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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 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Transient Triplet Metallopnictinidenes M–Pn (M = Pd II , Pt II ; Pn = P, As, Sb): Characterization and Dimerization

Nitrenes (R–N) have been subject to a large body of experimental and theoretical studies. The fundamental reactivity of this important class of transient intermediates has been attributed to their electronic structures, particularly the accessibility of triplet vs singlet states. In contrast, electronic structure trends along the heavier pnictinidene analogues (R–Pn; Pn = P–Bi) are much less systematically explored. We here report the synthesis of a series of metallodipnictenes, {M–Pn=Pn–M} (M = Pd II , Pt II ; Pn = P, As, Sb, Bi) and the characterization of the transient metallopnictinidene intermediates, {M–Pn} for Pn = P, As, Sb. Structural, spectroscopic, and computational analysis revealed spin triplet ground states for the metallopnictinidenes with characteristic electronic structure trends along the series. In comparison to the nitrene, the heavier pnictinidenes exhibit lower-lying ground state SOMOs and singlet excited states, thus suggesting increased electrophilic reactivity. Furthermore, the splitting of the triplet magnetic microstates is beyond the phosphinidenes {M–P} dominated by heavy pnictogen atom induced spin–orbit coupling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Geomechanical Framework for Secure CO 2 Storage in Fractured Reservoirs and Caprocks for Sedimentary Basins in theMidwest United States

This report presents final technical results for the project Geomechanical Framework for Secure CO 2 Storage in Fractured Reservoirs and Caprocks for Sedimentary Basins in the Midwest United States (DE-FE0023330). The project was a three-year effort consisting of seven technical tasks focused on defining geomechanical factors for CO 2 storage applications in deep saline rock formations in Ohio and the Midwest United States, because geomechancial issues have been identified as a significant risk factor for large-scale CO 2 storage applications. A basin-scale stress-strain analysis was completed to describe the geomechanical setting for rock formations of Ordovician-Cambrian age in Ohio and adjacent areas of the Midwest United States in relation to geologic CO 2 storage applications. The tectonic setting, stress orientation-magnitude, and geomechanical and petrophysical parameters for CO 2 storage zones and caprocks in the region were cataloged. Ten geophysical image logs were analyzed for natural fractures, borehole breakouts, and drilling-induced fractures. The logs indicated mostly less than 10 fractures per 100 vertical feet in the borehole, with mostly N65E principal stress orientation through the section. Geophysical image logs and other logs were obtained for three wells located near the sites where specific models were developed for geomechanical simulations: Arches site in Boone County, Kentucky; Northern Appalachian Basin site in Chautauqua County, New York; and E-Central Appalachian Basin site in Tuscarawas County, Ohio. For these three wells, 9,700 feet of image logs were processed and interpreted to provide a systematic review of the distribution within each well of natural fractures, wellbore breakouts, faults, and drilling induced fractures. There were many borehole breakouts and drilling-induced tensile fractures but few natural fractures. Concentrated fractures were present at the Rome-basal sandstone and basal sandstone-Precambrian contacts at the Arches and East-Central Appalachian Basin sites. Geophysical logs were utilized to develop local-scale geologic models by determining geomechanical and petrophysical parameters within the geologic formations. These data were ported to coupled fluid-flow and reservoir geomechanics multi-phase CO 2 injection simulations. The models were developed to emphasize the geomechanical layers within the CO 2 storage zones and caprocks. A series of simulations were completed for each site to evaluate whether commercial-scale CO 2 could be safely injected into each site, given site-specific geologic and geomechanical controls. This involved analyzing the simulation results for the integrity of the caprock, intermediate, and reservoir zones, as well quantifying the areal uplift at the surface. Simulation results were also examined to ensure that the stress-stress perturbations were isolated within the subsurface, and that there was only limited upward migration of the CO 2 . Simulations showed capacity to inject more than 10 million metric tons of CO 2 in a single well at the Arches and East Central Appalachian Basin sites without excessive geomechanical risks. Low-permeability rock layers at the Northern Appalachian Basin study area well resulted in very low CO 2 injection capacity. Fracture models developed for the sites suggests that the sites have sparse fracture network in the deeper Cambrian rocks. However, there were indicators in image logs of a moderate fracture matrix in the Rose Run Sandstone at the Northern Appalachian Basin site. Dual permeability fracture matrix simulations suggest the much higher injection rates may be feasible in the fractured interval. Guidance was developed for geomechanical site characterization in the areas of geophysical logging, rock core testing, well testing, and site monitoring. The guidance demonstrates that there is a suitable array of options for addressing geomechanical issues at CO 2 storage sites. Finally, a review of Marcellus and Utica-Point Pleasant shale gas wells and CO 2 storage intervals indicates that these items are vertically separated, except for the Oriskany sandstone and Marcellus wells in southwest Pennsylvania and northern West Virginia. Together, project results present a more realistic portrayal of geomechanical risk factors related to CO 2 storage for existing and future coal-fired power plants in Ohio.

58 GEOSCIENCES↗
DOE OSTI2026

Tunable Multisite Proton-Coupled Electron Transfer Mediators: Distinct Pathways for Substrate Reduction Versus Competing Hydrogen Evolution

Proton-coupled electron transfer (PCET) reagents have emerged as powerful tools for transferring net H atoms to organic substrates from relatively weak X–H bonds. One advantage of employing PCET reagents is the tunability of the X–H bond strength by independently varying their redox potential and/or p K a for selective substrate reductions; however, the rational development of modular catalytic PCET reagents based on these features remains underdeveloped. In this work, we address important mechanistic questions relevant to a dimethylaniline-appended cobaltocene PCET mediator that our lab has previously introduced. Specifically, we examine where protonation occurs within the reactive Co(II, NH) + intermediate of a Brønsted-base modified cobaltocene mediator, whether substrate reduction and hydrogen evolution reaction (HER) proceed by a common or bifurcated mechanistic pathway, and how the redox, acid–base, and structural properties of PCET mediators can dictate their reactivity and selectivity. We show that substrate compatibility can be tuned and, via a model study with N -aryl imine substrates, provide data pointing to a multisite PCET (MS-PCET) pathway. Moreover, we rigorously characterize the site of protonation in the reactive reduced, protonated form of the mediator, and through kinetic analysis establish that the pathway for undesired competing HER is fundamentally different and involves Cp-ring protonation. Our findings point to a high degree of flexibility in the design of reductive PCET mediators.

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

One Electron Multiple Proton Transfer in Model Organic Donor–Acceptor Systems: Implications for High-Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. In this work, we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analog, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g X -components of the electronicg-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g X -value of up to 0.003, but are not sensitive to the second proton transfer (E2PT). In the latter case, the change of the g X -value is much smaller (ca. 0.0001), which is too small to be distinguished even by high-frequency EPR. The 14 N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (> 0.001) in the g X -values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N 1 and N 2 positions of the imidazole.

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

PFLOTRAN modeling data and scripts associated with “Refining the Hydrogeologic Framework of a Large River Corridor Model Using Waterborne Transient Electromagnetics”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the publication “Refining the Hydrogeologic Framework of a Large River Corridor Model Using Waterborne Transient Electromagnetics” submitted to Water Resources Research (Terry et al. 2025). The data package contains the groundwater modeling dataset from PFLOTRAN software. It includes the python script for mesh generation, boundary condition setting, PFLOTRAN input deck formation and postprocessing. It couples groundwater flow and species transport for Hanford Reach river corridor and pipelines the model generation and processing. This model can be used to easily generate the model and analysis for Hanford site. It can also be adjusted to other hydrologic area with ease. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. The data package consists of 6 folders: (1) “data” contains all necessary data as input and intermediate data for processing; (2) “mesh” contains all mesh related files to generate mesh in Hanford Reach river corridor; (3) “model_run” contains the generated script for PFLOTRAN modeling; (4) “notebooks” contains all the Python script to generate the model; (5) “output” contains all the output from the computation; (6) “postprocessing” contains the Python script to generate scientific figure for manuscript. All files are .csv (comma-separated values), .h5 (HDF5 format), .in (input files), .ipynb (Jupyter notebooks), .p (Python pickle), .png (images), .PNG (images), .py (Python scripts), .pyc (Python bytecode), .r (R scripts), .sh (shell scripts), .txt (text files), .vtu (3D mesh/visualization format), .xz (compressed archive), or .zip (compressed archive).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Structures and diffusion of two-dimensional dusty plasmas on one-dimensional periodic substrates

Using numerical simulations, we examine the structure and diffusion of a two-dimensional dusty plasma (2DDP) in the presence of a one-dimensional periodic substrate (1DPS) as a function of increasing substrate strength. Both the pair correlation function perpendicular to the substrate modulation and the mean-squared displacement (MSD) of dust particles are calculated. It is found that both the structure and dynamics of 2DDP exhibit strong anisotropic effects, due to the applied 1DPS. As the substrate strength increases from zero, the structure order of dusty plasma along each potential well of 1DPS increases first probably due to the competition between the interparticle interactions and the particle-substrate interactions, and then decreases gradually, which may be due to the reduced dimensionality and the enhanced fluctuations. The obtained MSD along potential wells of 1DPS clearly shows three processes of diffusion in our studied 2DDP. Finally, between the initial ballistic and finally diffusive motion, there is the intermediate subdiffusion discovered here, which may result from the substrate-induced distortion of the caging dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Experimental and Computational Analysis of the Solvent‐Dependent O 2 /Li + ‐O 2 − Redox Couple: Standard Potentials, Coupling Strength, and Implications for Lithium–Oxygen Batteries

Abstract Understanding and controlling the kinetics of O 2 reduction in the presence of Li + ‐containing aprotic solvents, to either Li + ‐O 2 − by one‐electron reduction or Li 2 O 2 by two‐electron reduction, is instrumental to enhance the discharge voltage and capacity of aprotic Li‐O 2 batteries. Standard potentials of O 2 /Li + ‐O 2 − and O 2 /O 2 − were experimentally measured and computed using a mixed cluster‐continuum model of ion solvation. Increasing combined solvation of Li + and O 2 − was found to lower the coupling of Li + ‐O 2 − and the difference between O 2 /Li + ‐O 2 − and O 2 /O 2 − potentials. The solvation energy of Li + trended with donor number (DN), and varied greater than that of O 2 − ions, which correlated with acceptor number (AN), explaining a previously reported correlation between Li + ‐O 2 − solubility and DN. These results highlight the importance of the interplay between ion–solvent and ion–ion interactions for manipulating the energetics of intermediate species produced in aprotic metal–oxygen batteries.

Kwabi, David G.↗
DOE OSTI2016

Experimental and Computational Analysis of the Solvent‐Dependent O 2 /Li + ‐O 2 − Redox Couple: Standard Potentials, Coupling Strength, and Implications for Lithium–Oxygen Batteries

Abstract Understanding and controlling the kinetics of O 2 reduction in the presence of Li + ‐containing aprotic solvents, to either Li + ‐O 2 − by one‐electron reduction or Li 2 O 2 by two‐electron reduction, is instrumental to enhance the discharge voltage and capacity of aprotic Li‐O 2 batteries. Standard potentials of O 2 /Li + ‐O 2 − and O 2 /O 2 − were experimentally measured and computed using a mixed cluster‐continuum model of ion solvation. Increasing combined solvation of Li + and O 2 − was found to lower the coupling of Li + ‐O 2 − and the difference between O 2 /Li + ‐O 2 − and O 2 /O 2 − potentials. The solvation energy of Li + trended with donor number (DN), and varied greater than that of O 2 − ions, which correlated with acceptor number (AN), explaining a previously reported correlation between Li + ‐O 2 − solubility and DN. These results highlight the importance of the interplay between ion–solvent and ion–ion interactions for manipulating the energetics of intermediate species produced in aprotic metal–oxygen batteries.

Kwabi, David G.↗
DOE OSTI2025

Scaling microstructural processes in the sintering of ionic ceramics

A multi-scale framework, combining a multiphase field formulation and large deformation mechanics, was developed as a stepping stone to perform the data analytics of the microstructural level kinetics of a sintering solid. Relevant microstructural information from this framework, such as grain, stress, and porosity statistics, was scaled up to describe the macroscopic level sintering kinetics. Here, the developed formulation was applied to describe the electric field assisted sintering of Y 2 O 3 . Microstructural inhomogeneities in a multi-granular solid result in the formation of a field of compressive stress networks, which interleave with low compression and weakly tensile regions, defining a scaffolding for sintering concentration regions to develop. A Poisson effect-induced lateral stress network is also naturally self-induced as a result of the mechanical constraints imposed by the sintering apparatus. For long sintering times, localized shear stresses enhancing mass flow along grain boundaries and internal surfaces develop. Three-sided pores are removed by either vacancy transport to the surrounding pores, or move towards the external surfaces through grain boundary diffusion. Four- and higher order-sided pores stabilize because an equal amount of vacancies are gained and lost through the connecting grain boundaries. Grain dewetting contributes to pore coalescence, suggesting that pore kinetics and grain growth are coupled and should be analyzed in concert. The combined sintering and grain growth kinetics define six regimes of sintering behavior: (1) T, the transient regime; (2) E$_Υ$, the surface energy dominated, early sintering regime, where the grain growth exponent, p = 1, and the stress concentration factor, $f$ ~ $1/\hat{ρ}^{4.6}$; (3) E S , the stress dominated, early sintering regime, where p = 1 and $f$ ~ $1/\hat{ρ}^{4}$; (4) I$_Υ$, the surface energy dominated, intermediate sintering regime, where p = 2 and $f$ ~ $1/\hat{ρ}^{4.6}$; (5) I S , the stress dominated, intermediate sintering regime, where p = 2 and $f$ ~ $1/\hat{ρ}^{4}$; and (6) L, the late sintering regime, where p = 3 and $f$ ~ 1. At the macroscopic level, the rapid densification and suppression of grain growth observed in the electric field assisted sintering process is a consequence of the compounding effects of the underlying stress-, transport-, and interfacial-energy-induced energy minimization kinetics, as predicted by the multi-scale framework.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2018

Mechanism-based modeling of solute strengthening: Application to thermal creep in Zr alloy

In this paper, a crystallographic thermal creep model is proposed for Zr alloys that accounts for the hardening contribution of solutes via their time-dependent pinning effect on dislocations. The core-diffusion model proposed by Soare and Curtin (2008a) is coupled with a recently proposed constitutive modeling framework (Wang et al., 2017, 2016) accounting for the heterogeneous distribution of internal stresses within grains. The Coble creep mechanism is also included. This model is, in turn, embedded in the effective medium crystallographic VPSC framework and used to predict creep strain evolution of polycrystals under different temperature and stress conditions. The simulation results reproduce the experimental creep data for Zircaloy-4 and the transition between the low (n~1), intermediate (n~4) and high (n~9) power law creep regimes. This is achieved through the dependence on local aging time of the solute-dislocation binding energy. The anomalies in strain rate sensitivity (SRS) are discussed in terms of core-diffusion effects on dislocation junction strength. The mechanism-based model captures the primary and secondary creep regimes results reported by Kombaiah and Murty (2015a, 2015b) for a comprehensive set of testing conditions covering the 500–600 °C interval, stresses spanning 14–156 MPa, and steady state creep rates varying between 1.5·10 -9 s -1 to 2·10 -3 s -1 . There are two major advantages to this model with respect to more empirical ones used as constitutive laws for describing thermal creep of cladding: 1) specific dependences on the nature of solutes and their concentrations are explicitly accounted for; 2) accident conditions in reactors, such as RIA and LOCA, usually take place in short times, and deformation takes place in the primary, not the steady-state creep stage. Finally, as a consequence, a model that accounts for the evolution with time of microstructure is more reliable for this kind of simulation.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Synergistic Coupling of CO2 and H2O during Expansion of Clays in Supercritical CO2-CH4 Fluid Mixtures

A combination of in operando IR and XRD methods were used to investigate the interaction of variably hydrated supercritical CO2-CH4 fluids with Na/NH4/Cs substituted montmorillonites. Comparing the behavior of Na-clay exposed to CH4 versus CO2 dominant fluid phases demonstrated that CO2 disrupts the H-bond network of intercalated H2O. At relatively low potentials of H2O, CO2 facilitates H2O intercalation and expansion of the interlayer region of the Na-clay. In contrast, CO2 inhibited H2O intercalation but promoted expansion of the Cs-clay. The NH4-clay displayed intermediated behavior. Methane likely intercalated the clays but opportunistically, filling unoccupied space after CO2 and H2O actively expanded the interlayer region. By comparing and contrasting the behavior of the Cs and NH4 clays to the Na Clay we conclude that, whereas H2O is required for initial Na-clay expansion, CO2 synergistically facilitated expansion and hydration of Na-clay by mixing with H2O (the entropic contribution) and participating in the outer solvation sphere of Na (the enthalpic contribution). In contrast, CO2 can directly solvate interlayer Cs and NH4 and cause expansion in the absence of H2O; nonetheless, H2O and CO2 also act synergistically to facilitate expansion of the Cs and NH4 clays at low H2O concentrations.

Loring, John S.↗
DOE OSTI2013

Two-fluid simulations of driven reconnection in the mega-ampere spherical tokamak

In the merging-compression method of plasma start-up, two flux-ropes with parallel toroidal current are formed around in-vessel poloidal field coils, before merging to form a spherical tokamak plasma. This start-up method, used in the Mega-Ampere Spherical Tokamak (MAST), is studied as a high Lundquist number and low plasma-beta magnetic reconnection experiment. In this paper, 2D fluid simulations are presented of this merging process in order to understand the underlying physics, and better interpret the experimental data. These simulations examine the individual and combined effects of tight-aspect ratio geometry and two-fluid physics on the merging. The ideal self-driven flux-rope dynamics are coupled to the diffusion layer physics, resulting in a large range of phenomena. For resistive MHD simulations, the flux-ropes enter the sloshing regime for normalised resistivity η≲10{sup −5}. In Hall-MHD, three regimes are found for the qualitative behaviour of the current sheet, depending on the ratio of the current sheet width to the ion-sound radius. These are a stable collisional regime, an open X-point regime, and an intermediate regime that is highly unstable to tearing-type instabilities. In toroidal axisymmetric geometry, the final state after merging is a MAST-like spherical tokamak with nested flux-surfaces. It is also shown that the evolution of simulated 1D radial density profiles closely resembles the Thomson scattering electron density measurements in MAST. An intuitive explanation for the origin of the measured density structures is proposed, based upon the results of the toroidal Hall-MHD simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Fermi surface topology and nontrivial Berry phase in the flat-band semimetal Pd 3 Pb

A study of the Fermi surface of the putative topological semimetal Pd 3 Pb has been carried out using Shubnikov–de Haas (SdH) oscillations measured in fields of up to 60 T. Pd 3 Pb has garnered attention in the community due to a peculiar Fermi surface that has been proposed theoretically by Ahn, Pickett, and Lee, Phys. Rev. B 98 , 035130 (2018) to host a dispersionless band along X - Γ as well as multiple triply degenerate band crossings that, under the influence of spin-orbit coupling, lead to ten fourfold degenerate Dirac points. Analysis of the SdH oscillation data verifies the calculated multisheet Fermi surface, revealing a Γ centered spheroid that had not been resolved experimentally in prior studies. A comprehensive, angle-dependent analysis of the phase of the SdH oscillations convincingly demonstrates a nontrivial Berry phase for two bands along Γ - R , supporting the theoretical predictions, while simultaneously evidencing interference between extremal orbits that mimics a trivial Berry phase at intermediate angles.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Nascent energy distribution of the Criegee intermediate CH 2 OO from direct dynamics calculations of primary ozonide dissociation

Here, ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c -C 2 H 4 O 3 , the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H 2 COO) and formaldehyde (H 2 CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on newhigh-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 +/- 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (~30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum. Published by AIP Publishing.

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

Hund Physics Landscape of Two-Orbital Systems

Motivated by the recent discovery of superconductivity in infinite-layer nickelates RE 1–δ Sr δ NiO 2 (RE = Nd, Pr), we study the role of Hund coupling J in a quarter-filled two-orbital Hubbard model, which has been on the periphery of the attention. Here, a region of negative effective Coulomb interaction of this model is revealed to be differentiated from three- and five-orbital models in their typical Hund metal active fillings. We identify distinctive regimes including four different correlated metals, one of which stems from the proximity to a Mott insulator, while the other three, which we call “intermediate” metal, weak Hund metal, and valence-skipping metal, from the effect of J being away from Mottness. Defining criteria characterizing these metals is suggested, establishing the existence of Hund metallicity in two-orbital systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2000

Thermodynamics of Aqueous Organic Sulfur Compounds: A Key to the Organic Geochemistry of Hydrothermal Systems?

Hydrothermal environments are locations of varied geochemistry due to the disequilibrium between vent fluids and seawater. The disequilibrium geochemistry has been hypothesized to include reactions to synthesize organic compounds. Observations of the organic geochemistry of hydrothermal vent sites has received little attention. Experimental simulations of these environments, however, indicate that organic compounds may have difficulty forming in a purely aqueous environment. On the other hand, thiols. thioesters and disulfides have been implicated as reaction intermediates between CO or CO2 in experiments of carbon reduction in hydrothermal environments as well as in a variety of biological processes and other abiotic reactions (Wachtershauser, 1990, OLEB 20, 173; Heinen and Lauwers, 1996, OLEB 26, 13 1, Huber and Wachtershauser, 1997, Science 276, 245; Russell et al., 1998, in Thermophiles: The keys to molecular evolution and the origin of life?). The reduction of CO2 to thiols, for example, is observed using the FeS-H2S/FeS2 couple to provide the reducing power (see Schoonen et al., 1999, OLEB 29, 5). In addition, the enzyme involved in final stage of methanogenesis, coenzyme-M, is itself a thiol. Thus, organic sulfur compounds may hold the key to the organic chemistry leading to the origin of life at high temperatures. Understanding the biochemical processes of microorganisms that can live to temperatures at least as high as 113 C (Blochl et al., 1996, Extremophiles 1, 14) requires knowledge of the properties of the chemical reactions involved. In order to assess the role of aqueous organic sulfur compounds in hydrothermal organic geochemistry, we have been attempting to determine their thermodynamic properties. We have culled the literature to obtain the properties of organic sulfur compounds. We are able to calculate a number of essential properties, such as free energies of formation, from solubility data available in the literature together with standard properties of organic sulfur gases. However, a number of the properties for aqueous organic sulfur compounds have not been experimentally determined. Furthermore, most of thermodynamic data that are available are for 25 C and 1 bar. In order to determine reaction properties to temperatures and pressures appropriate to the hydrothermal conditions in which thermophilic organisms actually live, we use equations of state developed by Helgeson and co-workers (Helgeson et al., 1981, AJS 281, 1249). A key piece of information needed to go up in temperature is the partial molal heat capacity, which is one of the properties for which experimental data are unavailable for nearly all organic sulfur compounds. We have used correlation methods to determine the partial molal heat capacities and volumes of many organic solutes. These estimates allow us to asses the role of organic sulfur compounds during the reduction of carbon in hydrothermal settings. We will present these data, along with examples of the thermodynamic properties of reactions involving aqueous organic sulfur compounds.

Schulte, Mitchell↗
DOE OSTI2011

Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E

PDZ (PSD95/Discs large/ZO-1) domains are ubiquitous protein interaction motifs found in scaffolding proteins involved in signal transduction. Despite the fact that many PDZ domains show a limited tendency to undergo structural change, the PDZ family has been associated with long-range communication and allostery. One of the PDZ domains studied most in terms of structure and biophysical properties is the second PDZ ('PDZ2') domain from protein tyrosine phosphatase 1E (PTP1E, also known as PTPL1). Previously, we showed through NMR relaxation studies that binding of the RA-GEF2 C-terminal peptide substrate results in long-range propagation of side-chain dynamic changes in human PDZ2 [Fuentes, E. J., et al. (2004) J. Mol. Biol. 335, 1105-1115]. Here, we present the first X-ray crystal structures of PDZ2 in the absence and presence of RA-GEF2 ligand, determined to resolutions of 1.65 and 1.3 {angstrom}, respectively. These structures deviate somewhat from previously determined NMR structures and indicate that very minor structural changes in PDZ2 accompany peptide binding. NMR residual dipolar couplings confirm the crystal structures to be accurate models of the time-averaged atomic coordinates of PDZ2. The impact on side-chain dynamics was further tested with a C-terminal peptide from APC, which showed results nearly identical to those of RA-GEF2. Thus, allosteric transmission in PDZ2 induced by peptide binding is conveyed purely and robustly by dynamics. {sup 15}N relaxation dispersion measurements did not detect appreciable populations of a kinetic structural intermediate. Collectively, for ligand binding to PDZ2, these data support a lock-and-key binding model from a structural perspective and an allosteric model from a dynamical perspective, which together suggest a complex energy landscape for functional transitions within the ensemble.

59 BASIC BIOLOGICAL SCIENCES↗