification upon annealing, Surf.
Sci. 514 (2002) 376.
[152] S. Mezhenny, I. Lyubinetsky, W.J. Choyke, R.A. Wolkow, J.T. Yates Jr, Multiple bonding
structures of C2 H2 chemisorbed on Si(1 0 0), Chem. Phys. Lett. 344 (2001) 7.
[153] W. Kim, H. Kim, G. Lee, Y.K. Hong, K. Lee, C. Hwang, D.H. Kim, J.Y. Koo, Initial adsorption
configurations of acetylene molecules on the Si(0 0 1) surface, Phys. Rev. B 6419 (2001) 3313.
[154] W. Widdra, C. Huang, S.I. Yi, W.H. Weinberg, Coadsorption of hydrogen with ethylene and
acetylene on Si(1 0 0)-2 · 1, J. Chem. Phys. 105 (1996) 5605.
[155] M. Toscano, N. Russo, Interaction of acetylene with Si and Ge (1 0 0) surfaces: a theoretical study,
J. Mol. Catal. 55 (1989) 101.
[156] R. Miotto, A.C. Ferraz, A theoretical study of C2 H2 adsorption on the Ge(0 0 1) surface, Surf. Sci.
513 (2002) 422.
[157] J.L. Armstrong, E.D. Pylant, J.M. White, Thermal chemistry of biacetyl on Si(1 0 0), J. Vac. Sci.
Technol. A 16 (1998) 123.
[158] J.L. Armstrong, J.M. White, M. Langell, Thermal decomposition reactions of acetaldehyde and
acetone on Si(1 0 0), J. Vac. Sci. Technol. A 15 (1997) 1146.
[159] J.A. Barriocanal, D.J. Doren, Cycloaddition of carbonyl compounds on Si(1 0 0): new mecha-
nisms and approaches to selectivity for surface cycloaddition reactions, J. Am. Chem. Soc. 123
(2001) 7340.
[160] F. Tao, Z.H. Wang, M.H. Qiao, Q. Liu, W.S. Sim, G.Q. Xu, Covalent attachment of acetonitrile on
Si(1 0 0) through Si–C and Si–N linkages, J. Chem. Phys. 115 (2001) 8563.
[161] X. Lu, X. Xu, J.M. Wu, N.Q. Wang, Q. Zhang, Chemisorption of acetonitrile, pyridine, and
pyrazine on the Si(1 0 0)-2 · 1 surface: theoretical predictions, New J. Chem. 26 (2002) 160.
[162] F. Bournel, J. Gallet, S. Kubsky, G. Dufour, F. Rochet, M. Simeoni, F. Sirotti, Adsorption of
acetonitrile and acrylonitrile on Si(0 0 1)-2 · 1 at room temperature studied by synchrotron radiation
photoemission and NEXAFS spectroscopies, Surf. Sci. 513 (2002) 137.
[163] Y. Bu, L. Ma, M.C. Lin, Interaction of HCN/DCN with Si(1 0 0)-2 · 1, J. Phys. Chem. 97 (1993)
7081.
[164] F. Bacalzo-Gladden, D.G. Musaev, M.C. Lin, A model calculation for the isomerization and
decomposition of chemisorbed HCN on the Si(1 0 0)-2 · 1 surface, J. Chin. Chem. Soc-Taip. 46
(1999) 395.
[165] F. Bacalzo-Gladden, X. Lu, M.C. Lin, Adsorption , isomerization, and decomposition of HCN on
Si(1 0 0)-2 · 1: a computational study with a double-dimer cluster model, J. Phys. Chem. B 105 (2001)
4368.
[166] M.D. Ellison, J.S. Hovis, H.B. Liu, R.J. Hamers, Cycloaddition chemistry on silicon(0 0 1) surfaces:
the adsorption of azo-tert-butane, J. Phys. Chem. B 102 (1998) 8510.
[167] R. Konecny, D.J. Doren, Theoretical prediction of a facile Diels–Alder reaction on the Si(1 0 0)-2 · 1
surface, J. Am. Chem. Soc. 119 (1997) 11098.
[168] A.V. Teplyakov, M.J. Kong, S.F. Bent, Vibrational spectroscopic studies of Diels–Alder reactions
with the Si(1 0 0)-2 · 1 surface as a dienophile, J. Am. Chem. Soc. 119 (1997) 11100.
[169] J.S. Hovis, H.B. Liu, R.J. Hamers, Cycloaddition chemistry of 1,3-dienes on the silicon(0 0 1)
surface: competition between [4+2] reactions and [2+2] reactions, J. Phys. Chem. B 102 (1998) 6873.
[170] D.J. Doren, Private communication.
[171] M.J. Kong, A.V. Teplyakov, J. Jagmohan, J.G. Lyubovitsky, C. Mui, S.F. Bent, Interaction of C6
cyclic hydrocarbons with a Si(1 0 0)-2 · 1 surface: adsorption and hydrogenation reactions, J. Phys.
Chem. B 104 (2000) 3000.
[172] G.T. Wang, C. Mui, C.B. Musgrave, S.F. Bent, Cycloaddition of cyclopentadiene and dicyclopent-
adiene on Si(1 0 0)-2 · 1: comparison of monomer and dimer adsorption, J. Phys. Chem. B 103 (1999)
6803.
[173] S.W. Lee, L.N. Nelen, H. Ihm, T. Scoggins, C.M. Greenlief, Reaction of 1,3-cyclohexadiene with the
Ge(1 0 0) surface, Surf. Sci. 410 (1998) L773.
[174] M.D. Ellison, R.J. Hamers, Adsorption of phenyl isothiocyanate on Si(0 0 1): a 1,2-dipolar surface
addition reaction, J. Phys. Chem. B 103 (1999) 6243.
[175] J.A. Barriocanal, D.J. Doren, Reactions of nitromethane on Si(1 0 0): first-principles predictions,
J. Phys. Chem. B 104 (2000) 12269.
[176] J.A. Barriocanal, D.J. Doren, 1,3-Dipolar cycloadditions on Si(1 0 0)-2 · 1: theoretical studies of
novel attachment chemistry for organic monolayers, J. Vac. Sci. Technol. A 18 (2000) 1959.
[177] R.J. Hamers, Private communication.
[178] M.P. Schwartz, M.D. Ellison, S.K. Coulter, J.S. Hovis, R.J. Hamers, Interaction of p-conjugated
organic molecules with p-bonded semiconductor surfaces: structure, selectivity, and mechanistic
implications, J. Am. Chem. Soc. 122 (2000) 8529.
[179] L.A. Fang, J.M. Liu, S. Coulter, X.P. Cao, M.P. Schwartz, C. Hacker, R.J. Hamers, Formation of
p-conjugated molecular arrays on silicon (0 0 1) surfaces by heteroatomic Diels–Alder chemistry,
Surf. Sci. 514 (2002) 362.
[180] X. Lu, X. Xu, N.Q. Wang, Q. Zhang, M.C. Lin, Chemisorption and decomposition of thiophene
and furan on the Si(1 0 0)-2 · 1 surface: a quantum chemical study, J. Phys. Chem. B 105 (2001)
10069.
[181] U. Birkenheuer, U. Gutdeutsch, N. Rosch, Geometrical structure of benzene absorbed on Si(0 0 1),
Surf. Sci. 409 (1998) 213.
[182] B. Borovsky, M. Krueger, E. Ganz, Metastable adsorption of benzene on the Si(0 0 1)surface, Phys.
Rev. B 57 (1998) R4269.
[183] B.I. Craig, A theoretical examination of the chemisorption of benzene on Si(1 0 0)-2 · 1, Surf. Sci.
280 (1993) L279.
[184] S. Gokhale, P. Trischberger, D. Menzel, W. Widdra, H. Droge, H.P. Steinruck, U. Birkenheuer,
U. Gutdeutsch, N. Rosch, Electronic structure of benzene adsorbed on single-domain Si(0 0 1)-2 · 1:
a combined experimental and theoretical study, J. Chem. Phys. 108 (1998) 5554.
[185] G.P. Lopinski, T.M. Fortier, D.J. Moffatt, R.A. Wolkow, Multiple bonding geometries and binding
state conversion of benzene/Si(1 0 0), J. Vac. Sci. Technol. A 16 (1998) 1037.
[186] G.P. Lopinski, D.J. Moffatt, R.A. Wolkow, Benzene/Si(1 0 0): metastable chemisorption and binding
state conversion, Chem. Phys. Lett. 282 (1998) 305.
[187] M.J. Kong, A.V. Teplyakov, J.G. Lyubovitsky, S.F. Bent, NEXAFS studies of adsorption of
benzene on Si(1 0 0)-2 · 1, Surf. Sci. 411 (1998) 286.
[188] K.W. Self, R.I. Pelzel, J.H.G. Owen, C. Yan, W. Widdra, W.H. Weinberg, Scanning tun-
neling microscopy study of benzene adsorption on Si(1 0 0)-2 · 1, J. Vac. Sci. Technol. A 16 (1998)
1031.
[189] Y. Taguchi, Y. Ohta, T. Katsumi, K. Ichikawa, O. Aita, Photoemission study of benzene adsorbed
on Si surfaces, J. Electron. Spectrosc. 88 (1998) 671.
[190] R.A. Wolkow, G.P. Lopinski, D.J. Moffatt, Resolving organic molecule silicon scanning tunneling
microscopy features with molecular orbital methods, Surf. Sci. 416 (1998) L1107.
[191] W.A. Hofer, A.J. Fisher, G.P. Lopinski, R.A. Wolkow, Benzene on silicon: combining STM
experiments with first principles studies, Surf. Sci. 482 (2001) 1181.
[192] W.A. Hofer, A.J. Fisher, G.P. Lopinski, R.A. Wolkow, Adsorption of benzene on Si(1 0 0)-2 · 1:
adsorption energies and STM image analysis by ab initio methods, Phys. Rev. B 6308 (2001) 5314.
[193] P.L. Silvestrelli, F. Ancilotto, F. Toigo, Adsorption of benzene on Si(1 0 0) from first principles,
Phys. Rev. B 62 (2000) 1596.
[194] M. Staufer, U. Birkenheuer, T. Belling, F. Nortemann, N. Rosch, W. Widdra, K.L. Kostov,
T. Moritz, D. Menzel, The vibrational structure of benzene adsorbed on Si(0 0 1), J. Chem. Phys. 112
(2000) 2498.
[195] S. Alavi, R. Rousseau, T. Seideman, Toward control of surface reactions with a scanning tunneling
microscope: structure and dynamics of benzene desorption from a silicon surface, J. Chem. Phys. 113
(2000) 4412.
[196] A. Fink, D. Menzel, W. Widdra, Symmetry and electronic structure of benzene adsorbed on single-
domain Ge(1 0 0)-2 · 1 and Ge/Si(1 0 0)-2 · 1, J. Phys. Chem. B 105 (2001) 3828.
[197] A.V. Teplyakov, M.J. Kong, S.F. Bent, Diels–Alder reactions of butadienes with the Si(1 0 0)-2 · 1
surface as a dienophile: vibrational spectroscopy thermal desorption and near-edge X-ray absorption
fine structure studies, J. Chem. Phys. 108 (1998) 4599.
[198] C.H. Choi, M.S. Gordon, Cycloaddition reactions of 1,3-cyclohexadiene on the silicon(0 0 1) surface,
J. Am. Chem. Soc. 121 (1999) 11311.
[199] S.K. Coulter, J.S. Hovis, M.D. Ellison, R.J. Hamers, Reactions of substituted aromatic
hydrocarbons with the Si(0 0 1) surface, J. Vac. Sci. Technol. A 18 (2000) 1965.
[200] B. Borovsky, M. Krueger, E. Ganz, Scanning tunneling microscopy study of the adsorption of
toluene on Si(0 0 1), J. Vac. Sci. Technol. B 17 (1999) 7.
[201] T. Bitzer, T. Alkunshalie, N.V. Richardson, An HREELS investigation of the adsorption of benzoic
acid and aniline on Si(1 0 0)-2 · 1, Surf. Sci. 368 (1996) 202.
[202] T. Kugler, U. Thibaut, M. Abraham, G. Folkers, W. G€ opel, Chemically modified semiconductor
surfaces: 1,4-phenylenediamine on Si(1 0 0), Surf. Sci. 260 (1992) 64.
[203] R.M. Rummel, C. Ziegler, Room temperature adsorption of aniline (C6 H5 NH2 ) on Si(1 0 0)-2 · 1
observed with scanning tunneling microscopy, Surf. Sci. 418 (1998) 303.
[204] F. Tao, Z.H. Wang, G.Q. Xu, Formation of a benzoimine-like conjugated structure through the
adsorption of benzonitrile on Si(1 0 0), J. Phys. Chem. B 106 (2002) 3557.
[205] S.K. Coulter, M.P. Schwartz, R.J. Hamers, Sulfur atoms as tethers for selective attachment of
aromatic molecules to silicon (0 0 1) surfaces, J. Phys. Chem. B 105 (2001) 3079.
[206] M.H. Qiao, F. Tao, Y. Cao, Z.H. Li, W.L. Dai, J.F. Deng, G.Q. Xu, Cycloaddition reaction of
furan with Si(1 0 0)-2 · 1, J. Chem. Phys. 114 (2001) 2766.
[207] X. Lu, M.C. Lin, X. Xu, N.Q. Wang, Q. Zhang, Theoretical study of [4 + 2] cycloadditions of some
6- and 5-member ring aromatic compounds on the Si(0 0 1)-2 · 1 surface: correlation between binding
energy and resonance energy, Phys. Chem. Commun. (2001) 1.
[208] M.H. Qiao, Y. Cao, F. Tao, Q. Liu, J.F. Deng, G.Q. Xu, Electronic and vibrational properties of
thiophene on Si(1 0 0), J. Phys. Chem. B 104 (2000) 11211.
[209] H.D. Jeong, Y.S. Lee, S. Kim, Adsorbed state of thiophene on Si(1 0 0)-2 · 1 surface studied by
electron spectroscopic techniques and semiempirical methods, J. Chem. Phys. 105 (1996) 5200.
[210] G.B.D. Rousseau, V. Dhanak, M. Kadodwala, Photoemission studies of the surface reactivity of
thiophene on Si(1 0 0)-2 · 1, Si(1 1 1)-7 · 7, and Ge(1 0 0)-2 · 1, Surf. Sci. 494 (2001) 251.
[211] M.H. Qiao, Y. Cao, J.F. Deng, G.Q. Xu, Formation of covalent Si–N linkages on pyrrole
functionalized Si(1 0 0)-2 · 1, Chem. Phys. Lett. 325 (2000) 508.
[212] H.B. Luo, M.C. Lin, A computational study of the mechanism for self-assembly of N-pyrrolyl
radicals on Si(1 0 0)-2 · 1, Chem. Phys. Lett. 343 (2001) 219.
[213] Y. Bu, M.C. Lin, Surface chemistry of s-triazine on Si(1 0 0)-2 · 1, J. Phys. Chem. 98 (1994)
7871.
[214] X. Lu, M.C. Lin, X. Xu, N.Q. Wang, Q.N. Zhang, Diels–Alder addition of some 6- and 5-member
ring aromatic compounds on the Si(0 0 1)-2 · 1 surface: dependence of the binding energy on the
resonance energy of the aromatic compounds, Sci. China Ser. B 44 (2001) 473.
[215] T. Bitzer, T. Dittrich, T. Rada, N.V. Richardson, The electronic properties at the maleic anhydride/
Si(1 0 0)-2 · 1 interface, Chem. Phys. Lett. 331 (2000) 433.
[216] A. Lopez, T. Bitzer, T. Heller, N.V. Richardson, Adsorption of maleic anhydride on Si(1 0 0)-2 · 1,
Surf. Sci. 477 (2001) 219.
[217] W.A. Hofer, A.J. Fisher, T. Bitzer, T. Rada, N.V. Richardson, Tuning in on single molecular states:
adsorption sites and STM images of maleic anhydride on Si(1 0 0), Chem. Phys. Lett. 355 (2002) 347.
[218] T. Bitzer, T. Rada, N.V. Richardson, Inhibition of the [2 + 2] cycloaddition: maleic anhydride on
Si(1 0 0)-2 · 1, J. Phys. Chem. B 105 (2001) 4535.
[219] A. Lopez, T. Heller, T. Bitzer, N.V. Richardson, A vibrational study of the adsorption of glycine on
clean and Na modified Si(1 0 0)-2 · 1 surfaces, Chem. Phys. 277 (2002) 1.
[220] F. Tao, W.S. Sim, G.Q. Xu, M.H. Qiao, Selective binding of the cyano group in acrylonitrile
adsorption on Si(1 0 0)-2 · 1, J. Am. Chem. Soc. 123 (2001) 9397.
[221] C.H. Choi, M.S. Gordon, Cycloaddition reactions of acrylonitrile on the Si(1 0 0)-2 · 1 surface,
J. Am. Chem. Soc. 124 (2002) 6162.
[222] M.P. Schwartz, R.J. Hamers, The Role of Pi-conjugation in attachment of organic molecules to the
silicon (0 0 1) surface, Surf. Sci. 515 (2002) 75.
[223] A. Lopez, Q. Chen, N.V. Richardson, Combined STM, HREELS, and ab initio study of the
adsorption of uracil on Si(1 0 0)-2 1, Surf. Interf. Anal. 33 (2002) 441.
[224] A. Lopez, T. Bitzer, T. Heller, N.V. Richardson, Functional group selectivity in adsorption of
4-aminobenzoic acid on clean and Na modified Si(1 0 0)-2 · 1 surfaces, Surf. Sci. 480 (2001) 65.
[225] C.M. Greenlief, Reactions of organics, Telluride Workshop on Semiconductor Surface Chemistry,
1998.
[226] T. Bitzer, N.V. Richardson, Demonstration of an imide coupling reaction on a Si(1 0 0)-2 · 1 surface
by molecular layer deposition, Appl. Phys. Lett. 71 (1997) 662.
[227] C.G. Bochet, Photolabile protecting groups and linkers, J. Chem. Soc. Perk. T. 1 (2002) 125.
[228] D. Orain, J. Ellard, M. Bradley, Protecting groups in solid-phase organic synthesis, J. Comb. Chem.
4 (2002) 1.
[229] M. Schelhaas, H. Waldmann, Protecting group strategies in organic synthesis, Angew. Chem. Int.
Ed. 35 (1996) 2056.
[230] K. Yamaguchi, T. Kitabatake, M. Izawa, T. Fujiwara, H. Nishimura, T. Futami, Novel silane
coupling agents containing a photolabile 2-nitrobenzyl ester for introduction of a carboxy group on
the surface of silica gel, Chem. Lett. (2000) 228.
[231] J.W. Lyding, G.C. Abeln, T.C. Shen, C. Wang, J.R. Tucker, Nanometer-scale patterning and
oxidation of silicon surfaces with an ultrahigh-vacuum scanning tunneling microscope, J. Vac. Sci.
Technol. B 12 (1994) 3735.
[232] J.W. Lyding, T.C. Shen, J.S. Hubacek, J.R. Tucker, G.C. Abeln, Nanoscale patterning and
oxidation of H-passivated Si(1 0 0)-2 · 1 surfaces with an ultrahigh-vacuum scanning tunneling
microscope, Appl. Phys. Lett. 64 (1994) 2010.
[233] J.L. OÕBrien, S.R. Schofield, M.Y. Simmons, R.G. Clark, A.S. Dzurak, N.J. Curson, B.E. Kane,
N.S. McAlpine, M.E. Hawley, G.W. Brown, Towards the fabrication of phosphorus qubits for a
silicon quantum computer, Phys. Rev. B 6416 (2001) 1401.
[234] M. Bale, R.E. Palmer, Microfabrication of silicon tip structures for multiple-probe scanning
tunneling microscopy, J. Vac. Sci. Technol. B 20 (2002) 364.
[235] S.C. Minne, J.D. Adams, G. Yaralioglu, S.R. Manalis, A. Atalar, C.F. Quate, Centimeter scale
atomic force microscope imaging and lithography, Appl. Phys. Lett. 73 (1998) 1742.
[236] P. Vettiger, M. Despont, U. Drechsler, U. Durig, W. Haberle, M.I. Lutwyche, H.E. Rothuizen,
R. Stutz, R. Widmer, G.K. Binnig, The ‘‘millipede’’: more than one thousand tips for future AFM
data storage, IBM J. Res. Dev. 44 (2000) 323.
[237] P. Kruse, E.R. Johnson, G.A. DiLabio, R.A. Wolkow, Patterning of vinylferrocene on H–Si(1 0 0)
via self-directed growth of molecular lines and STM-induced decomposition, Nano Lett. 2 (2002)
807.

Filler 2003

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Filler 2003

Uploaded by

Copyright:

Available Formats

Progress in Surface Science 73 (2003) 1–56

Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA

Notes added during proof. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

It was considered landmark in the 1960Õs if a single transistor could be patterned

fundamental principles that govern pathway competition and product selectivity. As

3.1. Group-IV semiconductor surfaces

3.2. Structural theory

(a) Bonding functional groups

(b) Functional groups with non-bonding electrons

3.3. Competition, selectivity, and reaction control

Nucleophilic/electrophilic reactions are frequently observed in solution phase

4.1. Dative bonding and proton transfer

mass spectrometry (SIMS) [77,78], and temperature programmed desorption (TPD)

4.2. Donor–acceptor complexes

4.3. Non-local interactions

calization results in a binding energy for molecularly adsorbed ammonia of 26

4.4. Reactivity trends

Pericyclic reactions were originally proposed by Woodward and Hoﬀmann in

Of the diﬀerent types of pericyclic reactions, cycloadditions are widely used in

(a) (b) (c)

cycloadditions. Even though [2 + 2] cycloaddition reactions are classically symmetry

(a) Si(100)-2x1: [2+2] C=O Cycloaddition

(b) Ge(100)-2x1: α -CH Dissociation

5.2. [4 + 2] cycloaddition (Diels–Alder)

vided evidence for additional surface species at room temperature, identiﬁcation of

5.3. Dipolar addition

Two theoretical investigations by Barriocanal and Doren suggest that 1,3-dipoles

5.4. Group transfer (a-CH dissociation)

reaction of acetone is under kinetic control on Si(1 0 0)-2 · 1 and thermodynamic

The adsorption of aromatic compounds on semiconductor surfaces has received

Benzene Pyrrole Furan Thiophene

Styrene Toluene Xylene

Aniline Benzonitrile Benzoic Acid

It is well-known that the addition of substituent groups on an aromatic molecule

The concepts of aromaticity and resonance stabilization developed above for

(a) Proton Transfer Products

(b) Cycloaddition Products

6.4. Reactivity trends

Molecular Reactivity Reactivity on Semiconductor Surfaces

Now that the basic principles of the reactions of organic molecules on

[63]. On this surface, the [4 + 2] cycloaddition product through the conjugated

Fig. 27. (a) Keto and (b) enol tautomers of uracil.

A number of challenges toward successful vacuum functionalization still exist and

group. Glycine adsorbed on Si(1 0 0)-2 · 1 at room temperature results in HREELS

Notes added during proof

You might also like