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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 OSTI2020

Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy

Coordination-driven self-assembly has been extensively employed to construct a variety of discrete structures as a bottom-up strategy. However, mechanistic understanding regarding whether self-assembly is under kinetic or thermodynamic control is less explored. To date, such mechanistic investigation has been limited to distinct, assembled structures. It still remains a formidable challenge to study the kinetic and thermodynamic behavior of self-assembly systems with multiple assembled isomers due to the lack of characterization methods. Herein, we use a stepwise strategy which combined self-recognition and self-assembly processes to construct giant metallo-supramolecules with 8 positional isomers in solution. With the help of ultrahigh-vacuum, low-temperature scanning tunneling microscopy and scanning tunneling spectroscopy, we were able to unambiguously differentiate 14 isomers on the substrate which correspond to 8 isomers in solution. Through measurement of 162 structures, the experimental probability of each isomer was obtained and compared with the theoretical probability. Finally, such a comparison along with density functional theory (DFT) calculation suggested that although both kinetic and thermodynamic control existed in this self-assembly, the increased experimental probabilities of isomers compared to theoretical probabilities should be attributed to thermodynamic control.

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

Catalytic Transformation of Positional Nitrophenol Isomers on Highly Active Ag/Linde‐Type A4 Zeolite: A Comparative Analysis

Abstract The catalytic transformation of ortho‐( o‐ NP), meta‐( m‐ NP) and para‐nitrophenols ( p‐ NP) by Ag nanoparticles (Ag‐NPs) stabilised on zeolite A4 (ZA4) is presented for the first time. The catalysts are prepared by microwave‐assisted synthesis (Ag/ZA4‐MW) or ion exchange (Ag/ZA4‐IE). The results indicate that the nitrophenol reduction rate depends on the molecule structure and the presence of low‐coordinated metallic Ag‐NPs (∼2 nm and sub nanometric species). Meanwhile, the reactivity tendency depends on the synthesis methodology ( m‐ NP> p‐ NP> o‐ NP and o‐ NP> m‐ NP> p‐ NP for Ag/ZA4‐MW and Ag/ZA4‐IE, respectively). The turnover frequency (TOF) values estimated for nitrophenols reduction are superior for Ag/ZA4‐MW catalyst by several orders of magnitude compared with those obtained for Ag/ZA4‐IE catalyst. In addition, the catalyst exhibits remarkable catalytic stability for the reduction of p‐ NP even after the fifth consecutive catalytic run. The presently prepared catalysts are characterised by superior catalytic activity for the reduction of nitroaromatic compounds than similar Ag‐based materials reported in the literature.

Horta‐Fraijo, Patricia↗
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.↗
DOE OSTI2020

Cation, Anion, and Radical Isomers of C4H4N: Computational Characterization and Implications for Astrophysical and Planetary Environments

Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C 4 H 4 N may contribute to this signature. We have characterized seven isomers of C 4 H 4 N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH 2 CCHCNH + , a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C 4 H 4 N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.

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

Butterfly, Vinylidene-Like, Monobridged and Trans Structures of Si 2 H 2 + : Comparison to the Well-Characterized Neutral Si 2 H 2

This paper investigates four of the constitutional isomers of Si 2 H 2 + , namely the butterfly, vinylidene-like, monobridged, and trans structures. These isomer geometries were all studied using the CCSD(T) method with basis sets as large as cc-pV5Z. Higher level methods CCSDT and CCSDT(Q) were used for final energetics. It is found that the butterfly isomer has the lowest energy, followed by vinylidene-like and monobridged structures; the trans structure has the highest energy of the four. All structures were compared with their neutral counterparts. Partial charges are computed and it is found that all isomers share the positive charge between the silicon atoms. NBO analysis shows that the cation Si-Si bond order is reduced by 0.5 relative to the neutral versions of the same isomer in the case of the butterfly, vinylidene-like, and monobridged; and reduced by 0.6 for the trans isomer. Vibrational frequencies, infrared intensities, and dipole moments are predicted to encourage the spectroscopic identification of Si 2 H 2 + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗