Inner-Shell-Ionization-Induced Femtosecond Structural Dynamics of Water Molecules Imaged at an X-Ray Free-Electron Laser
Not Available
74 ATOMIC AND MOLECULAR PHYSICS↗
SEARCH · Search NASA
Results for “electronic structure of atoms and molecules”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules
Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optimization of La 2 NiO 4+δ Electrolysis Cell Oxygen Electrode through Surfactant-Enabled LaCoO 3±δ Nanocatalyst Deposition
Lanthanum nickelate (LNO) has shown promise as a Cr-resistant air electrode material for SOECs but has suboptimal surface oxygen exchange properties. Nanocoating of the LNO surface with lanthanum cobaltite (LCO) was chosen to improve cell performance as a surface oxygen conductor. The work focused on the implementation of a two-step nano-LCO film deposition utilizing catechol molecules in a porous LNO electrode. The subgoals of the work were to maintain nanosized LCO particles/ grains to increase active surface area and to control the regularity/ homogeneity of the coating across the microstructure. To achieve these goals, a novel surfactant-enhanced liquid infiltration method was utilized, where nucleation sites were spread across the electrode structure to control the location and size of LCO particles. Various catechol surfactant compositions were evaluated for their ability to control the kinetics of nanoparticle deposition and the homogeneity of the coating. Chelated LCO was characterized by X-ray diffraction (XRD), which found a substantial improvement in LCO formation with surfactant addition and determined polymerized norepinephrine to be the best-performing surfactant, with 88.4% pure LCO formed at low temperature. X-ray photoelectron spectroscopy (XPS) confirmed LCO nanostructures formed by the two-step infiltration process, showing no impurities and a stable perovskite structure. Deposition kinetics were analyzed using atomic force microscopy (AFM), correlating infiltration times and solution molarity to nanoparticle size and distribution, the results of which were confirmed in symmetrical cell samples by scanning electron microscopy (SEM). Electrochemical impedance spectroscopy (EIS) testing demonstrated substantial improvements in polarization resistance, where the nanocoating reduced the resistance by ∼55% to 0.152 Ω·cm 2 at 700 °C and 0.039 Ω·cm 2 at 800 °C. Electrical conductivity relaxation (ECR) at this temperature confirmed an improved surface oxygen exchange coefficient of the LCO + LNO heterostructure predicted by the Bode data from EIS, alongside a reduction in activation energy by about 30%.
Deposition↗
Benchmark Data Set of Crystalline Organic Semiconductors
This work reports a Benchmark Data set of Crystalline Organic Semiconductors to test calculations of the structural and electronic properties of these materials in the solid state. The data set contains 67 crystals consisting of mostly rigid molecules with a single dominant conformer, covering the majority of known structural types. The experimental crystal structure is available for the entire data set, whereas zero-temperature unit cell volume can be reliably estimated for a subset of 28 crystals. Using this subset, we benchmark r 2 SCAN-D3 and PBE-D3 density functionals. Then, for the entire data set, we benchmark approximate density functional theory (DFT) methods, including GFN1-xTB and DFTB3(3ob-3-1), with various dispersion corrections against r 2 SCAN-D3. Our results show that r 2 SCAN-D3 geometries are accurate within a few percent, which is comparable to the statistical uncertainty of experimental data at a fixed temperature, but the unit cell volume is systematically underestimated by 2% on average. The several times faster PBE-D3 provides an unbiased estimate of the volume for all systems except for molecules with highly polar bonds, for which the volume is substantially overestimated in correlation with the underestimation of atomic charges. Considered approximate DFT methods are orders of magnitude faster and provide qualitatively correct but overcompressed crystal structures unless the dispersion corrections are fitted by unit cell volume.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Machine learning dielectric screening for the simulation of excited state properties of molecules and materials
Accurate and efficient calculations of absorption spectra of molecules and materials are essential for the understanding and rational design of broad classes of systems. Solving the Bethe–Salpeter equation (BSE) for electron–hole pairs usually yields accurate predictions of absorption spectra, but it is computationally expensive, especially if thermal averages of spectra computed for multiple configurations are required. We present a method based on machine learning to evaluate a key quantity entering the definition of absorption spectra: the dielectric screening. We show that our approach yields a model for the screening that is transferable between multiple configurations sampled during first principles molecular dynamics simulations; hence it leads to a substantial improvement in the efficiency of calculations of finite temperature spectra. We obtained computational gains of one to two orders of magnitude for systems with 50 to 500 atoms, including liquids, solids, nanostructures, and solid/liquid interfaces. Importantly, the models of dielectric screening derived here may be used not only in the solution of the BSE but also in developing functionals for time-dependent density functional theory (TDDFT) calculations of homogeneous and heterogeneous systems. Overall, our work provides a strategy to combine machine learning with electronic structure calculations to accelerate first principles simulations of excited-state properties.
36 MATERIALS SCIENCE↗
Diabatic Valence-Hole States in the C 2 Molecule: “Putting Humpty Dumpty Together Again”
Despite the long history of spectroscopic studies of the C$_2$ molecule, fundamental questions about its chemical bonding are still being hotly debated. The complex electronic structure of C$_2$ is a consequence of its dense manifold of near-degenerate, low-lying electronic states. A global multi-state diabatic model is proposed here to disentangle the numerous configuration interactions within four symmetry manifolds of C$_2$ ($^{1}\Pi_g$, $^{3}\Pi_g$, $^{1}\Sigma_u^+$, and $^{3}\Sigma_u^+$). The key concept of our model is the existence of two "valence-hole" configurations, $2\sigma_g^22\sigma_u^11\pi_{u}^33\sigma_g^2$ for $^{1,3}\Pi_g$ states and $2\sigma_g^22\sigma_u^11\pi_{u}^43\sigma_g^1$ for $^{1,3}\Sigma_u^+$ states that derive from $3\sigma_g\leftarrow2\sigma_u$ electron promotion. The lowest-energy state from each of the four C$_2$ symmetry species is dominated by this type of valence-hole configuration at its equilibrium internuclear separation. Finally, as a result of their large binding energy (nominal bond order of 3) and correlation with the 2s$^2$2p$^2$+2s2p$^3$ separated-atom configurations, the presence of these valence-hole configurations has a profound impact on the $global$ electronic structure and unimolecular dynamics of C$_2$.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Fundamental Interactions of Bimetallic Cu x Pd y ( x + y = 4) Clusters Supported on the α-WC(0001) Surface and Their Performance for CO 2 Adsorption and Dissociation
The tungsten carbide α-WC(0001) surface, an active system for the activation of H 2 and important hydrogenation processes involving unsaturated hydrocarbons, can serve as a support of bimetallic clusters to produce materials with unique catalytic properties, opening routes for a wide range of technical applications. In particular, Cu x Pd y clusters are of particular interest because they combine metals with different properties. A stochastic method was applied to obtain the geometry of Cu x Pd y (x + y = 4) bare clusters, evaluating thousands of possibilities to obtain stable structures, yielding one isomer for Cu 4 , Cu 2 Pd 2 , Cu 1 Pd 3 , and Pd 4 and two isomers for Cu 3 Pd 1 . These clusters were supported on C and W terminations of the tungsten carbide (0001) surface, exploring all of the binding possibilities. The adsorption energies on the C and W terminations are in the ranges from −2.51 to −3.02 eV and from −2.26 to −3.30 eV, respectively. The strongest and weakest binding was seen for monometallic Cu 4 and Pd 4 clusters on both C and W terminations, while the Cu-Pd bimetallics have intermediate adsorption energies but lack a clear trend in terms of composition. The location of Cu x Pd y clusters over the (0001) surface induces a decrease in the work function relative to the pristine surface, while the cluster-surface Bader charge transfer and variations in the partial density of states point to changes in the electronic structure of the carbide atoms upon binding of the metallic clusters. The d-band center of the Cu x Pd y deposited on WC(0001) indicates an intermediate reactivity among Cu(111) and Pd(111) surfaces, modulating the reactivity with small numbers of Cu and Pd atoms, i.e., atom economy in catalyst design. The likelihood of existence of the most stable Cu x Pd y (x + y = 4) clusters in the temperature range of 298-400 K is 100%. The composite Cu x Pd y /α-WC(0001) (x + y = 4), is a nontrivial system since 22 isomers are needed to completely describe its structural properties. Among the isomers, seven structures are necessary to represent Cu 3 Pd 1 /α-WC(0001), five for Pd 4 /α-WC(0001), two for Cu 4 /α-WC(0001), and four for Cu 2 Pd 2 /α-WC(0001) and Cu 1 Pd 3 /α-WC(0001). The large number of cluster isomers supported on the tungsten carbide surface opens the door for several applications in the heterogeneous catalysis of the Cu x Pd y /α-WC(0001) composite, with the possibility of modulating the geometric, electronic, and chemical properties according to a desired application. Test studies for the adsorption of CO 2 indicate that the Cu x Pd y /α-WC(0001) composites are highly active for the adsorption and decomposition of the molecule, with bimetallic and admetal-carbide interactions playing a key role in the binding performance. In conclusion, this high activity indicates that these systems should be useful as catalysts for the conversion of CO 2 to oxygenates or light alkanes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Photothermal alternative to device fabrication using atomic precision advanced manufacturing techniques
The attachment of dopant precursor molecules to depassivated areas of hydrogen-terminated silicon templated with a scanning tunneling microscope (STM) has been used to create electronic devices with subnanometer precision, typically for quantum physics experiments. This process, which we call atomic precision advanced manufacturing (APAM), dopes silicon beyond the solid-solubility limit and produces electrical and optical characteristics that may also be useful for microelectronic and plasmonic applications. However, scanned probe lithography lacks the throughput required to develop more sophisticated applications. In this work, we demonstrate and characterize an APAM device workflow where scanned probe lithography of the atomic layer resist has been replaced by photolithography. An ultraviolet laser is shown to locally and controllably heat silicon above the temperature required for hydrogen depassivation on a nanosecond timescale, a process resistant to under- and overexposure. STM images indicate a narrow range of energy density where the surface is both depassivated and undamaged. Modeling that accounts for photothermal heating and the subsequent hydrogen desorption kinetics suggests that the silicon surface temperatures reached in our patterning process exceed those required for hydrogen removal in temperature-programmed desorption experiments. A phosphorus-doped van der Pauw structure made by sequentially photodepassivating a predefined area and then exposing it to phosphine is found to have a similar mobility and higher carrier density compared with devices patterned by STM. Lastly, it is also demonstrated that photodepassivation and precursor exposure steps may be performed concomitantly, a potential route to enabling APAM outside of ultrahigh vacuum.
nanoscale devices↗
Ab Initio modeling of Near-Edge EELS spectra for chemisorbed molecules
Abstract Electron energy loss spectroscopy (EELS) has recently been applied to probe chemisorbed molecules on metal nanostructures, but a fundamental understanding of the correlation between these spectra and the electronic structures of the adsorbates has been limited. We report here on the insights afforded by time-dependent density functional theory to decipher the energy loss near edge structure (ELNES) of EELS spectra associated with chemisorption. These first-principles calculations simulate the ELNES-EELS spectra for chemisorbed CO on various facets of Au and Pt. Computational predictions of key signatures such as the ‘red shift’ and reductions in the peak intensity of the 2 π * and 6 σ * peaks, as compared to free CO in the gas phase, are validated in comparison to experimentally collected EELS spectra. These signatures are revealed to arise from changes in the electronic structure in terms of unoccupied density of states associated with the chemisorption process. They are consistent with a Blyholder model that incorporates donation and back-donation of electrons. They are also characteristic of the chemisorption process, such as the choice of metal, site of adsorption and the coverage and distribution of adsorbates. Our simulations thus provide guidelines for the use of ELNES-EELS to characterize the atomic structure and adsorption property of nanostructured surfaces and facilitate the development of advanced nanomaterials for catalytic applications.
Materials Science↗
Truncating 2D Framework Materials Down to a Single Pore: Synthetic Approaches and Opportunities
Here, in this Accounts article, we summarize our recent work on truncating conjugated two-dimensional framework materials down to a single pore, or a single macrocycle. Conjugated 2D architectures have emerged as one of the most synthetically adaptable motifs for coupling semiconductivity and porosity in metal–organic frameworks (MOFs) and covalent organic frameworks (COFs). However, despite their prevalence, 2D architectures have several limitations. In particular, the strong interlayer π–π stacking can limit both processability and the accessibility of internal active sites. We have found that simple macrocycles preserve key aspects of 2D framework structure and function, including porosity and out-of-plane electrical conductivity, while providing improved processability, surface tunability, and mass transport properties. In this article, we first describe our synthetic approach and general design considerations. Specifically, we show how ditopic analogues of the tritopic ligands commonly found in the synthesis of 2D MOFs and COFs can be used to achieve a diverse library of conjugated macrocycles that resemble fragments of semiconducting frameworks in both form and function. The length of the peripheral side chains, the size of the aromatic core, and the solubility of intermediates are all key variables in favoring selective macrocycle formation over undesired linear polymers and oligomers. Next, we highlight the unique advantages that macrocycles provide, including improved processability, atomically precise surface tunability, and greater active site accessibility. In particular, the identity of the peripheral side chains dramatically impacts both solubility and colloidal stability as well as crystal size and morphology. We further show how the solution processability and nanoscale dimensions of macrocycles can simplify electronic device fabrication and improve electrochemical performance. Finally, we end with a forward-looking discussion on how macrocycles offer a unique bridge between conjugated molecules and extended frameworks, enabling new application areas and fundamental science.
charge transport↗
Determination of excited state molecular structures from time-resolved gas-phase X-ray scattering
We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-ångstrom resolution from time-resolved gas-phase scattering signals. The method, which is examined using time-resolved X-ray scattering data measured on the molecule N-methylmorpholine (NMM) at the Linac Coherent Light Source (LCLS), compares the experimentally measured scattering patterns against the simulated patterns corresponding to a large pool of molecular structures to determine the full set of structural parameters. In addition, we examine the influence of vibrational state distributions and find the effect negligible within the current experimental detection limits, despite that the molecules have a comparatively high internal vibrational energy. Here, the excited state structures determined using three structure pools generated using three different computational methods are in good agreement, demonstrating that the procedure is largely independent of the computational chemistry method employed as long as the pool is sufficiently expansive in the vicinity of the sought structure and dense enough to yield good matches to the experimental patterns.
74 ATOMIC AND MOLECULAR PHYSICS↗
Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups
Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. In this study, we observe the excited state dynamics following excitation with 266 nm UV light to the 1 ππ* (S 2 ) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron-withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the 1 nπ* (S 1 ) and 3 ππ* (T 1 ) states on a 1.6 ± 0.4 ps time scale, which is similar to the 1.5 ps time scale earlier observed for acetylacetone [ J. Am. Chem. Soc. 2017, 139, 16576—16583, DOI: 10.1021/jacs.7b07532]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Macromolecular crystallography and biology at the Linac Coherent Light Source
The Linac Coherent Light Source (LCLS) has significantly impacted the field of biology by providing advanced capabilities for probing the structure and dynamics of biological molecules with high precision. The ultrashort coherent X-ray pulses from the LCLS have enabled ultrafast, time-resolved, serial femtosecond crystallography that is inaccessible at conventional synchrotron light sources. Since the facility's founding, scientists have captured detailed insights into biological processes at atomic resolution and fundamental timescales. The ability to observe these processes in real time and under conditions closely resembling their natural state is transforming our approach to studying biochemical mechanisms and developing new medical and energy applications. This work recounts some of the history of the LCLS, advances in biological research enabled by the LCLS, key biological areas that have been impacted and how the LCLS has helped to unravel complex biological phenomena in these fields.
59 BASIC BIOLOGICAL SCIENCES↗
Spin–spin interactions in defects in solids from mixed all-electron and pseudopotential first-principles calculations
Abstract Understanding the quantum dynamics of spin defects and their coherence properties requires an accurate modeling of spin-spin interaction in solids and molecules, for example by using spin Hamiltonians with parameters obtained from first principles calculations. We present a real-space approach based on density functional theory for the calculation of spin-Hamiltonian parameters, where only selected atoms are treated at the all-electron level, while the rest of the system is described with the pseudopotential approximation. Our approach permits calculations for systems containing more than 1000 atoms, as demonstrated for defects in diamond and silicon carbide. We show that only a small number of atoms surrounding the defect needs to be treated at the all-electron level, in order to obtain an overall all-electron accuracy for hyperfine and zero-field splitting tensors. We also present results for coherence times, computed with the cluster correlation expansion method, highlighting the importance of accurate spin-Hamiltonian parameters for quantitative predictions of spin dynamics.
36 MATERIALS SCIENCE↗
Prediction of correlation energies using variational subspace valence bond
In the variational subspace valence bond (VSVB) [G. D. Fletcher, J. Chem. Phys. 142, 134112 (2015)] method, the electronic orbitals comprising the wave function correspond to chemically meaningful objects, such as bonds, lone pairs, atomic cores, and so on. Selected regions of a molecule (for example, a single chemical bond, as opposed to all the bonds) can be modeled with different levels of basis set and possible methods for modeling correlation from the other regions. The interactions between the components of a molecule (say, a bond and a neighboring orbital) can then be studied in detail for their impact on a chemical phenomenon while avoiding the expense of necessarily applying the higher levels and methods to the entire molecule. Here, this work presents the theoretical basis for modeling correlation effects between specific electron pairs by incorporating terms in the inter-electronic coordinates (“r 12 ”) into VSVB. The approach is validated with calculations on small systems using single-reference wave functions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational Study of Electron-Molecule Collisions Related to Low-Temperature Plasmas
Computational study of electron-molecule collisions not only complements experimental measurements, but can also be used to investigate processes not readily accessible experimentally. A number of ab initio computational methods are available for these types of calculations. Here we describe a recently developed technique, the finite element Z-matrix method, Analogous to the R-matrix, method, it partitions the space into regions and employs real matrix elements. However, unlike the implementation of the R-matrix method commonly used in atomic and molecular physics, the Z-matrix method is fully variational. In the present implementation, a mixed basis of finite elements and Gaussians is used to represent the continuum electron, thus offering full flexibility without imposing fixed boundary conditions. Numerical examples include the electron-impact dissociation of N2 via the metastable A3Su+ state, a process which may be important in the lower thermosphere, and the dissociation of the CF radical, a process of interest to plasma etching. To understand the dissociation pathways, large scale quantum chemical calculations have been carried out for all target states which dissociate to the lowest five limits in the case of N2, and to the lowest two limits in the case of CF. For N2, the structural calculations clearly show the preference for predissociation if the initial state is the ground X1 Sg+ state, but direct dissociation appears to be preferable if the initial state is the A3Su+ state. Multi-configuration SCF target functions are used in the collisional calculation.
Huo, Winifred M.↗
Multimetallic Metal-Organic Frameworks as Heterogeneous Catalysts for Gas Phase Hydroformylation and Hydrogenation Reactions
This project focused on the development bimetallic metal-organic frameworks (MOFs) as gas phase heterogeneous catalysts for hydrogenation and hydroformylation reactions. MOFs are a new class of hybrid inorganic/organic materials that are highly crystalline, with structures consisting of metal nodes of specific geometries connected by organic linkers. Although there have been a number of studies of catalysis at MOF nodes in solution, there is little experimental data in the literature for gas phase reactions despite the fact that industrial heterogeneous catalysis on MOFs is more economically viable than homogeneous catalysis. The use of MOFs as heterogeneous catalysts presents the unique opportunity to carefully control the composition, geometry and ensemble sizes of the active sites, which are all critical factors for the rational design of new catalysts. Specific objectives of the project are as follows: (1) to tailor the geometry, composition and ensemble size of the active sites; (2) to understand how the adsorption of molecules at metal sites can be modified by interactions with a neighboring metal site; (3) to determine how oxidation states of the metal change during reaction and how these states can be modified by metal-metal electronic interactions; and (4) to elucidate reaction mechanisms and intermediates. For these studies, we have chosen to investigate selective hydrogenation of hydrocarbons and hydroformylation, which are industrially relevant reactions. Our interdisciplinary team of Chen, Shustova and Vogiatzis/Henkelman provides critical expertise in novel MOF synthesis (Shustova), atomic-scale surface science and catalysis (Chen) and computational studies of reaction mechanisms (Vogiatzis/Henkelman) that are necessary for the development of these catalysts. We believe that this work will lead directly to the rational design of new catalysts that are versatile, highly active/selective and suitable for industrial processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Seniority eigenstate configuration interaction
Zero-seniority methods have shown great promise for the description of strongly correlated electronic systems. Other seniority sectors have been much less explored, and in particular, the maximal seniority sector and zero seniority have the same underlying algebraic structure. We introduce a seniority eigenstate configuration interaction in which the wave function is constrained to have good fixed local seniority for each paired orbital, by which we mean we partition orbitals into a pairing set with seniority zero, and a spin set with seniority one. Here, we show how to build the effective Hamiltonian for this ansatz, and demonstrate that high-seniority wave functions have unexpectedly excellent accuracy for strongly correlated fermionic systems, with accuracy competitive with or better than seniority zero for the Hubbard model and for the dissociation of the nitrogen molecule.
74 ATOMIC AND MOLECULAR PHYSICS↗