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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Mobility Selective Ion Soft-Landing and Characterization Enabled Using Structures for Lossless Ion Manipulation

In this study, while conventional ion-soft landing uses the mass-to-charge (m/z) ratio to achieve molecular selection for deposition, here we demonstrate the use of Structures for Lossless Ion Manipulation (SLIM) for mobility-based ion selection and deposition. The dynamic rerouting capabilities of SLIM were leveraged to enable the rerouting of a selected range of mobilities to a different SLIM path (rather than MS) that terminated at a deposition surface. A selected mobility range from a phosphazene ion mixture was rerouted and deposited with a current pulse (~150 pA) resembling its mobility peak. In addition, from a mixture of tetra-alkyl ammonium (TAA) ions containing chain lengths of C5–C8, selected chains (C6, C7) were collected on a surface, reconstituted into solution-phase, and subsequently analyzed with a SLIM-qToF to obtain an IMS/MS spectrum, confirming the identity of the selected species. Further, this method was used to characterize triply charged tungsten-polyoxometalate anions, PW 12 O 40 3– (WPOM). The arrival time distribution of the IMS/MS showed multiple peaks associated with the triply charged anion (PW 12 O 40 3– ), of which a selected ATD was deposited and imaged using TEM. Additionally, the identity of the deposited WPOM was ascertained using energy-dispersive (EDS) spectroscopy. Further, we present theory and computations that reveal ion landing energies, the ability to modulate the energies, and deposition spot sizes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Synthesis and Crystallization Behavior of Surfactants with Hexamolybdate as the Polar Headgroup

For this paper, alkyl chains with different lengths were covalently grafted onto the surface of hexamolybdate through the postfunctionalization protocol of polyoxometalates. The obtained compounds represent typical structures of the so-called giant surfactants. Unexpectedly, those surfactants with hexamolybdates as polar headgroups are able to crystallize, while single-crystal X-ray diffraction reveals that the crystallization behavior of the surfactants is highly dependent on the length of the alkyl chains. For surfactants with comparatively short alkyl chains (C6 and C10), the alkyl chains prefer to interact with tetrabutylammonium, the countercation of hexamolybdate. However, the alkyl chains tend to pack with each other to form a domain of alkyl chains in the surfactant with a longer alkyl chain (C18). Finally, the possible mechanism is that a long alkyl chain cannot be fully compatible with the short chain (C4) of tetrabutylammonium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Defining the Specificity of Carbohydrate–Protein Interactions by Quantifying Functional Group Contributions

Protein–carbohydrate interactions are significant in a wide range of biological processes, disruption of which has been implicated in many different diseases. The capability of glycan-binding proteins (GBPs) to specifically bind to the corresponding glycans allows GBPs to be utilized in glycan biomarker detection or conversely to serve as targets for therapeutic intervention. However, understanding the structural origins of GBP specificity has proven to be challenging due to their typically low binding affinities (mM) and their potential to display broad or complex specificities. Here we perform molecular dynamics (MD) simulations and post-MD energy analyses with the Poisson–Boltzmann and generalized Born solvent models (MM-PB/GBSA) of the Erythrina cristagalli lectin (ECL) with its known ligands, and with new cocrystal structures reported herein. While each MM-PB/GBSA parametrization resulted in different estimates of the desolvation free energy, general trends emerged that permit us to define GBP binding preferences in terms of ligand substructure specificity. Additionally, we have further decomposed the theoretical interaction energies into contributions made between chemically relevant functional groups. Based on these contributions, the functional groups in each ligand can be assembled into a pharmacophore comprised of groups that are either critical for binding, or enhance binding, or are noninteracting. It is revealed that the pharmacophore for ECL consists of the galactopyranose (Gal) ring atoms along with C6 and the O3 and O4 hydroxyl groups. This approach provides a convenient method for identifying and quantifying the glycan pharmacophore and provides a novel method for interpreting glycan specificity that is independent of residue-level glycan nomenclature. As a result, a pharmacophore approach to defining specificity is readily transferable to molecular design software and, therefore, may be particularly useful in designing therapeutics (glycomimetics) that target GBPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Flexible MOFs as Pressure-Tunable Filters for Hydrocarbon Separation

Metal–organic frameworks (MOFs) hold significant promise for separating gas mixtures, especially hydrocarbons. While the main focus in the field is the development of new adsorbents for specific separations of binary mixtures, a preferable situation would be using a single framework for separating various species. This has been achieved in some flexible MOFs, where ternary mixtures can be separated at different temperatures. Here, we propose a simple yet fascinating way of utilizing the flexibility of MOFs to create tunable filters as a function of external pressure. We thus replace the more costly temperature-driven tunability with a cost-efficient external-pressure tunability. As a proof-of-concept, we select the CaMOF flexible framework for C6 hydrocarbon separation, however, our results are applicable to other flexible framework and gas molecules. Furthermore, our findings provide mechanistic insight and guidelines to engineer separation filters by designing flexible pores with critical sizes that can be effectively manipulated by external pressure.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Impact of Backbone Rigidity on the Thermomechanical Properties of Semiconducting Polymers with Conjugation Break Spacers

There remains a lack of fundamental understanding in theroleofbackbonerigidityonthe thermomechanical properties of conjugated polymers. Here, we provide the first holistic approach to understand the fundamental influence of backbone rigidity on an n-type naphthalene diimide-based conjugated polymer, denoted by PNDI-Cx, through insertion of a flexible conjugation break spacer (CBS). CBS lengths are varied from fully conjugated with zero alkyl spacer (PNDI-C0) to a seven- carbon alkyl spacer (PNDI-C 7 ), with the CBS engineered into each repeat unit for systematic evaluation. Solution small-angle neutron scattering and oscillatory shear rheometry were employed to provide the first quantitative evidence of CBS influence over conjugated polymer chain rigidity and entanglement molecular weight (M e ), demonstrating a reduction in the Kuhn length from 521 to 36 Å for fully conjugated PNDI-C0 and PNDI-C6, respectively, as well as a nearly consistent Me of ~15 kDa upon the addition of CBS. Thermomechanical properties, such as elastic modulus and glass-transition temperature, were shown to decrease with an increasing length of CBS. An extraordinary ductility, upwards of 400% tensile strain before fracture, was observed for high-molecular-weight PNDI-C4, which we attribute to a high number of entanglements and disruption of crystallization. Furthermore, the deformation mechanism for PNDI-Cx was studied under strain through X-ray diffraction, polarized UV-vis spectroscopy, and atomic force microscopy. Overall, this work sheds light on the important role of backbone rigidity in designing flexible and stretchable conjugated polymers.

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

Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids

Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources to a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis, in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e., binding selectivity). We demonstrate this approach by identifying medium-chain (C8–C12) acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, which are products of thioesterase-catalyzed hydrolysis, are limited in natural abundance, compared to long-chain fatty acids; the limited supply leads to high costs of C6–C10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding of the highly active ‘TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C12 or C8 specificity, while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified 3 variants with enhanced production of dodecanoic acid (C12) and 27 variants with enhanced production of octanoic acid (C8). The top variants reached up to 49% C12 and 50% C8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of ‘TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of ‘TesA variants suggest that hydrophobic forces govern ‘TesA substrate specificity. Finally, we expect the design rules that we uncovered and the thioesterase variants that we identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain-length oleochemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

The influence of size, shape, and surface coating on the stability of aqueous nanoparticle suspensions

In response to the rapid development and emerging commercialization of nanoparticles, fundamental studies concerning the fate of nanoparticles in the environment are needed. Precise control over the nanoparticle size, shape, and surface coating of cadmium selenide particles modified with thiolate ligands has been used to analyze the effects of nanoparticle design on their stability in aqueous environments. Nanoparticle stability was quantified using the concept of critical coagulation concentration (CCC) in solutions of sodium chloride. These investigations characterized the instability of the ligand coatings, which varied directly with chain length of the capping ligands. The stability of the ligand coatings were characterized as a function of time, pH, and ionic strength. Ligand dissociation has been shown to be a primary mechanism for nanoparticle aggregation when short-chain (C2-C6) ligands are used in the ligand shell. Stable nanoparticle suspensions prepared with long chain ligands (C11) were used to characterize nanoparticle stability as a function of size and shape. A linear relationship between particle surface area and the CCC was discovered and was found to be independent of nanoparticle shape. Quantitative analysis of nanoparticle size, shape, and surface coating demonstrated the importance of ligand stability and particle surface area for the prediction of nanoparticle stability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Titanium-Beta Zeolites Catalyze the Stereospecific Isomerization of D-Glucose to L-Sorbose via Intramolecular C5-C1 Hydride Shift

Pure-silica zeolite beta containing Lewis acidic framework Ti 4+ centers (Ti-Beta) is shown to catalyze the isomerization of D-glucose to L-sorbose via an intramolecular C5–C1 hydride shift. Glucose–sorbose isomerization occurs in parallel to glucose–fructose isomerization on Ti-Beta in both water and methanol solvents, with fructose formed as the predominant product in water and sorbose as the predominant product in methanol (at 373 K) at initial times and over the course of >10 turnovers. Isotopic tracer studies demonstrate that 13 C and D labels placed respectively at the C1 and C2 positions of glucose are retained respectively at the C6 and C5 positions of sorbose, consistent with its formation via an intramolecular C5–C1 hydride shift isomerization mechanism. This direct Lewis acid-mediated pathway for glucose–sorbose isomerization appears to be unprecedented among heterogeneous or biological catalysts and sharply contrasts indirect base-mediated glucose–sorbose isomerization via 3,4-enediol intermediates or via retro-aldol fragmentation and recombination of sugar fragments. Measured first-order glucose–sorbose isomerization rate constants (per total Ti; 373 K) for Ti-Beta in methanol are similar for glucose and glucose deuterated at the C2 position (within a factor of ~1.1), but are a factor of ~2.3 lower for glucose deuterated at each carbon position, leading to H/D kinetic isotope effects expected for kinetically relevant intramolecular C5–C1 hydride shift steps. Optical rotation measurements show that isomerization of D-(+)-glucose (92% enantiomeric purity) with Ti-Beta in water (373 K) led to the formation of L-(-)-sorbose (73% enantiomeric purity) and D-(-)-fructose (87% enantiomeric purity) as the predominant stereoisomers, indicating that stereochemistry is preserved at carbon centers not directly involved in intramolecular C5–C1 or C2–C1 hydride shift steps, respectively. This new Lewis acid-mediated rearrangement of glucose to sorbose does not appear to have a metalloenzyme analog.

bio-inspired, hydrogen and fuel cells↗
DOE OSTI2012

Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad

Meta-cleavage product (MCP) hydrolases are members of the {alpha}/{beta}-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 {angstrom} resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of {sup 18}O into the benzoate produced during hydrolysis in H{sub 2}{sup 18}O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES{sup red}, previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.

Ruzzini, Antonio C.↗
DOE OSTI2023

XFEL Microcrystallography of Self-Assembling Silver n -Alkanethiolates

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd–even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd–even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd–even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. Finally, we conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Discovery and Early Clinical Evaluation of BMS-605339, a Potent and Orally Efficacious Tripeptidic Acylsulfonamide NS3 Protease Inhibitor for the Treatment of Hepatitis C Virus Infection

The discovery of BMS-605339 (35), a tripeptidic inhibitor of the NS3/4A enzyme, is described. This compound incorporates a cyclopropylacylsulfonamide moiety that was designed to improve the potency of carboxylic acid prototypes through the introduction of favorable nonbonding interactions within the S1' site of the protease. The identification of 35 was enabled through the optimization and balance of critical properties including potency and pharmacokinetics (PK). This was achieved through modulation of the P2* subsite of the inhibitor which identified the isoquinoline ring system as a key template for improving PK properties with further optimization achieved through functionalization. A methoxy moiety at the C6 position of this isoquinoline ring system proved to be optimal with respect to potency and PK, thus providing the clinical compound 35 which demonstrated antiviral activity in HCV-infected patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Effects of La2O3 on the Mixed Higher Alcohols Synthesis from Syngas over Co Catalysts: A Combined Theoretical and Experimental Study

The promoting role of lanthanum oxide (La{sub 2}O{sub 3}) in the catalytic synthesis of mixed higher (C{sub 2}-C{sub 6}) alcohols from syngas on Co-based catalysts was investigated using a combination of in situ and ex situ X-ray diffraction (XRD), photoelectron spectroscopy (XPS), catalyst reactivity performance studies, and ab initio molecular dynamics (AIMD) simulations. XRD measurements show that doping with La (0.5 wt %) onto activated carbon (AC) supported Co catalyst enhances the Co{sub 2}C phase formation, whereas the Co{sub 2}C phase formation is largely suppressed on alumina supported Co catalyst. A strong correlation of the selectivity toward alcohols with the ratio of Co{sub 2}C/Co particles present in the catalysts was observed. AIMD simulations suggest that on AC supports La exists as an oxide phase in the form of small clusters in the vicinity of Co particles. It was found that Co{sub 2}C formation is energetically favorable, especially for smaller Co particles because of the formation of surface carbide. Theoretical mechanistic studies indicate that oxygenated hydrocarbons can be formed on these catalysts by multiple routes involving the formation of CH{sub x}O and CH{sub x}CO species at the interface between the La{sub 2}O{sub 3} phase and Co/Co{sub 2}C. A detailed comparison with previous findings in the literature as well as discussion of the implications of these results upon the improvement of the selectivity of these catalysts toward higher alcohols is presented.

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

Structure and specificity of a permissive bacterial C-prenyltransferase

This study highlights the biochemical and structural characterization of the L-tryptophan C6 C-prenyltransferase (C-PT) PriB from Streptomyces sp. RM-5-8. In this work, PriB was found to be uniquely permissive to a diverse array of prenyl donors and acceptors including daptomycin. Two additional PTs also produced novel prenylated daptomycins with improved antibacterial activities over the parent drug.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria

Abstract Carbon-negative synthesis of biochemical products has the potential to mitigate global CO 2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL −1 ), as well as hexanoic acid (3.06 ± 0.03 gL −1 ) and 1-hexanol (1.0 ± 0.1 gL −1 ) at the best performance reported to date in this bacterium. We also generate Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL −1 in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Extending carbon chemistry at high-pressure by synthesis of CaC 2 and Ca 3 C 7 with deprotonated polyacene- and para-poly(indenoindene)-like nanoribbons

Metal carbides are known to contain small carbon units similar to those found in the molecules of methane, acetylene, and allene. However, for numerous binary systems ab initio calculations predict the formation of unusual metal carbides with exotic polycarbon units, [C 6 ] rings, and graphitic carbon sheets at high pressure (HP). Here we report the synthesis and structural characterization of a HP-CaC 2 polymorph and a Ca 3 C7 compound featuring deprotonated polyacene-like and para-poly(indenoindene)-like nanoribbons, respectively. We also demonstrate that carbides with infinite chains of fused [C6] rings can exist even at conditions of deep planetary interiors (~140 GPa and ~3300 K). Hydrolysis of high-pressure carbides may provide a possible abiotic route to polycyclic aromatic hydrocarbons in Universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Mechanistic Investigation of Solvent Extraction Based on Anion-Functionalized Ionic Liquids for Selective Separation of Rare-Earth Ions

In this study, solvation has been found to be a dominant mechanism in a comprehensive ionic liquid based extraction system for rare earth elements (REEs). Trioctylmethylammonium di(2-ethylhexyl)phosphate ([TOMA][DEHP]), an ionic-liquid extractant, was used in 1-alkyl-3-methylimidizolium bis[(trifluoromethyl)sulfonyl]imide ([Cnmim][NTf2], n = 4, 6, 8, 10) and 1-alkyl-3-methylimidizolium bis(perfluoroethanesulfonyl)imide ([Cnmim][BETI], n = 4, 6, 8, 10) for the separation of REEs. Surprisingly, a very similar extraction behavior was observed even as the carbon chain length on the ionic-liquid (IL) cation increased from butyl (C4) to hexyl (C6), to octyl (C8), to decyl (C10). This behavior is in sharp contrast to that exhibited by the conventional neutral extractants, whose extraction efficiencies are strongly dependent on the hydrophobicity of IL cations. Furthermore, the addition of IL cations ([Cnmim]+) or IL anions ([NTf2]- or [BETI]-) to the aqueous phase had little effect on the extraction behavior of the above extraction system, ruling out the strong involvement of the ion-exchange mechanism associated with traditional IL-based extraction systems. Results showed that the extractabilities and selectivities of REEs using [TOMA][DEHP] in [C10mim][NTf2]/[BETI] are several orders of magnitude better than those achieved using conventional organic solvent, diisopropylbenzene (DIPB). This study highlights the potential of developing a comprehensive IL-based extraction strategy for REEs separations.

Sun, Xiaoqi↗
DOE OSTI2016

Adsorption in zeolites using mechanically embedded ONIOM clusters

Here, we have explored mechanically embedded three-layer QM/QM/MM ONIOM models for computational studies of binding in Al-substituted zeolites. In all the models considered, the high-level-theory layer consists of the adsorbate molecule and of the framework atoms within the first two coordination spheres of the Al atom and is treated at the M06-2X/6-311G(2df,p) level. For simplicity, flexibility and routine applicability, the outer, low-level-theory layer is treated with the UFF. We have modelled the intermediate-level layer quantum mechanically and investigated the performance of HF theory and of three DFT functionals, B3LYP, M06-2X and ωB97x-D, for different layer sizes and various basis sets, with and without BSSE corrections. We have studied the binding of sixteen probe molecules in H-MFI and compared the computed adsorption enthalpies with published experimental data. We have demonstrated that HF and B3LYP are inadequate for the description of the interactions between the probe molecules and the framework surrounding the metal site of the zeolite on account of their inability to capture dispersion forces. Both M06-2X and ωB97x-D on average converge within ca. 10% of the experimental values. We have further demonstrated transferability of the approach by computing the binding enthalpies of n-alkanes (C1–C8) in H-MFI, H-BEA and H-FAU, with very satisfactory agreement with experiment. The computed entropies of adsorption of n-alkanes in H-MFI are also found to be in good agreement with experimental data. Finally, we compare with published adsorption energies calculated by periodic-DFT for n-C3 to n-C6 alkanes, water and methanol in H-ZSM-5 and find very good agreement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗