Adsorption and charge transfer interactions of bi-isonicotinic acid on Ag(111)

The adsorption and charge transfer dynamics of the organic molecule bi-isonicotinic acid (4,4′-dicarboxy-2,2′-bipyridine) on single crystal Ag(111) has been studied using synchrotron radiation-based photoemission, x-ray absorption and resonant core spectroscopies. Measurements for multilayer and monolayer coverage are used to determine the nature of the molecule-surface interactions and the molecular orientation. An experimental density of states for the monolayer with respect to the underlying metal surface is obtained by combining x-ray absorption spectroscopy at the N 1s edge and valence photoemission to measure the unoccupied and occupied valence states, respectively. This shows that the lowest unoccupied molecular orbital in the core-excited state lies energetically below the Fermi level of the surface allowing charge transfer from the metal into this orbital. Resonant photoelectron spectroscopy was used to probe this charge transfer in the context of super-spectator and super-Auger electron transitions. The results presented provide a novel interpretation of resonant core-level spectroscopy to explore ultra-fast charge transfer between an adsorbed organic molecule and a metal surface through the observation of electrons from the metal surface playing a direct role in the core-hole decay of the core-excited molecule

Exploring ultra-fast charge transfer and vibronic coupling with N 1s RIXS maps of an aromatic molecule coupled to a semiconductor

We present for the first time two-dimensional resonant inelastic x-ray scattering (RIXS) maps of multilayer and monolayer biisonicotinic acid adsorbed on the rutile TiO2(110) single crystal surface. This enables the elastic channel to be followed over the lowest unoccupied molecular orbitals resonantly excited at the N 1s absorption edge. The data also reveals ultra-fast intramolecular vibronic coupling, particularly during excitation into the LUMO-derived resonance. Both elastic scattering and the vibronic coupling loss features are expected to contain the channel in which the originally excited electron is directly involved in the core-hole decay process. This allows RIXS data for a molecule coupled to a wide bandgap semiconductor to be considered in the same way as the core-hole clock implementation of resonant photoemission spectroscopy (RPES). However, contrary to RPES measurements, we find no evidence for depletion of the participator channel under the conditions of ultra-fast charge transfer from the molecule to the substrate densities of states, on the timescale of the core-hole lifetime. These results suggest that the radiative core-hole decay processes in RIXS are not significantly modified by charge transfer on the femtosecond timescale in this system

Charge transfer from an adsorbed ruthenium-based photosensitizer through an ultra-thin aluminium oxide layer and into a metallic substrate

The interaction of the dye molecule N3 (cis-bis(isothiocyanato)bis(2,2-bipyridyl-4,4′-dicarbo-xylato)-ruthenium(II)) with the ultra-thin oxide layer on a AlNi(110) substrate, has been studied using synchrotron radiation based photoelectron spectroscopy, resonant photoemission spectroscopy, and near edge X-ray absorption fine structure spectroscopy. Calibrated X-ray absorption and valence band spectra of the monolayer and multilayer coverages reveal that charge transfer is possible from the molecule to the AlNi(110) substrate via tunnelling through the ultra-thin oxide layer and into the conduction band edge of the substrate. This charge transfer mechanism is possible from the LUMO+2 and 3 in the excited state but not from the LUMO, therefore enabling core-hole clock analysis, which gives an upper limit of 6.0 ± 2.5 fs for the transfer time. This indicates that ultra-thin oxide layers are a viable material for use in dye-sensitized solar cells, which may lead to reduced recombination effects and improved efficiencies of future devices

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".

This is the final version of the article. Available from American Society for Microbiology via the DOI in this record.Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.IMPORTANCE Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon-many of which occur in bacterioplankton from poorly understood lineages-have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these "microbial dark matter" taxa during hypoxia

Adsorption and charge transfer interactions of bi-isonicotinic acid on Ag(111)

The adsorption and charge transfer dynamics of the organic molecule bi-isonicotinic acid (4,4′-dicarboxy-2,2′-bipyridine) on single crystal Ag(111) has been studied using synchrotron radiation-based photoemission, x-ray absorption and resonant core spectroscopies. Measurements for multilayer and monolayer coverage are used to determine the nature of the molecule-surface interactions and the molecular orientation. An experimental density of states for the monolayer with respect to the underlying metal surface is obtained by combining x-ray absorption spectroscopy at the N 1s edge and valence photoemission to measure the unoccupied and occupied valence states, respectively. This shows that the lowest unoccupied molecular orbital in the core-excited state lies energetically below the Fermi level of the surface allowing charge transfer from the metal into this orbital. Resonant photoelectron spectroscopy was used to probe this charge transfer in the context of super-spectator and super-Auger electron transitions. The results presented provide a novel interpretation of resonant core-level spectroscopy to explore ultra-fast charge transfer between an adsorbed organic molecule and a metal surface through the observation of electrons from the metal surface playing a direct role in the core-hole decay of the core-excited molecule

On the suitability of high vacuum electrospray deposition for the fabrication of molecular electronic devices

We present a series of three studies investigating the potential application of high vacuum electrospray deposition to construct molecular electronic devices. Through the use of time of flight secondary ion mass spectrometry we explore the use of this novel deposition technique to fabricating multilayer structures using materials that are compatible with the same solvents and films containing a mixture of molecules from orthogonal solvents. Using x-ray photoelectron spectroscopy we study the deposition of a polymer blend using electrospray and find evidence of preferential deposition of one of the components

Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection

Influenza hemagglutinin (HA) is the primary target of the humoral response during infection/vaccination. Current influenza vaccines typically fail to elicit/boost broadly neutralizing antibodies (bnAbs), thereby limiting their efficacy. Although several bnAbs bind to the conserved stem domain of HA, focusing the immune response to this conserved stem in the presence of the immunodominant, variable head domain of HA is challenging. We report the design of a thermotolerant, disulfide-free, and trimeric HA stem-fragment immunogen which mimics the native, prefusion conformation of HA and binds conformation specific bnAbs with high affinity. The immunogen elicited bnAbs that neutralized highly divergent group 1 (H1 and H5 subtypes) and 2 (H3 subtype) influenza virus strains in vitro. Stem immunogens designed from unmatched, highly drifted influenza strains conferred robust protection against a lethal heterologous A/Puerto Rico/8/34 virus challenge in vivo. Soluble, bacterial expression of such designed immunogens allows for rapid scale-up during pandemic outbreaks

Ultra-fast intramolecular vibronic coupling revealed by RIXS and RPES maps of an aromatic adsorbate on TiO2(110)

Two-dimensional resonant inelastic x-ray scattering (RIXS) and resonant photoelectron spectroscopy (RPES) maps are presented for multilayer and monolayer coverages of an aromatic molecule (bi-isonicotinic acid) on the rutile TiO2(110) single crystal surface. The data reveals ultra-fast intramolecular vibronic coupling upon core-excitation from the N 1s orbital into the lowest unoccupied molecular orbital (LUMO) derived resonance. In the RIXS measurements this results in the splitting of the participator decay channel into a purely elastic line which disperses linearly with excitation energy, and a vibronic coupling channel at constant emission energy. In the RPES measurements the vibronic coupling results in a linear shift in binding energy of the participator channel as the excitation is tuned over the LUMO-derived resonance. Localisation of the vibrations on the molecule on the femtosecond timescale results in predominantly inelastic scattering from the core-excited state in both the physisorbed multilayer and the chemisorbed monolayer

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and ‘universal’ gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The ‘VirION’ (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature