Upgrade of the SPECIES beamline at the MAX IV Laboratory.

The SPECIES beamline has been transferred to the new 1.5 GeV storage ring at the MAX IV Laboratory. Several improvements have been made to the beamline and its endstations during the transfer. Together the Ambient Pressure X-ray Photoelectron Spectroscopy and Resonant Inelastic X-ray Scattering endstations are capable of conducting photoelectron spectroscopy in elevated pressure regimes with enhanced time-resolution and flux and X-ray scattering experiments with improved resolution and flux. Both endstations offer a unique capability for experiments at low photon energies in the vacuum ultraviolet and soft X-ray range. In this paper, the upgrades on the endstations and current performance of the beamline are reported.

A five-axis parallel kinematic mirror unit for soft X-ray beamlines at MAX†IV.

With the introduction of the multi-bend achromats in the new fourth-generation storage rings the emittance has decreased by an order of magnitude resulting in increased brightness. However, the higher brightness comes with smaller beam sizes and narrower radiation cones. As a consequence, the requirements on mechanical stability regarding the beamline components increases. Here an innovative five-axis parallel kinematic mirror unit for use with soft X-ray beamlines using off-axis grazing-incidence optics is presented. Using simulations and measurements from the HIPPIE beamline at the MAX IV Laboratory it is shown that it has no Eigen frequencies below 90 Hz. Its positioning accuracy is better than 25 nm linearly and 17-35 µrad angularly depending on the mirror chamber dimensions.

From Permeation to Cluster Arrays: Graphene on Ir(111) Exposed to Carbon Vapor.

Our scanning tunneling microscopy and X-ray photoelectron spectroscopy experiments along with first-principles calculations uncover the rich phenomenology and enable a coherent understanding of carbon vapor interaction with graphene on Ir(111). At high temperatures, carbon vapor not only permeates to the metal surface but also densifies the graphene cover. Thereby, in addition to underlayer graphene growth, upon cool down also severe wrinkling of the densified graphene cover is observed. In contrast, at low temperatures the adsorbed carbon largely remains on top and self-organizes into a regular array of fullerene-like, thermally highly stable clusters that are covalently bonded to the underlying graphene sheet. Thus, a new type of predominantly sp2-hybridized nanostructured and ultrathin carbon material emerges, which may be useful to encage or stably bind metal in finely dispersed form.

The SPECIES beamline at the MAX IV Laboratory: a facility for soft X-ray RIXS and APXPS.

SPECIES is an undulator-based soft X-ray beamline that replaced the old I511 beamline at the MAX II storage ring. SPECIES is aimed at high-resolution ambient-pressure X-ray photoelectron spectroscopy (APXPS), near-edge X-ray absorption fine-structure (NEXAFS), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS) experiments. The beamline has two branches that use a common elliptically polarizing undulator and monochromator. The beam is switched between the two branches by changing the focusing optics after the monochromator. Both branches have separate exit slits, refocusing optics and dedicated permanent endstations. This allows very fast switching between two types of experiments and offers a unique combination of the surface-sensitive XPS and bulk-sensitive RIXS techniques both in UHV and at elevated ambient-pressure conditions on a single beamline. Another unique property of the beamline is that it reaches energies down to approximately 27 eV, which is not obtainable on other current APXPS beamlines. This allows, for instance, valence band studies under ambient-pressure conditions. In this article the main properties and performance of the beamline are presented, together with selected showcase experiments performed on the new setup.

De novo biosynthesis of trans-cinnamic acid derivatives in Saccharomyces cerevisiae.

The production of natural aroma compounds is an expanding field within the branch of white biotechnology. Three aromatic compounds of interest are cinnamaldehyde, the typical cinnamon aroma that has applications in agriculture and medical sciences, as well as cinnamyl alcohol and hydrocinnamyl alcohol, which have applications in the cosmetic industry. Current production methods, which rely on extraction from plant materials or chemical synthesis, are associated with drawbacks regarding scalability, production time, and environmental impact. These considerations make the development of a sustainable microbial-based production highly desirable. Through steps of rational metabolic engineering, we engineered the yeast Saccharomyces cerevisiae as a microbial host to produce trans-cinnamic acid derivatives cinnamaldehyde, cinnamyl alcohol, and hydrocinnamyl alcohol, from externally added trans-cinnamic acid or de novo from glucose as a carbon source. We show that the desired products can be de novo synthesized in S. cerevisiae via the heterologous overexpression of the genes encoding phenylalanine ammonia lyase 2 from Arabidopsis thaliana (AtPAL2), aryl carboxylic acid reductase (acar) from Nocardia sp., and phosphopantetheinyl transferase (entD) from Escherichia coli, together with endogenous alcohol dehydrogenases. This study provides a proof of concept and a strain that can be further optimized for production of high-value aromatic compounds.

Increased availability of NADH in metabolically engineered baker's yeast improves transaminase-oxidoreductase coupled asymmetric whole-cell bioconversion.

BACKGROUND: Saccharomyces cerevisiae can be engineered to perform a multitude of different chemical reactions that are not programmed in its original genetic code. It has a large potential to function as whole-cell biocatalyst for one-pot multistep synthesis of various organic molecules, and it may thus serve as a powerful alternative or complement to traditional organic synthetic routes for new chemical entities (NCEs). However, although the selectivity in many cases is high, the catalytic activity is often low which results in low space-time-yields. In the case for NADH-dependent heterologous reductive reactions, a possible constraint is the availability of cytosolic NADH, which may be limited due to competition with native oxidative enzymes that act to maintain redox homeostasis. In this study, the effect of increasing the availability of cytosolic NADH on the catalytic activity of engineered yeast for transamination-reduction coupled asymmetric one-pot conversion was investigated. RESULTS: A series of active whole-cell biocatalysts were constructed by over-expressing the (S)-selective ω-transaminase (VAMT) from Capsicum chinense together with the NADH-dependent (S)-selective alcohol dehydrogenase (SADH) originating from Rhodococcus erythropolis in strains with or without deletion of glycerol-3-phosphate dehydrogenases 1 and 2 (GPD1 and GPD2). The yeast strains were evaluated as catalysts for simultaneous: (a) kinetic resolution of the racemic mixture to (R)-1-phenylethylamine, and (b) reduction of the produced acetophenone to (S)-1-phenylethanol. For the gpd1Δgpd2Δ strain, cell metabolism was effectively used for the supply of both amine acceptors and the co-factor pyridoxal-5'-phosphate (PLP) for the ω-transaminase, as well as for regenerating NADH for the reduction. In contrast, there was nearly no formation of (S)-1-phenylethanol when using the control strain with intact GPDs and over-expressing the VAMT-SADH coupling. It was found that a gpd1Δgpd2Δ strain over-expressing SADH had a 3-fold higher reduction rate and a 3-fold lower glucose requirement than the strain with intact GPDs over-expressing SADH. CONCLUSIONS: Overall the results demonstrate that the deletion of the GPD1 and GPD2 genes significantly increases activity of the whole-cell biocatalyst, and at the same time reduces the co-substrate demand in a process configuration where only yeast and sugar is added to drive the reactions, i.e. without addition of external co-factors or prosthetic groups.

Iron phthalocyanine on Cu(111): Coverage-dependent assembly and symmetry breaking, temperature-induced homocoupling, and modification of the adsorbate-surface interaction by annealing.

We have examined the geometric and electronic structures of iron phthalocyanine assemblies on a Cu(111) surface at different sub- to mono-layer coverages and the changes induced by thermal annealing at temperatures between 250 and 320 °C by scanning tunneling microscopy, x-ray photoelectron spectroscopy, and x-ray absorption spectroscopy. The symmetry breaking observed in scanning tunneling microscopy images is found to be coverage dependent and to persist upon annealing. Further, we find that annealing to temperatures between 300 and 320 °C leads to both desorption of iron phthalocyanine molecules from the surface and their agglomeration. We see clear evidence of temperature-induced homocoupling reactions of the iron phthalocyanine molecules following dehydrogenation of their isoindole rings, similar to what has been observed for related tetrapyrroles on transition metal surfaces. Finally, spectroscopy indicates a modified substrate-adsorbate interaction upon annealing with a shortened bond distance. This finding could potentially explain a changed reactivity of Cu-supported iron phthalocyanine in comparison to that of the pristine compound.

Correlation between stoichiometry and surface structure of the polar MgAl2O4(100) surface as a function of annealing temperature.

The correlation between surface structure, stoichiometry and atomic occupancy of the polar MgAl2O4(100) surface has been studied with an interplay of noncontact atomic force microscopy, X-ray photoelectron spectroscopy and surface X-ray diffraction under ultrahigh vacuum conditions. The Al/Mg ratio is found to significantly increase as the surface is sputtered and annealed in oxygen at intermediate temperatures ranging from 1073-1273 K. The Al excess is explained by the observed surface structure, where the formation of nanometer-sized pits and elongated patches with Al terminated step edges contribute to stabilizing the structure by compensating surface polarity. Surface X-ray diffraction reveals a reduced occupancy in the top two surface layers for both Mg, Al, and O and, moreover, vacancies are preferably located in octahedral sites, indicating that Al and Mg ions interchange sites. The excess of Al and high concentration of octahedral vacancies, very interestingly, indicates that the top few surface layers of the MgAl2O4(100) adopts a surface structure similar to that of a spinel-like transition Al2O3 film. However, after annealing at a high temperature of 1473 K, the Al/Mg ratio restores to its initial value, the occupancy of all elements increases, and the surface transforms into a well-defined structure with large flat terraces and straight step edges, indicating a restoration of the surface stoichiometry. It is proposed that the tetrahedral vacancies at these high temperatures are filled by Mg from the bulk, due to the increased mobility at high annealing temperatures.

Temperature-Dependent Selectivity and Detection of Hidden Carbon Deposition in Methane Oxidation.

Reaction products in heterogeneous catalysis can be detected either on the catalyst surface or in the gas phase after desorption. However, if atoms are dissolved in the catalyst bulk, then reaction channels can become hidden. This is the case if the dissolution rate of the deposits is faster than their formation rate. This might lead to the underestimation or even overlooking of reaction channels such as, e.g., carbon deposition during hydrocarbon oxidation reactions, which is problematic as carbon can have a significant influence on the catalytic activity. Here, we demonstrate how such hidden deposition channels can be uncovered by carefully measuring the product formation rates in the local gas phase just above the catalyst surface with time-resolved ambient pressure X-ray photoelectron spectroscopy. As a case study, we investigate methane oxidation on a polycrystalline Pd catalyst in an oxygen-lean environment at a few millibar pressure. By ramping the temperature between 350 and 525 °C, we follow the time evolution of the different reaction pathways. Only in the oxygen mass-transfer limit do we observe CO production, while our data suggests that carbon deposition also happens outside this limit.

2D Vanadium Sulfides: Synthesis, Atomic Structure Engineering, and Charge Density Waves.

Two ultimately thin vanadium-rich 2D materials based on VS2 are created via molecular beam epitaxy and investigated using scanning tunneling microscopy, X-ray photoemission spectroscopy, and density functional theory (DFT) calculations. The controlled synthesis of stoichiometric single-layer VS2 or either of the two vanadium-rich materials is achieved by varying the sample coverage and sulfur pressure during annealing. Through annealing of small stoichiometric single-layer VS2 islands without S pressure, S-vacancies spontaneously order in 1D arrays, giving rise to patterned adsorption. Via the comparison of DFT calculations with scanning tunneling microscopy data, the atomic structure of the S-depleted phase, with a stoichiometry of V4S7, is determined. By depositing larger amounts of vanadium and sulfur, which are subsequently annealed in a S-rich atmosphere, self-intercalated ultimately thin V5S8-derived layers are obtained, which host 2 × 2 V-layers between sheets of VS2. We provide atomic models for the thinnest V5S8-derived structures. Finally, we use scanning tunneling spectroscopy to investigate the charge density wave observed in the 2D V5S8-derived islands.

The new ambient-pressure X-ray photoelectron spectroscopy instrument at MAX-lab.

The new instrument for near-ambient-pressure X-ray photoelectron spectroscopy which has been installed at the MAX II ring of the Swedish synchrotron radiation facility MAX IV Laboratory in Lund is presented. The new instrument, which is based on a SPECS PHOIBOS 150 NAP analyser, is the first to feature the use of retractable and exchangeable high-pressure cells. This implies that clean vacuum conditions are retained in the instrument's analysis chamber and that it is possible to swiftly change between near-ambient and ultrahigh-vacuum conditions. In this way the instrument implements a direct link between ultrahigh-vacuum and in situ studies, and the entire pressure range from ultrahigh-vacuum to near-ambient conditions is available to the user. Measurements at pressures up to 10(-5) mbar are carried out in the ultrahigh-vacuum analysis chamber, while measurements at higher pressures are performed in the high-pressure cell. The installation of a mass spectrometer on the exhaust line of the reaction cell offers the users the additional dimension of simultaneous reaction data monitoring. Moreover, the chosen design approach allows the use of dedicated cells for different sample environments, rendering the Swedish ambient-pressure X-ray photoelectron spectroscopy instrument a highly versatile and flexible tool.

Water Chemistry beneath Graphene: Condensation of a Dense OH-H2O Phase under Graphene.

Room temperature oxygen hydrogenation below graphene flakes supported by Ir(111) is investigated through a combination of X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations using an evolutionary search algorithm. We demonstrate how the graphene cover and its doping level can be used to trap and characterize dense mixed O-OH-H2O phases that otherwise would not exist. Our study of these graphene-stabilized phases and their response to oxygen or hydrogen exposure reveals that additional oxygen can be dissolved into them at room temperature creating mixed O-OH-H2O phases with an increased areal coverage underneath graphene. In contrast, additional hydrogen exposure converts the mixed O-OH-H2O phases back to pure OH-H2O with a reduced areal coverage underneath graphene.

Graphene as an Adsorption Template for Studying Double Bond Activation in Catalysis.

Hydrogenated graphene (H-Gr) is an extensively studied system not only because of its capabilities as a simplified model system for hydrocarbon chemistry but also because hydrogenation is a compelling method for Gr functionalization. However, knowledge of how H-Gr interacts with molecules at higher pressures and ambient conditions is lacking. Here we present experimental and theoretical evidence that room temperature O2 exposure at millibar pressures leads to preferential removal of H dimers on H-functionalized graphene, leaving H clusters on the surface. Our density functional theory (DFT) analysis shows that the removal of H dimers is the result of water or hydrogen peroxide formation. For water formation, we show that the two H atoms in the dimer motif attack one end of the physisorbed O2 molecule. Moreover, by comparing the reaction pathways in a vacuum with the ones on free-standing graphene and on the graphene/Ir(111) system, we find that the main role of graphene is to arrange the H atoms in geometrical positions, which facilitates the activation of the O=O double bond.

CO-induced embedding of Pt adatoms in a partially reduced FeO(x) film on Pt(111).

The reduction of a single-layer FeO film grown on Pt(111) by CO at elevated pressures and temperatures has been studied through an interplay of scanning tunneling microscopy, ambient-pressure X-ray photoelectron spectroscopy, and density functional theory calculations. Exposure of the FeO thin film to CO at pressures between 1 and 30 Torr and temperatures between 500 and 530 K leads to formation of a honeycomb-structured Fe(3)O(2) film with hollow sites occupied by single Pt atoms extracted from the substrate surface. The formation of these adatoms is driven by an increase in CO adsorption energy. In addition, the structure incorporates undercoordinated Fe centers, which are proposed to have substantial effects on the catalytic properties of the surface.

Stable cation inversion at the MgAl2O4(100) surface.

From an interplay of atom-resolved noncontact atomic force microscopy, surface x-ray diffraction experiments, and density functional theory calculations, we reveal the detailed atomic-scale structure of the (100) surface of an insulating ternary metal oxide, MgAl2O4 (spinel). We surprisingly find that the MgAl2O4(100) surface is terminated by an Al and O-rich structure with a thermodynamically favored amount of Al atoms interchanged with Mg. This finding implies that so-called Mg-Al antisites, which are defects in the bulk of MgAl2O4, become a thermodynamically stable and integral part of the surface.

Modification of the size of supported clusters by coadsorption of an organic compound: gold and L-cysteine on rutile TiO2(110).

Using X-ray photoelectron spectroscopy we studied the coadsorption of the amino acid L-cysteine and gold on a rutile TiO(2)(110) surface under ultrahigh vacuum conditions. Irrespective of the deposition order, i.e., irrespective of whether L-cysteine or gold is deposited first, the primary interaction between L-cysteine and the gold clusters formed at the surface takes place through the deprotonated thiol group of the molecule. The deposition order, however, has a profound influence on the size of the gold clusters as well as their location on the surface. If L-cysteine is deposited first the clusters are smaller by a factor two to three compared to gold deposited onto the pristine TiO(2)(110) surface and then covered by L-cysteine. Further, in the former case the clusters cover the molecules and thus form the outermost layer of the sample. We also find that above a minimum gold cluster size the gold cluster/L-cysteine bond is stronger than the L-cysteine/surface bridging oxygen vacancy bond, which, in turn, is stronger than the gold cluster/vacancy bond.

Ammonia adsorption on iron phthalocyanine on Au(111): influence on adsorbate-substrate coupling and molecular spin.

The adsorption of ammonia on Au(111)-supported monolayers of iron phthalocyanine has been investigated by x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory calculations. The ammonia-induced changes of the x-ray photoemission lines show that a dative bond is formed between ammonia and the iron center of the phthalocyanine molecules, and that the local spin on the iron atom is quenched. This is confirmed by density functional theory, which also shows that the bond between the iron center of the metalorganic complex and the Au(111) substrate is weakened upon adsorption of ammonia. The experimental results further show that additional adsorption sites exist for ammonia on the iron phthalocyanine monolayer.

Adsorption of ammonia on multilayer iron phthalocyanine.

The adsorption of ammonia on multilayers of well-ordered, flat-lying iron phthalocyanine (FePc) molecules on a Au(111) support was investigated by x-ray photoelectron spectroscopy. We find that the electron-donating ammonia molecules coordinate to the metal centers of iron phthlalocyanine. The coordination of ammonia induces changes of the electronic structure of the iron phthalocyanine layer, which, in particular, lead to a modification of the FePc valence electron spin.

Gas Pulse-X-Ray Probe Ambient Pressure Photoelectron Spectroscopy with Submillisecond Time Resolution.

A setup capable of conducting gas pulse-X-ray probe ambient pressure photoelectron spectroscopy with high time resolution is presented. The setup makes use of a fast valve that creates gas pulses with an internal pressure in the mbar range and a rising edge of few hundreds of microseconds. A gated detector based on a fast camera is synchronized with the valve operation to measure X-ray photoemission spectra with up to 20 µs time resolution. The setup is characterized in several experiments in which the N2 gas is pulsed either into vacuum or a constant flow of another gas. The observed width of the pulse rising edge is 80 µs, and the maximum internal pulse pressure is ∼1 mbar. The CO oxidation reaction over Pt (111) was used to demonstrate the capability of the setup to correlate the gas phase composition with that of the surface during transient supply of CO gas into an O2 stream. Thus, formation of both chemisorbed and oxide oxygen species was observed prior to CO gas perturbation. Also, the data indicated that both the Langmuir-Hinshelwood and Mars-van-Krevelen mechanisms play an important role in the oxidation of carbon monoxide under ambient conditions.

Stroboscopic operando spectroscopy of the dynamics in heterogeneous catalysis by event-averaging.

Heterogeneous catalyst surfaces are dynamic entities that respond rapidly to changes in their local gas environment, and the dynamics of the response is a decisive factor for the catalysts' action and activity. Few probes are able to map catalyst structure and local gas environment simultaneously under reaction conditions at the timescales of the dynamic changes. Here we use the CO oxidation reaction and a Pd(100) model catalyst to demonstrate how such studies can be performed by time-resolved ambient pressure photoelectron spectroscopy. Central elements of the method are cyclic gas pulsing and software-based event-averaging by image recognition of spectral features. A key finding is that at 3.2 mbar total pressure a metallic, predominantly CO-covered metallic surface turns highly active for a few seconds once the O2:CO ratio becomes high enough to lift the CO poisoning effect before mass transport limitations triggers formation of a √5 oxide.