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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.

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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Chapter Twelve - Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease

HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D2O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Correlated particle transport enables biological free energy transduction

Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., they use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibrium and interacting systems. Here, we show that neglecting correlations fails to describe free energy transduction, mistakenly predicting an abundance of slippage and energy dissipation, even for networks that are near reversible and lack interactions among particle sites. Interestingly, linear charge transport chains are well described without including correlations, even for networks that are driven and include site-site interactions typical of biological electron transfer chains. We examine three specific bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a near-reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures), and a redox-coupled proton pump (as in complex IV of respiration).

bacterial nanowires↗
DOE OSTI2024

Isomer-specific, Cryogenic Ion Vibrational Spectroscopy Investigation of D2-and N2- Tagged, Protonated Formic Acid Complexes Using Two Color, IR-IR Photobleaching

Here we analyze cryogenic ion vibrational spectra of tagged protonated formic acid (PFA) with electronic structure and anharmonic vibrational calculations to establish the isomers generated by electrospray ionization (ESI) followed by buffer gas cooling to ~25 K. Two isomers are identified (the trans form (E,Z) and the cis form (E,E)) and generated in comparable abundance despite the fact that the calculated E,E structure lies 6.40 kJ mol-1 above the E,Z form. A large (~60 kJ mol-1) barrier separates them such that the E,E form can be kinetically trapped upon cooling in the ion trap. The anticooperativity between the H-bonds of the OH groups is explored by measuring the shift in the D2-bound OH fundamental when a second D2 is attached. Both isomers are observed in the N2-tagged counterparts, displaying the expected red-shifted OH bands. These results indicate that ESI generates both isomers and both must be considered when analyzing cluster spectra based on the PFA core ion.

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

Determinants for proton location and electron coupled proton transfer in hydrogen bonded pentafluorophenol-anion clusters

This work aims to reveal the determinant factors for proton locations and electron coupled proton transfer (ECPT) in biologically relevant hydrogen bonded systems. Pentafluorophenol-anion clusters [C6F5O-•H+•A-]- are chosen to model active sites of biological functions, with the anion A- being systematically varied to ensure the proton affinities (PAs) of the anions well cover the referenced PA of C6F5O- from being appreciably smaller, similar, and to significantly larger. Negative ion photoelectron spectroscopy of these clusters provides spectroscopic evidence showing that proton location in the anionic state is largely following the PA prediction, while ECPT is observed only for the clusters with the anion possessing the electron binding energy (EBE) significantly larger than that of the referenced C6F5O-. Theoretical calculations suggest these clusters are stabilized by forming single strong hydrogen bond between donor and acceptor, and the associated charge and MO analyses fully support the experimental observations. The current holistic cluster model study indicates that PA is the right determinant that can be used to predict the proton location and describe hydrogen bonding structures, while both PA and EBE of anionic groups play important roles in facilitating ECPT process. This work was supported by U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Science, Geosciences, and Biosciences (X.-B.W.), and performed using EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory, which is operated by Battelle Memorial Institute for the DOE. Part of this work was supported by the National Natural Science Foundation of China (No-11604046 for JZ; No. 11727810 for ZRS), as well as “Chenguang Program” by Shanghai Education Development Foundation, Shanghai Municipal Education Commission (No. 16CG38) and Natural Science Foundation of Shanghai (No. 16ZR1448100) (JZ).

Zhang, Jian↗
DOE OSTI2023

Beam Energy Dependence of Fifth- and Sixth-Order Net-Proton Number Fluctuations in Au + Au Collisions at RHIC

We report the beam energy and collision centrality dependence of fifth and sixth order cumulants (C 5 , C 6 ) and factorial cumulants (κ 5 , κ 6 ) of net-proton and proton distributions, from $\sqrt{s_{NN}}$=3-200 GeV Au+Au collisions at RHIC. The net-proton cumulant ratios generally follow the hierarchy expected from QCD thermodynamics, except for the case of collisions at $\sqrt{s_{NN}}$ = 3 GeV. C 6 /C 2 for 0-40\% centrality collisions is increasingly negative with decreasing $\sqrt{s_{NN}}$, while it is positive for the lowest $\sqrt{s_{NN}}$ studied. These observed negative signs are consistent with QCD calculations (at baryon chemical potential, μ B ≤ 110 MeV) that include a crossover quark-hadron transition. In addition, for $\sqrt{s_{NN}}$≥ 11.5 GeV, the measured proton κ n , within uncertainties, does not support the two-component shape of proton distributions that would be expected from a first-order phase transition. Taken in combination, the hyper-order proton number fluctuations suggest that the structure of QCD matter at high baryon density, μ B ~750 MeV ($\sqrt{s_{NN}}$ = 3 GeV) is starkly different from those at vanishing μ B ~20MeV ($\sqrt{s_{NN}}$ = 200 GeV and higher).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Inferring nuclear structure from heavy isobar collisions using Trajectum

Nuclei with equal number of baryons but varying proton number (isobars) have many commonalities, but differ in both electric charge and nuclear structure. Relativistic collisions of such isobars provide unique opportunities to study the variation of the magnetic field, provided the nuclear structure is well understood. In this work we simulate collisions using several state-of-the-art parametrizations of the ^{96}_{40} 40 96 Zr and ^{96}_{44} 44 96 Ru isobars and show that a comparison with the exciting STAR measurement [arXiv:2109.00131] of ultrarelativistic collisions can uniquely identify the structure of both isobars. This not only provides an urgently needed understanding of the structure of the Zirconium and Ruthenium isobars, but also paves the way for more detailed studies of nuclear structure using relativistic heavy ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

A STUDY OF SHORT-RANGE CORRELATED PAIR FORMATION MECHANISMS

Short-Range Correlations (SRCs) refers to pairs of nucleons that are temporary high density fluctuations with high relative momenta and lower center-of-mass momenta com pared to the nuclear Fermi momentum (kF). SRCs account for 20–25% of the nucleons in medium to heavy nuclei, make up essentially all nucleons with momentum greater than kF, and contribute most of the kinetic energy carried by nucleons in nuclei. The existing semi-inclusive and exclusive measurements only cover a handful of light nu clei or heavy elements. This does not allow for a systematic study of the dependence of SRC pairs on nuclear mass and proton-neutron asymmetry. It also does not allow for insights into SRC pairing mechanisms. Therefore, we systematically studied the individual probabilities for finding SRC protons in symmetric and neutron-rich asymmetric nuclei d, 9Be, 10B, 11B, 12C, 40Ca, 48Ca, 54Fe, and 197Au. We measured the (e,e'p) reaction in kinematics dominated by scattering off mean-field nucleons (k = kF) and nucleons in SRC pairs (k = kF) at the Thomas Jefferson National Accelerator Facility (JLab) in Hall C of the Continuous Electron Beam Accelerator Facility (CEBAF) in the Fall of 2022. The measured results were used to determine the SRC pairing probabilities for protons to examine how pairing depends on nuclear mass, proton-neutron asymmetry, and nuclear shell structure. The extracted cross-section ratios were also compared to theoretical calculations. We found that SRC pair formation depends more on the nuclear shell structure with sharp increases locally within the general trend of a slower increase with larger A. We also found that intra-shell pairing has a much larger influence than inter-shell pairing. Comparisons to theory suggest that angular momentum selection rules are important to SRC pair formation and can provide new constraints for new theoretical models.

Swan, Noah [Old Dominion Univ., Norfolk, VA (Unite↗
DOE OSTI2022

Laser spectroscopy for the study of exotic nuclei

Investigation into the properties and structure of unstable nuclei far from stability is a key avenue of research in modern nuclear physics. These efforts are motivated by the continual observation of unexpected structure phenomena in nuclei with unusual proton-to-neutron ratios. In recent decades, laser spectroscopy techniques have made significant contributions in our understanding of exotic nuclei in different mass regions encompassing almost the entire nuclear chart. This is achieved through determining multiple fundamental properties of nuclear ground and isomeric states, such as nuclear spins, magnetic dipole and electric quadrupole moments and charge radii, via the measurement of hyperfine structures and isotope shifts in the atomic or ionic spectra of the nuclei of interest. These properties offer prominent tests of recently developed state-of-the-art nuclear theory and help to stimulate new developments in improving the many-body methods and nucleon–nucleon interactions at the core of these models. With the aim of exploring more exotic short-lived nuclei located ever closer to the proton and neutron driplines, laser spectroscopy techniques, with their continuous technological developments towards higher resolution and higher sensitivity, are extensively employed at current- and next-generation radioactive ion beam facilities worldwide. Ongoing efforts in parallel promise to improve the availability of these even more exotic species at next-generation facilities. Very recently, an innovative application of laser spectroscopy on molecules containing short-lived nuclei has been demonstrated offering additional opportunities for several fields of research, e.g. fundamental symmetry studies and astrophysics. Here, in this review, the basic nuclear properties measurable with laser spectroscopy will be introduced. How these observables are associated with nuclear structure and nucleon–nucleon interactions will be discussed. Following this, a general overview of different laser spectroscopy methods will be given with particular emphasis on technical advancements reported in recent years. The main focus of this article is to review the numerous highlights that have resulted from studying exotic nuclei in different mass regions with laser spectroscopy techniques since the last edition in this series. Finally, the challenges facing the field in addition to future opportunities will be discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Design and structural assessment of the Spallation Neutron Source 2.0 MW target

The Proton Power Upgrade (PPU) project is underway at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory. The project will double the proton accelerator power from 1.4 MW to 2.8 MW, increase power to the First Target Station (FTS), and enable a future Second Target Station (STS). The power increase partly comes from raising proton energy from 1.0 GeV to 1.3 GeV. The STS will operate at 0.7 MW at 15 Hz when completed. Until then, PPU will provide the capability to operate the FTS at 2.0 MW at 60 Hz. Maximum power at the FTS to date has been 1.4 MW at 60 Hz with 1.0 GeV protons. A new mercury target module design to operate reliably under PPU conditions has been completed after a multi-year effort. The design philosophy and assessment of the structural analysis are described here. This target underwent an unprecedented design and analysis process for SNS using the latest engineering techniques and incorporating years of operating lessons and outcomes from R&D to meet structural design criteria. Finally, it also incorporates high-flow gas injection to further mitigate pulse fatigue stresses as well as cavitation damage to the mercury vessel.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Elastic scattering in the 12 N + 197 Au system at 𝐸 lab = 70 MeV

Halo structure is an interesting exotic configuration developed in some light weakly bound nuclei, where a valence particle orbits a nuclear core. Signatures of halo structure can be observed in the angular distributions of the elastic scattering induced by these nuclei at energies around the Coulomb barrier. There are some well-studied reactions with neutron-rich halo nuclei, such as 6 He and 11 Li . However, the information is scarce on the proton-rich side. Recent works confirm the halo structure in the 8B nuclei but still lack more experimental studies for other proton-halo candidates, such as 12 N and 17 F. In this work, we report experimental data for the elastic scattering of 12 N on 197 Au target at 𝐸 lab = 70 MeV. The 12 N is a proton-rich nucleus with proton separation energy 𝑆 𝑝 = 600 keV, which is higher than the 8 B (𝑆 𝑝 = 137 keV) and almost the same as the 17 F (𝑆 𝑝 = 601 keV). Data were obtained at the Cyclotron Institute of Texas A&M University where the 12 N radioactive beam was produced by the momentum achromatic recoil spectrometer. The calculation of the optical model was used to fit the measured angular distribution for the elastic scattering and to obtain the reaction cross section 𝜎 𝑅 . We also performed continuum discretized coupled-channel calculations to compare with the experimental data. The angular distribution of the elastic cross sections exhibits a suppression of the Fresnel peak. From the fitting of the optical model, we obtain the total reaction cross section, 𝜎 𝑅 = 1269 ± 41 mb. The agreement between the CDCC calculation and the experimental elastic scattering data is limited and the breakdown does not exhaust the measured 𝜎 𝑅 . The resulting reduced reaction cross section 𝜎 Red for 12 N + 197 Au is large and comparable to the one obtained for the 8 B + 208 Pb system. This suggests a strong decoupling of the valence proton from the core because of the low binding energy and a dynamic polarization effect. Here, more research is required to estimate the contribution of core excitation.

Elastic scattering reactions↗
DOE OSTI2023

A Joint Modeling/Experimental Approach to Characterize Ionization and Fragmentation of SOA Molecules with CIMS

The Molecular Dynamics technique Collective variable hyperdynamics (CVHD) interfaced with density functional tight-binding at the GFN1-xTB and GFN2-xTB levels of electronic structure theory has been applied to the H + GAG positively charged peptide system to explore the fragmentation of this simple tripeptide under relatively low temperature/energy conditions. Unlike conventional chemical dynamics simulations which can only be performed up to hundreds of picoseconds when coupled with semi-empirical Hamiltonians, CVHD is able to capture the long-time dynamics of multiple proton hopping, the formation of reversible ring structures, and ester rearrangement of the H + GAG system prior to fragmentation. The CVHD method applied to H + GAG is also able to uncover alternative fragmentation pathways not considered previously such as glycine fragmentation on the N-terminal side of the charged peptide and new cyclic cationic species. These findings in the H + GAG case have implications for other peptide systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Quasi-free scattering in inverse kinematics as a tool to unveil the structure of nuclei: A tribute to Mahir S. Hussein

Abstract Quasi-free scattering of electrons and protons has been extensively utilized in the past to study the single-particle structure of nuclei, clustering in light nuclei, and short-range correlated nucleon–nucleon pairs in nuclei. Recently, this approach has been applied in inverse kinematics using hydrogen targets. The characteristic features of this reaction and the experimental challenges and advantages of inverse-kinematics experiments are summarized. The applicability to radioactive beams opens a large research potential to study a variety of properties of neutron-to-proton asymmetric nuclei. Applications of quasi-free scattering in inverse kinematics and its potential are reviewed based on recent and ongoing research programs at different accelerator facilities worldwide.

Physics↗
DOE OSTI2022

Solvated Nuclear–Electronic Orbital Structure and Dynamics

Nonadiabatic dynamical processes such as proton-coupled electron transfer and excited state intramolecular proton transfer have been the subject of much research. One of the promising theoretical methods to describe these processes is the nuclear–electronic orbital (NEO) approach. This approach inherently accounts for nuclear quantum effects within quantum chemistry calculations, and it has recently been extended to directly simulate nonadiabatic processes with the development of real-time NEO methods. These processes can also be significantly dependent on the surrounding chemical environment, however, and capturing the effects of the environment is often necessary for analyzing experimentally relevant systems. This work couples the NEO density functional theory and real-time time-dependent density functional theory approaches with solvation through the polarizable continuum model. Here, the effects of this coupling are investigated for ground state properties, solvent-dependent vibrational frequencies, and direct excited state intramolecular proton transfer dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2025

Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Clarifying the 𝑁,𝑍 = 14 Shells near the Drip Lines from the Spectroscopy of 22 Si and 21 Al

Evidence for a (sub)-shell closure at 𝑍 = 14 has been observed from the spectroscopy of 22 Si and 21 Al . Using a fast 23 Si beam on a 9 Be target, several proton-decaying resonances have been populated in 21 Al and 22 Si , including the first measurement of the 2$^{+}_{1}$ state in 22 Si with an excitation energy of 2.352(55) MeV. Relative to the known 𝑁 = 14 subshell closure in 22 O , the 22 Si 2$^{+}_{1}$ excitation energy indicates the existence of a weakened 𝑍 = 14 subshell closure. To reproduce the new spectroscopic information and known 22 Al levels, the energy of the 1⁢𝑠 1/2 orbit must be substantially decreased, which imparts Thomas-Ehrman shifts to all excited states observed in the present Letter and explains the structure of nuclei in the 𝑠⁢𝑑 shell for this region of the proton drip line.

20 ≤ A ≤ 38↗
DOE OSTI2024

Identification of Unique Fragmentation Patterns of Fentanyl Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry

The opioid crisis in the United States is being fueled by the rapid emergence of new fentanyl analogs and precursors that can elude traditional library-based screening methods, which require data from known reference compounds. Since reference compounds are unavailable for new fentanyl analogs, we examined if fentanyls (fentanyl + fentanyl analogs) could be identified in a reference-free manner using a combination of electrospray ionization (ESI), high-resolution ion mobility (IM) spectrometry, high-resolution mass spectrometry (MS), and higher-energy collision-induced dissociation (MS/MS). We analyzed a mixture containing nine fentanyls and W-15 (a structurally similar molecule) and found that the protonated forms of all fentanyls uniquely exhibited two baseline separated IM distributions that produced different MS/MS patterns. Upon fragmentation, both IM distributions of all fentanyls produced two high intensity fragments resulting from amine site cleavages. The higher mobility distributions of all fentanyls also produced several low intensity fragments, but surprisingly, these same fragments exhibited much greater intensities in the lower mobility distributions. This observation demonstrates that many fragments of fentanyls predominantly originate from one of two different gas-phase structures (suggestive of protomers). Furthermore, increasing the water concentration in the ESI solution increased the intensity of the lower mobility distribution relative to the higher mobility distribution, which further supports that fentanyls exist as two gas-phase protomers. In conclusion, our new observations on the IM and MS/MS properties of fentanyls can be exploited to positively identify them as fentanyls without requiring reference libraries and will hopefully assist first responders and law enforcement in combating new and emerging fentanyls.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗