Selecting the Reaction Path in On-Surface Synthesis through the Electron Chemical Potential in Graphene.

The organometallic on-surface synthesis of the eight-membered sp2 carbon-based ring cyclooctatetraene (C8H8, Cot) with the neighboring rare-earth elements ytterbium and thulium yields fundamentally different products for the two lanthanides, when conducted on graphene (Gr) close to the charge neutrality point. Sandwich-molecular YbCot wires of more than 500 Å length being composed of an alternating sequence of Yb atoms and upright-standing Cot molecules result from the on-surface synthesis with Yb. In contrast, repulsively interacting TmCot dots consisting of a single Cot molecule and a single Tm atom result from the on-surface synthesis with Tm. While the YbCot wires are bound through van der Waals interactions to the substrate, the dots are chemisorbed to Gr via the Tm atoms being more electropositive compared to Yb atoms. When the electron chemical potential in Gr is substantially raised (n-doping) through backside doping from an intercalation layer, the reaction product in the synthesis with Tm can be tuned to TmCot sandwich-molecular wires rather than TmCot dots. By use of density functional theory, it is found that the reduced electronegativity of Gr upon n-doping weakens the binding as well as the charge transfer between the reaction intermediate TmCot dot and Gr. Thus, the assembly of the TmCot dots to long TmCot sandwich-molecular wires becomes energetically favorable. It is thereby demonstrated that the electron chemical potential in Gr can be used as a control parameter in an organometallic on-surface synthesis to tune the outcome of a reaction.

Tailoring magnetic anisotropy by graphene-induced selective skyhook effect on 4f-metals.

From macroscopic heavy-duty permanent magnets to nanodevices, the precise control of the magnetic properties in rare-earth metals is crucial for many applications used in our daily life. Therefore, a detailed understanding and manipulation of the 4f-metals' magnetic properties are key to further boosting the functionalization and efficiency of future applications. We present a proof-of-concept approach consisting of a dysprosium-iridium surface alloy in which graphene adsorption allows us to tailor its magnetic properties. By adsorbing graphene onto a long-range ordered two-dimensional dysprosium-iridium surface alloy, the magnetic 4f-metal atoms are selectively lifted from the surface alloy. This selective skyhook effect introduces a giant magnetic anisotropy in dysprosium atoms as a result of manipulating its geometrical structure within the surface alloy. Introducing and proving this concept by our combined theoretical and experimental approach provides an easy and unambiguous understanding of its underlying mechanism. Our study sets the ground for an alternative path on how to modify the crystal field around 4f-atoms and therefore their magnetic anisotropies.

Boron-Doped Graphene Nanoribbons: Electronic Structure and Raman Fingerprint.

We investigate the electronic and vibrational properties of bottom-up synthesized aligned armchair graphene nanoribbons of N = 7 carbon atoms width periodically doped by substitutional boron atoms (B-7AGNRs). Using angle-resolved photoemission spectroscopy and density functional theory calculations, we find that the dopant-derived valence and conduction band states are notably hybridized with electronic states of Au substrate and spread in energy. The interaction with the substrate leaves the bands with pure carbon character rather unperturbed. This results in an identical effective mass of ≈0.2 m0 for the next-highest valence band compared with pristine 7AGNRs. We probe the phonons of B-7AGNRs by ultrahigh-vacuum (UHV) Raman spectroscopy and reveal the existence of characteristic splitting and red shifts in Raman modes due to the presence of substitutional boron atoms. Comparing the Raman spectra for three visible lasers (red, green, and blue), we find that interaction with gold suppresses the Raman signal from B-7AGNRs and the energy of the green laser (2.33 eV) is closer to the resonant E22 transition. The hybridized electronic structure of the B-7AGNR-Au interface is expected to improve electrical characteristics of contacts between graphene nanoribbon and Au. The Raman fingerprint allows the easy identification of B-7AGNRs, which is particularly useful for device fabrication.

Self-energy matrices for electron transport calculations within the real-space finite-difference formalism.

The self-energy term used in transport calculations, which describes the coupling between electrode and transition regions, is able to be evaluated only from a limited number of the propagating and evanescent waves of a bulk electrode. This obviously contributes toward the reduction of the computational expenses in transport calculations. In this paper, we present a mathematical formula for reducing the computational expenses further without using any approximation and without losing accuracy. So far, the self-energy term has been handled as a matrix with the same dimension as the Hamiltonian submatrix representing the interaction between an electrode and a transition region. In this work, through the singular-value decomposition of the submatrix, the self-energy matrix is handled as a smaller matrix, whose dimension is the rank number of the Hamiltonian submatrix. This procedure is practical in the case of using the pseudopotentials in a separable form, and the computational expenses for determining the self-energy matrix are reduced by 90% when employing a code based on the real-space finite-difference formalism and projector-augmented wave method. In addition, this technique is applicable to the transport calculations using atomic or localized basis sets. Adopting the self-energy matrices obtained from this procedure, we present the calculation of the electron transport properties of C_{20} molecular junctions. The application demonstrates that the electron transmissions are sensitive to the orientation of the molecule with respect to the electrode surface. In addition, channel decomposition of the scattering wave functions reveals that some unoccupied C_{20} molecular orbitals mainly contribute to the electron conduction through the molecular junction.

First-principles calculation method for electron transport based on the grid Lippmann-Schwinger equation.

We develop a first-principles electron-transport simulator based on the Lippmann-Schwinger (LS) equation within the framework of the real-space finite-difference scheme. In our fully real-space-based LS (grid LS) method, the ratio expression technique for the scattering wave functions and the Green's function elements of the reference system is employed to avoid numerical collapse. Furthermore, we present analytical expressions and/or prominent calculation procedures for the retarded Green's function, which are utilized in the grid LS approach. In order to demonstrate the performance of the grid LS method, we simulate the electron-transport properties of the semiconductor-oxide interfaces sandwiched between semi-infinite jellium electrodes. The results confirm that the leakage current through the (001)Si-SiO_{2} model becomes much larger when the dangling-bond state is induced by a defect in the oxygen layer, while that through the (001)Ge-GeO_{2} model is insensitive to the dangling bond state.

Hypersensitivity Reactions to Oxaliplatin: Identifying the Risk Factors and Judging the Efficacy of a Desensitization Protocol.

PURPOSE: We examined the clinical data of patients treated with oxaliplatin to determine the risk factors of oxaliplatin-related hypersensitivity reaction (HSR). In addition, we evaluated the efficacy of rechallenging patients with HSRs with oxaliplatin using prophylactic agents or desensitization procedures. METHODS: This study consisted of 162 patients with colorectal cancer (88 men and 74 women) who were treated consecutively at the outpatient chemotherapy department at University Hospital, Kyoto Prefectural University of Medicine. Patients underwent chemotherapy, including oxaliplatin, between March 2006 and June 2012. We analyzed the patients' clinical backgrounds (eg, age, sex, performance status, disease stage, and allergic history) to uncover any connections to the development of HSR to oxaliplatin. In addition, we rechallenged 10 patients who had oxaliplatin-related HSR using prophylactic agents or desensitization procedures. FINDINGS: Of 162 patients, 28 (17.2%) developed oxaliplatin-related HSRs (16, 2, 9 and 1 patient had grade 1, 2, 3, and 4 HSRs, respectively). The total cumulative dose of oxaliplatin at the onset of the HSR was 301 to 1126 mg/m(2) (median, 582 mg/m(2)), and the first reactions developed in these patients after 5 to 17 infusions of oxaliplatin (median, 8 infusions). Logistic regression analysis indicated that sex (male: odds ratio = 3.624; 95% CI, 1.181-11.122; P = 0.024) and eosinophil count in peripheral blood (odds ratio = 35.118; 95% CI, 1.058-1166.007; P = 0.046) were independent variables for oxaliplatin-related HSRs. Rechallenging patients with prophylactic agents was successful in 2 (28.6%) of 7 patients who successfully completed their treatment. On the other hand, all 3 patients rechallenged with oxaliplatin using a desensitization protocol successfully completed their treatment without new HSRs. IMPLICATIONS: In this retrospective study, we observed that being male and having higher counts of peripheral eosinophil could be predictors for HSR to oxaliplatin. In addition, this study confirms that oxaliplatin desensitization protocol allows patients who developed HSRs to continue with their treatment. However, the optimum desensitization protocol for oxaliplatin administration in terms of tolerability and efficacy needs to be defined.

Real-space finite-difference calculation method of generalized Bloch wave functions and complex band structures with reduced computational cost.

Generalized Bloch wave functions of bulk structures, which are composed of not only propagating waves but also decaying and growing evanescent waves, are known to be essential for defining the open boundary conditions in the calculations of the electronic surface states and scattering wave functions of surface and junction structures. Electronic complex band structures being derived from the generalized Bloch wave functions are also essential for studying bound states of the surface and junction structures, which do not appear in conventional band structures. We present a novel calculation method to obtain the generalized Bloch wave functions of periodic bulk structures by solving a generalized eigenvalue problem, whose dimension is drastically reduced in comparison with the conventional generalized eigenvalue problem derived by Fujimoto and Hirose [Phys. Rev. B 67, 195315 (2003)]. The generalized eigenvalue problem derived in this work is even mathematically equivalent to the conventional one, and, thus, we reduce computational cost for solving the eigenvalue problem considerably without any approximation and losing the strictness of the formulations. To exhibit the performance of the present method, we demonstrate practical calculations of electronic complex band structures and electron transport properties of Al and Cu nanoscale systems. Moreover, employing atom-structured electrodes and jellium-approximated ones for both of the Al and Si monatomic chains, we investigate how much the electron transport properties are unphysically affected by the jellium parts.

Octithiophene on Cu(III) and Au(III): formation and electronic structure of molecular chains and films.

Adsorption and electronic structure of octithiophene (8T) molecules on Cu(III) and Au(III) surfaces are investigated using scanning tunneling microscopy (STM) and spectroscopy (STS) at room temperature. We find a large difference in adsorption behavior of 8T molecules on the two surfaces. At the initial stage of adsorption, 8T molecules are stabilized in the form of molecular chain on a terrace of Cu(III), whereas neither such chain structure nor isolated 8T molecules have been observed on a terrace of Au(III). By increasing the amount of adsorbed molecules, a disordered monolayer film is formed on Cu(III) while a well-ordered monolayer film is formed on Au(III). From the spectroscopic investigations using bias-dependent STM images and STS spectra and by comparing the data with theoretical calculations, it is found that the electronic property of 8T molecules in the molecular chain on Cu(III) is different from that of a free-standing 8T molecule while that in the monolayer film on Au(III) keeps original character of the free-standing 8T molecule. The present study shows that adsorption of 8T molecules on Cu(III) results in a formation of adsorption-induced states near the Fermi level.

Real-space calculations for electron transport properties of nanostructures.

Recent developments in the fabrication and investigation of conductors of atomic dimensions have stimulated a large number of experimental and theoretical studies on these nanoscale devices. In this paper, we introduce examples presenting the efficiencies and advantages of a first-principles transport calculation scheme based on the real-space finite-difference (RSFD) formalism and the overbridging boundary-matching (OBM) method. The RSFD method does not suffer from the artificial periodicity problems that arise in methods using plane-wave basis sets or the linear dependence problems that occur in methods using atomic basis sets. Moreover, the algorithm of the RSFD method is suitable for massively parallel computers and, thus, the combination of the RSFD and OBM methods enables us to execute first-principles transport calculations using large models. To demonstrate the advantages of this method, several applications of the transport calculations in various systems ranging from jellium nanowires to the tip and surface system of scanning tunneling microscopy are presented.

Chemical wiring and soldering toward all-molecule electronic circuitry.

Key to single-molecule electronics is connecting functional molecules to each other using conductive nanowires. This involves two issues: how to create conductive nanowires at designated positions, and how to ensure chemical bonding between the nanowires and functional molecules. Here, we present a novel method that solves both issues. Relevant functional molecules are placed on a self-assembled monolayer of diacetylene compound. A probe tip of a scanning tunneling microscope is then positioned on the molecular row of the diacetylene compound to which the functional molecule is adsorbed, and a conductive polydiacetylene nanowire is fabricated by initiating chain polymerization by stimulation with the tip. Since the front edge of chain polymerization necessarily has a reactive chemical species, the created polymer nanowire forms chemical bonding with an encountered molecular element. We name this spontaneous reaction "chemical soldering". First-principles theoretical calculations are used to investigate the structures and electronic properties of the connection. We demonstrate that two conductive polymer nanowires are connected to a single phthalocyanine molecule. A resonant tunneling diode formed by this method is discussed.

Atomic force microscopy and theoretical investigation of the lifted-up conformation of polydiacetylene on a graphite substrate.

The structure of a single polydiacetylene compound on a graphite substrate was investigated using atomic force microscopy (AFM). The linear conjugated polydiacetylenes were obtained through chain polymerization of a monomolecular layer of diacetylene compound on a graphite substrate under ultraviolet light irradiation. AFM observations revealed that the polydiacetylenes were imaged higher than the unpolymerized monomer rows. This result supports the 'lifted-up' conformation model, in which the polydiacetylene backbone is geometrically raised. To investigate why the polymer backbone is lifted, we also carried out first-principles density-functional calculations in the local density approximation. These calculations suggested that the steric hindrance between the alkyl side-chains of the monomers and the oligomer caused the lifted-up conformation.

One-dimensional surface reconstruction as an atomic-scale template for the growth of periodically striped Ag films.

The role of the In/Si(111)-(4 x 1)-In surface as an atomic-scale geometrical template for the growth of Ag thin films is clarified by scanning tunneling microscopy and low energy electron diffraction. Low-temperature grown Ag films are found to have stripe structures with a transverse periodicity equal to that of indium chains of the In/Si(111)-(4 x 1)-In. The stripes exhibit a structural transformation at the thickness of 6 monolayers (ML); this relaxation allows the stripes to persist up to a thickness as large as 30 ML (approximately = 7 nm) while maintaining their mean periodicity. We attribute this stability to a coincidental matching of the periodicity and the corrugation amplitude between the Ag film and the substrate, which is realized by periodic insertion of stacking faults into a Ag fcc crystal.

Mechanisms of electron transport through bellows-shaped fullerene tubes.

A bellows-shaped fullerene tube is featured by diameter modulation along the tube, where C60 molecules polymerize with tubular linkages between the molecules. The electronic structures of two types of bellows-shaped fullerene tube are theoretically found to exhibit band gaps indicating semiconducting characteristics. Although the effective masses of the conduction states of the two tubes are similar, these states have different spatial distributions. One of the two tubes is expected to exhibit thermally assisted electron transport.