ADSORPTION STATES AND SITE CONVERSIONS OF PHENYLACETYLENE ON Si(100)2 × 1 CALCULATED BY DFT

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

http://dx.doi.org/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 .


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)


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


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


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


(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.


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


possible control over the adsorption con¯gurations is easier exerted on the conversion

of the physisorbed states.

References

1. Hacker CA, Hamers RJ, J Phys Chem B 107:7689, 2003.2. Hung LS, Chen CH, Mater Sci Eng R 39:143, 2002.3. Shaw JM, Seidler PF, IBM J Res Dev 45:3, 2001.4. Hacker CA, Hamers RJ, J Phys Chem B 107:7689, 2003.5. Hung LS, Chen CH, Mater Sci Eng R 39:143, 2002.6. Tao F, Wang ZH, Lai Y, Xu GO, J Am Chem Soc 125:6687, 2003.7. Casaletto MP, Carbone M, Piancastelli MN, Horn K, Weiss K, Zanoni R, Surf Sci

582:48, 2005.8. Kim KY, Song BK, Jeong S, Kang H, J Phys Chem B 107:11987, 2003.9. Pluchery O, Coustel R, Witkowski N, Borensztein Y, J Phys Chem B 110:22635, 2006.10. Vanderbilt D, Phys Rev B 41(11):7892, 1990.11. Becke AD, Phys Rev A 38:3098, 1998.12. Lee C, Yang W, Parr RC, Phys Rev B 37:3098, 1988.13. Trouiller N and Martins J, Phys Rev B 43:1993, 1991.14. CPMD, Copyright IBM Corp. 1990�2006, Copyright MPI f€ur Festk€orperforschung

Stuttgart 1997�2001.15. Baroni S, Dal Corso A, De Gironcoli S, Giannozzi P, Cavazzoni C, Ballabio G, Scandolo

S, Chiarotti G, Focher P, Pasquarello A, Laasonen K, Trave A, Car R, Marzari N, KokaljA, http://www.pwscf.org/.

16. Shkrebtii AI, Di Felice R, Bertoni CM, Del Sole R, Phys Rev B 51:11201, 1995.17. Morrison I, Li JC, Jenkins S, Xantheas SS, Payne MC, J Phys Chem B 101:6146, 1997.18. Silvestrelli PL, Pulci O, Palummo M, Del Sole R, Ancilotto F, Phys Rev B 68:235306,

2003.19. Zhang QJ, Liu ZF, J Phys Chem C 113:5263, 2009.20. Lastapis M, Martin M, Riedel D, Hellner L, Comtet G, Dujardin G, Science 308:1000,

2005.


ADSORPTION STATES AND SITE CONVERSIONS OF PHENYLACETYLENE ON Si(100)2 × 1 CALCULATED BY DFT

Documents

Transcript of ADSORPTION STATES AND SITE CONVERSIONS OF PHENYLACETYLENE ON Si(100)2 × 1 CALCULATED BY DFT