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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 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO 3 Biological Crystallization

A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO 3 crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. Finally, this foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Local Electric Field Effects on Water Dissociation in Bipolar Membranes Studied Using Core–Shell Catalysts

The local electric field strength is thought to affect the rate of water dissociation (WD) in bipolar membranes (BPMs) at the catalyst–nanoparticle surfaces. Here, we study core–shell nanoparticles, where the core is metallic, semiconducting, or insulating, to understand this effect. The nanoparticle cores were coated with a WD catalyst layer (TiO2 or HfO2) via atomic layer deposition (ALD), and the morphology was imaged with transmission electron microscopy. Irrespective of the core material, these core–shell catalysts displayed comparable WD overpotentials at optimal mass loading, despite the hypothesized differences in the electric field strength across the catalyst particle suggested by continuum electrostatic simulations. Substantial atomic interdiffusion between the core and shell was ruled out by X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and diffuse reflectance optical measurements. However, the optimal mass loading of catalyst was roughly 1 order of magnitude higher for the conductive and high dielectric core materials than for the low dielectric insulating cores. These findings are consistent with the hypothesis that electric field screening within the core material focuses the electric field drop between particles such that larger film thicknesses can be tolerated. Collectively, these data support the idea that it is the local electric field at the molecular level that controls proton-transfer rates and that the metal core/dielectric-shell constructs introduced here modulate that field. Further materials and synthetic design may enable optimization of the electric field strength across the proton-transfer trajectory at the material surface.

Sarma, Prasad V↗
DOE OSTI2020

Vacuum Pyrolysis of Hybrid Poplar Milled Wood Lignin with Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Analysis of Feedstock and Products for the Elucidation of Reaction Mechanisms

The pyrolysis of lignocellulosic materials is a promising technique to produce fuels and chemicals. It is well known that the most abundant products of lignin pyrolysis are oligomeric molecules, known as pyrolytic lignin (PL). The chemical composition of PL has been extensively studied; however, there is still an important debate whether these oligomers are produced directly from the lignin or from the recombination of monomeric pyrolytic products. Existing theories are unable to describe the effect of vacuum on the distribution of pyrolysis products. Hybrid poplar milled wood lignin (MWL) was initially isolated and thoroughly characterized by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Chemical formulas were assigned to each oligomeric compound detected. The MWL was also subjected to vacuum pyrolysis in a modified pyroprobe at 250, 750, and 1000 mbar (absolute pressure), and the resulting liquid products were analyzed by FT-ICR MS. A new strategy to assign structural representations to the oligomeric PL products is proposed, based on the plausible pyrolysis reaction mechanisms of depolymerization/fragmentation applied to original MWL oligomer formulas. Our results support the hypothesis that PL is formed from the removal of moieties from primary lignin pyrolysis products with between three and five aromatic rings. This depolymerization/fragmentation allows the oligomers to reduce their molecular weights to the point where they can be removed from the reaction zone by direct vaporization. Furthermore, this phenomenon highlights the importance of pressure on removal mechanisms and their impact on the molecular weight of the resulting products from lignin pyrolysis.

09 BIOMASS FUELS↗
DOE OSTI2022

Numerical Study of PAHs and Soot Emissions from Gasoline–Methanol, Gasoline–Ethanol, and Gasoline– n -Butanol Blend Surrogates

Soot formation is an intricate phenomenon, and soot propensity of a fuel is interwoven with the fuel composition, physical and chemical properties, and combustion environment. Here, the present study examines the hypothesis that in addition to the chemical composition of the fuel, the sooting nature of the fuel is closely coupled with its chemical property known as octane sensitivity (S). With this motivation, the present study numerically investigates the effects of gasoline surrogate composition and its property, octane sensitivity (S), on polycyclic aromatic hydrocarbons (PAHs) and soot emissions. Four-component toluene primary reference fuel (TPRF)–alcohol blends, comprising iso-octane, n-heptane, toluene, and one of the three different alcohols- methanol, ethanol, and n-butanol, are used as gasoline surrogates. A total of 320 TPRF–alcohol mixtures, with S in the range of 1–10, are examined under laminar counterflow diffusion flame conditions. A detailed chemical mechanism coupled with a comprehensive soot model, which includes reactions for soot inception, surface growth, PAH condensation, and oxidation, is adopted. The analysis indicates that the toluene content in the fuel mixture has a prominent effect, while the alcohol content and octane sensitivity of the fuel have a weak correlation with the PAHs and soot. Thus, it is not clear if any of these three variables, namely, toluene content in the fuel, alcohol content in the fuel, and S, are individually sufficient to characterize the PAHs and soot across various blends. For this reason, a new variable (X CHO ) based on the elemental composition of the fuel mixture is identified and it is shown that X CHO along with S of the fuel characterize soot emissions satisfactorily. Further, a reaction path analysis indicates that the efficacy of alcohols in reducing soot emissions follows the order: methanol > ethanol > n-butanol.

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

Immobilizing Pertechnetate in Ettringite via Sulfate Substitution

Until recently, a nuclear waste form did not exist for the immobilization and long-term storage of the anionic form of radionuclide technetium-99 (99Tc), pertechnetate (TcO 4 - ). Across international nuclear waste sites, the inability to capture TcO 4 - poses a threat to the local environment due to the anion’s long half-life and environmental mobility under environmentally oxic conditions. To combat this challenge, most waste forms would capture 99Tc using materials that reduce TcO 4 - to Tc(IV) species, e.g. 99Tc oxides or 99Tc sulfides. However, this is a short-lived solution unless reducing capacities can be regenerated to last over the long life expectancy of some nuclear waste forms (~10,000 years). In light of recent experimental observations gained from the development of cementitious waste forms and unconfirmed hypotheses from the literature, this work explores how ettringite, a common mineral formed in cementitious materials with demonstrated success in incorporating oxyanions, may be used to immobilize TcO 4 - directly and over the life-time of the waste form. Using batch precipitation experiments, solid phase characterization techniques, and ab initio molecular dynamics simulations, we demonstrate herein successful incorporation of TcO 4 - into ettringite via substitution for SO 4 2- within the ettringite crystal structure. Here, these results are first of their kind and confirm the hypothesis that ettringite acts as an immobilizing mineral within cementitious waste forms for the highly mobile TcO 4 - oxyanion, enhancing the overall performance of these waste forms over time.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Distribution of Mn Oxidation States in Grassland Soils and Their Relationships with Soil Pores

Manganese (Mn) is known to be an active contributor to processing and cycling of soil organic carbon (C), yet the exact mechanisms behind its interactions with C are poorly understood. Plant diversity in terrestrial ecosystems drives feedback links between plant C inputs and soil pores, where the latter, in turn, impact the redox environment and Mn. This study examined associations between soil pores (>36 μm Ø) and Mn within intact soils from two grassland ecosystems, after their >6-year implementation in a replicated field experiment. In this work, we used μ-XRF imaging and XANES spectroscopy to explore spatial distribution patterns of Mn oxidation states, combined with X-ray computed microtomography and 2D zymography. A high plant diversity system (restored prairie) increased soil C and modified spatial distribution patterns of soil pores as compared to a single species system (monoculture switchgrass). In switchgrass, the abundance of oxidized and reduced Mn oxidation states varied with distance from pores consistently with anticipated O 2 diffusion, while in the soil from restored prairie, the spatial patterns suggested that biological activity played a greater role in influencing Mn distributions. Based on the findings, we propose a hypothesis that Mn transformations promote C gains in soils of high plant diversity grasslands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Wildfire Produces Transient Minerals: Speciation, Reactivity, and Fate of Iron and Manganese in Surface Soils Post Wildfire

Wildfire leads to the deposition of an ash layer at the land surface. This material typically has alkaline properties, abundant pyrogenic carbon, and elevated metal concentrations compared to surface soils. Here, we compare ash and surface soils collected three weeks and two years after the Glass Fire (St. Helena, California, USA) to determine how wildfire affects the speciation and reactivity of iron (Fe) and manganese (Mn), two micronutrients that influence many soil processes. Synchrotron-based analyses revealed that wildfire generated stable Fe oxides like maghemite (γ-Fe 2 O 3 ) and hematite (α-Fe 2 O 3 ) that likely derived from surface soil or mineral dust rather than the vegetation, and Mn oxides such as hausmannite (Mn 3 O 4 ) and bixbyite (Mn 2 O 3 ) that derived primarily from aboveground biomass. However, these pyrogenic minerals were absent in soils collected two years after the fire. Their loss from the soil surface may result from a combination of erosion, translocation to deeper soil layers, and chemical weathering. The latter hypothesis is supported by the enhanced mobilization of Fe and Mn from ash upon the addition of pyoverdine, a model biogenic ligand. The increased mobility of micronutrients from fire-derived minerals in ash in response to microbial and root exudation may facilitate postfire soil and vegetation recovery.

bixbyite↗
DOE OSTI2026

CO 2 Sorption in Moisture Swing Anion Exchange Resins for Direct Air Capture: Experimental Isotherm Determination and Modeling

Moisture swing (MS) sorption is a promising direct air capture (DAC) technology to achieve negative CO 2 emissions and counter global warming. Here, in this study, MS CO 2 sorption in a model MS sorbent, IRA900, was investigated. IRA900 is a macroporous commercial strong-base anion exchange resin (AER) with quaternary ammonium functional groups. A rigorous CO 2 desorption process was developed to desorb all CO 2 from the sample and obtain CO 2 sorption isotherms as a function of relative humidity, CO 2 partial pressure, and temperature. CO 2 sorption increased with decreasing relative humidity, decreasing temperature, and increasing CO 2 partial pressure. Remarkably, the total CO 2 uptake from the sorption isotherms matched the ion exchange capacity (IEC) of the material, suggesting a stoichiometry of one CO 2 molecule reacting per active site. An isotherm model for CO 2 sorption starting with empty sorption sites (i.e., with the AER in the OH – form) described the experimental data well, supporting the hypothesis that the bicarbonate-loaded AER fully unloaded to the OH – state following rigorous CO 2 desorption. CO 2 sorption kinetics were studied, and carbon diffusion coefficients were estimated as a function of %RH and CO 2 partial pressure. Overall, this study provides a roadmap for the systematic evaluation of MS CO 2 DAC materials.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Volatilized Ammonia Supports Subterranean Ecosystems with Unusual Nitrogen Isotopic Signatures

The Frasassi cave system hosts a robust subterranean ecosystem based on microbial lithoautotrophy. Curiously, acidic biofilms forming above degassing sulfidic cave streams, and the invertebrates that feed on them, are extremely depleted in nitrogen-15 (δ 15 N values less than −20‰). In this study, we tested the hypothesis that these low δ 15 N values result from the volatilization, trapping, and uptake of ammonia degassed from circumneutral streams. We found that dissolved ammonium in the streams had δ 15 N values near +3‰, whereas NH 3(g) in the cave atmosphere above streams exhibited δ 15 N values as low as −27‰, consistent with fractionation by NH 3 volatilization. Extremely acidic condensation droplets on cave walls efficiently trapped airborne NH 3 , accumulating up to 4 mM NH 4 + with δ 15 N values as low as −29‰, thereby confirming volatilized and trapped ammonia as the primary N source to cave wall biofilms and the extensive subsurface ecosystem they support. Airborne ammonia trapping represents a novel mechanism for biological N acquisition and provides abundant N for growth in an extreme subsurface environment that otherwise receives very limited nutrient input.

Nitrogen↗
DOE OSTI2022

Mechanistic Interpretations and Insights for the Oxidative Dehydrogenation of Propane via CO 2 over Cr 2 O 3 /Al 2 O 3 Catalysts

Oxidative dehydrogenation (ODH) of alkanes using carbon dioxide as a soft oxidant has recently emerged as a potentially attractive alternative to steam cracking for the production of light olefins. To elucidate reaction pathways and their dependence on the operating conditions, CO 2 -assisted propane dehydrogenation over a redox-active Cr 2 O 3 /Al 2 O 3 catalyst was examined in a packed bed reactor as a function of temperature, Cr 2 O 3 /CO 2 feed ratio, and residence time. Previous ODH studies have largely focused on CO 2 -rich conditions with the aim of preventing coke formation. However, at T = 600 °C the present study finds that the use of propane-rich conditions (1 ≤ C 3 H 8 /CO 2 ≤ 2.5) maximizes propylene production and selectivity while maintaining catalyst stability. In this work, it is postulated that the selective Mars van Krevelen dehydrogenation process is optimized at these ratios. Excess CO 2 apparently promotes nonselective dehydrogenation and dry reforming pathways that generate additional CO, adversely impacting catalyst stability via the Bouduard reaction. This hypothesis is supported by complementary investigations of the reverse water gas shift reaction and thermodynamic analysis. The findings and methodology presented here are likely applicable to related ODH processes with other alkanes and redox-active catalysts.

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

Impact of Solution Chemistry on Growth and Structural Features of Mo-Substituted Spinel Iron Oxides

The effect of crystallizing solution chemistry on the chemistry of subsequently as-grown materials was investigated for Mo-substituted iron oxides prepared by thermally activated co-precipitation. In the presence of Mo ions, we find that varying the oxidation state of the iron precursor from Fe(II) to Fe(III) causes a progressive loss of atomic long-range order with the stabilization of 2-4 nm particles for the sample prepared with Fe(III). The oxidation state of the Fe precursor also affects the distribution of Fe and Mo cations within the spinel structure. Increasing the Fe precursor oxidation state gives decreased Fe-ion occupation and increased Mo-ion occupation of tetrahedral sites, as revealed by the extended X-ray absorption fine structure. The stabilization of Mo within tetrahedral sites appears to be unexpected, considering the octahedral preferred coordination number of Mo(VI). The analysis of the atomic structure of the sample prepared with Fe(III) indicates a local ordering of vacancies and that the occupation of tetrahedral sites by Mo induces a contraction of the interatomic distances within the polyhedra as compared to Fe atoms. Moreover, the occupancy of Mo into the thermodynamic site preference of a Mo dopant in Fe 2 O 3 assessed by density functional theory calculations points to a stronger preference for Mo substitution at octahedral sites. Hence, we suggest that the synthetized compound is thermodynamically metastable, that is, kinetically trapped. Such a state is suggested to be a consequence of the tetrahedral site occupation by Mo ions. The population of these sites, known to be reactive sites enabling particle growth, is concomitant with the stabilization of very small particles. Furthermore, we confirmed our hypothesis by using a blank experiment without Mo ions, further supporting the impact of tetrahedral Mo ions on the growth of iron oxide nanoparticles. Our findings provide new insights into the relationships between the Fechemistry of the crystallizing solution and the structural features of the as-grown Mo-substituted Fe-oxide materials.

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

Role of Pairwise Reactions on the Synthesis of Li 0.3 La 0.57 TiO 3 and the Resulting Structure–Property Correlations

The performance of single-ion conductors is highly sensitive to the material’s defect chemistry. Tuning these defects is limited for solid-state reactions as they occur at particle–particle interfaces, which provide a complex evolving energy landscape for atomic rearrangement and product formation. In this report, we investigate the (1) order of addition and (2) lithium precursor decomposition temperature and their effect on the synthesis and grain boundary conductivity of the perovskite lithium lanthanum titanium oxide (LLTO). We use an intimately mixed sol–gel, a solid-state reaction of Li precursor + La 2 O 3 + TiO 2 , and Li precursor + amorphous La 0.57 TiO x as different chemical routes to change the way in which the elements are brought together. The results show that the perovskite can accommodate a wide range of Li deficiencies (upward of 50%) while maintaining the tetragonal LLTO structure, indicating that X-ray diffraction (XRD) is insufficient to fully characterize the chemical nature of the product (i.e., Li-deficient LLTO may behave differently than stoichiometric LLTO). Variations in the relative intensities of different reflections in XRD suggest variations in the La ordering within the crystal structure between synthesis methods. Furthermore, the choice of the precursor and the order of addition of the reactants lower the time required to form a pure phase. Density functional theory calculations of the formation energy of possible reaction intermediates support the hypothesis that a greater thermodynamic driving force to form LLTO leads to a greater LLTO yield. Here, the retention of lithium is correlated with the thermal decomposition temperature of the Li precursor and the starting material mixing strategy. Taking the results together suggests that cations that share a site with Li should be mixed early to avoid ordering. Such cation ordering inhibits Li motion, leading to higher Li ion resistance.

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

Controlling Extraction of Rare Earth Elements Using Functionalized Aryl-vinyl Phosphonic Acid Esters

Ligands that can discriminate between individual rare earth elements are important for production of these critical elements. A set of aryl-vinyl phosphonic acid ligands for extracting rare earth elements were designed and synthesized under the hypothesis that the strength of the rare earth-ligand interactions could be tuned by changing the dipole moment of the ligand. The ligands were synthesized via a two-step reaction procedure using a Heck coupling reaction to functionalize vinyl phosphonic acid, followed by Steglich esterification to obtain high-purity styryl phosphonic acid monoesters with varying dipole moments along the P-C bond. The metal binding strength and composition of the rare earth complexes formed with these styryl phosphonic acid monoesters were experimentally studied by liquid-liquid extraction techniques, while DFT calculations were performed to determine the dipole moments of the free and complexed ligands and the electronic structure of the complexes formed. All three prepared ligands were much stronger extracting agents for europium(III) than the dialkylphosphonic acids usually used for this separation. However, the order of increasing extraction strength was found to match the order of the decreasing calculated dipole moment along the P-C bond of the three styryl-based ligands, rather than correlating with increasing ligand basicity, as reflected by the pK a of the ligands. Finally, these findings suggest that this approach can be used to systematically alter the extraction strength of aromatic phosphonic monoesters for rare earth element purification.

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

Double Intramolecular 1,2 C–H Addition of o -Methyl Groups To Form Ruthenium Pincer Double Tuck-In Complexes

Ruthenium pincer complexes have a rich history of coordination and reaction chemistries. In this work, we report our discoveries of previously unreported Ru pincer coordination geometries. We found that mono tuck-in κ 4 -ArPN H PRuLCl complexes react with NaN(SiMe 3 ) 2 producing double tuck-in mer-κ 5 -ArPN H PRuL complexes. Interestingly, when κ 4 -MesPN H PRuCl is dehydrohalogenated, the resulting double tuck-in complex binds N 2 , forming the nitrogen complex κ 5 -MesPN H PRuN 2 . Further, the mer-κ 5 -ArPN H PRuL complexes thermally isomerize to the fac-κ 5 -ArPN H PRuL isomers, which is an uncommon reaction for pincer complexes. The mer-κ 5 -ArPN H PRuL complexes react with CO and CO 2 to form amide κ 4 -ArPN H PRu(CO)L or carbamate κ 5 -ArPN(CO 2 )PRuL complexes, respectively, supporting the hypothesis that the κ 4 -ArPNPRuL amide intermediates are accessible and reactive.

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

Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin

Serum albumin is the most abundant protein in blood plasma, and it is involved in multiple biological processes. Serum albumin has recently been adapted for improving biomaterial integration with bone tissue, and studies have shown the importance of this protein in bone repair and regeneration. However, the mechanism of action is not yet clear. In stark contrast, other studies have demonstrated that albumin blocks cell adhesion to surfaces, which is seen as a limitation to its bone healing role. These apparent contradictions suggest that the conformation of albumin facilitates its bioactivity, leading to enhanced bone repair. Serum albumin is known to play a major role in maintaining the calcium ion concentration in blood plasma. Due to the prevalence of calcium at bone repair and regeneration sites, it has been hypothesized that calcium binding to serum albumin triggers a conformational change, leading to bioactivity. In the current study, molecular modeling approaches including molecular docking, atomic molecular dynamics (MD) simulation, and coarse-grained MD simulation were used to test this hypothesis by investigating the conformational changes induced in bovine serum albumin by interaction with calcium ions. The computational results were qualitatively validated with experimental Fourier-transform infrared spectroscopy analysis. We find that free calcium ions in solution transiently bind with the three major loops in albumin, triggering a conformational change where N-terminal and C-terminal domains separate from each other in a partial unfolding process. The separation distance between these domains was found to correlate with the calcium ion concentration. The experimental data support the simulation results showing that albumin has enhanced conformational heterogeneity upon exposure to intermediate levels of calcium, without any significant secondary structure changes.

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

All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System

Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.

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

Folding Coarse-Grained Oligomer Models with PyRosetta

Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta’s ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. Here, we show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.

36 MATERIALS SCIENCE↗