RT-EOM-CCSD Calculations of Inner and Outer Valence Ionization Energies and Spectral Functions.

Photoelectron spectroscopy (PES) is a standard experimental method for material characterization, but its interpretation can be hampered by its reliance on standard materials. To facilitate the study of unknown systems, theoretical methods are desirable. Here, we present a real-time equation-of-motion coupled cluster (RT-EOM-CC) approach for valence PES, extending our core-level development. We demonstrate that RT-EOM-CC yields ionization energies and spectral functions in good agreement with experimental and CI-based results, even for some more correlated cases.

NWChem: Recent and Ongoing Developments.

This paper summarizes developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0.0). Specifically, we focus on functionality, along with input blocks, that is accessible in the current stable release (NWChem 7.2.0) and in the "master" development branch, interfaces to quantum computing simulators, interfaces to external libraries, the NWChem github repository, and containerization of NWChem executable images. Some ongoing developments that will be available in the near future are also discussed.

Real-Time Equation-of-Motion Coupled-Cluster Cumulant Green's Function Method: Heterogeneous Parallel Implementation Based on the Tensor Algebra for Many-Body Methods Infrastructure.

We report the implementation of the real-time equation-of-motion coupled-cluster (RT-EOM-CC) cumulant Green's function method [ J. Chem. Phys. 2020, 152, 174113] within the Tensor Algebra for Many-body Methods (TAMM) infrastructure. TAMM is a massively parallel heterogeneous tensor library designed for utilizing forthcoming exascale computing resources. The two-body electron repulsion matrix elements are Cholesky-decomposed, and we imposed spin-explicit forms of the various operators when evaluating the tensor contractions. Unlike our previous real algebra Tensor Contraction Engine (TCE) implementation, the TAMM implementation supports fully complex algebra. The RT-EOM-CC singles (S) and doubles (D) time-dependent amplitudes are propagated using a first-order Adams-Moulton method. This new implementation shows excellent scalability tested up to 500 GPUs using the Zn-porphyrin molecule with 655 basis functions, with parallel efficiencies above 90% up to 400 GPUs. The TAMM RT-EOM-CCSD was used to study core photoemission spectra in the formaldehyde and ethyl trifluoroacetate (ESCA) molecules. Simulations of the latter involve as many as 71 occupied and 649 virtual orbitals. The relative quasiparticle ionization energies and overall spectral functions agree well with available experimental results.

Real-time equation-of-motion CC cumulant and CC Green's function simulations of photoemission spectra of water and water dimer.

Newly developed coupled-cluster (CC) methods enable simulations of ionization potentials and spectral functions of molecular systems in a wide range of energy scales ranging from core-binding to valence. This paper discusses the results obtained with the real-time equation-of-motion CC cumulant (RT-EOM-CC) approach and CC Green's function (CCGF) approaches in applications to the water and water dimer molecules. We compare the ionization potentials obtained with these methods for the valence region with the results obtained with the coupled-cluster with singles, doubles, and perturbative triples formulation as a difference of energies for N and N - 1 electron systems. All methods show good agreement with each other. They also agree well with the experiment with errors usually below 0.1 eV for the ionization potentials. We also analyze unique features of the spectral functions, associated with the position of satellite peaks, obtained with the RT-EOM-CC and CCGF methods employing single and double excitations, as a function of the monomer OH bond length and the proton transfer coordinate in the dimer. Finally, we analyze the impact of the basis set effects on the quality of calculated ionization potentials and find that the basis set effects are less pronounced for the augmented-type sets.

Ab initio calculation of X-ray and related core-level spectroscopies: Green's function approaches.

X-Ray and related spectroscopies are powerful probes of atomic, vibrational, and electronic structure. In order to unlock the full potential of such experimental techniques, accurate and efficient theoretical and computational approaches are essential. Here we review the status of a variety of first-principles and nearly first principles techniques for X-ray spectroscopies such as X-ray absorption, X-ray emission, and X-ray photoemission, with a focus on Green's function based methods. In particular, we describe the current state of multiple scattering Green's function techniques available in the FEFF10 code and cumulant Green's function techniques for including the effects of many-body electronic excitations. Illustrative examples are shown for a variety of materials and compared with other theoretical and experimental results.

Database of ab initio L-edge X-ray absorption near edge structure.

The L-edge X-ray Absorption Near Edge Structure (XANES) is widely used in the characterization of transition metal compounds. Here, we report the development of a database of computed L-edge XANES using the multiple scattering theory-based FEFF9 code. The initial release of the database contains more than 140,000 L-edge spectra for more than 22,000 structures generated using a high-throughput computational workflow. The data is disseminated through the Materials Project and addresses a critical need for L-edge XANES spectra among the research community.

Energy-Dependent Relative Cross Sections in Carbon 1s Photoionization: Separation of Direct Shake and Inelastic Scattering Effects in Single Molecules.

We demonstrate that the possibility of monitoring relative photoionization cross sections over a large photon energy range allows us to study and disentangle shake processes and intramolecular inelastic scattering effects. In this gas-phase study, relative intensities of the carbon 1s photoelectron lines from chemically inequivalent carbon atoms in the same molecule have been measured as a function of the incident photon energy in the range of 300-6000 eV. We present relative cross sections for the chemically shifted carbon 1s lines in the photoelectron spectra of ethyl trifluoroacetate (the "ESCA" molecule). The results are compared with those of methyl trifluoroacetate and S-ethyl trifluorothioacetate as well as a series of chloro-substituted ethanes and 2-butyne. In the soft X-ray energy range, the cross sections show an extended X-ray absorption fine structure type of wiggles, as was previously observed for a series of chloroethanes. The oscillations are damped in the hard X-ray energy range, but deviations of cross-section ratios from stoichiometry persist, even at high energies. The current findings are supported by theoretical calculations based on a multiple scattering model. The use of soft and tender X-rays provides a more complete picture of the dominant processes accompanying photoionization. Such processes reduce the main photoelectron line intensities by 20-60%. Using both energy ranges enabled us to discern the process of intramolecular inelastic scattering of the outgoing electron, whose significance is otherwise difficult to assess for isolated molecules. This effect relates to the notion of the inelastic mean free path commonly used in photoemission studies of clusters and condensed matter.

A consistent path for phase determination based on transmission electron microscopy techniques and supporting simulations.

This work addresses aspects for the analysis of industrial relevant materials via transmission electron microscopy (TEM). The complex phase chemistry and structural diversity of these materials require several characterization techniques to be employed simultaneously; unfortunately, different characterization techniques often lack connection to yield a complete and consistent picture. This paper describes a continuous path, starting with the acquisition of 3D diffraction data - alongside classical high-resolution imaging techniques - and linking the structural characterization of hard metal industrial samples with energy-loss fine-structure simulations, quantitative electron energy-loss (EEL) and energy-dispersive X-ray (EDX) spectroscopy. Thereby, the compositional analysis of a MAX phase indicated an offset of the hydrogenic, theoretical sensitivity factors, originating from poorly-adjusted screening factors. In a next step, these results were matched against quantitative compositions and parameters obtained from X-ray spectroscopy data, carried out synchronously with EELS.

Extended X-Ray Absorption Fine Structure of ZrW2O8: Theory vs. Experiment.

Extended x-ray absorption fine structure (EXAFS) is well-suited for investigations of structure and disorder of complex materials. Recently, experimental measurements and analysis of EXAFS have been carried out to elucidate the mechanisms responsible for the negative thermal expansion (NTE) in zirconium tungstate (ZrW2O8). In contrast to previous work suggesting that transverse O-displacements are largely responsible, the EXAFS analysis suggested that correlated rotations and translations of octahedra and tetrahedra within the structure are a major source. In an effort to resolve this controversy, we have carried out ab initio calculations of the structure, lattice vibrations, and EXAFS of ZrW2O8 based on real-space multiple-scattering calculations using the FEFF9 code and auxiliary calculations of structure and Debye-Waller factors. We find that the theoretical simulations are consistent with observed EXAFS, and show that both of the above mechanisms contribute to the dynamical structure of ZrW2O8.

High-throughput computational X-ray absorption spectroscopy.

X-ray absorption spectroscopy (XAS) is a widely-used materials characterization technique. In this work we present a database of computed XAS spectra, using the Green's formulation of the multiple scattering theory implemented in the FEFF code. With more than 500,000 K-edge X-ray absorption near edge (XANES) spectra for more than 40,000 unique materials, this database constitutes the largest existing collection of computed XAS spectra to date. The data is openly distributed via the Materials Project, enabling researchers across the world to access it for free and use it for comparisons with experiments and further analysis.

Efficient Calculation of the Negative Thermal Expansion in ZrW2O8.

We present a study of the origin of the negative thermal expansion (NTE) on ZrW2O8 by combining an efficient approach for computing the dynamical matrix with the Lanczos algorithm for generating the phonon density of states in the quasi-harmonic approximation. The simulations show that the NTE arises primarily from the motion of the O-sublattice, and in particular, from the transverse motion of the O atoms in the W-O and W-O-Zr bonds. In the low frequency range these combine to keep the WO4 tetrahedra rigid and induce internal distortions in the ZrO6 octahedra. The force constants associated with these distortions become stronger with expansion, resulting in negative Grüneisen parameters and NTE from the low frequency modes that dominate the positive contributions from the high frequency modes. This leads us to propose an anharmonic, two-frequency Einstein model that quantitatively captures the NTE behavior.

Anomalous Structural Disorder in Supported Pt Nanoparticles.

Supported Pt nanocatalysts generally exhibit anomalous behavior, including negative thermal expansion and large structural disorder. Finite temperature DFT/MD simulations reproduce these properties, showing that they are largely explained by a combination of thermal vibrations and low-frequency disorder. We show here that a full interpretation is more complex and that the DFT/MD mean-square relative displacements (MSRD) can be further separated into vibrational disorder, "dynamic structural disorder" (DSD), and long-time equilibrium fluctuations of the structure dubbed "anomalous structural disorder" (ASD). We find that the vibrational and DSD components behave normally, increasing linearly with temperature while the ASD decreases, reflecting the evolution of mean nanoparticle geometry. As a consequence the usual procedure of fitting the MSRD to normal vibrations plus temperature-independent static disorder results in unphysical bond strengths and Grüneisen parameters.

X-ray and Electron Spectroscopy of Water.

Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the O 1s level or the valence band is the basis of photoelectron spectroscopy. Excitation between the O 1s and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.

How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II.

First principle calculations of extended X-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S0(2) and Debye-Waller values as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first-principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.

Real-space multiple-scattering Hubbard model calculations for d- and f-state materials.

Calculations are presented of the electronic structure and X-ray spectra of materials with correlated d- and f-electron states based on the Hubbard model, a real-space multiple-scattering formalism and a rotationally invariant local density approximation. Values of the Hubbard parameter are calculated ab initio using the constrained random-phase approximation. The combination of the real-space Green's function with Hubbard model corrections provides an efficient approach to describe localized correlated electron states in these systems, and their effect on core-level X-ray spectra. Results are presented for the projected density of states and X-ray absorption spectra for transition metal- and lanthanide-oxides. Results are found to be in good agreement with experiment.

Polarization dependent high energy resolution X-ray absorption study of dicesium uranyl tetrachloride.

Dicesium uranyl tetrachloride (Cs2UO2Cl4) has been a model compound for experimental and theoretical studies of electronic structure of U(VI) in the form of UO2(2+) (uranyl ion) for decades. We have obtained angle-resolved electronic structure information for oriented Cs2UO2Cl4 crystal, specifically relative energies of 5f and 6d valence orbitals probed with extraordinary energy resolution by polarization dependent high energy resolution X-ray absorption near edge structure (PD-HR-XANES) and compare these with predictions from quantum chemical Amsterdam density functional theory (ADF) and ab initio real space multiple-scattering Green's function based FEFF codes. The obtained results have fundamental value but also demonstrate an experimental approach, which offers great potential to benchmark and drive improvement in theoretical calculations of electronic structures of actinide elements.

Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases.

Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new 'multi-point cross-correlation' technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

Effects of adsorbate coverage and bond-length disorder on the d-band center of carbon-supported Pt catalysts.

Determination of the factors that affect the d-band center of catalysts is required to explain their catalytic properties. Resonant inelastic X-ray scattering (RIXS) enables direct imaging of electronic transitions in the d-band of Pt catalysts in real time and in realistic environmental conditions. Through a combination of in situ, temperature-resolved RIXS measurements and theoretical simulations we isolated and quantified the effects of bond-length disorder and adsorbate coverage (CO and H2) on the d-band center of 1.25 nm size Pt catalysts supported on carbon. We found that the decrease in adsorbate coverage at elevated temperatures is responsible for the d band shifts towards higher energies relative to the Fermi level, whereas the effect of the increase in bond-length disorder on the d-band center is negligible. Although these results were obtained for a specific case of non-interacting support and weak temperature dependence of the metal-metal bond length in a model catalyst, this work can be extended to a broad range of real catalysts.

The status of strontium in biological apatites: an XANES/EXAFS investigation.

Osteoporosis represents a major public health problem through its association with fragility fractures. The public health burden of osteoporotic fractures will rise in future generations, due in part to an increase in life expectancy. Strontium-based drugs have been shown to increase bone mass in postmenopausal osteoporosis patients and to reduce fracture risk but the molecular mechanisms of the action of these Sr-based drugs are not totally elucidated. The local environment of Sr(2+) cations in biological apatites present in pathological and physiological calcifications in patients without such Sr-based drugs has been assessed. In this investigation, X-ray absorption spectra have been collected for 17 pathological and physiological calcifications. These experimental data have been combined with a set of numerical simulations using the ab initio FEFF9 X-ray spectroscopy program which takes into account possible distortion and Ca/Sr substitution in the environment of the Sr(2+) cations. For selected samples, Fourier transforms of the EXAFS modulations have been performed. The complete set of experimental data collected on 17 samples indicates that there is no relationship between the nature of the calcification (physiological and pathological) and the adsorption mode of Sr(2+) cations (simple adsorption or insertion). Such structural considerations have medical implications. Pathological and physiological calcifications correspond to two very different preparation procedures but are associated with the same localization of Sr(2+) versus apatite crystals. Based on this study, it seems that for supplementation of Sr at low concentration, Sr(2+) cations will be localized into the apatite network.