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The origin of dielectric constant enhancement in high-temperature (high glass transition temperature Tg) polymer dilute nanocomposites is investigated via Infrared (IR) Spectroscopy applied through Atomic Force Microscope (AFM) and density functional theory (DFT) calculations. The dielectric constant can be greatly enhanced by trace nanofiller loadings (

Electromechanical (EM) coupling—the conversion of energy between electric and mechanical forms—in ferroelectrics has been used for a broad range of applications. Ferroelectric polymers have weak EM coupling that severely limits their usefulness for applications. We introduced a small amount of fluorinated alkyne (FA) monomers (k 33 ) of 88% and a piezoelectric coefficient ( d 33 ) >1000 picometers per volt. These values make this solution-processed polymer competitive with ceramic oxide piezoelectrics, with the potential for use in distinct applications.

The mechanism of the recently discovered enhancement of dielectric properties in dilute polymer-nanoparticle composites is investigated by experiments and computer simulations. We show that the weakening of the hydrogen bonds between the nanoparticles and the polymer chains reduces the polymer-nanoparticle composite's dielectric enhancement. The subsequent multiscale simulations investigate the attachment of solvated highly dipolar polymers to oxide nanoparticles, which leads to deposition of nanoparticle-polymer blobs during solution casting and a reduced density compared to a neat polymer film. Coarse-grained simulations of nanocomposite morphology are followed by molecular dynamics and density functional theory calculations of permittivities. The increased free volume in the nanocomposite enables easier reorientation of monomer dipoles with an applied electric field, and thus a higher dielectric permittivity. The numerical results are in excellent agreement with experimental data for PEEU and PEI nanocomposites.

Solid-state narrow-band light emitters are on-demand for quantum optoelectronics. Current approaches based on defect engineering in low-dimensional materials usually introduce a broad range of emission centers. Here, we report narrow-band light emission from covalent heterostructures fused to the edges of graphene nanoribbons (GNRs) by controllable on-surface reactions from molecular precursors. Two types of heterojunction (HJ) states are realized by sequentially synthesizing GNRs and graphene nanodots (GNDs) and then coupling them together. HJs between armchair GNDs and armchair edges of the GNR are coherent and give rise to narrow-band photoluminescence. In contrast, HJs between the armchair GNDs and the zigzag ends of GNRs are defective and give rise to nonradiative states near the Fermi level. At low temperatures, sharp photoluminescence emissions with peak energy range from 2.03 to 2.08 eV and line widths of 2-5 meV are observed. The radiative HJ states are uniform, and the optical transition energy is controlled by the band gaps of GNRs and GNDs. As these HJs can be synthesized in a large quantity with atomic precision, this finding highlights a route to programmable and deterministic creation of quantum light emitters.

The first-principles simulations are used to search and identify a potential candidate for the single-atom catalysts (SACs). By exploring the stability, clustering tendency, and catalytic activity ...

Phonons are fundamental to understanding the dynamical and thermal properties of materials. However, first-principles phonon calculations are usually limited to moderate-size systems due to their high computational requirements. We implemented the finite displacement method (FDM) in the highly parallel real-space multigrid (RMG) suite of codes to study phonon properties. RMG scales from desktops to clusters and supercomputers containing thousands of nodes, fully supports graphics processing units (GPUs), including multiple GPUs per node, and is very suitable for large-scale electronic structure calculations. It is used as the core computational kernel to calculate the force constants matrix with FDM. By comparing with other widely used density functional theory packages and experimental data from inelastic neutron scattering, we demonstrate that RMG is very accurate in calculating forces at small displacements from equilibrium positions. The calculated phonon band structures and vibrational spectra for a variety of different systems are in very good agreement with plane-wave-based density functional theory codes, Quantum ESPRESSO, CASTEP and VASP, and these results have been validated comparing with inelastic neutron scattering experimental data measured at the VISION spectrometer at the Spallation Neutron Source.

Understanding the reaction mechanisms of dehydrogenative Caryl–Caryl coupling is the key to directed formation of π-extended polycyclic aromatic hydrocarbons. Here we utilize isotopic labeling to identify the exact pathway of cyclodehydrogenation reaction in the on-surface synthesis of model atomically precise graphene nanoribbons (GNRs). Using selectively deuterated molecular precursors, we grow seven-atom-wide armchair GNRs on a Au(111) surface that display a specific hydrogen/deuterium (H/D) pattern with characteristic Raman modes. A distinct hydrogen shift across the fjord of Caryl–Caryl coupling is revealed by monitoring the ratios of gas-phase by-products of H2, HD, and D2 with in situ mass spectrometry. The identified reaction pathway consists of a conrotatory electrocyclization and a distinct [1,9]-sigmatropic D shift followed by H/D eliminations, which is further substantiated by nudged elastic band simulations. Our results not only clarify the cyclodehydrogenation process in GNR synthesis but also present a rational strategy for designing on-surface reactions towards nanographene structures with precise hydrogen/deuterium isotope labeling patterns., Selective deuterations were exploited to synthesize graphene nanoribbons on Au(111) surface with a specific H/D pattern on edges, allowing the determination of cyclodehydrogenation reaction pathway within the framework of pericyclic reactions.

Significantly enhanced electromechanical responses are inherent to piezoelectric materials at the morphotropic phase boundary (MPB). Here we reveal that conformational competition between the trans-planar and 3/1-helical phases of poly(vinylidene fluoride–trifluoroethylene) P(VDF-TrFE) occurs intramolecularly rather than intermolecularly to induce the formation of MPB. We attribute significantly enhanced piezoelectric properties observed near MPB to the polarization rotation between energetically degenerate trans-planar and 3/1-helical phases. Our results offer design principles to search for new MPB polymers from a molecular perspective.

The influence of substrate steps on the bottom-up synthesis of atomically precise graphene nanoribbons (GNRs) on an Au(111) surface is investigated. Straight surface steps are found to promote the assembly of long and compact arrays of polymers with enhanced interchain π-π stacking interactions, which create a steric hindrance effect on cyclodehydrogenation to suppress the H passivation of polymer ends. The modified two-stage growth process results in periodic arrays of GNRs with doubled average length near step edges.

The precise atomic structure of a metal contact significantly affects the performance of nanoscale electronic devices. We use an accurate, DFT-based non-equilibrium Green’s function method to evaluate various metal contacts with graphene or graphene nanoribbons. For surface metal contacts not chemically bound to graphene, Ti contacts have lower resistance than those of Au, Ca, Ir, Pt, and Sr. However, as an edge contact, Ti has larger resistance than Au. Bridging O atoms at Ti and Au edge contacts lowers the transmission by over 30%.

Relaxor ferroelectrics exhibit outstanding dielectric, electromechanical and electrocaloric properties, and are the materials of choice for acoustic sensors, solid-state coolers, transducers and actuators1-4. Despite more than five decades of intensive study, relaxor ferroelectrics remain one of the least understood material families in ferroelectric materials and condensed matter physics5-14. Here, by combining X-ray diffraction, atomic force microscope infrared spectroscopy and first-principles calculations, we reveal that the relaxor behaviour of ferroelectric polymers originates from conformational disorder, completely different from classic perovskite relaxors, which are typically characterized by chemical disorder. We show that chain chirality is essential to the formation of the disordered helix conformation arising from local distortions of gauche torsional angles, which consequently give rise to relaxor properties in polymers. This study not only sheds light on the fundamental mechanisms of relaxor ferroelectrics, but also offers guidance for the discovery of new ferroelectric relaxor organic materials for flexible, scalable and biocompatible sensor and energy applications.

The development of robust, adaptive software and algorithms that can fully exploit exascalecapabilities and future computing architectures is critical to designing advanced materials anddevices with targeted properties. We have developed an open-source code that discretizes theDFT equations on real-space grids that are distributed over the nodes of a massively parallelsystem via domain decomposition. Multigrid techniques are used to dramatically accelerateconvergence while only requiring nearest neighbor communications. The real-space multigrid(RMG) code achieves full plane wave accuracy and scales from desktops and clusters tosupercomputers consisting of ~200k cores and 20k GPUs, including the Cray XE-XK systemsand the new IBM-NVIDIA pre-exascale Summit. Multilevel parallelization with MPI, threadsand/or Cuda/HIP programming enables adaptation to future exascale supercomputers. RMG isdistributed via www.rmgdft.org, with over 3,800 downloads do date. Advanced functionalitiesare provided through interfaces to other codes, including QMCPACK, BerkeleyGW, Phonopy,and ALAMODE.

The anharmonic phonon behavior in zirconium hydrides and deuterides, including ϵ-ZrH2, γ-ZrH, and γ-ZrD, has been investigated from aspects of inelastic neutron scattering (INS) and lattice dynamics calculations within the framework of density functional theory (DFT). The harmonic model failed to reproduce the spectral features observed in the experimental data, indicating the existence of anharmonicity in those materials and the necessity of further explanations. Here, we present a detailed study on the anharmonicity in zirconium hydrides/deuterides by exploring the 2D potential energy surface of hydrogen/deuterium atoms and solving the corresponding 2D single-particle Schrödinger equation to obtain the eigenfrequencies, which are then convoluted with the instrument resolution. The convoluted INS spectra qualitatively describe the anharmonic peaks in the experimental INS spectra and demonstrate that the anharmonicity originates from the deviations of hydrogen potentials from quadratic behavior in certain directions, the effects are apparent for the higher-order excited vibrational states, but small for the ground and first excited states.

Electrical contact to low-dimensional (low-D) materials is a key to their electronic applications. Traditional metal contacts to low-D semiconductors typically create gap states that can pin the Fermi level (EF). However, low-D metals possessing a limited density of states at EF can enable gate-tunable work functions and contact barriers. Moreover, a seamless contact with native bonds at the interface, without localized interfacial states, can serve as an optimal electrode. To realize such a seamless contact, one needs to develop atomically precise heterojunctions from the atom up. Here, we demonstrate an all-carbon staircase contact to ultranarrow armchair graphene nanoribbons (aGNRs). The coherent heterostructures of width-variable aGNRs, consisting of 7, 14, 21, and up to 56 carbon atoms across the width, are synthesized by a surface-assisted self-assembly process with a single molecular precursor. The aGNRs exhibit characteristic vibrational modes in Raman spectroscopy. A combined scanning tunneling m...

In the bottom-up synthesis of graphene nanoribbons (GNRs) from self-assembled linear polymer intermediates, surface-assisted cyclodehydrogenations usually take place on catalytic metal surfaces. Here we demonstrate the formation of GNRs from quasi-freestanding polymers assisted by hole injections from a scanning tunnelling microscope (STM) tip. While catalytic cyclodehydrogenations typically occur in a domino-like conversion process during the thermal annealing, the hole-injection-assisted reactions happen at selective molecular sites controlled by the STM tip. The charge injections lower the cyclodehydrogenation barrier in the catalyst-free formation of graphitic lattices, and the orbital symmetry conservation rules favour hole rather than electron injections for the GNR formation. The created polymer–GNR intraribbon heterostructures have a type-I energy level alignment and strongly localized interfacial states. This finding points to a new route towards controllable synthesis of freestanding graphitic layers, facilitating the design of on-surface reactions for GNR-based structures., A key step in the on-surface synthesis of graphene nanoribbons is thermal annealing of polymer precursors on a metal substrate. Here, Ma et al. decouple the cyclodehydrogenation reaction from the catalytic metal substrate and grow graphene nanoribbons by injecting charges at molecular sites.

It is a great challenge in dielectric polymers to achieve a high dielectric constant while maintaining low dielectric loss and high operating temperatures. Here we report that by blending two glassy state dipolar polymers i.e., poly(arylene ether urea) (PEEU, K=4.7) and an aromatic polythiourea (ArPTU, K=4.4) to form a nanomixture, the resulting blend exhibits a very high dielectric constant, K=7.5, while maintaining low dielectric loss (

Functionalized carbon nanotubes have great potential for nanoscale sensing applications, yet many aspects of their sensing mechanisms are not understood. Here, two paradigmatic sensor configurations for detection of biologically important molecules are investigated through ab initio calculations: a non-covalently functionalized nanotube for glucose detection and a covalently functionalized nanotube for ethylene detection. Glucose and ethylene control key life processes of humans and plants, respectively, despite of their structural and chemical simplicity. The sensors' electrical conductance and transmission coefficients are evaluated at the full density-functional theory level via the non-equilibrium Green's function method. We also investigate the effects of the density of the receptors, the band gaps of the nanotubes, the source-drain voltages, and the atomic modification of the receptor on detection sensitivities. A clear atomistic picture emerges about the mechanisms involved in glucose and ethylene sensing. While semiconducting nanotubes exhibit good sensitivities in both cases, the current through metallic nanotubes is only weakly affected by analyte attachment. These quantitative results could guide the design of improved sensors.

Graphene nanoribbons (GNRs) can be synthesized from molecular precursors with atomic precision. A prominent case is the 7-atom-wide armchair GNR made from 10,10′-dibromo-9,9′-bianthryl (DBBA) precursors on metal substrates through dehalogenation/polymerization followed by cyclodehydrogenation. We investigate the key aspects of the cyclodehydrogenation process by evaluating the energy profiles of various reaction pathways using density functional theory and the nudged elastic band method. The metal substrate plays a critical catalytic role by providing stronger adsorption for products and facilitating H desorption. For polyanthrylene on an extra layer of GNR on Au, the underlying GNR insulates it from the Au substrate and increases the reaction barriers, rendering the polyanthrylene “quasi-freestanding”. However, positive charge injection can induce localized cyclodehydrogenation. We find that this is due to the stabilization of an intermediate state through an arenium ion mechanism and favorable orbital symmetries. These results provide mechanistic insight into the effects of the metal substrate and charge injection on cyclodehydrogenation during GNR synthesis and offer guidance for the design and growth of new graphitic structures.

Precision control of interfacial structures and electronic properties is the key to the realization of functional heterostructures. Here, utilizing the scanning tunneling microscope (STM) both as a manipulation and characterization tool, we demonstrate the fabrication of a heterostructure in a single atomically precise graphene nanoribbon (GNR) and report its electronic properties. The heterostructure is made of a seven-carbon-wide armchair GNR and a lower band gap intermediate ribbon synthesized bottom-up from a molecular precursor on an Au substrate. The short GNR segments are directly written in the ribbon with an STM tip to form atomic precision intraribbon heterostructures. Based on STM studies combined with density functional theory calculations, we show that the heterostructure has a type-I band alignment, with manifestations of quantum confinement and orbital hybridization. Our finding demonstrates a feasible strategy to create a double barrier quantum dot structure with atomic precision for novel functionalities, such as negative differential resistance devices in GNR-based nanoelectronics., 17 pages, 6 figures

Down-scaling device dimensions to the nanometer range raises significant challenges to traditional device design, due to potential current leakage across nanoscale dimensions and the need to maintain reproducibility while dealing with atomic-scale components. Here we investigate negative differential resistance (NDR) devices based on atomically precise graphene nanoribbons. Our computational evaluation of the traditional double-barrier resonant tunneling diode NDR structure uncovers important issues at the atomic scale, concerning the need to minimize the tunneling current between the leads while achieving high peak current. We propose a new device structure consisting of multiple short segments that enables high current by the alignment of electronic levels across the segments while enlarging the tunneling distance between the leads. The proposed structure can be built with atomic precision using a scanning tunneling microscope (STM) tip during an intermediate stage in the synthesis of an armchair nanoribbon. An experimental evaluation of the band alignment at the interfaces and an STM image of the fabricated active part of the device are also presented. This combined theoretical-experimental approach opens a new avenue for the design of nanoscale devices with atomic precision., 19 pages, 6 figures

We propose the Pd monolayer (ML) on ZrC(0 0 1) surface as an effective catalyst for the dissociation of oxygen by density functional theory calculations. We find that the coverage of Pd has a conspicuous impact on the adsorption and dissociation of O2. The strong interaction between the Pd atoms and the ZrC(0 0 1) support enhances the reactivity and stability of the electrocatalyst. By comparing the binding energies of Pd-Pd and Pd-C, we conclude that the Pd adatoms do not aggregate to form a cluster and prefer to form a monolayer when the coverage is low. With a monolayer of coverage, the C sites are fully saturated by adsorbed Pd atoms, which prevent the oxidation of the ZrC(0 0 1) surface. The dissociation activity of O2 on PdML/ZrC(0 0 1) is predicted to be a rival of or even surpass Pt(1 1 1). In addition, the high mobility of the dissociated oxygen atoms on PdML/ZrC(0 0 1) also benefits the later reaction step for ORR.

Both experimental results and theoretical models suggest the decisive role of the filler-matrix interfaces on the dielectric, piezoelectric, pyroelectric, and electrocaloric properties of ferroelectric polymer nanocomposites. However, there remains a lack of direct structural evidence to support the so-called interfacial effect in dielectric nanocomposites. Here, a chemical mapping of the interfacial coupling between the nanofiller and the polymer matrix in ferroelectric polymer nanocomposites by combining atomic force microscopy-infrared spectroscopy (AFM-IR) with first-principles calculations and phase-field simulations is provided. The addition of ceramic fillers into a ferroelectric polymer leads to augmentation of the local conformational disorder in the vicinity of the interface, resulting in the local stabilization of the all-trans conformation (i.e., the polar β phase). The formation of highly polar and inhomogeneous interfacial regions, which is further enhanced with a decrease of the filler size, has been identified experimentally and verified by phase-field simulations and density functional theory (DFT) calculations. This work offers unprecedented structural insights into the configurational disorder-induced interfacial effect and will enable rational design and molecular engineering of the filler-matrix interfaces of electroactive polymer nanocomposites to boost their collective properties.

Piezoelectricity—the direct interconversion between mechanical and electrical energies—is usually remarkably enhanced at the morphotropic phase boundary of ferroelectric materials1–4, which marks a transition region in the phase diagram of piezoelectric materials and bridges two competing phases with distinct symmetries1,5. Such enhancement has enabled the recent development of various lead and lead-free piezoelectric perovskites with outstanding piezoelectric properties for use in actuators, transducers, sensors and energy-harvesting applications5–8. However, the morphotropic phase boundary has never been observed in organic materials, and the absence of effective approaches to improving the intrinsic piezoelectric responses of polymers9,10 considerably hampers their application to flexible, wearable and biocompatible devices. Here we report stereochemically induced behaviour in ferroelectric poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) copolymers, which is similar to that observed at morphotropic phase boundaries in perovskites. We reveal that compositionally tailored tacticity (the stereochemical arrangement of chiral centres related to the TrFE monomers11,12) can lead to intramolecular order-to-disorder evolution in the crystalline phase and thus to an intermediate transition region that is reminiscent of the morphotropic phase boundary, where competing ferroelectric and relaxor properties appear simultaneously. Our first-principles calculations confirm the crucial role of chain tacticity in driving the formation of this transition region via structural competition between the trans-planar and 3/1-helical phases. We show that the P(VDF-TrFE) copolymer with the morphotropic composition exhibits a longitudinal piezoelectric coefficient of −63.5 picocoulombs per newton, outperforming state-of-the-art piezoelectric polymers10. Given the flexibility in the molecular design and synthesis of organic ferroelectric materials, this work opens up the way for the development of scalable, high-performance piezoelectric polymers.

The stability of graphene nanoribbons (GNRs) against oxidation is critical for their practical applications. Here we study both the thermal stability and the oxidation process of the ambient-exposed armchair GNRs with a width of seven carbon atoms (7-aGNR), grown on an Au(111) surface. The atomic scale evolution of the armchair edges and the zigzag ends of the aGNRs after annealing at different temperatures are revealed by using scanning tunneling microscopy, Raman spectroscopy, x-ray photoelectron spectroscopy, and first-principles calculations. We observe evidence that the zigzag ends start to be oxidized and decomposed at 180 \ifmmode^\circ\else\textdegree\fi{}C, while the armchair edges are intact at 430 \ifmmode^\circ\else\textdegree\fi{}C but become oxidized at 520 \ifmmode^\circ\else\textdegree\fi{}C. Two different oxygen species are identified at the armchair edges, namely the hydroxyl pair and the epoxy bonding motif with one oxygen bonded to two edge carbons. These oxidization species modify the electronic properties of the pristine 7-aGNRs, with a band-gap reduction from 2.6 to 2.3 eV and 1.9 eV for the hydroxyl pair- and epoxy-terminated edges, respectively. These findings demonstrate the oxidation stability of both the zigzag and armchair edges of GNRs, and they provide an opportunity to harness the high density of edge atoms in applications such as GNR-based high-temperature oxygen sensors.

RMG (Real Space Multigrid) is an open-source real-space DFT-based electronic structure code for quantum simulations of materials. Designed for scalability, RMG has been run successfully on systems with thousands of GPU nodes and hundreds of thousands of CPU cores, reaching multipetaflops performance. An extensive default set of pseudopotentials, both norm-conserving and ultrasoft, is built-in. RMG is highly portable and runs on Linux/UNIX, Windows and Mac OS X workstations and desktops, as well supercomputers. RMG is distributed at https://www.rmgdft.org, including sources, scripts and binaries for common platforms.

Self-assembled monolayers are the basis for molecular nanodevices, flexible surface functionalization, and dip-pen nanolithography. Yet self-assembled monolayers are typically created by a rather inefficient process involving thermally driven attachment reactions of precursor molecules to a metal surface, followed by a slow and defect-prone molecular reorganization. Here we demonstrate a nonthermal, electron-induced approach to the self-assembly of phenylacetylene molecules on gold that allows for a previously unachievable attachment of the molecules to the surface through the alkyne group. While thermal excitation can only desorb the parent molecule due to prohibitively high activation barriers for attachment reactions, localized injection of hot electrons or holes not only overcomes this barrier but also enables an unprecedented control over the size and shape of the self-assembly, defect structures, and the reverse process of molecular disassembly from a single molecule to a mesoscopic length scale. Electron-induced excitation may therefore enable new and highly controlled approaches to molecular self-assembly on a surface.

Supramolecular self-assembly on well-defined surfaces provides access to a multitude of nanoscale architectures, including clusters of distinct symmetry and size. The driving forces underlying supramolecular structures generally involve both graphoepitaxy and weak directional nonconvalent interactions. Here we show that functionalizing a benzene molecule with an ethyne group introduces attractive interactions in a 2D geometry, which would otherwise be dominated by intermolecular repulsion. Furthermore, the attractive interactions enable supramolecular self-assembly, wherein a subtle balance between very weak CH/π bonding and molecule-surface interactions produces a well-defined "magic" dimension and chirality of supramolecular clusters. The nature of the process is corroborated by extensive scanning tunneling microscopy/spectroscopy (STM/S) measurements and ab initio calculations, which emphasize the cooperative, multicenter characters of the CH/π interaction. This work points out new possibilities for chemical functionalization of π-conjugated hydrocarbon molecules that may allow for the rational design of supramolecular clusters with a desired shape and size.

A series of chiral β -arylalkyl-1 H -1,2,4-triazole derivatives were prepared and both their in vitro antifungal activities against Penicillium digitatum and binding activity toward CYP51 protein of P. digitatum (PdCYP51) were tested. In general, the in vitro inhibitory activities of R - and S -enantiomers were in good agreement with the corresponding binding activities in cultured cells. Furthermore, the preliminary molecular docking modeling of representative compounds are described to provide more insight into their stereoselective interaction, as well as further rationalize the observations of the activities of chiral azoles as demethylase inhibitors for defense against postharvest pathogens.

Unlike single-C(60)-based devices, molecular assemblies based on two or more appropriately connected C(60) molecules have the potential to exhibit negative differential resistance (NDR). In this work, we evaluate electron transport properties of molecular devices built from two C(60) molecules connected by an alkane chain, using a nonequilibrium Green function technique implemented within the framework of density functional theory. We find that electronic conduction in these systems is mediated by the lowest unoccupied molecular orbitals (LUMOs) of C(60), as in the case of a single-C(60)-based device. However, as the positions of the LUMOs are pinned to the chemical potentials of their respective electrodes, their relative alignment shifts with applied bias and leads to a NDR at a very low bias. Furthermore, the position and magnitude of the NDR can be tuned by chemical modification of the C(60) molecules. The role of the attached molecules is to shift the LUMO position and break the symmetry between the forward and reverse currents. The NDR feature can also be controlled by changing the length of the alkane linker. The flexibility and richness of C(60)-based molecular electronics components point to a potentially promising route for the design of molecular devices and chemical sensors.

The prion protein (PrP) is responsible for a group of neurodegenerative diseases called the transmissible spongiform encephalopathies. The normal function of PrP has not yet been discovered, but indirect evidence suggests a linkage to its ability to bind copper. In this article, low-copper-concentration bindings of Cu 2+ to PrP are investigated by using a recently developed hybrid density functional theory (DFT)/DFT method. It is found that at the lowest copper concentrations, the binding site consists of 4 histidine residues coordinating the copper through ε imidazole nitrogens. At higher concentrations, 2 histidines are involved in the binding, one of them in the axial position. These results are in good agreement with existing experimental data. Comparison of free energies for all modes of coordination shows that when enough copper is available, the binding sites will spontaneously rearrange to accommodate more copper ions, despite the fact that binding energy per copper ion decreases with concentration. These findings support the hypothesis that PrP acts as a copper buffer in vivo, protecting other proteins from the attachment of copper ions. Using large-scale classical molecular dynamics, we also probe the structure of full-length copper-bound PrP, including its unfolded N-terminal domain. The results show that copper attachment leads to rearrangement of the structure of the Cu-bonded octarepeat region and to development of turns in areas separating copper-bound residues. These turns make the flexible N-terminal domain more rigid and thus more resistant to misfolding. The last result suggests that copper binding plays a beneficial role in the initial stages of prion diseases.

Quantum transport properties of porphyrin-bridged p-n junctions with Si leads are investigated by ab initio calculations. It is shown that this system exhibits strong negative differential resistance (NDR) peaks, whose magnitude and position can be controlled by the doping levels of the leads and by changing the central transition metal atom of the porphyrin. These results are explained by bias-induced on-off switching of resonant tunneling channels associated with specific molecular orbitals. The predicted behavior is general and should be observable for other organic molecules bridging doped semiconducting leads.

A radiation damage database with emphasis on spallation interactions is described. Currently, the database contains damage energy, displacement, helium, and hydrogen cross sections for 23 elemental targets irradiated by proton and neutron projectiles up to 3.2 GeV. In this paper, the focus is on proton-induced helium cross sections, but it is shown that for high energies (above about 500 MeV) proton- and neutron-induced helium cross sections are almost equal. The cross section calculations were run on the Cascade–Exciton Model code (no options) and also on the Bertini code with three nuclear level-density models and multistage pre-equilibrium model on and off. Calculation and experimental results are compared. For various targets, we tried to determine which code and options give best agreement with experiment. In some cases, such determinations are uncertain, partly because of limited and conflicting experimental information and partly perhaps because of the need for modifications in the codes.

Conventional semiconducting devices are rapidly approaching their physical limits, encouraging an increasing number of researchers across multiple disciplines to attempt to devise innovative ways to decrease the size and increase the performance of critical features in microelectronic circuits. One possible route is based on the idea of using molecules and molecular structures as functional electronic devices. While impressive experimental progress toward the realization of molecular electronics has been achieved, full insight into the potential for molecular-based electronics requires accurate theoretical investigations of the processes governing their functioning. In the present study, we show that large-scale quantum electronic structure calculations coupled with nonequilibrium Green function theory can be employed to determine quantum conductance on practical length scales. The combination of state-of-the-art quantum mechanical methods, efficient numerical algorithms, and high-performance computing allows for realistic evaluation of properties at length scales that are routinely reached experimentally. Two illustrations of the method are presented. First, we investigate the electron transport properties of a Si/organic-molecule/Si junction, using a numerically optimized basis. Second, quantum chemical calculations using up to 104 basis functions are carried out to investigate amphoteric doping of carbon nanotubes by encapsulation of organic molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Novel carbon nanotube-metal cluster structures are proposed as prototype systems for molecular recognition at the nanoscale. Ab initio calculations show that already the bare nanotube cluster system displays some specificity because the adsorption of ammonia on a carbon nanotube-Al cluster system is easily detected electrically, while diborane adsorption does not provide an electrical signature. Since there are well-established procedures for attaching molecular receptors to metal clusters, these results provide a "proof-of-principle" for the development of novel, high-specificity molecular sensors.

Large-scale quantum electronic structure calculations coupled with nonequilibrium Green function theory are employed for determining quantum conductance on practical length scales. The combination of state-of-the-art quantum mechanical methods, efficient numerical algorithms, and high performance computing allows for realistic evaluation of properties at length scales that are routinely reached experimentally. Two illustrations of the method are presented. First, quantum chemical calculations using up to 104 basis functions are used to investigate the amphoteric doping of carbon nanotubes by encapsulation of organic molecules. As a second example, we investigate the electron transport properties of a Si/organic molecule/Si junction using a numerically optimized basis.

In the last couple of years there has been much methodological and computational progress in the modelling of optical properties from first principles .R ef lectance anisotropy spectra (RAS) can now be calculated with true predictive power and can thus be used to draw conclusions directly on the surface geometry. In the present work we study two potentially very interesting applications for RAS: the oxidation of Si(001) and the functionalization of the Si surface with organic molecules. Our calculations confirm experimental indications that the polarity of the interface-induced optical anisotropy is reversed layer by layer with increasing oxide thickness. The oscillation of the RAS amplitude should thus allow for the quantitative monitoring of the vertical progression of the oxidation. Our results for Si(001) surfaces modified by cyclopentene and 9,10-phenanthrenequinone adsorption show a strong sensitivity of the RAS signal with respect to the adsorption geometry. Comparison with experimental data shows that cyclopentene most probabl ya dsorbs vi aa cycloaddition reaction with the Si surface dimers, while phenanthrenequinone seems to adsorb across two Si dimers.

In the last couple of years there has been much methodological and computational progress in the modeling of optical properties from first principles. While the calculation of non-linear optical coefficients is still hampered by numerical limitations— demonstrated here for the case of bulk GaAs—linear optical spectra can now be calculated accurately and with true predictive power, even for large and complex surface structures. This allows on one hand for a much better understanding of the origin of specific features such as surface optical anisotropies. We find that in particular microscopic electric fields at the surface induce slight deformations of bulk-like wavefunctions and thus give rise to optical anisotropies even from sub-surface layers. On the other hand, from the comparison of measured and calculated spectra, one can now confidently reach conclusions on the surface geometry. This short review focuses on the simulation of reflectance anisotropy spectroscopy. The clean, hydrogenated and uracil- covered Si(001) surface is used to illustrate the microscopic origin of surface optical anisotropies and the present state-of-the-art in computational modeling of optical spectra. 2003 Elsevier B.V. All rights reserved. PACS: 78.68.qm; 78.66.Fd; 78.66.Db; 78.66.Qn

Calculations are underway to determine radiation damage (displacement, helium, and hydrogen production) at the entrance window of the SINQ Target 3 (Mark II Type). Damage production rates were determined in two ways. In Method 1, the displacement, He, and H cross-sections were folded into the proton and neutron fluxes to give the three defect production rates separately for protons and neutrons. In Method 2, MCNPX with a computer model of SINQ was used directly to calculate the three production rates due to the combined effects of protons and neutrons. The production rates at the central tip of the target by Method 1 are 4.1 and 0.47 dpa/yr per mA for protons and neutrons, respectively, giving a total of 4.6 dpa/yr per mA. By Method 2 using several approaches, we obtain a range of production rates from 3.6 to 4.1 dpa/yr per mA. For helium, the production rates are calculated to be about 1000 and a range from 950 to 1580 appmHe/yr per mA, respectively. LAHET calculations indicate that the helium is completely retained in the irradiated aluminum. For hydrogen, the calculations indicate that perhaps only about half of the hydrogen produced is retained. Method 1 gives about 3500 appmH/yr per mA retained and Method 2 gives a range from 3500 to 4400 appmH/yr per mA.

The structure of the ( $3\ifmmode\times\else\texttimes\fi{}2$) reconstruction of $\ensuremath{\beta}$-SiC(001) surface has been identified by comparing reflectance anisotropy spectra calculated from first principles with recent measurements. Only the calculations for the two-adlayer asymmetric-dimer model agree with experiment. The two prominent peaks at 3.6 and 5.0 eV found experimentally are assigned to electronic transitions between surface and bulklike electronic states. A further pronounced anisotropy at 2.0 eV, due to transitions between surface states, is predicted.

Structural and electronic properties of silicate adlayers on $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$-reconstructed C-terminated $(0001\ifmmode\bar\else\textasciimacron\fi{})$ and Si-terminated (0001) surfaces of hexagonal $6H\ensuremath{-}\mathrm{SiC}$ have been studied using the ab initio pseudopotential supercell method. Two significantly different structural models, previously suggested on the basis of a quantitative low-energy electron diffraction (LEED) analysis for the two adsorbate systems, have been investigated. Both of these models have been considered for both surfaces and the four respective structures have been optimized by total energy minimization calculations. The two structures with the lowest formation energy confirm the interpretation of the LEED data. In addition, they allow us to address the physical origin of the distinctly different reconstruction models for the two surfaces. The electronic structure of these surfaces according to local density approximation calculations is presented and discussed. Both models yield a number of oxygen-induced bound states and resonances within the projected valence band region and a band of localized dangling-bond states within the projected gap. Within the local density approximation, this dangling-bond band turns out to be half-filled in both cases, giving rise to metallic surfaces in contradiction to experiment. Therefore, the systems have also been studied within the framework of the Hubbard model and by employing the local-spin-density approximation. In both cases semiconducting surfaces are obtained in agreement with experiment. The dangling-bond bands resulting within the Hubbard-model calculation, in particular, are in quantitative agreement with most recent angle-resolved photoemission spectroscopy data for a ${\mathrm{Si}}_{2}{\mathrm{O}}_{3}$ silicate adlayer on $\mathrm{SiC}(0001\ifmmode\bar\else\textasciimacron\fi{}).$