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The characteristics of interaction between six transition-metal porphyrines and the Ag(111) surface are detailed here as resulted from DFT calculations. Van der Waals interactions as well as the strong correlation in 3d orbitals of transition metals were taken into account in all calculations, including the structural relaxation. For each system we investigate four relative positions of the metallic atom on top the surface. We show that the interaction between the transition metal and silver is the result of a combination between the dispersion interaction, charge transfer and weak chemical interaction. The detailed analysis of the physical properties, such as dipolar and magnetic moments and the molecule–surface charge transfer, analyzed for different geometric configurations allows us to propose qualitative models, relevant for the understanding of the self-assembly processes and related phenomena.

Acenes and azaacenes lie at the core of molecular materials' applications due to their important optical and electronic features. A critical aspect is provided by their heteroatom multiplicity, which can strongly affect their properties. Here we report pyrazinacenes containing the dihydro-decaazapentacene and dihydro-octaazatetracene chromophores and compare their properties/functions as a model case at an oxidizing metal substrate. We find a distinguished, oxidation-state-dependent conformational adaptation and self-assembly behaviour and discuss the analogies and differences of planar benzo-substituted decaazapentacene and octaazatetracene forms. Our broad experimental and theoretical study reveals that decaazapentacene is stable against oxidation but unstable against reduction, which is in contrast to pentacene, its C-H only analogue. Decaazapentacenes studied here combine a planar molecular backbone with conformationally flexible substituents. They provide a rich model case to understand the properties of a redox-switchable pi-electronic system in solution and at interfaces. Pyrazinacenes represent an unusual class of redox-active chromophores. Acenes are a promising class of organic materials with distinctive electronic and optical properties. Here decaazapentacene and octaazatetracenes are prepared and their self-assembly behaviour at different oxidation states is analysed. Práce se zabývá studiem pyrazinacenů obsahujících dihydro-dekaazapentacenové a dihydro-oktaazatetracenové chromofory a porovnáním jejich vlastností při modelovém chování na oxidačním kovovém substrátu. Byla nalezena odlišná, na oxidačním stavu závislá konformační adaptace a samouspořádající se chování. Byly připraveny dekaazapentaceny a oktaazatetraceny a analyzováno jejich samoorganizující se chování v různých oxidačních stavech.

Using first-principles calculations, we investigate the binding energy for six transition metal - phthalocyanine molecules adsorbed on Au(111). We focus on the effect of translation on molecule - surface physical properties; van der Waals interactions as well as the strong correlation in d orbitals of transition metals are taken into account in all calculations. We found that dispersion interaction and charge transfer have the dominant role in the molecule-surface interaction, while the interaction between the transition metal and gold has a rather indirect influence over the physics of the molecule-surface system. A detailed analysis of the physical properties of the adsorbates at different geometric configurations allows us to propose qualitative models to account for all values of interface dipole charge transfer and magnetic moment of metal-phthalocyanines adsorbed on Au(111).

We present a theoretical investigation that addresses the most important aspects of the interaction between α-glycero-phosphatidyl-choline and Au(111) surface. For the density functional calculations we employed both traditional exchange-correlation functionals and newly developed vdW-D2 corrected one. The comparison between these functionals allows us to spot the role of van der Waals effects into the molecule– surface interaction. The effect of an external field applied to the molecule–surface system was also explicitly investigated. Our results reveal a complex picture where the molecular adsorption is dominated by the interplay between a weak molecule–surface interaction and a rather important deformation energy of the adsorbed molecule. In the presence of an external electric field, the choline moiety provided the strongest response in terms of binding energy as well as geometric configuration of the adsorbate.

We present density functional theory investigations on the electronic structure properties for three derivatives of trioxotriangulene that were recently used as electrode materials in Li–ion batteries. We compare the results obtained by standard GGA exchange–correlation functionals with those based on recently developed van der Waals exchange–correlation functionals for the free molecules and bulk structures. This allows us to point out the importance of van der Waals interaction for the stability of the structures as well as the main characteristics of the electronic structures.

Using first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts.

We have investigated the ballistic transport for Mn, Fe-porphyrin molecules in contact with Au(111) electrodes by using density functional theory. We show that the information resulted from the projected density of electronic states does not provide a complete picture of the transport mechanism. Instead, we propose a methodology based on the concept of the orbital projected transmissions for selected groups of atoms. We have found that the transmission channels for occupied states can be assigned to short range scattering processes at gold-molecule interface, while for the states above Fermi level the transmission takes place via long range scattering processes. The interplay between these two conduction mechanisms is responsible for the transport path in metal-porphyrin; our model is in qualitative agreement with the existing experimental data on transport pathway on single porphyrin molecules.

We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.