We present a systematic investigation of molecule-metal interactions for transition-metal phthalocyanines (TMPc, with TM = Fe, Co, Ni, Cu) adsorbed on Ag(100). Scanning tunneling spectroscopy and density functional theory provide insight into the charge transfer and hybridization mechanisms of TMPc as a function of increasing occupancy of the 3d metal states. We show that all four TMPc receive approximately one electron from the substrate. Charge transfer occurs from the substrate to the molecules, inducing a charge reorganization in FePc and CoPc, while adding one electron to ligand π-orbitals in NiPc and CuPc. This has opposite consequences on the molecular magnetic moment: in FePc and CoPc the interaction with the substrate tends to reduce the TM spin, whereas in NiPc and CuPc an additional spin is induced on the aromatic Pc ligand, leaving the TM spin unperturbed. In CuPc, the presence of both TM and ligand spins leads to a triplet ground state arising from intramolecular exchange coupling between d and π electrons. In FePc and CoPc the magnetic moment of C and N atoms is antiparallel to that of the TM. The different character and symmetry of the frontier orbitals in the TMPc series leads to varying degrees of hybridization and correlation effects, ranging from the mixed-valence (FePc, CoPc) to the Kondo regime (NiPc, CuPc). Coherent coupling between Kondo and inelastic excitations induces finite-bias Kondo resonances involving vibrational transitions in both NiPc and CuPc and triplet-singlet transitions in CuPc.

Electronic transport properties of single-molecule junctions have been widely measured by several techniques, including mechanically controllable break junctions, electromigration break junctions, and by means of scanning tunneling microscopes. In parallel, many theoretical tools have been developed and refined for describing such transport properties and for obtaining numerical predictions. Most prominent among these theoretical tools are those based upon density functional theory. In this review, theory and experiment are critically compared, and this confrontation leads to several important conclusions. The theoretically predicted trends nowadays reproduce the experimental findings well for series of molecules with a single well-defined control parameter, such as the length of the molecules. The quantitative agreement between theory and experiment usually is less convincing, however. Two main sources for the quantitative discrepancies can be identified. Experimentally, the atomic structure of the junction typically realized in the measurement is not well known, so simulations rely on plausible scenarios. In theory, correlation effects can be included only in approximations that are difficult to control for experimentally relevant situations. Therefore, one typically expects qualitative agreement with present modeling tools; in exceptional cases a quantitative agreement has already been achieved. For further progress, benchmark systems are required that are sufficiently well defined by experiment to allow quantitative testing of the approximation schemes underlying the theoretical modeling. Several key experiments can be identified suggesting that the present description may even be qualitatively incomplete in some cases. Such key experimental observations and their current models are also discussed here, leading to several suggestions for extensions of the models toward including dynamic image charges, electron correlations, and polaron formation.

A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudoatomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here we describe the more recent implementations on top of that core scheme, which include: full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, DFT+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, densityfunctional perturbation theory, efficient Van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modelling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various postprocessing utilities. SIESTA has also been a) Electronic mail:

We study the impact of electrode band structure on transport through single--molecule junctions by measuring the conductance of pyridine--based molecules using Ag and Au electrodes. Our experiments are carried out using the scanning tunneling microscope based break--junction technique and are supported by density functional theory based calculations. We find from both experiments and calculations that the coupling of the dominant transport orbital to the metal is stronger for Au--based junctions when compared with Ag--based junctions. We attribute this difference to relativistic effects, which results in an enhanced density of d--states at the Fermi energy for Au compared with Ag. We further show that the alignment of the conducting orbital relative to the Fermi level does not follow the work function difference between two metals and is different for conjugated and saturated systems. We thus demonstrate that the details of the molecular level alignment and electronic coupling in metal--organic interfaces do not follow simple rules, but are rather the consequence of subtle local interactions.

Note:The published version in Nature Materials contains an extended manuscript and comprehensive supplementary information. . One of the primary experimental methods to reveal the mechanisms behind electronic transport through metal-molecule interfaces is the study of conductance as a function of molecule length in molecular junctions [4][5][6][7][8][9][10][11][12][13][14] . Previous studies focused on transport governed either by coherent tunneling or hopping, both at low conductance. However, the upper limit of conductance across molecular junctions has not been explored, despite the great potential for efficient information transfer, charge injection and recombination processes at high conductance. Here, we study the conductance properties of highly transmitting metal-molecule-metal interfaces, using a series of single-molecule junctions based on oligoacenes with increasing length. We find that the conductance saturates at an upper limit where it is independent of molecule length. Furthermore, we show that this upper limit can be controlled by the character of the orbital hybridization at the metal-molecule interface. Using two prototype systems, in which the molecules are contacted by either Ag or Pt electrodes, we reveal two different origins for the saturation of conductance. In the case of Ag-based molecular junctions, the conductance saturation is ascribed to a competition between energy level alignment and level broadening, while in the case of Pt-based junctions, the saturation is attributed to a band-like transport. The results are explained by an intuitive model, backed by ab-initio transport calculations. Our findings shed light on the mechanisms that constrain the conductance at the high transmission limit, providing guiding principles for the design of highly conductive metal-molecule interfaces.In order to study the conductance characteristics of highly transmitting molecular junctions, strong electronic coupling is required between the molecule and the electrodes, as well as within the molecule itself 10,11,15,16 . These conditions are achieved in this work by direct hybridization between the π-orbitals of the oligoacene molecules and the frontier orbitals of the metal electrodes, without employing anchoring groups such as thiols that can act as spacers between the orbitals of the molecular backbone and the frontier orbitals of the metal 13,15 . The oligoacenes (Fig. 1a) are linear π-conjugated molecules that can be viewed as short graphene nanoribbons 17 , whose electronic structure is subject to an ongoing research 18 . We study the evolution of conductance as a function of molecule length and compare the conductance characteristics of

Organic electronics offers prospects of functionality for science, industry and medicine that are new as compared with silicon technology and available at a very low material cost. Among the plethora of organic molecules available for materials design, polymers and oligomers are very promising, for example, because of their mechanical flexibility. They consist of repeated basic units, such as benzene rings, and the number of these units N determines their excitation gap, a property that is often used in proposals of organic photovoltaics. Here, we show that contrary to a widely held belief the magnitudes of excitation gaps do not always decay monotonously with N, but can oscillate due to the presence of a 'Dirac cone' in the band structure. With an eye on the more fundamental question how a molecular wire becomes metallic with increasing length, our research suggests that the process can exhibit incommensurate oscillations.

The interaction of individual electrons with vibrations has been extensively studied. However, the nature of electron-vibration interaction in the presence of many-body electron correlations such as a Kondo state has not been fully investigated. Here, we present transport measurements on a Copper-phthalocyanine molecule, suspended between two silver electrodes in a break-junction setup. Our measurements reveal both zero bias and satellite conductance peaks, which are identified as Kondo resonances with a similar Kondo temperature. The relation of the satellite peaks to electron-vibration interaction is corroborated using several independent spectroscopic indications, as well as ab initio calculations. Further analysis reveals that the contribution of vibration-induced inelastic current is significant in the presence of a Kondo resonance.

We have developed a multi-orbital approach to compute the electronic structure of a quantum impurity using the non-crossing approximation. The calculation starts with a mean-field evaluation of the system's electronic structure using a standard quantum chemistry code; here we use density functional theory (DFT). We transformed the one-electron structure into an impurity Hamiltonian by using maximally localized Wannier functions. Hence, we have developed a method to study the Kondo effect in systems based on an initial one-electron calculation. We have applied our methodology to a copper phthalocyanine molecule chemisorbed on Ag(100), and we have described its spectral function for three different cases where the molecule presents a single spin or two spins with ferro- and anti-ferromagnetic exchange couplings. We find that the use of broken-symmetry mean-field theories such as Kohn-Sham DFT cannot deal with the complexity of the spin of open-shell molecules on metal surfaces and extra modeling is needed.