Search NASA⌕ Search

SEARCH · Search NASA

Results for “ultrafast molecular dynamics”

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.

At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Effect of Core-Hole Shape on Attosecond Valence Electron Dynamics

Rapid X-ray ionization of a core electron is known to induce the attosecond motion of valence electrons; however, the effect of core-hole shape on the triggered dynamics remains relatively unknown. In this work, the sub-four fs response of prototypical functionalized/heterocyclic/polycyclic molecules was simulated using real-time time-dependent density functional theory (RT-TDDFT), a sudden approximation core-hole, and phenomenologically Auger–Meitner (AM) decay. These molecules included fluorobenzene, chlorobenzene, bromobenzene, phenol, thiophenol, pyridine, phosphorus, and azulene. It is observed that the valence electron dynamics are essentially independent of the core-hole created, provided that it is ionized from an inner-shell orbital and not an inner-valence orbital. This has broad implications for free-electron laser studies of X-ray pumped attosecond processes since the flexibility in edge allows for a wide range of experimental modalities, core-holes with longer AM lifetimes, and molecular targets.

aromatic compounds↗
DOE OSTI2024

Ultrafast nuclear dynamics in double-core-ionized water molecules

Double-core-hole (DCH) states in isolated-water and heavy-water molecules, resulting from the sequential absorption of two x-ray photons, have been investigated. Here, a comparison of the subsequent Auger emission spectra from the two isotopes provides direct evidence of ultrafast nuclear motion during the 1.5-fs lifetime of these DCH states. Our numerical results align well with the experimental data, providing for various DCH states an in-depth study of the dynamics responsible of the observed isotope effect.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Femtosecond dynamics and coherence of ionic retro-Diels–Alder reactions

Ultrafast tunnel ionization enables femtosecond time-resolved dynamic measurements of the retro-Diels–Alder reactions of positively charged cyclohexene, norbornene, and dicyclopentadiene. Unlike the reaction times of 500–600 ps that are observed following UV excitation of neutral species, on the ionic potential energy surfaces, these reactions occur on a single picosecond timescale and, in some cases, exhibit vibrational coherence. In the case of norbornene, a 270 cm –1 vibrational mode is found to modulate the retro-Diels–Alder reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Two-dimensional electronic–vibrational spectroscopy: Exploring the interplay of electrons and nuclei in excited state molecular dynamics

Two-dimensional electronic-vibrational spectroscopy (2DEVS) is an emerging spectroscopic technique which exploits two different frequency ranges for the excitation (visible) and detection (infrared) axes of a 2D spectrum. In contrast to degenerate 2D techniques, such as 2D electronic or 2D infrared spectroscopy, the spectral features of a 2DEV spectrum report cross correlations between fluctuating electronic and vibrational energy gaps rather than autocorrelations as in the degenerate spectroscopies. The center line slope of the spectral features reports on this cross correlation function directly and can reveal specific electronic-vibrational couplings and rapid changes in the electronic structure, for example. The involvement of the two types of transition moments, visible and infrared, makes 2DEVS very sensitive to electronic and vibronic mixing. 2DEV spectra also feature improved spectral resolution, making the method valuable for unraveling the highly congested spectra of molecular complexes. The unique features of 2DEVS are illustrated in this paper with specific examples and their origin described at an intuitive level with references to formal derivations provided. Although early in its development and far from fully explored, 2DEVS has already proven to be a valuable addition to the tool box of ultrafast nonlinear optical spectroscopy and is of promising potential in future efforts to explore the intricate connection between electronic and vibrational nuclear degrees of freedom in energy and charge transport applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A quantitative model of charge injection by ruthenium chromophores connecting femtosecond to continuous irradiance conditions

A kinetic framework for the ultrafast photophysics of tris(2,2-bipyridine)ruthenium(II) phosphonated and methyl-phosphonated derivatives is used as a basis for modeling charge injection by ruthenium dyes into a semiconductor substrate. By including the effects of light scattering, dye diffusion, and adsorption kinetics during sample preparation and the optical response of oxidized dyes, quantitative agreement with multiple transient absorption datasets is achieved on timescales spanning femtoseconds to nanoseconds. In particular, quantitative agreement with important spectroscopic handles—the decay of an excited state absorption signal component associated with charge injection in the UV region of the spectrum and the dynamical redshift of a ~500 nm isosbestic point—validates our kinetic model. Pseudo-first-order rate coefficients for charge injection are estimated in this work, with an order of magnitude ranging from 10 11 to 10 12 s –1 . The model makes the minimalist assumption that all excited states of a particular dye have the same charge injection coefficient, an assumption that would benefit from additional theoretical and experimental exploration. Here, we have adapted this kinetic model to predict charge injection under continuous solar irradiation and find that as many as 68 electron transfer events per dye per second take place, significantly more than prior estimates in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light–matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Excited-State Dynamics during Primary C–I Homolysis in Acetyl Iodide Revealed by Ultrafast Core-Level Spectroscopy

In typical carbonyl-containing molecules, bond dissociation events follow initial excitation to $nπ_{C=O}$$^*$ states. However, in acetyl iodide, the iodine atom gives rise to electronic states with mixed $nπ_{C=O}$$^*$ and $nπ_{C–I}$$^*$ character, leading to complex excited-state dynamics, ultimately resulting in dissociation. Using ultrafast extreme ultraviolet (XUV) transient absorption spectroscopy and quantum chemical calculations, we present an investigation of the primary photodissociation dynamics of acetyl iodide via time-resolved spectroscopy of core-to-valence transitions of the I atom after 266 nm excitation. The probed I 4d-to-valence transitions show features that evolve on sub-100-fs time scales, reporting on excited-state wavepacket evolution during dissociation. These features subsequently evolve to yield spectral signatures corresponding to free iodine atoms in their spin–orbit ground and excited states with a branching ratio of 1.1:1 following dissociation of the C–I bond. Calculations of the valence excitation spectrum via equation-of-motion coupled cluster with single and double substitutions (EOM-CCSD) show that initial excited states are of spin-mixed character. From the initially pumped spin-mixed state, we use a combination of time-dependent density functional theory (TDDFT)-driven nonadiabatic ab initio molecular dynamics and EOM-CCSD calculations of the N$_{4,5}$ edge to reveal a sharp inflection point in the transient XUV signal that corresponds to rapid C–I homolysis. Here, by examining the molecular orbitals involved in the core-level excitations at and around this inflection point, we are able to piece together a detailed picture of C–I bond photolysis in which d → σ* transitions give way to d → p excitations as the bond dissociates. We also report theoretical predictions of short-lived, weak 4d → 5d transitions in acetyl iodide, validated by weak bleaching in the experimental transient XUV spectra. This joint experimental–theoretical effort has thus unraveled the detailed electronic structure and dynamics of a strongly spin–orbit coupled system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Influence of pump laser fluence on ultrafast myoglobin structural dynamics

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern whether this experimental approach allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions. Here we describe ultrafast pump–probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe–CO bond distance (predicted by recent quantum wavepacket dynamics) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump–probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump–probe experiments such that mechanistically relevant insight emerges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers

Despite the crucial role of various insulin analogs in achieving satisfactory glycemic control, a comprehensive understanding of their in-solution dynamic mechanisms still holds the potential to further optimize rapid insulin analogs, thus significantly improving the well-being of individuals with Type 1 Diabetes. Here, we employed hydrogen-deuterium exchange mass spectrometry to decipher the molecular dynamics of newly modified and functional insulin analog. A comparative analysis of H/D dynamics demonstrated that the modified insulin exchanges deuterium atoms faster and more extensively than the intact insulin aspart. Additionally, we present new insights derived from our 2.5 Å resolution X-ray crystal structure of modified hexamer insulin analog at ambient temperature. Furthermore, we obtained a distinctive side-chain conformation of the Asn3 residue on the B chain (AsnB3) by operating a comparative analysis with a previously available cryogenic rapid-acting insulin structure (PDB_ID: 4GBN). The experimental conclusions have demonstrated compatibility with modified insulin’s distinct cellular activity, comparably to aspart. Additionally, the hybrid structural approach combined with computational analysis employed in this study provides novel insight into the structural dynamics of newly modified and functional insulin vs insulin aspart monomeric entities. It allows further molecular understanding of intermolecular interrelations driving dissociation kinetics and, therefore, a fast action mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ultrafast studies of elusive chemical reactions in the gas phase

The chemical composition of the interstellar medium and planetary atmospheres is constantly in flux as atoms and molecules collide and interact with high-energy particles such as electrons, protons, and photons. These transformative processes ultimately lead to the coalescence of molecules and eventually the birth of stars. Our understanding of these chemical ecosystems relies on models that synthesize data from gas-phase experiments, providing insights into reaction cross sections. This Review examines efforts to delve into the fundamental bond-forming and bond-breaking dynamics that occur during bimolecular and electron-initiated reactions. Furthermore, these experiments involve clever approaches to establish a time reference and the collision geometry necessary for tracking atomic motion with femtosecond time resolution. Findings from these efforts enhance present models and improve predictions for molecule-molecule and electron-molecule collisions.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Revealing Hot and Long-Lived Metastable Spin States in the Photoinduced Switching of Solvated Metallogrid Complexes with Femtosecond Optical and X-ray Spectroscopies

An atomistic understanding of the photoinduced spin-state switching (PSS) within polynuclear systems of d 4 –d 7 transition metal ion complexes is required for their rational integration into light-driven reactions of chemical and biological interest. However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. Herein, the PSS in a solvated triiron(II) metallogrid complex is characterized using transient optical absorption and X-ray emission spectroscopies on the femtosecond time scale. The complementary measurements reveal the photoinduced creation of energy-rich (hot) and long-lived quintet states, whose dynamics differ critically from their mononuclear congeners. We report this finding opens major prospects for developing novel schemes in solution-phase spin chemistry that are driven by the dynamic PSS process in compact oligometallic arrays.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Controlling the helicity of light by electrical magnetization switching

Controlling the intensity of emitted light and charge current is the basis of transferring and processing information. By contrast, robust information storage and magnetic random-access memories are implemented using the spin of the carrier and the associated magnetization in ferromagnets. In this study, the missing link between the respective disciplines of photonics, electronics and spintronics is to modulate the circular polarization of the emitted light, rather than its intensity, by electrically controlled magnetization. Here we demonstrate that this missing link is established at room temperature and zero applied magnetic field in light-emitting diodes through the transfer of angular momentum between photons, electrons and ferromagnets. With spin-orbit torque a charge current generates also a spin current to electrically switch the magnetization. This switching determines the spin orientation of injected carriers into semiconductors, in which the transfer of angular momentum from the electron spin to photon controls the circular polarization of the emitted light. The spin-photon conversion with the nonvolatile control of magnetization opens paths to seamlessly integrate information transfer, processing and storage. Our results provide substantial advances towards electrically controlled ultrafast modulation of circular polarization and spin injection with magnetization dynamics for the next-generation information and communication technology, including space-light data transfer. The same operating principle in scaled-down structures or using two-dimensional materials will enable transformative opportunities for quantum information processing with spin-controlled single-photon sources, as well as for implementing spin-dependent time-resolved spectroscopies.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Attosecond delays in X-ray molecular ionization

The photoelectric effect is not truly instantaneous, but exhibits attosecond delays that can reveal complex molecular dynamics. Sub-femtosecond duration light pulses provide the requisite tools to resolve the dynamics of photoionization. Accordingly, the past decade has produced a large volume of work on photoionization delays following single photon absorption of an extreme ultraviolet (XUV) photon. However, the measurement of time-resolved core-level photoionization remained out of reach. The required x-ray photon energies needed for core-level photoionization were not available with attosecond tabletop sources. We have now measured the x-ray photoemission delay of core-level electrons, and here report unexpectedly large delays, ranging up to 700 attoseconds in NO near the oxygen K-shell threshold. These measurements exploit attosecond soft x-ray pulses from a free-electron laser (XFEL) to scan across the entire region near the K-shell threshold. Furthermore, we find the delay spectrum is richly modulated, suggesting several contributions including transient trapping of the photoelectron due to shape resonances, collisions with the Auger-Meitner electron that is emitted in the rapid non-radiative relaxation of the molecule, and multi-electron scattering effects. Finally, the results demonstrate how x-ray attosecond experiments, supported by comprehensive theoretical modelling, can unravel the complex correlated dynamics of core-level photoionization.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Insight into the Chemistry of PETN Under Shock Compression Through Ultrafast Broadband Mid-Infrared Absorption Spectroscopy

In this study, thin films of pentaerythritol tetranitrate (PETN) were shock compressed using the laser driven shock apparatus at Los Alamos National Laboratory (LANL). Two spectroscopic probes were available to this apparatus: visible white light transient absorption spectroscopy (VIS) from 400 to 700 nm and mid-infrared transient absorption spectroscopy (MIR) from 1150 to 3800 cm –1 . Important PETN vibrational modes are the symmetric and antisymmetric NO 2 stretches at 1280 and 1650 cm –1 , respectively, as well as CH stretches at ~2900 cm –1 . Shock strength was varied from approximately 3 to 55 GPa to span from the chemically unreactive regime to the regime in which fast chemical reaction took place on the 250 ps time scale of the measurements. VIS and MIR results suggest irreversible chemistry was induced in PETN at pressures above 30 GPa. At lower shock pressures, the spectroscopy showed minimal changes attributable to pressure induced effects. Under the higher-pressure reactive conditions, the frequency region at the antisymmetric NO 2 stretch mode had a significantly increased absorption while the region around the symmetric NO 2 stretch did not. No observable increased absorption occurred in the higher frequency regions where CH-, NH-, and OH- bond absorptions would be observed. A broad absorption appeared on the shoulder at the red-edge of the CO 2 vibrational band around 2200 cm –1 . In addition to the experiments, reactive molecular dynamics were carried out under equivalent shock conditions to correlate the evolution of the infrared spectrum to molecular processes. The simulations show results consistent to experiments up to 30 GPa but suggest that NO and NO 2 related features provided the strongest contributions to the shocked infrared changes. Proposed mechanisms for shocked PETN chemistry are analyzed as consistent or inconsistent with the data presented here. Our experimental data suggests C≡O or N 2 O bond formation, nitrite formation, and absence of significant hydroxyl or amine concentrations in the initial chemistry steps in PETN shocked above 30 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Accuracy of XAS theory for unraveling structural changes of adsorbates: CO on Ni(100)

Studying surface reactions using ultrafast optical pump and X-ray probe experiments relies on accurate calculations of X-ray spectra of adsorbates for correct identification of the spectral signatures and their dynamical evolution. We show that experimental XAS can be well reproduced for the different binding sites in a static prototype system CO/Ni(100) at a standard DFT (GGA) level of theory, using a plane-wave basis and pseudopotentials. This validates its utility in analyzing ultrafast X-ray probe experiments. The accuracy of computed relative core level binding energies is about 0.2 eV, representing a lower limit for which spectral features can be resolved with this method. We also show that the commonly used Z +1 approximation gives very good core binding energy shifts overall. However, we find a discrepancy for CO adsorbed in the hollow site, which we assign to the significantly stronger hybridization in hollow bonding than in on-top.

74 ATOMIC AND MOLECULAR PHYSICS↗