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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Electrochemistry in the Large Tunnels of Lithium Postspinel Compounds

Lithium spinels (Li MM 'O 4 ) are an important class of mixed-cation materials that have found uses in batteries, catalysis, and optics. Postspinels are a series of related framework structures with the AMM 'O 4 host composition that are formed with larger A -site cations, typically under high pressure. Postspinels have one-dimensional tunnel structures with pores that are larger than those in spinel and triangular in cross-section, but they are relatively unexplored as intercalation electrodes. While lithium postspinels have been previously found to be thermodynamically stable only at high pressures, we have identified a synthetic pathway that produces the lithium-containing materials at ambient pressure using an ion-exchange process from the corresponding sodium postspinels. Here, in this work, we report the synthesis and a survey of the electrochemical properties of 10 new lithium CaFe 2 O 4 -type postspinel compounds where M = Mn 3+ , V 3+ , Cr 3+ , Rh 3+ , Fe 2+ , Mg 2+ , Co 2+ and M ' = Ti 4+ and/or Sn 4+ . Although complete delithiation is not achieved during electrochemical cycling, many of the lithium postspinels have substantial charge storage capacity in Li battery cells owing to the ability of the large framework tunnels to accommodate more than one lithium ion per formula unit. Multiple redox couples are accessed for LiMnSnO 4 , Li 0.96 Mn 0.96 Sn 1.04-x Ti x O 4 , Li 0.96 V 0.96 Ti 1.04 O 4 , Li 0.96 Cr 0.96 Ti 1.04 O 4 , and LiFe 0.5 Ti 1.5 O 4 . Compositions with moderate or poor lithium cyclability are also discussed for comparison. Redox mechanisms and trends are identified by comparing this new redox-active framework to related spinels, ramsdellites, and 'Na 0.44 MnO 2 ' structures, and from density functional theory (DFT) electronic structures. Operando diffraction shows complex structural responses to lithium insertion and extraction in this postspinel framework. A DFT framework was proposed to identify promising lithium postspinel phases that could be accessed metastably under ambient pressure conditions and to assess their stability to lithium insertion and extraction. This work suggests that CaFe 2 O 4 -type hosts are a promising new class of lithium-ion energy storage materials.

25 ENERGY STORAGE↗
DOE OSTI2020

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↗
DOE OSTI2022

Mercury Removal from Contaminated Water by Wood-Based Biochar Depends on Natural Organic Matter and Ionic Composition

Biochars can remove potentially toxic elements, such as inorganic mercury [Hg(II)] from contaminated waters. However, their performance in complex water matrices is rarely investigated, and the combined roles of natural organic matter (NOM) and ionic composition in the removal of Hg(II) by biochar remain unclear. Here, we investigate the influence of NOM and major ions such as chloride (Cl – ), nitrate (NO 3 – ), calcium (Ca 2+ ), and sodium (Na + ) on Hg(II) removal by a wood-based biochar (SWP700). Multiple sorption sites containing sulfur (S) were located within the porous SWP700. In the absence of NOM, Hg(II) removal was driven by these sites. Ca 2+ bridging was important in enhancing removal of negatively charged Hg(II)-chloro complexes. In the presence of NOM, formation of soluble Hg-NOM complexes (as seen from speciation calculations), which have limited access to biochar pores, suppressed Hg(II) removal, but Cl – and Ca 2+ could still facilitate it. The ability of Ca 2+ to aggregate NOM, including Hg-NOM complexes, promoted Hg(II) removal from the dissolved fraction (<0.45 μm). Hg(II) removal in the presence of Cl – followed a stepwise mechanism. Weakly bound oxygen functional groups in NOM were outcompeted by Cl – , forming smaller-sized Hg(II)-chloro complexes, which could access additional intraparticle sorption sites. Therein, Cl – was outcompeted by S, which finally immobilized Hg(II) in SWP700 as confirmed by extended X-ray absorption fine structure spectroscopy. We conclude that in NOM containing oxic waters, with relatively high molar ratios of Cl – : NOM and Ca 2+ : NOM, Hg(II) removal can still be effective with SWP700.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Desorption of Phosphate from Iron-Bearing Soil Minerals by a Plant Secondary Metabolite

In soils, phosphorus readily adsorbs to the surfaces of ubiquitous iron (oxyhydr)oxide minerals, rendering it less accessible to plants and microorganisms. Plants have a number of strategies to access iron, among them the secretion of redox-active metabolites from their roots. Although these strategies likely increase the bioavailability of surface-adsorbed phosphorus through reductive dissolution, their effect on phosphorus cycling has not yet been investigated. We tested the ability of fraxetin, a coumarin-type redox-active metabolite produced by the model plant Arabidopsis thaliana and other dicotyledon plant species, to reductively solubilize phosphate from the surface of ferrihydrite. Our findings show that, at low and neutral pH, fraxetin increased aqueous phosphate concentrations under both oxic and anoxic conditions; at high pH, it was only effective in anoxic experiments. Additionally, a combination of liquid chromatography–mass spectrometry and spectroscopic methods demonstrated substantial fraxetin adsorption to the mineral surface but showed that iron reduction did not alter the mineral structure or change the nature of the chemical environment of the phosphorus atom over short time scales. These results provide evidence that the secretion of redox-active metabolites from roots is likely to be an effective phosphorus acquisition tactic in iron-rich soils.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A Semi-Empirical Density Law for Ternary, Homogeneous PuCl 3 /HCl/H 2 O Solutions

Nuclear material operations pose unique hazards that are not encountered in other chemical, energy, or manufacturing industries. One of these hazards is the potential for a nuclear criticality accident when handling fissile isotopes such as 235 U and 239 Pu. These hazards are particularly high when fissile material is dissolved in solution as the neutron behaviors of the system can change rapidly with the physical and chemical changes accessible in solution. Current estimates of solution density used for criticality safety are outdated and hinder fissile material handling. Developing new estimates for these safety calculations requires experimental characterization and the derivation of empirical density models. We have derived a density law describing PuCl 3 /HCl/H 2 O solutions from experimental data characterizing solution density. Density data was treated using a Pitzer-derived eight-parameter equation, defining density as a function of analyte concentrations, temperature, and interactions between these variables. The model is predictive across the concentration and temperature ranges from which it was derived. The potential effects of varying oxidation states of plutonium, which are easily accessible in aqueous media, on the bulk solution density of the ternary system were also investigated. The resulting Pitzer-derived density law was applied to a nuclear criticality safety model, and the impact of the experimental characterization of solution density relative to previous estimates was demonstrated to be significant and suggest that the current approach to estimating density in nuclear criticality safety calculations may lead to overly conservative controls.

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

A Solid-State Support for Separating Astatine-211 from Bismuth

Increasing access to the short-lived α-emitting radionuclide astatine-211 ( 211 At) has the potential to advance targeted α-therapeutic treatment of disease and to solve challenges facing the medical community. For example, there are numerous technical needs associated with advancing the use of 211 At in targeted α-therapy, e.g., improving 211 At chelates, developing more effective 211 At targeting, and characterizing in vivo 211 At behavior. There is an insufficient understanding of astatine chemistry to support these efforts. The chemistry of astatine is one of the least developed of all elements on the periodic table, owing to its limited supply and short half-life. Increasing access to 211 At could help address these issues and advance understanding of 211 At chemistry in general. Here, we contribute an extraction chromatographic processing method that simplifies 211 At production in terms of purification. It utilizes the commercially available Pre-Filter resin to rapidly (<1.5 h) isolate 211 At from irradiated bismuth targets (Bi decontamination factors ≥876 000), in reasonable yield (68–55%) and in a form that is compatible for subsequent in vivo study. We are excited about the potential of this procedure to address 211 At supply and processing/purification problems.

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

Probing Mg Intercalation in the Tetragonal Tungsten Bronze Framework V 4 Nb 18 O 55

While commercial Li-ion batteries offer the highest energy densities of current rechargeable battery technologies, their energy storage limit has almost been achieved. Therefore, there is considerable interest in Mg batteries, which could offer increased energy densities in comparison to Li-ion batteries if a high-voltage electrode material, such as a transition-metal oxide, can be developed. However, there are currently very few oxide materials which have demonstrated reversible and efficient Mg 2+ insertion and extraction at high voltages; this is thought to be due to poor Mg 2+ diffusion kinetics within the oxide structural framework. Here, in this paper, the authors provide conclusive evidence of electrochemical insertion of Mg 2+ into the tetragonal tungsten bronze V 4 Nb 18 O 55 , with a maximum reversible electrochemical capacity of 75 mA h g –1 , which corresponds to a magnesiated composition of Mg 4 V 4 Nb 18 O 55 . Experimental electrochemical magnesiation/demagnesiation revealed a large voltage hysteresis with charge/discharge (1.12 V vs Mg/Mg 2+ ); when magnesiation is limited to a composition of Mg 2 V 4 Nb 18 O 55 , this hysteresis can be reduced to only 0.5 V. Hybrid-exchange density functional theory (DFT) calculations suggest that a limited number of Mg sites are accessible via low-energy diffusion pathways, but that larger kinetic barriers need to be overcome to access the entire structure. The reversible Mg 2+ intercalation involved concurrent V and Nb redox activity and changes in crystal structure, as confirmed by an array of complementary methods, including powder X-ray diffraction, X-ray absorption spectroscopy, and energy-dispersive X-ray spectroscopy. Consequently, it can be concluded that the tetragonal tungsten bronzes show promise as intercalation electrode materials for Mg batteries.

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

Impact of Pendant Amine Basicity on Electrochemically-Promoted Cobalt Hydride Formation: Kinetic and Mechanistic Analysis

Here, we report the role of pendant amine basicity on the proton-coupled electron transfer (PCET) reactivity for the conversion of [Co III Cp(P Ph 2 N R 2 )(CH 3 CN)] 2+ complexes to [HCo III Cp(P Ph 2 N R 2 )] + , which is a key transformation involved in catalytic CO 2 conversion to formate and in H 2 evolution. Three complexes were studied, where the amine substituent (R) varies from benzyl, methoxyphenyl, or phenyl. In previous work on the benzyl system, we showed that the amine on the P Ph 2 N Bn 2 ligand serves as a kinetically accessible protonation site and enables three participating hydride formation mechanisms. In this work, a combination of electrochemical measurements and theoretical calculations were used to show that the electronic donation at the pendant amine influences the accessible PCET mechanism and proton transfer kinetics related to cobalt hydride formation under analogous reaction conditions. Notably, the amine with the most electron-donating substituent correlates to the lowest barrier for amine protonation, and specific cobalt hydride formation mechanisms can be shut off for the amine with the least electron-donating substituent. The mechanistic and kinetic changes upon modulation of the amine substituent have great implications for overall catalytic efficiency and selectivity, especially to generate the cobalt hydride intermediate involved in selective CO 2 reduction to formate. This work shows how to exploit kinetic basicity using ligand-cooperative design to facilitate PCET reactions involved in energy related transformations.

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

Toward a Diverse Next-Generation Energy Workforce: Teaching Artificial Photosynthesis and Electrochemistry in Elementary Schools through Active Learning

Artificial photosynthesis is a promising approach to generate commodity chemicals using abundant chemical feedstocks and renewable energy sources. Despite its importance, affordable and effective hands-on classroom activities that demonstrate artificial photosynthesis and teach key concepts, especially for primary school students, are lacking. Educating young students on this topic is a critical step in the development of the next-generation energy workforce, especially one that is diverse in race and gender. Here, we hypothesize that an effective approach to educate a broad range of young students on the topic of artificial photosynthesis is through the use of an active learning-based lesson plan that employs cheap and accessible materials. This hypothesis is confirmed by evaluating the understanding of fifth grade students with a survey before and after a lesson plan on artificial photosynthesis that uses active-learning techniques and uses safe and highly accessible materials (baking soda, tap water, plastic jars, Ni coil, alligator clips, and a solar cell) to perform solar-powered water splitting. The lesson plan and survey questions are designed to align with the educational outcomes for fifth grade classrooms in California and to address four general learning objectives: (1) Motivations of Artificial Photosynthesis, (2) Applications of Artificial Photosynthesis, (3) Inputs and Outputs of Artificial Photosynthesis, and (4) Engineering Design for Artificial Photosynthesis. The survey data demonstrate a statistically significant improvement in overall student understanding from the lesson plan. Importantly, the data show that the lesson plan presented here is effective at narrowing the performance gap between minority students and overly represented groups.

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

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. In this work, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (~98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ~1.5 million atoms is discussed in the context of MuMMI.

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

A Data Deposition Platform for Sharing Nuclear Magnetic Resonance Data

Nuclear magnetic resonance (NMR) data are rarely deposited in open databases, leading to loss of critical scientific knowledge. Existing data reporting methods (images, tables, lists of values) contain less information than raw data, and are poorly standardized. Together, these issues limit FAIR (findable, accessible, interoperable, reusable) access to these data, which in turn creates barriers for compound dereplication and the development of new data-driven discovery tools. Existing NMR databases are either not designed for natural products data, or employ complex deposition interfaces that disincentivize deposition. Journals, including the Journal of Natural Products (JNP), are now requiring data submission as part of the publication process, creating the need for a streamlined, user-friendly mechanism to deposit and distribute NMR data. Recently, our team reported the development of the Natural Products Magnetic Resonance Database (NP-MRD; www.np-mrd.org). Here in this paper we present a new data deposition platform for the NP-MRD project that is designed to enable users to deposit NMR data for published or submitted manuscripts in under five minutes. This platform includes a suite of automated data extraction and standardization tools, together with a simple-to-use web-based interface and detailed error reporting to simplify the data deposition process and is available at www.np-mrd.org/submissions.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Photodissociation Dynamics of CH 2 OO on Multiple Potential Energy Surfaces: Experiment and Theory

UV excitation of the CH 2 OO Criegee intermediate across most of the broad span of the (B 1A') – (X 1A') spectrum results in prompt dissociation to two energetically accessible asymptotes: O ( 1 D) + H 2 CO (X 1 A 1 ) and O ( 3 P) + H 2 CO (a 3A"). Dissociation proceeds on multiple singlet potential energy surfaces that are coupled by two regions of conical intersection (CoIn). Velocity map imaging (VMI) studies reveal a bimodal total kinetic energy (TKER) distribution for the O ( 1 D) + H 2 CO (X 1 A 1 ) products with the major and minor components accounting for ca. 40% and ca. 20% on average of the available energy (E avl ), respectively. The unexpected low TKER component corresponds to highly internally excited H 2 CO (X 1 A 1 ) products accommodating ca. 80% of E avl . Full dimensional trajectory calculations suggest that the bimodal TKER distribution of the O ( 1 D) + H 2 CO (X 1 A 1 ) products originates from two different dynamical pathways: a primary pathway (69%) evolving through one CoIn region to products and a smaller component (20%) sampling both CoIn regions enroute to products. Those that access both CoIn regions likely give rise to the more highly internally excited H 2 CO (X 1 A 1 ) products. The remaining trajectories (11%) dissociate to O ( 3 P) + H 2 CO (a 3 A") products after traversing through both CoIn regions. Here, the complementary experimental and theoretical investigation provides insight on the photodissociation of CH 2 OO via multiple dissociation pathways through two regions of CoIn that control the branching and energy distributions of products.

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

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. Here we find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

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

Interpreting the Operando XANES of Surface-Supported Subnanometer Clusters: When Fluxionality, Oxidation State, and Size Effect Fight.

X-ray absorption near edge structure (XANES) spectroscopy is widely used for operando catalyst characterization. We show that, for highly fluxional supported nanoclusters, the customary extraction of the oxidation state of the metal from the XANES data by fitting to the bulk standards is highly questionable. The XANES signatures as well as the apparent oxidation state for such clusters arise from a complex combination of many factors, and not only from the chemical composition in reaction conditions (e.g., oxygen content in oxidizing atmosphere). The thermally accessible isomerization and population of several structurally distinct cluster forms, cluster-support interaction, and intrinsic size effects all impact the metal oxidation state and XANES signal. We demonstrate this on copper oxide clusters with different compositions, Cu4Ox(x = 2-5) and Cu5Oy (y = 3, 5), deposited on amorphous alumina and ultrananocrystalline diamond, for which we computed the XANES spectra and compare the results to the experiment. We show in addition that fitting the experimental spectrum to calculated spectra of supported clusters can, in contrast, provide good agreement and insight into the spectrum-composition-structure relation. Experimental XANES interpreted using the proposed fitting scheme shows the partial reduction of Cu oxide clusters at rising temperatures, and pinpoints the specific stoichiometries that dominate in the ensemble of cluster states as the temperature changes.

Zandkarimi, Borna↗
DOE OSTI2022

Capacitance of Carbon Nanotube/Graphene Composite Electrodes with [BMIM + ][BF$_4^–$]/Acetonitrile: Fixed Voltage Molecular Dynamics Simulations

The capacitance of nanoporous carbon electrode materials is dictated by the physical interactions with electrolyte ions and molecules at the accessible interior electrode surface. While significant progress has been made in designing and synthesizing carbon materials with well-defined and relatively homogeneous nanoporosity, the majority of materials remain heterogeneous, and the resulting properties reflect an average over this distribution. In this regard, computer simulations can be a valuable tool to predict or validate structure/property relationships by systematically investigating well-defined, model electrode morphologies. In this work, we utilize fixed-voltage molecular dynamics simulations to predict structure/capacitance relationships for five different model morphologies of carbon nanotube/graphene (CNT/G) composite electrodes with 1-butyl-3-methylimidazolium tetrafluoroborate/acetonitrile electrolyte. The CNT/G electrode models are inspired by experimental “layer-by-layer” syntheses and strike a balance between realism and computational tractability. Comparison between different model electrode architectures elucidates important structure/property relationships. We find that CNT/graphene contact points serve as “hot spots” with significantly enhanced charge separation relative to the rest of the electrode. Furthermore, we demonstrate a specific nanoconfinement motif that provides substantial 3–4$\times$ enhancement of local capacitance, resulting in a ~40% increase of the total electrode differential capacitance. Because the accessible surface area of the model CNT/G electrodes is precisely determined, a comparison of per-area capacitance across systems is unambiguous. Our results thus complement a prior computational demonstration of capacitance enhancement in nanoconfinement while elucidating additional interaction motifs at CNT/G electrochemical interfaces.

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

Elucidation of Ultrafast Decay, Vibrational Beating, and Slow Decay Processes of Excited Azulene

Azulene’s nonradiative decay dynamics and kinetics from its singlet excited-states were studied using mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) combined with trajectory surface-hopping nonadiabatic molecular dynamics (NAMD) and Fermi’s golden rule (FGR) rate theory. The NAMD dynamics reproduce experimental observations that the S 1 → S 0 decay is accelerated and exhibits a crossover from mono- to biexponential kinetics with increasing excess vibrational energy. Minimum-energy-path analyses reveal a continuous S 1 /S 0 conical-intersection seam slightly above the S 1 minimum, providing readily accessible funnels. Time-resolved normal-mode projections reveal selective energy funneling into C–C stretching modes at 1272, 1528, and 1692 cm –1 . Constructive combinations of the latter two modes appear to promote rapid access to the conical-intersection seam, whereas their beating at ∼ 160 fs imposes a natural limit on the decrease of the decay time upon a further increase of excess energies, suggesting that their interference delays the decay. Here, the FGR rate calculation data for the S 1 → S 0 transition reaffirm that the nonradiative decay proceeds mainly near or through the conical intersection, rather than via simple nonadiabatic derivative coupling around the minimum of S 1 . On the other hand, the FGR rates indicate that S 2 decays predominantly to S 0 , as the S 2 –S 1 vibronic coupling is exceptionally weak, which serves as a primary cause for azulene’s characteristic anti-Kasha emission.

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

Open-Source and FAIR Research Software for Proteomics

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Inter-Leaflet Phospholipid Exchange Impacts the Ligand Density Available for Protein Binding at Supported Lipid Bilayers

Phospholipid bilayers formed at solid-liquid interfaces have garnered interest as mimics of cell-membranes to model association reactions of proteins with lipid-bilayer-tethered ligands. Despite the importance of understanding how ligand density in a lipid bilayer impacts the protein-ligand association response, relating the ligand-modified lipid fraction to the absolute density of solution-accessible ligands in a lipid bilayer remains a challenge in interfacial quantitative analysis. In this work, confocal-Raman microscopy is employed to quantify the association of anti-biotin IgG with a small fraction of biotinylated lipids dispersed in either gel-phase or liquid-crystalline supported lipid bilayers, deposited on the interior surfaces of wide-pore silica surfaces. We examine the question whether inter-leaflet lipid translocation contributes to the population of solution-accessible biotin ligands on the distal leaflet of a supported lipid bilayer by comparing their protein accumulation response with ligands dispersed in lipid monolayers on nitrile-derivatized silica surfaces. The binding of antibody to biotin ligands dispersed in gel-phase bilayers exhibited an equivalent biotin-coverage response as the accumulation of IgG onto gel-phase monolayers, indicating that gel-phase bilayer symmetry was preserved. This result contrasts with the ~60% greater anti-biotin capture observed at fluid-phase bilayers compared to fluid-phase monolayers prepared at equivalent biotin fractions. This enhanced protein capture is attributed to biotin-capped lipids being transferred from the surface-associated proximal leaflet of the bilayer to the solution-exposed distal leaflet by the inter-leaflet exchange or lipid flip-flop, a facile process in fluid-phase supported lipid bilayers. Here, the results suggest caution in interpreting the results of quantitative studies of protein binding to lipid-tethered ligands dispersed in fluid-phase phospholipid bilayers.

36 MATERIALS SCIENCE↗