First principles theory of organic molecules on metal surfaces : formate, 3-thiophene-carboxylate and glycinate on Cu(110)

We have performed ab initio calculations for the understanding of the interaction between organic molecules and the Cu(110) surface. We have used the program package EStCoMPP (Electronic Structure Code for Material Properties and Processes) that is based on density functional theory, pseudopotential and supercell approaches. In order to accurately describe the molecule-metal surface interaction we have implemented the generalized gradient approximation (GGA) for the exchange- correlation functional in the EStCoMPP-package. The gradient-corrected exchange- correlation functional can be evaluated using two schemes: a traditional scheme (using the second order derivatives whose calculation requires the use of a high- quality representation of the density on the FFT-grid) and a new scheme proposed by White and Bird (in this formulation the total exchange-correlation potential and energy are exactly calculated on a minimum FFT-grid by using a product of first order gradients instead of second order derivatives.). In addition, a new scheme to calculate the partial core-correction charge in real space has been implemented. A series of pseudopotentials have been generated: Si, Cd, S, Ti, O, Cu, N, C, Pt, Ga and Sr. Several calculations including various bulk crystals and molecules have been performed in order to verify the accuracy of our generated pseudopotentials, and the approximations to the exchange-correlation functional. All tests show that our results are in good agreement with the experimental and theoretical data in the literature. Cadmium Complexes in Si and Ge: Using the local density approximation (LDA) we have performed calculations to search for the correct local geometry of the Cd-vacancy and Cd-interstitial complexes in Si and Ge. We found that for both Si and Ge the substitutional Cd-vacancy complex is unstable and relaxes to a split vacancy complex with the Cd on the bond center site. For the Cd-interstitial complex we obtained a highly symmetrical split configuration as well. For these geometries a collaboration group has calculated the electric field gradients (EFG's) of these complexes and found that they are in good agreement with experiments. The main part of this thesis is the investigation of the bonding of several molecules to the Cu(110) surface via carboxylate group: formate, 3-thiophene carboxylate (planar molecules) and glycinate (3-dimensional structure). Formate molecule: Several geometries corresponding to low and high coverages of formate molecules in a (2x2) unit cell on clean and oxygen-precovered Cu surface have been optimized. For all configurations we found that the molecule is sitting with its molecular plane perpendicular to the Cu(110)-surface. For low coverage (one formate molecule in the unit cell) we found that in the stable configuration the molecule is in a bridge position (each oxygen of the carboxylate group binds a single copper atom so that the carboxylate group forms a bridge between two nearest-neighbor copper atoms along to [110] direction). The Cu surface atoms that are not binding directly to oxygen atoms show inward relaxations as on the clean Cu(110) surface. In contrast, nearly no relaxation relative to the ideal unrelaxed Cu(110) surface is found for the Cu atoms that are forming the bonds with O atoms. At high coverage (two formate molecules in the unit cell) the most stable configuration is the one with both molecules in bridge positions. The Cu-surface atoms show outward relaxations larger than in the low coverage case. In the case of oxygen-precovered Cu-surface, at high coverage of formate molecules, we find again that the stable configuration is the one with both molecules in bridge positions. A large outward relaxation of the Cu surface layer is found. The extra oxygen atom (the 0.25ML oxygen monolayer) is only slightly displaced from its fourfold hollow site starting position. This oxygen atom binds more strongly to the second layer Cu atom than to the first layer atoms. The Cu-O bond length is practically the same in all configurations and does not depend on the coverage ratio. The main changes due to oxygen coverage are in the first interlayer relaxations. With increasing coverage the first Cu-surface layer relaxes towards the positions corresponding to the unrelaxed (110) surface, and for the oxygen precovered surface the inward relaxation for the clean Cu(110) surface is over-compensated and turned into a large outward relaxation. 3-thiophene carboxylate molecule: Four different geometries corresponding to a (2x1) unit cell (high coverage) of 3-thiophene carboxylate molecules on Cu(110) surface have been optimized. In the final stable configuration the molecule sits perpendicular to the surface in bridge position above the first Cu-surface layer with the carboxylate group oriented along to the [110] direction. The most important change due to adsorption is in the geometry of the molecule. In the gas phase the single molecule has a planar geometry with an extended p-system over the thiophene ring and carboxylate group. The adsorption of the molecule breaks this planarity. There are strong lateral interactions that appear between the hydrogen atoms of neighboring thiophene rings. As a consequence, in the adsorbed molecules the thiophene rings are rotated by 24° relative to the carboxylate group. The relaxations of the Cu-surface layer are almost the same as those of the clean Cu(110) surface. Glycinate molecule: In the case of the glycinate molecules adsorbed on the Cu(110) surface (two molecules in a (3x2) unit cell) several geometries have been optimized. The most stable one was found to be a heterochiral configuration configuration where both enantiomers are present in the unit cell with zero degree rotated relative to each other. The molecules are lying flat and bind to the surface via both functional groups (carboxylate -OCO- and amino H2N-). In this configuration short and strong Cu-N and Cu-O bonds are formed. The hydrogen atoms that are binding the carbon atom are non-equivalent and distinct relative to the surface: one bond direction is almost parallel and the other is perpendicular to the surface. This makes the carbon atom a chiral center in the molecule. The N and one O atom are slightly displaced from on-top Cu-sites. The other O atom is forming a bridge between two Cu-surface atoms along to [100] direction. The carboxylate group is no longer perpendicular to the surface as in the case of formate or 3-thiophene carboxylate molecules. For the glycinate-Cu(110) system, the Cu-O bonds are 0.22- 0.29 Å larger than in the case of the formate- or 3-thiophene-carboxylate-Cu(110) systems. There are interactions between the adsorbed glycinate molecules via hydrogen bonds. The stable configuration shows a glide plane symmetry that is also observed in the experiments. 1

Grantor dc:publisher

Publikationsserver der RWTH Aachen University

Year dc:date

2004

Author dc:creator

• Atodiresei, Nicolae

Contributors dc:contributor

• Schroeder, Kurt

• info:eu-repo/classification/ddc/530
• Kupfer
• Kristallfläche
• Formiate
• Monoschicht
• Glycinderivate
• Dichtefunktionalformalismus
• Thiophenderivate
• Carboxylate
• Physik
• First Principles Theory
• Organic Molecules
• Metal Surfaces

Statement dc:rights

• info:eu-repo/semantics/openAccess

Language dc:language

eng

Identifier

https://publications.rwth-aachen.de/search?p=id:%22RWTH-CONV-115084%22

OAI record oai:identifier

https://publications.rwth-aachen.de/oai2d?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Apublications.rwth-aachen.de%3A52894