Physical Chemistry Chemical Physics

This paper is published as part of a PCCP Themed Issue on:

Interfacial Systems Chemistry: Out of the Vacuum, Through the Liquid, Into the

Cell

Guest Editors: Professor Armin Gölzhäuser (Bielefeld) & Professor Christof Wöll (Karlsruhe)

Editorial

Interfacial systems chemistry: out of the vacuum—through the liquid—into the cell Phys. Chem. Chem. Phys., 2010 DOI: 10.1039/c004746p

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Is there a Au–S bond dipole in self-assembled monolayers on gold? LinJun Wang, Gerold M. Rangger, ZhongYun Ma, QiKai Li, Zhigang Shuai, Egbert Zojer and Georg Heimel, Phys. Chem. Chem. Phys., 2010 DOI: 10.1039/b924306m

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Structural characterization of self-assembled monolayers

of pyridine-terminated thiolates on gold

Jinxuan Liu,a Bjorn Schupbach,b Asif Bashir,c Osama Shekhah,d Alexei Nefedov,d

Martin Kind,bAndreas Terfort*

band Christof Woll*

d

Received 17th November 2009, Accepted 8th February 2010

First published as an Advance Article on the web 4th March 2010

DOI: 10.1039/b924246p

Self-assembled monolayers (SAMs) fabricated on Au(111) substrates from a homologous series

of pyridine-terminated organothiols have been investigated using ultra high vacuum infrared

reflection adsorption spectroscopy (UHV-IRRAS), X-ray photoelectron spectroscopy (XPS),

scanning tunnelling microscopy (STM) and near-edge X-ray absorption fine structure (NEXAFS)

spectroscopy. A total of 4 different pyridine-based organothiols have been investigated, consisting

of a pyridine unit, one or two phenyl units, a spacer of between one and three methylene units

and, finally, a thiol unit. For all pyridine-terminated thiols the immersion of Au-substrates in the

corresponding ethanolic solutions was found to result in the formation of highly ordered and

densely packed SAMs. For an even number of the methylene spacers between the SH group and

the aromatic moieties, the SAM unit-cell is rather large, ð5ffiffiffi

3p� 3Þrect, whereas in case of an odd

number of methylene units a smaller unit cell is adopted, ð2ffiffiffi

3p�

ffiffiffi

3pÞR30�. The tilt angle of the

molecules amounts to 151. In contrast to expectation, the pyridine-terminated organic surfaces

exposed by the corresponding SAMs showed a surprisingly strong resistance with regard to

protonation.

Introduction

Although self-assembled monolayers (SAMs) prepared

from thiols on gold have been investigated for more than

twenty-five years, this field is still developing quickly because

of the diversity and numerous potential applications of these

organic thin films.1–6 Whereas in earlier work on SAMs the

focus was on n-alkanethiolates on gold to unravel funda-

mental aspects of film formation, structure and properties1,3

in later years aromatic thiolates have attracted an increasing

amount of attention. This interest results from the higher

rigidity of the molecular backbones which in many cases have

allowed for a better control of the monolayer structure.7–14

Today, SAMs gain an increasing importance with regard

to the generation of organic surfaces exposing predefined

functionalities.15 Attaching an appropriate function, e.g.

–COOH,16–19 –SH,20–23 –NH224–26 or –OH18,27 at the

o-position of the organothiol allows to tailor the wettability

and the reactivity of the organic surfaces exposed by the

SAMs, which have numerous potential applications in

molecular electronics,28–31 electrochemistry,32–36 or bio-

chemistry.37–42 A particularly exciting new field of SAM

application is interface-based supramolecular chemistry,

where organic monolayers are used as substrates to anchor

and grow highly complex materials like metal–organic frame-

works (MOFs).43–51 Pyridine-terminated SAMs represent a

particularly interesting type of organic substrates. The

nitrogen lone pair electrons of the pyridine unit exposed at

the surface can act as Lewis base. This functionality has e.g.

been used for the complexation of Pd salts, which were then

reduced electrochemically to yield metallic Pd particles.52,53

Pyridine-terminated surfaces have also been used to enhance

the rate of heterogeneous electron transfer between electrodes

and the solution phase of biological species.54 Recent

studies have revealed that the chemical activity of pyridine-

terminated SAMs, e.g. with regard to protonation55,56

or interaction with water57 is quite complicated. The

properties cannot be predicted in a straightforward fashion

from the properties of pyridine in solution, the special

properties of pyridine-terminated surfaces clearly need further

investigations.

The first studies of pyridine-terminated SAMs were carried

out using 4-mercapto-pyridine.52,54,58,59 More recently, SAMs

formed from other pyridine-functionalized thiols or disulfides

have been investigated55–57 to improve the understanding of

factors that influence film growth, the reactivity of this class of

monolayers and their applicability as anchoring layer for e.g.,

metal–organic frameworks.46,50 Here, we present a compre-

hensive study of SAMs prepared from a series of four related

pyridine-terminated thiols with backbones comprising of both

aliphatic and aromatic parts. Fig. 1 shows schematic drawings

of SAMs formed from (4-(4-pyridyl)phenyl)methanethiol

(PP1), (4-(4-(4-pyridyl)phenyl)phenyl)methanethiol (PPP1),

2-(4-(4-(4-pyridyl)phenyl)phenyl)ethanethiol (PPP2) and 3-(4-

(4-(4-pyridyl)phenyl)phenyl)propanethiol (PPP3) on Au(111).

a Lehrstuhl fur Physikalische Chemie I, Ruhr-Universitat Bochum,44780 Bochum, Germany

b Institut fur Anorganische und Analytische Chemie,Goethe-Universitat Frankfurt am Main, 60325 Frankfurt, Germany

c Interface Chemistry and Surface Engineering, Max-Planck-Institutfur Eisenforschung, 40237 Dusseldorf, Germany

d Institute of Functional Interfaces, Karlsruhe Institute of Technology,74800 Karlsruhe, Germany

This journal is �c the Owner Societies 2010 Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 | 4459

PAPER www.rsc.org/pccp | Physical Chemistry Chemical Physics

These films were thoroughly characterized employing a variety

of surface-analytical techniques.

Experimental

Synthesis of pyridine-terminated Organothiols

The pyridine-terminated organothiols were obtained employing

a newly established synthesis route which will be described

elsewhere.60

Preparation of the self-assembled monolayers

The SAMs made from PP1, PPP1, PPP2 and PPP3 were

prepared by immersing Au substrates into 20 mM ethanolic

solutions of the corresponding pyridine-terminated organo-

thiols for 20–24 h. After removal of the samples from solution,

they were rinsed with ethanol and dried in a stream of N2.

For spectroscopic studies (UHV-IRRAS, XPS and NEXAFS),

the following method to obtain substrates with Au(111)

surfaces was employed: a 150 nm gold (Chempur, 99.99%)

layer at a rate of 1 nm s�1 was deposited onto a Si(100) wafer

(Wacker). An 8 nm titanium (Chempur, 99.8%) layer was

deposited at a rate of 0.15 nm s�1 as an adhesion layer between

the Si substrate and the Au layer. Metal deposition was carried

out using a commercial vaporisator (Leybold Univex 300).

The deposition rate was monitored using a quartz crystal

microbalance.

For the STM measurements, freshly cleaved mica sheets

(Mahlwerk Neubauer-Friedrich Geffers) were heated to

280 1C for about two days inside the evaporation chamber

to remove residual water and other contaminations from the

ambient. Subsequently, a 140 nm gold layer (99.995%

Chempur) was deposited by thermal evaporation at a sub-

strate temperature of 280 1C and a pressure of B10�7 mbar

using the above-mentioned vaporisator. The substrate was

cooled down to room temperature in the evaporation chamber

after deposition and was then flame annealed using a butane–

oxygen flame directly before SAM preparation. Using this

procedure, Au substrates with well-defined terraces exhibiting

a (111) surface orientation are obtained routinely.61,62

For the protonation experiments, freshly prepared Au/Si

substrates covered with pyridine-terminated SAMs were

immersed into (1) 0.5 M sulfuric acid (H2SO4) aqueous

solution for about 40 min, followed by rinsing with dimethyl-

formamide and drying with N2 before characterization by IR

spectroscopy at ambient conditions (2) 10 mM trifluoromethane-

sulfonic acid (TfOH) solution in a 9 : 1 mixture of CCl4 and

CH3CN as solvent for about 5 min. Subsequently the samples

were stored in the load lock chamber of a UHV apparatus

(see below) and kept for about one hour at a pressure of

B10�7 mbar before recording of IR spectra under UHV

conditions.

Infrared (IR) spectroscopy

Bulk spectra of the organothiols investigated here for KBr

pellets were obtained using a dry-air purged BioRad Excalibur

FTS-3000 FTIR-spectrometer equipped with a DTGS

detector. IRRA spectra of the SAMs were recorded with a

UHV apparatus (Prevac) with an attached FTIR spectro-

meter (Bruker VERTEX 80v) which has been described

elsewhere.63–66 The base pressure of the measurement chamber

amounted to 2 � 10�10 mbar. All spectra were acquired with a

resolution of 2 cm�1. Some additional IRRA spectra were

taken under ambient conditions with the BioRad spectrometer.

All IRRA spectra were recorded in grazing incidence

reflection mode at an angle of incidence amounting to 801

relative to the surface normal using liquid nitrogen cooled

mercury cadmium telluride (MCT) narrow band detectors.

Perdeuterated hexadecanethiol-SAMs on Au/Si were used for

reference measurements.

XPS

The X-ray photoelectron spectroscopy (XPS) measurements

were performed in a UHV apparatus based on a modified

Leybold XPS system with a double-anode X-ray source. For

the measurements reported here, an Al Ka X-ray source with

an energy resolution of about 0.8 eV was used at normal

incidence. The base pressure of the apparatus was below

3 � 10�10 mbar. The energy scales of all spectra were

referenced to the Au 4f7/2 peak located at a binding energy

Fig. 1 Schematic drawings of the pyridine-terminated SAMs.

4460 | Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 This journal is �c the Owner Societies 2010

of 84.0 eV. To estimate the layer thickness of the investigated

SAMs, they were mounted on the sample holder together with

a reference sample covered with a SAM of a known thickness

(n-decanethiolate SAM). By this means, for both pyridine-

terminated samples and reference sample the geometric

conditions (i.e., distance and angles of X-ray gun and energy

analyzer toward the sample) were identical.

STM

STM micrographs were recorded under ambient conditions

employing a Jeol JSPM 4210 microscope using tips prepared

mechanically by cutting a 0.25 mm Pt/Ir (80 : 20) wire

(Goodfellow). The tunneling current with respect to the

sample varied from 0.1 to 0.4 nA and the sample bias from

�200 to 600 mV. No tip-induced changes were observed for

these tunneling conditions.

NEXAFS

The NEXAFS measurements were performed at the dipole

beamline HE-SGM of the synchrotron storage ring BESSY II

in Berlin (Germany). All NEXAFS measurements were

carried out with linearly polarized radiation (polarization

factor P E 82%67) with an energy resolution of better than

350 meV. NEXAFS spectra were recorded at the C K-edge

and the N K-edge in the partial electron yield mode with a

retarding voltage of �150 V at the C K-edge and �250 V at

the N K-edge, respectively. In the partial electron yield mode,

retarding potentials are applied to assure that only near-

surface electrons are detected.91 The NEXAFS raw data were

normalized in a multi step procedure by considering the

incident photon flux, which was monitored by the photo-

current on the gold grid, and using the background signal of

the clean Au substrate. A carbon contamination of a gold grid

with a characteristic peak at 284.81 eV was registered

simultaneously with each spectrum and served as a reference

for photon energy calibration. To determine the molecular

orientation from the linear dichroism, spectra were recorded

for 5 different incidence-angles y of the synchrotron radiation

(y = 20, 30, 55, 70 and 901 with respect to the surface).

Theoretical calculations of IR and NEXAFS spectra

Theoretical values of the vibrational frequencies of the isolated

molecules have been performed by employing quantum-

chemical DFT calculations using the Gaussian 03 program

package.68 The employed approach (functional, basis sets) was

the same as used in a previous publication55 on a related

system (B3LYP/cc pvDZ). The computed IR-frequencies

have been scaled with the same factor of 0.967.55 The

computational results were used to aid the assignment of the

vibrational bands and to estimate the directions of the corres-

ponding transition dipole moments (TDMs).

In order to provide a reliable basis for the assignment of the

features in the experimental NEXAFS data, in particular with

regard to understanding the origin of the splitting in the C 1s

p* resonance, and in order to gain more insight into the

conformation of the chemisorbed molecules within the SAMs,

a series of calculations with the quantum chemistry program

package StoBe69 were carried out. StoBe can deal with rather

large molecules and clusters and has specific implementations

to reliably describe inner-shell spectroscopies.70,71

Results

IR spectroscopy

Like other organic substrates with a reactive termination

(e.g., OH,27 COOH16), the surfaces of pyridine-terminated

SAMs are prone to adsorption of water57 at ambient

conditions, which might give rise to protonation.55 To avoid

such contaminations of the organic surfaces exposed by the

SAMs by water and other molecules at ambient conditions,

the acquisition of IR-spectra for the SAMs studied here has

been carried out under ultra high vacuum conditions using the

UHV-IR apparatus mentioned above. No further annealing

was applied after transfer of the samples into UHV.

Fig. 2–5 display the UHV-IRRA spectra recorded for PP1-,

PPP1-, PPP2-, and PPP3-SAMs (panels a) together with

additional bulk IR spectra recorded for KBr pellets (panels b)

and the results of ab initio calculations (panels c). The assign-

ment of the vibrational features as listed in Table 1

was carried out using these theoretical results as well as

assignments provided in previous work.72–74 Generally, a very

satisfying agreement between the theoretical and experimental

band positions is observed. Comparison of the SAM spectra

and the bulk (KBr) spectra confirms that organic thin layers of

PP1, PPP1, PPP2, and PPP3 have formed upon immersion of

the Au-substrates into the respective ethanolic solutions. All

IR-bands observed for the SAMs also appear in the respective

bulk spectra. Some IR bands, however, are only present in the

KBr data (e.g. the SH stretching mode 6 at about 2570 cm�1)

or are markedly attenuated in the UHV-IRRA spectra with

regard to the bulk data. While the disappearance of the SH

stretching mode can be explained with the cleavage of the SH

bond (and subsequent formation of a S–Au bond), the

attenuation of several other bands result from the so-called

surface selection rule governing IR-spectroscopy on

metals.75,76 According to this rule, vibrational modes with a

Fig. 2 Experimental and calculated spectra of PP1-species. Panel a:

UHV-IRRA spectrum of the PP1-SAM, panel b: bulk spectrum of

PP1 taken from KBr pellets, panel c: calculated spectra of the isolated

PP1 molecule. Calculated spectra are given in arbitrary units of

absorption.

This journal is �c the Owner Societies 2010 Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 | 4461

transition dipole moment (TDM) orientated parallel to a

metal surface cannot be seen in IR spectroscopy.

XPS

XP spectra recorded from PP1-, PPP1-, PPP2-, PPP3-SAMs

on polycrystalline gold substrates are shown in Fig. 6.The C 1s

line profiles in Fig. 6 turn out to be rather asymmetric

indicating that the different C atoms exhibit different chemical

shifts. Therefore, two components were used to fit the C 1s

spectra after a Shirley background subtraction. The results of

the fitting process are listed in Table 2. Similar asymmetric line

profiles are present in the high quality XP spectra reported

by Silien et al.56 for a PP3 (i.e. 3-(4-(4-pyridyl)phenyl)

propanethiol -SAM on Au(111) and by Zubavichus et al.57

for a PP0 (i.e. 3-(4-mercaptophenyl)pyridine)-SAM on

Au(111). The authors of these studies assign the component

at higher energy to the ortho- and para-C atoms of the pyridine

ring and the lower energy component to the other C atoms of

PP3. The intensity ratios of the components in the spectra of

the PP1-, PPP1-, PPP2-, and PPP3-SAMs are generally in

accordance with this interpretation. Note, however, that the

limited signal-to-noise ratio in our XP spectra does not allow

for a more detailed analysis of the intensities of the C 1s

components.

The N 1s region shown in Fig. 6 can be well described by a

single component located at 399.0, 398.7, 398.7 and 398.9 eV

for the PP1-, PPP1-, PPP2- and PPP3-SAMs, respectively.

These positions are in accordance with the presence of a

non-protonated pyridine rings. For a protonated pyridine-

terminated SAM substantially higher binding energies,

400.4 eV, were reported in previous work.59

No other peaks than those of C, N and Au could be found

in the XP spectra of the SAMS investigated in this study.

From the XPS data film thicknesses of the SAMs were

obtained by evaluating the ratios of the Au 4f7/2 and the C 1s

intensities (IAu and IC) and using a decanethiolate SAM on Au

as a reference system.17–19

ICIAuðsampleÞ

ICIAuðreferenceÞ

¼ 1� e�dsample

lC1s-AromaticðECÞ

e�dsamplelAuðEAuÞ

� e�dreferencelAu4f ðEAuÞ

1� e�dreference

lC1s-AliphaticðECÞ

ð1Þ

The photoelectron escape depths l of gold and carbon

depend on the X-ray source as well as the density of the layer

material; for Al Ka (1486.6 eV) they amount to lAu4f = 45 A

at a photoelectron kinetic energy of EAu = 1402 eV

and lC1s-Aliphatic = 35 A, lC1s-Aromatic = 27.3 A77 at a

photoelectron kinetic energy of EC = 1202 eV. For thickness

of the decanethiolate SAM a value of 13.1 A78 was used,

corresponding to a tilt angle of the molecules of 301

with respect to the surface normal and an Au–S distance

of 2 A.79,80

Using eqn (1) thicknesses of 10.4 � 1 A, 14.4 � 1 A,

14.8 � 1 A, and 17.2 � 1 A were obtained for the PP1-,

PPP1-, PPP2-, and PPP3-SAMs, respectively. Fig. 7 displays

the experimental results together with data points representing

the maximum SAM thickness given by the full length of the

Fig. 3 Experimental and calculated spectra of PPP1-species. Panel a:

UHV-IRRA spectrum of the PPP1-SAM, panel b: bulk spectrum of

PPP1 taken from KBr pellets, panel 3: calculated spectra of the

isolated PPP1 molecule. Calculated spectra are given in arbitrary units

of absorption.

Fig. 4 Experimental and calculated spectra of PPP2-species. Panel a:

UHV-IRRA spectrum of the PPP2-SAM, panel b: bulk spectrum of

PPP2 taken from KBr pellets, panel c: calculated spectra of the

isolated PPP2 molecule. Calculated spectra are given in arbitrary units

of absorption.

Fig. 5 Experimental and calculated spectra of PPP3-species. Panel a:

UHV-IRRA spectrum of the PPP3-SAM, panel b: bulk spectrum of

PPP3 taken from KBr pellets, panel c: calculated spectra of the

isolated PPP3 molecule. Calculated spectra are given in arbitrary units

of absorption.

4462 | Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 This journal is �c the Owner Societies 2010

corresponding molecules. Theoretical thicknesses assuming a

tilt angle of 151 with respect to the surface normal are also

provided (see discussion).

STM

In Fig. 8 STMmicrographs recorded for the SAMs made from

PP1, PPP1, PPP2 and PPP3 on Au(111) are shown. The

images with lower resolution (labeled a) exhibit a morphology

characteristic for thiolate SAMs on gold, monatomic

steps separating large terraces decorated by so-called

‘‘etch-pits’’,81–84 round depressions with diameters of

5–10 nm and a depth of 2.5 A, equal to the height of a single

gold layer.85–87 While the density and diameter of these

depressions are comparable for the PP1-, PPP1- and

PPP3-SAMs, for the PPP2-SAM the depressions have

substantially larger diameters and a lower density.

The high-resolution STM micrographs of the SAMs

displayed in columns b and c show the monolayers with

molecular resolution. The structure of PPP2-SAM is charac-

terized by domains with an average size of about 20 nm. For

the other SAMs the domain sizes are somewhat smaller, the

average value amounts to 5–10 nm. In column c, we have

added two lines (A and B) to the STMmicrographs in order to

denote the high-symmetry crystallographic directions. In

column d we show cross-section height profiles taken along

Table 1 Vibrational frequencies of pyridine-terminated species as obtained from the calculated, bulk and SAM spectra, together with theassignment and the orientation of their transition dipole moments

Band position/cm�1

No. Assignmenta TDM

PP1 PPP1 PPP2 PPP3

Calc. Bulk SAM Calc. Bulk SAM Calc. Bulk SAM Calc. Bulk SAM

1 n CH arom > 3089 3077 3093 3074 3032 3089 3078 3038 30782 n CH Ph J 3070 3058 3040 3072 3056 2983 3067 3060 3033 3060 30573 n CH Py ? 3047 3034 3027 3046 3034 2964 2949 3032 2987 3046 3031 30294 nas CH2 > 3018 2930 2923 3018 2926 2929 3011 2964 2987 2933 2925

2977 29295 nsym CH2 / 2962 2907 2855 2962 2847 2855 2954 2900 2926 2933 2852 2851

2937 2841 28536 n SH 2563 2568 2555 2553 2757 2538 2576 25347 g CC Py J 1590 1598 1596 1590 1596 1595 1590 1591 1595 1590 1596 15978 g CC arom > 1567 1578 1578 1553 1563 1561 1553 1563 1563 1553 1563 1562

1537 1541 1541 1529 1538 1543 1529 1539 1538 1529 1540 15409 dbend CH arom J 1499 1517 1516 1485 1504 1505 1485 1484 1505 1485 1505 1506

1466 1487 1487 1464 1485 1484 1369 1507 1484 1464 1486 148510 dbend CH2 / 1428 1441 1441 1433 1468

1415 145811 g CC arom > 1400 1404 1405 1426 1405 1426 1404 1425

1387 1421 1389 1409 1384 1389 1406 1407 1389 1411 13831381 1400 1381 1399 1381 1401

12 gCH2 > 1272 1292 128513 dbendCH arom + g CH2 / 1221 1230 1232 1220 1231 1228 1203 1231 1224 1197 1231 1240

1199 1205 1203 1184 1204 1213 1185 1221 1184 1185 1222 122814 dbend CH Ph + g CC Py J 983 1003 1004 983 1003 1005 983 1004 1004

a Explanation of band assignments: dbend: bending mode; g CC: CC-vibration, wagging mode; Py: band is attributed mainly to a vibration mode of

the pyridine ring; Ph: band is attributed mainly to a vibration mode of the phenyl ring(s); arom: band is attributed to all aromatic rings of the

molecule; n: stretching mode; nsym: symmetric stretching mode; nas: asymmetric stretching mode; Explanation of the orientation of the transition

dipole moment (TDM) of the bands:>: TDM perpendicular to the molecular axis defined as line through the N-atom and the phenyl; C-atom that

binds to the aliphatic chain; J: TDM almost of completely parallel to the molecular axis; /: TDM neither parallel nor perpendicular to the

molecular axis; ?: band consists of more than one resonance with different orientations of the TDM; In some cases, especially in the CH stretching

region, the assignments may be simplifying or uncertain.

Fig. 6 XP spectra of PP1, PPP1, PPP2 and PPP3-SAMs on Au(111).

This journal is �c the Owner Societies 2010 Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 | 4463

the lines displayed in column c. The structural data of all

SAMs are summarized in Table 3.

Analysis of the high-resolution STM images reveals that the

structural properties of three of the four investigated SAMs,

PP1-, PPP1- and PPP3-SAMs are quite similar. In each case,

the unit cells are oblique with an angle of about 57–581

between lines A and B. The lattice constants along the

directions A and B amounts to 5.7–6.4 � 0.2 A and

10.3–11.1 � 0.2 A, respectively. For these three SAMs, the

height-profiles show one maximum per unit cell along

direction A and two maxima of different height along direction

B. This suggests the presence of two inequivalent molecules

per unit cell.

The PPP2-SAM has a significantly different structure with

an almost rectangular unit cell. The angle between directions

A and B as indicated in Fig. 8 amounts to 841, the

lattice constants along A and B amount to 9.9 � 0.1 A and

25.9 � 0.2 A, respectively. Like for the other SAMs, the height

profiles for the PPP2-SAM reveal one maximum per unit cell

along direction A, but four maxima with different heights per

unit cell along direction B.

Experimental NEXAFS spectra

In Fig. 9 we display C1s and N1s NEXAFS spectra recorded

for PP1-, PPP1-, PPP2-, and PPP3-SAMs at different angles of

incidence. All spectra exhibit a number of characteristic

absorption resonances due to excitations from the respective

core-levels into p* and s* orbitals of the aromatic rings as well

as into molecular orbitals of Rydberg character. The assign-

ment of the individual resonances as provided in Table 4 and 5

is based on previous publications reporting NEXAFS and

inner shell electron energy loss (ISEEL) spectra of related

aromatic compounds.88–90 For the present study, the main

purpose of the NEXAFS spectra is to determine the molecular

orientation from an analysis of the dichroism of the 1s-p1*excitations located at around 285 eV in the C K-egde

spectra and slightly below 400 eV in the N K-edge spectra.

Accordingly, we focus our attention mainly on these

1s-p*-resonances. The insets in Fig. 9 clearly demonstrate

that the C K-edge 1s-p1* transition consists of at least two

components located at 285.35 eV and 285.65 eV (PP1-SAM)

and 285.2 and 285.6 eV (PPP1-, PPP2-, PPP3-SAMs),

respectively.

Both carbon and nitrogen K-edge NEXAFS spectra reveal a

pronounced dichroism, the strongest variations of intensity

with angle of incidence are observed for the 1s-p1* resonances.An analysis of this dichroism allows determining the tilt angles

of the molecules with respect to the substrate surface. For

molecules adsorbed on a surface with an at least threefold

symmetry, the relationship of the NEXAFS resonance

intensity Ip* of the 1s-p* transitions and the X-ray

radiation incidence angle y relative to the surface can be

expressed as:91,92

Ip* p P�cos2 y�(1 � 32sin2 a) + 1

2sin2 a (2)

where P denotes the degree of polarization of the incident

X-ray light and a the average tilt angle of the transition dipole

moments (TDMs) governing the particular excitation with

respect to the surface normal.

Application of eqn (2) to the C K-edge and N K-edge 1s-p1*transition intensities yields values for the molecular tilt angle aof 671, 681, 641, and 651 (C K-edge), and 611, 611, 581 and 591

(N K-edge) for the PP1-, PPP1-, PPP2-, and PPP3-SAMs,

respectively.

Calculated NEXAFS spectra

The presence of at least two components in the C1s-p*excitations has already been reported in previous studies on

pyridine88–90,93 and other organic compounds containing

pyridine moieties.56,57 Zubavichus et al.57 reported a split

resonance for a PP0-SAM on Au(111) and Silien et al.56 for

a PP3-SAM on Au(111). While Zubavichus et al. did not

discuss the origin of this splitting in more detail, Silien et al.

assigned the component at lower energy (285.05 eV) to the

Table 2 Results of the evaluation of XP spectra recorded from PP1, PPP1, PPP2 and PPP3-SAMs on Au(111). The FWHM for the gold, carbonand nitrogen peak fits is given in the parentheses. See text for explanation of obtaining binding energy, intensity and layer thickness

Sample

Binding energy/eV Intensity/cps eV

Layer thickness/AAu 4f7/2 C 1s C 1s N 1s Au 4f7/2 C 1s C 1s N 1s

PP1 84.0 (1.2) 284.5 (1.3) 285.9 (1.3) 399.1 (1.5) 12 528 756 249 135 10.4 � 1PPP1 84.0 (1.2) 284.4 (1.3) 285.4 (1.3) 398.7 (1.5) 13 417 1269 261 126 14.4 � 1PPP2 84.0 (1.2) 284.4 (1.3) 285.8 (1.3) 398.7 (1.5) 12 978 1212 228 106 14.8 � 1PPP3 84.0 (1.2) 284.6 (1.3) 285.7 (1.3) 398.8 (1.5) 12 345 1435 258 102 17.2 � 1

Fig. 7 Thicknesses of the pyridine-terminated monolayers as

obtained from the analysis of the XPS data (’), from the theoretical

values for upright and fully extended molecules on the Au surface (J),

and from applying a tilt angle of 151 as suggested from evaluation of

the experimental and theoretical NEXAFS data (n).

4464 | Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 This journal is �c the Owner Societies 2010

excitation into the lowest unoccupied p (E2u) orbital of the

phenyl ring and into the lowest unoccupied p (B1) orbital of

the pyridine ring, whereas the component at higher energy

(285.6 eV) was attributed to the excitation into the p (A2)

orbital of the pyridine ring.

The same assignment was proposed in an earlier NEXAFS-

study on pyridine adsorbed on Ni(111).94 However, in later

combined experimental and theoretical studies on gas phase

pyridine and pyridine monolayers on ZnO(0001)89,90 it has

been shown that in case of pyridine in fact both components

are due to excitations into the p (B1) orbital. A theoretical

analysis revealed that the splitting does not result from

different final states but from different initial states, i.e. a

chemical shift of the 1s core levels of the ortho-, meta- and

para-C-atoms in the pyridine ring. The same assignment was

proposed in a recent study of pyridine monolayers on

Si(100).93

A major problem with the assignment of the two compo-

nents in C 1s-p* proposed by Silien et al.56 for PP3 is the

intensity ratios of the components found in the NEXAFS

spectra of the investigated molecules. Assuming that the

C 1s-p* transition probabilities in both the phenyl and the

pyridine units are similar, one would expect substantially

different intensities because the component at higher energy

(285.6 eV) originates from only two C-atoms (the pyridine

ortho C-atoms) while the component at lower energy

(285.05 eV) is due to the rest of the aromatic C-atoms

(i.e. 6 or 12 from the phenyl unit(s) and 3 (meta and para)

from the pyridine unit). However, in the NEXAFS spectra of

Fig. 8 STM images of PP1, PPP1, PPP2 and PPP3 SAMs on gold/mica recorded at different resolutions. The sizes of the unit cells are inferred

from the averaged distances in the cross-section height profiles (1)d–(4)d taken along the lines labelled A and B in (1)a–(1)d. The PPP2-SAM has a

unit cell different from the PP1, PPP1, and PPP3-SAMs. See text for discussion.

Table 3 Structural data of the PP1-, PPP1-, PPP2-, and PPP3-SAMsas obtained from the STM images, together with structural data ofideal overlayers on Au(111)

a (1) a/A b/A Ratio b/a

Pyridine terminated-SAMsPP1 58 5.8 � 0.2 10.3 � 0.2 1.8 � 0.3PPP1 57 6.4 � 0.2 11.1 � 0.1 1.7 � 0.3PPP2 84 9.9 � 0.1 25.9 � 0.2 2.6 � 0.3PPP3 58 5.7 � 0.2 11.1 � 0.2 1.7 � 0.3Overlayer structures

ð2ffiffiffi

3p�

ffiffiffi

3pÞR30� 60 5.0 10.0 2.0

ð5ffiffiffi

3p� 3Þrect 90 8.7 24.9 2.9

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PP0,57 PP356 and PP1 (reported in this study) both

components of the 1s-p1* resonance are of roughly the same

intensity. Increasing the number of phenyl units attached to

the pyridine-moiety by one leads to an intensity ratio that is

constant for the PPP1-, PPP2- and PPP3-SAMs; in all cases a

higher intensity of the component at lower energy is observed.

This indicates that the component at lower energy is at least

predominantly due to the phenyl units.

Still, the difference between the intensities of both compo-

nents is quite low. This might be due to various facts that

complicate the interpretation of the NEXAFS data: (a) the

transition probabilities of the C atoms in the phenyl and in the

pyridine units (or even within the pyridine moiety) might

differ, (b) the C atoms of the investigated molecules could

have chemical shifts different from those in the pyridine

molecule, (c) other transitions than into p (B1) have to be

taken into account, e.g. into p (A2), (d) there is also a

vibrational fine structure to be considered (as discussed in

ref. 90), and (e) a non-coplanar arrangement of the aromatic

rings might influence the absorption probability (see discussion).

In view of these ambiguities as regards the assignment of the

various contributions to the C 1s-p* transition we have used

the StoBe program package69 to calculate NEXAFS spectra of

the isolated PP1 molecule for different internal twist angles

between the two aromatic rings of the molecule. Fig. 10 shows

theoretical results for the isolated PP1molecule (panels b-d)

in comparison to the experimental spectrum (panel a) of the

PP1-SAM. The experimental data were recorded close to

the so-called magic angle.91 For this photon incidence angle

the influence of linear dichroism on relative NEXAFS

resonance intensities can be largely excluded.

The agreement between the experimental and theoretical

results is quite satisfying. With regard to experiment the two

contributions to the C 1s-p* transition are slightly shifted and

the splitting is somewhat smaller. A more detailed analysis of

the theoretical results reveals that phenyl and pyridine C

atoms contribute to both components, as can be seen from

the summarized contribution of the phenyl and pyridine ring C

atoms shown in panels b–d of Fig. 10. We thus conclude

that the splitting is not due to two different final states but

instead to a different binding energy of the initial state

(see discussion above).

For similar molecules (namely pyridine,90 benzene95 and

naphthalene95) it has been found that an analysis of the C 1s

p* resonance is further complicated by a vibrational structure,

which in the present study has not been taken into account.

For these reasons, for the analysis of the dichroism (see below)

Fig. 9 Carbon K-edge and nitrogen K-edge NEXAFS spectra of

PP1-, PPP1-, PPP2-, and PPP3-SAMs on Au(111) recorded at different

incidence angles. To keep the figure as simple as possible, only

the spectra recorded at grazing incidence (y = 201), the magic angle

(y = 551) and normal incidence (y = 901) are displayed. The insets in

the C K-edge spectra show the region from 284–287 eV with the 1s-p1*transition that consists of at least two components, whereas the 1s-p1*transition of the N K-edge spectra shows only one maximum.

Table 4 Photon energy positions in eV and assignments (only thefinal orbital) of the C K-edge NEXAFS resonances for PP1-, PPP1-,PPP2-, and PPP3-SAMs on Au(111) and reference data for benzeneand pyridine. The labeling p1* and p2* refers to the nomenclature forbenzene. R denotes the transition to a Rydberg state. The p1*transition in the spectra of pyridine and the SAMs investigated in thisstudy show two maxima. See explanation in the text

Species p1* R p2* s1* s2*

Benzene 285.2a,b 287.2a 288.9a,b,c 293.5a,b 300.2a

285.0c 287.2b 293.3c 299.8b

300.1c

Pyridine 285.3d 287.4a 289.2a 294.2a 300.1a

285.5e 289.1c 294.1c 301.0c

285.1 + 285.7f

PP1-SAM 285.35 + 285.65 287.75 289.25 294.15 302.65PPP1-SAM 285.2 + 285.6 288.1 289.2 293.6 302.7PPP2-SAM 285.2 + 285.6 288.1 289.3 293.6 302.9PPP3-SAM 285.2 + 285.6 288.2 289.3 293.6 303.0

a Gas phase, taken from ref. 88. b Gas phase, taken from ref. 119.c Solid phase, taken from ref. 88. d Gas phase, taken from ref. 88. Due

to limited spectral resolution, the authors of this publication only

found one maximum. e Solid phase, taken from ref. 88. Due to limited

spectral resolution, the authors of this publication only found one

maximum. f Taken from ref. 89.

Table 5 Photon energy positions in eV and assignments (only thefinal orbital) of the N K-edge NEXAFS resonances for PP1-, PPP1-,PPP2-, PPP3-SAMs on Au(111) and reference data for pyridine

Species p1*(b1) p2*(a2) p3*(a1) s1* s2*

Pyridine 398.8a,b,c 400.2c 402.7a 408.0a,b 414.3a,b

403.3b

402.6c

PP1-SAM 398.9 400.5 402.8 408.8 415.8PPP1-SAM 398.6 400.5 402.6 408.6 415.6PPP2-SAM 398.6 400.5 402.5 408.9 415.7PPP3-SAM 398.6 400.5 402.6 408.9 415.8

a Gas phase, taken from ref. 88. b Solid phase, taken from ref. 88.c Gas phase, taken from ref. 90.

4466 | Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 This journal is �c the Owner Societies 2010

no attempt was made to distinguish between the phenyl and

pyridine contributions, only total the integrated intensity of

the C 1s p* resonance was used for the analysis.

Protonation behavior of the pyridine-terminated SAMs

The chemical activity of the pyridine-terminated organic

surface exposed by the different pyridine-based SAMs studied

here with regard to protonation was tested using the procedure

described in the experimental section. This experiment was

also performed to compare the chemical behavior of the SAMs

studied here with the findings reported previously for the

protonation behaviour of PP3.56 All SAMs investigated in

this work were found to yield very similar results. In the

following we will only discuss the case of the PP1-SAM. Panel

a of Fig. 11 shows the IR spectrum as recorded for the pristine

PP1-SAM. After immersion in a 0.5 M solution of sulfuric

acid, no changes in the IR spectrum are observed, see panel b.

After immersing the SAM into a solution of the stronger acid

trifluoromethanesulfonic acid, however, the IR spectrum

shows characteristic changes that indicate a protonation

(the appearance of a strong new band at B1690 cm�1 is

discussed in detail and assigned to a protonated species e.g.

in ref. 55 and references therein).

In order to rule out that the lack of any evidence of

protonation after immersion in sulfuric acid (which was

reported in ref. 56) is due to the quality of the SAMs,

additional protonation experiments were carried out with

SAMs prepared on fresh and also on aged substrates. In other

studies the quality of the SAM has been shown to critically

influence the chemical activity of the organic surface.21 In the

present case no differences could be found for SAMs with

different structural quality, in no case did we find any evidence

for a protonation after immersion in sulfuric acid. In addition,

a SAM prepared from PP3 as provided from the authors of

ref. 56 was investigated in our laboratory. In contrast to the

results of Silien et al.,56 this SAM could not be protonated

with sulfuric acid but only by using trifluoromethanesulfonic

acid. The reasons for this obvious discrepancy to the

previously published results by Silien et al.56 are unknown.

Note that care was taken to carry out the protonation experi-

ment with sulfuric acid using exactly the same procedure as

described in ref. 56.

Discussion

Monolayer formation

The IR data displayed in Fig. 2–5 clearly indicate the presence

of a well-defined SAM consisting of the corresponding

Fig. 10 Comparison of (a) the experimental NEXAFS spectrum of

the PP1-SAM on Au(111) recorded at the magic angle and NEXAFS

spectra of PP1 molecules calculated using the StoBe program package.

Spectra have been calculated for three different internal twist angles oof the aromatic rings: (b) 361, (c) 181, and (d) coplanar conformation

(01). Both maxima of the p* resonance have contributions from both

phenyl and pyridine ring C atoms.

Fig. 11 Result of protonation experiments of the pyridine-terminated

SAMs, here demonstrated by the example of the PP1-SAM. Panel a)

shows the UHV-IRRA spectrum of the untreated SAM, panel b) the

IRRA spectrum of the SAM recorded at atmospheric pressure after

immersing into 0.5 M aqueous H2SO4. The spectrum shows no

substantial differences compared to the one of the untreated SAM

indicating that no protonation did happen. Panel c) shows the

UHV-IRRA spectrum of the SAM after immersing in 10 mM solution

of trifluoromethanesulfonic acid in a 9 : 1 mixture of CCl4 and CH3CN

as solvent. The SAMs of the other thiols investigated in this study

behaved similar.

This journal is �c the Owner Societies 2010 Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 | 4467

pyridine-terminated thiolates on the Au surface. The band

intensities and the absence of any SH related bands in the

SAM spectra as well as the SAM-thicknesses as deduced

from the XPS data (Fig. 7) are fully consistent with a

SAM-structure as depicted in Fig. 1.

Orientation of the molecules with respect to the surface

When interpreting the IR spectra of the SAMs, the surface

selection rule can be applied to gain some qualitative informa-

tion on the orientation of the molecules relative to the

substrate surface. The simplest way to proceed is to search

for bands where the band intensities are lower in the SAM

than for the bulk (KBr) sample. A comparison of the data

shown in Fig. 2–5 reveals that this is the case for the bands 8

and 11 which are assigned to the gCC arom vibrations.

According to the theoretical calculations, these bands have

TDMs oriented perpendicular to the molecular axis defined by

the line through the N-atom and the phenyl C-atom that binds

to the methylene group. This observation thus supports the

presence of oriented monomers within the SAM, with the

molecular axis of the pyridine-based molecules orientated

perpendicular to the Au-substrate.

All IR band intensities are consistent with such an upright

orientation of PP1 as indicated in Table 1. Note, that a

pronounced overlapping of the CH stretching bands and their

rather small intensities complicates the analysis for these

stretching modes (3040 cm�1–2923 cm�1).

Similar conclusions can be drawn for the other SAMs

investigated in this study: in all IRRA spectra, the bands with

an orientation of their TDM perpendicular to the molecular

axis (1, 8, 10, 11) are attenuated whereas the bands exhibiting

an orientation of the TDM parallel to the molecular axis

(7, 9, 13, 14) are not attenuated. The fact that band 2 is

slightly attenuated despite a parallel TDM and the fact that

band 4 is not attenuated despite perpendicular TDM can be

explained by the arguments provided above.

In conclusion, the band intensities in the IR spectra of the

SAMs are in accord with the assumption that well-oriented

monolayers of organothiolates have been formed on the

substrate surface with an upright orientation of the

organothiolate moieties.

When considering the results obtained by NEXAFS

spectroscopy we would like to point out that the values aCobtained from the C K-edge dichroism correspond to an

average of the tilt angles of the TDMs of all aromatic rings

of the respective molecules (will below be referred to as

‘‘average tilt angle’’), whereas the values aN obtained from

the N K-edge dichroism corresponds to the tilt angle of the

TDM of the pyridine moiety only (referred to below as

‘‘pyridine unit tilt angle’’). The TDM tilt angles obtained for

the SAMs investigated in this study are different, the average

tilt angle mounts to 64–681 and the pyridine unit tilt angle: to

58–611. These differences are considered significant.

In case of a PP3-SAM on Au(111), different tilt angles for

the pyridine and the phenyl unit have already been reported by

Silien et al.56 A possible reason for this observation is that the

molecules are bent upon adsorption on the gold surface, i.e.

that the molecular axes of the pyridine unit and the subsequent

phenyl unit are not parallel as for the free molecule. Since such

a distortion is energetically quite unfavourable, we feel that we

can rule out this explanation and will not consider it any

further. Instead, we follow the authors of ref. 56 in favoring

another explanation for the present experimental results,

namely the presence of tilted molecules in connection with a

non-coplanar conformation of the individual aromatic rings.

For a given orientation of the molecular axis (described by the

tilt angle b with respect to the surface normal), different

orientations a of the TDMs of the 1s-p1* resonance can be

obtained in dependence on the rotation g of the aromatic ring

with respect to the molecular axis. The external twist angle g isdefined such that g= 0 when the TDM is in the plane spanned

by the surface normal and the molecular axis. An illustration

of the angles a, b and g can be found in Fig. 1 of ref. 96.

Following this definition of the angles, the relationship

between them is ref. 91:

cos a = sin b cos g (3)

The values for a obtained from an analysis of the C K-edge

and the N K-edge spectra will be different if the twist angle g ofthe pyridine unit is different from the average of the aromatic

moieties in the molecule, i.e. if the aromatic rings are twisted

with respect to each other. The difference between the twist

angles g is equal to the internal twist angle o of the aromatic

rings. In the bulk phase, polyphenyl molecules tend to have

smaller internal twist angles compared to the gas phase. For

biphenyl and several terphenyls in the bulk the averages of the

absolute values of o have been found to be about 151 at room

temperature.97–103 For the free molecules, however, these

values are much larger, e.g. for gas phase biphenyl a value

of 40 � 51 has been reported.104,105

A first indication that the twist angle between the pyridine

ring and the subsequent phenyl ring is not zero is provided by

a geometry optimization using Gaussian68 for the free PP1

molecules, which yields a value of 361, similar to that reported

for free biphenyl molecules.104,105

In principle, the presence of a non-zero torsion angle could

also have an effect on the NEXAFS-spectra since a torsion will

reduce the mixing of the p*-MOs of the individual rings.

To explore this possibility, NEXAFS spectra of PP1 were

simulated using StoBe69 for different values of o. The corres-ponding results are displayed in Fig. 10. Panel d displays the

calculation result for a coplanar conformation (o = 01),

in panel c the spectrum for an intermediate value is shown

(o = 181). Panel a of Fig. 10 shows the experimental

NEXAFS spectrum recorded at an angle close to the magic

angle to exclude any influence of molecular orientation. The

theoretical results reveal that there is indeed a substantial

variation for relative NEXAFS intensities with the internal

twist angle. Comparison of experimental PP1-SAM data and

theoretical spectra shows the best agreement for the inter-

mediate torsion angle of 181.

The tilt angle b of the molecular axis of PP1 can be

estimated from the experimental values aC and aN using

eqn (3) and the relationship between the twist angles of the

pyridine unit and the phenyl unit:

gphenyl � gpyridine = o (4)

4468 | Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 This journal is �c the Owner Societies 2010

Assuming that the PP1 molecules chemisorbed on the Au

surface actually have an internal twist angle of o = 181 and

that aC is equivalent to the arithmetic average of the TDM tilt

angles of the pyridine and the phenyl units, a value of 151 is

obtained for the tilt angle b.Although the estimate for o is rather approximate and

despite the fact that the analysis is additionally complicated

by the fact that a for the phenyl ring is not directly available,

we take these results as a strong indication that indeed the

aromatic rings within PP1 and the other pyridine-based

molecules are substantially twisted and that the tilt angle bof the molecular axes relative to the surface normal is rather

small. A value of b = 151 is fully consistent with the other

results of this study, e.g. the attenuation of IRRAS bands with

TDMs perpendicular to the molecular axis and the layer

thicknesses derived from XPS as can be seen by comparison

of the experimental layer thickness of PP1 and the calculated

layer thickness assuming a tilt angle of 151 in Fig. 7.

Although NEXAFS spectra were calculated only for PP1,

we propose a rather small tilt angle b also for the PPP1- and

PPP3-SAMs. This hypothesis is based on the fact that (a) the

dichroism in the NEXAFS spectra is very similar for all

molecules, (b) the IR spectra of all SAMs indicate that the

adsorbed molecules stand quite upright on the surface and (c)

the experimentally obtained layer thicknesses are in

accordance with such small tilt angles. Concerning point c,

PPP2-SAMs are slightly different. In this case the thickness

extracted from the XPS data as displayed in Fig. 7 give rise to

the assumption that the tilt angle is distinctly larger than 151.

In a previous investigation of biphenyl-based thiol SAMs on

gold and silver14 an alteration of molecular tilt angles has been

found that depends on the number of alkyl spacers between

the anchor group and the aromatic rings. Like for the

PP1-, PPP1-, and PPP3-SAMs investigated in this study, the

SAMs formed from biphenyl-based thiols with odd numbers

of methylene spacers were found to have smaller tilt angles

than those with even numbers of methylene spacers. The

results displayed in Fig. 7 indicate that the SAMs investigated

in this study show similar behavior. The STM data lead to a

similar conclusion (see below).

Lateral packing within the organic thin layers

The STM data as shown in Fig. 8 and listed in Table 3 indicate

that the lateral packing of the PP1-, PPP1- and PPP3-SAMs

on the Au(111) substrate is similar to a commensurate

ð2ffiffiffi

3p�

ffiffiffi

3pÞR30�

overlayer structure. There was no indication for a

Moire-structure in the experimental data. The PPP2-SAM

structure is markedly different; the STM data can be best

explained by formation of a ð5ffiffiffi

3p� 3Þrect overlayer on the

Au(111) surface, although the experimentally observed

periodicity along direction A is slightly larger than the value

expected from this u. Again, there was no indication for a

Moire-structure in the experimental data.

In earlier STM studies on SAMs formed from o-biphenyl-alkanethiols on Au(111) with 1-6 methylene spacers

between the organic moeietiy and the S-atom7,10 the same

ð2ffiffiffi

3p�

ffiffiffi

3pÞR30� and ð5

ffiffiffi

3p� 3Þrect structures were found for

thiols with odd and even spacer numbers, respectively. The

authors of ref. 7 and 10 explained this phenomenon by the

competition of the energetically most favourable Au–S–C

bond angle and the intermolecular packing forces between

the thiolate molecules which is dependent on the number of

spacers. A recent theoretical study106 corroborates this

hypothesis. A similar effect with regard to the orientation of

the termination CH3-group, has been found in the case of

various n-alkanethiols.107–110 In NEXAFS-based studies on

SAMs of biphenylalkanethiols14 and terphenylthiols,111 for

thiolates with odd numbers of methylene spacers, a smaller tilt

angle of the molecular axes has been found in comparison to

the thiolates with even numbers of methylene spacers. This

was rationalized as follows: on Au(111), the sulfur atom tends

to be sp3-hybridized112,113 and thus the Au–S–C bond angle

amounts to B1041.14,108,110,114–116 Therefore, for an odd

number of methylene spacers the bond that connects the

backbone with the aromatic moiety is expected to ‘‘stick

up’’, which leads to a rather upright aromatic termination.

An even number of methylene spacers however is expected to

lead to a more flat lying aromatic termination.

Since all the above considerations apply also for the present

case of the pyridine-based thiols we conclude that the

differences in intermolecular interaction between the biphenyl

units and the pyridine-phenyl and pyridine-biphenyl units

considered here are so small that the lateral packing is not

affected. We thus propose the structures shown in Fig. 12 for

the 4 different SAMs studied here.

Structural model

The proposed structural models of the PP1-, PPP1-, PPP2- and

PPP3-SAMs are displayed in Fig. 12. Since there is no

straightforward experimental method to assess the sulfur

Fig. 12 Model of molecular arrangements of the pyridine-terminated

thiols on Au(111). (a) Top view and (b) side view of the

ð2ffiffiffi

3p�

ffiffiffi

3pÞR30� structure of the PPP1- -SAM as example for the

three SAMs with odd numbers of methylene spacers, (c) top view and

(d) side view of the ð5ffiffiffi

3p� 3Þrect structure of the PPP2-SAM. In (a)

and (c) the unit cells are denoted by white solid lines. Note that

the sulfur binding sites (three-fold hollow site) have been chosen

arbitrarily. See text for detailed discussion of the model.

This journal is �c the Owner Societies 2010 Phys. Chem. Chem. Phys., 2010, 12, 4459–4472 | 4469

binding sites on the gold surface, they have been chosen

arbitrarily. The herringbone-like orientation with respect to

the neighbour-molecules has been proposed on the basis of

previous theoretical calculations for biphenyl-(BP)-based

SAMs.106 Moreover, such structure could be directly observed

in a STM study on anthraceneselenol-SAMs on gold.117

The structures proposed are analogous to those observed of

BP-based SAMs, a ð2ffiffiffi

3p�

ffiffiffi

3pÞR30� alike structure for the

pyridine-based organothiols with an anchor containing an odd

number of methylene units, PP1, PPP1 and PPP3 and a

different structure, best described as ð5ffiffiffi

3p� 3Þrect for the

organothiol containing an anchor chain with an even number

of methylene units.

For terphenyl-based SAMs, similar structures,

ð2ffiffiffi

3p�

ffiffiffi

3pÞR30� and ð5

ffiffiffi

3p� 3Þrect for odd numbers and

even numbers of methylene spacers, respectively, were found

in a systematic STM study.118 The results reported here

indicate that the mechanisms governing the structure of SAMs

formed from oligophenyl thiols also dictate the packing of

similar organothiolates where the terminal phenyl ring is

replaced by a pyridine function. The free electron pair and

the dipole moment of pyridine appear to have no significant

influence on the structure within the SAM, a result which is of

special importance in the context of the design of organic

surfaces with predictable structure and arbitrary functional

termination.

Conclusions

In the present work different surface-analytical techniques

have been used to characterize the formation of a homologous

series of pyridine-terminated SAMs on Au(111) and their

molecular arrangements on the substrate surface. It has been

shown that well ordered and densely packed monolayer films

can be prepared by immersion of gold substrates into ethanolic

solutions of the respective thiols at room temperature. From

experimental and ab initio calculated NEXAFS spectra as well

as from IRRAS data it can be inferred that for all investigated

SAMs the orientation of the individual thiolates is almost

perpendicular to the substrate surface. The thiolates in the

PPP2-SAM have a somewhat larger tilt angle than in the other

pyridine-terminated SAMs. A comparison of experimental

and theoretical NEXAFS spectra provides strong evidence

for a non-coplanar conformation of the aromatic rings in the

PP1-SAM. Structural models consistent with all the experi-

mental findings are presented in Fig. 12. While the SAMs from

PP1, PPP1 and PPP3 adopt a ð2ffiffiffi

3p�

ffiffiffi

3pÞR30� structure, for

the PPP2-SAM a ð5ffiffiffi

3p� 3Þrect—like structure is observed.

The chemical behavior of the SAMs was probed by protona-

tion experiments. All SAMs behaved in a very similar way.

Immersion into aqueous H2SO4 did not show any effect,

whereas immersion into solutions of trifluoromethanesulfonic

acid clearly resulted in protonation of the organic pyridine-

terminated surfaces. The similarity of the lateral packing

within the pyridine-oligophenyl based SAMs reported here

to the analogous case of biphenyl- and terphenyl-based SAMs

suggests that the difference in intermolecular interactions induced

by replacing the terminal phenyl unit by a pyridine unit is not

sufficiently strong to affect the structure of the SAMs.

Acknowledgements

This work was supported by the European Union (FP6 STReP

SURMOF, NMP4-CT-2006-032109). Traveling costs for

synchrotron measurements were provided by the German

BMBF through Grant No. 05ESXBA/5. J.L. thanks the

IMPRS of SurMat for a research grant. B.S. and A.T.

appreciate financial support by the DFG through the graduate

school 611 (‘‘Functional materials’’). The authors would

like to thank Paul Bagus for valuable contributions to the

discussion of the experimental and calculated NEXAFS data

and the authors of ref. 56, especially Manfred Buck, for

discussion of the protonation results and for providing PP3

molecules.

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