First principles theory of organic molecules on metal surfaces: formate, 3-Thiophene-carboxylate and glycinate on Cu(110) [Elektronische Ressource] / vorgelegt von Nicolae Atodiresei
185 pages
English

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First principles theory of organic molecules on metal surfaces: formate, 3-Thiophene-carboxylate and glycinate on Cu(110) [Elektronische Ressource] / vorgelegt von Nicolae Atodiresei

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First Principles Theory of Organic Molecules on Metal surfaces: Formate, 3-Thiophene-carboxylate and Glycinate on Cu(110) Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der Rheinisch-Westfälischen Technischen Hochschule Aachen zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigte Dissertation vorgelegt von Master of Science Nicolae Atodiresei aus Pacani (Romania) Berichter: Herr apl. Prof. Dr. rer. nat. Kurt Schroeder Herr Univ.-Prof. Dr. rer. nat. Stefan Blügel Tag der mündlichen Prüfung: 12. Oktober 2004 Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verügbar. Contents Introduction 7 Chapter 1 Density Functional Theory 11 1.1. Density Functional Theory 16 1.2. The Kohn-Sham Formulation 19 1.3. Exchange-Correlation Terms in Density Functional Theory 20 1.3.1. Local Density Approximation (LDA) 22 1.3.2. Generalized Gradient Approximation (GGA) Chapter 2 Density Functional Theory in a Plane Wave implementation 24 2.1. Supercell Approach 25 2.2. Bloch’s Theorem and the Plane-Wave Basis Set 26 2.3. Kohn-Sham Equations in Plane-Wave Form r27 2.4 k -point Sampling Chapter 3 Pseudopotentials 28 3.1. Pseudopotentials 30 3.2. Generation of Norm-Conserving Pseudopotentials 3.3. Semi-local Pseudopotential and 32 Kleinman-Bylander Form of the Pseudopotential 33 3.4. The PAW Pseudopotential 35 3.5. Partial Core-Correction 36 3.6.

Informations

Publié par
Publié le 01 janvier 2004
Nombre de lectures 20
Langue English
Poids de l'ouvrage 14 Mo

Extrait

First Principles Theory of Organic Molecules on Metal surfaces:
Formate, 3-Thiophene-carboxylate and Glycinate on Cu(110)
Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der
Rheinisch-Westfälischen Technischen Hochschule Aachen
zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften
genehmigte Dissertation
vorgelegt von
Master of Science
Nicolae Atodiresei
aus Pacani (Romania)

Berichter:
Herr apl. Prof. Dr. rer. nat. Kurt Schroeder
Herr Univ.-Prof. Dr. rer. nat. Stefan Blügel


Tag der mündlichen Prüfung: 12. Oktober 2004

Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verügbar. Contents

Introduction 7
Chapter 1
Density Functional Theory
11 1.1. Density Functional Theory
16 1.2. The Kohn-Sham Formulation
19 1.3. Exchange-Correlation Terms in Density Functional Theory
20 1.3.1. Local Density Approximation (LDA)
22 1.3.2. Generalized Gradient Approximation (GGA)
Chapter 2
Density Functional Theory in a Plane Wave implementation
24 2.1. Supercell Approach
25 2.2. Bloch’s Theorem and the Plane-Wave Basis Set
26 2.3. Kohn-Sham Equations in Plane-Wave Form
r
27 2.4 k -point Sampling
Chapter 3
Pseudopotentials
28 3.1. Pseudopotentials
30 3.2. Generation of Norm-Conserving Pseudopotentials
3.3. Semi-local Pseudopotential and
32 Kleinman-Bylander Form of the Pseudopotential
33 3.4. The PAW Pseudopotential
35 3.5. Partial Core-Correction
36 3.6. General Scheme for Pseudopotential Generation
38 3.7. Coments on the Generation of the Pseudopotentials

3Chapter 4
The EStCoMPP-Program
40 4.1. The Energy Minimization
4.2. Explicit Form of the Equations in the EStCoMPP-program
43 The Kinetic Energy
43 The local Energy
45 The Non-local Part of the Energy
47 The Ewald-Energy
47 The Hellman-Feynman Forces
49 The Loop-Structure and the Algorithms
50 4.3. Iterative Eigenvalue Determination
51 4.4. The Electronic Self-consistency and Molecular Relaxation Loops
Chapter 5
Cadmium Complexes in Si and Ge 53

Chapter 6
Formate on Cu(110) surface
58 6.1 Introduction
61 6.2 Formate Free Radical
64 6.3 Formate-Cu(110) Surface Systems
70 6.4 “Low Formate Coverage”
73 6.5 “High Formate Coverage”
76 6.6 Oxygen Precovered Cu(110), “High Formate Coverage”
Chapter 7
3-Thiophene carboxylate on Cu(110) surface
81 7.1 Introduction
83 7.2 3-Thiophene Carboxylate Free Radical
87 7.3 3-Thiophene Carboxylate-Cu(110) System
Chapter 8
Glycinate on Cu(110)-Surface
99 8.1 Generalities
100 8.2 Chirality and the Biological Importance
100 8.3 Experimental Structure Determination
103 8.4 Glycinate Free Radical
4106 8.5 Glycinate-Cu(110) System
113 Energetics and Bond Strength
116 Atomic and Electronic Structure
Summary 122

Appendixes
Appendix A.1.
127 Functional (variational) derivative
Appendix A.2.
129 Exchange-correlation terms in DFT
Appendix A.3.
Explicit formula of the terms used in calculation of exchange-correlation
131 energy and potential
Appendix A.4.
133 Formulae
Appendix A.5.
Details about the GGA implementation in
140 the subroutines of EStCoMPP-Program
Appendix B
143 Partial core-correction in real space
Appendix C
144 Parameters and tests of the PAW-pseudopotentials
Appendix D
178 PLDOS for clean Cu(110) surface

180 Bibliography



5



6Introduction
New ways have to be explored if the miniaturization of the electronic devices
is to continue at the same pace as in the last decades. Besides incurring in
exponentially increasing fabrication costs, the down-scaling of (optical) lithographic
processes in the “top-down” approach for silicon chip manufacturing will soon lead to
fundamental physical limits [IO00]. An alternative possibility is to explore the so-
called “bottom-up” approach, which is based on the formation of functional devices
out of prefabricated molecular building blocks with intrinsic electronic properties - an
area generally referred to as molecular electronics and nanodevices. Molecules
can be viewed as the ultimate limit of electronic devices, since their size is about 1nm.
By using appropriately designed organic molecules, the density of transistors per chip
5might potentially be increased by up to a factor of 10 compared to present standards
[IGA00, RT00].
The possibility of tailoring organic molecules with particular properties, the
tunability of their characteristics, and the efficiency and flexibility of deposition
methods, are reasons for a strong effort to show their applicability as competitive
materials with respect to inorganic semiconductors. The idea of being able to control
and explore ways to incorporate organic functions into existing technologies and to
build molecule-based nanoscale electronic circuits with rectifying, logic and
switching functions has stimulated experimental attempts to build such molecular
electronics, and theoretical efforts to describe and predict their properties.
Organic functionalisation of the metallic surfaces has important applications,
e.g. in catalysis, sensors, adhesion, corrosion inhibition, molecular recognition,
optoelectronics and lithography [Rav03]. Electronic transport involving molecules is
attracting increasing interest because single molecules might be able to control
electron transport. The inclusion of biological active molecules and the concept of
bioelectronic devices add further weight to this idea. Within such a technological
complex, it is clear that the development of future organic/inorganic interfaces is
critically dependent on establishing a fundamental understanding of the various
bonding and lateral interactions that govern the ultimate orientation, conformation and
two dimensional organization of these molecules at the surface.
As a consequence, in all cases, molecule-surface interaction plays a vital role,
since the binding and ordering of molecules on surfaces is in general controlled by a
delicate balance between competing molecule-substrate and intermolecular
interactions. Another consequence of the complex interactions involved, certain
7molecular behavior, although valid for molecules in the gas phase, cannot be
transferred a priori to a situation, in which the molecules are adsorbed on the
substrate. For example, the exact adsorption conformation may play an important role
when measuring the conductance through a single molecule.
During recent years a whole range of highly sophisticated experimental
techniques have been developed for testing the properties of the molecules on surfaces
[IFF03]: AES (Auger electron spectroscopy), AFM (atomic force spectroscopy),
EELS or HREELS (high resolution electron energy loss spectroscopy), LEED (low
energy electron diffraction), STM (scanning tunneling microscopy), STS (scanning
tunneling spectroscopy), XPD (X-ray photoelectron diffraction), XPS (X-ray
photoelectron spectroscopy). All these techniques offer valuable insights into the
ordering of molecules on the surfaces and into molecule-surface interactions. In
general, the information obtained with some of the experimental techniques (as AES,
LEED, HREELS, XPD, XPS) is averaged over large areas of the sample substrate
compared to the characteristic molecular distances on the surface. Although high-
resolution STM/STS can manipulate matter with atomic scale precision the
information obtained in most of the molecule-substrate cases is not free of
ambiguities. This clearly limits the ability to yield information on local properties,
which is essential in the present context.
A fundamental new insight into the very detailed binding geometries and
ordering of the molecules on surfaces and specificity of the interaction that occur
between anchored molecules can be obtained by performing ab initio calculations.
Among many fascinating questions connected with the problem of adsorption, two
basic ones can be answered using ab initio methods: the first refers to the structure
and energies of the adsorbed molecules and the second, perhaps more subtle question,
is concerned with the way in which the electronic properties of the substrate material
and the molecules are modified by the adsorption.
The basis of ab initio calculations is the density functional theory (DFT),
which states that the ground state properties of a many-electron system are
exclusively determined by the electron density. It has been shown that the quantum
mechanical many-particle problem can be mapped onto a system of non-interacting
electrons moving in an effective potential. Using the generalized gradient
approximation (GGA) for the exchange-correlation functional, the pseudopotential
method in a supercell approach, i.e. reciprocal space formulation [IZC79], and
iterative numerical methods for solving the single-particle equations [Fle87], the ab
initio method can be applied to large and complex molecular-surface systems.
For this purpose we have develop

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