First-Principles Modeling of Optically Active Organic Molecules in Solar Cell Devices and Biological Environments

With the increasing cognition of the importance of organic molecules, they are widely applied in printing, biological and pharmacological fields, because of their special capabilities of harvesting solar light, scavenging free radicals, and chelating metal ions. During the past decades, the unique photoelectronic and photochemical properties of organic molecules, such as phthalocyanine, cyanidin, and their relevant derivatives, attract tremendous attention, because they provide an excellent opportunity to solve the worldwide energy crisis by converting directly the solar light to electricity. The surface morphology and electronic interaction of these organic molecules with other molecules, surfaces or interfaces play a critical role in determining the performance of the electronic and optical devices based on organic molecules. In this thesis, we focus on the investigation of several selected organic molecules, and their interaction with molecules, inorganic semiconductors, and organic semi-conductors, by using first-principles electronic structure calculations based on density functional theory, and time-dependent density functional theory. Particular attention is paid to the atomic structure, electronic and optical properties of organic molecules and the corresponding interfaces. The focus of this thesis is on the following aspects of the organic molecules: (i) The complexation mechanism of flavonoids with metal ions. The most likely chelation site for Fe is the 3-hydroxyl-4-carbonyl group, followed by 4-carbonyl-5-hydroxyl group and the 3'-4' hydroxyl (if present) of quercetin. A complex of two quercetin molecules with a single Fe ion is energetically more stable, however, six orbitals of Fe in the three quercetin complex are saturated by three perpendicular molecules to form and octahedral configurations. Furthermore, the optical absorbance spectra serves as signatures to identify various complexes. (ii) The electronic coupling between a dye molecule (Cyanidin) and a TiO2 nanowire. Upon molecular adsorption on TiO2 [010]-wire, cyanidin will be deprotonated into the quinonoidal form. This results in its highest occupied molecular orbitals being located in the middle of TiO2 bandgap and its lowest occupied molecular orbitals being close to the TiO2 conduction band minimum, in turn enhancing visible light absorption. Moreover, the excited electrons are injected into TiO2 conduction band within a time scale of 50 fs with negligible electron-hole recombination. (iii) The atomic and electronic structure of copper (fluoro-)phthalocyanine and graphene. When adsorbed on graphene, F16CuPc molecules prefer to form a close-packed hexagonal lattice with two-ordered alternating α and β stripes, whereas CuPc would like to form a square lattice. In addition, phthalocyanine adsorption modifies the electronic structure of graphene introducing intensity smoothing at 2-3 eV below and a small peak at ∼0.4 eV above the Dirac point in the density of states. And finally, (iv) the electronic interaction between CuPc and fullerene. For CuPc/C60 molecular complex, CuPc prefers to lie flat on the C60 surface rather than taking the standing-up molecular orientation. The favorable adsorption site for CuPc is the bridge site of C60 with one N-Cu-N bond of CuPc being parallel to a C-C bond of C60. Based on the analysis of the molecular complex, we predict that CuPc/C60(001) thin film heterojunction adopting the lying-down molecular orientation should have a higher efficiency of charge transfer in comparison with the relevant CuPc/C60(111) heterojunction with the standing-up arrangement.

Properties of copper (fluoro-)phthalocyanine layers deposited on epitaxial graphene

Efthimios Kaxiras, Sheng Meng, Jun Ren

We investigate the atomic structure and electronic properties of monolayers of copper phthalocyanines (CuPc) deposited on epitaxial graphene substrate. We focus in particular on hexadecafluorophthalocyanine (F16CuPc), using both theoretical and experimental (scanning tunneling microscopy STM) studies. For the individual CuPc and F16CuPc molecules, we calculated the electronic and optical properties using density functional theory (DFT) and time-dependent DFT and found a red-shift in the absorption peaks of F16CuPc relative to those of CuPc. In F16CuPc, the electronic wavefunctions are more polarized toward the electronegative fluorine atoms and away from the Cu atom at the center of the molecule. When adsorbed on graphene, the molecules lie flat and form closely packed patterns: F16CuPc forms a hexagonal pattern with two well-ordered alternating alpha and beta stripes while CuPc arranges into a square lattice. The competition between molecule-substrate and intermolecular van der Waals interactions plays a crucial role in establishing the molecular patterns leading to tunable electron transfer from graphene to the molecules. This transfer is controlled by the layer thickness of, or the applied voltage on, epitaxial graphene resulting in selective F16CuPc adsorption, as observed in STM experiments. In addition, phthalocyanine adsorption modifies the electronic structure of the underlying graphene substrate introducing intensity smoothing in the range of 2-3 eV below the Dirac point (E-D) and a small peak in the density of states at similar to 0.4 eV above E-D. (C) 2011 American Institute of Physics. [doi:10.1063/1.3590277]

American Institute of Physics2011

On-Surface Assembly and Reactions of Organic Molecules in Ultra-High Vacuum

Claudius Morchutt

This thesis comprises the study of two types of 2D materials, those stabilized by non-covalent and those by covalent interactions. They are synthesized and studied on well-defined metallic surfaces in ultra-high vacuum (UHV). The self-assembly of terephthalic acid (TPA) on Ag(100) is explored. TPA stays intact upon deposition at room temperature (RT) and forms islands stabilized by hydrogen bonds. TPA islands influence the homoepitaxial growth of silver and reduce the sticking coefficient of Ag atoms. At RT Ag atoms intercalate TPA islands which are not disrupted. In contrast, TPA molecules in conjunction with Mg atoms on Ag(100) results in tip-induced altering of the surface. The electric field between tip and sample interacts with Mg atoms and TPA, which leads to a restructuring of the step-edges during scanning. Moreover, the self-assembly of the organic semiconductor 2,7-dicyano[1]benzothiene[3,2-b]benzothiophene (cBTBT) on Ag(111) at RT is presented. The pro-chiral molecules form compact islands with a chevron-like structure containing both enantiomers. Deposition of Fe atoms leads to an amorphous metal-organic coordination network (MOCN). Statistical analysis reveals that conformational entropy plays a critical part in its stabilization. Phase segregation into spatially homogeneously crystalline domains of molecules and metal atoms upon annealing suggests that the amorphous network is kinetically trapped at RT during the preparation process. The second part presents the on-surface synthesis of 2D polymers via different coupling schemes. First, the Ullmann coupling on Au(111) is explored. The molecule 1,3,5-tris(4-bromophenyl)benzene (TBPB) debrominates upon annealing and polyphenylene is formed. To investigate the influence of metal substrates on the dehalogenation, a single layer of hexagonal boron nitride as well as graphene grown on Ni(111) is introduced. On both surfaces TBPB forms self-assembly islands stabilized by halogen bonds, while on bare Ni(111) the substrate-molecule interaction dominates resulting in structures without long-range order. Upon annealing on both surfaces dehalogenation is induced and 2D nanostructures are formed. On bare Ni(111) the precursor molecules merely decompose. The experimental annealing temperatures are consistent with debromination barriers calculated by DFT. An example of the synthesis of tailor-made 2D structures by using particularly designed precursor molecules is also given. A terminal alkyne with a triazine core undergoes on-surface Glaser coupling and cyclotrimerization on Au(111) resulting in nitrogen doped 2D polymers. Finally, a comprehensive study of the on-surface decarboxylation reaction of 1,3,5-tris(4-carboxyphenyl)benzene (TCPB) on Cu(111) is presented. TCPB deprotonates upon deposition on Cu(111) at RT and self-assembles in compact islands. The self-assembly is stabilized by ionic hydrogen bonds between deprotonated and negatively charged oxygen atoms and hydrogen atoms of neighboring molecules. Annealing leads to decarboxylation and formation of 2D nanostructures. The reaction occurs in a clean fashion because CO2 leaves the surface. In addition, STS reveals that the lowest unoccupied molecular orbital (LUMO) of the 2D polymer is destabilized compared to the LUMO of the monomer although the pi-electron system is more extended in the polymer. The decarboxylation impacts the energy position of the LUMO to a greater extend which is corroborated by DFT calculations.

EPFL2016

Design of Surface-Supported Bio-inspired Networks for CO2 and O2 Activation at Room Temperature

Daniel Eduardo Hurtado Salinas

The structure of a biological system defines its function. Therefore, nature has developed sophisticated systems that catalyze chemical reactions that are vital for life on earth. For instance, the photosynthesis is a biological process that is partially regulated by the metallo-enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), whose function is to catalyze the capture and transfer of CO2 into organic molecules. This carboxylation reaction occurs at the active site, where a magnesium ion (Mg2+) is bound to organic molecules with carboxylate (COO-) and amine (NH2) functional groups. In the last decades, supramolecular chemistry has proven to be a valid approach to replicate the structural characteristics of these natural metal-organic systems. Metal atoms and organic molecules are used as building blocks to form two-dimensional (2D) metal-organic networks (MONs) on metal surfaces, through a self-assembly process that occurs spontaneously. In these systems the molecules bind to the metal centers and control their oxidation states that, as found in metallo-enzymes, is crucial to perform a catalytic task. Therefore, these supramolecular assemblies show promising features to be explored for heterogeneous catalysis. The main objective of this thesis is to reverse the structure-function equation, that is: instead of finding specific functions of well-known 2D structures for future applications, 2D structures are designed to reproduce the specific functions of well-known bio-systems. Thus, inspired in the structure of the active site of RuBisCO, 2D Mg-based supramolecular assemblies are rationally designed on Cu(100) or Mg(0001) surfaces at room temperature (RT) as a platform for CO2 adsorption. This work is the first study of self-assembly of alkaline earth metal atoms (Mg) with organic molecules ((1,4-benzenedicarboxylic acid (TPA) and 2,4,6-tris(4-aminophenyl)-1,3,5-triazine (TAPT)) on metal surfaces. The first part of this thesis investigates the self-assembly of TAPT molecules. Scanning Tunneling Microscopy (STM) and High Resolution X-ray Photoemission Spectroscopy (HR-XPS) demonstrate that the molecules typically semi-deprotonate to form MONs with the adatoms from the host substrates. The exposure of these structures to CO2 results in the carboxylation of the amino groups. The second part proves that the COOH moieties of TPA molecules fully-deprotonate to form homo-molecular structures. The incorporation of Mg adatoms result in ionic MONs, which reproduce the carboxylate environment of the active site of RuBiSCO. STM, XPS and Density Functional Theory (DFT) analyze the structural changes, the chemical reactions and charge transfer during either the CO2 or O2 adsorption on the Mg2+ centers. The last part focusses on the co-deposition of both molecules to form 2D metallic-hetero-molecular networks with Mg2+ centers. The role of the Mg2+ centers as active sites for molecular adsorption and model systems for gas storage is studied. STM reveals that CO2 partially modifies the network towards a configuration that resembles the active site of RuBisCO. The formation of 3D structures to enhance CO2 adsorption is also evaluated.