Self-energy corrected DFT-NEGF for conductance in molecular junctions: an accurate and efficient implementation for TRANSIESTA package applied to Au electrodes.

In view of the development and the importance that the studies of conductance through molecular junctions is acquiring, robust, reliable and easy-to-use theoretical tools are the most required. Here, we present an efficient implementation of the self-energy correction to density functional theory non-equilibrium Green functions method for TRANSIESTA package. We have assessed the validity of our implementation using as benchmark systems a family of acene complexes with increasing number of aromatic rings and several anchoring groups. Our theoretical results show an excellent agreement with experimentally available measurements assuring the robustness and accuracy of our implementation.

A simple model to engineer single-molecule conductance of acenes by chemical disubstitution.

Understanding and controlling electrical conductivity at the single-molecule level is of fundamental importance for the development of new molecular electronic devices. This ideally requires considering the many different options offered by the molecular structure, the nature of the electrodes, and all possible molecule-electrode anchoring configurations, which is experimentally tedious and theoretically very expensive. Here we present a systematic theoretical study of the conductance of di-amino, di-methylthio and di-(4-methylthio)phenyl acenes, from benzene to pentacene, and for all possible distributions of two identical linkers symmetrically placed on opposite sides of the same ring. We show that, for all investigated compounds, the relative variation of the conductance is well explained by the variations of the HOMO energies as predicted by a simple extended-Hückel approach, i.e., without the need for further input from more elaborate calculations. The model predicts quite nicely that diamino acenes are better conductors than their corresponding dimethylthio analogues, and both much better than the di-(4-methylthio)phenyl counterparts, irrespective of the linkers' relative positions. It also predicts, for a given pair of linkers, the variations in the conductance resulting from changing the acene size and/or the relative position of the linkers. These variations can be as large as an order of magnitude, and therefore can be used to engineer molecular conductance. Finally, we show that a similar approach should be useful to predict trends in the relative conductance of a large variety of disubstituted acene isomers, including various linkers.

Quantifying Image Charge Effects in Molecular Tunnel Junctions Based on Self-Assembled Monolayers of Substituted Oligophenylene Ethynylene Dithiols.

A number of factors contribute to orbital energy alignment with respect to the Fermi level in molecular tunnel junctions. Here, we report a combined experimental and theoretical effort to quantify the effect of metal image potentials on the highest occupied molecular orbital to Fermi level offset, εh, for molecular junctions based on self-assembled monolayers (SAMs) of oligophenylene ethynylene dithiols (OPX) on Au. Our experimental approach involves the use of both transport and photoelectron spectroscopy to extract the offsets, εhtrans and εhUPS, respectively. We take the difference in these quantities to be the image potential energy eVimage. In the theoretical approach, we use density functional theory (DFT) to calculate directly eVimage between positive charge on an OPX molecule and the negative image charge in the Au. Both approaches yield eVimage ∼ -0.1 eV per metal contact, meaning that the total image potential energy is ∼-0.2 eV for an assembled junction with two Au contacts. Thus, we find that the total image potential energy is 25-30% of the total offset εh, which means that image charge effects are significant in OPX junctions. Our methods should be generally applicable to understanding image charge effects as a function of molecular size, for example, in a variety of SAM-based junctions.

Dynamic Covalent Properties of a Novel Indolo[3,2-b]carbazole Diradical.

This work describes the synthesis and properties of a dicyanomethylene-substituted indolo[3,2-b]carbazole diradical ICz-CN. This quinoidal system dimerises almost completely to (ICz-CN)2 , which contains two long C(sp3 )-C(sp3 ) σ-bonds between the dicyanomethylene units. The minor open-shell ICz-CN component in the solid-state mixture was identified by EPR spectroscopy. Cyclic voltammetry and UV-visible spectroelectrochemical data, as well as comparison with reference monomer ICz-Br reveal that the nature of the one-electron oxidation of (ICz-CN)2 at ambient temperature and ICz-CN at elevated temperature is very similar in all these compounds due to the prevailing localization of their HOMO on the ICz backbone. The peculiar cathodic behaviour reflects the co-existence of (ICz-CN)2 and ICz-CN. The involvement of the dicyanomethylene groups stabilizes the close-lying LUMO and LUMO+1 of (ICz-CN)2 and especially ICz-CN compared to ICz-Br, resulting in a distinctive cathodic response at low overpotentials. Differently from neutral ICz-CN, its radical anion and dianion are remarkably stable under ambient conditions. The UV/Vis(-NIR) electronic transitions in parent (ICz-CN)2 and ICz-CN and their different redox forms have been assigned convincingly with the aid of TD-DFT calculations. The σ-bond in neutral (ICz-CN)2 is cleaved in solution and in the solid-state upon soft external stimuli (temperature, pressure), showing a strong chromism from light yellow to blue-green. Notably, in the solid state, the monomeric diradical species is predominantly formed under high hydrostatic pressure (>1 GPa).

Single-Molecule Conductance of 1,4-Azaborine Derivatives as Models of BN-doped PAHs.

The single-molecule conductance of a series of BN-acene-like derivatives has been measured by using scanning tunneling break-junction techniques. A strategic design of the target molecules has allowed us to include azaborine units in positions that unambiguously ensure electron transport through both heteroatoms, which is relevant for the development of customized BN-doped nanographenes. We show that the conductance of the anthracene azaborine derivative is comparable to that of the pristine all-carbon anthracene compound. Notably, this heteroatom substitution has also allowed us to perform similar measurements on the corresponding pentacene-like compound, which is found to have a similar conductance, thus evidencing that B-N doping could also be used to stabilize and characterize larger acenes for molecular electronics applications. Our conclusions are supported by state-of-the-art transport calculations.

[High cholesterol diet modifies the repairing effect of the hepatocyte growth factor]. / La dieta alta en colesterol altera el proceso reparador del factor de crecimiento de hepatocitos.

Currently, fatty liver represents a serious public health problem in the Western world. In our country, a large amount of food rich in cholesterol is consumed. Cholesterol is an important component in lipid rafts, where many receptors for growth factors are localized, so its functionality could be altered in the presence of high cholesterol concentration. Hepatocyte growth factor (HGF) and its receptor c-Met are known to promote repair after an injury. The aim in the present work was to study the effect of a high cholesterol diet in the molecular repair process mediated by HGF in hepatocytes and liver tissue. Data show a delay in the activation of the HGF-mediated signaling cascade which results in a deficient repair process, that in the case of a continuous aggression could favor the progression of liver damage.

Delocalization-to-localization charge transition in diferrocenyl-oligothienylene-vinylene molecular wires as a function of the size by Raman spectroscopy.

In going from short to large size thienylene-vinylene diferrocenyl cations, the transition from a charge delocalized to a localized state is addressed by resonance Raman spectroscopy and supported by theoretical model chemistry. The shorter members, dimer and tetramer, display conjugated structures near the cyanine limit of bond length equalization as a result of the strong interferrocene charge resonance, producing a full charge delocalized mixed valence system. In the longest octamer, charge resonance vanishes and the cation is localized at the bridge center (the mixed valence property disappears). The hexamer is at the delocalized-to-localized turning point. Solvent and variable-temperature Raman measurements highlight this borderline property. A detailed structure-property correlation of bond length alternation data and Raman frequencies is proposed to account for the whole set of spectroscopic properties, with emphasis on the changes observed with the size of the molecular wire.

Diferrocenyl oligothiophene wires: Raman and quantum chemical study of valence-trapped cations.

A combination of Raman spectroscopy and density functional theory calculations is used to describe the structural and spectroscopic properties of the different isomeric cations of diferrocenyl quaterthiophenes. Isomerisation of the thienyl ß-positions provides site selective oxidation, which gives rise to species that can interconvert by moving the charge over the bridge. The spectroscopic study allows us to describe a sequence of stationary trapped cationic, either ferrocenyl or thienyl, states which constitutes an energy cascade of accessible sites through which the charge transfer can proceed.

Enhanced functionality for donor-acceptor oligothiophenes by means of inclusion of BODIPY: synthesis, electrochemistry, photophysics, and model chemistry.

We have synthesized several new push-pull oligothiophenes based on the boron dipyrromethene (BODIPY) moiety as the electron acceptor and the more well-known oligothiophenes substituted with N,N-dialkylamino functions to enhance their electron-donor ability. A complete characterization of the electronic properties has been carried out; it consists of their photophysical, electrochemical, and vibrational properties. The compounds have been studied after chemical treatment with acids and after oxidation. In this regard, they can be termed as NIR dyes and amphoteric redox electroactive molecules. We have described the presence of dual fluorescence in these molecules and fluorescence quenching either by energy transfer or, in the push-pull molecules, by electron exchange. The combination of electrochemical and proton reversibility along with the interesting optical properties of the new species offer an interesting platform for sensor and material applications.

Quinoidal oligothiophenes: towards biradical ground-state species.

A family of quinoidal oligothiophenes, from the dimer to the hexamer, with fused bis(butoxymethyl)cyclopentane groups has been extensively investigated by means of electronic and vibrational spectroscopy, electrochemical measurements, and density functional calculations. The latter predict that the electronic ground state always corresponds to a singlet state and that, for the longest oligomers, this state has biradical character that increases with increasing oligomer length. The shortest oligomers display closed-shell quinoidal structures. Calculations also predict the existence of very low energy excited triplet states that can be populated at room temperature. Aromatization of the conjugated carbon backbone is the driving force that determines the increasing biradical character of the ground state and the appearance of low-lying triplet states. UV/Vis, Raman, IR, and electrochemical experiments support the aromatic biradical structures predicted for the ground state of the longest oligomers and reveal that population of the low-lying triplet state accounts for the magnetic activity displayed by these compounds.

Ferrocenyl-ended thieno-vinylene oligomers: donor-acceptor polarization and mixed-valence properties with emphasis on the raman mapping of localized-to-delocalized transitions.

What's your role? New oligothiophene-vinylene compounds have been synthesized to study the role of the conjugated chain in two different cases (see scheme; MV=mixed valence). The electronic and molecular structures were analyzed by means of electronic, X-ray photoelectron, and Raman spectroscopy, together with thermo spectroscopy, electrochemistry, and DFT calculations.New oligothiophene-vinylene compounds have been synthesized in order to study the role of the conjugated chain in two different cases: 1) when push-pull action operates between an electron-donor and an electron-acceptor group at the ends of the thiophene-vinylene conjugated chain, and 2) when mixed-valence action is induced by single oxidation of the same chain functionalized at both terminal positions with ferrocene groups leading to competition between the donor groups. The electronic and molecular structures are analyzed by means of electronic, X-ray photoelectron and Raman spectroscopies, together with thermospectroscopy, electrochemistry and density functional theory calculations. The cyclic voltammetry processes have been followed by spectrochemistry. It is shown that the radical cation of the diferrocenyl derivative is a class III mixed-valence system (i.e., fully delocalized) according to its Raman spectrum. Moreover, by Raman thermo-spectroscopy the thermal transition of this radical cation from a delocalized (class III, room temperature) to a localized (class II, -160 degrees C) state is scanned. In all cases the Raman study is paralleled by an electronic absorption spectroscopic analysis. Structure-property relationships are proposed for molecules of two important fields of very active research as that of the non-linear optics (i.e., organic optoelectronic) and that of the mixed-valence systems (i.e., charge-transfer processes).