Simulation of Rough Electrodes Coupled with Structural Dynamics
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Dankesreiter, Benjamin Thomas↗
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Ultrafast population and structural dynamics of a Ni-bipyridine photoredox catalyst reveal a significant deactivation pathway
The ultrafast excited state pathways and dynamics of NiII-bipyridine complexes influence the yield of photochemical processes involved in their catalytic cross-coupling reactions. Here we present ultrafast Ni K x-ray emission spectroscopy (XES) and x-ray solution scattering (XSS) of a NiII-bipyridine aryl halide complex, [Ni(t-Bubpy)(o-tol)Br], to quantify the excited state population dynamics and structural changes of the pre-catalyst. Due to the local spin-sensitivity of XES, the population dynamics of metal-to-ligand charge transfer (MLCT) and metal-centered (MC) excited states is established. A rapid ground state recovery pathway is newly identified, representing a significant deactivation pathway during photocatalysis. Furthermore, the pseudotetrahedral structure of the long-lived MC excited state is unambiguously identified and refined by XSS. The results advance our understanding of the ultrafast relaxation mechanisms that impact the photocatalytic mechanism and yield for NiII-bipyridine aryl halide cross-coupling catalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.
59 BASIC BIOLOGICAL SCIENCES↗
Deciphering Dynamic Structural and Mechanistic Complexity in Cu/CeO2/ZSM-5 Catalysts for the Reverse Water-Gas Shift Reaction
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99 GENERAL AND MISCELLANEOUS↗
Origin of core-to-core x-ray emission spectroscopy sensitivity to structural dynamics
Recently, coherent structural dynamics in the excited state of an iron photosensitizer was observed through oscillations in the intensity of Kα x-ray emission spectroscopy (XES). Understanding the origin of the unexpected sensitivity of core-to-core transitions to structural dynamics is important for further development of femtosecond time-resolved XES methods and, we believe, generally necessary for interpretation of XES signals from highly non-equilibrium structures that are ubiquitous in photophysics and photochemistry. Here, we use multiconfigurational wavefunction calculations combined with atomic theory to analyze the emission process in detail. The sensitivity of core-to-core transitions to structural dynamics is due to a shift of the minimum energy metal–ligand bond distance between 1s and 2p core-hole states. A key effect is the additional contraction of the non-bonding 3s and 3p orbitals in 1s core-hole states, which decreases electron– electron repulsion and increases overlap in the metal–ligand bonds. The effect is believed to be general and especially pronounced for systems with strong bonds. The important role of 3s and 3p orbitals is consistent with the analysis of radial charge and spin densities and can be connected to the negative chemical shift observed for many transition metal complexes. The XES sensitivity to structural dynamics can be optimized by tuning the emission energy spectrometer, with oscillations up to ±4% of the maximum intensity for the current system. The theoretical predictions can be used to design experiments that separate electronic and nuclear degrees of freedom in ultrafast excited state dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures
Not Available
Zhou, Bing-Rui↗
Structure, Dynamics, and Reactivity for Light Alkane Oxidation of Fe(II) Sites Situated in the Nodes of a Metal–Organic Framework
Metal organic frameworks (MOFs), with their crystalline, porous structures, can be synthesized to incorporate a wide range of catalytically active metals in tailored surroundings. These materials have potential as catalysts for conversion of light alkanes, feedstocks available in large quantities from shale gas that are changing the economics of manufacturing commodity chemicals. Mononuclear high-spin (S = 2) Fe(II) sites situated in the nodes of the MOF MIL-100(Fe) convert propane via dehydrogenation, hydroxylation, and overoxidation pathways in reactions with the atomic oxidant N 2 O. Pair distribution function analysis, N 2 adsorption isotherms, X-ray diffraction patterns, and infrared and Raman spectra confirm the single-phase crystallinity and stability of MIL-100(Fe) under reaction conditions (523 K in vacuo, 378–408 K C 3 H 8 + N 2 O). Density functional theory (DFT) calculations illustrate a reaction mechanism for the formation of 2-propanol, propylene, and 1-propanol involving the oxidation of Fe(II) to Fe(III) via a high-spin Fe(IV)$=$O intermediate. The speciation of Fe(II) and Fe(III) in the nodes and their dynamic interchange was characterized by in situ X-ray absorption spectroscopy and ex situ Mössbauer spectroscopy. Furthermore, the catalytic relevance of Fe(II) sites and the number of such sites were determined using in situ chemical titrations with NO. N 2 and C 3 H 6 production rates were found to be first-order in N 2 O partial pressure and zero-order in C3H8 partial pressure, consistent with DFT calculations that predict the reaction of Fe(II) with N 2 O to be rate determining. DFT calculations using a broken symmetry method show that Fe-trimer nodes affecting reaction contain antiferromagnetically coupled iron species, and highlight the importance of stabilizing high-spin (S = 2) Fe(II) species for effecting alkane oxidation at low temperatures (<408 K).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter
Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. In this study, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca 2+ ) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.
54 ENVIRONMENTAL SCIENCES↗
Structural Dynamics in UV Curable Resins Resolved by In Situ 3D Printing X-ray Photon Correlation Spectroscopy
Additive manufacturing (AM) is a promising technique to rapidly produce polymeric materials into complex 3-dimensional (3D) geometries. While AM is widespread and relevant for a range of applications, implementation in industry has outpaced our fundamental understanding of polymer dynamics and structure development during the printing process. Characterization and quantification of such dynamics is necessary to optimize final material properties and design future materials and processes for 3D printing. Here, we utilize X-ray photon correlation spectroscopy (XPCS) to measure spatial and time-resolved, out-of-equilibrium dynamics during direct ink write (DIW) 3D printing. Specifically, we investigate the progression of structural dynamics in a dual cure (UV/thermal) nanocomposite during and directly after printing. As the filament is printed and cured in situ, the relaxation processes of the cross-linking network are measured through the dynamics of inorganic filler particles. The characteristic relaxation time of the dynamics is calculated through the intensity–intensity autocorrelation function g 2 and directly correlated to the printing process parameters, such as printhead velocity and UV light intensity. The time-resolved evolution of nanoscale dynamics follows a power-law dependence as the filament is cured. Additionally, bulk rheological characterizations reveal the macroscopic solidification of the resin, providing correlation of material properties across a wide range of length and time scales. Overall, the measurement of multiscale, out-of-equilibrium dynamics provides insight into the development of structure in polymer nanocomposite filaments during 3D printing and is used to further understand the influence of such parameters on the AM process.
36 MATERIALS SCIENCE↗
Direct Observation of Transient Structural Dynamics of Atomically Thin Halide Perovskite Nanowires
Halide perovskite is a unique dynamical system, whose structural and chemical processes happening across different timescales have significant impact on its physical properties and device-level performance. However, due to its intrinsic instability, real-time investigation of the structure dynamics of halide perovskite is challenging, which hinders the systematic understanding of the chemical processes in the synthesis, phase transition, and degradation of halide perovskite. Here, we show that atomically thin carbon materials can stabilize ultrathin halide perovskite nanostructures against otherwise detrimental conditions. Moreover, the protective carbon shells enable atomic-level visualization of the vibrational, rotational, and translational movement of halide perovskite unit cells. Albeit atomically thin, protected halide perovskite nanostructures can maintain their structural integrity up to an electron dose rate of 10,000 e – /Å 2 ·s while exhibiting unusual dynamical behaviors pertaining to the lattice anharmonicity and nanoscale confinement. Here, our work demonstrates an effective method to protect beam-sensitive materials during in situ observation, unlocking new solutions to study new modes of structure dynamics of nanomaterials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
State Space Reconstruction from Embeddings of Partial Observables in Structural Dynamic Systems for Structure-Preserving Data-Driven Methods.
Abstract not provided.
Najera-Flores, David↗
Sparse and Random Sampling Techniques for High-Resolution, Full-Field, BSS-Based Structural Dynamics Identification from Video
Video-based techniques for identification of structural dynamics have the advantage that they are very inexpensive to deploy compared to conventional accelerometer or strain gauge techniques. When structural dynamics from video is accomplished using full-field, high-resolution analysis techniques utilizing algorithms on the pixel time series such as principal components analysis and solutions to blind source separation the added benefit of high-resolution, full-field modal identification is achieved. An important property of video of vibrating structures is that it is particularly sparse. Typically video of vibrating structures has a dimensionality consisting of many thousands or even millions of pixels and hundreds to thousands of frames. However the motion of the vibrating structure can be described using only a few mode shapes and their associated time series. As a result, emerging techniques for sparse and random sampling such as compressive sensing should be applicable to performing modal identification on video. This work presents how full-field, high-resolution, structural dynamics identification frameworks can be coupled with compressive sampling. The techniques described in this work are demonstrated to be able to recover mode shapes from experimental video of vibrating structures when 70% to 90% of the frames from a video captured in the conventional manner are removed.
47 OTHER INSTRUMENTATION↗
Nonadiabatic coupling of the dynamical structure to the superconductivity in YSr 2 Cu 2.75 Mo 0.25 O 7.54 and Sr 2 CuO 3.3
A crucial issue in cuprates is the extent and mechanism of the coupling of the lattice to the electrons and the superconductivity. Here we report Cu K edge extended X-ray absorption fine structure measurements elucidating the internal quantum tunneling polaron (iqtp) component of the dynamical structure in two heavily overdoped superconducting cuprate compounds, tetragonal YSr 2 Cu 2.75 Mo 0.25 O 7.54 with superconducting critical temperature, T c = 84 K and hole density p = 0.3 to 0.5 per planar Cu, and the tetragonal phase of Sr 2 CuO 3.3 with T c = 95 K and p = 0.6. In YSr 2 Cu 2.75 Mo 0.25 O 7.54 changes in the Cu-apical O two-site distribution reflect a sequential renormalization of the double-well potential of this site beginning at T c , with the energy difference between the two minima increasing by ~6 meV between T c and 52 K. Sr 2 CuO 3.3 undergoes a radically larger transformation at T c , >1-Å displacements of the apical O atoms. The principal feature of the dynamical structure underlying these transformations is the strongly anharmonic oscillation of the apical O atoms in a double-well potential that results in the observation of two distinct O sites whose Cu–O distances indicate different bonding modes and valence-charge distributions. The coupling of the superconductivity to the iqtp that originates in this nonadiabatic coupling between the electrons and lattice demonstrates an important role for the dynamical structure whereby pairing occurs even in a system where displacements of the atoms that are part of the transition are sufficiently large to alter the Fermi surface. The synchronization and dynamic coherence of the iqtps resulting from the strong interactions within a crystal would be expected to influence this process.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Model Order Reduction of Nonviscously Damped Structural Dynamic Models
A reduced order modeling capability has been developed to reduce the computational burden associated with time-domain solutions of structural dynamic models with linear viscoelastic materials. The discretized equations-of-motion produce convolution integrals resulting in a linear system with nonviscous damping forces. The challenge associated with the reduction of nonviscously damped, linear systems is the selection and computation of the appropriate modal basis to perform modal projection. The system produces a nonlinear eigenvalue problem that is challenging to solve and requires use of specialized algorithms not readily available in commercial finite element packages. This SAND report summarizes the LDRD discoveries of a reduction scheme developed for monolithic finite element models and provides preliminary investigations to extensions of the method using component mode synthesis. In addition, this report provides a background overview of structural dynamic modeling of structures with linear viscoelastic materials, and provides an overview of a new code capability in Sierra Structural Dynamics to output the system level matrices computed on multiple processors.
97 MATHEMATICS AND COMPUTING↗
Ultrafast X-Ray Scattering Measurements of Coherent Structural Dynamics on the Ground-State Potential Energy Surface of a Diplatinum Molecule
We present x-ray free electron laser experiments addressing ground-state structural dynamics of the diplatinum anion Pt 2 POP 4 following photoexcitation. The structural dynamics are tracked with < 100 fs time resolution by x-ray scattering, utilizing the anisotropic component to suppress contributions from the bulk solvent. The x-ray data exhibit a strong oscillatory component with period 0.28 ps and decay time 2.2 ps, and structural analysis of the difference signal directly shows this as arising from ground-state dynamics along the PtPt coordinate. Here, these results are compared with multiscale Born-Oppenheimer molecular dynamics simulations and demonstrate how off-resonance excitation can be used to prepare a vibrationally cold excited-state population complemented by a structure-dependent depletion of the ground-state population which subsequently evolves in time, allowing direct tracking of ground-state structural dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Anisotropic structural dynamics of monolayer crystals revealed by femtosecond surface X-ray scattering
Ultrafast X-ray scattering is one of the primary tools to track intrinsic crystallographic evolution with atomic accuracy in real time. However, its application to study nonequilibrium structural properties at the two-dimensional limit remains a long-standing challenge due to a significant reduction of diffraction volume and complexity of data analysis. Here, we report femtosecond surface X-ray diffraction in combination with crystallographic model-refinement calculations to quantify the ultrafast structural dynamics of monolayer WSe 2 crystals supported on a substrate. We found the absorbed optical photon energy is preferably coupled to the in-plane lattice vibrations within one picosecond whereas the out-of-plane lattice vibration amplitude remains unchanged during the first ten picoseconds. The model-assisted fitting suggests an asymmetric intralayer spacing change upon excitation. The observed nonequilibrium anisotropic structural dynamics agrees with first-principles modelling in both real and momentum space, marking the distinct structural dynamics of monolayer crystals from their bulk counterparts.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Optical transient grating pumped X-ray diffraction microscopy for studying mesoscale structural dynamics
Abstract A fundamental understanding of materials’ structural dynamics, with fine spatial and temporal control, underpins future developments in electronic and quantum materials. Here, we introduce an optical transient grating pump and focused X-ray diffraction probe technique (TGXD) to examine the structural evolution of materials excited by modulated light with a precisely controlled spatial profile. This method adds spatial resolution and direct structural sensitivity to the established utility of a sinusoidal transient-grating excitation. We demonstrate TGXD using two thin-film samples: epitaxial BiFeO 3 , which exhibits a photoinduced strain (structural grating) with an amplitude proportional to the optical fluence, and FeRh, which undergoes a magnetostructural phase transformation. In BiFeO 3 , structural relaxation is location independent, and the strain persists on the order of microseconds, consistent with the optical excitation of long-lived charge carriers. The strain profile of the structural grating in FeRh, in comparison, deviates from the sinusoidal excitation and exhibits both higher-order spatial frequencies and a location-dependent relaxation. The focused X-ray probe provides spatial resolution within the engineered optical excitation profile, resolving the spatiotemporal flow of heat through FeRh locally heated above the phase transition temperature. TGXD successfully characterizes mesoscopic energy transport in functional materials without relying on a specific transport model.
36 MATERIALS SCIENCE↗
Exactly and Easily Applying Experimental Boundary Conditions in Computational Structural Dynamics
Most experimental setups and environment specifications define acceleration loads on the component. However, Sierra Structural Dynamics cannot apply acceleration boundary conditions in modal transient analysis. Modal analysis of these systems and environments must be done through the application of a huge artificial force to a large fictitious point mass. Introducing a large mass into the analysis is a common source of numerical error. In this report we detail a mathematical procedure to directly apply acceleration boundary conditions in modal analyses without the requirement of adding a non-physical mass to the system. We prototype and demonstrate this procedure in Matlab and scope the work required to integrate this procedure into Sierra Structural Dynamics.
97 MATHEMATICS AND COMPUTING↗