Search NASA⌕ Search

SEARCH · Search NASA

Results for “Proton structure”

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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Synthesis and anticancer effects of conjugates of doxorubicin and unsaturated fatty acids (LNA and DHA)

Doxorubicin (DOX) is a leading cytostatic drug with many adverse effects in use. We are still looking for methods that will allow us to preserve the therapeutic effect against the tumor cells and reduce the toxicity to the normal cells. In our work, we obtained amide derivatives of DOX by reaction of the amino group with α-linolenic (LNA) and docosahexaenoic (DHA) acids (2, 3), as well as double-substituted derivatives via amide and ester linkages (4, 5). The structures of the compounds were confirmed by Proton Nuclear Magnetic Resonance (1H NMR), Carbon-13 Nuclear Magnetic Resonance (13C NMR), and High Resolution Mass Spectrometry (HRMS) analyses. For all compounds 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) assay was used to determine the cytotoxic effect on human cancer cell lines (SW480, SW620, and PC3) and Chinese hamster lung fibroblasts (V79) that were used as a control. The cytotoxic activity was established by calculation of the inhibitory concentration IC{sub 50}. In addition, a cytotoxic capacity against tumor cells for tested compounds was expressed as a selectivity factor (selectivity index, SI). Lactate dehydrogenase (LDH) assay was performed for all compounds to assess the level of cell damage. To explain the basic mechanism of cell death induction the Annexin V-FITC/IP flow cytometry analysis was investigated. We found that all studied conjugates exhibit lower cytotoxicity but higher selectivity than DOX. Among the all derivatives, the conjugates formed by the amide and ester linkages (4, 5) were found to be more promising compared with conjugates (2, 3) formed only by the amide linkage. They show high cytotoxicity toward the tumor cell lines and moderate cytotoxicity towards the normal cell line.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.

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

Large-scale physically accurate modelling of real proton exchange membrane fuel cell with deep learning

Proton exchange membrane fuel cells, consuming hydrogen and oxygen to generate clean electricity and water, suffer acute liquid water challenges. Accurate liquid water modelling is inherently challenging due to the multi-phase, multi-component, reactive dynamics within multi-scale, multi-layered porous media. In addition, currently inadequate imaging and modelling capabilities are limiting simulations to small areas (<1 mm 2 ) or simplified architectures. Herein, an advancement in water modelling is achieved using X-ray micro-computed tomography, deep learned super-resolution, multi-label segmentation, and direct multi-phase simulation. The resulting image is the most resolved domain (16 mm 2 with 700 nm voxel resolution) and the largest direct multi-phase flow simulation of a fuel cell. This generalisable approach unveils multi-scale water clustering and transport mechanisms over large dry and flooded areas in the gas diffusion layer and flow fields, paving the way for next generation proton exchange membrane fuel cells with optimised structures and wettabilities.

25 ENERGY STORAGE↗
DOE OSTI2021

Mass measurements of 99–101 In challenge ab initio nuclear theory of the nuclide 100 Sn

The tin isotope 100 Sn is of singular interest for nuclear structure due to its closed-shell proton and neutron configurations. It is also the heaviest nucleus comprising protons and neutrons in equal numbers—a feature that enhances the contribution of the short-range proton–neutron pairing interaction and strongly influences its decay via the weak interaction. Decay studies in the region of 100 Sn have attempted to prove its doubly magic character but few have studied it from an ab initio theoretical perspective, and none of these has addressed the odd-proton neighbours, which are inherently more difficult to describe but crucial for a complete test of nuclear forces. Here we present direct mass measurements of the exotic odd-proton nuclide 100 In, the beta-decay daughter of 100 Sn, and of 99 In, with one proton less than 100 Sn. We use advanced mass spectrometry techniques to measure 99 In, which is produced at a rate of only a few ions per second, and to resolve the ground and isomeric states in 101 In. The experimental results are compared with ab initio many-body calculations. The 100-fold improvement in precision of the 100 In mass value highlights a discrepancy in the atomic-mass values of 100 Sn deduced from recent beta-decay results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio

Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Insights into the possible existence of a soft dipole mode in He 8

With an extreme neutron-to-proton ratio of N/Z = 3, 8 He provides an ideal laboratory for the study of a variety of exotic phenomena, such as the emergence of a soft dipole mode that is dominated by transitions into the continuum. In this contribution, a covariant density-functional theory (DFT) framework is used to compute ground-state properties and the dipole response of 8 He. Although 8 He is admittedly too light for DFT to be applicable, the great merit of the approach is that the spurious contamination associated with the center-of-mass motion is guaranteed to decouple from the physical response. Given that a strong mixing between the isoscalar and isovector dipole modes is expected for a system with such a large neutron-proton asymmetry as 8 He, the narrow structures that emerged at low energies in the isovector dipole response are attributed to the shift of the spurious strength to zero (or near zero) excitation energy. Furthermore, the theoretical framework implemented here disfavors the emergence of a soft dipole mode in 8 He.

6 ≤ A ≤ 19↗
DOE OSTI2024

Reduction of spectroscopic overlap across the Z = 8 shell in neutron-rich nuclei

The recent discovery and spectroscopic measurements of 27 O and 28 O suggests the disappearance of the N = 20 shell structure in these neutron-rich oxygen isotopes. We measured one- and two-proton removal cross sections from 27 F and 29 N, respectively, extracting spectroscopic factors and comparing them to shell model overlap functions coupled with eikonal reaction model calculations. The invariant mass technique was used to reconstruct the two-body ( 24 O + n) and three-body ( 24 O + 2n) decay energies from knockout reactions of 27 F (106.2 MeV/u) and 29 Ne (112.8 MeV/u) beams impinging on a 9 Be target. The one-proton removal from 27 F strongly populated the ground state of 26 O and the extracted cross section of $3.4^{+0.3}_{-1.5}$ mb agrees with eikonal model calculations that are normalized by the shell model spectroscopic factors and account for the systematic reduction factor observed for single nucleon removal reactions within the models used. For the two-proton removal reaction from 29 Ne an upper limit of 0.08 mb was extracted for populating states in 27 O decaying though the ground state of 26 O. The measured upper limit for the population of the ground state of 26 O in the two-proton removal reaction from 29 Ne indicates a significant difference in the underlying nuclear structure of 27 F and 29 Ne.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Overcoming the Conductance versus Crossover Trade-off in State-of-the-Art Proton Exchange Fuel-Cell Membranes by Incorporating Atomically Thin Chemical Vapor Deposition Graphene

Permeance–selectivity trade-offs are inherent to polymeric membranes. In fuel cells, thinner proton exchange membranes (PEMs) could enable higher proton conductance and increased power density with lower area-specific resistance (ASR), smaller ohmic losses, and lower ionomer cost. However, reducing thickness is accompanied by an increase in undesired species crossover harming performance and long-term efficiency. Here, we show that incorporating atomically thin monolayer graphene synthesized via scalable chemical vapor deposition (CVD) and tunable defect density into PEMs (Nafion, ~5–25 μm thick) can allow for reduced H 2 crossover (~34–78% of Nafion of a similar thickness) while maintaining adequate areal proton conductance for applications (>4 S cm –2 ). In contrast to most prior work using >50 μm symmetric Nafion sandwich structures, we elucidate the interplay of graphene defect density and Nafion proton transport resistance on the performance of Nafion|graphene composite membranes and find high-quality low-defect density CVD graphene (G) supported on Nafion 211 (~25 μm); i.e., N211|G has a high areal proton conductance (~6.1 S cm –2 ) and the lowest H 2 crossover (~0.7 mA cm –2 ). Fully functional centimeter-scale N211|G fuel-cell membranes demonstrate performance comparable to that of state-of-the-art Nafion N211 at room temperature as well as standard operating conditions (~80 °C, ~150–250 kPa-abs) with H 2 /air (power density ~0.57–0.63 W cm –2 ) and H 2 /O 2 feed (power density ~1.4–1.62 W cm –2 ) and markedly reduced H 2 crossover (~53–57%).

25 ENERGY STORAGE↗
DOE OSTI2021

Calculations versus measurements for residual dose rates from SNS spent structures

Here, residual dose rate measurements were conducted on target vessel #13 and proton beam window #5 after extraction from their service locations. These measurements are used to verify calculation methods of radionuclide inventory assessment that are typically performed for nuclear waste characterization and transportation of these structures. Neutronics analyses for predicting residual dose rates are carried out using the transport code MCNPX and the transmutation code CINDER90. For transport analyses a complex and rigorous geometry model of the structures and their surroundings are applied. The neutronics analyses are carried out using the Bertini and CEM high energy physics models for simulating particles interactions above the table-based cross section range. Finally, obtained calculational results are analyzed and compared to the measured dose rates and overall show good agreement within 25%, which shows applicability of the methods used in analyses.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Metastable multimeric G-quadruplex 2′FY-RNA aptamers that selectively bind pyoverdines

Two 2′FY-RNA aptamers with distinct sequences were selected for specific binding to pyoverdine-Pf5 (PVD-Pf5), increasing chromophore fluorescence upon binding. They also recognized the peptide portion of pyoverdines, as shown by their differential specificity for related variants. Computational analysis and experimental data (NMM binding, CD spectra) identified G-quadruplex structures that were thermally metastable but reformed in the presence of PVD-Pf5. Further structural studies mainly with one aptamer revealed imino proton peaks in 1D H-NMR and pressure stability up to 2 kbar. Electrophoretic evidence identified dimeric G-quadruplexes formed by the 2′FY-RNA aptamers and their RNA equivalents. While cations were necessary for PVD-Pf5 binding, they were not required for G-quadruplex formation. Given the established role of G-quadruplexes as protein interaction sites, multimeric G-quadruplexes offer a potential framework for structure-based regulatory mechanisms in cellular RNAs. In addition to previously characterized multimeric G-quadruplexes, these aptamers contribute novel sequences that expand the repertoire of known multimeric G-quadruplexes.

2′FY-RNA↗
DOE OSTI2020

Investigating Liquid Water Transport in Different Pore Structure of Gas Diffusion Layers for PEMFC Using Lattice Boltzmann Method

Proton exchange membrane fuel cells (PEMFC) require a gas diffusion layer (GDL) to aid in the transport of liquid fuel to the catalyst layer. In this work, direct modeling using the Lattice Boltzmann Method (LBM) was applied to X-ray CT scans of four different carbon gas diffusion layers to understand the mass transport properties through the samples. Three injection orientations were used to study local saturation levels, water evolution through the sample, and mass transport behavior at breakthrough conditions. The LBM, combined with computational fluid dynamic modeling techniques, can accurately predict liquid saturation at the macro and micro scale, which provides more insight into the mass transport phenomena through the GDL. The change of pore structure and orientation in both the in-plane and through-plane determines the path that liquid water must take, which could aid or impact PEMFC performance. The outcomes from this work will also benefit any research that needs knowledge of internal mass transport qualities of gas diffusion media.

Sepe, M.↗
DOE OSTI2024

Cu(II) Stability and UV-Induced Electron Transfer in a Metal–Organic Hybrid: An EPR, DFT, and Crystallographic Characterization of Copper-Doped Zinc Creatininium Sulfate

Single-crystal X-ray diffraction and electron paramagnetic resonance (EPR) spectroscopic experiments, complemented by quantum chemical DFT calculations, were carried out on the copper-doped metal–organic hybrid and Tutton salt analogue zinc creatininium sulfate to determine its crystal structure, to characterize the electronic structure of the doped Cu(II) binding site, and to propose a pathway for an excited-state, proton-coupled electron transfer (PCET) process in UV-exposed crystals. The crystal structure is isomorphous to that of cadmium creatininium sulfate, which has the transition ion, not in direct coordination with the creatinine, but forming a hexahydrate complex, which is bridged to a creatininium through an intervening sulfate ion. The EPR g (2.446, 2.112, 2.082) and copper hyperfine (A Cu : -327, -59.6, 10.8 MHz) tensor parameters are consistent with doped copper replacing host zinc in the metal–hexahydrate complex. These parameters are similar to those observed for copper hexahydrate in doped Tutton salt systems at low temperature, where the unpaired electron occupies mainly the copper 3d x 2 –y 2 orbital. At room temperature in the Tutton systems, vibration couplings stemming from a dynamic Jahn–Teller effect cause tensor averaging which results in a reduction in their maximum g-tensor and hyperfine tensor values. However, like for the doped isomorphous Cd creatinine crystal, the Cu(II) EPR exhibits little, or no room temperature averaging compared to its low temperature pattern. Samples exposed to 254 nm UV light generate a carbon-centered free radical species, characterized by an isotropic g-tensor (g = 2.0029) and an alpha-proton hyperfine coupling (-24 -14 +4 G). These parameters identify it as a creatinine radical cation formed by the oxidative release of one of its C2 methylene hydrogens. DFT calculations confirm the unpaired electronic structures of both the Cu(II) site and free radical. The growth in radical concentration with an increase in the UV exposure time coincides with a decrease in the copper EPR signal, indicating a coupled light-induced oxidation reduction process. A comparison of the crystal structure with the EPR parameters and DFT results provides evidence for a UV-induced PCET.

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

Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues

We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR–IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. Here, these observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.

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

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

Pyridoxal 5’-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Predominant Proton Insertion during Electrochemical Cycling of ε-VOPO 4 in a Nonaqueous Ca-Ion Electrolyte

Calcium-ion batteries (CIBs) are promising for next-generation energy storage systems. However, many reported Ca-ion storage mechanisms lack direct structural evidence, raising concerns that the observed electrochemistry may instead originate from proton insertion. Herein, we investigate the electrochemical cycling of a VOPO 4 electrode in an aprotic Ca electrolyte with trace water to clarify the charge storage mechanism. While electrochemistry, elemental analysis, and X-ray absorption spectroscopy seem to support Ca-ion intercalation in the VOPO 4 electrode, X-ray diffraction and electron microscopy unequivocally show proton insertion as the predominant charge storage mechanism. The apparent variation of Ca content in the electrode with the state of charge is attributed to the formation and dissolution of Ca-containing precipitates on the surface of VOPO 4 particles. Our work demonstrates the propensity of proton participation in the intercalation reaction in Ca-ion batteries and the necessity of structural evidence in understanding reactions in multivalent electrochemical systems.

Wang, Jiwei [Binghamton University, NY (United Sta↗
DOE OSTI2023

New Structure in the Deuteron

Here, we demonstrate that a paradigm shift from considering the deuteron as a system of a bound proton and neutron to that of a pseudovector system in which we observe a proton and neutron results in the possibility of probing a new “incomplete” P-statelike structure on the light front (LF). This occurs at extremely large internal momenta, which can be achieved in a high energy transfer electrodisintegration of the deuteron. Investigating the deuteron on the light front, where the vacuum fluctuations are suppressed, we found that this new structure, together with the conventional S and D states, is leading order in transferred energy of the reaction and thus not suppressed on the light front. The incompleteness of the observed P state results in a violation of the angular condition that can happen only if the deuteron contains non-nucleonic structures, such as Δ Δ, N*⁢N or hidden color components. We demonstrate that experimentally verifiable signatures of incomplete P states are angular anisotropy of the light front momentum distribution of the nucleon in the deuteron, as well as an enhancement of the tensor polarization strength beyond the S- and D-wave predictions at large internal momenta in the deuteron.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

NMR investigation of proton transport in polybenzimidazole/polyphosphoric acid membranes prepared via novel synthesis route

Here, in this work, we present a molecular-level view of the structural changes in polybenzimidazole (PBI) membranes doped with phosphoric acid (PA) generated by a novel membrane fabrication technique. The modified PA doped membranes displayed unprecedented ionic conductivity at elevated temperatures, comparable to the starting PBI gel membranes prepared by the commonly used PPA process, while also exhibiting enhanced mechanical properties. To elucidate the cause of these effects, we used multi-nuclear ( 1 H, 13 C, 31 P) 1D PFG, MAS and CPMAS, and 2D HETCOR magnetic resonance (NMR) techniques to characterize the structure and dynamics of the modified film and the original gel PBI membranes. 1 H diffusivity measurements show significantly enhanced proton diffusivity, both in magnitude and in lower activation energy, which were consistent with its high ionic conductivity despite the lower PA content compared to the original gel membrane. CPMAS experiments further substantiated that the location of these distinct phosphate environments as being close to the polymer network. Finally, the phosphate groups in the modified membrane were revealed to be strongly bounded to each other and to the PBI polymer backbone in contrast to the combination of weakly and strongly bounded groups of the original gel membrane.

74 ATOMIC AND MOLECULAR PHYSICS↗