Verlag des Forschungszentrums Jülich
JUEL-4152
Atodiresei, N.
First Principles Theory of Organic Molecules on Metal surfaces
185 S., 2004
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 socalled
“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
might potentially be increased by up to a factor of 105 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
molecular 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 highresolution
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 developed in our group the program package
EStCoMPP, an “Electronic Structure Code for Materials Properties and Processes”,
which has been used throughout this thesis. It is an ab initio molecular dynamics
program in the spirit of Car and Parrinello based on a plane-wave basis set. The
physical system is represented as a periodical supercell. The EStCoMPP program
contains the projector-augmented-wave method (PAW) in a formulation similar to the
one proposed by Blöchl [Blö94], but also includes elements of a pseudocharge
method proposed by M. Weinert [Wei81] for the full potential linearized augmented
plane wave method. It is optimally suited for calculating forces exerted on the atoms
and to determine the equilibrium structures of complex systems of surfaces and
molecule-surface systems. The program package contains the EStCoMPPVisualization
Tool (EStCoMPP-VT) [AA02] that is used to visualize the position
of the atoms in the unit cell and electron densities calculated with EStCoMPP-program.
We shortly describe the basics of the DFT in Chapter 1 including the
generalized gradient approximation to the exchange-correlation functional, which is
used to describe molecules and molecule-surface systems accurately. Chapter 2
contains the description of the plane-wave representation of the density functional
theory, and Chapter 3 is devoted to the pseudopotential concept and generation of the
pseudopotentials in the Kleinman-Bylander and the PAW formalism. As the final
chapter of the theoretical background Chapter 4 contains the flow diagram of the
EStCoMPP-code and the implementation of all theoretical ideas.
In order to verify the accuracy of the results obtained with our program we
have calculated the geometrical structure of Cd impurities with vacancies and
interstitials in Si/Ge bulk. Our results, which are presented in Chapter 5, have been
used by a collaborating group (using a KKR all-electron method) and the specific
geometry has been properly assigned to the measured electric field gradient (EFG) in
Si/Ge.
In order to understand the interface organic molecules-metallic substrate it is
important to study model systems in detail. In this thesis the structure (bonding
geometry and electronic structure) and local order of several molecular layers on
Cu(110) surface have been investigated. Formate, 3-thiophene carboxylate or
glycinate molecules form such molecular layers. All these molecules contain the
carboxylate group but their geometrical structures differ: while formate and 3-
thiophene carboxylate are planar molecules the glycinate has a 3-dimensional
geometry. All investigated molecules chemically bind to Cu(110) via the carboxylate
group. A lot of very complex organic and biological molecules, which are interesting
from the surface science point of view, use the carboxyl group as an anchoring group
to bind to metal surfaces. For recent reviews on molecular adsorption see [Rav03],
[BR03].
Formic acid is the simplest molecule that contains a carboxyl group. The
adsorption of formic acid on copper single crystal surfaces, in particular Cu(110), has
attracted considerable attention due to the identification of formate as a key stable
intermediate in methanol synthesis which is carried out commercially using copperbased
catalysts. Formic acid adsorbs at the Cu(110) surface the result being a
perpendicular formate-molecular layer on the metallic surface. Chapter 6 of the thesis
is concerned with the bonding geometry and electronic structure of formate molecules
for different coverages on clean and oxygen-precovered Cu(110) surfaces.
The family of five-membered heterocycles, which includes 3-thiophene
carboxylic acid, is the main constituent of the polymeric organic conductors. There is
an increasing interest in the adhesion and growth of oriented polymeric materials on
surfaces. Many investigations are performed in order to understand the properties of
the polymer-precursor-substrate interfaces. With such information it should be
possible to fabricate a specific polymer-surface structure, of which chemistry and
physics can be controlled and optimized to achieve specifically desired properties.
The chemical adsorption of 3-thiophene carboxylic on theCu(110) surface produces
an ordered 3-thiophene carboxylate molecular layer in which the molecules are
perpendicular on the surface. Chapter 7 of this thesis investigates the bonding to the
surface, the lateral interactions, the orientation and alignment of adsorbed 3-thiophene
carboxylate molecules on Cu(110) surface.
The study of bonding geometries of model species such as simple aminoacids
can assist the interpretation of more complex systems including aspects of
biochemically and chirally active films. For example, the structures, conformations
and local ordering in the self-assembled monolayers determine the possible
interaction with other incoming species in the process of molecular recognition. The
functional groups involved in the bonding of the molecule to the surface will not be
available for coupling to other species from the surrounding medium. Glycine is the
simplest aminoacid, it has an important function in the neurotransmitter system.
Glycine adsorption on the Cu(110) surface produces a flat layer of glycinate
molecules, binding to the surface via both functional groups (carboxylate and amino).
Some experiments suggested the formation of heterochiral domains (two molecules
where both enantiomers are present in the unit cell) as well as homochiral domains
(two molecules of one enantiomer type are in the unit cell), other experiments report
the existence of only heterochiral domains. Chapter 8 of this thesis is concerned with
the study of the bonding properties of the glycinate molecules and the stability of
possible different domains that can be formed at the Cu(110) surface. The results
obtained allow a unique assignment of the registry of glycinate molecules at the
Cu(110) surface.
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