The C 1s NEXAFS spectrum of benzene below threshold: Rydberg or valence character of the unoccupied σ-type orbitals

Structures of Gas-Phase Hydrated Phosphotyrosine Revealed by Soft X-ray Action Spectroscopy

Gas-phase near-edge X-ray absorption mass spectrometry (NEXAMS) was employed at the carbon and oxygen K-edges to probe the influence of a single water molecule on the protonated phosphotyrosine molecule. The results of the photodissociation experiments revealed that the water molecule forms two bonds, with the phosphate group and another chemical group. By comparing the NEXAMS spectra at the carbon and oxygen K-edges with density functional theory calculations, we attributed the electronic transitions responsible for the observed resonances, especially the transitions due to the presence of the water molecule. We showed that the water molecule leads to a specific spectral feature in the partial ion yield of hydrated fragments at 536.4 eV. Moreover, comparing the NEXAMS spectra with the calculated structures allowed us to identify three possible structures for singly hydrated phosphotyrosine that agree with the observed fragmentation and resonances.

Signatures of the Bromine Atom and Open-Shell Spin Coupling in the X-ray Spectrum of the Bromobenzene Cation

Tabletop X-ray spectroscopy measurements at the carbon K-edge complemented by ab initio calculations are used to investigate the influence of the bromine atom on the carbon core-valence transitions in the bromobenzene cation (BrBz⁺). The electronic ground state of the cation is prepared by resonance-enhanced two-photon ionization of neutral bromobenzene (BrBz) and probed by X-rays produced by high-harmonic generation (HHG). Replacing one of the hydrogen atoms in benzene with a bromine atom shifts the transition from the 1s_C* orbital of the carbon atom (C*) bonded to bromine by ∼1 eV to higher energy in the X-ray spectrum compared to the other carbon atoms (C). Moreover, in BrBz⁺, the X-ray spectrum is dominated by two relatively intense transitions, 1s_C→π* and 1s_C*→σ*(C*-Br), where the second transition is enhanced relative to the neutral BrBz. In addition, a doublet peak shape for these two transitions is observed in the experiment. The 1s_C→π* doublet peak shape arises due to the spin coupling of the unpaired electron in the partially vacant π orbital (from ionization) with the two other unpaired electrons resulting from the transition from the 1s_C core orbital to the fully vacant π* orbitals. The 1s_C*→σ* doublet peak shape results from several transitions involving σ* and vibrational C*-Br mode activations following the UV ionization, which demonstrates the impact of the C*-Br bond length on the core-valence transition as well as on the relaxation geometry of BrBz⁺.

Density functionals for core excitations

The core excitation energies and related principal ionization energies are obtained for selected molecules using several density functionals and compared with benchmark equation-of-motion coupled cluster (EOM-CC) results. Both time-dependent and time-independent formulations of excitation spectra in the time-dependent density functional theory and the EOM-CC are employed to obtain excited states that are not always easily accessible with the time-independent method. Among those functionals, we find that the QTP(00) functional, which is only parameterized to reproduce the five IPs of water, provides excellent core IPs and core excitation energies, consistently yielding better excitation and ionization energies. We show that orbital eigenvalues of KS density functional theory play an important role in determining the accuracy of the excitation and photoelectron spectra.

X-ray Spectroscopy Fingerprints of Pristine and Functionalized Graphene

In this work, we demonstrate how to identify and characterize the atomic structure of pristine and functionalized graphene materials from a combination of computational simulation of X-ray spectra, on the one hand, and computer-aided interpretation of experimental spectra, on the other. Despite the enormous scientific and industrial interest, the precise structure of these 2D materials remains under debate. As we show in this study, a wide range of model structures from pristine to heavily oxidized graphene can be studied and understood with the same approach. We move systematically from pristine to highly oxidized and defective computational models, and we compare the simulation results with experimental data. Comparison with experiments is valuable also the other way around; this method allows us to verify that the simulated models are close to the real samples, which in turn makes simulated structures amenable to several computational experiments. Our results provide ab initio semiquantitative information and a new platform for extended insight into the structure and chemical composition of graphene-based materials.

The nuts and bolts of core-hole constrainedab initiosimulation forK-shell x-ray photoemission and absorption spectra

X-ray photoemission (XPS) and near edge x-ray absorption fine structure (NEXAFS) spectroscopy play an important role in investigating the structure and electronic structure of materials and surfaces.Ab initiosimulations provide crucial support for the interpretation of complex spectra containing overlapping signatures. Approximate core-hole simulation methods based on density functional theory (DFT) such as the delta-self-consistent-field (ΔSCF) method or the transition potential (TP) method are widely used to predictK-shell XPS and NEXAFS signatures of organic molecules, inorganic materials and metal-organic interfaces at reliable accuracy and affordable computational cost. We present the numerical and technical details of our variants of the ΔSCF and TP method (coined ΔIP-TP) to simulate XPS and NEXAFS transitions. Using exemplary molecules in gas-phase, in bulk crystals, and at metal-organic interfaces, we systematically assess how practical simulation choices affect the stability and accuracy of simulations. These include the choice of exchange-correlation functional, basis set, the method of core-hole localization, and the use of periodic boundary conditions (PBC). We particularly focus on the choice of aperiodic or periodic description of systems and how spurious charge effects in periodic calculations affect the simulation outcomes. For the benefit of practitioners in the field, we discuss sensible default choices, limitations of the methods, and future prospects.

Table-Top X-ray Spectroscopy of Benzene Radical Cation

Ultrafast table-top X-ray spectroscopy at the carbon K-edge is used to measure the X-ray spectral features of benzene radical cations (Bz⁺). The ground state of the cation is prepared selectively by two-photon ionization of neutral benzene, and the X-ray spectra are probed at early times after the ionization by transient absorption using X-rays produced by high harmonic generation (HHG). Bz⁺ is well-known to undergo Jahn-Teller distortion, leading to a lower symmetry and splitting of the π orbitals. Comparison of the X-ray absorption spectra of the neutral and the cation reveals a splitting of the two degenerate π* orbitals as well as an appearance of a new peak due to excitation to the partially occupied π-subshell. The π* orbital splitting of the cation, elucidated on the basis of high-level calculations in a companion theoretical paper [Vidal et al. J. Phys. Chem. A. http://dx.doi.org/10.1021/acs.jpca.0c08732], is discovered to be due to both the symmetry distortion and even more dominant spin coupling of the unpaired electron in the partially vacant π orbital (from ionization) with the unpaired electrons resulting from the transition from the 1s_C core orbital to the fully vacant π* orbitals.

Interplay of Open-Shell Spin-Coupling and Jahn-Teller Distortion in Benzene Radical Cation Probed by X-ray Spectroscopy

We report a theoretical investigation and elucidation of the X-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization and the measurement of the carbon K-edge spectra of both species using a table-top high-harmonic generation source are described in the companion experimental paper [Epshtein, M.; et al. J. Phys. Chem. A http://dx.doi.org/10.1021/acs.jpca.0c08736]. We show that the 1s_C → π transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence of the unpaired (spectator) electron in the π-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1s_C → π* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation. The prominent split structure of the 1s_C → π* band of the cation is attributed to the interplay between the coupling of the core → π* excitation with the unpaired electron in the π-subshell and the Jahn-Teller distortion. The calculations attribute most of the splitting (∼1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and we estimate the additional splitting due to structural relaxation to be around ∼0.1-0.2 eV. These results suggest that X-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Teller effect in the benzene cation.

A simple molecular orbital picture of RIXS distilled from many-body damped response theory

Ab initio calculations of resonant inelastic x-ray scattering (RIXS) often rely on damped response theory, which prevents the divergence of response solutions in the resonant regime. Within the damped response theory formalism, RIXS moments are expressed as the sum over all electronic states of the system [sum-over-states (SOS) expressions]. By invoking resonance arguments, this expression can be reduced to a few terms, an approximation commonly exploited for the interpretation of computed cross sections. We present an alternative approach: a rigorous formalism for deriving a simple molecular orbital picture of the RIXS process from many-body calculations using the damped response theory. In practical implementations, the SOS expressions of RIXS moments are recast in terms of matrix elements between the zero-order wave functions and first-order frequency-dependent response wave functions of the initial and final states such that the RIXS moments can be evaluated using complex response one-particle transition density matrices (1PTDMs). Visualization of these 1PTDMs connects the RIXS process with the changes in electronic density. We demonstrate that the real and imaginary components of the response 1PTDMs can be interpreted as contributions of the undamped off-resonance and damped near-resonance SOS terms, respectively. By analyzing these 1PTDMs in terms of natural transition orbitals, we derive a rigorous, black-box mapping of the RIXS process into a molecular orbital picture. We illustrate the utility of the new tool by analyzing RIXS transitions in the OH radical, benzene, para-nitroaniline, and 4-amino-4'-nitrostilbene. These examples highlight the significance of both the near-resonance and off-resonance channels.

Surface chemistry of 2,3-dibromosubstituted norbornadiene/quadricyclane as molecular solar thermal energy storage system on Ni(111)

Dwindling fossil fuels force humanity to search for new energy production routes. Besides energy generation, its storage is a crucial aspect. One promising approach is to store energy from the sun chemically in strained organic molecules, so-called molecular solar thermal (MOST) systems, which can release the stored energy catalytically. A prototypical MOST system is norbornadiene/quadricyclane (NBD/QC) whose energy release and surface chemistry need to be understood. Besides important key parameters such as molecular weight, endergonic reaction profiles, and sufficient quantum yields, the position of the absorption onset of NBD is crucial to cover preferably a large range of sunlight's spectrum. For this purpose, one typically derivatizes NBD with electron-donating and/or electron-accepting substituents. To keep the model system simple enough to be investigated with photoemission techniques, we introduced bromine atoms at the 2,3-position of both compounds. We study the adsorption behavior, energy release, and surface chemistry on Ni(111) using high-resolution X-ray photoelectron spectroscopy (HR-XPS), UV photoelectron spectroscopy, and density functional theory calculations. Both Br₂-NBD and Br₂-QC partially dissociate on the surface at ∼120 K, with Br₂-QC being more stable. Several stable adsorption geometries for intact and dissociated species were calculated, and the most stable structures are determined for both molecules. By temperature-programmed HR-XPS, we were able to observe the conversion of Br₂-QC to Br₂-NBD in situ at 170 K. The decomposition of Br₂-NBD starts at 190 K when C-Br bond cleavage occurs and benzene and methylidene are formed. For Br₂-QC, the cleavage already occurs at 130 K when cycloreversion to Br₂-NBD sets in.

Electronic structures and spectral characteristics of the six C32 fullerene isomers

In this paper, the six C₃₂ isomers which were of crucial importance in the manufacture of new electronic components were identified by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS). For the discernment, geometry optimizations of the six isomers have been carried out, and the C1s XPS and NEXAFS spectra have been simulated in the frame of density functional theory (DFT). XPS spectra, as accurately reflection of different chemical environments where a particular element was located, provided an effective way to identify the six isomers of C₃₂. The NEXAFS spectra, which were commonly used in the electronic structure detection, captured information of unoccupied orbital and showed many recognizable characteristics. To further investigate the source of spectral features, the spectral components calculated from different types of carbon atoms in each C₃₂ isomer also have been well explored and discussed.

Births in the United States, 2017

This report presents selected highlights from 2017 final birth data on key demographic, health care utilization, and infant health indicators. General fertility rates (the number of births per 1,000 females aged 15-44 years) and teen birth rates are presented by race and Hispanic origin. The use of Medicaid as the source of payment for the delivery and preterm birth rates are presented by the age of the mother. Data for 2017 are compared with 2016 for each indicator.

Identification of Four C40 Isomers by Means of a Theoretical XPS/NEXAFS Spectra Study

XPS and NEXAFS spectra of four stable C₄₀ isomers [29( C₂), 31( C _s), 38( D₂), and 39( D_{5 d})] have been investigated theoretically. We combined density functional theory and the full core hole potential method to simulate C 1s XPS and NEXAFS spectra for nonequivalent carbon atoms of four stable C₄₀ fullerene isomers. The NEXAFS showed obvious dependence on the four C₄₀ isomers, and XPS spectra are distinct for all four isomers, which can be employed to identify the four stable structures of C₄₀. Furthermore, the individual components of the spectra according to different categories have been investigated, and the relationship between the spectra and the local structures of C atoms was also explored.

Theoretical Identification of the Six Stable C84 Isomers by IR, XPS, and NEXAFS Spectra

Six stable C₈₄ isomers satisfying isolated pentagon rule (IPR) have been theoretically identified by infrared (IR), X-ray photoelectron (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra. The XPS and NEXAFS spectra at the K-edge for all nonequivalent carbon atoms were simulated by the density functional theory method. NEXAFS spectra show stronger dependence than IR and XPS spectra on the six C₈₄ isomers, which can be properly used for isomer identification. Furthermore, spectral components of total spectra for carbon atoms in different local environment have been explored.

Spectroscopic characterization of the on-surface induced (cyclo)dehydrogenation of a N-heteroaromatic compound on noble metal surfaces

Connecting polycyclic aromatic hydrocarbons by on-surface chemistry.

Polyphenylsilole multilayers--an insight from X-ray electron spectroscopy and density functional theory

We present a combined investigation by means of X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy of condensed multilayers of two polyphenylsiloles, namely hexaphenylsilole (HPS) and tetraphenylsilole (TPS). Both compounds exhibit very similar spectroscopic signatures, whose interpretation is aided by density functional theory (DFT) calculations. High-resolution XPS spectra of the Si 2p and C 1s core levels of these multilayers indicate a positively charged silicon ion flanked by two negatively charged adjacent carbon atoms in the silole core of both molecules. This result is corroborated quantitatively by DFT calculations on isolated HPS (TPS) molecules, which show a natural bond orbital partial charge of +1.67 e (+1.58 e) on the silicon and -0.34 e (-0.58 e) on the two neighbouring carbon atoms in the silole ring. These charges are conserved in direct contact with a Cu(111) substrate for films of submonolayer coverage, as evidenced by the Si 2p XPS data. The C K-edge NEXAFS spectra of HPS and TPS multilayers exhibit distinct and differing features. Their main characteristics reappear in the simulated spectra and are assigned to the different inequivalent carbon species in the molecule. The angle-dependent measurements hardly reveal any dichroism, i.e., the molecular π-systems are not uniformly oriented parallel or perpendicular with respect to the surface. Changes in the growth conditions of TPS, i.e., a reduction of the substrate temperature from 240 K to 80 K during deposition, lead to a broadening of both XPS and NEXAFS signatures, as well as an upward shift of the Si 2p and C 1s binding energies, indicative of a less ordered growth mode at low temperature.

Chemical-state analysis of organic semiconductors using soft X-ray absorption spectroscopy combined with first-principles calculation

The chemical states of organic semiconductors were investigated by total-electron-yield soft X-ray absorption spectroscopy (TEY-XAS) and first-principles calculations. The organic semiconductors, pentacene (C(22)H(14)) and pentacenequinone (C(22)H(12)O(2)), were subjected to TEY-XAS and the experimental spectra obtained were compared with the 1s core-level excited spectra of C and O atoms, calculated by a first-principles planewave pseudopotential method. Excellent agreement between the measured and the calculated spectra were obtained for both materials. Using this methodology, we examined the chemical states of the aged pentacene, and confirmed that both C-OH and C═O chemical bonds are generated by exposure to air. This result implies that not only oxygen but also humidity causes pentacene oxidation.

Time-dependent density functional theory calculations of the spectroscopy of core electrons

Recent advances in X-ray sources have led to a renaissance in spectroscopic techniques in the X-ray region. These techniques that involve the excitation of core electrons can provide an atom specific probe of electronic structure and provide powerful analytical tools that are used in many fields of research. Theoretical calculations can often play an important role in the analysis and interpretation of experimental spectra. In this perspective, we review recent developments in quantum chemical calculations of X-ray absorption spectra, focusing on the use of time-dependent density functional theory to study core excitations. The practical application of these calculations is illustrated with examples drawn from surface science and bioinorganic chemistry, and the application of these methods to study X-ray emission spectroscopy is explored.

Structure and excitonic coupling in self-assembled monolayers of azobenzene-functionalized alkanethiols

Optical properties and the geometric structure of self-assembled monolayers of azobenzene-functionalized alkanethiols have been investigated by UV/visible and near edge X-ray absorption fine structure spectroscopy in combination with density-functional theory. By attaching a trifluoro-methyl end group to the chromophore both the molecular tilt and twist angle of the azobenzene moiety are accessible. Based on this detailed structural analysis the energetic shifts observed in optical reflection spectroscopy can be qualitatively described within an extended dipole model. This substantiates sizable excitonic coupling among the azobenzene chromophores as an important mechanism that hinders trans to cis isomerization in densely packed self-assembled monolayers.

L-tyrosine on Ag(111): universality of the amino acid 2D zwitterionic bonding scheme?

We present a combined study of the adsorption and ordering of the l-tyrosine amino acid on the close-packed Ag(111) noble-metal surface in ultrahigh vacuum by means of low-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. On this substrate the biomolecules self-assemble at temperatures exceeding 320 K into linear structures primarily following specific crystallographic directions and evolve with larger molecular coverage into two-dimensional nanoribbons which are commensurate with the underlying atomic lattice. Our high resolution topographical STM data reveal noncovalent molecular dimerization within the highly ordered one-dimensional nanostructures, which recalls the geometrical pattern already seen in the l-methionine/Ag(111) system and supports a universal bonding scheme for amino acids on smooth and unreactive metal surfaces. The molecules desorb for temperatures above 350 K, indicating a relatively weak interaction between the molecules and the substrate. XPS measurements reveal a zwitterionic adsorption, whereas NEXAFS experiments show a tilted adsorption configuration of the phenol moiety. This enables the interdigitation between aromatic side chains of adjacent molecules via parallel-displaced pi-pi interactions which, together with the hydrogen-bonding capability of the hydroxyl functionality, presumably mediates the emergence of the self-assembled supramolecular nanoribbons.

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111)

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C(9)H(10) isomers trans-methylstyrene, alpha-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s-->pi(*) transitions which are explained by different coupling of the pi-electron system of the C(6) ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbed molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations.

Combined X-ray Absorption Spectroscopy and Density Functional Theory Examination of Ferrocene-Labeled Peptides

A combination of soft X-ray absorption spectroscopy (XAS) measurements and StoBe density functional theory (DFT) calculations has been used to study the electronic structures of the ferrocene-labeled peptides Fc-Pro(n)-OBz (n = 1-4). Excellent agreement between the measured and the simulated data is observed in all cases, and the origin of all major spectral features was assigned. The breaking of the degeneracy of the ferrocene 3e(2u)-like unoccupied molecular orbital under the influence of a substituent attached to a Cp ring was observed experimentally. The influence of the bonding environment on the O 1s and N 1s XAS spectra was examined. A corrected assignment of one of the major features in the Fe 2p XAS spectra of ferrocene is proposed and supported by the DFT simulations, as well as the measured spectra.

Spectroscopic analysis of small organic molecules: A comprehensive near-edge x-ray-absorption fine-structure study of C6-ring-containing molecules

We report high-resolution C 1s near-edge x-ray-absorption fine-structure (NEXAFS) spectra of the C6-ring-containing molecules benzene (C6H6), 1,3- and 1,4-cyclohexadiene (C6H8), cyclohexene (C6H10), cyclohexane (C6H12), styrene (C8H8), and ethylbenzene (C8H10) which allow us to examine the gradual development of delocalization of the corresponding pi electron systems. Due to the high experimental resolution, vibrational progressions can be partly resolved in the spectra. The experimental spectra are compared with theoretical NEXAFS spectra obtained from density-functional theory calculations where electronic final-state relaxation is accounted for. The comparison yields very good agreement between theoretical spectra and experimental results. In all cases, the spectra can be described by excitations to pi*- and sigma*-type final-state orbitals with valence character, while final-state orbitals of Rydberg character make only minor contributions. The lowest C 1s-->1pi* excitation energy is found to agree in the (experimental and theoretical) spectra of all molecules except for 1,3-cyclohexadiene (C6H8) where an energy smaller by about 0.6 eV is obtained. The theoretical analysis can explain this result by different binding properties of this molecule compared to the others.