ADSORPTION STATES AND SITE CONVERSIONS
OF PHENYLACETYLENE ON Si(100)2� 1
CALCULATED BY DFT
MARILENA CARBONE*,‡ and RUGGERO CAMINITI†
*Department Chemical Science and Technologies
University Tor Vergata Via della Ricerca Scienti¯ca
1-00133 Roma, Italy†Department Chemistry, University La Sapienza
P.le A. Moro, 5-00185 Roma, Italy‡[email protected]
Received 14 June 2011Accepted 12 March 2012
The adsorption on Si(100)2� 1 of PhenylAcetilene (PA), a bifunctional molecule with a phenyl
ring and a triple bond, may occur through each group, selectively, or both functional groups
simultaneously. The most favorable adsorption sites upon adsorption were calculated by DFT.Furthermore, several energy barriers were calculated: The ones connecting the physisorbed to
the chemisorbed states, as well as the interconversion barriers of di®erent chemisorbed states.
The conversion of physisorbed-to-chemisorbed states has barriers of 0.11�0.19 eV. The barriersof sites inter-conversions are all higher (1.11�1.36 eV) and suggest a di±cult post-chemisorp-
tion surface rearrangement.
Keywords: Silicon; adsorption; bi-functionality; DFT.
1. Introduction
The adsorption of bi- or multi-functional molecules on Si(100)2� 1 provides the tool
to generate a homogeneous molecular layer, though preserving a functional group,
either for further reactions or providing charge-transfer capabilities1 or °uorescence.2
In Si-based devices with a uniform layer of organic molecules as well as in single-
molecule devices, the key of the device fabrication is the correct arrangement of the
functional group(s). In other words, it is important to be capable of controlling the
speci¯c conditions of device production, both in terms of selective adsorption and/or
post-adsorption manipulation.
Si(100)2� 1 may act as an adsorption template. From a morphological point of
view it is made of dimers which may direct the self-organization of molecules, due to
the presence of a � bond, that gives rise to a cycloadditions.
1089
Journal of Theoretical and Computational Chemistry
Vol. 11, No. 5 (2012) 1089�1099
#.c World Scienti¯c Publishing CompanyDOI: 10.1142/S0219633612500721
Monolayers of �-conjugated organic molecules on semiconductors are of special
interest as they have the ability to function as electrically active interfaces at the
metal�molecule�semiconductor junctions.3 They possess very promising optoelec-
tronic properties such as anisotropic electrical conductivity, high charge mobility,
electro-optical switching behavior, etc.4�6 Phenylacetylene (PA) is a prototypical
alkyne that has two chemically active sites: One is the acetylene triple bond and
another is �-conjugation of benzene ring. As a result, this molecule, such as phenol7
can undergo di®erent adsorption con¯gurations depending on which of these sites
takes part in chemical bonding with the surface atoms of silicon.8 If the adsorption
occurs through the acetylene group in a [2þ 2] addition, i.e. a dimerization of �
bonds into cyclobutane, then the rich �-conjugation of benzene may exhibit inter-
esting optoelectronic properties and it can also be a good functional site for further
attachment of organic molecules.
The interaction with the surface involving (also) a phenyl ring, instead, would be
associated to a loss of aromaticity and, because of this, be less favorable than a [2þ 2]
addition.
At variance with this, STM observations of PA on Si(100)2� 1 indicate two
di®erent prevalent adsorption con¯gurations,9 one of which involving a [2þ 2]
addition of the triple bond and the other one also the phenyl ring.
In this paper we present a DFT study of PA adsorption on Si(100)2� 1 aiming at
identifying the most stable adsorption sites, both physi- and chemisorbed as well as
possible pathways which may lead to di®erent adsorption con¯gurations. Further-
more, the likelihood of post-adsorption manipulation is evaluated in terms of energy
barrier for inter-conversion between adsorption sites. We performed a series of
geometry optimization routines and connected the most representative outcomes as
starting points for barrier calculations by nudged elastic bands (NEBs).
We found that the [2þ 2] cycloaddition yields the most stable chemisorption state
(on top) and that adsorption con¯gurations which involve both functional groups
simultaneously have a smaller adsorption energy (butterflyþ U). The adsorption
con¯gurations which occur through the phenyl ring-only are, instead, far less
favorable. Physisorbed states, precursors of the most stable chemisorbed states, were
also singled out. We found that the physisorbed states, which are most likely to end
up in the butter°y and on top con¯guration have comparable energy barriers. As for
the inter-conversions between con¯gurations we found relatively high barriers, which
make it di±cult to envisage the post-adsorption manipulation for the creation of a
uniform Phenyl Acetylene layer on Si(100)2� 1.
2. Method
All electronic structure calculations were performed using periodic density functional
theory and the ultrasoft Vanderbilt pseudopotential method10 the BLYP
implementation11,12 and expanding Kohn�Sham orbitals on a plane wave basis set.
The calculations have been carried out using norm-conserving Trouiller�Martins
1090 M. Carbone & R. Caminiti
pseudopotentials.13 We adopted the CPMD code14 for the geometry optimizations
and Quantum Espresso for probing a reaction pathway by NEB,15 after making sure
we obtained the same adsorption energies for the selected systems with the two codes
using the same functionals and pseudopotentials. Kinetic-energy cuto®s for wave-
functions was 816.2 eV (60 Ryd.) This converges the total energy to within 0.01 eV/
atom. p(4� 2) supercell of Si(100) was used to model the adsorption of PA on silicon
surface. This corresponds to a cluster of Si190H16 with 10 layers of Si atoms and 8
surface dimers and a monolayer of hydrogen atoms to saturate the dangling bonds on
the lower side of the slab. The surface size allowed the optimization of the PA,
regardless of the adsorbate position with respect to the surface. The vacuum region
between supercells was about 14�A in the [001] direction. All the atoms except the
bottom Si and H layers were allowed to relax. It was veri¯ed that, by starting with
the unreconstructed, clean Si(100) surface, the optimization procedure correctly
reproduces asymmetric surface dimers, with a dimer bond length and a buckling
angle in good agreement with previous highly converged ab-initio calculations.16
The sampling for the Brillouin zone includes a set of eight special k-points. The
minimum energy reaction path is mapped out with the climbing image nudged elastic
band (CI-NEB) method by optimizing the inserted nine images between the given
initial state and the given ¯nal state. In one case, i.e. for the transition from the inter-
Dimers to the on top con¯guration, 15 images were inserted, due to the presence of
two transition states. The imaginary vibrational frequency of each transition state is
calculated using the dynamic matrix method17 to further con¯rm the saddle point
along each reaction pathway.
For the adsorption energy (AE), we follow the convention that an exothermic
adsorption process produces a positive value for its adsorption energy.
3. Results and Discussion
3.1. Stability of the con¯gurations
Since PA is a bifunctional molecule, it may react with the silicon surface through
either the triple bond or with the phenyl ring or both functional groups simul-
taneously. Geometry optimizations were performed on all three types of adsorption
con¯gurations. In Fig. 1(a) the PA is sketched and the carbon atoms are numbered,
in order to facilitate further presentations. In Fig. 1(b) the surface dimers are labelled
with letters, to distinguish their position.
The outcomes of the geometry optimizations are reported in Fig. 2 and the cor-
responding adsorption energies in Table 1. Bond length and angles are reported in
Table 2.
The selective adsorption of PA through the � system has been evaluated for
di®erent con¯gurations, i.e. with the triple bond on top of a silicon dimer or between
dimers of adjacent rows (Figs. 2(a) and 2(b)). Adsorption models where both
functional groups simultaneously interacting with the surface are sketched in
Figs. 2(d)�2(f). Finally, models where PA is selectively bonded through the phenyl
Adsorption States and Site Conversions of PhenylAcetylene 1091
ring are reported in Figs. 2(g) and 2(h). Along with them, two physisorbed states are
also represented, which are likely to be precursors of two of the chemisorbed states
(Figs. 2(j) and 2(k)). The adsorption through the acetylenic electrons on top of a
silicon dimer can be depicted as a [2þ 2] reaction process. The outcome, sketched in
Fig. 2(a) is the most energetically favorable con¯guration, with an AE of 2.69 eV.
Upon adsorption, the triple bond becomes more similar to a double one, with a
(a) (b)
Fig. 1. (a) A sketch of Phenyl Acetilene. The carbon atoms are numbered 1 through 8. C1 and C2 are the
acetylenic carbons, C3 through C8 the phenyl ones. (b) A sketch of the surface dimers. The silicon atoms
are labelled A through P.
(a) (b)
Fig. 2. Front and top view of Phenyl Acetilene adsorbed on Si(100)2� 1 in several con¯gurations: (a) On
top, (b) on top TP, (c) inter Dimers, (d) butter°y along the Dimers, (e) butterflyþD, (f) butterflyþ U ,(g) ½4þ 2� di� �, (h) vertical, (i) Phys 1, and (j)Phys 2. * indicates the down atoms next to the bond Si�C1
in the butterflyþD con¯guration, # marks the up ones, next to the bond Si�C1 in the butterflyþ U .
1092 M. Carbone & R. Caminiti
C1�C2 bond length of 1.37�A and C1�C2�C3 angle no longer linear, but of 108:8�,hence closer to an sp2 hybridization. Furthermore, the phenyl ring may be included
in the same plane of the double bond, or be tilted by 40�. This corresponds to an local
minimum with an AE of 2.53 eV and is indicated ad on top tilted Phenyl (TP).
(c) (d)
(e) (f)
(g) (h)
(i) (j)
Fig. 2. (Continued)
Adsorption States and Site Conversions of PhenylAcetylene 1093
Acetylene on top of a dimer of Si(100)2� 1 has a similar adsorption energy.
Silvestrelli et al.18 found in their paper an AE of 2.75 eV, which is to be compared to
2.69 eV we ¯nd for PA. The similarity of the adsorption energies of simple acetylene
and acetylene conjugated to a phenyl ring allows the depiction of the functional
groups as behaving like building blocks, with the triple bond interacting as decoupled
from the presence of the phenyl ring.
The AE decreases to AE¼ 1.48 eV, when of the acetylenic bond interacts with
dimers of adjacent rows (Inter Dimers con¯guration Fig. 2(c)). This can no longer be
considered a [2þ 2] adsorption, since the overall process requires the rearrangement
of two dimers (with associated energy loss), whilst the energy gain comes only from
the cyclobutene formation.
Interactions between the silicon surface and PA through both the phenyl ring and
the acetylenic electrons occur in the butter°y con¯gurations and involve 3 PA atoms:
C1, C4, and C7. We calculated the energy of three of such con¯gurations, i.e. with
the acetylenic moiety along dimers of the same row (butter°y AR or butter°y Along
the Raw) Fig. 2(c) or between dimer rows. The latter may be characterized by a bond
of the C1 atom with a \down" atom of a dimer, hence the C1-Silicon neighbors two
\up" atoms (butterfly þ U or butterfly next to \up"atoms) as in Fig. 2(d) or vice
versa, the bond may occur with an \up" atom, and, then, the C1-Silicon
bond neighbors two \down" atoms (butterfly þ D or next to \down" atoms) as in
Fig. 2(e). The adsorption energies are similar for the butter°y AR and butterflyþ U
con¯gurations: 1.57 and 1.51 eV, respectively. At variance with this, the formation of a
silicon�carbon bond, next to two \up" atoms leads to a decrease of the AE of the
butterflyþD to 1.24 eV.
In the addition process leading to the butter°ies con¯gurations, the acetylenic
bond deviates only slightly from the linearity, with a C1�C2�C3 angle of 177� for
the butter°ies con¯gurations across the dimers and 165� for the butter°y AR. This isalso re°ected in the formation of two consecutive double bonds (or allenic bonds),
with similar C1�C2 and C2�C3 bond distances at � 1.3�A (1.29 and 1.31�A for
Table 1. Phenylacetilene-Si(100)2� 1 adsorption energy in variouscon¯gurations.
Model Functional group involved Adsorption energy (eV)
On top Acetylene 2.69On top TP Acetylene 2.53
Butterflyþ U Acetylene þ Phenyl 1.57
Butter°y AR Acetylene þ Phenyl 1.51
Inter Dimers Acetylene 1.48½4þ 2� di� � Acetylene þ Phenyl 1.27
ButterflyþD Acetylene þ Phenyl 1.24
Vertical Phenyl 0.60
Phys 1 0.44Phys 2 0.40
1094 M. Carbone & R. Caminiti
Tab
le2.
Phenylacetilene-Si(100)2�1:Bon
ddistancesan
dan
gles.Theletterscorrespon
dto
thelabelsof
thesilicondim
ersas
reportedin
Fig.1(b).Cfollow
edby
number
isaPA
carbon
atom
asnumbered
inFig.1(a).
Bon
dBon
dBon
dBon
dBon
dTorsion
Mod
elBond
length/� A
Bond
length/� A
Bon
dlength/� A
Bon
dlength/� A
Bon
dlength/� A
Angle
Degrees/�
Angle
Degrees/�
angle
Degrees/�
Ontop
C1{H
1.919
C2{G
1.900
C1{C
21.369
C1{C
2{K
108.84
C1{C
2{C
3129.98
OntopTP
C1{H
1.913
C2{G
1.914
C1{C
21.364
C1{C
2{K
105.82
C1{C
2{C
3132.33
C1{C
2{C
3{C
844.21
ButterflyþU
C1{G
1.958
C8{F
1.981
C5{J
2.128
C1{C
21.286
C2{C
31.361
G{C
1{C
2120.50
C1{C
2{C
3177.02
Butter°yAR
C1{G
1.968
C7{K
1.980
C4{L
2.088
C1{C
21.287
C2{C
31.360
G{C
1{C
2108.20
C1{C
2{C
3164.48
InterDim
ers
C1{G
1.967
C2{F
1.955
C1{C
21.37
G{C
1{C
2130.35
C1{C
2{C
3121.45
½4þ2�di��
C1{G
1.918
C4{K
1.997
C1{C
21.319
C2{C
31.335
G{C
1{C
2118.51
C1{C
2{C
3164.49
ButterflyþD
C1{F
1.949
C8{G
1.992
C5{K
1.992
C1{C
21.291
C2{C
31.364
F{C
1{C
2122.21
C1{C
2{C
3177.40
Vertical
C4{J
1.972
C5{I
2.019
C4{C
51.579
J{C
4{C
5102.60
C1{C
2{C
3176.35
Phys
1C4{s
G3.510
Phys
2C4{G
3.420
Adsorption States and Site Conversions of PhenylAcetylene 1095
butterflyþ U , 1.29�A and 1.36�A for butter°y AR, and 1.32�A and 1.34�A for
butterflyþD, respectively).
Another [2þ 2] addition involving the phenyl ring yields a di-� bonded PA on a
silicon dimer through C4 and C5 (Fig. 2(f)), with an AE of 1.27 eV.
A lower AE is associated to the interaction of the PA exclusively through the
phenyl ring. This requires a [2þ 2] addition with breaking of the aromaticity and loss
of the conjugation energy. As a consequence, the AE of the vertical con¯guration
(Fig. 2(h)) is only 0.60 eV.
Two physisorbed states, Phys 1 and Phys 2 were singled out, in con¯gurations
which may be precursors of the on top and the butter°y þU con¯gurations. They are
at 3.5�A (Sidown�C2) and 3.4�A (Sidown�C1) away from the surface and adsorption
energies of 0.44 and 0.40 eV respectively. They are sketched in Figs. 2(i) and 2(j),
respectively.
3.2. Conversion pathways
In the calculation of the conversion pathways, we checked whether there is a bar-
rierless reaction pathway from vacuum to the each adsorption states. This condition
is veri¯ed and generally plotted in Fig. 3(a).
We have, then, calculated the barriers for the conversions of the physisorbed
states Phys 1 andPhys 2 into the on top and the butterflyþ U chemisorbed states,
respectively. Both additions of PA to the Si(100)2� 1 are facile. Similar to other
unsaturated hydrocarbons,19 PA can form an asymmetric � complex, Phys 1, with
the acetylene group interacting with the down Si atom, as shown in Fig. 2(i).
Starting from such � complexes, the barrier leading to the formation of intradimer
product is no more than 0.19 eV. The associated imaginary frequency (IF) is
�120 cm�1. The orientation of the phenyl ring makes only a small di®erence in the
barrier. The reaction goes through a simultaneous tightening of the Si \down"-C1
and Si \up"-C2 bonds (transition state) and then proceeds till completion.
The addition through both phenyl ring and acetylene bond starts from the
physisorbed structure Phys 2 and proceeds with a small barrier, even lower than for
the direct [2þ 2] addition. It requires a concerted interaction of PA with two silicon
dimers of di®erent rows (sketched in Fig. 3(a)). The major rearrangement occuring in
the transition state is the loss of planarity of the phenyl ring.
As noted already for styrene on Si(100)2� 1,19 the presence of the acetylenic bond
actually makes the phenyl ring more reactive, and the concerted addition involving
both phenyl and acetylenic bonds displays only a small barrier, 0.11 eV (IF, 0.95 cm�1Þ.The two pathways, leading to the on top and butterflyþ U con¯gurations are
characterized by similar parameters, i.e. (i) similar adsorption energies for the Phys 1
and Phys 2 states, both adsorbing barrierless from vacuum and (ii) low conversion
barriers into the corresponding chemisorbed states.
Inter-conversion pathways were also calculated: The pathways examined are those
converting the on top adsorption into an inter-Dimers one, or into a butterflyþ U
1096 M. Carbone & R. Caminiti
(Fig. 3(b), top and medium plots). Conversions between di®erent con¯gurations on
the silicon surface are not uncommon. Biphenyl, a molecule where two phenyl rings
are connected to each other shows a fast switch property on Si(100)2� 1 at room
temperature.20
The conversion of PA from on top to the inter-Dimers con¯guration proceeds in
two steps, with two energy barriers, which correspond to the rearrangements of the
dimers upon the shift of the PA on the surface. The ¯rst step has a barrier of 1.11 eV
(IF �237 cm�1) which corresponds to the weakening of the C2-Si(1st dimer) bond.
An intermediate is, then, reached at an energy level 0.40 eV lower, where C1, C2, and
C3 of PA are realigned. Then, a further shift of the adsorbate along the dimer
(a) (b)
Fig. 3. (a) Upper plot: Reaction pathways of PA from from vacuum to the physisorbed state on
Si(100)2� 1 and then, to the corresponding chemisorbed state. Middle plot: Transition from Phys 1 to on
top con¯guration. Bottom plot: Transition from Phys 2 to butterflyþ U con¯guration. (b) Upper plot:
Transition from inter Dimer to on top con¯guration. Middle plot: Transition from butterflyþ U to on top
con¯guration. Bottom plot: Transition from butterflyþD to butterflyþ U con¯guration.
Adsorption States and Site Conversions of PhenylAcetylene 1097
direction causes a rearrangement of the second Si dimer with an associated barrier of
0.49 eV (162 cm�1), followed by the achievement of the ¯nal on top con¯guration.
The transition from the on top to the butterflyþ U con¯guration occurs in a
single step, with an energy barriers of 1.33 eV (IF �195 cm�1). The transition state is
characterized by shift of the PA in along the dimers direction and a partial rotation
of the phenyl ring and regain of the aromatic character.
The height of barriers in both transitions excludes room temperature di®usion or
inter-conversions of the con¯gurations. Therefore, the simultaneous presence of two
adsorption con¯gurations observed experimentally is most probably related to the
comparable barriers of the Phys1-to-onTop and Phys2-to-butterflyþ U transitions.
Finally, a check was made on possible conversion between butter°ies con¯gur-
ations, the butterflyþD and the butterflyþ U . The energy pro¯le shows a single
step transition, though rather broad. The energy barrier is 1.36 (IF �200 cm�1) eV
high and corresponds to a state of the PA 90� rotated along the z-axis, with respect to
the initial con¯guration, with recovered aromaticity and distant 3.4 and 3.5�A from
the ¯rst and the second dimer rows, respectively.
The high transition barrier excludes surface movements for this type of site, as it
is the case for bi-phenyl.
Most signi¯cant bond lengths of the transition states are reported in Table 3.
4. Conclusions
The adsorption of bifunctional Phenyl Acetilene on Si(100)2� 1 was investigated by
DFT. Optimization routines were applied to di®erent adsorption sites where one or
both functional groups were simultaneously involved in the adsorption process and
the correponding energies were calculated. The adsorption through acetylene on top
of a dimer is the most favorable one.
Two physisorption states Phys 1 and Phys 2 were singled out, both adsorbing bar-
rierless. Their conversion into chemisorbed states proceeds with similar energy barriers.
The relatively high inter-conversions barriers between selected chemisorption
sites excludes a post-chemisorption surface rearrangement. This suggests that a
Table 3. Signi¯cant bond lengths in the transition states. But. is the shortening of butter°y. InterD is the
inter-Dimers con¯guration, T1 and T2 are the ¯rst and second transition states in the the inter-Dimers toon top conversion.
Bond Bond Bond Bond
Model Bond length/�A Bond length/�A Bond length/�A Bond length/�A
Phys 1-on top E{F 2.375 G{H 2.412 C1{H 2.399 C2{G 2.251
Phys 2-But:þ U E{F 2.442 I{J 2.515 F{C8 2.285 J{C5 2.375
InterD-on top T1 E{F 2.824 G{H 2.508 C1{G 1.901 C2{F 3.404InterD-on top T2 E{F 2.380 G{H 3.329 C1{H 2.299 C2{G 1.851
But:þ U-But:þD C1{F 4.124 C1{G 3.912 C4{K 3.434 C8{J 3.075
Butter°y-on top E{F 2.289 G{H 2.667 C1{H 2.753 C2{G 1.976
1098 M. Carbone & R. Caminiti
possible control over the adsorption con¯gurations is easier exerted on the conversion
of the physisorbed states.
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Adsorption States and Site Conversions of PhenylAcetylene 1099
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