Molecular networks through surface-mediated reactions [Elektronische Ressource] : from hydrogen bonds to covalent links / Hermann Walch

Molecular Networks Through
Surface-Mediated Reactions - From
Hydrogen Bonds to Covalent Links
Dissertation
der Fakultät für Geowissenschaften
der Ludwig-Maximilians-Universität
München
Hermann Walch
München, den 14. September 2010Erstgutachter: Prof. Dr. Markus Lackinger
Zweitgutachter: Prof. Dr. Wolfgang M. Heckl
16. Februar 2011Disputation:Contents
Table of Contents i
Abbreviations iii
Abstract v
1 Motivation 1
2 Experimental Methods 3
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Scanning Tunneling Microscopy . . . . . . . . . . . . . . . . . . . . . . 4
2.2.1 Basic Principle . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2.2 Theoretical Description . . . . . . . . . . . . . . . . . . . . . . . 5
2.2.3 Imaging Molecules . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.3 UHV System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.3.2 Modifications of the Omicron VT STM . . . . . . . . . . . . . . 10
2.3.3 Electron Beam Tip Heater . . . . . . . . . . . . . . . . . . . . . 11
3 Molecule-Molecule Interactions 13
3.1 Non-Covalent Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.2 Metal-Coordination Bonds . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.3 Covalent Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4 Molecule-Substrate-Interactions and Reactivity 23
4.1 Physisorption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.2 Chemisorption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.3 Active Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.4 2D Adatom Gas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
5 Summary 35
6 Publications 37
6.1 Isotopological Supramolecular Networks from Melamine and Fatty Acids 37
6.2 Surface mediated synthesis of 2D covalent organic frameworks:
1,3,5-tris(4-bromophenyl)benzeneongraphite(001),Cu(111),andAg(110) 51
6.3 Material and Orientation dependent activity for heterogeneously cat-
alyzed carbon-bromine bond homolysis . . . . . . . . . . . . . . . . . . 65
iContents
6.4 On the Scalability of Supramolecular Networks - High Packing Density
vs Optimized Hydrogen Bonds in Tricarboxylic Acid Monolayers . . . . 73
6.5 ExtendedTwo-dimensionalMetal-OrganicFrameworksBasedonThiolate-
Copper Coordination Bonds . . . . . . . . . . . . . . . . . . . . . . . . 91
References 97
Acknowledgements 109
Curriculum Vitae 111
iiAbbreviations
AFM atomic force microscope
BTB 1,3,5-benzenetribenzoic acid
COF covalent-organic framework
DFT density functional theory
DOS density of states
FCC face centered cubic
HOMO highest occupied molecular orbital
HOPG highly oriented pyrolytic graphite
LDOS local density of states
LEED low energy electron diffraction
LUMO lowest unoccupied molecular orbital
MOF metal-organic framework
PDOS projected density of states
RAHB resonance-assisted hydrogen bonding
SAM self-assembled monolayer
SPA-LEED spot profile analysis - low energy electron diffraction
STM scanning tunneling microscope
TBB 1,3,5-tris-(4-bromophenyl)benzene
TCBPB 1,3,5-tris[4’-carboxy(1,1’-biphenyl-4-yl)]benzene
TMA trimesic acid
TDS thermal desorption spectroscopy
TMB 1,3,5-tris(4-mercaptophenyl)benzene
TPD temperature programmed desorption
TSK terrace-step-kink
UHV ultrahigh vacuum
iiiAbstract
This thesis deals with adsorption, self-assembly, and surface reactions of organic
molecules on solid substrates, with the aim to fabricate higher hierarchical two-
dimensional (2D) structures. It is of genuine interest in materials science to develop
strategies and methods for reproducible growth of extended molecular assemblies with
specific and desired chemical, physical and functional properties. The experimental
technique used was Scanning Tunneling Microscopy (STM) - an outstanding method
to gain real space information of the atomic-scale realm of adsorbates on crystalline
surfaces.
The investigated systems are characterized by a complex interplay between adsorbate-
adsorbate interactions and adsorbate-substrate interactions. In one series of experi-
ments this could be illustrated through self-assembly of hydrogen bonded heteromeric
molecular networks on a chemically relatively inert graphite substrate. In this case,
van-der-Waals forces between adsorbate and substrate have to be balanced with in-
termolecular hydrogen bonds in concert with weaker van-der-Waals forces. Since the
magnitude of van-der-Waals forces between adsorbates and substrates correlates with
the contact area, this type of interaction becomes more dominant for larger molecules.
By stronger interactions which do not depend on molecule size, it was also possible
to grow isotopological molecular networks, i.e. networks following a similar building
plan. By varying for instance the length of aliphatic spacers, supramolecular struc-
tures with tuneable lattice parameter could be formed.
Studies of organic molecules on chemically more active metal substrates show that
more complex processes can be involved. In particular the concept of reactivity and
surface-catalyzed reactions are discussed and illustrated by an intuitive example. It is
demonstratedthatstrongmolecule-substrateinteractioncaninduceunimolecularreac-
tions such as deprotonation of molecules or more generally dissociation of intramolec-
ular bonds. This interaction strength, thus substrate reactivity is highly influenced by
a variety of factors which include material, crystallographic surface orientation, and
temperature. Further more the importance of so-called active sites on crystal surfaces,
i.e. special sites with significantly increased interaction strength, is taken into account
and exemplified with experimental results. Exploiting these fundamental principles,
C-Br bond scission of brominated aromatic compounds was demonstrated upon ad-
sorption on reactive substrates and followed by successful incorporation in covalently
bonded networks. However, irreversibility of covalent bonds prevents similar control
and error correction mechanisms over the system as compared to hydrogen bonded
networks. A high defect density and a low degree of ordering is the consequence for
the resulting 2D structures.
Inafinalsetofexperimentsaromaticthiolmoleculescouldbeassembledintohighlyor-
vContents
dered structures via metal-coordination bonds. The 2D gas of freely diffusing adatoms
of a copper surface was thermally excited to finally transform a trithiolate precursor
structure into metal-coordination networks via Cu-S metal coordination bonds. Two
different coordination geometries were observed giving rise to the formation of two
morphologically distinct phases. These studies revealed the impact of the adatom gas
for surface reactivity and chemistry of metals.
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