The binding of multi functional organic molecules on silicon surfaces 3

The Binding of Multi-functional Organic Molecules on Silicon Surfaces

Chapter 3 Adsorption of Nitrogen-containing Aromatic
Molecules on Si(111)-7×7
3.1 Motivation
The reactivity and reaction mechanisms of aromatic molecules with the Si-dangling
bonds of Si(111)-7×7 have been explored [1-6]. For five-membered heterocyclic
molecules, thiophene [1] and furan [2] react with the adjacent adatom-rest atom pair
through their two α-carbon atoms to form C-Si σ-linkages, denoted as a [4+2]-like
cycloaddition. In the case of pyrrole, the dissociative adsorption via the breakage of its NH bond was observed to be the dominant reaction channel [3]. The resulting fragments of
pyrrolyl and H-atom are bonded to adjacent adatom and rest atom, respectively. Among
the six-membered aromatic systems, benzene readily reacts with the surface, forming a
di-σ bonded 1,4-cyclohexadiene-like surface intermediate through the [4+2] addition
reaction [4, 5]. Replacing one of the C-atoms in benzene ring by N-atom results in
pyridine with a non-even electronic density distribution. A dative bonding between the
electron-rich N-atom of pyridine and electron-deficient Si-adatoms was detected in
addition to the di-σ binding configuration through the N-atom and its opposite C-atom
[6]. To further understand the effect of constituent ring atoms on the reactivity, nitrogencontaining aromatic molecules (pyrazine, pyrimidine, and s-triazine) are interesting
systems for investigation.

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

3.2 Pyrazine adsorption
3.2.1 High-resolution electron energy loss spectroscopy
Figure 3.1 shows the high-resolution electron energy loss spectra of Si(111)-7×7
exposed to pyrazine at 110 K. The vibrational frequencies and their assignments for
physisorbed and chemisorbed molecules on a Si(111)-7×7 surface are listed in the Table
3.1. This table clearly shows that the vibrational features of physisorbed pyrazine

(Figures 3.1c,d, e) are in excellent agreement with the IR spectrum of liquid pyrazine [7,
8]. Among these vibrational signatures, the peak at 3071 cm-1 is assigned to the (sp2) C-H
stretching modes of the molecule. The feature at 1556 cm-1 is related to the conjugated
C=C (N) stretching vibration.
The vibrational features of chemisorbed pyrazine taken at low exposures (Figure
3.1a) or obtained after annealing the multilayer pyrazine-covered sample to 300 K to
drive away all the physisorbed molecules and retain only the chemisorbed molecules
(Figure 3.1f), however, are significantly different. Losses at 497, 712, 905, 1065, 1230,
1615, and 3071 cm-1 can be readily resolved. Compared to physisorbed molecules,
chemisorbed pyrazine does not lead to obvious variations in the stretching frequency of C
(sp2)-H. This result indicates that the C atoms of the molecule are not involved in the
chemical binding with the surface (A C (sp3)-H vibrational peak, red-shifted by 80-100
cm-1 from the C (sp2)-H stretching mode, would be expected if the C atoms were
involved in binding with Silicon surface dangling bonds). The 1615 cm-1 loss observed is
attributed to the non-conjugated C=C stretching vibration in the chemisorbed pyrazine.
This assignment is consistent with the results obtained for liquid 1,4-cyclohexadiene (at
1639cm-1) [9], and chemisorbed benzene (at 1635 cm-1) [5] and chlorobenzene (at

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

1628cm–1) [10] on Si(111)-7×7 with a 1,4-hexadiene-like surface intermediate. On the
other hand, the loss feature at 497 cm-1 is associated with the Si-N stretching mode,
consistent with previous studies on the binding of unsaturated N-containing organic
molecules on Si surfaces through the N-Si linkages [11-13]. Furthermore, we did not
observe any peak at ~2055 cm -1 associated with the Si-H stretching mode [14], indicating
the molecular nature of chemisorbed pyrazine on the Si(111)-7×7 surface. The detailed
assignments are tabulated in Table 3.1. The main vibrational features of chemisorbed

pyrazine correlates well with the calculated vibrational frequencies for chemisorbed
pyrazine on Si(111)-7×7. The details of DFT theoretical modeling will be given in
Section 3. 5.
To further confirm our assignments, pyrazine-d4 adsorption was also studied in our
HREELS experiments. Figure 3.2 presents the vibrational features of physisorbed
pyrazine-d4 and the saturated chemisorption molecules on Si(111)-7×7. A new peak at
2291 cm-1 is identified and attributed to the C (sp2)-D stretching in the vibrational
spectrum of physisorbed pyrazine-d4 (Figure 3.2a), replacing the C (sp2)-H stretching
mode at 3071 cm-1 for physisorbed molecules (Figure 3.1e). Upon chemisorption (Figure
3.2b), the =C-D stretching mode remains at the almost same vibrational frequency,
retaining sp2 hybridization for all four carbon atoms of the chemisorbed pyrazine on
Si(111)-7×7. This result clearly illustrates that the C-atoms do not directly bind to the
silicon surface dangling bonds. In addition, the spectrum of chemisorbed pyrazine-d4
(Figure 3.2b) also shows the characteristic vibrational modes of the unconjugated C=C at
1595 cm-1 and Si-N at 512 cm-1, further confirming our vibrational assignment for
chemisorbed pyrazine on Si(111)-7×7 surfaces. The absence of C (sp3)-H (D) stretching

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

mode, together with the formation of C-N bond and unconjugated C=C bond, suggests
that pyrazine is directly bonded to the adjacent adatom and rest-atom on Si(111)-7×7
through the two para-nitrogen atoms, forming the two new Si-N sigma linkage.
3.2.2 X-ray photoelectron spectroscopy
The N (1s) and C (1s) spectra of pyrazine following a sequence of exposure at
110 K are shown in Figure 3.3 and Figure 3.4, respectively. At very low exposures, the N
1s spectra show a main peak centered at 399.0 eV. With increasing the exposure from 3.0
to 8.0L, the peak at 400.6 eV preferentially grows, suggesting its physisorption nature. C

1s spectra also present a similar evolution as a function of pyrazine dosage. When the
dosage is below 0.5L, the main feature is the peak at 285.8 eV. At a high exposure of
8.0L, the 286.6 eV peak dominates the spectra, attributable to physisorbed pyrazine. The
binding energy of N 1s and C 1s core level for physisorbed pyrazine on Si(111)-7×7 is in
excellent with the results of condensed pyrazine on Au.[15] Compared to the value
(284.7 eV) of physisorbed benzene [16], the higher C 1s BE of 286.6 eV observed for
physisorbed pyrazine is due to the effect of the more electronegative N-atoms
incorporated in the aromatic ring.
To unambiguously assign these peaks, chemisorbed monolayer was obtained by
annealing the multilayer pyrazine-covered surface (8.0L) to 300 K to drive away all
physisorbed molecules. Chemisorbed pyrazine gives a single nearly symmetrical peak for
the N 1s core level (Figure 3.3h) centered at 399.0 eV. Its narrow FWHM of ~ 1.4 eV,
close to the overall resolution of our XPS spectrometer, suggests that the two N-atoms in
chemisorbed pyrazine are chemically indistinguishable. Compared with the value of
400.6 eV observed for physisorbed pyrazine, the chemisorption on Si(111)-7×7 results in

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

a significant down-shift of 1.6 eV in the binding energy of N (1s). The large magnitude of
this shift strongly demonstrates that the nitrogen atoms are directly bonded to the surface
reactive sites. Similar trend was previously observed for (CH3)N=N(CH3) on Si surfaces,
N 1s binding energy changing from 400.8 eV for physisorbed molecules to a value of
399.0 eV for chemisorbed state with direct Si-N bond formation.[17]
Figure 3.4h shows the corresponding C 1s spectrum for pyrazine chemisorbed on
Si(111)-7×7. A single peak at 285.8 eV can be readily resolved, suggesting the existence
of only one chemically distinguishable form of carbon in chemisorbed species. This C 1s
peak (285.8 eV) is noticed to be ~ 1.2 eV higher than the value of 284.6 eV observed for

the C-atom directly linked to surfaces through the Si-CH2- group [18, 19]. Its down-shift
of 0.8 eV from the value (286.6 eV) of physisorbed molecules can be attributed to the
increase of electron density on these carbon atoms upon chemisorption. Pyrazine binds to
an adjacent pair of adatom-rest atom through its two para-nitrogen atoms, forming N-Si
linkages. The chemisorption process is expected to destroy the ring π-bond or aromaticity.
This blocks the electron-withdrawing effect of nitrogen atoms through π-bonding,
subsequently enhancing the electron density of carbon atoms and down-shift in C 1s in
chemisorbed pyrazine compared to physisorbed molecules.
The inset of Figure 3.4 presents the ratio of AC1s / ASi2p as a function of pyrazine
exposure at room temperature. The value for each point was obtained by averaging three
separate measurements to reduce possible errors. AC1s is the C 1s peak area of
chemisorbed pyrazine at 300 K. The saturation of the AC1s / ASi2p ratio indicates the
completion of chemisorption. To estimate its absolute saturation coverage, XPS
measurements for pyrazine-saturated Si(111)-7×7 are compared to those of chemisorbed

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

benzene. The saturation coverage of benzene, θ

benzene,

was known to be ~ 0.10, defined

as the ratio of the reacted adatoms to the 49 silicon atoms in a unit cell [20]. This value
becomes ~0.42 if the coverage is defined as the ratio between the reacted adatoms and the
total adatoms on Si(111) )-7×7. The peak-area ratio, (AC1s / ASi2p) for pyrazine-saturated
Si(111)-7×7 is 0.301, whereas a saturation ratio of 0.488 was also found for chemisorbed

benzene, which corresponds to an absolute coverage of 0.42 [20]. After considering the
numbers of carbon atoms in these two molecules, the saturation coverage, θpyrazine is
estimated to be ~ 0.39 [= 0.42 × 0.301 / 0.488 × 6 / 4]. This value approximately
corresponds to 5 pyrazine molecules / unit cell.”
3.3 Pyrimidine adsorption
3.3.1 High-resolution electron energy loss spectroscopy
Figure 3.5 shows the high resolution electron energy loss spectra of pyrimidine
exposed Si(111)-7×7 at 110 K as a function of exposure. The vibrational frequencies and
their assignments for physisorbed and chemisorbed molecules are summarized in Table
3.2. Vibrational signatures at 384, 712, 1021, 1220, 1402, 1547, 3074 cm-1 can be clearly
identified in the spectrum of physisorbed molecules (Figures 3.5c, d, e). These vibrational
features of physisorbed pyrimidine are in excellent agreement with the IR and Raman
vibrational energies of liquid-phase pyrimidine with in ~20 cm-1 (Table 3.2)[21-24].
Among them, the peak at 3074 cm-1 is assigned to the C (sp2)-H stretching mode; the
feature at 1547 cm-1 is related to the conjugated C=C (N) stretching vibration.
The vibrational features of chemisorbed pyrimidine at low exposures or obtained by
annealing the multilayer pyrimidine exposed sample to 300 K to drive away all the
physisorbed molecules and only retain the chemisorbed molecules are shown in Figure

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

3.5a and Figure 3.6b, respectively. Losses at 530, 620, 748, 893, 998, 1202, 1621, 2891,
3074 cm-1 can be readily resolved. The absence of the Si-H stretching around 2000-2100
cm-1 [14] suggests the nature of molecular chemisorption for pyrimidine on Si(111)-7×7.
Compared to the physisorbed molecules, interesting changes are noticed. The C-H
stretching of chemisorbed molecules presents as an obvious doublet at 3074 and 2891
cm-1. Previous studies showed that benzene can be covalently attached to Si(111)-7×7

through [4+2]-like cycloaddition to form two new Si-C σ-bond linkages [5], evidenced
by the doublet at ~3050 and ~2908cm-1 assigned to C(sp2)-H and C(sp3)-H stretching
modes, respectively. Based on a similar argument, the two ν(C-H) peaks at 3074 and
2891cm-1 observed in Figure 3.6b suggest the occurrence of one or more C-atoms
rehybridizing from sp2 to sp3. The formation of Si-C linkage is further supported by the
appearance of a vibrational feature at 530 cm-1 [25]. In addition, a new peak at 1621 cm-1
is resolved, attributable to non-conjugated C=C(N) stretching vibration in chemisorbed
pyrimidine. This assignment is consistent with the results obtained for liquid 1,4cyclohexadiene (at 1639cm-1) [9], and chemisorbed benzene (at 1635 cm-1) [5] and
chlorobenzene (at 1628cm–1) [10] on Si(111)-7×7 with a 1,4-cyclohexadiene-like surface
intermediate. The fact of forming non-conjugated surface species rules out the possibility
of [2+2]-like addition mechanisms. Furthermore, new intensities appearing 620 cm-1
(Figure 3.6b), can be assigned to the stretching modes of the Si-N bonds in the
chemisorbed molecules. This result clearly reveals that pyrimidine binding to the surfaces
directly involves the nitrogen atoms as well. The detailed assignments are tabulated in
Table 3.2. The main vibrational features of chemisorbed pyrimidine correlate well with
the calculated vibrational frequencies of the 1,4-N, C-dihydropyrimidine-like structure on

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

Si(111)-7×7 from our DFT calculations, confirming our assignments for chemisorbed
pyrimidine on Si(111)- 7×7.
Our HREELS results show that upon chemisorption, the coexistence of C(sp2)-H
and C(sp3)-H stretching modes is observed together with the appearance of the nonconjugated C=C(N) vibrational feature(at 1621 cm-1) as well as the formation of the Si-N
and Si-C bonds. Thus, our vibrational observation strongly suggests that pyrimidine
covalently bonds to the adjacent adatom and rest-atom on Si(111)-7×7 through a nitrogen
atom and its para-carbon atom to form Si-N and Si-C di-σ via the [4+2]-like
cycloaddition mechanism. This is also further supported by the XPS results.

3.3.2 X-ray photoelectron spectroscopy
Figure 3.7b shows the N 1s photoemission spectra of chemisorbed pyrimidine
obtained by annealing the sample with multilayer pyrimidine (Figure 3.7a) prepared at
110K to 300K. N 1s photoemission spectrum of physisorbed molecules (Figure 3.7a)
contains a symmetric peak at 400.4 eV with a typical FWHM (~1.2 eV) under our XPS
resolution. This binding energy is consistent with that of condensed pyrimidine on Au.[15]
Compared to physisorption, however, significant changes can be found in the N 1s
spectrum of chemisorbed molecules, broadened with a nearly symmetric flat-top shape.
This strongly suggests the significant modification on the electronic properties of
nitrogen atoms after chemisorption. The broad N 1s photoemission band of chemisorbed
molecules can be fitted into two peaks centered at 400.4 and 399.0 eV, demonstrating the
existence of two chemically different nitrogen atoms. The ratio of integrated peak areas
for these two peaks is 49.8%: 51.2%, approximately 1:1. Thus, the large down-shift of

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

1.4eV in the core level for one of the nitrogen atoms confirms its participation in the
cycloaddition with reactive sites on Si(111)-7×7, consistent with our vibrational analyses.
Figure 3.8 shows the fitted C 1s XPS spectra for physisorbed and chemisorbed
pyrimidine on Si(111)-7×7. The C 1s spectrum of physisorbed molecules is deconvoluted
into three peaks centered at 287.9, 287.1 and 285.7 eV with equal FWHM and an area
ratio of 24%: 52%: 24%, approximately 1:2:1 (Figure 3.8a), in excellent accordance with
the results of condensed pyrimidine on Au [15]. Our results showed that the BEs of C1
and C2 separated by 0.8 eV are ~2.2 eV higher than that of the C3 atom. The detailed
assignment is listed in Table 3.3. Due to the higher electron negativity of nitrogen atoms,
the neighboring C-atoms are expected to have a lower electron density, subsequently a
higher BE of the C 1s core level. Thus, the peaks at 287.9 and 285.7eV can be attributed

to C1 and C3, respectively, whereas the intensity at 287.1 eV is contributed by the two C2atoms [15]. Similarly, the C1s spectrum of chemisorbed molecules is be fitted into three
peaks at 285.3, 286.5, and 287.5 eV with the same FWHM and an area ratio of 50%: 24%:
26%, approximately 2:1:1. According to the HREELS results, chemisorbed pyrimidine
has 1,4-N, C-dihydropyrimidine-like structure. In this configuration, one of the C2-atoms
and its para-nitrogen atom are covalently linked to surface silicon atoms. Thus the peak at
285.3eV can be reasonably assigned to the C2 atom directly bonded to silicon surface and
C3-atom. The large chemical shift of 1.8 eV in the core-level of this C2-atom, compared
to these in physisorbed molecules, is attributable to its enhanced electron density after
bonding with the Si-atom. The peaks at 287.5eV and 286.5eV are associated with C1 and
unreacted C2-atom, respectively, slightly down-shifted from their values of physisorbed
molecules. Their down-shift can be attributed to the increase of electron density on these

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

carbon atoms upon chemisorption. The chemisorption process is expected to destroy the
ring π-bond or aromaticity. This blocks the electron-withdrawing effect of nitrogen atoms
through π-bonding, subsequently enhancing the electron density of carbon atoms and
down-shift in C 1s in chemisorbed pyrimidine compared to physisorbed molecules.
3.3.3 Ultraviolet photoelectron spectroscopy
He II valence band spectra following a sequence of pyrimidine exposures at 110 K
are shown in Figure 3.9. The orbital constitution of physisorbed pyrimidine is shown in
the form of the bar graph below Curve g, shifted to account for the work function and
final state relaxation effects when condensed on solid-state surfaces. For a clean Si(111)7×7 surface [26, 27], the existence of two peaks at 0.3 (S1) and 0.7 (S2) (Figure 3.9)
below EF

is due to the dangling bond surface states at adatoms and rest atoms,

respectively, according to the STM studies of a clean Si(111)-7×7 surface [26, 27].
Increasing pyrimidine exposure leads to the gradual attenuation of the surface states and
total quenching around 2.4 L exposures. The disappearance of the surface states may be
caused by the consumption of surface dangling bonds and redistribution of their electron
density at the pyrimidine / Si(111)-7×7 interface.
Upon 3.2 L exposure at 110 K, a physisorbed multilayer results in four dominant
features at 12.12(D), 9.37(C), 6.62(B), and 5.15(A) eV. The energy separations between
two successive levels agree well with those gas-phase values [28, 29]. A large body of
evidence concerning the electronic structures of pyrimidine has been accumulated [3033]. The four bands of A, B, C, and D observed for physisorbed molecules in our
experiment can be assigned to πc=c(N) (2b1), n (7b2), πc=c(N) + n (11a1), and πc=c(N) (1b1),
respectively.

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

The UPS of chemisorbed pyrimidine was obtained after annealing the sample preexposed to 6.4 L of pyrimidine at 110 K to 300 K to drive away all the physisorbed
molecules. From Figure 3.9, it is noted that the relative intensities of peaks B and C,
mainly contributed from the “lone pair” electrons of nitrogen atoms in pyrimidine, are
almost the same for both the physisorbed and chemisorbed pyrimidine on Si(111)-7×7,
disproving the formation of dative bond through the charge transfer of nitrogen lone pair
electrons to the electron deficient Si-adatoms. On the other hand, compared to the UPS
spectrum of physisorbed (Figure 3.9h), a significant reduction in the relative intensities of
peak A, D (π

c=c(N))

can be noticed for chemisorbed pyrimidine (Figure 3.9i). The

difference shows the participation of π

c=c(N)

orbital in the interaction with Si surface

states, consistent with the observations of HREELS and XPS studies.
3.4 S-triazine adsorption
3.4.1 High-resolution electron energy loss spectroscopy
Figure 3.10 shows the high-resolution electron energy loss spectra recorded as a
function of s-triazine exposure on Si(111)-7×7. Figures 3.10d and 3.10e display the
vibrational features for physisorbed multilayer s-triazine after exposing 0.8 and 1.6 L
onto the Si(111)-7×7 surface at 110K, respectively. The loss features at 345, 730, 993,
1161, 1396, 1550, and 3053 cm-1 are readily resolved, which are in good agreement with
the IR and Raman spectroscopic data of gas-phase within ~15cm-1.[34, 35] Among these
vibrational signatures, the peak at 1550 cm-1 is assigned to the C-N stretching modes of
the aromatic ring. The features at 3053 is related to the (sp2)C-H stretching mode. The
detailed assignments for physisorbed and chemisorbed s-tirazine together with the IR and
Raman spectroscopic data of gas-phase s-triazine [34, 35] are listed in Table 3.4.

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

The vibrational features of chemisorbed s-triazine at low exposures (Figure 3.10a)
or prepared after annealing the multilayer triazine-covered sample to 300 K (Figure
3.11b), present interesting changes. Losses at 503, 670, 940, 1204, 1359, 1635, 2909,
3036 cm-1 can be readily resolved. Compared to the physisorbed s-triazine, the C-H
stretching of chemisorbed molecules presents an obvious doublet at 3036 and 2909 cm-1.

The two ν(C-H) peaks observed in Figure 3.11b suggest the occurrence of one or more Catoms rehybridizing from sp2 to sp3. In addition, the C=N stretching vibration in the
chemisorbed s-triazine shows significant shifts (85 cm-1) comparing to the spectrum of
physisorbed molecules, indicating the disruption of aromaticity of s-triazine and
formation of the unconjugated C=N stretching mode. A similar assignment was made for
the nonconjugated C=C in chemisorbed benzene (at 1635 cm-1)[5], chlorobenzene (at
1628cm-1) [10] on Si(111)-7×7 and liquid 1,4-cyclohexadiene (at 1639cm-1).[9] The
absence of the Si-H stretching around 2000-2100 cm-1 [14] suggests the nature of
molecular chemisorption for s-triazine on Si(111)-7×7. The detailed assignments are
tabulated in Table 3.4.
The present HREELS results are markedly different from the previous work on
Si(100) surface by Lin et al.[36] The coexistence of two hybridization states of carbon
atoms is clearly resolved, as evidenced by the observation of two separate vibrational
losses of 2905 and 3035 cm-1 for chemisorbed s-triazine on Si(111)-7×7. The failure to
observe this splitting in their work [36] may partly be attributable to the lower
instrumental resolution (fwhm ~80 cm-1) compared to an energy resolution of ~55 cm-1 in
this experiment. The present experimental findings suggest the formation of chemical
bonds between a carbon atom and it pare-nitrogen atom in s-triazine and two adjacent Si

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

atoms with dangling bonds. S-triazine is therefore di-σ-bonded to a pair of neighboring
adatom and rest atom on Si(111)-7×7, forming a 1,4-N, C-dihydrotriazine-like structure.
3.4.2 X-ray photoelectron spectroscopy
Figure 3.12b shows the C 1s photoemission spectra of chemisorbed s-triazine
obtained by annealing the sample with multilayer s-triazine (Figure 3.12a) prepared at
110K to 300K. C 1s photoemission spectrum of physisorbed molecules (Figure 3.12a)
contains a symmetric peak at 287.9 eV. This binding energy is consistent with that of

condensed s-triazine on Si(100) [36]. Compared to physisorption, the C 1s spectrum of
chemisorbed molecules broadened somewhat. This strongly suggests the significant
modification on the electronic properties of carbon atoms after chemisorption. The broad
C 1s photoemission band of chemisorbed molecules can be fitted into two peaks centered
at 287.4 and 286.0 eV, demonstrating the existence of two chemically different carbon
atoms. The ratio of integrated peak areas for these two peaks is 66.4 %: 33.6 %,
approximately 2:1. Thus, the large down-shift of 1.9 eV in the core level for one of the
carbon atoms confirms its participation in the cycloaddition with reactive sites on
Si(111)-7×7, consistent with the observation of the C(sp3)-H (at 2905cm-1) stretching
mode in HREELS results.
Figure 3.13 shows the N 1s photoemission spectra of physisorbed (Figure 3.13a)
and chemisorbed (Figure 3.3b) s-triazine at 110K. N 1s photoemission spectrum of
physisorbed molecules (Figure 3.13a) contains a symmetric peak at 400.6 eV, consistent
with previous studies.[15, 36] Compared to physisorption, the broad N 1s photoemission
band of chemisorbed molecules can be fitted into two peaks centered at 400.4 and 399.0
eV, demonstrating the existence of two chemically different nitrogen atoms. The ratio of

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

integrated peak areas for these two peaks is 69.5 %: 30.5 %, approximately 2:1. Thus, the
large down-shift of 1.6 eV in the core level for one of the nitrogen atoms suggests its
participation in the cycloaddition with reactive sites on Si(111)-7×7.
3. 5 DFT theoretical calculations
Based on the reaction mechanisms of functional group on the silicon surface, there
are three possible ways for nitrogen-containing molecules (pyrazine, pyrimidine, and striazine) binding on Si(111)-7×7: (a) the interaction of lone-pair electrons at its N atom
with the Si dangling bond to form a dative bond, similar to the case of pyridine on
Si(100) or Si(111)-7×7 [6, 38]; (b) [2+2]-like cycloaddition through a C=N or C=C bond;

c) [4+2]-like cycloaddition through two para-carbon atoms or two para nitrogen atoms or
a carbon atom and its para-nitrogen atom of the conjugated C=N and C=C groups. DFT
theoretical calculations were carried out to obtain the optimized geometric structures and
energies for these possible adsorption configurations.
Figure 3.14 presents the optimized geometries of the local minima for the
pyrazine/Si9H12, pyrimidine/Si9H12, and s-triazine/Si9H12 model systems. The adsorption
energies are given in Table 3.5. The calculation result reveals that the [4+2]-like
cycloadditions is thermodynamically favored compared to the [2+2]-like reactions. In the
[2+2]-like cycloadditions for pyrazine / Si(111), pyrimidine / Si(111), and s-triazine /
Si(111) systems, only one C=C, or C=N bond is involved in the di-σ bonding
configuration. Considering the direct distance (~4.45 Å) between two adjacent adatom
and rest atom based on the DAS (Dimer Adatom Stacking fault) model of Si(111)-7×7
[38, 39] and typical bond length of Si-C (1.8-2.1 Å), Si-N (1.7-1.8 Å) [40], the C-C or C-

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

N bonds are expected to be much stretched in the adsorption intermediate, implying the
instability of [2+2]-like cycloadducts.
3.6 Discussion
3.6.1 Binding configuration for chemisorbed nitrogen-containing aromatic
molecules on Si(111)-7×7
3.6.1.1 Pyrazine
In the vibrational studies, the retention of sp2 configuration for all four carbon atoms
in chemisorbed intermediate was evidenced in the detection of only one (sp2) C-H
stretching at 3071 cm-1 without any intensity at 2900 cm-1 for (sp3) C-H stretching. This
clearly rules out the possibility for these reactions involving carbon atoms. Indeed, the
HREELS results show that upon chemisorption, all the vibrational modes related to (sp2)

C-H remain unchanged and unconjugated C=C vibrational feature at 1615 cm-1 was
evidenced. Thus, the vibrational observation strongly suggests that pyrazine covalently
bonds to the adjacent adatom and rest-atom on Si(111)-7×7 through two para-nitrogen
atoms to form di-Si-N-σ via the [4+2]-like cycloaddition mechanism. This is also in
good agreement with the XPS results and the prediction of DFT calculations.
In the XPS studies of chemisorbed molecules, the binding energy of N 1s of
chemisorbed pyrazine displays large chemical shift of 1.6 eV from that of physisorbed
multilayer, which implies the direct involvement of N-atoms in pyrazine binding on
Si(111)-7×7. The N (1s) binding energy of 399.0 eV for pyrazine on Si(111)-7×7 coupled
with the down-shift (1.6 eV) is in good agreement with results obtained for other
molecules covalently attached to the silicon surface through the direct bonding of their Natoms with the Si surface reactive sites [17].

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The Binding of Multi-functional Organic Molecules on Silicon Surfaces

Chemisorbed pyrazine gives a single C 1s peak at 285.8 eV, down-shifted by 0.8
eV from that of physisorbed multilayer (286.6 eV). This binding energy is in fact nearly
1.2 eV higher than the value (284.6 eV) found for the Si-C σ-linkages [17, 18]. Thus, the
C 1s intensity observed for chemisorbed pyrazine can not be attributed to the C-atoms
bonding with the surface Si-atoms. The fact of observing the 0.8 eV down-shift for the C
1s core level can be explained considering the structural changes and electron redistribution in chemisorbed pyrazine depicted in the theoretical model. The attachment of
two para-nitrogen atoms to the adjacent adatom and rest atom significantly tilts the
molecular plane and removes the aromaticity. As a result, the π-electron polarization
towards the nitrogen atoms occurring in physisorbed pyrazine does not exist in
chemisorbed state. This enhances the relative electron density at the carbon atoms in the
resulting 1,4-N,N-dihydropyrazine-like surface intermediate, subsequently lowering the
C 1s binding energy. This is consistent with our experimental conclusion that pyrazine
selectively binds on the Si(111)-7×7 through two para-nitrogen atoms with the adjacent

adatom and rest-atom.
The observation of only the [2+4]-like reaction through two para-nitrogen atoms in
the experiment is well consistent with the calculation result. The absence of the binding
configuration of pyrazine mode (IV) in Figure 3.14 through the two opposite-carbon
atoms can be reasonable explained as following: a) the Si-N bond is much stronger than
the Si-C bond. The calculation result reveals that the [4+2]-like cycloadditions through
two nitrogen atoms (33.3 kcal·mol-1) is thermodynamically favored compared to the
[4+2]-like reaction through two carbon atoms; b) the higher selectivity of the attachment
of nitrogen atoms on Si(111)-7×7 reactive sites over the carbon atoms due to the

65


The Binding of Multi-functional Organic Molecules on Silicon Surfaces

electronic charge interaction. The nitrogen atom is partially negatively charged center,
and the adatom is partially positively charged center. Their interaction directs the
attachment of nitrogen atom onto the adatom, and consequently the molecule onto a
adatom-rest-atom pair. This possible explains the selectivity from the kinetic point of
view.

Thus,

the

[2+4]-like

reaction

through

two

para-nitrogen

atoms

is

thermodynamically and kinetically preferential with the formation of di-σ N-Si linkages.
3.6.1.2 Pyrimidine and s-triazine
The HREELS results of pyrimidine and s-triazine on Si(111)-7×7 are markedly
different from the spectra of pyrazine on the same surface. The coexistence of two
hybridization states of carbon atoms is clearly resolved, as evidenced by the observation
of two separate vibrational losses of

2891, 3074 cm-1 and 2905, 3035 cm-1 for

chemisorbed pyrimidine and s-triazine on Si(111)-7×7, respectively. In addition, the
C=N(C) stretching vibration in the chemisorbed pyrimidine and s-triazine shows
significant shifts comparing to the spectrum of physisorbed molecules, indicating the
disruption of aromaticity of pyrimidine and s-triazine and formation of the unconjugated
C=N (C) stretching mode. Thus, the vibrational observation suggests that pyrimidine and
s-triazine covalently bonds to the adjacent adatom and rest-atom on Si(111)-7×7 through
a carbon atom and its para-nitrogen atom via the [4+2]-like cycloaddition mechanism.
The large down-shift of 1.6 eV (1.4eV) in the core level for one of the nitrogen atoms
suggests its participation in the cycloaddition with reactive sites on Si(111)-7×7,
consistent with vibrational analyses.
3.6.2 Dative bonds

66


The Binding of Multi-functional Organic Molecules on Silicon Surfaces

In contrast to the pyridine/Si(111) system, there is no observation of the formation
of dative bonds for pyrazine, pyrimidine and s-triazine chemisorbed on Si(111)-7×7. The
absence of dative bonds for pyrazine, pyrimidine, and s-triazine / Si(111) can be
reasonable explained as following: a) Pyridine molecule is a better electron donor. The
electron density of nitrogen atom in pyridine is higher than that in pyrazine, pyrimidine,
and s-triazine, as evidenced by the lower binding energy of N 1s core level for
physisorbed pyridine (400.0eV) as compared to that for physisorbed pyrazine (400.6eV),
pyrimidine (400.4 eV), and s-triazine (400.6 eV). b) The dative bonds for pyridine/Si(111)
is more stable. DFT calculations show that the heat of formation of dative bond for
pyrazine, pyrimidine, and s-triazine/Si(111) is lower than that for pyridine/Si(111) by
12.2, 4.0, 21.6 kcal/mol, respectively. Moreover, compared to the dative bonded states,
the 1,4-N, N-dihydropyrazine-like, 1.4-N, C-dihydropyrimidine, and 1,4-N, Cdihydrotriazine binding configurations are thermodynamically favorable by 19, 14.6, 25.2
kcal/mol, respectively; however, the heat of formation of dative-bonded product (26.4
kcal/mol) is comparable to that of the [4+2]-like addition product (26.7 kcal/mol) for
pyridine/Si(111) system.
The binding of nitrogen-containing aromatic molecules (pyrazine, pyrimidine, and striazine) on Si(111)-7×7 surface involves their nitrogen atom through a [4+2]-like
cycloaddition. The attachment of nitrogen atoms to the silicon dangling bonds is possibly
attributable to a barrierless pathway passing through a dative-bonded precursor. The
nitrogen atoms with lone-pair electrons can possibly act as donor to provide electrons to
form a dative-bonded precursor with electron-deficient Si dangling bonds on adatoms,
possibly lowering the energy barrier of surface reactions. For pyrimidine and s-triazine,

67

The Binding of Multi-functional Organic Molecules on Silicon Surfaces

nitrogen atoms are situated in “meta” position to each other, leading to the direct binding
of one nitrogen and its para-carbon atoms to silicon surface. In the case of pyrazine, two
para nitrogen atoms reacted with the surface sites in the formation of two N-Si linkages.
This possibly explains the selectivity from the kinetic point of view for nitrogencontaining aromatic molecules binding on Si(111)-7×7 surface.

4.7 Conclusions
In summary, a combined experimental and theoretical approach has been employed
to systemically investigate the nitrogen-containing aromatic molecules (pyrazine,
pyrimidine, and s-triazine) adsorption on Si(111)-7×7.
(1) Chemisorption of pyrazine on Si(111)- 7×7 leads to the formation of di-σ N-Si
linkages .
(2) Pyrimidine and s-triazine covalently bonds to the adjacent adatom and rest-atom
on Si(111)-7×7 through a carbon atom and its para-nitrogen atom via the [4+2]like cycloaddition mechanism.
(3) In contrast to the pyridine/Si(111) system, there is no observation of the
formation of dative bonds for pyrazine, pyrimidine and s-triazine chemisorbed on
Si(111)-7×7.

68


3071

1615

Pyrazine / Si(111)-7x7
110 K

769

1030
1215
1408
1556

402

497
712
905
1065
1230

The Binding of Multi-functional Organic Molecules on Silicon Surfaces

f 300 K

e 3.0 L
d 2.0 L
55 cm

-1

c 1.5 L
b 1.0 L
x2
a 0.5 L

-500

0

500

1000 1500 2000 2500 3000 3500 4000
-1

Wavenumber (cm )

Figure 3.1 HREELS spectra of pyrazine on Si(111)-7×7 as a function of exposure at 110
K. Ep=5.0eV, specular geometry. Figure 3.1f is the difference spectrum of saturated
chemisorption monolayer.

69


Pyrazine-d4/Si(111)-7x7

2304

110 K

55 cm

-500

0

-1

2291

624
846
998
1262
1512

414

1087
1249
1595

512
902

The Binding of Multi-functional Organic Molecules on Silicon Surfaces

Chemisorption
(b)

Physisorption
(a)

500 1000 1500 2000 2500 3000 3500 4000
-1

Wavenumber (cm )

Figure 3.2 HREELS spectra of the physisorbed and saturated chemisorption pyrazine-d4
on Si(111)-7×7.

70


The Binding of Multi-functional Organic Molecules on Silicon Surfaces

Pyrazine / Si(111)-7x7

XPS

399.0
110 K

400.6

N 1s

Intensity (a.u)

x2
h 300 K

x 0.5
g 8.0 L
f 5.0 L
e 3.0 L
d 1.5 L
c 1.0 L

b 0.5 L
a0L
406

404

402

400

398

396

394

392

390

Binding Energy (eV)

Figure 3.3 N 1s XPS spectra of pyrazine on Si(111)-7×7 at 110 K as a function of
exposure. Figure 3.3h is the difference spectrum of saturated chemisorption monolayer.

71


The Binding of Multi-functional Organic Molecules on Silicon Surfaces

0.8

XPS

0.6

AC1s/ ASi2p

286.6

110 K

285.8

0.7

Pyrazine/Si(111)-7x7

0.5

Benzene

0.488

0.4

Pyrazine

0.3

0.301

0.2
0.1
0.0
0

4

8

12

16

20

24

Exposure

Intensity (a.u)

C 1s
h 300 K

g 8.0 L
f 5.0 L
e 3.0 L
d 1.5 L

c 1.0 L
b 0.5 L
a0L
292

290

288

286

284

282

280

278

276

Binding Energy (eV)

Figure 3.4 C 1s XPS spectra of pyrazine on Si(111)-7×7 at 110 K as a function of
exposure. Figure 3.4h is the difference spectrum of saturated chemisorption monolayer.
The inset plots the XPS peak area ratio, AC1s / ASi2p, for pyrazine and benzene on Si(111)7×7 as a function of exposure at 300 K, where the dotted lines represent the saturation of
chemisorption.

72

The Binding of Multi-functional Organic Molecules on Silicon Surfaces

Pyrimidine / Si(111)-7x7
3074

1021
1220
1402
1547

712

Intensity (a.U)

384

110 K

e 5.0 L

d 3.0 L

55 cm

c 1.6 L

-1

b 0.8 L

x2

a 0.4 L
2891

-500

0

500

1000 1500 2000 2500 3000 3500 4000
-1

Wavenumber (cm )

Figure 3.5 HREELS spectra of pyrimidine on Si(111)-7×7 as a function of exposure at
110 K. Ep=5.0eV, specular geometry.

73


The Binding of Multi-functional Organic Molecules on Silicon Surfaces

530
620

Pyrimidine / Si(111)-7x7

55 cm

2891
3074

1621

1021
1220
1402
1547

712

384

Intensity (a.u)

748
893
998
1202

110 K

Chemisorption

x 1.5
(b)

-1

Physisorption

(a)

-500

0

500

1000 1500 2000 2500 3000 3500 4000
-1

Wavenumber(cm )

Figure 3.6 HREELS spectra of the physisorbed and saturated chemisorption pyrimidine
on Si(111)-7×7.

74