Robust nanotube-based nanosensor designed for the detection of explosive molecules.

The adequate determination and detection of explosive molecules is key to introducing improvements in areas related to safety, whose progress depends on an adequate and rapid determination of dangerous substances. To detect explosives down to the molecular level and accurately discriminate between different but somehow similar substances, it is necessary to design sensors that can differentiate them uniquely and efficiently. In this study, we present a new generation nanoscale sensor based on carbon nanotubes with an adapted nanopore shape that is capable of effectively discriminating between five types of explosive compounds (TATP, RDX, PENT, HMX and DNT). We show that the interaction of each compound with the walls of the nanotubes induces changes in transmission and current that allows clear differentiation of each type of molecule. Interestingly, the transport properties do not depend on the orientation of the molecules within the nanopore in most cases, making it a robust device with high reproducibility and stability. The results also show that these systems can lead to relatively high thermoelectric performances and, furthermore, the Seebeck coefficient can be used to discriminate between them.

Selective Sensing of DNA Nucleobases with Angular Discrimination.

The fast and precise selective sensing of DNA nucleobases is a long-pursued method that can lead to huge advances in the field of genomics and have an impact on aspects such as the prevention of diseases, health enhancement, and, in general, all types of medical treatments. We present here a new type of nanoscale sensor based on carbon nanotubes with a specific geometry that can discriminate the type of nucleobase and also its angle of orientation. The proper differentiation of nucleobases is essential to clearly sequence DNA chains, while angular discrimination is key to improving the sensing selectivity. We perform first-principle and quantum transport simulations to calculate the transmission, conductance, and current of the nanotube-based nanoscale sensor in the presence of the four nucleotides (A, C, G, and T), each of them rotated 0, 90, 180, or 270°. Our results show that this system is able to effectively discriminate between the four nucleotides and their angle of orientation. We explain these findings in terms of the interaction between the phosphate group of the nucleotide and the nanotube wall. The phosphate specifically distorts the electronic structure of the nanotube depending on the distance and the orientation and leads to nontrivial changes in the transmission. This work provides a method for finer and more precise sequential DNA chains.

Towards nanotube-based sensors for discrimination of drug molecules.

The proper detection of drug molecules is key for applications that have an impact in several fields, ranging from medical treatments to industrial applications. In case of illegal drugs, their correct and fast detection has important implications that affect different parts of society such as security or public health. Here we present a method based on nanoscale sensors made of carbon nanotubes modified with dopants that can detect three types of drug molecules: mephedrone, methamphetamine and heroin. We show that each molecule produces a distinctive feature in the density of states that can be used to detect it and distinguish it from other types of molecules. In particular, we show that for semiconducting nanotubes the inclusion of molecules reduces the gap around the Fermi energy and produces peaks in the density of states below the Fermi energy at positions that are different for each molecule. These results prove that it is possible to design nanoscale sensors based on carbon nanotubes tailored with dopants, in such a way that they might be able to discriminate between different types of compounds and, especially, drug molecules whose proper recognition has important consequences in different fields.

Thermoelectric Response Enhanced by Surface/Edge States in Physical Nanogaps.

Current solid-state thermoelectric converters have poor performance, which typically renders them useless for practical applications. This problem is evidenced by the small figures of merit of typical thermoelectric materials, which tend to be much smaller than 1. Increasing this parameter is then key for the development of functional devices in technologically viable applications that can work optimally. We propose here a feasible and effective design of new thermoelectric systems based on physical gaps in nanoscale junctions. We show that, depending on the type of features, i.e., the character of surface/edge states, on both sides of the gap, it is possible to achieve high figures of merit. In particular, we show that, for configurations that have localized states at the surfaces/edges, which translate into sharp resonances in the transmission, it is possible to achieve large Seebeck coefficients and figures of merit by carefully tuning their energy and their coupling to other states. We calculate the thermoelectric coefficients as a function of different parameters and find non-obvious behaviors, such as the existence of a certain coupling between the localized and bulk states for which these quantities have a maximum. The highest Seebeck coefficients and figures of merit are achieved for symmetric junctions, which have the same coupling between the localized state and the bulk states on both sides of the gap. The features and trends of the thermoelectric properties and their changes with various parameters that we find here can be applied not only to systems with nanogaps but also to many other nanoscale junctions, such as those that have surface states or states localized near the contacts between the nanoscale object and the electrodes. The model presented here can, therefore, be used to characterize and predict the thermoelectric properties of many different nanoscale junctions and can also serve as a guide for studying other systems. These results pave the way for the design and fabrication of stable next-generation thermoelectric devices with robust features and improved performance.

Effect of Impurity Adsorption on the Electronic and Transport Properties of Graphene Nanogaps.

Graphene stands out as a versatile material with several uses in fields that range from electronics to biology. In particular, graphene has been proposed as an electrode in molecular electronics devices that are expected to be more stable and reproducible than typical ones based on metallic electrodes. In this work, we study by means of first principles, simulations and a tight-binding model the electronic and transport properties of graphene nanogaps with straight edges and different passivating atoms: Hydrogen or elements of the second row of the periodic table (boron, carbon, nitrogen, oxygen, and fluoride). We use the tight-binding model to reproduce the main ab-initio results and elucidate the physics behind the transport properties. We observe clear patterns that emerge in the conductance and the current as one moves from boron to fluoride. In particular, we find that the conductance decreases and the tunneling decaying factor increases from the former to the latter. We explain these trends in terms of the size of the atom and its onsite energy. We also find a similar pattern for the current, which is ohmic and smooth in general. However, when the size of the simulation cell is the smallest one along the direction perpendicular to the transport direction, we obtain highly non-linear behavior with negative differential resistance. This interesting and surprising behavior can be explained by taking into account the presence of Fano resonances and other interference effects, which emerge due to couplings to side atoms at the edges and other couplings across the gap. Such features enter the bias window as the bias increases and strongly affect the current, giving rise to the non-linear evolution. As a whole, these results can be used as a template to understand the transport properties of straight graphene nanogaps and similar systems and distinguish the presence of different elements in the junction.

The CECAM electronic structure library and the modular software development paradigm.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.

Dynamically Stable Topological Phase of Arsenene.

First-principles calculations based on density functional theory (DFT) are used to investigate the electronic structures and topological phase transition of arsenene under tensile and compressive strains. Buckling in arsenene strongly depends on compressive/tensile strain. The phonons band structures reveal that arsenene is dynamically stable up to 18% tensile strain and the frequency gap between the optical and acoustic branches decreases with strain. The electronic band structures show the direct bandgap decreases with tensile strain and then closes at 13% strain followed by band inversion. With spin-orbit coupling (SOC), the 14% strain-assisted topological insulator phase of arsenene is mainly governed by the p-orbitals. The SOC calculated bandgap is about 43 meV. No imaginary frequency in the phonons is observed in the topological phase of arsenene. The dynamically stable topological phase is accessed through Z2 topological invariant ν using the analysis of the parity of the wave functions at the time-reversal invariant momentum points. The calculated ν is shown to be 1, implying that arsenene is a topological insulator which can be a candidate material for nanoelectronic devices.

In-situ formation of one-dimensional coordination polymers in molecular junctions.

We demonstrate the bottom-up in-situ formation of organometallic oligomer chains at the single-molecule level. The chains are formed using the mechanically controllable break junction technique operated in a liquid environment, and consist of alternating isocyano-terminated benzene monomers coordinated to gold atoms. We show that the chaining process is critically determined by the surface density of molecules. In particular, we demonstrate that by reducing the local supply of molecules within the junction, either by lowering the molecular concentration or by adding side groups, the oligomerization process can be suppressed. Our experimental results are supported by ab-initio simulations, confirming that the isocyano terminating groups display a high tendency to form molecular chains, as a result of their high affinity for gold. Our findings open the road for the controlled formation of one-dimensional, single coordination-polymer chains as promising model systems of organometallic frameworks.

Mechanically controlled quantum interference in graphene break junctions.

The ability to detect and distinguish quantum interference signatures is important for both fundamental research and for the realization of devices such as electron resonators1, interferometers2 and interference-based spin filters3. Consistent with the principles of subwavelength optics, the wave nature of electrons can give rise to various types of interference effects4, such as Fabry-Pérot resonances5, Fano resonances6 and the Aharonov-Bohm effect7. Quantum interference conductance oscillations8 have, indeed, been predicted for multiwall carbon nanotube shuttles and telescopes, and arise from atomic-scale displacements between the inner and outer tubes9,10. Previous theoretical work on graphene bilayers indicates that these systems may display similar interference features as a function of the relative position of the two sheets11,12. Experimental verification is, however, still lacking. Graphene nanoconstrictions represent an ideal model system to study quantum transport phenomena13-15 due to the electronic coherence16 and the transverse confinement of the carriers17. Here, we demonstrate the fabrication of bowtie-shaped nanoconstrictions with mechanically controlled break junctions made from a single layer of graphene. Their electrical conductance displays pronounced oscillations at room temperature, with amplitudes that modulate over an order of magnitude as a function of subnanometre displacements. Surprisingly, the oscillations exhibit a period larger than the graphene lattice constant. Charge-transport calculations show that the periodicity originates from a combination of the quantum interference and lattice commensuration effects of two graphene layers that slide across each other. Our results provide direct experimental observation of a Fabry-Pérot-like interference of electron waves that are partially reflected and/or transmitted at the edges of the graphene bilayer overlap region.

Spin signatures in the electrical response of graphene nanogaps.

We analyse the electrical response of narrow graphene nanogaps in search for transport signatures stemming from spin-polarized edge states. We find that the electrical transport across graphene nanogaps having perfectly defined zigzag edges does not carry any spin-related signature. We also analyse the magnetic and electrical properties of nanogaps whose electrodes have wedges that possibly occur in the currently fabricated nanogaps. These wedges can host spin polarized wedge low-energy states due to the bipartite nature of the graphene lattice. We find that these spin-polarized low-energy modes give rise to low-voltage signatures in the differential conductance and to distinctive features in the stability diagrams. These are caused by fully spin-polarized currents.

Multifunctional nanostructured Co-doped ZnO: Co spatial distribution and correlated magnetic properties.

In this report we present a systematic structural and magnetic analysis of Co-doped ZnO nanoparticles prepared via a microwave-assisted hydrothermal route. The structural data confirm the incorporation of Co ions into the wurtzite ZnO lattice and a Co concentration mainly near/at the surface of the nanoparticles. This Co spatial distribution is set to passivate the surface of the ZnO nanoparticles, inhibiting the nanoparticle growth and suppressing the observation of a ferromagnetic phase. Based on experimental and theoretical results we propose a kinetic-thermodynamic model for the processes of nucleation and growth of the Co-doped ZnO nanoparticles, and attribute the observed ferromagnetic order to a ferromagnetism associated with specific defects and adsorbed elements at the surface of the nanoparticle. Our findings give valuable contribution to the understanding of both the doping process at the nanoscale and the nature of the magnetic properties of the Co-doped ZnO system.

Spin-state dependent conductance switching in single molecule-graphene junctions.

Spin-crossover (SCO) molecules are versatile magnetic switches with applications in molecular electronics and spintronics. Downscaling devices to the single-molecule level remains, however, a challenging task since the switching mechanism in bulk is mediated by cooperative intermolecular interactions. Here, we report on electron transport through individual Fe-SCO molecules coupled to few-layer graphene electrodes via π-π stacking. We observe a distinct bistability in the conductance of the molecule and a careful comparison with density functional theory (DFT) calculations allows to associate the bistability with a SCO-induced orbital reconfiguration of the molecule. We find long spin-state lifetimes that are caused by the specific coordination of the magnetic core and the absence of intermolecular interactions according to our calculations. In contrast with bulk samples, the SCO transition is not triggered by temperature but induced by small perturbations in the molecule at any temperature. We propose plausible mechanisms that could trigger the SCO at the single-molecule level.

Thermoelectricity in vertical graphene-C60-graphene architectures.

Recent studies of single-molecule thermoelectricity have identified families of high-performance molecules. However, in order to translate this discovery into practical thin-film energy-harvesting devices, there is a need for an understanding of the fundamental issues arising when such junctions are placed in parallel. This is relevant because controlled scalability might be used to boost electrical and thermoelectric performance over the current single-junction paradigm. As a first step in this direction, we investigate here the properties of two C60 molecules placed in parallel and sandwiched between top and bottom graphene electrodes. In contrast with classical conductors, we find that increasing the number of parallel junctions from one to two can cause the electrical conductance to increase by more than a factor of 2. Furthermore, we show that the Seebeck coefficient is sensitive to the number of parallel molecules sandwiched between the electrodes, whereas classically it should be unchanged. This non-classical behaviour of the electrical conductance and Seebeck coefficient are due to inter-junction quantum interference, mediated by the electrodes, which leads to an enhanced response in these vertical molecular devices.

Synthesis and Single-Molecule Conductance Study of Redox-Active Ruthenium Complexes with Pyridyl and Dihydrobenzo[b]thiophene Anchoring Groups.

The ancillary ligands 4'-(4-pyridyl)-2,2':6',2''-terpyridine and 4'-(2,3-dihydrobenzo[b]thiophene)-2,2'-6',2"-terpyridine were used to synthesize two series of mono- and dinuclear ruthenium complexes differing in their lengths and anchoring groups. The electrochemical and single-molecular conductance properties of these two series of ruthenium complexes were studied experimentally by means of cyclic voltammetry and the scanning tunneling microscopy-break junction technique (STM-BJ) and theoretically by means of density functional theory (DFT). Cyclic voltammetry data showed clear redox peaks corresponding to both the metal- and ligand-related redox reactions. Single-molecular conductance demonstrated an exponential decay of the molecular conductance with the increase in molecular length for both the series of ruthenium complexes, with decay constants of ßPY =2.07±0.1 nm(-1) and ßBT =2.16±0.1 nm(-1) , respectively. The contact resistance of complexes with 2,3-dihydrobenzo[b]thiophene (BT) anchoring groups is found to be smaller than the contact resistance of ruthenium complexes with pyridine (PY) anchors. DFT calculations support the experimental results and provided additional information on the electronic structure and charge transport properties in those metal|ruthenium complex|metal junctions.

Systematic pseudopotentials from reference eigenvalue sets for DFT calculations: Pseudopotential files.

We present in this article a pseudopotential (PP) database for DFT calculations in the context of the SIESTA code [1-3]. Comprehensive optimized PPs in two formats (psf files and input files for ATM program) are provided for 20 chemical elements for LDA and GGA exchange-correlation potentials. Our data represents a validated database of PPs for SIESTA DFT calculations. Extensive transferability tests guarantee the usefulness of these PPs.

Redox control of thermopower and figure of merit in phase-coherent molecular wires.

We demonstrate how redox control of intra-molecular quantum interference in phase-coherent molecular wires can be used to enhance the thermopower (Seebeck coefficient) S and thermoelectric figure of merit ZT of single molecules attached to nanogap electrodes. Using first principles theory, we study the thermoelectric properties of a family of nine molecules, which consist of dithiol-terminated oligo (phenylene-ethynylenes) (OPEs) containing various central units. Uniquely, one molecule of this family possesses a conjugated acene-based central backbone attached via triple bonds to terminal sulfur atoms bound to gold electrodes and incorporates a fully conjugated hydroquinonecentral unit. We demonstrate that both S and the electronic contribution Z el T to the figure of merit ZT can be dramatically enhanced by oxidizing the hydroquinone to yield a second molecule, which possesses a cross-conjugated anthraquinone central unit. This enhancement originates from the conversion of the pi-conjugation in the former to cross-conjugation in the latter, which promotes the appearance of a sharp anti-resonance at the Fermi energy. Comparison with thermoelectric properties of the remaining seven conjugated molecules demonstrates that such large values of S and Z el T are unprecedented. We also evaluate the phonon contribution to the thermal conductance, which allows us to compute the full figure of merit ZT = Z el T/(1 + κ p/κ el), where κ p is the phonon contribution to the thermal conductance and κ el is the electronic contribution. For unstructured gold electrodes, κ p/κ el â‰«âƒ’ 1 and therefore strategies to reduce κ p are needed to realize the highest possible figure of merit.

Simplifying the conductance profiles of molecular junctions: the use of the trimethylsilylethynyl moiety as a molecule-gold contact.

Conductance across a metal|molecule|metal junction is strongly influenced by the molecule-substrate contacts, and for a given molecular structure, multiple conductance values are frequently observed and ascribed to distinct binding modes of the contact at each of the molecular termini. Conjugated molecules containing a trimethylsilylethynyl terminus, -C≡CSiMe(3) give exclusively a single conductance value in I(s) measurements on gold substrates, the value of which is similar to that observed for the same molecular backbone with thiol and amine based contacting groups when bound to under-coordinated surface sites.

Correlations between molecular structure and single-junction conductance: a case study with oligo(phenylene-ethynylene)-type wires.

The charge transport characteristics of 11 tailor-made dithiol-terminated oligo(phenylene-ethynylene) (OPE)-type molecules attached to two gold electrodes were studied at a solid/liquid interface in a combined approach using an STM break junction (STM-BJ) and a mechanically controlled break junction (MCBJ) setup. We designed and characterized 11 structurally distinct dithiol-terminated OPE-type molecules with varied length and HOMO/LUMO energy. Increase of the molecular length and/or of the HOMO-LUMO gap leads to a decrease of the single-junction conductance of the linearly conjugate acenes. The experimental data and simulations suggest a nonresonant tunneling mechanism involving hole transport through the molecular HOMO, with a decay constant ß = 3.4 ± 0.1 nm(-1) and a contact resistance R(c) = 40 kΩ per Au-S bond. The introduction of a cross-conjugated anthraquinone or a dihydroanthracene central unit results in lower conductance values, which are attributed to a destructive quantum interference phenomenon for the former and a broken π-conjugation for the latter. The statistical analysis of conductance-distance and current-voltage traces revealed details of evolution and breaking of molecular junctions. In particular, we explored the effect of stretching rate and junction stability. We compare our experimental results with DFT calculations using the ab initio code SMEAGOL and discuss how the structure of the molecular wires affects the conductance values.

Long-range electron tunnelling in oligo-porphyrin molecular wires.

Short chains of porphyrin molecules can mediate electron transport over distances as long as 5-10 nm with low attenuation. This means that porphyrin-based molecular wires could be useful in nanoelectronic and photovoltaic devices, but the mechanisms responsible for charge transport in single oligo-porphyrin wires have not yet been established. Here, based on electrical measurements of single-molecule junctions, we show that the conductance of the oligo-porphyrin wires has a strong dependence on temperature, and a weak dependence on the length of the wire. Although it is widely accepted that such behaviour is a signature of a thermally assisted incoherent (hopping) mechanism, density functional theory calculations and an accompanying analytical model strongly suggest that the observed temperature and length dependence is consistent with phase-coherent tunnelling through the whole molecular junction.