University of Groningen

Surface-confined molecular assemblyEnache, Mihaela

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APPENDIX A 

177 

Appendix A

Figure A1. Overview STM image 2t t(200× 200 nm ,U = 2V, I = 20 pA) for

deposition of 0.2 ML of molecule 2 on Ag(111). The self-aggregation of molecule 2 results mainly in 1D chains. This is not identifiable due to the large scale. The chains exhibit mainly the double row structure character as are discussed in Section 3.3.

APPENDIX A 

178 

Figure A2. Bonding geometries observed for the double row structures. (a)

High-resolution STM image 2t t(5.5× 3 nm ,U = 1.3V, I = 100 pA) , and (b)

the corresponding molecular model. (b) The dotted blue lines indicate the H-bonds formed between neighboring molecules 2. In addition, the corresponding bond lengths are given as derived from the STM data. The dotted pink line indicates the distance (repulsive interaction) between the O atoms of neighboring molecules. All distances are given in Å.

Additional information for Figure 3.5 in Section 3.3:

A few experimental and theoretical studies of alkane chains on metal

surfaces (mainly on Au(hkl)) [Dub92][Wet98][Lav98][Lee10][Yin01]

suggested that the hydrocarbons’ contributions to the activation energy

for desorption can be divided into additive contributions of atoms and

groups of atoms (CH2, CH3 fragments in this case). Roughly, the CH2

and CH3 contributions were estimated to 6.2 kJ/mol (64 meV) and 15.5

kJ/mol (160 meV), which in the case of molecule 2 corresponds to 0.35

eV for each chain (0.7 eV per molecule 2). Hence, to lift up the chains

the system pays an energetic penalty (<1 eV) which is compensated by

APPENDIX A 

179 

the gain in entropy and by minimization of the area occupied per

molecule.

APPENDIX B 

180 

Appendix B

Figure B1. Overview STM image 2t t(30×30 nm ,U = 1.5V, I = 25 pA) ,

acquired at 77 K) of the molecule 1 and 2 bicomponent system at low coverage showing the coexistence of three supramolecular structures: straight chains (I), zigzag chains (II) and a polygonal structure (III). The white arrow marks the orientation of the underlying Ag substrate.

Figure B2. (a) – (f) Detailed STM images for the different supramolecular structures observed for the mixture of molecule 1 and 2 on Ag(111) at low coverage together with the superposition of their molecular models on the

APPENDIX B 

181 

STM images: (a) – (b) straight chains 25.3×6.2 nm ; (c) – (d) zigzag chains

24.9×4.3 nm ; (e) – (f) polygonal structure 25.4×5.2 nm ; (g) – (i) Tentative

adsorption models for the supramolecular structures shown above. (Scanning

parameters: t tU =1.5V, I = 25 pA).

Figure B3. (a) STM image 2t t(7.2× 5.8 nm ,U = -0.2V, I = 4 pA) for the

mixture of molecule 1 and 2 on Ag(111) for a total coverage of 0.5 ML1,2. The molecules arrange in zigzag rows. The unit cell, which contains four molecules, is drawn on the STM image. (b) Suggested adsorption model of the densely packed arrangement: molecule 1 adopts two different adsorption configurations on the surface, the 0° and 15° rotational geometries, respectively, while molecule 2 adopts only the 30° configuration (see Figure 3.3, Chapter 3). (c) Molecular model of the densely packed arrangement showing the intermolecular interactions. Two molecules 1 within the same zigzag row exhibit an angle of 75° and interact via triple H-bonding (marked in yellow) with molecules 2 (type C2 interaction). Molecules 1 in adjacent zigzag rows interact via double H-bonding (marked in orange).

APPENDIX B 

182 

Figure B4. (a) Large-scale STM image 2t t(87× 97 nm ,U =1.6V, I = 20 pA)

showing different rotational domains of the close-packed arrangement of molecules 1 and 2 on Ag(111).(b) Detailed STM image

2t t(35× 39 nm ,U = 0.7V, I = 92 pA) showing three rotational domains. Their

rotational orientation differs by multiples of 60° (white arrows) as well as by

(n× 60 + 15)° with n Î [1,6] (yellow arrow). The unit cells for two different

domains are drawn in blue and red on the STM image. The green arrow indicates the principal direction of the Ag substrate. (c) Proposed molecular model for the domains marked in (b). The blue (red) unit cell is rotated

clockwise (anti-clockwise) by 7.5° with respect to the [110] direction. This

operation leads to a set of unit cells rotated clockwise (anti-clockwise) and which have a rotational angle of 60° with respect to each other.

APPENDIX B 

183 

Figure B5. Two unit cells corresponding to two rotational domains. The unit

cells are rotated o15 with respect to each other.

APPENDIX C 

184 

Appendix C

The formation of individual porous units.

For the construction of polygonal porous structures on the Ag(111)

surface (Figure 2), two experimental pathways were identified: (a) a

sequential deposition of molecules 2 and 1 (molecular ratio 11:12, and a

molecular coverage of the individual units not larger than 0.1 ML) on

the Ag(111) surface held at room temperature (RT), followed by a post-

annealing step (at a temperature between 333-338 K for 30 min) and a

cooling until the sample reached RT. (b) A sequential deposition of

molecules 2 and 1 (molecular ratio 11:12, and a molecular coverage of

the individual units not larger than 0.1 ML) on a warm Ag(111) surface

held at 338 K during deposition, followed by a smooth cooling down of

the sample similar as in (a). The latter method has proven to be the

more efficient for the pore formation on the Ag(111) surface.

Two crucial experimental parameters involved in the process of pore

formation were identified: (a) the annealing procedure and (b) the

molecule deposition sequence. (a) The annealing step at 338 K has a

major role in the formation of the polygonal porous structure on the

surface because: (i) enough energy is supplied to the system to explore

the reversibility of the H-bonds (bond formation and bond breaking)

until an equilibrium structure is formed, namely the porous unit; (ii) the

diffusion is increased and thus, the collision probability between the

molecules, a process which increases the chances for the

complementary units to recognize each other on the surface. (b) From

the homomolecular organization of molecule 1 [Mat09] and molecule 2

APPENDIX C 

185 

[Ena13a] on Ag(111) we observed that the unit of molecule 2 is mobile

on the surface at RT, while the unit of molecule 1 forms a H-bonded

hexagonal network. In order to avoid the homomolecular self-assembly

of 1 into the hexagonal network, which will lead to a phase separation

in the bi-component system, first the molecule 2 has to be deposited on

the Ag(111).

Figure C1. (a) High-resolution STM image

,2(30×30 nm t tU = 1.8 V, I = 33 pA) of the molecule 1 and 2 bi-component system. The blue dashed rectangle indicates two mirror-symmetric porous units. (b) Molecular model corresponding to the area marked by the blue dashed rectangle in (a). The black dashed line indicates the orientation of the

mirror plane which follows the -

[112] substrate direction. The magenta and cyan ellipses indicate H-bonding interactions between the two mirror-symmetric pores. The black/white arrows indicate the high symmetry directions of the substrate.

APPENDIX D

186

Appendix D

D.1 Experimental set-up

The NIXSW experiments were performed at the ID32 beamline

of the European Synchrotron Radiation Facility (ESRF). The

experimental set-up was designed specifically for NIXSW experiments.

In particular, the X-ray beam is directed perpendicular to the Bragg

planes of the sample. The reflected beam hits a fluorescence screen,

where its intensity is measured with the help of a photodiode. In order

to detect the photoelectrons, an analyzer, which is situated at an angle

of θ 45° with respect to the X-ray beam direction, is used.

During an NIXSW experiment the following quantities (signals) have

to be measured in order to derive the coherent fraction and coherent

position of an element under study:

- An XPS spectrum of an element core level. From this XPS spectrum

the photoelectron yield (Y), which represents the integrated

photoelectron intensity after background subtraction, is obtained.

- A signal/quantity proportional to the reflectivity R.

- The so-called “ 0mesh _ I ”, which is a signal proportional to the

intensity of the incoming X-ray beam measured after the beam crosses

the last slit before entering the UHV chamber. Because the intensity of

the beam is not constant during measurements, the knowledge of this

parameter is fundamental for accurate normalization of the reflectivity

and the absorption yield.

APPENDIX D

187

In order to evaluate the XSW measurement data a three-step

process has to be followed. First, the off-Bragg high-resolution XPS

spectra are evaluated and a fitting model is developed. In this step,

information about the stoichiometry and the number of chemically

different atoms of the same species has to be considered and accounted

for in the model. After a suitable XPS model is developed, it has to be

transferred from the off-Bragg XPS to the XSW data set. Each XSW

data set consists of 20-30 XPS spectra taken consecutively at a photon

energy of 2eV around the Bragg energy1. Relative intensities are

fixed for peaks which stem from the same atom (for example a main

peak and its satellite), but are free to change between peaks of different

origin (with respect to the adsorption position). The absolute energy

position and the FWHM of the components are fixed for each XSW

data set. Afterwards, the complete data set is fitted and the integrated

intensity of each component, as well as the integrated intensity of the

complete spectrum after background subtraction, are extracted. All data

processing of the first two steps is done in CasaXPS [Fin]. The third

step is the XSW yield fit done using Torricelli software [Mer12]. In this

step, the reflectivity and the photoelectron yield curve corresponding to

each XSW dataset are fitted in order to extract the cF and cP of the

dataset.

1 The (111) reflection was used.

APPENDIX D

188

D.2 XPS acquisition parameters

During an NIXSW experiment it is crucial to optimize the

following XPS acquisition parameters:

- The pass energy of the energy analyzer. The lower the pass energy,

the better (smaller) the resolution of the analyzer (ΔE) will be.

- The size of the kinetic energy window of the photoemitted electrons

detected by the analyzer. The larger the window, the better the

background can be defined which helps the fitting of the PE spectra.

- The energy step, which represents the energy distance between two

consecutive data points. The smaller the energy step, the more accurate

the PE spectra will be, and accordingly, the easier to fit.

- The time per step, known as the “dwell” time, which represents the

acquisition time of one data point. A longer time per step results in

better statistics and thus, a smoother spectrum.

- The number of repeats which represents the number of times a

spectrum is measured before being averaged and saved in a file.

In order to have good data statistics, it is best to acquire the PE

spectra with low pass energy, a large kinetic energy window, small

energy step, a large dwell time, and a sufficiently high number of

repetitions. Unfortunately, this leads to long acquisition times, which

were not possible for our system of interest, TAPP on Cu(111), due to

its sensitivity to beam damage. Accordingly, a compromise had to be

found such that beam damage is avoided while at the same time

resolution and statistics of the acquired data are good enough to resolve

possible core-level chemical shifts. First the beam damage was studied.

Unfortunately, after irradiating the same spot on the sample for 45

minutes the peak intensity of the N1s spectra significantly changed.

APPENDIX D

189

Accordingly, we limited our time per measurement point to 40 min.

Second, high-resolution XPS spectra were acquired in order to develop

the best fitting routines for the C1s and N1s XPS spectra. For example,

for the low temperature phase of TAPP on Cu(111), the high-resolution

XPS spectra were acquired with 100 ms/step, a kinetic energy window

of 26 eV (30 eV) for the N1s (C1s) core level, a 0.1 eV kinetic energy

step, a pass energy 29.35 eV and 5 (2) repeats for the N1s (C1s) core

level. For the high-resolution XPS data, in contrast to the XSW-XPS

data, a larger window for the kinetic energy was used in order to define

the background better. For the XSW-XPS data we used the same pass

energy of 29.35 eV in order to easily transfer the fitting routine

developed for the high-resolution XPS spectra to the XSW-XPS data

without the need for major adjustments. Furthermore, the photon

energy used for the high-resolution XPS spectra was slightly lower than

the Bragg energy (~2966 eV).

D.3 XPS background

The photoelectron yield of an atomic species is defined as the

difference between the photoelectron (PE) spectrum of the atomic

species adsorbed on the surface and the background (BG)2. Thus, it is

important to properly define the background in order to eliminate any

contribution of the substrate signal from the photoelectron yield to the

adsorbate signal. If the background subtraction is not done carefully,

the corresponding vertical adsorption height of the adsorbate atom

would be altered by the substrate contribution, which might lead to a

misinterpretation of the data.

2 The background represents the PE intensity coming from the substrate.

APPENDIX D

190

In this thesis, only a Shirley background was used to subtract the

contributions of the substrate. The best fit for the XPS spectra

discussed in this thesis resulted from PE lines modeled by Voigt

functions with 30% Lorentzian contribution, while the satellites are

fitted with a pure Gaussian function. The software used to analyze the

XPS data is called CasaXPS [Fai]. To extract the coherent fraction and

coherent position the Torricelli software was used [Mer12].

D.4 Overview of the prepared samples

During the XSW beamtime, multiple samples of TAPP/Cu(111)

were prepared in order to perform the XSW experiments. Three

samples were prepared for the herringbone assembly (Table C.1) and

three samples for the porous network (Table C.2). Different positions

on the sample(s) were measured (which are called ‘datasets’ in Table

C.1). From each position (dataset) a coherent position value and

coherent fraction value were obtained. By averaging these values, a

final average coherent fraction and coherent position is obtained (the

average vertical adsorption heights for the nitrogen and the carbon

atoms of TAPP in the herringbone assembly and porous network

structure are shown in Figure 4.9).

Herringbone Sample Mlu Olu Plu Dataset C1s N1s C1s N1s C1s N1s

Nr. of XSW datasets

4 5 6 8 3 8

Coverage (Å) 3.65

(2.8 + 0.85) ~3.4 ~3.4

meas osampleT ( C) -61 -61 -61

APPENDIX D

191

Table C.1 TAPP/Cu(111): Summary of the samples prepared for the herringbone assembly. In total, three different samples were prepared (Mlu, Olu, Plu) and the parameters for each sample are reported.

Porous network Sample Flu Hlu Qlu Dataset C1s N1s C1s N1s C1s N1s

Nr. of XSW datasets

5 5 5 5 5 5

Coverage(Å) 4.11

(1.54+1.65+0.92) 3.71

(1.5+2.21) 3.4

meas osampleT ( C) RT RT -61

Table C.2 Summary of the samples prepared for the porous network. Three different samples were prepared (Flu, Hlu, Qlu) and the parameters for each sample are reported. The Qlu sample was measured at 77K, in contrast with the other two samples (Flu, Hlu) which were measured at RT.

APPENDIX D

192

D.5 N1s XPS spectra of TAPP/Cu(111)

Figure C.1 N1s XPS spectra of TAPP/Cu(111) for (a) the herringbone, (b) the porous network, and (c) the chains. The fitting and the assignment of the peaks is shown. (a) Two main components were considered (N1, N2) to fit the spectrum. An overall satellite for both main components (Sat) was also taken into account for the fitting procedure. In the left inset table, the positions (eV), FWHM (eV) and relative area (%) of the fitting components N1 (blue component), N2 (red component) and Sat (light blue dotted line), are given as resulted from the fitting of the raw data with no constraints imposed. Only for

APPENDIX D

193

the herringbone assembly, two peaks are visible and taken into account in the fitting procedure (NI, N2). For (b) and (c) only one main component was assumed together with a Sat.

C.5 XPS spectra of 1ML uracil on Cu(111)

Figure C.2. XP spectra of 1 ML uracil on Cu(111) as a function of annealing temperature (Adapted with permission from [Pap12]. Copyright (2016) American Chemical Society).

SUMMARY & CONCLUSIONS 

172

Summary & Conclusions

In this thesis, the self-assembly of specially synthesized organic

molecules adsorbed on well-defined metal surfaces was studied by means of

Scanning Tunneling Microscopy (STM), X-ray photoelectron spectroscopy

(XPS) and X-ray standing waves (XSW). The aim of this work is to

understand the underlying interaction mechanisms for the formation of well-

defined self-assembled nanostructures. Such understanding is fundamental to

the controlled fabrication of complex functional surfaces with desired

properties and functions.

In Chapter 3, the controlled formation of supramolecular bicomponent

networks on Ag(111) through molecular recognition utilizing hydrogen

bonding is reported. Two molecular linkers, one linear and one angular,

where specifically designed with complementary H-bonding recognition

sites in order to build pre-programmed low-dimensional assemblies on

surfaces via triple H-bonding. Molecule 1, a linear linker, bears two 2,6-

di(acetylamino)pyridine recognition sites (NH–N–NH, donor(D)-

acceptor(A)-donor(D)) connected to a 1, 4-disubstituted central phenyl ring

through ethynyl spacers. The angle between the ethynyl spacers is 180°.

Molecule 2, an angular linker, has two uracil moieties (CO–NH–CO, ADA)

attached to a 2,3-disubstituted phenyl ring through ethynyl spacers with an

angle of 60° between the ethynyl spacers. At each uracil group, a hexyl chain

is attached.

First, each molecular linker was investigated individually on the

Ag(111) surface. The linear linker, when deposited on Ag(111) held at room

CHAPTER 6 – SUMMARY & CONCLUSIONS 

173

temperature, arranges in a commensurate hexagonal porous network held

together by double H-bonds formed between neighboring molecules. The

self-organization of the angular unit on Ag(111) was studied as a function of

coverage. By increasing the molecular coverage, a phase transformation

occurs from a disordered to an ordered 2-dimensional (2D) phase. At low

and intermediate molecular coverages, a glassy phase consisting of 1D

chains and 2D aggregates is observed, while close to a first complete

molecular layer, a well-ordered 2D close-packed phase forms. The delicate

balance of the molecule-substrate and molecule-molecule interactions is

responsible for the structure formation. The main driving forces responsible

for the structure formations are: (i) the uracil self-complementarity, resulting

in uracil-uracil pairs through two C=O···H–N H-bonds and (ii) the steric

demands of the alkyl chains. We found that the coverage dependent phase

behavior is due to a mutual interplay between entropic (mainly due to the

alkyl chains) and enthalpic contributions to the Gibbs free energy of the

system, i.e. the system evolves towards a state of lower free energy and

higher structural stability.

In the case of the bicomponent system, based on the molecular

recognition between the linear and the angular linker, by tuning the substrate

temperature we could successfully drive the system into only one pre-

programmed structure consisting of pores. In this way, we provide a viable

method towards the fabrication of patterned materials which can serve as a

template for accommodating nanoscale objects (molecules) exhibiting

specific functionalities. To prove this concept, we could show that the porous

network can act as a host for guest molecules (zinc octaethylporphyrin,

ZnOEP).

SUMMARY & CONCLUSIONS 

174

Finally, the electronic properties of the pores were theoretically

investigated and the capability of the pores to confine the electrons of the Ag

surface state was explored. For future work, it will be interesting to

determine the experimental eigenvalues and the low density of states

(LDOS) patterns for the porous network and compare it with the theoretical

predictions. The bicomponent system provides a unique environment to

exploit the confinement properties of an individual pore unit and an island of

pores. Thus, it will be interesting to perform a comparison of the Scanning

Tunneling Spectroscopy (STS) for an individual pore and an island of pores.

Another promising experiment will be to fill the porous unit with a

functional molecule (for example a molecular switch) and exploit its on/off

properties inside the pore in an individual pore, as well as in an island of

pores.

In Chapter 4, the temperature induced phase behavior of a perylene

derivative 1,3,8,10-tetraazaperopyrene (TAPP) deposited on Cu(111) is

presented. The perylene core of TAPP has a pyrimidine ring attached at each

end as a functional group. In the submonolayer regime, deposition of TAPP

on a Cu(111) substrate held at -90 °C results in the formation of small

patches of an ordered close-packed assembly. The TAPP molecules arrange

in a so-called herringbone assembly, which is stabilized via hydrogen

bonding and van der Waals (vdW) forces [Mat10] [MatThesis]. Deposition

of TAPP on Cu(111) held at 150 °C results in the formation of a highly

ordered metal-coordinated porous network structure [Bjö10] [Mat10].

Deposition of TAPP on Cu(111) held at 250 °C leads to the formation of 1D

chains made up from covalently linked TAPP monomers [Mat08] [Mat10].

The vertical adsorption height of the molecule was determined with the help

of XSW measurements for two particular phases, the herringbone phase and

CHAPTER 6 – SUMMARY & CONCLUSIONS 

175

the porous network phase. Thus, the bonding mechanism of TAPP on

Cu(111) in the herringbone phase and the porous network could be clarified.

In the herringbone phase, the molecules interact with the Cu surface

through the non-protonated nitrogen species which are very close to the

surface (2.53 Å) and through the perylene core (which is situated at 2.63 Å

above the surface) of TAPP. The H-bonding between neighboring TAPP

molecules is responsible for the molecule-molecule interactions. The H-

bonding takes place between the protonated nitrogen of one TAPP and the

non-protonated nitrogen of a neighboring TAPP. Furthermore, the difference

in the vertical adsorption height of the protonated and non-protonated

nitrogen atoms of TAPP induces a distortion in the planar shape of the

molecule. In the case of the porous network, the incorporation of the Cu

adatoms in the network leads to an increase of the vertical adsorption height

of TAPP, which indicates a fundamental change of molecule-substrate

interaction, attributed to the two-fold coordination between nitrogen and Cu

adatoms. Furthermore, in the case of the porous network, the metal

coordination mediates both, the intermolecular as well as the molecule-

substrate interactions. Thus, the perylene backbone is no longer needed to

anchor the molecule to the substrate. A suggestion for a future experiment

will be to use the Non-Contact Atomic Force Microscopy (nc-AFM) with a

QPlus sensor to directly image the chemical bonds and the intramolecular

feature of TAPP in all phases on Cu(111). For TAPP in the herringbone

phase it will help to clarify the assignment of the protonated nitrogen. For the

porous network phase it will be interesting to look at the crossing and see if

the native Cu adatoms can be resolved, and if somehow there is a fingerprint

of the Cu-N bond.

SUMMARY & CONCLUSIONS 

176

In Chapter 5, the self-assembly properties of two ZnII porphyrin

isomers on Cu(111) were studied at different coverages by means of STM.

Both isomers are substituted in their meso-position by two 3,5-di(tert-

butyl)phenyl and two rod-like 4’-cyanobiphenyl groups, respectively. In the

trans-isomer, the two 4’-cyanobiphenyl groups are opposite to each other,

whereas they are located perpendicular in the cis-isomer. In the

submonolayer regime, the cis-substituted porphyrins self-assemble to form

oligomeric macrocycles held together by antiparallel CN CN dipolar

interactions and H-bonding (C N H C ). Cyclic trimers and tetramers

occur most frequently but everything from cyclic dimers to hexamers were

observed. Upon annealing of the samples at temperatures higher than 150°C,

dimeric macrocyclic structures were observed, in which the two porphyrins

are bridged by native Cu adatoms, under formation of two CN Cu CN

coordination bonds. It was shown how flexible 4’-cyanobiphenyl

substituents can adapt to very different geometries if supported by strong

adsorbate–substrate interactions due to their elongated structure as well as

diverse 4’-cyanobiphenyl bonding motifs. The substrate influence was

dominant in all detected structures on Cu(111). The trans-isomer forms

linear chains on Cu(111) at low coverage, whereas for higher coverage the

molecules assemble in a periodic, densely-packed structure. The close-

packed structure is held together by antiparallel dipole-dipole interactions in

one dimension, and vdW interactions in the other. The strong influence of

the substrate is visible since the porhyrins are aligned along the Cu(111)

direction. These findings reveal the complexity of supramolecular structure

formation induced by the interplay between molecule–substrate and

molecule–molecule interactions.

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SAMENVATTING & CONCLUSIES 

219 

Samenvatting & Conclusies

In dit proefschrift wordt de zelfassemblage van speciaal gesynthetiseerde

moleculen op goed gedefinieerde metalen oppervlakken bestudeert door

middel van Scanning Tunneling Microscopie (STM), Röntgen Foto-

elektron Spectroscopie (XPS) en Staande Röntgengolven (XSW). Het

doel van dit werk is om de interactiemechanismes te begrijpen die ten

grondslag liggen aan de formatie van goed gedefinieerde zelf

geassembleerde nanostructuren. Dit begrip is fundamenteel voor de

fabricage van complexe functionele oppervlakken met wenselijke

eigenschappen en functies.

In hoofdstuk 3 is de gecontroleerde formatie, door moleculaire

herkenning middels waterstofbruggen, van supramoleculaire twee

component netwerken op Ag(111) beschreven. Twee moleculaire

linkers, een lineair en een gehoekt, zijn ontworpen met complementaire

herkenningspunten voor waterstofbruggen om zo een voorbestemd laag

gedimensioneerde assemblage te vormen op oppervlakken. Molecuul 1,

de lineaire linker, draagt twee 2,6-di(acetylamino)pyridine

herkenningspunten (NH-N-NH, donor(D)-acceptor(A)-donor(D)

functionaliteit) die zijn verbonden met een 1,4-gesubstitueerde centrale

phenyl ring door ethynyl moleculen. De hoek tussen de ethynyl

moleculen is 180°. Molecuul 2, de gehoekte linker, heeft twee uracil

moeieties (CO-NH-CO, ADA functionaliteit) die zijn verbonden met een

2,3-gesubstitueerde phenyl ring door ethynyl moleculen waartussen de

hoek 60° bedraagt. Elke uracil groep is gebonden aan een hexyl keten.

Allereerst zijn de moleculaire linkers individueel onderzocht op een

Ag(111) oppervlak. De lineaire linker vormt bij depositie op Ag(111)

gehouden op kamertemperatuur een evenwijdig hexagonaal poreus

netwerk, dat samengehouden wordt door tweevoudige waterstofbruggen

SAMENVATTING & CONCLUSIES 

220 

tussen naburige moleculen. De zelfassemblage van de gehoekte linker op

Ag(111) was bestudeerd als functie van de dekkingsgraad. Bij een

toenemende bedekking door moleculen vindt er een fase transformatie

plaats van wanorde naar een geordende 2-dimensionale (2D) fase. Bij

een lage tot intermediaire moleculaire bedekking van het oppervlak is

een glasachtige fase bestaande uit 1D ketens en 2D aggregaten

geobserveerd. Dicht bij het vormen van een complete moleculaire laag

vormt zich een goed geordende 2D dichtgepakte fase. Het delicate balans

tussen het molecuul-substraat en molecuul-molecuul interacties is

verantwoordelijk voor de structuur formatie. De belangrijkste krachten

voor de formatie van structuren zijn: (i) De zelf-complementariteit van

uracil dat resulteert in uracil-uracil paren formatie door twee C=O···H-

N waterstofbruggen en (ii) de sterische hinder van de alkyl ketens.

Bevonden is dat het dekkingsgraad afhankelijke fasegedrag gevolg is van

een wederzijdse wisselwerking tussen entropie en enthalpie contributies

aan de Gibbs vrije energie van het systeem, i.e. het systeem evolueert

naar een staat van lagere vrije energie en hogere structuur stabiliteit.

In het geval van het twee componenten systeem, gebaseerd op de

moleculaire herkenning tussen de lineaire en gehoekte linker, kan het

systeem gestuurd worden naar een enkel voorgeprogrammeerde

structuur bestaande uit poriën door het afstellen van de substraat

temperatuur. Deze manier demonstreert een mogelijke methode

voorwaarts naar de fabricage van sjabloon materialen, die kunnen dienen

als template om nanoschaal objecten (moleculen) met specifieke

functionaliteiten te accommoderen. Dit concept is bewezen door aan te

tonen dat een poreus netwerk kan functioneren als gastheer voor

moleculen (zink octaethylporphyrin, ZnOEP).

SAMENVATTING & CONCLUSIES 

221 

Ten slotte zijn de elektronische eigenschappen van de poriën theoretisch

onderzocht en is de capaciteit van de poriën om de elektronen in de

oppervlakte toestanden van Ag op te sluiten verkend. Voor toekomstige

werkzaamheden is het interessant om de experimentele eigenwaardes en

de patronen van de Lokale Dichtheid van Toestanden (LDOS) te meten

voor poreuze netwerken en dit te vergelijken met de theoretische

voorspellingen. Het twee componenten systeem biedt een unieke

omgeving om de eigenschappen van opsluiting in een individuele porie

en eilanden van poriën te exploiteren. Zodoende is het interessant om een

vergelijking uit te voeren tussen Scanning Tunneling Spectroscopie

(STS) voor een individuele porie en een eiland van poriën. Nog een

veelbelovend experiment is om een poreuze eenheid te vullen met een

functioneel molecuul (e.g. een moleculaire switch) en zijn uit/aan

eigenschappen te exploiteren in een individuele porie alsmede een eiland

van poriën.

In hoofdstuk 4 is het temperatuur geïnduceerde fase gedrag van het

perylene afgeleide 1,3,8,10-tetraazaperopyrene (TAPP) gedeponeerd op

Cu(111) gepresenteerd. De perylene kern van TAPP heeft een

pyrimidine ring gebonden elk eind dat fungeert als functionele groep.

Depositie van TAPP in het submonolaag regime op een Cu(111)

substraat gehouden op -90 °C, resulteert in de formatie van kleine

regionen met geordende dichtgepakte formaties. De TAPP moleculen

rangschikken zich in een zogenaamd visgraat structuur, dit wordt

gestabiliseerd door waterstofbruggen en van der Waals (vdW) krachten

[Mat10][MatThesis]. Depositie van TAPP op Cu(111) gehouden op

150°C resulteert in de formatie van een sterk geordend metaal

gecoördineerd poreus netwerk. [Bjö] [Mat10]. Depositie van TAPP op

Cu(111) gehouden op 250°C leidt tot de formatie van 1D ketens

SAMENVATTING & CONCLUSIES 

222 

opgebouwd uit covalent gebonden TAPP monomeren [Mat08] [Mat10].

De adsorptiehoogte van het molecuul is bepaald met XSW metingen

voor de visgraat en poreuze fase. Zodoende kon het

bindingsmechanisme van TAPP op Cu(111) voor beide fases

opgehelderd worden.

In de visgraat fase hebben de moleculen interactie met het Cu oppervlak

door het niet geprotoneerde stikstof dat zich erg dicht bij het oppervlak

begeeft (2.53 Å) en door de perylene kern (dat 2.63 Å boven het

oppervlak is gesitueerd) van TAPP. De waterstofbruggen tussen

naburige TAPP moleculen zijn verantwoordelijk voor de molecuul-

molecuul interacties. De waterstofbrug vindt plaats tussen het

geprotoneerde stikstok van een TAPP met de niet-geprotoneerde stikstof

van een naburige TAPP. Het verschil in adsorptie hoogte van het

geprotoneerde en niet geprotoneerde stikstof van TAPP induceert een

distorsie in de vlakke vorm van het molecuul. In het geval van het

poreuze netwerk leidt de incorporatie van Cu adatoenm in het netwerk

tot een verhoging van de adsorptie hoogte van TAPP, dit geeft een

fundamenteel verschil aan van molecuul-substraat interactie dat

toegekend kan worden aan de tweevoudige coördinatie tussen stikstof en

Cu adatomen. Bij het poreuze netwerk medieert de metaal coördinatie

zowel de intermoleculaire alsmede de molecuul-substraat interacties.

Zodoende is de perylene ruggengraat niet langer nodig om het molecuul

te ankeren aan het substraat. Een suggestie voor een toekomstig

experiment is om Contactloze Atoomkrachtmicroscopie (nc-AFM) met

een QPlus sensor te gebruiken om een direct beeld van de chemische

bindingen en intramoleculaire kenmerken van TAPP en al zijn fases op

Cu(111). Dit zal helpen om het geprotoneerde stikstof toe te wijzen in

TAPP in de visgraat fase. Voor het poreuze netwerk is het interessant om

SAMENVATTING & CONCLUSIES 

223 

te kijken naar de kruising en vast te stellen of de inheemse Cu adatomen

opgehelderd kunnen worden en of er mogelijk een vingerafdruk van de

Cu-N binding te zien is.

In hoofdstuk 5 zijn de zelfassemblage eigenschappen van twee ZnII

porfyrine isomeren op Cu(111) bestudeerd bij verschillende

dekkingsgraden met STM. Beide isomeren zijn gesubstitueerd in hun

meso-configuratie door twee 3,5-di(tert-butyl)phenyl en twee

staafachtige 4’-cyanobiphenyl groepen. In het trans-isomeer bevinden

de twee 4’-cyanobiphenyl groepen tegenover elkaar staan, dit in

tegenstelling tot het cis-isomeer waarbij ze haaks op elkaar staan. In het

submonolaag regime vormen de cis-gesubstitueerde porfyrines zichzelf

tot oligomeric macrocycles bij elkaar gehouden door anti-parallelle

CN CN dipolaire interacties en waterstofbruggen ( C N H C ).

Het meest voorkomend zijn de cyclische trimeren en tetrameren echter

is er van alles geobserveerd, van cyclische dimeren tot hexameren. Na

annealing van de samples tot temperaturen boven 150°C konden er

macrocyclische structuren worden geobserveerd, waarin twee porfyrines

bruggen vormen met inheemse Cu adatomen onder de formatie van twee

CN Cu CN gecoördineerde bindingen. Het is gedemonstreerd hoe

flexibel 4’-cyanobiphenyl substituanten kunnen aanpassen aan erg

verschillende geometrieën als het ondersteund word door sterke

adsorbaat-substraat interacties. Deze sterke interacties zijn mogelijk

door de uitgerekte structuur alsmede de diverse 4’-cyanobiphenyl

bindingsmotieven. De invloed van het substraat was dominant bevonden

in elke geobserveerde structuur op Cu(111). Het trans-isomeer vormt

lineaire ketens op Cu(111) bij lage dekkingsgraad, terwijl bij hoge

dekkingsgraad de moleculen een periodieke dichtgepakte structuur

vormen. De dichtgepakte structuur wordt bij elkaar gehouden door anti-

SAMENVATTING & CONCLUSIES 

224 

parallelle dipool-dipool interacties in één dimensie en vdW interactie in

een andere dimensie. De sterke invloed van het substraat is zichtbaar

sinds de porfyrines zich ordenen langs de Cu(111) richting. Deze

bevindingen onthullen de complexiteit van de supramoleculaire structuur

vorming geïnduceerd door de wisselwerking tussen molecuul-substraat

en molecuul-molecuul interacties.

LIST OF PUBLICATIONS 

225 

List of publications

1) M. Enache, L. Maggini, A. Llanes-Pallas, T. A. Jung, M. Riello, A. De Vita, D. Bonifazi, M. Stöhr “Programming linear and cyclic bicomponent H-bonded supramolecular nanostructures: solution vs. surface studies” In manuscript

2) M. Enache, M. Matena, J. Björk, J. Lobo-Checa, J. Zegenhagen, L. H. Gade, T. A. Jung, M. Stöhr “Insight into the bonding mechanism of a perylene derivative on Cu(111)” In manuscript

3) K. Müller, M. Enache, M. Stöhr “Confinement properties of 2D porous molecular networks on metal surfaces” J. Phys.: Condens. Matter 28, 2016, 153003

4) M. Enache, L. Maggini, A. Llanes-Pallas, T. A. Jung, D. Bonifazi, M. Stöhr “Coverage dependent disorder-to-order phase ttransformation of an uracil-derivative on Ag(111)” J. Phys. Chem. C, 2014, 118, 15286-15291

5) C. Iacovita, P. Fesser, S. Vijayaraghavan, M. Enache, M. Stöhr, F. Diederich, T. A. Jung “Controlling the dimensionality and structure of supramolecular porphyrin assemblies by their functional substituents: dimers, chains, and close packed 2D assemblies” Chem. Eur. J. 2012, 18, 14610

6) M. Matena, M. Stöhr, T. Riehm, J. Björk, S. Martens, M. S. Dyer, M. Persson, J. Lobo-Checa, K. Müller, M. Enache, H. Wadepohl, J. Zegenhagen, T. A. Jung, L. H. Gade “Aggregation and contingent metal/surface reactivity of tetraazaperopyrene (TAPP) on Cu(111)” Chem. Eur. J. 2010, 16, 2079

7) J. Björk, M. Matena, M. S. Dyer, M. Enache, J. Lobo-Checa, L. Gade, T. Jung, M. Stöhr, M. Persson “STM fingerprint of molecule-adatom interactions in a self-assembled metal-organic surface coordination network on Cu(111)” Phys. Chem. Chem. Phys. 2010, 12, 8815

8) M. Matena, A. Llanes-Pallas, M. Enache, T. A. Jung, J. Wouters, B. Champagne, M. Stöhr, D. Bonifazi “Conformation-controlled networking of H-bonded assemblies on surfaces”

LIST OF PUBLICATIONS 

226 

Chem. Commun., 2009, 3525 9) L.-A. Fendt, M. Stöhr, N. Wintjes, M. Enache, T. A. Jung, F. Diederich

“Modification of supramolecular binding motifs induced by substrate registry: formation of self-assembled macrocycles and chain-like patterns” Chem. Eur. J. 2009, 15, 11139

10) I. Enculescu, M. Sima, M. Enculescu, M. Enache, V. Vasile and R. Neumann “Influence of geometrical properties on light emission of ZnO nanowires” Optical Materials 2007, 30, 72

11) I. Enculescu, M. Sima, M. Enculescu, M. Enache, L. Ion, S. Antohe, R. Neumann “Deposition and properties of CdTe nanowires prepared by template replication” Phys. Stat. Sol. (b) 2007, 244, 1607

12) M. Sima, I. Enculescu, M. Sima, M. Enache, E. Vasile, J.-P. Ansermet “ZnO:Mn:Cu nanowires prepared by template method” Phys. Stat. Sol. (b) 2007, 244, 1522

13) I. Enculescu, M. Sima, M. Enculescu, C. Ghica, M. Enache, R. Neumann “Preparation of metallic nanowires with magnetic properties using the template method” J.Optoelec. and Adv. Mat. 2007, 9, 1468

ACKNOWLEDGMENTS 

227 

Acknowledgments

Without the support of many people in many places, this thesis could not

have been written… . I would like to take the opportunity to thanks

first of all, to my PhD mentor Prof. Meike Stöhr for believing in

me, for giving me the opportunity to work in her research group and

for her unconditioned guidance during the past years. I was

extremely fortunate to have her as my supervisor, who gave me the

freedom to explore on my own, and at the same time the guidance

to recover when I drifted away from the main purpose. Her

suggestions and help made it so much easier to accomplish my work.

Without her explanations, help with data analysis, unlimited

patience and critical approach, many of the things written in this

work would not be there. Dear Meike, along my PhD, beside your

constant scientific support, you also have been my best and closest

friend. Without your constant care and persistence (especially in

2010 when you basically insisted over and over till I finally ‘gave

up’ and decided to take care of my health) I am sure we wouldn’t

have reached this point. This thesis is my accomplishment as much

as is yours. None of this would have been possible without you, on

the scientific and personal side as well. Thank you for always

believing in me, and for the fact that you never gave up on me.

Prof. Petra Rudolf for agreeing to be my co-promotor and for her

valuable suggestions during my PhD in Groningen.

Prof. B. Noheda Pinuaga, Prof. T.Linderoth and Prof. H.

Zandvliet for accepting to co-referee my PhD thesis.

ACKNOWLEDGMENTS 

228 

Prof.T. Palstra for his support and understanding regarding my

situation and helping me to come back at Zernike Institute for

Advance Materials and finish my thesis.

Prof. Thomas Jung for giving me the opportunity to start my PhD

at the Department of Physics of the University of Basel.

Basel crew (Nanolab): Dr. Jorge Lobo-Checa, Dr. Manfred Matena,

Dr. Serpil Boz, Dr. Tomáš Samuely, Stefan Schnell. In particular I

would like to show my gratitude to Jorge for being the person who

introduced me to UHV. Without his initial guidance I am sure my

progress along my PhD would have been different. Furthermore,

together with Jorge, Manfred and Meike we have been for many

beam times together, where we shared lots of funny memories. A

special thanks goes to Tomáš, who was my closest friend in Basel,

and we shared a lots of nice memories in the lab, and outside the lab

as well.

The STM group in Groningen (Anh, Stefano, Kathrin, Juan, Nico,

Leonid, Jun, Bay, Flo) for providing a nice group atmosphere during

the years. Leonid and Nico thank you for accepting to be my

paranymphs. In particular, I would like to thank Jos for his help with

translating the Dutch summary of my thesis. A special thanks goes

to Yvonne, for her help and support during my PhD. I would also

like to thank Hilke for his extraordinary technical skills which help

us have our experiments running in the lab. My special thanks go to

my office mate in Groningen, Naureen. Thank you for creating such

a friendly atmosphere in our office and for ‘just being there’ when

needed.

All the collaborators without whom this work wouldn’t have been

possible. the group of Prof. D. Bonifazi, Prof. F. Diederich, and

ACKNOWLEDGMENTS 

229 

Prof. L. H. Gade. I profoundly appreciate the friendly collaboration

with Dr. Jonas Björk. His theoretical input and many helpful

discussions significantly improved the quality of my thesis.

Daphne for all her support through the time, for encouraging,

helping and always being there. Without your support along the last

years, this thesis wouldn’t have been completed and I wouldn’t have

been at this point in my life. Thank you Daphne for never giving up

on me either.

My high school physics teacher, Victoria Olaru, for ‘seeing’ me at

the right time and guiding me towards science and higher education.

I will always be grateful for your patience and support over the

years.

My partner Angie, to whom I would like to express my special

gratitude and love as being one of the most important people in my

life for the last (almost) two years, to whom I cannot thank enough

for her patience, love and support during this time.

My father, my uncle (Nenea Adi) and my aunt (Tanti Flori) and Zori

for their unconditional support. I will always be grateful for my

parents’ support during my studies, although I know sometimes it

was really a financial struggle for them to do so. Furthermore, I was

lucky enough to be ‘let in’, accepted as one of their own and loved

by Adela’s family. I will always be grateful for their (Mami, Oni,

Mamitica, and Adi)’s unconditioned love and support. Adela, you

have been my forever best friend (as I know you for 16 years now),

the person on whom I could and still can always count on, my little

sister, and you are another person in my life who never gave up on

me. When I was sick and hard to deal with, you never gave up. You

tried your best to help me, even when I was giving you a really hard

ACKNOWLEDGMENTS 

230 

time. I will always appreciate your help and I hope to some point I

will be able to ‘pay you back’. I would also like to thank Cipri for

trying to have the patience to deal with me, and for his unconditional

support when I most needed it. I will always be grateful to both of

you.

Unfortunately, my mom and my brother did not manage to see me

finishing this thesis, but I know both of them are really proud of me

there.