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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.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Compositional analysis of organosolv poplar lignin by using high-performance liquid chromatography/high-resolution multi-stage tandem mass spectrometry

Organosolv treatment is an efficient and environmentally friendly process to degrade lignin into small compounds. The capability of characterizing the individual compounds in the complex mixtures formed upon organosolv treatment is essential for the optimization of the further lignin conversion processes and for the rational genetic engineering of plants used to produce lignin in order to improve lignin properties. In this study, an organosolv poplar lignin sample was initially analyzed by high-resolution mass spectrometry coupled with negative-ion mode electrospray ionization ((-)ESI HRMS). Lignin monomers and dimers were found to constitute the majority of the compounds in the organosolv lignin sample. Larger lignin oligomers, such as trimers and tetramers, and some not lignin-related compounds, were also detected. A high-performance liquid chromatograph/linear quadrupole ion trap/orbitrap mass spectrometer capable of multi-stage high-resolution tandem mass spectrometry experiments (HRMS n ), equipped with an (-)ESI source (HPLC/(-)ESI HRMS n ), was employed to separate the unknown compounds in the organosolv mixture and to obtain structural information for the deprotonated compounds via collision-activated dissociation (CAD) HRMS n experiments. To improve the understanding of the CAD behavior of deprotonated lignin-related compounds, 16 deprotonated model compounds with different functionalities and linkage types were examined. This approach enabled the assignment of likely structures for several lignin monomers, dimers, trimers, and tetramers, and some not lignin-related compounds, most likely fatty acids. Based on the proposed structures, compounds in the organosolv lignin sample contain β-O-4, 5–5, β-5, and possibly also 4-O-5 linkages. Most compounds contain G- and S-monomeric units although a small amount of H-units were also detected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Potential energy profile for the Cl + (H 2 O) 3 → HCl + (H 2 O) 2 OH reaction. A CCSD(T) study

Four different reaction pathways are initially located for the reaction of Cl atom plus water trimer Cl + (H 2 O) 3 → HCl + (H 2 O) 2 OH using a standard DFT method. As found for the analogous fluorine reaction, the geometrical and energetic results for the four chlorine pathways are closely related. However, the energetics for the Cl reaction are very different from those for fluorine. Here in this paper, we investigate the lowest-energy chlorine pathway using the “gold standard” CCSD(T) method in conjunction with correlation-consistent basis sets up to cc-pVQZ. Structurally, the stationary points for the water trimer reaction Cl + (H 2 O) 3 may be compared to those for the water monomer reaction Cl + H 2 O and water dimer reaction Cl + (H 2 O) 2 . Based on the CCSD(T) energies, the title reaction is endothermic by 19.3 kcal mol -1 , with a classical barrier height of 16.7 kcal mol -1 between the reactants and the exit complex. There is no barrier for the reverse reaction. The Cl … (H 2 O) 3 entrance complex lies 5.3 kcal mol -1 below the separated reactants. The HCl … (H 2 O) 2 OH exit complex is bound by 8.6 kcal mol -1 relative to the separated products. The Cl + (H 2 O) 3 reaction is somewhat similar to the analogous Cl + (H 2 O) 2 reaction, but qualitatively different from the Cl + H 2 O reaction. It is reasonable to expect that the reactions between the chlorine atom and larger water clusters may be similar to the Cl + (H 2 O) 3 reaction. The potential energy profile for the Cl + (H 2 O) 3 reaction is radically different from that for the valence isoelectronic F + (H 2 O) 3 system, which may be related to the different bond energies between HCl and HF.

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

In situ studies of reversible solid–gas reactions of ethylene responsive silver pyrazolates

Solid–gas reactions and in situ powder X-ray diffraction investigations of trinuclear silver complexes {[3,4,5-(CF 3 ) 3 Pz]Ag} 3 and {[4-Br-3,5-(CF 3 ) 2 Pz]Ag} 3 supported by highly fluorinated pyrazolates reveal that they undergo intricate ethylene-triggered structural transformations in the solid-state producing dinuclear silver–ethylene adducts. Despite the complexity, the chemistry is reversible producing precursor trimers with the loss of ethylene. Less reactive {[3,5-(CF 3 ) 2 Pz]Ag} 3 under ethylene pressure and low-temperature conditions stops at an unusual silver–ethylene complex in the trinuclear state, which could serve as a model for intermediates likely present in more common trimer–dimer reorganizations described above. Complete structural data of three novel silver–ethylene complexes are presented together with a thorough computational analysis of the mechanism.

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

The impact of stacking and phonon environment on energy transfer in organic chromophores: computational insights

Energy transfer in organic materials is extensively studied due to many applications in optoelectronics. The electronic and vibrational relaxations within molecular assemblies can be influenced by stacking arrangements or additions of a backbone that unites them. Here, we present the computational study of the photoexcitation dynamics of a perylene diimide monomer, and face-to-face stacked dimer and trimer. By using non-Energy transfer in organic materials is extensively studied due to many applications in optoelectronics. The electronic and vibrational relaxations within molecular assemblies can be influenced by stacking arrangements or additions of a backbone that unites them. In this work, we present the computational study of the photoexcitation dynamics of a perylene diimide monomer, and face-to-face stacked dimer and trimer. By using non-adiabatic excited-state molecular dynamics simulations, we show that the non-radiative relaxation is accelerated with the number of stacked molecules. This effect is explained by differences in the energy splitting between states that impacts their corresponding nonadiabatic couplings. Additionally, our analysis of the vibronic dynamics reveals that the passage through the different conical intersections that participate in the relaxation of the stacked systems, activate a positive feedback mechanism. This effect involves a narrow set of vibrational normal modes that accelerate the process by increasing the efficiency of its vibronic dynamics. In contrast, an addition of a biologically inspired backbone slows down the relaxation rate due to its participation in the vibronic dynamics of the molecular stacking arrangements. Our results suggest the stacking arrangements and common backbones as strategies to modulate the efficiency of electronic and vibrational relaxation of diimide-based systems and other molecular aggregates.

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

Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism

BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae, where both are symmetric trimers composed of three “binding”-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure-Spin-Transport Anomaly in Quasi-One-Dimensional Ba9Fe3Te15 under High Pressure

Recently, a series of novel compounds Ba3MX5 (M= Fe, Ti, V; X=Se, Te) with hexagonal crystal structures composed of quasi-1-dimensional (1D) magnetic chains has been synthesized by our research team using high-pressure and high-temperature methods. The initial hexagonal phases persist to the maximum achievable pressure, while spin configurations and magnetic interactions may change dramatically as a result of considerable reductions in interchain separations upon pressurization. These compounds therefore offer unique possibilities for studying the evolution of intrinsic electronic structures in quasi-1D magnetic systems. Here we present a systematic investigation of Ba9Fe3Te15, in which the interchain separations between trimerized 1D chains (~10.2 Å) can be effectively modulated by external high pressure. The crystal structure especially along the 1D chains exhibits an abnormal expansion at ~5GPa, which accompanies trimerization entangled anomalous mixed-high-low spin transition. An insulator-metal transition has been observed under high pressure as a result of charge-transfer gap closing. Pressure-induced superconductivity emerges at 26GPa, where the charge-transfer gap fully closes, 3D electronic configuration forms and local spin fully collapses.

Zhang, Jun↗
DOE OSTI2025

Sliding dynamics of skyrmion molecular crystals

Using both atomistic and particle-based simulations, we investigate the current-driven dynamics of skyrmions on two-dimensional periodic substrates when there are multiple skyrmions per substrate minimum. At zero drive, the system forms pinned skyrmion molecular crystal states consisting of dimers, trimers, or dimer-trimer mixtures that have both positional and orientational order. On a square substrate lattice, the motion above depinning occurs via a running soliton that travels completely transverse to the applied current. This motion is generated by a torque from the Magnus force, which rotates the n-mer states perpendicular to the applied current. At higher drives, the flow becomes disordered while the Hall angle diminishes and gradually approaches the intrinsic value. In some cases, we also find directional locking where the Hall angle becomes locked to certain symmetry directions of the substrate over a range of currents. The transitions into and out of directionally locked states are accompanied by negative differential mobility in which the net velocity decreases as the drive increases. In conclusion, on a triangular substrate, we find no transverse mobility effects, but still observe directionally locked motion.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Unraveling excitation energy transfer assisted by collective behaviors of vibrations

Abstract We investigate how collective behaviors of vibrations such as cooperativity and interference can enhance energy transfer in a nontrivial way, focusing on an example of a donor–bridge–acceptor trimeric chromophore system coupled to two vibrational degrees of freedom. Employing parameters selected to provide an overall uphill energy transfer from donor to acceptor, we use numerical calculations of dynamics in a coupled exciton–vibration basis, together with perturbation-based analytics and calculation of vibronic spectra, to identify clear spectral features of single- and multi-phonon vibrationally-assisted energy transfer (VAET) dynamics, where the latter include up to six-phonon contributions. We identify signatures of vibrational cooperation and interference that provide enhancement of energy transfer relative to that obtained from VAET with a single vibrational mode. We observe a phononic analogue of two-photon absorption, as well as a novel heteroexcitation mechanism in which a single phonon gives rise to simultaneous excitation of both the trimeric system and the vibrational degrees of freedom. The impacts of vibrations and of the one- and two-phonon VAET processes on the energy transfer are seen to be quite different in the weak and strong site–vibration coupling regimes. In the weak coupling regime, two-phonon processes dominate, whereas in the strong coupling regime up to six-phonon VAET processes can be induced. The VAET features are seen to be enhanced with increasing temperature and site–vibration coupling strength, and are reduced in the presence of dissipation. We analyze the dependence of these phenomena on the explicit form of the chromophore–vibration couplings, with comparison of VAET spectra for local and non-local couplings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2

The emergence of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created the need for development of new therapeutic strategies. Understanding the mode of viral attachment, entry and replication has become a key aspect of such interventions. The coronavirus surface features a trimeric spike (S) protein that is essential for viral attachment, entry and membrane fusion. The S protein of SARS-CoV-2 binds to human angiotensin converting enzyme 2 (hACE2) for entry. Herein, we describe glycomic and glycoproteomic analysis of hACE2 expressed in HEK293 cells. We observed high glycan occupancy (73.2 to 100%) at all seven possible N-glycosylation sites and surprisingly detected one novel O-glycosylation site. To deduce the detailed structure of glycan epitopes on hACE2 that may be involved in viral binding, we have characterized the terminal sialic acid linkages, the presence of bisecting GlcNAc and the pattern of N-glycan fucosylation. We have conducted extensive manual interpretation of each glycopeptide and glycan spectrum, in addition to using bioinformatics tools to validate the hACE2 glycosylation. Our elucidation of the site-specific glycosylation and its terminal orientations on the hACE2 receptor, along with the modeling of hACE2 glycosylation sites can aid in understanding the intriguing virus-receptor interactions and assist in the development of novel therapeutics to prevent viral entry. Here, the relevance of studying the role of ACE2 is further increased due to some recent reports about the varying ACE2 dependent complications with regard to age, sex, race and pre-existing conditions of COVID-19 patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases

The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Many-body expansion for light nuclear systems

Here we extend the many-body expansion (MBE), previously applied to hydrogen bonded and molecular systems, to the light nuclear systems 3 H and 3 He by considering the nucleonic degrees of freedom as fundamental in the expansion. The analysis is based on the Pauli nucleonic dynamics (PND) model, a simple antisymmetrized dynamical code, inspired by the sophisticated constrained molecular dynamics (CoMD) model. The total energy of the 2 H nucleus is calculated with this model at -2.312 MeV, which is within 4% of the experimental value of -2.225 MeV. The application of the MBE yields results for the three-body term in the 3 H nucleus that is comparable with previous estimates, while it is reported for the first time for the nucleus of 3 He . The energies of 3 H and 3 He that include the sum of the one- and two-body terms with the model are - 6.97 ± 0.21 MeV and - 6.19 ± 0.21 MeV and the three-body terms, estimated from the difference of the sum of the one- and two-body terms from the experimentally measured energies, are -1.51 ± 0.21 MeV and -1.53 ± 0.21 MeV, respectively. The MBE for the 3 H and 3 He nuclei is qualitatively similar to the one previously reported for the water trimer: the two- and three-body terms are negative with the latter amounting to ~3% of the former. Additionally, the three-body terms correspond to about 16–23% of the total energy of the bound systems, a percentage that is also comparable to the one in the water trimer (17%). In this manner, the MBE analysis can be applied to light nuclear systems following the same protocol as the one that has been previously extensively used for hydrogen bonded molecular systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis

We report multicopper oxidases (MCOs) represent a diverse family of enzymes that catalyze the oxidation of either an organic or a metal substrate with concomitant reduction of dioxygen to water. These enzymes contain variable numbers of cupredoxin domains, two, three or six per subunit, and rely on four copper ions, a single type I copper and three additional copper ions organized in a trinuclear cluster (TNC), with one type II and two type III copper ions, to catalyze the reaction. Here, two crystal structures and the enzymatic characterization of Marinithermus hydrothermalis MCO, a two-domain enzyme, are reported. This enzyme decolorizes Congo Red dye at 70°C in the presence of high halide concentrations and may therefore be useful in the detoxification of industrial waste that contains dyes. In two distinct crystal structures, MhMCO forms the trimers seen in other two-domain MCOs, but differs from these enzymes in that four trimers interact to create a dodecamer. This dodecamer of MhMCO forms a closed ball-like structure and has implications for the sequestration of bound divalent metal ions as well as substrate accessibility. In each subunit of the dodecameric structures, a Trp residue, Trp351, located between the type I and TNC sites exists in two distinct conformations, consistent with a potential role in facilitating electron transfer in the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural basis of broad HIV neutralization by a vaccine-induced cow antibody

Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo–electron microscopy, and site-directed mutagenesis, we structurally and functionally elucidate the mode of binding of a potent bnAb (NC-Cow1) elicited in cows by immunization with the HIV envelope (Env) trimer BG505 SOSIP.664. The exceptionally long (60 residues) third complementarity-determining region of the heavy chain (CDR H3) of NC-Cow1 forms a mini domain (knob) on an extended stalk that navigates through the dense glycan shield on Env to target a small footprint on the gp120 CD4 receptor binding site with no contact of the other CDRs to the rest of the Env trimer. These findings illustrate, in molecular detail, how an unusual vaccine-induced cow bnAb to HIV Env can neutralize with high potency and breadth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microsecond dynamics control the HIV-1 Envelope conformation

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization

The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence.

Virology↗
DOE OSTI2022

Pseudomonas aeruginosa C-Terminal Processing Protease CtpA Assembles into a Hexameric Structure That Requires Activation by a Spiral-Shaped Lipoprotein-Binding Partner

Pseudomonas aeruginosa CtpA is a carboxyl-terminal processing protease that partners with the outer membrane lipoprotein LbcA to degrade at least five cell wall-associated proteins, four of which are cell wall hydrolases. This activity plays an important role in supporting P. aeruginosa virulence in a mouse model of acute pneumonia. However, almost nothing is known about the molecular mechanisms underlying CtpA and LbcA function. Here, we used structural analysis to show that CtpA alone assembles into an inactive hexamer comprising a trimer of dimers, which limits its substrate access and prevents nonspecific degradation. The adaptor protein LbcA is a right-handed open spiral with 11 tetratricopeptide repeats, which might wrap around a substrate to deliver it to CtpA for degradation. By structure-guided mutagenesis and functional assays, we also showed that the interfaces of the CtpA trimer of dimers and an N-terminal helix of LbcA are important for LbcA-mediated substrate degradation by CtpA both in vitro and in vivo. This work improves our understanding of the molecular mechanism of the LbcA-CtpA proteolytic system and reveals some striking differences from the arrangements found in some other bacterial CTPs.

structural biology↗