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At least 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Side chain dynamics in semiconducting polymer MEH-PPV

We report that the characteristic nanoscale dynamics of the alkyl side groups in the light-emitting polymer poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] have been investigated using quasi-elastic neutron scattering (QENS). The measurements were taken below the polymer's glass transition (T ≤ T g ≃ 353 K), where the main backbone is in a rigid state and does not contribute to the broadening of the QENS signal. An analytical diffusion model consisting of a static term and two dynamical components, characterizing the flexible side groups, provide an excellent fit to the experimental data. The two observed dynamical processes are all localized in character, with no meaningful dependence on temperature. The faster process, with characteristic timescale of ~18 ps at room temperature (RT), can be linked to the average mobility of the terminal protons of the alkyl chain, while the slower process, with characteristic timescale of ~170 ps at RT, to those protons at the other end of the alkyl chain, closest to the backbone. Lastlyl, while the fraction of mobile protons contributing to the QENS signal increases with increasing temperature, the characteristic timescale and confining volume within which the protons are able to move locally depend chiefly on the polymer conformational state.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Stereochemistry of polypeptoid chain configurations

Abstract Like polypeptides, peptoids, or N ‐substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N ‐substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. One hundred thirty‐two monomer dihedral angle pairs were compared to the calculated energy landscape for the peptoid Ramachandran plot, and were found to fall within the expected minima. Interestingly, only two regions of the backbone dihedral angles ϕ and ψ were found to be populated that are mirror images of each other. Furthermore, these two conformers are present in both cis and trans forms. Thus, there are four primary conformers that are sufficient to describe almost all known backbone conformations for peptoid oligomers, despite conformational constraints imposed by a variety of side chains, macrocyclization, or crystal packing forces. Because these conformers are predominant in peptoid structure, and are distinct from those found in protein secondary structures, we propose a simple naming system to aid in the description and classification of peptoid structure.

Spencer, Ryan K.↗
DOE OSTI2020

A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids

Microbial cell factories have been extensively engineered to produce free fatty acids (FFAs), key components of crucial nutrients, soaps, industrial chemicals, and fuels. Yet, our ability to control the specificity of microbially synthesized FFAs is still limited for medium-chain fatty acids (MCFAs), which is mainly due to lack of high-throughput approaches for FFA analysis. Here we report a mass spectrometry (MS)-based method for rapid profiling of MCFAs in Saccharomyces cerevisiae by using membrane lipids as a proxy. Specially, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) MS was used to detect shorter acyl chain phosphatidylcholines from membrane lipids and the m/z peak ratio at 730 and 758 was used as an index for improved MCFA production. This yeast colony-based method can be performed at a rate of ~2 second per sample, which is much faster than the gold standard gas chromatography (GC)-MS (typically > 30 min per sample). To demonstrate the power of this method, we performed site-saturation mutagenesis of the yeast fatty acid synthase and identified 9 mutants that resulted in improved MCFA production relative to the wild-type strain. This colony-based MALDI-ToF MS screening method offers an alternative way for engineering microbial fatty acid compositions in a high-throughput manner.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular Simulations of the Chain Length Dependent Adsorption of C7‐C14 n ‐Alkanes in ZIF‐8

Recent experiments show that the diffusivities of C8 and C10 n-alkanes in ZIF-8 are higher than those of C7 and C9, respectively. We investigated this unusual ‘odd-even' effect by simulating the adsorption of C7-C14 n-alkanes in ZIF-8 using hybrid Monte Carlo molecular simulations. The resultant adsorption isotherms, guest-host energies, isosteric heats, and chain length distributions are analyzed for trends among the n-alkanes. ZIF-8 cages filled with n-alkanes are characterized using a combination of image processing and data science to quantify the differences in packing that occur with chain length. In conclusion, results indicate that packing changes drastically from C7 to C8 and from C9 to C10, which is consistent with the diffusion trends previously reported in experiments.

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

Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine‐Residue Low Complexity Peptide, as Probed by 2 H Solid‐State NMR

Abstract Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid‐state NMR to assess rotameric inter‐conversions and other dynamic modes of the methionine in the context of a nine‐residue random‐coil peptide (RC9) with the low‐complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine‐containing systems, characterized previously. Namely, the M35 of hydrated amyloid‐β 1–40 in the three‐fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)‐methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.

Vugmeyster, Liliya↗
DOE OSTI2023

Optimizing Renewable Ammonia Production for a Sustainable Fertilizer Supply Chain Transition

Local renewable ammonia production using electrolytic hydrogen is an emerging approach to alleviate emissions attributed to synthetic nitrogen fertilizer production while also insulating against fluctuations in fertilizer prices and mitigating transportation costs and emissions. However, replacing ammonia currently produced using fossil fuels will not be immediate. To this end, we develop a supply chain transition model, which first optimizes the design and hourly operation of new renewable ammonia facilities to minimize production costs and then optimizes the annual installation timing, production scale, and location of these new renewable facilities along with ammonia transportation to meet county resolution demands. The objective is to augment and eventually replace conventional ammonia market imports in an economically competitive manner. We performed a case study for Minnesota's ammonia supply chain and found that a full transition to in-state renewable production by 2032 is optimal. This is incentivized by the U.S. federal government's clean hydrogen production credits. This transition results in 99 % reduction in carbon intensity along with stable supply costs below $475 per metric tonne. New renewable production facilities are an order of magnitude smaller than existing conventional plants. They use both wind and solar resources and operate dynamically to minimize expensive battery and hydrogen storage capacities.

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

Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand‐Binding Cavity

Abstract Stabilization of amyloidogenic immunoglobulin light chains (LCs) by binding of small molecule “kinetic stabilizers” is under development as a novel treatment for light chain amyloidosis. From a high‐throughput screen, we previously identified 16 full‐length (FL) LC stabilizers from five distinct chemotypes. We then obtained structural biological information on two classes of hits, coumarins and hydantoins, revealing that both chemotypes bind to a pocket at the V L −V L interface of the FL LC dimer. Here, we report crystal structures of three screening hits from two other chemotypes, diaryl hydrazones and sulfones, in complex with an amyloidogenic FL LC. While two of these hits bind to the previously identified pocket, one diaryl hydrazone binds to a different pocket bisected by the C 2 symmetry axis of the dimer. These data further expand on the FL LC stabilizer‐binding surface that could be used in design of more potent FL LC aggregation inhibitors.

Chemistry↗
DOE OSTI2019

Investigating Chain Dynamics in Highly Crosslinked Polymers using Solid–State 1 H NMR Spectroscopy

Solid state 1 H NMR line–shape analysis and (double quantum) DQ 1 H NMR experiments have been used to investigate the segmental and polymer chain dynamics as a function of temperature for a series of thermosetting epoxy resins produced using different diamine curing agents. In these thermosets, chemical crosslinks introduce topological constraints leading to residual stresses during curing. Materials containing a unique ferrocene–based diamine (FcDA) curing agent were evaluated to address the role of the ferrocene fluxional process on the atomic–level polymer dynamics. Here, at temperatures above the glass transition temperature ( T g), the DQ 1 H NMR experiments provided a measure of the relative effective crosslink and entanglement densities for these materials and revealed significant polymer chain dynamic heterogeneity in the FcDA–cured thermosets.

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

RrA, an enzyme from Rhodospirillum rubrum , is a prototype of a new family of short‐chain L‐asparaginases

Abstract L‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum , reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

Abstract Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self‐avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N‐terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10–58°C, with a Flory exponent, ν , >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti‐freeze protein (red‐sfAFP) is unaffected by temperature and ionic strength and persists as a near‐SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red‐sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red‐sfAFP had minimal effect on ν . Water remained a good solvent even with 21 consecutive glycine residues ( ν > 0.5), and red‐sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine‐rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Electrically Driven Dynamics of Few‐Chain NbSe 3

An in situ transmission electron microscopy study of few‐chain NbSe 3 encapsulated within the hollow core of carbon nanotubes is presented, where the tube/chain system is subjected to applied axial electrical currents. Electromigration and thermal excitation forces result in collective and individual chain dynamics, with concomitant radial deformations of the encapsulating tubes.

Pham, Thang↗
DOE OSTI2026

Side-Chain Nanophase Separation Broadens the Double-Gyroid Stability Window in PS–PODMA Diblock Copolymers

Expanding access to bicontinuous network phases in block copolymers remains an important challenge because the double gyroid (DG) phase is usually stable only within a narrow composition window in conventional diblock copolymers. Here, we show that poly(styrene-block-octadecyl methacrylate) (PS-b-PODMA) exhibits an unusually broad DG window. Small-angle X-ray scattering measurements across a wide composition range reveal lamellar and hexagonally packed cylindrical phases at higher polystyrene fractions. In contrast, the DG phase appears over 0.22 ≤ fPS ≤ 0.35, with DG/BCC and DG/HEX coexistence near fPS = 0.18 and 0.40, respectively. This broad DG window is much wider than those reported for neat diblock copolymers and is not readily explained by conformational asymmetry alone. Wide-angle X-ray scattering detects a characteristic signature of nanophase separation within the PODMA-rich domains, indicating that side-chain ordering introduces an additional internal length scale. These results suggest that hierarchical side-chain nanophase separation modifies packing frustration and curvature selection, thereby broadening DG stability and providing a new molecular design strategy for stabilizing complex network morphologies.

Seko, Tamio↗
DOE OSTI2015

On the central charge extension of the $\mathcal{N}$ =4 SYM spin chain

In this paper it is argued that the central charge extension of the Coulomb branch of $\mathcal{N}$ = 4 SYM theory appears as a limit of Beisert’s central charge extension of the planar $\mathcal{N}$ = 4 spin chain in the presence of boundaries. These boundaries are interpreted as D-branes that source the central charge and are realized as giant gravitons and dual giant gravitons in the AdS dual. The BPS states that correspond to short representations of the centrally extended algebra on the spin chain can stop from existing when they cross walls of stability that depend on the position of the branes. These walls can be understood easily at weak coupling in the SU(2) sector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins

Abstract Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

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

Computational Errors in the Calculation of Long Radioactive Decay Chains

For safety security of objects utilizing atomic energy, the effect of numerical errors on the calculation of the activity and integrals of the activity in time when using Bateman’s formula and Siewers’ algorithm to calculate radioactive decay chains is investigated. The smallest errors obtain when using Siewers’ algorithm and Bateman’s formula together with long arithmetic. It is shown that the standard calculations of radioactive decay chains according to Bateman’s formula with double precision lead to significant errors. However, these errors have almost no effect on the dose characteristics of mixtures of radionuclides. The analysis is based on data contained in ICRP Publication No. 107.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

X-Ray Photoelectron Spectroscopy of Imidazolium Zwitterionic Salts: Comparison to Acetate Analogs and the Impact of the Alkyl Chain Length on the Charge Distribution

We investigate two imidazolium zwitterionic salts, 1,3-dimethylimidazolium-2-carboxylate and 1-butyl-3-methylimidazolium-2-carboxylate, together with 1-butyl-3-methylimidazolium acetate using X-ray photoelectron spectroscopy. The electronic environment of each element for the two zwitterionic salts is analyzed. Due to the electron-withdrawing effect of the imidazoliumcation, the binding energies of Ccarboxyl 1s and O 1s for zwitterionic salts are higher than those of 1-butyl-3-methylimidazolium acetate. The impact of the alkyl chain length on the charge distribution is also illustrated. It suggests that the electron-withdrawing effect of the imidazoliumcation decreases along with the increasing of the alkyl chain length.

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

Spectral-Luminescent Properties of Alkoxysilane–Metallophthalocyanine Conjugates Covalently Bonded to the Polymeric Chains of Silicate Gel Materials

Conjugates of metal hydroxyl phthalocyanines (М(ОН){sub n}Рс; М = Si, Ge, Al, Ga) with 3-aminopropyltriethoxysilane (APTEOS) are synthesized. By means of the sol-gel method, polymeric silicate gel materials doped with the (APTEOS){sub n}–М(ОН){sub n}Рс conjugates are prepared: the latter form structural links in the composition of the copolymer with the siloxane fragments of the polymeric chains (in the case of n = 2) or are ″grafted″ to such chains in the form of side substituents (n = 1). It is shown by spectral-luminescent and kinetic spectroscopy methods that the (APTEOS){sub n}–М(ОН){sub n}Рс conjugates, on the introduction into a silicate gel material, retain their molecular structure and the photophysical characteristics of MPc in the monomeric form. The obtained macromolecular substances are promising as monomeric dopants in new functional materials for optics and quantum electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Shocks, Rarefaction Waves, and Current Fluctuations for Anharmonic Chains

The nonequilibrium dynamics of anharmonic chains is studied by imposing an initial domain-wall state, in which the two half lattices are prepared in equilibrium with distinct parameters. Here, we analyse the Riemann problem for the corresponding Euler equations and, in specific cases, compare with molecular dynamics. Additionally, the fluctuations of time-integrated currents are investigated. In analogy with the KPZ equation, their typical fluctuations should be of size t 1/3 and have a Tracy–Widom GUE distributed amplitude. The proper extension to anharmonic chains is explained and tested through molecular dynamics. Our results are calibrated against the stochastic LeRoux lattice gas.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗