High-resolution K-shell photoabsorption measurements of simple molecules

Blade Coating Poly(3-hexylthiophene): The Importance of Molecular Weight on Thin-Film Microstructures

Poly(3-hexylthiophene) is one of the most prevalent and promising conjugated polymers for use in organic electronics. However, the deposition of this material in thin films is highly dependent on the process, such as blade coating versus spin coating and material properties such as molecular weight. Typically, large polymer dispersity makes it difficult to isolate the effect of molecular weight without considering a distribution. In this study, we characterize oligothiophenes of exactly 8, 11, and 14 repeat units, which were deposited into thin films by varying blade coating conditions and postdeposition annealing. From synchrotron-based grazing incidence wide-angle X-ray scattering (GIWAXS), scanning transmission X-ray microscopy (STXM) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS), Raman microscopy, optical microscopy, and X-ray diffraction (XRD), it was suggested that higher molecular weight polymers exhibit a fast-forming crystalline polymorph (form-1) while low molecular weight polymers exhibit a slow forming polymorph (form-2) with large domain boundaries. As molecular weight is gradually increased, the polymorph formed transitions from form-1 and form-2, where 11 repeat unit oligomers display both polymorphs. We also found that processing conditions can increase the formation of the form-2 polymorph. We also report improved organic thin film transistor (OTFT) performance when form-1 is present. Overall, oligothiophene polymorph formation is highly dependent on the molecular weight and processing conditions, providing critical insight into the importance of polymer weight control in the development of thin-film electronics based on conjugated polymers.

Variational Quantum Computation of Molecular Linear Response Properties on a Superconducting Quantum Processor

Simulating response properties of molecules is crucial for interpreting experimental spectroscopies and accelerating materials design. However, it remains a long-standing computational challenge for electronic structure methods on classical computers. While quantum computers hold the promise of solving this problem more efficiently in the long run, existing quantum algorithms requiring deep quantum circuits are infeasible for near-term noisy quantum processors. Herein, we introduce a pragmatic variational quantum response (VQR) algorithm for response properties, which circumvents the need for deep quantum circuits. Using this algorithm, we report the first simulation of linear response properties of molecules including dynamic polarizabilities and absorption spectra on a superconducting quantum processor. Our results indicate that a large class of important dynamical properties, such as Green's functions, are within the reach of near-term quantum hardware using this algorithm in combination with suitable error mitigation techniques.

All-Electron BSE@GW Method for K-Edge Core Electron Excitation Energies

We present an accurate computational approach to calculate absolute K-edge core electron excitation energies as measured by X-ray absorption spectroscopy. Our approach employs an all-electron Bethe-Salpeter equation (BSE) formalism based on GW quasiparticle energies (BSE@GW) using numeric atom-centered orbitals (NAOs). The BSE@GW method has become an increasingly popular method for the computation of neutral valence excitation energies of molecules. However, it was so far not applied to molecular K-edge excitation energies. We discuss the influence of different numerical approximations on the BSE@GW calculation and employ in our final setup (i) exact numeric algorithms for the frequency integration of the GW self-energy, (ii) G₀W₀ and BSE starting points with ∼50% of exact exchange, (iii) the Tamm-Dancoff approximation and (iv) relativistic corrections. We study the basis set dependence and convergence with common Gaussian-type orbital and NAO basis sets. We identify the importance of additional spatially confined basis functions as well as of diffuse augmenting basis functions. The accuracy of our BSE@GW method is assessed for a benchmark set of small organic molecules, previously used for benchmarking the equation-of-motion coupled cluster method [Peng et al., J. Chem. Theory Comput., 2015, 11, 4146], as well as the medium-sized dibenzothiophene (DBT) molecule. Our BSE@GW results for absolute excitation energies are in excellent agreement with the experiment, with a mean average error of only 0.63 eV for the benchmark set and with errors <1 eV for the DBT molecule.

Theoretical Calculation of Core-Excited States along Dissociative Pathways beyond Second-Order Perturbation Theory

We extend the multireference driven similarity renormalization (MR-DSRG) method to compute core-excited states by combining it with a GASSCF treatment of orbital relaxation and static electron correlation effects. We consider MR-DSRG treatments of dynamical correlation truncated at the level of perturbation theory (DSRG-MRPT2/3) and iterative linearized approximations with one- and two-body operators [MR-LDSRG(2)] in combination with a spin-free exact-two-component (X2C) one-electron treatment of scalar relativistic effects. This approach is calibrated and tested on a series of 16 core-excited states of five closed- and open-shell diatomic molecules containing first-row elements (C, N, and O). All GASSCF-MR-DSRG theories show excellent agreement with experimental adiabatic transitions energies, with mean absolute errors ranging between 0.17 and 0.35 eV, even for the challenging partially doubly excited states of the N₂⁺ molecule. The vibrational structure of all these transitions, obtained from using a full potential energy scan, shows a mean absolute error as low as 25 meV for DSRG-MRPT2 and 12/13 meV for DSRG-MRPT3 and MR-LDSRG(2). We generally find that a treatment of dynamical correlation that goes beyond the second-order level in perturbation theory improves the accuracy of the potential energy surface, especially in the bond-dissociation region.

Analysis of Cr(VI) Bioremediation by Citrobacter freundii Using Synchrotron Soft X-ray Scanning Transmission X-ray Microscopy

Scanning transmission X-ray microscopy (STXM) was utilized for analysing the bioremediation of Cr(VI) by Citrobacter freundii, a species of gram-negative bacteria. The biosorption and bioreduction processes were analysed by the chemical mapping of cells biosorbed at different concentrations of Cr(VI). STXM spectromicroscopy images were recorded at O K-edge and Cr L-edge. A thorough analysis of the X-ray absorption features corresponding to different oxidation states of Cr in the biosorbed cell indicated the coexistence of Cr(III) and Cr(VI) at higher concentrations. This signifies the presence of partially reduced Cr(VI) in addition to biosorbed Cr(VI). In addition, the Cr(III) signal is intense compared with Cr(VI) at different regions of the cell indicating excess of reduced Cr. Speciation of adsorbed Cr was analysed for the spectral features of biosorbed cell and comparison with Cr standards. Analysis of absorption onset, L3/L2 ratio and absorption fine structure concludes that adsorbed Cr is predominantly present as Cr(III) hydroxide or oxyhydroxide. The evolution of absorption features in the duration of biosorption process was also studied. These time lapse studies depict the gradual decrement in Cr(VI) signal as biosorption proceeds. A strong evidence of interaction of Cr with the cell material was also observed. The obtained results provide insights into the biosorption process and chemical speciation of Cr on the cells.

Internal molecular conformation of organic glasses: A NEXAFS study

The origin of the exceptional stability of molecular glasses grown by physical vapor deposition (PVD) is not well understood. Differences in glass density have been correlated with thermodynamic stability for thin films of N,N'-Bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD) grown by PVD at specific substrate temperatures below the glass transition temperature. However, the relationship between the internal conformation of glass molecules and the thermodynamic properties of molecular glasses is not well studied. We use carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectroscopy to examine different TPD sample preparations in which differences in the thermodynamic stability of the glass are known. Density functional theory simulations of the NEXAFS spectra of TPD allow us to attribute spectroscopic differences to changes in the internal conformation of the TPD molecule and relate this conformation to the stability of the TPD glass. This provides a direct experimental measurement of the internal conformation of molecules forming an organic glass.

Calculating absorption dose when X-ray irradiation modifies material quantity and chemistry

X-ray absorption is a sensitive and versatile tool for chemical speciation. However, when high doses are used, the absorbed energy can change the composition, amount and structure of the native material, thereby changing the aspects of the absorption process on which speciation is based. How can one calculate the dose when X-ray irradiation affects the chemistry and changes the amount of the material? This paper presents an assumption-free approach which can retrieve from the experimental data all dose-sensitive parameters - absorption coefficients, composition (elemental molecular units), material densities - which can then be used to calculate accurate doses as a function of irradiation. This approach is illustrated using X-ray damage to a solid film of a perfluorosulfonic acid fluoropolymer in a scanning transmission soft X-ray microscope. This new approach is compared against existing dose models which calculate the dose by making simplifying assumptions regarding the material quantity, density and chemistry. While the detailed measurements used in this approach go beyond typical methods to experimental analytical X-ray absorption, they provide a more accurate quantitation of radiation dose, and help to understand mechanisms of radiation damage.

New and Efficient Equation-of-Motion Coupled-Cluster Framework for Core-Excited and Core-Ionized States

We present a fully analytical implementation of the core-valence separation (CVS) scheme for the equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method for calculations of core-level states. Inspired by the CVS idea as originally formulated by Cederbaum, Domcke, and Schirmer, pure valence excitations are excluded from the EOM target space and the frozen-core approximation is imposed on the reference-state amplitudes and multipliers. This yields an efficient, robust, practical, and numerically balanced EOM-CCSD framework for calculations of excitation and ionization energies as well as state and transition properties (e.g., spectral intensities, natural transition, and Dyson orbitals) from both the ground and excited states. The errors in absolute excitation/ionization energies relative to the experimental reference data are on the order of 0.2-3.0 eV, depending on the K-edge considered and on the basis set used, and the shifts are systematic for each edge. Compared to a previously proposed CVS scheme where CVS was applied as a posteriori projection only during the solution of the EOM eigenvalue equations, the new scheme is computationally cheaper. It also achieves better cancellation of errors, yielding similar spectral profiles but with absolute core excitation and ionization energies that are systematically closer to the corresponding experimental data. Among the presented results are calculations of transient-state X-ray absorption spectra, relevant for interpretation of UV-pump/X-ray probe experiments.

Spectral Distribution of Oscillator Strength for Core-to-Valence Transitions probed by using X-ray Absorption and Total Electron Yield Modes

Changes in spectral distribution of oscillator strength for core-to-valence transitions probed by X-ray absorption and total electron yield (TEY) modes are studied in more detail. The quantitative analysis of their redistribution in TEY due to the saturation effect is performed by applying the model M ˜ $\tilde M$ -function method suggested by Flesch et al. J. Chem. Phys. 138 (2013) 144302. The model M ˜ $\tilde M$ -function method is generalized to account for the saturation-induced distortion of the line shape of the transitions embedded into the core ionization continua and located below them. It is shown that TEY measurements produce essential changes not only in the relative intensity of the transitions but also shift upward the transition energy, broaden the Lorentzian and Gaussian widths and enhance the line asymmetry. The Gaussian width of the TEY signal undergoes the most substantial broadening though the Lorentzian width increases significantly too. The saturation-induced distortion of the line shapes is not negligible even if the well-known escape-to-penetration condition is valid.

Introduction of soft X-ray spectromicroscopy as an advanced technique for plant biopolymers research

Soft X-ray absorption spectroscopy coupled with nano-scale microscopy has been widely used in material science, environmental science, and physical sciences. In this work, the advantages of soft X-ray absorption spectromicroscopy for plant biopolymer research were demonstrated by determining the chemical sensitivity of the technique to identify common plant biopolymers and to map the distributions of biopolymers in plant samples. The chemical sensitivity of soft X-ray spectroscopy to study biopolymers was determined by recording the spectra of common plant biopolymers using soft X-ray and Fourier Transform mid Infrared (FT-IR) spectroscopy techniques. The soft X-ray spectra of lignin, cellulose, and polygalacturonic acid have distinct spectral features. However, there were no distinct differences between cellulose and hemicellulose spectra. Mid infrared spectra of all biopolymers were unique and there were differences between the spectra of water soluble and insoluble xylans. The advantage of nano-scale spatial resolution exploited using soft X-ray spectromicroscopy for plant biopolymer research was demonstrated by mapping plant cell wall biopolymers in a lentil stem section and compared with the FT-IR spectromicroscopy data from the same sample. The soft X-ray spectromicroscopy enables mapping of biopolymers at the sub-cellular (~30 nm) resolution whereas, the limited spatial resolution in the micron scale range in the FT-IR spectromicroscopy made it difficult to identify the localized distribution of biopolymers. The advantages and limitations of soft X-ray and FT-IR spectromicroscopy techniques for biopolymer research are also discussed.

Thermodynamic and spectroscopic properties of oxygen on silver under an oxygen atmosphere

Comparing experimental and theoretical XPS and XANES suggest that unreconstructed atomic oxygen is not present on the silver surface at oxygen chemical potentials relevant for epoxidation.

Dissociation of core-valence doubly excited states in NO followed by atomic Auger decay

The decay processes of core-valence doubly excited states near the N K edge of NO have been studied using electron spectroscopy. Electron yields measured as a function of photon energy and kinetic energy enable the clear identification of atomic Auger lines associated with the dissociation of doubly excited states. The atomic Auger lines exhibit Doppler profiles, allowing the entire reaction scheme of such dissociation processes to be determined.

Carbon K-edge spectra of carbonate minerals

Carbon K-edge X-ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280-320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K-edge and Ca L-edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X-ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K-edge, exhibited significantly different spectra at the Ca L-edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.

Complementary effects of multi-protein components on biomineralization in vitro

The extracellular matrix (ECM) is composed of mixed protein fibers whose precise composition affects biomineralization. New methods are needed to probe the interactions of these proteins with calcium phosphate mineral and with each other. Here we follow calcium phosphate mineralization on protein fibers self-assembled in vitro from solutions of fibronectin, elastin and their mixture. We probe the surface morphology and mechanical properties of the protein fibers during the early stages. The development of mineral crystals on the protein matrices is also investigated. In physiological mineralization solution, the elastic modulus of the fibers in the fibronectin-elastin mixture increases to a greater extent than that of the fibers from either pure protein. In the presence of fibronectin, longer exposure in the mineral solution leads to the formation of amorphous calcium phosphate particles templated along the self-assembled fibers, while elastin fibers only collect calcium without any mineral observed during early stage. TEM images confirm that small needle-shape crystals are confined inside elastin fibers which suppress the release of mineral outside the fibers during late stage, while hydroxyapatite crystals form when fibronectin is present. These results demonstrate complementary actions of the two ECM proteins fibronectin and elastin to collect cations and template mineral, respectively.

PolLux: a new facility for soft x-ray spectromicroscopy at the Swiss Light Source

We report on the successful installation and operation of a scanning transmission x-ray microspectroscope (STXM) at the PolLux facility at the Swiss Light Source. This integration of an advanced STXM with improved sample handling capabilities and a novel beamline provides unique capabilities. PolLux uses linearly or circularly polarized x-rays from a bending magnet with an extended photon energy range (200-1400 eV). It is therefore well suited to determine a sample's quantitative chemical composition, molecular orientation, or thickness of organic as well as condensed matter materials. The local magnetic state of magnetic thin films is accessible through fast helicity switching by steering the electron beam off axis through the bending magnet. Ex vacuo girder movers allow fast and highly reproducible (<1 microm) alignment of the instrument with respect to the photon beam. The present spatial resolution is approximately 20 nm, limited by the zone plates utilized. The instrument has the stability and positional resolution to operate with much higher resolution optics as it becomes available. In addition to characterization experiments, we present several typical examples from materials research and environmental science to exemplify the capabilities.

X-ray absorption and resonant Auger spectroscopy of O2 in the vicinity of the O 1s-->sigma* resonance: experiment and theory

We report on an experimental and theoretical investigation of x-ray absorption and resonant Auger electron spectra of gas phase O(2) recorded in the vicinity of the O 1s-->sigma(*) excitation region. Our investigation shows that core excitation takes place in a region with multiple crossings of potential energy curves of the excited states. We find a complete breakdown of the diabatic picture for this part of the x-ray absorption spectrum, which allows us to assign an hitherto unexplained fine structure in this spectral region. The experimental Auger data reveal an extended vibrational progression, for the outermost singly ionized X (2)Pi(g) final state, which exhibits strong changes in spectral shape within a short range of photon energy detuning (0 eV>Omega>-0.7 eV). To explain the experimental resonant Auger electron spectra, we use a mixed adiabatic/diabatic picture selecting crossing points according to the strength of the electronic coupling. Reasonable agreement is found between experiment and theory even though the nonadiabatic couplings are neglected. The resonant Auger electron scattering, which is essentially due to decay from dissociative core-excited states, is accompanied by strong lifetime-vibrational and intermediate electronic state interferences as well as an interference with the direct photoionization channel. The overall agreement between the experimental Auger spectra and the calculated spectra supports the mixed diabatic/adiabatic picture.

X-ray microscopy study of chromonic liquid crystal dry film texture

Soft x-ray spectromicroscopy has been used to investigate the degree of the molecular alignment of sulfonated benzo[de]benzo[4.5]imidazo[2,1-a]isoquinoline[7,1], a lyotropic chromonic liquid crystal (LCLC). LCLC thin films cast from concentrated aqua solution (20%wt.) , aligned by shear flow and dried, show strong linear dichroism in their C-, N-, O-, S- K edge near edge x-ray spectra (NEXAFS). The carbon K edge has been used for quantitative evaluation of the orientational texture of the films at a submicron spatial scale. This has verified there is predominantly in-plane alignment of the LC director. To highlight the role of hydrophobic-hydrophilic interactions, two stereoisomers of the same dye has been synthesized with different positioning of terminal sulfonate groups, in the form of a mixture of isomers with sulfonate groups in 2,10 and 2,11 positions (Y104 compound) and in a 5,10-disulfo arrangement (Y105). Both compounds develop characteristic herringbone-type texture with similar domain sizes. Polarized optical microscopy and higher resolution x-ray microscopy show sinusoidal-like undulations of the molecular director, with occasional crisscross appearance. Such behavior is found to be consistent with earlier observation of striations, characteristic of the columnar phase. The drastic difference in the degree of undulation ( +/-15 degrees in Y104 and +/-7 degrees in Y105 films) and long period of undulation (approaching the film thickness) requires further analysis. It was also found that the degree of in-plane order within domains changes from 0.8 for Y104 to >0.9 in Y105 films.

Hybrid exchange-correlation functional for core, valence, and Rydberg excitations: core-valence-Rydberg B3LYP

The core-valence-Rydberg Becke's three-parameter exchange (B3)+Lee-Yang-Parr (LYP) correlation functional (CVR-B3LYP) is proposed as a means to improve descriptions of Rydberg excitations of core-valence B3LYP (CV-B3LYP). CV-B3LYP describes excitations from both core and occupied valence orbitals to unoccupied valence orbitals with high accuracy but fails to describe those to Rydberg orbitals. CVR-B3LYP, which adopts the appropriate portions of Hartree-Fock exchange for unoccupied valence and Rydberg regions separately, overcomes the disadvantage of CV-B3LYP. Numerical assessment confirms that time-dependent density functional theory calculations with CVR-B3LYP succeed in describing not only core excitations but also Rydberg excitations with reasonable accuracy.

Oxygenated Interface on Biomass Burn Tar Balls Determined by Single Particle Scanning Transmission X-ray Microscopy

Carbonaceous particles originating from biomass burning can account for a large fraction of organic aerosols in a local environment. Presently, their composition, physical and chemical properties, as well as their environmental effects are largely unknown. Tar balls, a distinct type of highly spherical carbonaceous biomass burn particles, have been observed in a number of field campaigns. The Yosemite Aerosol Characterization Study that took place in summer 2002 occurred during an active fire season in the western United States; tar balls collected during this field campaign are described in this article. Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure spectroscopy are used to determine the shape, structure, and size-dependent chemical composition of approximately 150 individual spherical particles ranging in size from 0.15 to 1.2 mum. The elemental composition of tar balls is approximately 55% atomic carbon and approximately 45% atomic oxygen. Oxygen is present primarily as carboxylic carbonyls and oxygen-substituted alkyl (O-alkyl-C) functional groups, followed by moderate amounts of ketonic carbonyls. The observed chemical composition, density, and carbon functional groups are distinctly different from soot or black carbon and more closely resemble high molecular weight polymeric humic-like substances, which could account for their reported optical properties. A detailed examination of the carboxylic carbonyl and O-alkyl-C functional groups as a function of particle size reveals a thin oxygenated interface layer. The high oxygen content, as well as the presence of water-soluble carboxylic carbonyl groups, could account for the reported hygroscopic properties of tar balls. The presence of the oxygenated layer is attributed to atmospheric processing of biomass burn particles.

Effect of chain length and substrate temperature on the growth and morphology of n-alkane thin films

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and microscopy has been used to study the orientational morphology of thin films of the linear alkanes n-C36H74 and n-C60H122, prepared by vacuum deposition onto NaCl (001) surfaces at ambient and elevated substrate temperatures. The orientational morphology, specifically, the nature of domains with lateral and normal orientation, is explored as a function of the chain length and the substrate temperature. It is found that the longer n-C60H122 molecules are laterally oriented on the substrate surface within the investigated substrate temperatures but that the morphology of these thin films varies with substrate temperature. The shorter n-C36H74 molecules are partially laterally oriented at low substrate temperature and are completely normally oriented at high substrate temperature. The relative magnitude of "side-by-side" and "end-to-end" intermolecular interactions leads to the formation of highly ordered alkane structures with a high aspect ratio. The formation of complex, nanoscale orientational morphologies are rationalized by considering kinetic and thermodynamic effects, in particular, the relative enthalpic and entropic contributions to the free energy associated with the different molecular orientations.