Electronic structure approach for complex silicas

Three-Center Tight-Binding Together with Multipolar Auxiliary Functions

We present an ab initio tight-binding method that allows to improve on the effective potential and minimal basis approximations employed in semiempirical calculations. Three-center expansions are used to evaluate the zeroth-order Hamiltonian matrix elements and repulsive energy terms in the spirit of the Horsfield method. Self-consistency is handled by expanding atomic orbital products in an auxiliary basis following the work of Giese and York, combined with a two-center expansion of the exchange-correlation kernels. Together with nonminimal main basis sets (double-ζ plus polarization), we show that the resulting method trades a modest amount of accuracy for a significant gain in speed, compared to that of numerical atomic orbital density functional theory, in calculations on small molecules, bulk compounds, and metal nanoclusters.

Transition mechanism of the coverage-dependent polymorphism of self-assembled melamine nanostructures on Au(111)

Molecular self-assembled films have recently attracted increasing attention within the field of nanotechnology as they offer a route to obtain new materials. However, careful selection of the molecular precursors and substrates, as well as exhaustive control of the system evolution is required to obtain the best possible outcome. The three-fold rotational symmetry of melamine molecules and their capability to form hydrogen bonds make them suitable candidates to synthesize this type of self-assembled network. In this work, we have studied the polymorphism of melamine nanostructures on Au(111) at room temperature. We find two coverage-dependent phases: a honeycomb structure (α-phase) for submonolayer coverage and a close-packed structure (β-phase) for full monolayer coverage. A combined scanning tunnel microscopy and density functional theory based-calculations study of the transition regime where both phases coexist allows describing the mechanism underlying this coverage driven phase transition in terms of the changes in the molecular lateral tension.

Destructive quantum interference in meta-oligo(phenyleneethynylene) molecular wires with gold-graphene heterojunctions

Quantum interference (QI) is well recognised as a significant contributing factor to the magnitude of molecular conductance values in both single-molecule and large area junctions. Numerous structure-property relationship studies have shown that para-connected oligo(phenyleneethynylene) (OPE) based molecular wires exemplify the impact of constructive quantum interference (CQI), whilst destructive quantum interference (DQI) effects are responsible for the orders of magnitude lower conductance of analogous meta-contacted OPE derivatives, despite the somewhat shorter effective tunnelling distance. Since molecular conductance is related to the value of the transmission function, evaluated at the electrode Fermi energy, T(EF), which in turn is influenced by the presence and relative energy of (anti)resonances, it follows that the relative single-molecule conductance of para- and meta-contacted OPE-type molecules is tuned both by the anchor group and the nature of the electrode materials used in the construction of molecular junctions (gold|molecule|gold vs. gold|molecule|graphene). It is shown here that whilst amine-contacted junctions show little influence of the electrode material on molecular conductance due to the similar electrode-molecule coupling through this anchor group to both types of electrodes, the weaker coupling between thiomethyl and ethynyl anchors and the graphene substrate electrode results in a relative enhancement of the DQI effect. This work highlights an additional parameter space to explore QI effects and establishes a new working model based on the electrode materials and anchor groups in modulating QI effects beyond the chemical structure of the molecular backbone.

Nonuniform STM Contrast of Self-Assembled Tri-n-octyl-triazatriangulenium Tetrafluoroborate on HOPG

We have assembled 4,8,12-tri-n-octyl-4,8,12-triazatrianguleniumtetrafluoroborate (TATA-BF4) on highly oriented pyrolytic graphite (HOPG) and have studied the structure and tunneling properties of this self-assembled monolayer (SAM) using scanning tunneling microscopy (STM) under ambient conditions. We show that the triazatriangulenium cations TATA+ form hexagonally packed structures driven by the interaction between the aromatic core and the HOPG lattice, as evidenced by density functional theory (DFT) modeling. According to the DFT results, the three alkyl chains of the platform tend to follow the main crystallographic directions of HOPG, leading to a different STM appearance. The STM contrast of the SAM shows that the monolayer is formed by two types of species, namely, TATA+ with BF4- counterions on top and without them. The cationic TATA+ platform gives rise to a seemingly higher appearance than neutral TATA-BF4, in contrast to observations made on metallic substrates. The variation of the STM tunneling parameters does not change the relative difference of contrast, revealing the stability of both species on HOPG. DFT calculations show that TATA-BF4 on HOPG has sufficient binding energy to resist dissociation into TATA+ and BF4-, which might occur under the action of the electric field in the tunneling gap during STM scanning.

Toward a QUBO-Based Density Matrix Electronic Structure Method

Density matrix electronic structure theory is used in many quantum chemistry methods to "alleviate" the computational cost that arises from directly using wave functions. Although density matrix based methods are computationally more efficient than wave function based methods, significant computational effort is involved. Because the Schrödinger equation needs to be solved as an eigenvalue problem, the time-to-solution scales cubically with the system size in mean-field type approaches such as Hartree-Fock and density functional theory and is solved as many times in order to reach charge or field self-consistency. We hereby propose and study a method to compute the density matrix by using a quadratic unconstrained binary optimization (QUBO) solver. This method could be useful to solve the problem with quantum computers and, more specifically, quantum annealers. Our proposed approach is based on a direct construction of the density matrix using a QUBO eigensolver. We explore the main parameters of the algorithm focusing on precision and efficiency. We show that, while direct construction of the density matrix using a QUBO formulation is possible, the efficiency and precision have room for improvement. Moreover, calculations performed with quantum annealing on D-Wave's new Advantage quantum computer are compared with results obtained with classical simulated annealing, further highlighting some problems of the proposed method. We also suggest alternative methods that could lead to a more efficient QUBO-based density matrix construction.

Oligothiophene molecular wires at graphene-based molecular junctions

The use of graphene as a new type of electrode at molecular junctions has led to a renewal of molecular electronics. Indeed, the symmetry breaking induced by the graphene electrode yields different electronic behaviors at the molecular junction and in particular enhanced conductance for longer molecules. In this respect, several studies involving different molecular backbones and anchoring groups have been performed. Here in the same line, we consider oligopthiophene based hybrid gold-graphene junctions and we measure their electrical properties using the STM-I(s) method in order to determine their attenuation factor and the effect of specific anchoring groups. The results are supported by density functional theory (DFT) calculations, and exhibit a similar behavior to what is observed at alkane-based junctions.

Where do the counterions go? Tip-induced dissociation of self-assembled triazatriangulenium-based molecules on Au(111)

Chemical coupling of functional molecules on top of the so-called platform molecules allows the formation of functional self-assembled monolayers (SAMs). An often-used example of such a platform is triazatriangulenium (TATA), which features an extended aromatic core providing good electronic contact to the underlying metal surface. Here, we present a study of the SAM formation of a TATA platform on Au(111) employing scanning tunneling microscopy (STM) under ambient atmospheric conditions. In solution, the TATA platform is stabilized by BF4 counterions, while after deposition on a gold substrate, the localization of the BF4 counterions remains unknown. We used 1,2,4-trichlorobenzene as a solvent of TATA-BF4 to induce SAM formation on a heated (∼50 °C) Au substrate. We show by STM how to detect and distinguish TATA-BF4 from TATA platforms, which lost their BF4 counterions. Finally, we observe a change of the counterion position on the SAM during the STM scanning, which we explain by an electric-field-induced decrease of the electrostatic interaction in TATA-BF4 on the surface. We applied DFT calculations to reveal the influence of the gold lattice and the electric field of the STM tip on the stability of TATA-BF4 physisorbed on the surface.

Size-Selective Carbon Clusters as Obstacles to Graphene Growth on a Metal

Chemical vapor deposition (CVD) on metals is so far the best suited method to produce high-quality, large-area graphene. We discovered an unprecedentedly large family of small size-selective carbon clusters that form together with graphene during CVD. Using scanning tunneling microscopy (STM) and density functional theory (DFT), we unambiguously determine their atomic structure. For that purpose, we use grids based on a graphene moiré and a dilute atomic lattice that unambiguously reveal the binding geometry of the clusters. We find that the observed clusters bind in metastable configurations on the substrate, while the thermodynamically stable configurations are not observed. We argue that the clusters are formed under kinetic control and establish that the evolution of the smallest clusters is blocked. They are hence products of surface reactions in competition with graphene growth, rather than intermediary species to the formation of extended graphene, as often assumed in the literature. We expect such obstacles to the synthesis of perfect graphene to be ubiquitous on a variety of metallic surfaces.

Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

Densely-packed ZnTPPs Monolayer on the Rutile TiO2(110)-(1×1) Surface: Adsorption Behavior and Energy Level Alignment

The adsorption of a densely packed Zinc(II) tetraphenylporphyrin monolayer on a rutile TiO₂(110)-(1×1) surface has been studied using a combination of experimental and theoretical methods, aimed at analyzing the relation between adsorption behavior and barrier height formation. The adsorption configuration of ZnTPP was determined from scanning tunnel microscopy (STM) imaging, density functional theory (DFT) calculations and STM image simulation. The corresponding energy alignment was experimentally determined from X-ray and UV-photoemission spectroscopies and inverse photoemission spectroscopy. These results were found in good agreement with an appropriately corrected DFT model, pointing to the importance of local bonding and intermolecular interactions in the establishment of barrier heights.

fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems

In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

Calculated photo-isomerization efficiencies of functionalized azobenzene derivatives in solar energy materials: azo-functional organic linkers for porous coordinated polymers

Recently, we used a local orbital density functional theory code called FIREBALL, to study the photoisomerization process in azobenzene derivatives for solar energy materials. Azobenzene functional groups undergo photoisomerization upon light irradiation or application of heat. Zhou et al (2012 J. Am. Chem. Soc. 134 99-102) showed that these azobenzenes can then be introduced into metal-organic frameworks via an organic linker in order to create a reversible switch for CO2 adsorption. In this manuscript, we examined how the addition of organic linkers (isophthalic acid) changes the relaxation times, isomerization mechanism, and quantum yield for both the cis↔trans pathways. We then tuned these properties by substituting functional groups, finding an increase in quantum yield as well as improved optical properties.

Mechanism of a molecular photo-switch adsorbed on Si(100)

We present a combined scanning tunneling microscopy and density functional theory study of a compact molecular photoswitch on a Si(100) surface.

Self-organisation of inorganic elements on Si(001) mediated by pre-adsorbed organic molecules

A combined theoretical and experimental study on the adsorption of an isolated benzonitrile molecule on the Si(001) surface, followed by the adsorption of Al (group III), Pb (carbon group) and Ag (transition metal) is presented.

Tailoring the structure of two-dimensional self-assembled nanoarchitectures based on ni(ii) -salen building blocks

The synthesis of a series of Ni(II) -salen-based complexes with the general formula of [Ni(H2 L)] (H4 L=R(2) -N,N'-bis[R(1) -5-(4'-benzoic acid)salicylidene]; H4 L1: R(2) =2,3-diamino-2,3-dimethylbutane and R(1) =H; H4 L2: R(2) =1,2-diaminoethane and R(1) =tert-butyl and H4 L3: R(2) =1,2-diaminobenzene and R(1) =tert-butyl) is presented. Their electronic structure and self-assembly was studied. The organic ligands of the salen complexes are functionalized with peripheral carboxylic groups for driving molecular self-assembly through hydrogen bonding. In addition, other substituents, that is, tert-butyl and diamine bridges (2,3-diamino-2,3-dimethylbutane, 1,2-diaminobenzene or 1,2-diaminoethane), were used to tune the two-dimensional (2D) packing of these building blocks. Density functional theory (DFT) calculations reveal that the spatial distribution of the LUMOs is affected by these substituents, in contrast with the HOMOs, which remain unchanged. Scanning tunneling microscopy (STM) shows that the three complexes self-assemble into three different 2D nanoarchitectures at the solid-liquid interface on graphite. Two structures are porous and one is close-packed. These structures are stabilized by hydrogen bonds in one dimension, while the 2D interaction is governed by van der Waals forces and is tuned by the nature of the substituents, as confirmed by theoretical calculations. As expected, the total dipolar moment is minimized.

The role of charge transfer in the energy level alignment at the pentacene/C60 interface

Understanding the mechanism of energy level alignment at organic-organic interfaces is a crucial line of research to optimize applications in organic electronics. We address this problem for the C60-pentacene interface by performing local-orbital Density Functional Theory (DFT) calculations, including the effect of the charging energies on the energy gap of both organic materials. The results are analyzed within the induced density of interface states (IDIS) model. We find that the induced interface potential is in the range of 0.06-0.10 eV, in good agreement with the experimental evidence, and that such potential is mainly induced by the small, but non-negligible, charge transfer between the two compounds and the multipolar contribution associated with pentacene. We also suggest that an appropriate external intercompound potential could create an insulator-metal transition at the interface.

Carbon tips for all-carbon single-molecule electronics

We present here an exhaustive ab initio study of the use of carbon-based tips as electrodes in single-molecule junctions. Motivated by recent experiments, we show that carbon tips can be combined with other carbon nanostructures, such as graphene, to form all-carbon molecular junctions with molecules like benzene or C60. Our results show that the use of carbon tips can lead to relatively conductive molecular junctions. However, contrary to junctions formed with standard metals, the conductance traces recorded during the formation of the all-carbon single-molecule junctions do not exhibit clear conductance plateaus, which can be attributed to the inability of the hydrogenated carbon tips to form chemical bonds with the organic molecules. Additionally, we explore here the use of carbon tips for scanning tunneling microscopy and show that they are well suited for obtaining sample images with atomic resolution.

Selective catalytic production of 5-hydroxymethylfurfural from glucose by adjusting catalyst wettability

The development of highly-efficient catalysts for conversion of glucose and fructose to 5-hydroxymethylfurfural (HMF) is of great importance. In this work, theoretical simulations form the basis for rational design and synthesis of a superhydrophobic mesoporous acid, that can completely prevent HMF hydration, giving HMF as sole product from full conversion of fructose. Interestingly, the combined superhydrophobic solid acid and superhydrophilic solid base catalysts are very efficient for one-pot conversion of glucose to HMF, giving a yield as high as 95.4 %. The excellent catalytic data in the conversion of glucose to HMF is attributed to the unique wettabilities of the solid acid and base catalysts.

Divacancies in carbon nanotubes and their influence on electron scattering

First-principles calculations are applied to study the formation energies of various divacancy defects in armchair and zigzag carbon nanotubes of varying diameter, and the transport properties for the corresponding structures. Our explicit ab initio calculations confirm that the lateral 585 divacancy is the most stable defect in small diameter tubes, with the 555 777 divacancy becoming more stable in armchair tubes larger than (30, 30). Evaluating the electron transmission as a function of diameter and chirality for a range of defects, the strongest scattering is found for the 555 777 divacancy configuration, which is observable in electrical spectroscopy experiments. Finally, validation of an approximation relating contributions from independent scattering sites enables the study of the characteristic localization length in large diameter tubes. Despite the fixed number of channels, localization lengths increase with increasing diameter and can exceed 100 nm for typical defect densities.

Exploring the T-Θ phase diagram of S adsorbed on Au(111) substrate on the Θ = 0.5 ML line

Theoretical results for the adsorption of half of a monolayer of S on Au(111) are presented. The simulations were made using a density functional theory (DFT) tight binding approach combined with classical molecular dynamics at 800, 500, 300, 150 and 1 K. By considering a minimal (2 × √3) unit cell, two stable adsorbed phases are found: a dimeric one and another forming a rhomboidal structure depending on the preparation of the sample at high temperatures. Optimized calculations at T = 0 K indicate that the stability of the dimeric phase is due to the increase of the binding energies between sulfur atoms. Enforcing previous results (Gómez-Carrillo et al 2011 Phys. Chem. Chem. Phys. 13 461) it is verified that at high temperatures (T > 300 K) sulfur atoms have a high mobility which allows migration among different adsorption sites. The mobility decreases with the temperature and, as in the previous work, a thermal barrier of 25-30 meV is found. On enlarging the unit cell new agglomerates are found, in good agreement with experimental data.

First-principles study of stability of the bcc and ω phases of a low Al concentration Nb1-xAlx alloy

The phase stability and site occupancy of bcc (body centered cubic) Nb(5)Al and slightly rearranged atomic structures have been examined by means of first-principles calculations. In order to use first-principles methods, a periodic cell is required and we used ordered Nb(5)Al compounds as a tractable example of a low Al concentration Nb(1 - x)Al(x) alloy (in this case, for about 17 at.% Al). The instability against an ω-structure atomic displacement was also studied, since this structure is detrimental to ductility. Mulliken population analysis was used to provide an understanding of the hybridization between the atoms and the electronic origin of the site occupancy and instability of the underlying bcc structures. By making calculations for several different configurations of the Nb-Al system we estimated the strengths of the Nb-Nb and Nb-Al bonds. It is shown that the stability of the underlying bcc phases is directly related to Nb-Nb and Nb-Al first-nearest-neighbor interactions. The first-principles calculations were extended to finite temperature by including various contributions to the free energy. In particular, the vibrational free energy was calculated within the quasiharmonic approximation, and it is shown that the contribution of the low energy modes to the lattice entropy helps to stabilize ordered bcc phases against ω-type phase transformations. Semi-quasi-random structures were employed to study the stability of the ordered and disordered bcc phases. Our study showed, in agreement with experiment, that the ω, ordered, and disordered phases can coexist in a nonequilibrium state at finite temperature.

An ab initio two-center tight-binding approach to simulations of complex materials properties

We describe theab initioconstruction of two-center tight-binding (TB) hamiltonians, which at a properly chosen input density upon non-selfconsistent solution of the related Kohn-Sham equations transform the energy within density-functional theory (DFT) into a tight-bindinglike expression. In cases, where the electron density of the interacting many-atom structure in good approximation may be represented as a sum of atomic-like densities, the method has been shown to operate highly transferable, being particularly successful in determining the properties of low-energy silicon clusters, in predicting the structure and vibrational signatures of fullerene oligomers, amorphous carbons and carbon nitrides and in simulating elementary growth reactions on diamond surfaces. The uncertainties within the standard non-SCF DF-TB-variant, however, increase if the chemical bonding is controlled by a delicate charge balance between different atomic constituents, as e.g. in organic molecules and in polar semiconductors. Therefore, we extend the standard TB-approach to the operation in a selfconsistent-charge mode(SCC-DFTB)in order to improve total energies, forces, and transferability in the presence of considerable long-range Coulomb interactions. By using a variational technique, we derive a transparent and readily calculable expression for the iterative modification of Hamiltonian matrix elements and show, that the final energy is a second order approximation to the total energy in density-functional theory,see M. Elstner et al., this Symposium.First successful applications to surface studies of GaAs and dislocation modeling in GaN will be presented.

Theoretical study of electronic and transport properties of PPy-Pt(111) and PPy-C(111):H interfaces

We present a first-principles study of promising hybrid organic-inorganic interface systems consisting of a polypyrrole (PPy) chain sandwiched between metallic Pt(111) or hydrogen-terminated diamond C(111):H electrodes. We combine ab initio density-functional-theory total energy calculations, Green's function approach and the complex band-structure method in order to determine electronic and transport properties of those organic-semiconductor/metal (semiconductor) interfaces. We analyze one- and multi-bond nanocontact formation including structural modification (H desorption) as well as PPy length dependence. For selected ground state configurations of the considered interface systems we study their energetics and structural properties. Through the analysis of the local density of states, in particular isosurfaces of the charge density, the mechanism of the charge transfer and the charge neutrality levels are determined. The voltage dependence of the electrical conductance and the I-V characteristics are compared to the transport properties based on the complex band-structure method. The obtained results support recent experiments, where PPy nanowires are formed via electrochemical synthesis and placed between platinum or diamond microelectrodes.

Modelling energy level alignment at organic interfaces and density functional theory

A review of our theoretical understanding of the band alignment at organic interfaces is presented with particular emphasis on the metal/organic (MO) case. The unified IDIS (induced density of interface states) and the ICT (integer charge transfer) models are reviewed and shown to describe qualitatively and semiquantitatively the barrier height formation at those interfaces. The IDIS model, governed by the organic CNL (charge neutrality level) and the interface screening includes: (a) charge transfer across the interface; (b) the "pillow" (or Pauli) effect associated with the compression of the metal wavefunction tails; and (c) the molecular dipoles. We argue that the ICT-model can be described as a limiting case of the unified IDIS-model for weak interface screening. For a fully quantitative understanding of the band alignment at organic interfaces, use of DFT (density functional theory) or quantum chemistry methods is highly desirable. In this Perspective review, we concentrate our discussion on DFT and show that conventional LDA or GGA calculations are limited by the "energy gap problem of the organic materials", because the LDA (or GGA) Kohn-Sham energy levels have to be corrected by the self-interaction energy of the corresponding wavefunction, to provide the appropriate molecule transport energy gap. Image potential and polarization effects at MO interfaces tend to cancel these self-interaction corrections; in particular, we show that for organic molecules lying flat on Cu and Ag, these cancellations are so strong that we can rely on conventional DFT to calculate their interface properties. For Au, however, the cancellations are weaker making it necessary to go beyond conventional DFT. We discuss several alternatives beyond conventional LDA or GGA. The most accurate approach is the well-known GW-technique, but its use is limited by its high demanding computer time. In a very simple approach one can combine conventional DFT with a "scissor" operator which incorporates self-interaction corrections and polarization effects in the organic energy levels. Hybrid potentials combined with conventional DFT represent, probably, the best alternative for having a simple and accurate approach for analyzing organic interfaces. The problem then is to find an appropriate one for both the metal and the organic material in a plane-wave formulation; we show, however, how to overcome this difficulty using a local-orbital basis formulation. As examples of these alternatives, we present some DFT-calculations for several organic interfaces, using either the scissor operator or a hybrid potential, which can be interpreted in terms of the unified IDIS-model.

Spin fluctuation effects on the conductance through a single Pd atom contact

A controversy about the conductance through single atoms still exists. There are many experiments where values lower than the quantum unity G(0) = 2e(2)/h have been found associated to Kondo regimes with high Kondo temperatures. Specifically in the Pd single atom contact, conductance values close to G(0)/2 at room temperature have been reported. In this work we propose a theoretical analysis of a break junction of Pd where the charge fluctuation in the single atom contact is limited to the most probable one: [Formula: see text]. The projected density of states and the characteristics of the electron transport are calculated by using a realistic description of the interacting system. A Kondo regime is found where the conductance values and their dependence on temperature are in good agreement with the experimental trends observed in the conduction of single molecule transistors based on transition metal coordination complexes.

Mechanical and electrical properties of stretched clean and H-contaminated Pd-nanowires

We analyze theoretically the formation of stretched Pd-nanowires and their interaction with hydrogen. In our approach, we simulate the nanowire stretching process using a first-principles molecular-dynamics method to obtain realistic atomic geometries of the contact in its final stages before the nanowire breaks. The electrical conductance of the nanowire is also calculated at each point of the deformation path. For the clean Pd-nanowire in the last stages of the deformation process we find that the nanowire develops, first, a one-atom-neck and, at the end, a dimer whose bond is finally broken. For these atomic configurations, the calculated electrical conductances are in good agreement with the experimental evidence. The interaction with hydrogen is analyzed adsorbing one or two H atoms on the Pd-nanowire for different configurations along the stretching process. In the case of one H atom we obtain geometries with conductances in the range 0.8-1.4G(0), while for two H atoms we find conductance plateaus with values ∼0.5G(0) and ∼1.0G(0). These results are in excellent agreement with the experimental evidence for nanocontact breaking in an H(2) atmosphere and indicate that the conductance peak around 0.5G(0) observed experimentally is associated with nanowires where two H atoms have been adsorbed.

Controlled self-organization of atom vacancies in monatomic gallium layers

Ga adsorption on the Si(112) surface results in the formation of pseudomorphic Ga atom chains. Compressive strain in these atom chains is relieved via creation of adatom vacancies and their self-organization into meandering vacancy lines. The average spacing between these line defects can be controlled, within limits, by adjusting the chemical potential mu of the Ga adatoms. We derive a lattice model that quantitatively connects density functional theory (DFT) calculations for perfectly ordered structures with the fluctuating disorder seen in experiment and the experimental control parameter mu. This hybrid approach of lattice modeling and DFT can be applied to other examples of line defects in heteroepitaxy.

Electronic Structures and Conductivity in Peptide Nanotubes

Self-assembling cyclic D,L-peptide nanotubes are electronically insulating and possess wide band gaps (E(g) > 4 eV). Our ab initio electronic structure calculations indicate that the presence of aromatic rings in the side chain of peptide nanotubes significantly reduces the band gap. We investigate the conductivity of the modified peptide nanotubes through calculations of the electron tunneling probability. The electron tunneling probability through a molecule depends on the length of the molecule, L, as e-beta(E)L, where the tunneling beta(E)-factor is strongly energy-dependent. We have calculated beta(E) in three types of peptide nanotubes that have different sequences of amino acid residue, (L-Gln, D-Ala)(4), (L-Gln, D-Leu)(4) and (L-Gln, D-Phe)(4), using the complex band structure approach. We find large beta values near midgap, making these peptide nanotubes a poor tunneling conductor.

Measuring single molecule conductance with break junctions

Single-molecule conductance measurements made under potential control provide a critical link between chemical and molecular electronic data. These measurements are made possible by the STM break-junction method introduced recently, but questions remain about its reliability. Here we report the use of a logarithmic current-to-voltage converter to examine a wide range of currents in an STM break junction study of octanedithiol, clearly showing both the gold-quantum wire regime and the single molecule conductance regime. We find two sets of molecular currents that we tentatively ascribe to different bonding geometries of the molecules in the break junction.

Anderson localization in carbon nanotubes: defect density and temperature effects

The role of irradiation induced defects and temperature in the conducting properties of single-walled (10, 10) carbon nanotubes has been analyzed by means of a first-principles approach. We find that divacancies modify strongly the energy dependence of the differential conductance, reducing also the number of contributing channels from two (ideal) to one. A small number of divacancies (5-9) brings up strong Anderson localization effects and a seemly universal curve for the resistance as a function of the number of defects. It is also shown that low temperatures, about 15-65 K, are enough to smooth out the fluctuations of the conductance without destroying the exponential dependence of the resistivity as a function of the tube length.

Tuning the conductance of single-walled carbon nanotubes by ion irradiation in the Anderson localization regime

Carbon nanotubes are a good realization of one-dimensional crystals where basic science and potential nanodevice applications merge. Defects are known to modify the electrical resistance of carbon nanotubes; they can be present in as-grown carbon nanotubes, but controlling their density externally opens a path towards the tuning of the electronic characteristics of the nanotube. In this work, consecutive Ar+ irradiation doses are applied to single-walled nanotubes (SWNTs) producing a uniform density of defects. After each dose, the room-temperature resistance versus SWNT length (R(L)) along the nanotube is measured. Our data show an exponential dependence of R(L) indicating that the system is within the strong Anderson localization regime. Theoretical simulations demonstrate that mainly di-vacancies contribute to the resistance increase induced by irradiation, and that just a 0.03% of di-vacancies produces an increase of three orders of magnitude in the resistance of a SWNT of 400 nm length.

Formation of atom wires on vicinal silicon

The feasibility of creating atomic wires on vicinal silicon surfaces via pseudomorphic step-edge decoration has been analyzed for the case of Ga on Si(112). Scanning tunneling microscopy and density functional theory calculations indicate the formation of Ga zigzag chains intersected by quasiperiodic vacancy lines or "misfit dislocations." This structure strikes a balance between the system's drive towards chemical passivation and its need for strain relaxation in the atom chains. Spatially fluctuating disorder, intrinsic to the reconstruction, originates from the two symmetry-degenerate orientations of the zigzag chains on vicinal Si.