Enantiospecificity in NMR enabled by chirality-induced spin selectivity.

Spin polarization in chiral molecules is a magnetic molecular response associated with electron transport and enantioselective bond polarization that occurs even in the absence of an external magnetic field. An unexpected finding by Santos and co-workers reported enantiospecific NMR responses in solid-state cross-polarization (CP) experiments, suggesting a possible additional contribution to the indirect nuclear spin-spin coupling in chiral molecules induced by bond polarization in the presence of spin-orbit coupling. Herein we provide a theoretical treatment for this phenomenon, presenting an effective spin-Hamiltonian for helical molecules like DNA and density functional theory (DFT) results on amino acids that confirm the dependence of J-couplings on the choice of enantiomer. The connection between nuclear spin dynamics and chirality could offer insights for molecular sensing and quantum information sciences. These results establish NMR as a potential tool for chiral discrimination without external agents.

Evolution of point defects in pulsed-laser-melted Ge1-xSnxprobed by positron annihilation lifetime spectroscopy.

Direct-band-gap Germanium-Tin alloys (Ge1-xSnx) with high carrier mobilities are promising materials for nano- and optoelectronics. The concentration of open volume defects in the alloy, such as Sn and Ge vacancies, influences the final device performance. In this article, we present an evaluation of the point defects in molecular-beam-epitaxy grown Ge1-xSnxfilms treated by post-growth nanosecond-range pulsed laser melting (PLM). Doppler broadening - variable energy positron annihilation spectroscopy and variable energy positron annihilation lifetime spectroscopy are used to investigate the defect nanostructure in the Ge1-xSnxfilms exposed to increasing laser energy density. The experimental results, supported with ATomic SUPerposition calculations, evidence that after PLM, the average size of the open volume defects increases, which represents a raise in concentration of vacancy agglomerations, but the overall defect density is reduced as a function of the PLM fluence. At the same time, the positron annihilation spectroscopy analysis provides information about dislocations and Ge vacancies decorated by Sn atoms. Moreover, it is shown that the PLM reduces the strain in the layer, while dislocations are responsible for trapping of Sn and formation of small Sn-rich-clusters.

The contribution of intermolecular spin interactions to the London dispersion forces between chiral molecules.

Dispersion interactions are one of the components of van der Waals (vdW) forces that play a key role in the understanding of intermolecular interactions in many physical, chemical, and biological processes. The theory of dispersion forces was developed by London in the early years of quantum mechanics. However, it was only in the 1960s that it was recognized that for molecules lacking an inversion center, such as chiral and helical molecules, there are chirality-sensitive corrections to the dispersion forces proportional to the rotatory power known from the theory of circular dichroism and with the same distance scaling law R-6 as the London energy. The discovery of the chirality-induced spin selectivity effect in recent years has led to an additional twist in the study of chiral molecular systems, showing a close relation between spin and molecular geometry. Motivated by it, we propose in this investigation to describe the mutual induction of charge and spin-density fluctuations in a pair A-B of chiral molecules by a simple physical model. The model assumes that the same fluctuating electric fields responsible for vdW forces can induce a magnetic response via a Rashba-like term so that a spin-orbit field acting on molecule B is generated by the electric field arising from charge density fluctuations in molecule A (and vice versa). Within a second-order perturbative approach, these contributions manifest as an effective intermolecular exchange interaction. Although expected to be weaker than the standard London forces, these interactions display the same R-6 distance scaling.

A nanographene disk rotating a single molecule gear on a Cu(111) surface.

On Cu(111) surface and in interaction with a single hexa-tert-butylphenylbenzene molecule-gear, the rotation of a graphene nanodisk was studied using the large-scale atomic/molecular massively parallel simulator molecular dynamics simulator. To ensure a transmission of rotation to the molecule-gear, the graphene nanodisk is functionalized on its circumference bytert-butylphenyl chemical groups. The rotational motion can be categorized underdriving, driving and overdriving regimes calculating the locking coefficient of this mechanical machinery as a function of external torque applied to the nanodisk. The rotational friction with the surface of both the phononic and electronic contributions is investigated. For small size graphene nanodisks, the phononic friction is the main contribution. Electronic friction dominates for the larger disks putting constrains on the experimental way of achieving the transfer of rotation from a graphene nanodisk to a single molecule-gear.

S-layer protein-AuNP systems for the colorimetric detection of metal and metalloid ions in water.

Bacterial surface layer proteins (S-layer) possess unique binding properties for metal ions. By combining the binding capability of S-layer proteins with the optical properties of gold nanoparticles (AuNP), namely plasmonic resonance, a colorimetric detection system for metal and metalloid ions in water was developed. Eight S-layer proteins from different bacteria species were used for the functionalization of AuNP. The thus developed biohybrid systems, AuNP functionalized with S-layer proteins, were tested with different metal salt solutions, e.g. Indium(III)-chloride, Yttrium(III)-chloride or Nickel(II)-chloride, to determine their selective and sensitive binding to ionic analytes. All tested S-layer proteins displayed unique binding affinities for the different metal ions. For each S-layer and metal ion combination markedly different reaction patterns and differences in concentration range and absorption spectra were detected by UV/vis spectroscopy. In this way, the selective detection of tested metal ions was achieved by differentiated analysis of a colorimetric screening assay of these biohybrid systems. A highly selective and sensitive detection of yttrium ions down to a concentration of 1.67 × 10-5 mol/l was achieved with S-layer protein SslA functionalized AuNP. The presented biohybrid systems can thus be used as a sensitive and fast sensor system for metal and metalloid ions in aqueous systems.

Green function, quasi-classical Langevin and Kubo-Greenwood methods in quantum thermal transport.

With the advances in fabrication of materials with feature sizes at the order of nanometers, it has been possible to alter their thermal transport properties dramatically. Miniaturization of device size increases the power density in general, hence faster electronics require better thermal transport, whereas better thermoelectric applications require the opposite. Such diverse needs bring new challenges for material design. Shrinkage of length scales has also changed the experimental and theoretical methods to study thermal transport. Unsurprisingly, novel approaches have emerged to control phonon flow. Besides, ever increasing computational power is another driving force for developing new computational methods. In this review, we discuss three methods developed for computing vibrational thermal transport properties of nano-structured systems, namely Green function, quasi-classical Langevin, and Kubo-Green methods. The Green function methods are explained using both nonequilibrium expressions and the Landauer-type formula. The partitioning scheme, decimation techniques and surface Green functions are reviewed, and a simple model for reservoir Green functions is shown. The expressions for the Kubo-Greenwood method are derived, and Lanczos tridiagonalization, continued fraction and Chebyshev polynomial expansion methods are discussed. Additionally, the quasi-classical Langevin approach, which is useful for incorporating phonon-phonon and other scatterings is summarized.

Nanowire sensors monitor bacterial growth kinetics and response to antibiotics.

Miniaturized and cost-efficient methods aiming at high throughput analysis of microbes are of great importance for the surveillance and control of infectious diseases and the related issue of antimicrobial resistance. Here we demonstrate a miniature nanosensor based on a honeycomb-patterned silicon nanowire field effect transistor (FET) capable of detection of bacterial growth and antibiotic response in microbiologically relevant nutrient media. We determine the growth kinetics and metabolic state of Escherichia coli cells in undiluted media via the quantification of changes in the source-drain current caused by varying pH values. Furthermore, by measuring the time dependent profile of pH change for bacterial cultures treated with antibiotics, we demonstrate for the first time the possibility of electrically distinguishing between bacteriostatic and bactericidal drug effects. We believe that the use of such nanoscopic FET devices enables addressing parameters that are not easily accessible by conventional optical methods in a label-free format, i.e. monitoring of microbial metabolic activity or stress response.

Molecular design driving tetraporphyrin self-assembly on graphite: a joint STM, electrochemical and computational study.

Tuning the intermolecular interactions among suitably designed molecules forming highly ordered self-assembled monolayers is a viable approach to control their organization at the supramolecular level. Such a tuning is particularly important when applied to sophisticated molecules combining functional units which possess specific electronic properties, such as electron/energy transfer, in order to develop multifunctional systems. Here we have synthesized two tetraferrocene-porphyrin derivatives that by design can selectively self-assemble at the graphite/liquid interface into either face-on or edge-on monolayer-thick architectures. The former supramolecular arrangement consists of two-dimensional planar networks based on hydrogen bonding among adjacent molecules whereas the latter relies on columnar assembly generated through intermolecular van der Waals interactions. Scanning Tunneling Microscopy (STM) at the solid-liquid interface has been corroborated by cyclic voltammetry measurements and assessed by theoretical calculations to gain multiscale insight into the arrangement of the molecule with respect to the basal plane of the surface. The STM analysis allowed the visualization of these assemblies with a sub-nanometer resolution, and cyclic voltammetry measurements provided direct evidence of the interactions of porphyrin and ferrocene with the graphite surface and offered also insight into the dynamics within the face-on and edge-on assemblies. The experimental findings were supported by theoretical calculations to shed light on the electronic and other physical properties of both assemblies. The capability to engineer the functional nanopatterns through self-assembly of porphyrins containing ferrocene units is a key step toward the bottom-up construction of multifunctional molecular nanostructures and nanodevices.

Electron-beam induced synthesis of nanostructures: a review.

As the success of nanostructures grows in modern society so does the importance of our ability to control their synthesis in precise manners, often with atomic precision as this can directly affect the final properties of the nanostructures. Hence it is crucial to have both deep insight, ideally with real-time temporal resolution, and precise control during the fabrication of nanomaterials. Transmission electron microscopy offers these attributes potentially providing atomic resolution with near real time temporal resolution. In addition, one can fabricate nanostructures in situ in a TEM. This can be achieved with the use of environmental electron microscopes and/or specialized specimen holders. A rather simpler and rapidly growing approach is to take advantage of the imaging electron beam as a tool for in situ reactions. This is possible because there is a wealth of electron specimen interactions, which, when implemented under controlled conditions, enable different approaches to fabricate nanostructures. Moreover, when using the electron beam to drive reactions no specialized specimen holders or peripheral equipment is required. This review is dedicated to explore the body of work available on electron-beam induced synthesis techniques with in situ capabilities. Particular emphasis is placed on the electron beam-induced synthesis of nanostructures conducted inside a TEM, viz. the e-beam is the sole (or primary) agent triggering and driving the synthesis process.

pH measurements of FET-based (bio)chemical sensors using portable measurement system.

In this study we demonstrate the sensing capabilities of a portable multiplex measurement system for FET-based (bio)chemical sensors with an integrated microfluidic interface. We therefore conducted pH measurements with Silicon Nanoribbon FET-based Sensors using different measurement procedures that are suitable for various applications. We have shown multiplexed measurements in aqueous medium for three different modes that are mutually specialized in fast data acquisition (constant drain current), calibration-less sensing (constant gate voltage) and in providing full information content (sweeping mode). Our system therefore allows surface charge sensing for a wide range of applications and is easily adaptable for multiplexed sensing with novel FET-based (bio)chemical sensors.

Ion fluxes and electro-osmotic fluid flow in electrolytes around a metallic nanowire tip under large applied ac voltage.

Motivated by the analysis of electrochemical growth of metallic nanowires from solution, we studied ion fluxes near nanoelectrodes in a binary symmetric electrolyte on the basis of the modified Poisson-Nernst-Planck equations in the strongly nonlinear region at large applied ac voltage. For an approximate calculation of the electric field near the nanowire tip, concentric spherical blocking electrodes were considered with radius of the inner electrode being of typically a few ten nanometers. The spatiotemporal evolution of the ion concentrations within this spherical model was calculated numerically by using the finite element method. The potential drop at the electric double layer, the electric field enhancement at the electrode surface, and the field screening in the bulk solution were determined for different bulk concentrations, ac voltages, and frequencies. The appearance of ac electro-osmotic fluid flow at the tip of a growing metallic nanowire is discussed, based on an estimation of the body force in the liquid near the nanowire tip, which was modeled by a cylinder with hemispherical cap. Electric field components tangential to the electrode surface exist near the contact between cylinder and hemisphere. Our analysis suggests that ac electro-osmotic flow causes an additional convective transport of metal complexes to the tip of the growing metal nanowire and thus affects the nanowire growth velocity.

Vibrational heating in single-molecule switches: an energy-dependent density-of-states approach.

In recent experiments, it has been shown that the switching rate of single-molecule switches can show a rather complicated dependence on the applied bias voltage. Here, we discuss a minimal model which describes the switching process in terms of inelastic scattering processes of the tunneling electron by specific molecular vibrations. One important point is the introduction of an energy-dependent electronic density of states around the Fermi energy. The influence of different model parameters on the switching rate is studied and we show that the inclusion of a variable density of states allows us to understand the non-monotonic behavior of the switching rate observed in some experiments.

Probing charge transport in oxidatively damaged DNA sequences under the influence of structural fluctuations.

We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic structure calculations to formulate a coarse-grained charge transport model. The influence of solvent- and DNA-mediated structural fluctuations is encoded in the obtained time series of the electronic charge transfer parameters. Within the Landauer approach to charge transport, we perform a detailed analysis of the conductance and current time series obtained by sampling the electronic structure along the molecular dynamics trajectory, and find that the inclusion of 8-oxoG damages into the DNA sequence can induce a change in the electrical response of the system. However, solvent-induced fluctuations tend to mask the effect, so that a detection of such sequence modifications via electrical transport measurements in a liquid environment seems to be difficult to achieve.

Dielectrophoretic growth of platinum nanowires: concentration and temperature dependence of the growth velocity.

The growth velocity of platinum nanowires in an aqueous solution of K(2)PtCl(4) is investigated as a function of the metal complex concentration and temperature. The solution is specially prepared to provide mainly the neutral complex cis-[PtCl(2)(H(2)O)(2)] for growing nanowires by dielectrophoresis. The measured growth velocities indicate diffusion-limited nanowire growth at low concentration and high temperature in qualitative agreement with a theoretical analysis that includes the diffusion of metal complexes and the dielectrophoretic force on the complexes. At concentrations greater than 100 µM and low temperature, different behavior is observed, suggesting the growth rate to be limited by the deposition reaction of platinum at the nanowire tip. The enhancement of the K(+) concentration is found to support nanowire growth. Possible reasons for a rate limitation and for the difference between observed and calculated nanowire growth velocities are discussed.

Multiscale modeling of nanowire-based Schottky-barrier field-effect transistors for sensor applications.

We present a theoretical framework for the calculation of charge transport through nanowire-based Schottky-barrier field-effect transistors that is conceptually simple but still captures the relevant physical mechanisms of the transport process. Our approach combines two approaches on different length scales: (1) the finite element method is used to model realistic device geometries and to calculate the electrostatic potential across the Schottky barrier by solving the Poisson equation, and (2) the Landauer-Büttiker approach combined with the method of non-equilibrium Green's functions is employed to calculate the charge transport through the device. Our model correctly reproduces typical I-V characteristics of field-effect transistors, and the dependence of the saturated drain current on the gate field and the device geometry are in good agreement with experiments. Our approach is suitable for one-dimensional Schottky-barrier field-effect transistors of arbitrary device geometry and it is intended to be a simulation platform for the development of nanowire-based sensors.

Conformation dependence of DNA exciton parentage.

Singlet electronic excitations of DNA duplex trimers and tetramers with regular homogeneous base-pair sequences ((dA)n.(dT)n and (dG)n.(dC)n, with n=3, 4) have been investigated in vacuo using semiempirical quantum chemistry in a Zerner's Intermediate Neglect of Differential Overlap (ZINDO) approximation. Frequencies, oscillator strengths, and single-electron assignments of many-electron transitions have been calculated as functions of all 12 possible conformational modes of DNA duplexes. Specific DNA conformational modes responsible for significant changes in the exciton parentage (onset or arrest of the charge-transfer excitons' involvement into observable electronic transition spectra) are revealed. These computational results are thoroughly discussed in connection with numerous data of the most recent relevant experiments.

Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches.

We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

Quantum transport through a DNA wire in a dissipative environment.

Electronic transport through DNA wires in the presence of a strong dissipative environment is investigated. We show that new bath-induced electronic states are formed within the band gap. These states show up in the linear conductance spectrum as a temperature dependent background and lead to a crossover from tunneling to thermal activated behavior with increasing temperature. Depending on the strength of the electron-bath coupling, the conductance at the Fermi level can show a weak exponential or even an algebraic length dependence. Our results suggest a new environmentally induced transport mechanism. This might be relevant for the understanding of molecular conduction experiments in liquid solution, such as those recently performed on poly(GC) oligomers in a water buffer (B. Xu et al., Nano Lett. 2004, 4, 1105).

Model evaluation for glycolytic oscillations in yeast biotransformations of xenobiotics.

Anaerobic glycolysis in yeast perturbed by the reduction of xenobiotic ketones is studied numerically in two models which possess the same topology but different levels of complexity. By comparing both models' predictions for concentrations and fluxes as well as steady or oscillatory temporal behavior we answer the question what phenomena require what kind of minimum model abstraction. While mean concentrations and fluxes are predicted in agreement by both models we observe different domains of oscillatory behavior in parameter space. Generic properties of the glycolytic response to ketones are discussed.

A three terminal ring interferometer logic gate.

We propose a carbon-based logic gate where and, or, and xor logic operations are available. It consists of a carbon nanotube (CNT) ring coupled to three external CNT-leads, two of them used as input channels, and the third as the output channel. The total transmission for two inputs displays characteristic interference effects. The constructive interference leads to total transmission significantly larger than that for a single input and validates and gates, whereas the destructive interference corresponds to xor gates. For or gates a negligible interference between the transmittance of each single inputs is needed.