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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Self-Inhibition Phenomena in Cu 3 Pt Oxidation by CO 2

Here, this study investigates the oxidation behavior of Cu 3 Pt(100) in CO 2 using a combination of ambient-pressure X-ray photoelectron spectroscopy, mass spectroscopy, and density functional theory modeling. Our in situ measurements reveal the simultaneous oxidation and reduction of Cu 2 O due to the opposing effects of atomic oxygen and CO generated from dissociative CO 2 adsorption, leading to a dynamic equilibrium state of simultaneously occurring redox reactions. Complementary atomistic calculations elucidate the inhibitory effects of subsurface Pt enrichment and the counteracting roles of CO 2 and CO in surface oxidation and reduction. These results provide mechanistic insights into the dissociative pathway of CO 2 molecules and dynamic evolution of surface composition and reactivity of Cu-based alloy catalysts in CO 2 -rich environments, with broader implications for tuning gas–surface reactions by manipulating gas reactants or solid surface composition.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Atomic Dynamics of Multi‐Interfacial Migration and Transformations

Redox-induced interconversions of metal oxidation states typically result in multiple phase boundaries that separate chemically and structurally distinct oxides and suboxides. Directly probing such multi-interfacial reactions is challenging because of the difficulty in simultaneously resolving the multiple reaction fronts at the atomic scale. Using the example of CuO reduction in H 2 gas, a reaction pathway of CuO → monoclinic m-Cu 4 O 3 → Cu 2 O is demonstrated and identifies interfacial reaction fronts at the atomic scale, where the Cu 2 O/m-Cu 4 O 3 interface shows a diffuse-type interfacial transformation; while the lateral flow of interfacial ledges appears to control the m-Cu 4 O 3 /CuO transformation. Together with atomistic modeling, it is shown that such a multi-interface transformation results from the surface-reaction-induced formation of oxygen vacancies that diffuse into deeper atomic layers, thereby resulting in the formation of the lower oxides of Cu 2 O and m-Cu 4 O 3 , and activate the interfacial transformations. In conclusion, these results demonstrate the lively dynamics at the reaction fronts of the multiple interfaces and have substantial implications for controlling the microstructure and interphase boundaries by coupling the interplay between the surface reaction dynamics and the resulting mass transport and phase evolution in the subsurface and bulk.

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

Effect of iron redox ratio on the structures of boroaluminosilicate glasses

Iron oxide is commonly found in natural or industrial glass compositions and can exist as ferrous (Fe 2+ ) or ferric (Fe 3+ ) species, with their ratios depending on glass composition, temperature, pressure and the redox reactions during the glass forming process. The iron redox ratio plays an important role on silicate glass structures and consequently various properties. This work aims to study the effect of iron oxide, and particularly the iron redox ratio, on the structures of borosilicate and boroaluminosilicate glasses using molecular dynamics simulations with newly developed iron potential parameters that are compatible with the borosilicate potentials. The results provide detailed cation coordination states of both iron species and the effect of redox ratio on boron coordination and other structural features. Particularly, competition for charge compensating modifier cations (such as Na + ) among the fourfold-coordinated cations such as B 3+ , Al 3+ , and Fe 3+ is investigated by calculating the cation–cation pair distribution functions and coordination preferential ratios. The results show that the trivalent ferric ions, with a shorter Fe–O bond distance and better defined first coordiation shell with mainly four-fold coordination, act as a glass former whereas the divalent ferrous ions mainly play the role of glass modifier. The ferrous/ferric ratio (Fe 2+ /Fe 3+ ) was found to affect the glass chemistry and hence glass properties by regulating the amount of four-coordinated boron, the fraction of non-briding oxygen and other features. Finally, the results are compared with available experimental data to gain insights of the complex structures and charge compensation schemes of the glass system.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Light-Driven Ultrafast Polarization Manipulation in a Relaxor Ferroelectric

Relaxor ferroelectrics have been intensely studied for decades based on their unique electromechanical responses which arise from local structural heterogeneity involving polar nanoregions or domains. Here, we report first studies of the ultrafast dynamics and reconfigurability of the polarization in freestanding films of the prototypical relaxor 0.68PbMg 1/3 Nb 2/3 O 3 -0.32PbTiO 3 (PMN-0.32PT) by probing its atomic-scale response via femtosecond-resolution, electron-scattering approaches. By combining these structural measurements with dynamic phase-field simulations, we show that femtosecond light pulses drive a change in both the magnitude and direction of the polarization vector within polar nanodomains on few-picosecond time scales. This study defines new opportunities for dynamic reconfigurable control of the polarization in nanoscale relaxor ferroelectrics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Novel Technique for Developing Linearized Convex System Models from Experimentally Derived Data

This paper presents a novel technique for generating a convex system model from an experimentally derived data set which features variance among repeated measurements. The convex system model developed as a test case characterizes the dynamic system losses of a vanadium redox flow battery as a function of the active power output and the battery state of charge. The technique hinges on a pre-cleaning via clustering procedure which precedes the formation of a planar convex hull comprised of triangular simplices. The clustering procedure efficiently reduces the experimental data set while mitigating variance among repeated measurements and removes outliers. Ultimately, the lower evelope of the planar convex hull serves as the desired convex system model. The proposed technique reduces systematic model error which is otherwise present when directly developing a planar convex hull model based on an unreduced data set.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Multi-Scale Lithofacies and Chemostratigraphic Analysis of Two Middle Devonian Marcellus Shale Wells in Northern West Virginia, USA

The Marcellus Shale Energy and Environmental Laboratory (MSEEL) consists of two project areas within the dry gas producing region of the Marcellus shale play in Monongalia County, West Virginia. MSEEL is a collaborative field project led by West Virginia University, with Northeast Natural Energy LLC, several industrial partners, and sponsored by the US Department of Energy National Energy Technology Laboratory. The study areas are drilled approximately 8.5 miles apart to better understand the vertical and lateral changes in stratigraphy over a short distance. Two vertical pilot wells, MIP-3H and Boggess 17H were drilled in the fall of 2015 and spring of 2019, respectively. Core was recovered from the MIP-3H (API: 47-061-01707-00-00) 112 feet (34m) between depths of 7445 to 7557 feet, and from the Boggess 17H (API: 47-061-01812-00-00) 139 feet (42m) between depths of 7908 and 8012 ft. A full suite of triple combo (gamma ray, neutron, density logs), image logs, and advanced logging tools were run in both wells and calibrated to core analysis. Core analysis includes medical computed tomography (CT) scans, mineralogy and chemostratigraphy determined from handheld X-Ray fluorescence (hhXRF) and X-Ray powder diffraction (XRD) measurements, and determination of total organic content (TOC). Lithofacies were determined at core-scale using traditional core description techniques and medical CT-scan images. Log-scale facies are based on mineralogy and TOC data and developed using petrophysical logging data calibrated to core data (XRD and pyrolysis data). Chemostratigraphic analysis utilized hhXRF data to determine the major and trace element trends in the cores. In the two wells six shale lithofacies were recognized at the core and log scale. Both wells show organic-rich facies (TOC > 6.5%) primarily in the middle and lower Marcellus, with a slight decrease in thickness of this interval in the Boggess 17H. This interval is interpreted as an increase in paleo-productivity (increased Ni, Zn, and V), decreased sedimentation (decreased detrital proxies), and anoxic to euxinic conditions (increased Mo and chalcophile elements). Paleo-redox conditions in both wells are dynamic throughout deposition transitioning between euxinic/anoxic to dysoxic/oxic. This trend is seen through elemental proxies and calcite/pyrite concretion distributions.

03 NATURAL GAS↗
DOE OSTI2024

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dynamic operation of metal-supported solid oxide electrolysis cells

Symmetric-structure metal-supported solid oxide fuel cells and electrolysis cells (MS-SOFCs, MS-SOECs) offer several advantages over conventional solid oxide cells, including the use of inexpensive materials, high mechanical strength, and rapid ramp-up ability. Aggressive operation of MS-SOCs in fuel cell mode is well-established, including extremely fast start-up, redox tolerance, and imbalanced pressure. Here, we extend dynamic operation to MS-SOCs in SOEC mode with high steam content for both small button cells and a large rectangular cell, including: steam cycling, thermal cycling, redox cycling and power cycling. Steam cycling entailed switching between 3:97 and 50:50 steam:hydrogen ratio. For thermal cycling, the temperature was rapidly varied between 150°C and 700°C for 50 cycles. Redox cycling involved switching the steam side gas between 50 % humidified H 2 and 50 % humidified N 2 for 5 cycles. Power cycling was performed by operating the cell under variable current density, resulting in cell voltage between 1.3V and 2.8V. Degradation rates for each testing strategy were compared to a baseline cell, and found to be similar. In conclusion, the excellent tolerance to dynamic operation increases confidence that MS-SOECs will be compatible with dynamic or intermittent renewable resources.

08 HYDROGEN↗
DOE OSTI2023

Model simulations of Plum Island Ecosystems LTER low marsh site using ELM-PFLOTRAN

Model simulations using the E3SM Land Model (ELM) coupled to the PFLOTRAN reactive transport model via the Alquimia interface. The simulations were conducted for a tidal salt marsh at the Plum Island Ecosystems LTER near Rowley, Massachusetts, USA. Model simulations were forced using site-specific tidal cycles and salinity, and the simulations used a biogeochemical reaction network including aerobic decomposition, sulfate reduction, iron reduction, and methanogenesis. Model outputs include simulated carbon stocks, carbon dioxide and methane fluxes, and porewater concentrations of key solutes related to sulfur, iron, and carbon cycling. The model simulations included a saline simulation (with tidal sulfate inputs), a fresh simulation (with low salinity and low sulfate inputs), and a saline simulation with lower vegetation productivity to represent the effect of salinity on vegetation. These simulations were conducted to demonstrate that a new model framework incorporating subsurface redox and biogeochemical interactions into a land surface model could reproduce measured surface greenhouse gas fluxes and biogeochemical dynamics in tidal marsh ecosystems, and to test whether including redox interactions in a land surface model would allow the model to resolve contrasts in biogeochemical cycling and greenhouse gas production between saline and freshwater wetlands.The data package includes gzipped tar archives (which can be expanded using standard tar and gzip utilities) of model outputs from three model configurations: saline subsurface and reduced vegetation productivity related to salinity; saline subsurface with vegetation productivity not reduced; and freshwater. Also included are code for the modified E3SM model, Alquimia interface, and PFLOTRAN reactive transport simulator in gzipped tar format; plain text parameter and configuration files; python code files for visualizing model output and defining model configurations; and model output, tide and salinity forcing, and configuration files in netCDF format. See the README.md file in the data package for a detailed description of all files contained in the package. All files are in netCDF (.nc), gzipped tar archive (.tar.gz or .tgz), or text (all other files).Updated: May 13, 2024. Model output, E3SM code, PFLOTRAN input files, and python codes for visualizing results were updated to reflect changes made for the manuscript revision. The updated archive reflects the code and model output from the final accepted manuscript. Changes included updated reaction parameters reflecting improved parameterization and additional comparisons with field measurements. E3SM code changes included better support for multiple grid cells and improved flow and transport parameterization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Warming Stimulates Iron-Mediated Carbon and Nutrient Cycling in Mineral-Poor Peatlands

We know that iron (Fe) plays a key role in elemental cycling at terrestrial–aquatic interfaces by stabilizing carbon (C), phosphorus (P), and nutrient cations through physicochemical associations and by potentially releasing these elements following the reduction of Fe(III) to Fe(II). However, the ecosystem-scale importance of Fe redox cycling and its responses to climate change remain unclear in precipitation-fed peatlands (bogs), C-rich wetlands with very low mineral content. We tested impacts of Fe redox cycling on C and nutrient release in two bogs in northern Minnesota and in Spruce and Peatland Responses Under Changing Environments (SPRUCE), an ecosystem-scale warming experiment. Concentrations of Fe(III) declined from the peat surface to 50 cm depth (31 to 0.5 µmol g -1 ) and co-occurred with Fe(II) (10 to 30 µmol g -1 ). Chemical reduction of Fe(III) released C and P from variably saturated (0–30 cm) peat (106–1006 µmol C g -1 ; 0.6–5 µmol P g -1 ), and Fe-bound C was similar to previous measurements from upland mineral soils. Concentrations of Fe(II) and dissolved organic carbon (DOC) were strongly (R 2 = 0.56–0.78) and positively correlated in water samples measured at SPRUCE enclosure outlets and ambient near-surface porewater. Concentrations of Fe(II) also correlated positively with P at warmer SPRUCE temperature treatments and increased with experimental warming, but stabilized at the highest temperature treatments as water depth declined. Although bogs have low total mineral content, mass balance measurements indicated that atmospheric deposition could in principle sustain significant Fe cycling and hydrologic losses in these ecosystems. Overall, Fe redox cycling significantly impacted C and nutrient dynamics in these mineral-poor bogs, contributing to strong correlations between Fe(II) and DOC in water samples. Increased Fe(III) reduction with warmer temperatures will likely promote peatland C and nutrient release, impacting ecosystem C budgets both directly and indirectly by enhancing decomposition and productivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Proton dynamics in water confined at the interface of the graphene–MXene heterostructure

Heterostructures of 2D materials offer a fertile ground to study ion transport and charge storage. Here, we use ab initio molecular dynamics to examine the proton-transfer/diffusion and redox behavior in a water layer confined in the graphene-Ti 3 C 2 O 2 heterostructure. We find that in comparison with the similar interface of water confined between Ti 3 C 2 O 2 layers, the proton redox rate in the dissimilar interface of graphene-Ti 3 C 2 O 2 is much higher, owing to the very different interfacial structure as well as the interfacial electric field induced by an electron transfer in the latter. Water molecules in the dissimilar interface of the graphene-Ti 3 C 2 O 2 heterostructure form a denser hydrogen-bond network with a preferred orientation of water molecules, leading to an increase in proton mobility with proton concentration in the graphene-Ti 3 C 2 O 2 interface. As the proton concentration further increases, proton mobility decreases due to increasingly more frequent surface redox events that slow down proton mobility due to binding with surface O atoms. Our work provides important insights into how the dissimilar interface and their associated interfacial structure and properties impact proton transfer and redox in the confined space.

2D materials↗
DOE OSTI2024

Integrating Tide‐Driven Wetland Soil Redox and Biogeochemical Interactions Into a Land Surface Model

Abstract Redox processes, aqueous and solid‐phase chemistry, and pH dynamics are key drivers of subsurface biogeochemical cycling and methanogenesis in terrestrial and wetland ecosystems but are typically not included in terrestrial carbon cycle models. These omissions may introduce errors when simulating systems where redox interactions and pH fluctuations are important, such as wetlands where saturation of soils can produce anoxic conditions and coastal systems where sulfate inputs from seawater can influence biogeochemistry. Integrating cycling of redox‐sensitive elements could therefore allow models to better represent key elements of carbon cycling and greenhouse gas production. We describe a model framework that couples the Energy Exascale Earth System Model (E3SM) Land Model (ELM) with PFLOTRAN biogeochemistry, allowing geochemical processes and redox interactions to be integrated with land surface model simulations. We implemented a reaction network including aerobic decomposition, fermentation, sulfate reduction, sulfide oxidation, methanogenesis, and methanotrophy as well as pH dynamics along with iron oxide and iron sulfide mineral precipitation and dissolution. We simulated biogeochemical cycling in tidal wetlands subject to either saltwater or freshwater inputs driven by tidal hydrological dynamics. In simulations with saltwater tidal inputs, sulfate reduction led to accumulation of sulfide, higher dissolved inorganic carbon concentrations, lower dissolved organic carbon concentrations, and lower methane emissions than simulations with freshwater tidal inputs. Model simulations compared well with measured porewater concentrations and surface gas emissions from coastal wetlands in the Northeastern United States. These results demonstrate how simulating geochemical reaction networks can improve land surface model simulations of subsurface biogeochemistry and carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗
DOE OSTI2026

The Use of Microelectrodes in Molten Salt Electrochemistry

Molten salts have attracted considerable interest as essential media for advanced high-temperature technologies, including molten salt reactors, thermal energy storage, high-temperature electrolysis, and pyrochemical processing. Their ability to remain stable in liquid form at elevated temperatures, combined with favorable thermophysical properties and wide electrochemical windows, makes them highly suitable for applications involving heat transfer, energy storage, and hightemperature electrochemical processing. However, despite these advantages, molten salts present challenges due to their chemically reactive nature at high-temperatures, especially in the presence of oxidizing impurities. Salt chemistry can fluctuate through interactions with impurities over time, or fuel burnup in the case of molten salt reactors, often leading to the dissolution of metal species. This dynamic environment not only results in complex redox behavior but also promotes corrosion, which is rarely uniform and frequently manifests as localized degradation driven by structural materials’ compositional differences, electrochemical imbalances, and microstructural susceptibilities.

Kim, Changkyu [University of Wisconsin-Madison, WI↗
DOE OSTI2021

Activation of anionic redox in d 0 transition metal chalcogenides by anion doping

Expanding the chemical space for designing novel anionic redox materials from oxides to sulfides has enabled to better apprehend fundamental aspects dealing with cationic-anionic relative band positioning. Pursuing with chalcogenides, but deviating from cationic substitution, we here present another twist to our band positioning strategy that relies on mixed ligands with the synthesis of the Li 2 TiS 3-x Se x solid solution series. Through the series the electrochemical activity displays a bell shape variation that peaks at 260 mAh/g for the composition x = 0.6 with barely no capacity for the x = 0 and x = 3 end members. We show that this capacity results from cumulated anionic (Se 2– /Se n– ) and (S 2– /S n– ) and cationic Ti 3+ /Ti 4+ redox processes and provide evidence for a metal-ligand charge transfer by temperature-driven electron localization. Moreover, DFT calculations reveal that an anionic redox process cannot take place without the dynamic involvement of the transition metal electronic states. These insights can guide the rational synthesis of other Li-rich chalcogenides that are of interest for the development of solid-state batteries.

25 ENERGY STORAGE↗
DOE OSTI2022

Single-Molecule Chemical Reactions Unveiled in Molecular Junctions

Understanding chemical processes at the single-molecule scale represents the ultimate limit of analytical chemistry. Single-molecule detection techniques allow one to reveal the detailed dynamics and kinetics of a chemical reaction with unprecedented accuracy. It has also enabled the discoveries of new reaction pathways or intermediates/transition states that are inaccessible in conventional ensemble experiments, which is critical to elucidating their intrinsic mechanisms. Thanks to the rapid development of single-molecule junction (SMJ) techniques, detecting chemical reactions via monitoring the electrical current through single molecules has received an increasing amount of attention and has witnessed tremendous advances in recent years. Research efforts in this direction have opened a new route for probing chemical and physical processes with single-molecule precision. This review presents detailed advancements in probing single-molecule chemical reactions using SMJ techniques. We specifically highlight recent progress in investigating electric-field-driven reactions, reaction dynamics and kinetics, host–guest interactions, and redox reactions of different molecular systems. Finally, we discuss the potential of single-molecule detection using SMJs across various future applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Competitive Pi-Stacking and H-Bond Piling Increase Solubility of Heterocyclic Redoxmers

Redoxmers are organic molecules that carry electric charge in flow batteries. In many instances, they consist of heteroaromatic moieties modified with appended groups to prevent stacking of the planar cores and increase solubility in liquid electrolytes. This higher solubility is desired as it potentially allows achieving greater energy density in the battery. However, the present synthetic strategies often yield bulky molecules with low molarity even when they are neat and still lower molarity in liquid solutions. Fortunately, there are exceptions to this rule. Here, we examine one well-studied redoxmer, 2,1,3-benzothiadiazole, which has solubility similar to 5.7 M in acetonitrile at 25 degrees C. We demonstrate computationally and prove experimentally that the competition between two packing motifs, face-to-face it-stacking and random N-H bond piling, introduces frustration that confounds nucleation in crowded solutions. Our findings and examples from related systems suggest a complementary strategy for the molecular design of redoxmers for high energy density redox flow cells.

25 ENERGY STORAGE↗