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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Energetic and structural control of polyspecificity in a multidrug transporter

Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood. Using multiparametric deep mutational scanning across eight substrates and two energy conditions, we deconvolute the contributions of substrate recognition, energetic coupling, and protein stability, providing an integrated, high-resolution view of multidrug transport. We find that substrate specificity arises from a distributed network of residues extending beyond the binding site, with mutations that reshape binding, coupling, conformational flexibility, and membrane interactions. Further, we apply a pH-based selection scheme to measure the effect of mutation on pH-dependent transport efficiency. By integrating these data, we reveal a fundamental relationship between efficiency and promiscuity: Highly efficient variants exhibit broad substrate profiles, while inefficient variants are narrower. In conclusion, these findings establish a direct link between energy coupling and polyspecificity, uncovering the biochemical logic underlying multidrug transport.

Biological Sciences↗
DOE OSTI2025

A low-temperature, one-step synthesis for monazite can transform monazite into a readily usable advanced nuclear waste form

It has been demonstrated that monazite-type materials are excellent candidates for nuclear waste forms, and hence, their facile synthesis is of great importance for the needed sequestration of existing nuclear waste. The synthesis of monazite, LaPO 4 , requires inconveniently high temperatures near 1000°C and generally involves the conversion of the presynthesized rhabdophane, LaPO 4 •nH 2 O, to the LaPO 4 monazite phase. During this structure transformation, the rhabdophane converts irreversibly to the thermodynamically stable monoclinic monazite structure. A low-temperature (185° to 260°C) mild hydrothermal acid-promoted synthesis of monazite is described that can both transform presynthesized rhabdophane or assemble reagents to the monoclinic monazite structure. The pH dependence of this reaction is detailed, and its applicability to the LnPO 4 (Ln = La, Ce, Pr, Nd, Sm-Gd), Ca 0.5 Th 0.5 PO 4 , and Sr 0.5 Th 0.5 PO 4 systems is discussed. The crystal growth of Ca 0.5 Th 0.5 PO 4 and Sr 0.5 Th 0.5 PO 4 is described, and their crystal structures were reported. In situ x-ray diffraction studies, performed as a function of temperature, provide insight into the structure transformation process.

Biogeochemistry↗
DOE OSTI2024

Synthesis and Characterization of Silver-Modified Nanoporous Silica Materials for Enhanced Iodine Removal

In aquatic environments, the presence of iodine species, including radioactive isotopes like 129 I and I 2 , poses significant environmental and health concerns. Iodine can enter water resources from various sources, including nuclear accidents, medical procedures, and natural occurrences. To address this issue, the use of natural occurring nanoporous minerals, such as zeolitic materials, for iodine removal will be explored. This study focuses on the adsorption of iodine by silver-modified zeolites (13X-Ag, 5A-Ag, Chabazite-Ag, and Clinoptilolite-Ag) and evaluates their performance under different conditions. All materials were characterized using scanning electron microscopey (SEM), energy-dispersive X-ray spectroscopy (EDS), powdered X-ray diffraction (P-XRD), Fourier-transform infrared spectrometry (FTIR), and nitrogen adsorption studies. The results indicate that Chabazite-Ag exhibited the highest iodine adsorption capacity, with an impressive 769 mg/g, making it a viable option for iodine removal applications. 13X-Ag and 5A-Ag also demonstrated substantial adsorption capacities of 714 mg/g and 556 mg/g, respectively, though their behavior varied according to different models. In contrast, Clinoptilolite-Ag exhibited strong pH-dependent behavior, rendering it less suitable for neutral to slightly acidic conditions. Furthermore, this study explored the impact of ionic strength on iodine adsorption, revealing that Chabazite-Ag is efficient in low-salinity environments with an iodine adsorption capacity of 51.80 mg/g but less effective in saline conditions. 5A-Ag proved to be a versatile option for various water treatments, maintaining its iodine adsorption capacity across different salinity levels. In contrast, Clinoptilolite-Ag exhibited high sensitivity to ionic competition, virtually losing its iodine adsorption ability at a NaCl concentration of 0.1 M. Kinetic studies indicated that the pseudo-second-order model best describes the adsorption process, suggesting chemisorption mechanisms dominate iodine removal. Chabazite-Ag exhibited the highest initial adsorption rate with a k 2 value of 0.002 mg g -1 h -1 , emphasizing its superior adsorption capabilities. Chabazite and Clinoptilolite, naturally occurring minerals, provide eco-friendly solutions for iodine adsorption. Chabazite superior iodine removal highlights its value in critical applications and its potential for addressing pressing environmental challenges.

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

Modeling supercritical CO 2 flow and mineralization in reactive host rocks with PFLOTRAN v7.0

Understanding the flow and reactivity of CO 2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO 2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO 2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO 2 -reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO 2 in situ to simultaneously dissolve host rock minerals and mineralize CO 2 as carbonates. Engineering rapid CO 2 mineralization in the subsurface is attractive because of the increased density of stored CO 2 , the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO 2 -brine flow and reactive transport for a wide range of injection and production applications involving reactive CO 2 -brine systems. These developments are based on the well established and trusted CO 2 flow capabilities in the STOMP-CO 2 simulator. New capabilities added to PFLOTRAN include new CO 2 -brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO 2 verify the newly developed CO 2 -brine flow capabilities. Demonstrations of coupled CO 2 -brine flow modeling and reactive transport show how CO 2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO 2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.

Critical Minerals↗
NASA NTRS1982

Carbon catalyzed SO2 oxidation by NO2 and O3

The oxidation of SO2 to sulfate on carbon particles by trace quantities of NO2 and O3 was studied. Particulate carbon black was either: (1) directly exposed on the pan of a microbalance to various humidified mixtures of SO2 and oxidant gas and the resultant weight gains monitored, or (2) the gas mixtures were bubbled through aqueous suspensions of carbon black and pure water blanks. In each set of experiments the run times were varied appropriately and the yields of sulfate were determined analytically. Conversion of SO2 to sulfate was thus characterized as a function of exposure time and of oxidant gas. Carbon black was determined to be an excellent catalyst for SO2 oxidation to sulfate by both NO2 and O3. No saturation effects were observed in either experimental approach. Conversions of SO2 to sulfate did not appear pH dependent.

Cofer, W. R., III↗
NASA NTRS1985

Soluble minerals in chemical evolution. I - Adsorption of 5-prime-AMP on CaSO4 - A model system

The adsorption of 5-prime-AMP onto solid CaSO4-2H2O was studied in a saturated suspension as a function of pH and electrolyte concentration. The adsorption is pH-dependent and is directly correlated with the charge on the 5-prime-AMP molecule which is determined by the state of protonation of the N-1 nitrogen of the purine ring and the phosphate oxygens. It is proposed that the binding that occurs between the nucleotide and the salt is electrostatic in nature. The adsorption decreases with increasing ionic strength of the solution which means that in a fluctuating environment of wetting and drying cycles, a biomolecule similar to 5-prime-AMP could be expected to desorb during the drying phase. The results indicate that CaSO4-2H2O can serve as a concentrating surface for biomolecules. The significance of this is discussed with regard to the possible role of soluble minerals and their surfaces in a geochemical model consistent with the evolution of the earth and the origin of life.

Orenberg, J. B.↗
NASA NTRS1985

Effects of tyrosine-26 and tyrosine-64 nitration on the photoreactions of bacteriorhodopsin

The photoreactions of nitrated bacteriorhodopsin (bR) are examined. Flash-induced difference spectra of bR, bR with aminotyrosine in position 26 (bR-N26R) and bR with aminotyrosine in position 64 are analyzed. It is observed that changes in the actinic wavelength (from 520 to 500 or 580 nm) have no affect on the shape of the spectra and the formation and decay kinetics of the O and M intermediates. Nitration of tyrosine-64 decreases the chromophore absorbance, shifts the absorption maximum to 535 nm, and affects photocycle kinetics independent of the pK of its phenolic group. Light-dark adaptation spectra for bR are studied. The kinetics of the M and O intermediates in bR with nitrotyrosine in position 64 (bR-N64) and bR with aminotyrosine in position 64 and bR with nitrotyrosine in position 26 and bR-N26R are described and compared to bR; the pH dependence and M and O decay rates are considered. The deprotonation of bR-N64 during the photoreaction cycle and the effects of nitration on the activity of proton pumping are investigated.

Scherrer, P.↗
NASA NTRS2003

Ionic signaling in plant gravity and touch responses

Plant roots are optimized to exploit resources from the soil and as each root explores this environment it will encounter a range of biotic and abiotic stimuli to which it must respond. Therefore, each root must possess a sensory array capable of monitoring and integrating these diverse stimuli to direct the appropriate growth response. Touch and gravity represent two of the biophysical stimuli that plants must integrate. As sensing both of these signals requires mechano-transduction of biophysical forces to biochemical signaling events, it is likely that they share signal transduction elements. These common signaling components may allow for cross-talk and so integration of thigmotropic and gravitropic responses. Indeed, signal transduction events in both plant touch and gravity sensing are thought to include Ca(2+)- and pH-dependent events. Additionally, it seems clear that the systems responsible for root touch and gravity response interact to generate an integrated growth response. Thus, primary and lateral roots of Arabidopsis respond to mechanical stimuli by eliciting tropic growth that is likely part of a growth strategy employed by the root to circumvent obstacles in the soil. Also, the mechano-signaling induced by encountering an obstacle apparently down-regulates the graviperception machinery to allow this kind of avoidance response. The challenge for future research will be to define how the cellular signaling events in the root cap facilitate this signal integration and growth regulation. In addition, whether other stimuli are likewise integrated with the graviresponse via signal transduction system cross-talk is an important question that remains to be answered.

Review↗
NASA NTRS2002

4,4,4-trifluoro-3-(indole-3-)butyric acid promotes root elongation in Lactuca sativa independent of ethylene synthesis and pH

We studied the mode of action of 4,4,4-trifluoro-3- (indole-3-) butyric acid (TFIBA), a recently described root growth stimulator, on primary root growth of Lactuca sativa L. seedlings. TFIBA (100 micromoles) promoted elongation of primary roots by 40% in 72 h but inhibited hypocotyl growth by 35%. TFIBA induced root growth was independent of pH. TFIBA did not affect ethylene production, but reduced the inhibitory effect of ethylene on root elongation. TFIBA promoted root growth even in the presence of the ethylene biosynthesis inhibitor L-alpha-(2-aminoethoxyvinyl)glycine. TFIBA and the ethylene-binding inhibitor silver thiosulphate (STS) had a similar effect on root elongation. The results indicate that TFIBA-stimulated root elongation was neither pH-dependent nor related to inhibition of ethylene synthesis, but was possibly related to ethylene action.

Non-NASA Center↗
NASA NTRS2002

The growing world of expansins

Expansins are cell wall proteins that induce pH-dependent wall extension and stress relaxation in a characteristic and unique manner. Two families of expansins are known, named alpha- and beta-expansins, and they comprise large multigene families whose members show diverse organ-, tissue- and cell-specific expression patterns. Other genes that bear distant sequence similarity to expansins are also represented in the sequence databases, but their biological and biochemical functions have not yet been uncovered. Expansin appears to weaken glucan-glucan binding, but its detailed mechanism of action is not well established. The biological roles of expansins are diverse, but can be related to the action of expansins to loosen cell walls, for example during cell enlargement, fruit softening, pollen tube and root hair growth, and abscission. Expansin-like proteins have also been identified in bacteria and fungi, where they may aid microbial invasion of the plant body.

NASA Discipline Plant Biology↗
NASA NTRS1994

Autolysis and extension of isolated walls from growing cucumber hypocotyls

Walls isolated from cucumber hypocotyls retain autolytic activities and the ability to extend when placed under the appropriate conditions. To test whether autolysis and extension are related, we treated the walls in various ways to enhance or inhibit long-term wall extension ('creep') and measured autolysis as release of various saccharides from the wall. Except for some non-specific inhibitors of enzymatic activity, we found no correlation between wall extension and wall autolysis. Most notably, autolysis and extension differed strongly in their pH dependence. We also found that exogenous cellulases and pectinases enhanced extension in native walls, but when applied to walls previously inactivated with heat or protease these enzymes caused breakage without sustained extension. In contrast, pretreatment of walls with pectinase or cellulase, followed by boiling in methanol to inactivate the enzymes, resulted in walls with much stronger expansin-mediated extension responses. Crude protein preparations from the digestive tracts of snails enhanced extension of both native and inactivated walls, and these preparations contained expansin-like proteins (assessed by Western blotting). Our results indicate that the extension of isolated cucumber walls does not depend directly on the activity of endogenous wall-bound autolytic enzymes. The results with exogenous enzymes suggest that the hydrolysis of matrix polysaccharides may not induce wall creep by itself, but may act synergistically with expansins to enhance wall extension.

NASA Discipline Plant Biology↗
NASA NTRS1997

Assembly and enlargement of the primary cell wall in plants

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

NASA Discipline Plant Biology↗
NASA NTRS2011

One-carbon (bio ?) Geochemistry in Subsurface Waters of the Serpentinizing Coast Range Ophiolite

Serpentinization - the aqueous alteration of ultramafic rocks - typically imparts a highly reducing and alkaline character to the reacting fluids. In turn, these can influence the speciation and potential for metabolism of one-carbon compounds in the system. We examined the aqueous geochemistry and assessed the biological potential of one-carbon compounds in the subsurface of the McLaughlin Natural Reserve (Coast Range Ophiolite, California, USA). Fluids from wells sunk at depths of 25-90 meters have pH values ranging from 9.7 to 11.5 and dissolved inorganic carbon (DIC concentrations) generally below 60 micromolar. Methane is present at concentrations up to 1.3 millimolar (approximately one-atmosphere saturation), and hydrogen concentrations are below 15 nanomolar, suggesting active consumption of H2 and production of CH4. However, methane production from CO2 is thermodynamically unfavorable under these conditions. Additionally, the speciation of DIC predominantly into carbonate at these high pH values creates a problem of carbon availability for any organisms that require CO2 (or bicarbonate) for catabolism or anabolism. A potential alternative is carbon monoxide, which is present in these waters at concentrations 2000-fold higher than equilibrium with atmospheric CO. CO is utilized in a variety of metabolisms, including methanogenesis, and bioavailability is not adversely affected by pH-dependent speciation (as for DIC). Methanogenesis from CO under in situ conditions is thermodynamically favorable and would satisfy biological energy requirements with respect to both Gibbs Energy yield and power.

McLaughlin Natural Reserve↗
NASA NTRS2017

Investigation of Global Particulate Nitrate from the AeroCom Phase III Experiment

An assessment of global particulate nitrate and ammonium aerosol based on simulations from nine models participating in the Aerosol Comparisons between Observations and Models (AeroCom) phase III study is presented. A budget analysis was conducted to understand the typical magnitude, distribution, and diversity of the aerosols and their precursors among the models. To gain confidence regarding model performance, the model results were evaluated with various observations globally, including ground station measurements over North America, Europe, and east Asia for tracer concentrations and dry and wet depositions, as well as with aircraft measurements in the Northern Hemisphere mid-to-high latitudes for tracer vertical distributions. Given the unique chemical and physical features of the nitrate occurrence, we further investigated the similarity and differentiation among the models by examining (1) the pH-dependent NH3 wet deposition; (2) the nitrate formation via heterogeneous chemistry on the surface of dust and sea salt particles or thermodynamic equilibrium calculation including dust and sea salt ions; and (3) the nitrate coarse-mode fraction (i.e., coarse/total). It is found that HNO3, which is simulated explicitly based on full O3-HOx-NOx-aerosol chemistry by all models, differs by up to a factor of 9 among the models in its global tropospheric burden. This partially contributes to a large difference in NO3(-), whose atmospheric burden differs by up to a factor of 13. The atmospheric burdens of NH3 and NHC 4 differ by 17 and 4, respectively. Analyses at the process level show that the large diversity in atmospheric burdens of NO3(-), NH3, and NHC4(+) is also related to deposition processes. Wet deposition seems to be the dominant process in determining the diversity in NH3 and NHC 4 lifetimes. It is critical to correctly account for contributions of heterogeneous chemical production of nitrate on dust and sea salt, because this process overwhelmingly controls atmospheric nitrate production (typically greater than 80 %) and determines the coarse- and fine-mode distribution of nitrate aerosol.

Ammonium aerosol based on simulations↗
DOE OSTI2025

Chemical Functional Groups Regulate Ion Concentrations and pHs in Nanopores

Understanding ion behaviors in functionalized nanopores is essential to deciphering reactions in both natural and engineered systems, such as sediments, biological ion channels, and membranes. While many efforts have shown the modified ion behaviors in the functionalized nanopores, a direct measurement and analysis to show how chemical functional groups affect ion concentrations in nanopores are critically needed. In this work, we present a plasmonic nanosensor that can measure the local concentrations of protons, anions (phosphate, nitrate, sulfate, and arsenate), and cations (mercury, lead, and copper) in functionalized nanopores, and we compare their concentrations in nanopores with the corresponding bulk concentrations. Notably, chemical functional groups induced ion concentrations differently in nanopores. In pristine nanopores and methyl- and phenyl-functionalized nanopores, we discovered an unexpected concurrence of an enhanced anion concentration and a suppressed cation concentration. In addition, the nanopore pH is dependent on bulk solution compositions and can be lower by 2.5 units, even when the bulk solution is well-buffered. In contrast, for hydrophilic (amine, thiol, and carboxyl) nanopores, pH depended on the p K a of the functional groups, and the heavy metal concentrations depended on chemical interactions with the functional groups. Our findings provide a better understanding of water chemistry in nanopores and can help precisely control ions in nanopores to benefit the design of membrane-based desalination techniques, CO 2 storage, and porous catalysts.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1996

Was Ferrocyanide a Prebiotic Reagent?

Hydrogen cyanide is the starting material for a diverse array of prebiotic syntheses, including those of amino acids and purines. Hydrogen cyanide also reacts with ferrous ions to give ferrocyanide, and so it is possible that ferrocyanide was common in the early ocean. This can only be true if the hydrogen cyanide concentration was high enough and the rate of reaction of cyanide with ferrous ions was fast enough. We show experimentally that the rate of formation of ferrocyanide is rapid even at low concentrations of hydrogen cyanide in the pH range 6-8, and therefore an equilibrium calculation is valid. The equilibrium concentrations of ferrocyanide are calculated as a function of hydrogen cyanide concentration, pH and temperature. The steady state concentration of hydrogen cyanide depends on the rate of synthesis by electric discharges and ultraviolet light and the rate of hydrolysis, which depends on pH and temperature. Our conclusions show that ferrocyanide was a major species in the prebiotic ocean only at the highest production rates of hydrogen cyanide in a strongly reducing atmosphere and at temperatures of 0 C or less, although small amounts would have been present at lower hydrogen cyanide production rates. The prebiotic application of ferrocyanide as a source of hydrated electrons, as a photochemical replication process, and in semi-permeable membranes is discussed.

Keefe, Anthony D.↗
NASA NTRS1997

An Accurate Potential Energy Surface for H2O

We have carried out extensive high quality ab initio electronic structure calculations of the ground state potential energy surface (PES) and dipole moment function (DMF) for H2O. A small adjustment is made to the PES to improve the agreement of line positions from theory and experiment. The theoretical line positions are obtained from variational ro-vibrational calculations using the exact kinetic energy operator. For the lines being fitted, the root-mean-square error was reduced from 6.9 to 0.08 /cm. We were then able to match 30,092 of the 30,117 lines from the HITRAN 96 data base to theoretical lines, and 80% of the line positions differed less than 0.1 /cm. About 3% of the line positions in the experimental data base appear to be incorrect. Theory predicts the existence of many additional weak lines with intensities above the cutoff used in the data base. To obtain results of similar accuracy for HDO, a mass dependent correction to the PH is introduced and is parameterized by simultaneously fitting line positions for HDO and D2O. The mass dependent PH has good predictive value for T2O and HTO. Nonadiabatic effects are not explicitly included. Line strengths for vibrational bands summed over rotational levels usually agree well between theory and experiment, but individual line strengths can differ greatly. A high temperature line list containing about 380 million lines has been generated using the present PES and DMF

Schwenke, David W.↗
DOE OSTI2024

UV-Vis spectrophotometric determination of rare earth elements (REE) speciation at near-neutral to alkaline pH. Part I: m-cresol purple properties from 25-75 °C and Er hydrolysis

The speciation and mobility of rare earth elements (REE) strongly depends on pH which controls the formation of charged aqueous hydroxyl species. The latter potentially play an important role in controlling heavy REE adsorption on clay minerals in near-neutral to alkaline waters such as in regolith-hosted REE mineral deposits. However, accurate REE hydrolysis constants are needed for developing geochemical models that can predict the role of these charged species in natural systems. Here, we develop a robust experimental UV-Vis spectrophotometric method using m-cresol purple to determine in situ pH from 25 to 75 °C. This method is used to derive the average ligand number and hydrolysis constants of erbium (Er) at 25 °C in aqueous solutions with low ionic strength (≤ 0.001 mol/L) at pH from ~7 to 9.5 and in the presence of Er concentrations from 0 to 0.057 mM. The average ligand number ranges between 1 and 3 indicating that Er(OH) 2+ , Er(OH) 2 + and Er(OH) 3 0 control speciation in the experiments. The logarithm of the Er hydrolysis constants (log*β n ° , n= 1 to 3) derived at infinite dilution for the reaction Er 3+ + nH 2 O = Er(OH) n 3-n + nH + are: *β 1 ° = –7.22 ± 0.10, *β 2 ° = –14.52 ± 0.08, *β 3 ° = –23.24 ± 0.04. Implementation of these experimental data into a geochemical model indicates that the Er(OH) 2 + and Er(OH) 3 0 species are both stable in a much wider pH range than previously predicted. Consequently, the positively charged REE hydroxyl complexes can potentially control the fractionation of light vs. heavy REE via adsorption as observed in the formation of certain regolith-hosted REE deposits.

58 GEOSCIENCES↗