DFT study of alkanethiol self-assembled monolayers on gold(111) surfaces [Elektronische Ressource] / von Edmanuel Torres

Edmanuel Torres, Mb 014, 492

Sujets

• Physik

Informations

• Publié par: ruhr-universitat_bochum
• Publié le: 01 janvier 2009
• Nombre de lectures: 33
• Langue: English
• Poids de l'ouvrage: 17 Mo

Extrait

DFT Study of Alkanethiol
Self-assembled Monolayers on
Gold(111) Surfaces
DISSERTATION
zur
Erlangung des Grades
,,Doktors der Naturwissenschaften”
an der Fakult¨at fu¨r Physik und Astronomie
der Ruhr-Universit¨at Bochum
von
Edmanuel Torres
aus
Kolumbien
Bochum20091. Gutachter Prof. Dr. J¨org Neugebauer
2. Gutachter Prof. Dr. Dr. h.c. Hartmut Zabel
Datum der Disputation 6. Juli 2009Abstract
Self-assembled monolayers (SAMs) of thiols on gold surfaces are of great interest
because of the growing number of potential applications in fields such as molecular
electronics, nanotechnology or biosciences. The development of future applications of
alkanethiol SAMs in nanosciences requires methods that can reproduce with precision
the desired properties.
√ √
◦Alkanethiols on gold(111) surfaces adopt a ( 3× 3)R30 commensurate lattice
and may manifest c(4×2) superlattice modulations in the high density regime. Until
now six different high density phases have been reported. Alkanethiol SAMs have
been intensively studied during the last two decades. In spite of this, experiment
and theoretical calculations have persistently disagreed. One of the most remarkable
controversies is whether the molecules adsorb on top or at a site close to the bridge
site.
In this thesis, the SAM structures for alkanethiols with short and intermediate
chains were studied on unreconstructed and reconstructed gold(111) surfaces. The
presented results shed light on some of the thiol SAM controversies. The steric effects
due to the chain length suggest that long chain thiols may show higher ordered SAM
structures. Two SAM structures were found favorable on unreconstructed gold(111)
for each thiol, indicating that different domains may coexist. Vacancies formation
inside SAMs are favorable and may lead to point defects. A new more stable c(4×
2) structure including adatom reconstructions satisfactorily reproduces the structural
characteristics reported from experiments is presented. The simulated STM image
exhibits a zigzag modulation that is frequently observed in STM experiments. The
results also indicate that the SAM may stabilize by a stepwise mechanism in which
adatom-vacancy pairs are created and vacancies are subsequently pushed out of the
dense domains. A plausible mechanism for the formation of gold vacancy islands, as
seen in experiments, arises from this stabilization process.Contents
1 Introduction 7
1.1 Alkanethiol building blocks . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.2 The Gold(111) substrate . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.3 Preparation of alkanethiol SAMs on Au(111) . . . . . . . . . . . . . . . 12
1.4 Structures of alkanethiol SAMs on Au(111) . . . . . . . . . . . . . . . . 13
√ √
◦1.4.1 The ( 3× 3)R30 lattice . . . . . . . . . . . . . . . . . . . . 15
1.4.2 The c(4×2) superlattice . . . . . . . . . . . . . . . . . . . . . . 17
1.5 Previous theoretical studies of alkanethiol SAMs . . . . . . . . . . . . . 21
1.6 Issues of Alkanethiol SAM studies . . . . . . . . . . . . . . . . . . . . . 24
1.7 Alkanethiol SAM applications . . . . . . . . . . . . . . . . . . . . . . . 25
2 Basis of Electronic Structure Methods 27
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.2 Born-Oppenheimer approximation . . . . . . . . . . . . . . . . . . . . . 29
2.3 Hartree-Fock theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.4 Variational principle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.5 Density functional theory. . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.5.1 Hohenberg and Kohn theorems . . . . . . . . . . . . . . . . . . 35
2.5.1.1 First theorem . . . . . . . . . . . . . . . . . . . . . . . 35
2.5.1.2 Second theorem . . . . . . . . . . . . . . . . . . . . . . 36
2.5.2 Kohn-Sham equation . . . . . . . . . . . . . . . . . . . . . . . . 37
i2.5.3 Exchange-correlation functionals . . . . . . . . . . . . . . . . . . 39
2.6 Computational methods . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.6.1 Basis set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.6.1.1 Localized basis sets . . . . . . . . . . . . . . . . . . . . 41
2.6.1.2 Plane waves . . . . . . . . . . . . . . . . . . . . . . . . 43
2.6.1.3 Numerical functions . . . . . . . . . . . . . . . . . . . 44
2.6.2 Pseudopotentials . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.6.3 Augmented Plane Wave . . . . . . . . . . . . . . . . . . . . . . 47
2.6.4 Projector augmented-wave method . . . . . . . . . . . . . . . . 47
2.6.5 Structure optimization . . . . . . . . . . . . . . . . . . . . . . . 48
2.6.5.1 Hellmann-Feynman forces . . . . . . . . . . . . . . . . 49
2.6.5.2 Conjugate-gradients . . . . . . . . . . . . . . . . . . . 50
2.6.5.3 Quasi-Newton . . . . . . . . . . . . . . . . . . . . . . . 50
2.7 Tersoff-Hamann STM simulations . . . . . . . . . . . . . . . . . . . . . 51
3 Modeling 53
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.2 Basics of Crystal Structures . . . . . . . . . . . . . . . . . . . . . . . . 54
3.3 Supercell Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.3.1 Periodic Systems . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.3.2 Aperiodic Systems . . . . . . . . . . . . . . . . . . . . . . . . . 59
3.3.3 Molecular Adlayers . . . . . . . . . . . . . . . . . . . . . . . . . 60
3.4 Computational Details . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
4 The Gold substrate 63
4.1 Bulk Gold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
4.2 Surface Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
5 Alkanethiol monolayers on Gold(111) 71
5.1 Structure of Alkanethiol Molecules . . . . . . . . . . . . . . . . . . . . 73
ii√ √
◦5.2 The ( 3× 3)R30 Lattice . . . . . . . . . . . . . . . . . . . . . . . . 74
5.2.1 Chain Length effects in SAMs on Unreconstructed Au(111) Sur-
faces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
5.2.2 Favorable Structures on Unreconstructed Au(111) . . . . . . . . 82
5.2.3 Ethanethiol SAMs on Reconstructed Au(111) . . . . . . . . . . 85
5.2.4 Favorable Structures on Reconstructed Au(111) . . . . . . . . . 89
5.3 The c(4×2) Superlattice . . . . . . . . . . . . . . . . . . . . . . . . . . 91
5.3.1 Phase Transformation by Gold Adatoms . . . . . . . . . . . . . 91
5.3.2 The c(4×2) structures . . . . . . . . . . . . . . . . . . . . . . . 92
5.3.3 Mechanisms for Vacancy Island formation . . . . . . . . . . . . 95
5.4 STM Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
6 Conclusion and Outlook 105
Bibliography 108
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