Search NASA⌕ Search

SEARCH · Search NASA

Results for “positional isomers”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Positional Isomer of P3HB by Stereoselective Polymerization of Racemic α-Methyl-β-propiolactone Delivers Polyethylene-like Properties

Biobased and biodegradable poly(3-hydroxybutyrolactone) (P3HB) has long been considered as a more sustainable alternative to petroleum-based, nonbiodegradable polyolefins, but its properties are far off from its polyolefin (polyethylene, PE, and polypropylene, PP) counterpart’s unique set of thermal (low T g below −20 °C and high T m > 100 °C) and mechanical (high ductility >350%) characteristics. Here, we report that a positional isomer of P3HB, poly(3-hydroxy-2-methylpropionate) (P3H2MP), synthesized by catalyst-controlled stereoselective polymerization of racemic α-methyl-β-propiolactone, can match that demanding set of thermomechanical properties of PE. In particular, isotactic-rich P3H2MP, readily synthesized under ambient conditions, reaches high M n close to one million Da, T g down to −25 °C, T m up to 115 °C, tensile strength up to 64 MPa, and toughness up to 131 MJ m –3 , thus mechanically outperforming PE while maintaining a comparable low T g and high T m combination. A P3H2MP-based triblock copolymer further widens the low-high temperature window from T g = −29 °C to T m = 186 °C, resembling those of PP. These results show that P3H2MP exhibits the unique combination of thermomechanical properties matching those of high-performance polyolefins.

Biopolymers↗
DOE OSTI2025

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗
DOE OSTI2025

Hydride Migration within RhH 2 Ag 19 Superatom: A Combined Neutron Diffraction and DFT Analysis

Abstract An investigation combining neutron diffraction and DFT allows determining the most likely hydride migration pathway within the icosahedral metal framework of [RhH 2 Ag 19 {S 2 P(O n Pr) 2 } 12 ] (RhH 2 Ag 19 ). Starting from the experimentally derived solid‐state structures, a computational analysis is able to reveal an energetically favorable migration pathway with a maximum energy barrier of 4.2 kcal mol −1 . The two hydrides migrate simultaneously within the Rh@Ag 12 icosahedral core, traversing several positional isomers. This study expands the understanding of hydride dynamics in nanoclusters and provides critical insights into the structural flexibility of the superatom framework. These findings have significant implications for hydrogen storage, catalysis, and the design of advanced hydride‐containing materials.

Chemistry↗
DOE OSTI2025

Ultrafast Correlation Energy Estimator

A virtually no-cost method is proposed that can compute the correlation energies of general, covalently bonded, organic, and inorganic molecules (including conjugated π-electron systems) with a well-defined dominant Lewis structure at the accuracy of 99.5% of the near-exact values determined by the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] in the complete-basis-set (CBS) limit. This Correlation Energy Per Bond (CEPB) method assigns a partial correlation energy to each bond type (characterized by the identities of the two atoms forming the bond and its integer bond order) and to a lone pair, regardless of the bond length, bond angle, sp-hybridization, π-electron conjugation, ionicity, noncovalent interactions, etc. At its current stage, the method is mainly suitable for near-equilibrium geometries. The correlation energies per bond are determined by a fit to the CCSD(T)/CBS benchmarks. It can neither improve the equilibrium structures nor discern conformers or positional isomers, yet its accuracy for reaction energies rivals that of the second-order Møller–Plesset perturbation theory, which is far more expensive. Its promising performance underscores the possibility that surprisingly compact, chemically intuitive molecular fragments exist into which correlation energies can be partitioned, leading to various ultrafast correlation-energy estimators tailored to different purposes.

Binding energy↗
DOE OSTI2025

dynamics of organic-mineral interactions at the metal oxide-solution interface as studied via binding energetics (Final report)

This project focused on addressing longstanding fundamental and experimental uncertainties on how dissolved organic substances (DOS) interact with metal oxide surface under environmentally relevant conditions. By leveraging a custom-built real-time, in-tandem flow adsorption microcalorimetry-UV-Vis/fluorescence spectroscopy platform, we characterized the binding energetics, kinetics and mechanistic pathways driving DOS-metal oxide interactions at temporal resolution on the order of 1-5 seconds. We studied a diverse suite of model organic compounds/substances – including monocarboxylates (e.g. acetate and benzoate), di-carboxylates (oxalate and succinate), amino acids, amino-based nanparticles and natural organic matter – interacting at the mineral-water interface of structurally- and/or chemically distinct metal oxides (including SiO2, boehmite, ferrihydrite, and γ-Al2O3). Our results indicated that DOS-metal oxide interactions are governed by multi-step reaction pathways, often switching between distinct, resolvable enthalpy- and entropy-driven non-electrostatic or electrostatic configurations. To quantify these interactions, we developed and implemented an analytical workflow that integrates peak deconvolution and Monte-Carlo based error propagation to determine site-specific thermodynamic and kinetic parameters for individual binding/debinding events. In addition to resolving apparent first-order rate constants of each event, we were able to quantify associated apparent equilibrium constants as well as free energy, enthalpy and entropy contribution to the activation and subsequent progression of the binding/debinding process across compounds, compound class and metal oxide surfaces. The kinetic-thermodynamic data produced in this study captured how the interplay between oxide surface reactivity and DOS molecular structure jointly drives binding-debinding dynamics. Notably, that at pH below PZC of the oxide surface, neutral species were heavily involved in monocarboxylate binding, while anionic species drove dicarboxylate binding. Also, that among amino acids 1) positional isomers show distinctive binding characteristics to each other while enantiomers show no significant differences in binding characteristics, 2) molecules that bind via outer-sphere complexation show a larger entropic shift between binding and debinding with no impact on oxide surface while 3) inner-sphere interactions increased anion exchange capacity of the oxide surface. The new insights and data from this work has great potential for improving predictive modeling of carbon dynamics and specifically organic-mineral interactions in environmental and industrial systems.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1992

The effects of growth temperature on the methyl sterol and phospholipid fatty acid composition of Methylococcus capsulatus (Bath)

Growth of Methylococcus capsulatus (Bath) at temperatures ranging from 30 to 50 C resulted in changes to the whole cell lipid constituents. As temperature was lowered, the overall proportion of hexadecenoic acid (C16:1) increased, and the relative proportions of the Delta9, Delta10, and Delta11 C16:1 double bond positional isomers changed. Methyl sterol content also increased as the growth temperature was lowered. The highest amounts of methyl sterol were found in 30 C cells and the lowest in 50 C cells (sterol-phospholipid ratios of 0.077 and 0.013, respectively). The data are consistent with a membrane modulating role for the sterol produced by this prokaryotic organism.

Jahnke, Linda L.↗
NASA NTRS1992

The effects of growth temperature on the methyl sterol and phospholipid fatty acid composition of Methylococcus capsulatus (Bath)

Growth of Methylococcus capsulatus (Bath) at temperatures ranging from 30 to 50 degrees C resulted in changes to the whole cell lipid constituents. As temperature was lowered, the overall proportion of hexadecenoic acid (C16:1) increased, and the relative proportions of the delta 9, delta 10 and delta 11 C16:1 double bond positional isomers changed. Methyl sterol content also increased as the growth temperature was lowered. The highest amounts of methyl sterol were found in 30 degrees C cells and the lowest in 50 degrees C cells (sterol-phospholipid ratios of 0.077 and 0.013, respectively). The data are consistent with a membrane modulating role for the sterol produced by this prokaryotic organism.

Jahnke, L. L.↗
NASA NTRS1994

Identification of Methanotrophic Biomarker Lipids in the Symbiont-Containing Gills of Seep Mussels

Mussels collected from hydrocarbon seeps in the Gulf of Mexico grow with methane as sole carbon and energy source due to a symbiotic association with methane-oxidizing bacteria. Transmission electron micrographs of mussel gills show cells with stacked intracytoplasmic membranes similar to type I methanotrophic bacteria. Methanotrophs are known to synthesize several types of cyclic triterpenes, hopanoids and methyl sterols, as well as unique monounsaturated fatty acid, double bond positional isomers that serve as biomarkers for this group. Lipid analysis of dissected mussels demonstrated the presence of these biomarkers predominantly in the gill tissue with much smaller amounts in mantle and remaining body tissues. Gill tissue contained 1150 micrograms/g dry wt. of hopanepolyol derivatives and diplopterol while the mantle tissue contained only 17 micrograms/g. The C16 monounsaturated fatty acids (16:1) characteristic of type I methanotrophic membranes dominated the gill tissue making up 53% of the total while only 5% 16:1 was present in the mantle tissue. The methyl sterol distribution was more dispersed. The predominant sterol in all tissues was cholesterol with lesser amounts of other desmethyl and 4-methyl sterols. The gill and mantle tissues contained 3461 micrograms (17% methyl) and 2750 micrograms (5% methyl) sterol per gm dry wt., respectively. Methyl sterol accounted for 44% of the sterol esters isolated from the gill, suggesting active demethylation of the methanotrophic sterols in this tissue. The use of lipid biomarkers could provide an effective means for identifying host-symbiont relationships.

Jahnke, L. L.↗
NASA NTRS1995

Identification And Survival Of Bacteriohopanepolyol In A Hot Spring Microbial Mat

The polar lipids of a hot spring microbial mat located in Yellowstone National Park were examined for the presence of bacteriohopanepolvols (BHP). BHP are a group of molecules consisting of a hopanoid (peotacyclic triterpene) linked via a n-alkyl polyhydroxylated chain to a variety of polar end groups. BHP have been isolated in varying amounts from phylogenetically diverse eubacterial groups including cyanobacteria, methanotrophs and the Rhodospirillaceae. The hopanoids are excellent biomarkers and have been detected in sedimentary rocks as old as 1.7 bya. In order to interpret the ancient organic record, it is important to understand the abundance, source and fate of such biomarker compounds in microbial mats. A 40 sq cm mat section was taken from a 52 to 55 C site in the effluent channel of Octopus Spring and was sampled vertically over approximately 16 mm. The first 5-6 mm was sectioned into a top green layer (310 mg dry weight) and several subjacent, deep orange layers (240 and 250 mg, respectively). The lower 10 mm of the mat was sectioned into two gelatinous orange layers containing a siliceous gritty material (260 and 440 mg) which increased with depth, and a bottom layer composed almost exclusively of siliceous sinter (4.1 g). The progressive decrease in total organic carbon from 45% in the top green layer to only 4% in the bottom layer reflects the observed increase in siliceous deposition. GC-MS analysis of the phospholipid and glycolipid fatty acids yielded predominantly saturated normal chain acids, n-15 to n-18, and iso-branched acids, i-15 to i-17. Small amounts of unsaturated fatty acids (16:1, two positional isomers of 18:1, and two cyclopropyl acids, C(sub 17) and C(sub 19)) were present mainly in the top layer. Esterified fatty acid which is a good index for intact cellular membrane, i.e. viable organisms, was highest in the top two layers (203 and 231 micro g/mg total lipid, respectively) and gradually decreased to 66 micro g/mg total lipid in the bottom layer. Small amounts of BHP were present in all six layers, however in this case, BHP was lowest in the top green and subjacent deep-orange layers (118 and 172 micro g/mg total lipid, respectively) and increased with depth reaching almost 400 micro g/mg in the bottom two layers. This data suggest that BHP are survivina the initial phase of mat degradation and may be preferentially enriched in any organic record of such thermal environments. The relatively low level of BHP in the top layer also suggests that cyanobacteria may not be the major source of BHP in this mat. Since Chloroflexus a major component of the deep-orange layer has been reported to lack BHP, this material may prove a valuable biomarker for some other mat inhabitant. Further isotopic characterization of this BHP should help resolve this finding.

Janke, Linda L.↗
NASA NTRS1995

Identification of Methanotrophic Lipid Biomarkers in Cold-Seep Mussel Gills: Chemical and Isotopic Analysis

A lipid analysis of the tissues of a cold-seep mytilid mussel collected from the Louisiana slope of the Gulf of Mexico was used in conjunction with a compound-specific isotope analysis to demonstrate the presence of methanotrophic symbionts in the mussel gill tissue and to demonstrate the host's dependence on bacterially synthesized metabolic intermediates. The gill tissue contained large amounts of group-specific methanotrophic biomarkers, bacteriohopanoids, 4-methylsterols, lipopolysaccharide-associated hydroxy fatty acids, and type I-specific 16:1 fatty acid isomers with bond positions at delta-8, delta-10, and delta-ll. Only small amounts of these compounds were detected in the mantle or other tissues of the host animal. A variety of cholesterol and 4-methylsterol isomers were identified as both free and steryl esters, and the sterol double bond positions suggested that the major bacterially derived gill sterol(11.0% 4(alpha)-methyl-cholesta-8(14), 24-dien-3(beta)-ol) was converted to host cholesterol (64.2% of the gill sterol was cholest-5-en-3(beta)-ol). The stable carbon isotope values for gill and mantle preparations were, respectively, -59.0 and -60.4 per thousand for total tissue, -60.6 and -62.4 per thousand for total lipids, -60.2 and -63.9 per thousand for phospholipid fatty acids, and -71.8 and -73.8 per thousand for sterols. These stable carbon isotope values revealed that the relative fractionation pattern was similar to the patterns obtained in pure culture experiments with methanotrophic bacteria further supporting the conversion of the bacterial methyl-sterol pool.

Jahnke, Linda L.↗
DOE OSTI2025

OzMALDI: A Gas-Phase, In-Source Ozonolysis Reaction for Efficient Double-Bond Assignment in Mass Spectrometry Imaging with Matrix-Assisted Laser Desorption/Ionization

Lipids make up an important class of biomolecules with diverse structures and varied chemical functions. This diversity is a major challenge in chemical analysis and limits our understanding of biological functions and regulation. A major way lipid isomers differ is by double-bond (db) position, and analyzing db-isomers is especially challenging for mass spectrometry imaging (MSI). Ozonolysis can be used to determine the dbposition and has been paired with MSI before. However, previous techniques require increased analysis time to allow for gas-phase reactions within an ion trap or ion mobility cell or additional sample preparation time to allow for offline ozonation. Here, we introduce a new ozonolysis method inside the matrix-assisted laser desorption-ionization (MALDI) source, termed OzMALDI, that simultaneously produces ozonides from all unsaturated lipids. This allows us to determine db-positions without adding additional reaction time while maintaining the high mass resolution provided by Orbitrap MS. This new technique is especially effective at determining multiple db-positions in lipids containing polyunsaturated fatty acids, which is a limitation of many previous techniques. OzMALDI-MSI was applied to the analysis of rat brain and genetically engineered Camelina and soybean seed samples, demonstrating the utility of this method and uncovering novel biological information.

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

Microcanonical Kinetics of Water-Mediated Proton Transfer in 4ABAH + ·(H 2 O) n = 4–6 Clusters (ABA = Aminobenzoic Acid): A Model System for Size-Dependent Relaxation to Ergodic Behavior

Here, we leverage the unique properties of the 4ABAH + · (H 2 O) n clusters (ABA = 4-aminobenzoic acid, n = 4−6) to quantitatively address how a finite, isolated system evolves into an ergodic condition starting from localized arrangements in configuration space. This system adopts two distinct structural isomers in which water molecules cluster around the cationic centers of its two protomers with widely separated positive charge centers. These isomers arise from excess proton attachment to either the acid (O) or amino (N) group on opposite sides of the benzene ring. Both forms are captured and kinetically trapped using cryogenic ion methods and then selectively vibrationally excited through their mutually exclusive IR bands involving NH and OH stretching fundamentals. Because the IR excitation lies below the water binding energy, the system can evolve to explore slow, rare events that lead to the interconversion between the two isomers. The rates of these intracluster reactions are determined by using a pump−probe scheme involving ∼5 ns IR pump and UV probe lasers. The rates occur on the microsecond time scale, leading to steady state populations of the isomers, thus revealing the cluster size-dependent fractionation between the two species at microcanonical equilibrium. The steady state distributions are correlated with the expected trend in the cluster size-dependent reaction energetics, which are in turn consistent with changes in the relative densities of states of the two species. These results thus provide an unusually clear example in which complex, protic-solvent-mediated chemical transformations are captured within a finite system at a precisely determined internal energy.

Rana, Abhijit [Yale Univ., New Haven, CT (United S↗
NASA NTRS1990

The Chemical Basis for the Origin of the Genetic Code and the Process of Protein Synthesis

A model for the origin of protein synthesis. The essential features of the model are that 5'-AMP and perhaps other monoribonucleotides can serve as catalysts for the selective synthesis of L-based peptides. A unique set of characteristics of 5'-AMP is responsible for the selective catalysts and these characteristics are described in detail. The model involves the formation of diesters as intermediates and selectivity for use of the L-isomer occurs principally at the step of forming the diester. However, in the formation of acetyl phenylalanine-AMP monoester there is a selectivity for esterification by the D-isomer. Data showing this selectivity is presented. This selectivity for D-isomer disappears after the first step. The identity was confirmed of all four of possible diesters of acetyl-D- and -L phenylaline with 5'-AMP by nuclear magnetic resonance (NMR). The data using flourescence and NMR show the Trp ring can associate with the adenine ring more strongly when the D-isomer is in the 2' position than it can when in the 3' position. These same data also suggest a molecular mechanisim for the faster esterificaton of 5'-AMP by acetyl-D-phenylaline. Some new data is also presented on the possible structure of the 2' isomer of acetyl-D-tryptophan-AMP monoester. The HPLC elution times of all four possible acetyl diphenylalanine esters of 5'-AMP were studied, these peptidyl esters will be products in the studies of peptide formation on the ribose of 5'-AMP. Other studies were on the rate of synthesis and the identity of the product when producing 3'Ac-Phe-2'tBOC-Phe-AMP diester. HPLC purification and identification of this product were accomplished.

Lacey, James C., Jr.↗
DOE OSTI2025

Efficient Self-Sensitized Photochemical CO 2 Reduction Using [Re(bpy 2+ )(CO) 3 (I)] 2+ and [Re(bpy 2+ )(CO) 3 (CH 3 CN)] 3+ Photocatalysts with Pendent Ammonium Cations

Rhenium(I) tricarbonyl complexes fac-[Re(bpy)(CO) 3 (L)]n + are the classical examples of self-sensitized photocatalysts capable of the dual roles of light absorption and catalysis. Here, in this work, a series of dicationic halido or tricationic solvento complexes fac-[Re(bpy 2+ )(CO) 3 X] n+ (PF 6 ) n (where X = Cl - or I - (n = 2), or CH 3 CN (n = 3) and bpy 2+ is bipyridine modified by two -CH 2 -(NMe3) + tetra-alkylammonium cations) have been investigated as self-sensitized and sensitized CO 2 reduction photocatalysts. Four structural isomers differing in the cation position have been tested in N,Nʹ-dimethylacetamide solvent (DMA) using 1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzimidazole (BIH) as the electron donor, and the position of the cationic pendants has a significant impact on the catalyst turnover number and quantum efficiency (ϕ). Up to 455 self-sensitized turnovers of CO and a high photon efficiency (ϕ CO ) of 22% have been achieved. Time-resolved infrared spectroscopy and theoretical calculations were used to characterize the catalytic cycle including the ligand exchange between one-electron reduced (OER) halido and solvento species as well as the binding of CO 2 to the putative two-electron reduced (TER) species. The CO 2 -reactive TER catalyst was formed by disproportionation or intramolecular electron transfer between two forms of the OER catalyst as indicated by the formation of the fully oxidized catalyst concurrent with CO 2 binding. When [Ru(bpy) 3 ] 2+ was used as a sensitizer, catalyst durability improved, and the selectivity toward formate increased as high as 3.3:1 over CO (total TON = 1370) due to acidification of the reaction, which promotes formation of the hydride intermediate, as BIH was consumed and deprotonated.

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

Selective carboxylation of alkenes with CO 2 to form unsaturated carboxylic acid on Sc-exchanged MFI zeolite

Utilization of CO 2 in chemical synthesis as C1 carbon feedstock to introduce a carboxylic group into alkene is valuable for producing unsaturated carboxylic acids. Selective carboxylation of alkenes at targeted positions can be used to regulate the production of such specific unsaturated carboxylic acids or functionalize hydrocarbon plastics that possess residual C=C double bonds. In this study, we investigated the carboxylation of 1-butene and 2-butene (as representative alkene) with CO 2 on Sc-exchanged MFI zeolites using density functional theory calculations. Here, we find that similar to ethylene, the carboxylation of butene is also rate-limited by the β–H transfer. We examined carboxylation at the C1 and C2 positions of 1-butene and cis and trans isomers for 2-butene. Based on activation barriers of the β–H transfer, our results demonstrate that Sc-MFI zeolite preferably carboxylates at the terminal position of butene. In the case of 2-butene, carboxylation of the trans isomer is more favorable than the cis isomer. Furthermore, We show that the energy of degenerate orbitals of C, O and H atoms (involved in the β–H transfer) in the metallalactone ring regulates the activation energy of the β–H transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗