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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 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events

Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. The mechanism of DnaG remains unclear due to the paucity of structural information on DnaG in complexes with other replisome components. Furthermore we report the first crystal structures of noncovalent DnaG–DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis. In another structure, DNA in the active site of DnaG mimics the primer, providing insight into mechanisms for the nucleotide transfer and DNA translocation. In conjunction with the recent cryo-EM structure of the bacteriophage T7 replisome, this study yields a model for primer elongation and hand-off to DNA polymerase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Exposing Key Vibrational Contributions to Properties of Organic Molecular Solids with High Signal, Low Frequency Neutron Spectroscopy and Ab Initio Simulations

Stability and response of supramolecular forms is important to many areas in materials science, and contributions from vibrations can be crucial. In this study, we have collected the first spectra of organic molecular crystals and polymorphic cocrystals using the next-generation, high-signal VISION spectrometer in the far-infrared (FIR) and mid-infrared (MIR) range. Unambiguously different spectral signatures were found for carbamazepine and two polymorphs of the carbamazepine-saccharin cocrystal, including numerous modes undetectable with optical methods. For FIR-range frequencies, in addition to correct calculation of peak positions, accurate line-shape features were reproducible by simulation using ab initio vibrational calculations. Finally, high confidence spectral assignments and thermochemical information for this region are thus expected, and a benchmark for vibrational ab initio calculations is provided, creating a significant addition to methods used in investigation and design of organic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Key Chemical Kinetic Steps in Reaction Mechanisms for Fuels from Biomass: A Perspective

Detailed chemical kinetic modeling has been a significant part of combustion research since the entry of the computer into the research community. For most of that time, fuels have largely been provided from petrochemicals, and the combustion chemistry that was developed reflected that source of fuels. Furthermore, renewable fuels from biomass have always made important contributions as fuel sources. Current trends show that renewable fuels are gaining an even more important role as fuel sources, and chemical kinetic modeling of those fuels is playing an essential role in these advances. Interactions between fuels research and chemical kinetic modeling are discussed in this paper, with emphasis on the close and continuous coupling between them. In many cases, new fuels from biomass have structural or compositional features never before seen in real fuels, so entirely new reaction mechanisms are required.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[ a ]pyrene Biodegradation in Sediments by Microbial Electrochemistry

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[ a ]pyrene (B a P) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c -type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased B a P bioavailability and increased degradation rates. In conclusion, tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of B a P enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Computational Study of an Iron(II) Polypyridine Electrocatalyst for CO 2 Reduction: Key Roles for Intramolecular Interactions in CO 2 Binding and Proton Transfer

A solar-driven conversion of CO 2 into fuels by artificial photosynthesis would not only mitigate the greenhouse effect but also provide an alternative to obtain fuels in a renewable fashion. To this end, the new iron polypyridine catalyst [Fe(bpy NHEt PY2Me)L 2 ] 2+ (L = H 2 O, CH 3 CN) was recently developed for the electrochemical reduction of CO 2 to CO. Here, we performed density functional theory (DFT) electronic structure calculations to shed light on a possible pathway for CO 2 reduction and the origin of the selectivity between CO 2 reduction versus the hydrogen evolution reaction. The metal center remains Lewis acidic throughout the reduction process due to ligand loss and mainly ligand-based reduction stabilized by antiferromagnetic coupling to a high-spin Fe(II) center. This results in a high barrier for hydride formation but a facile addition and activation of CO 2 via an η 2 coordination and stabilizing hydrogen bonding by the amine group. The second unoccupied equatorial coordination site opens up the possibility for an intramolecular protonation with a coordinated water ligand. This facilitates protonation because not only CO 2 but also the proton source H 2 O is activated and properly aligned for a proton transfer due to the Fe-OH 2 bond; consequently, both protonation steps are facile. The moderate ligand field allows a rapid ligand exchange for a second intramolecular protonation step and facilitates an exergonic CO release. The lower selectivity of the related [Fe(bpy OH PY2Me)L 2 ] 2+ complex can be related to its more acidic second coordination sphere, which enables an intramolecular proton transfer that is kinetically competitive with CO 2 addition.

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

Cation-poor complex metallic alloys in Ba(Eu)–Au–Al(Ga) systems: Identifying the keys that control structural arrangements and atom distributions at the atomic level

Four complex intermetallic compounds BaAu 6±x Ga 6±y (x = 1, y = 0.9) (I), BaAu 6±x Al 6±y (x = 0.9, y = 0.6) (II), EuAu 6.2 Ga 5.8 (III), and EuAu 6.1 Al 5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn 13 -type structure (cF104–112, Fm3C), III (tP52, P4/nbm) is derived from the tetragonal Ce 2 Ni 17 Si 9 -type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution (“coloring scheme”). Chemical bonding analyses for two different “EuAu 6 Tr 6 ” models reveal maximization of the number of heteroatomic Au–Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the “EuAu 6 Tr 6 ” models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu 6.2 Ga 5.8 (III) and EuAu 6.1 Al 5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at T C = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. As a result, the effective moments of 8.3 μB/f.u., determined from Curie–Weiss fits, point to divalent oxidation states for europium in both III and IV.

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

Identification of Potent and Selective Inhibitors of Acanthamoeba : Structural Insights into Sterol 14α-Demethylase as a Key Drug Target

Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii. The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC 50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Quantification of Key Peroxy and Hydroperoxide Intermediates in the Low-Temperature Oxidation of Dimethyl Ether

Dimethyl ether (DME) oxidation is a model chemical system with a small number of prototypical reaction intermediates that also has practical importance for low-carbon transportation. Although it has been studied experimentally and theoretically, ambiguity remains in the relative importance of competing DME oxidation pathways in the low-temperature autoignition regime. To focus on the primary reactions in DME autoignition, we measured the time-resolved concentration of five intermediates, CH 3 OCH 2 OO (ROO), OOCH 2 OCH 2 OOH (OOQOOH), HOOCH 2 OCHO (hydroperoxymethyl formate, HPMF), CH 2 O, and CH 3 OCHO (methyl formate, MF), from photolytically initiated experiments. We performed these studies at P = 10 bar and T = 450-575 K, using a high-pressure photolysis reactor coupled to a time-of-flight mass spectrometer with tunable vacuum-ultraviolet synchrotron ionization at the Advanced Light Source. Our measurements reveal that the timescale of ROO decay and product formation is much shorter than predicted by current DME combustion models. The models also strongly underpredict the observed yields of CH 2 O and MF and do not capture the temperature dependence of OOQOOH and HPMF yields. Adding the ROO + OH $\rightarrow$ RO + HO 2 reaction to the chemical mechanism (with a rate coefficient approximated from similar reactions) improves the prediction of MF. Increasing the rate coefficients of ROO ↔ QOOH and QOOH + O 2 ↔ OOQOOH reactions brings the model predictions closer to experimental observations for OOQOOH and HPMF, while increasing the rate coefficient for the QOOH $\rightarrow$ 2 CH 2 O + OH reaction is needed to improve the predictions of formaldehyde. In conclusion, to aid future quantification of DME oxidation intermediates by photoionization mass spectrometry, we report experimentally determined ionization cross-sections for ROO, OOQOOH, and HPMF.

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

Determining Key Factors for the Open-Loop Control of Molecular Fragmentation Using Shaped Strong Fields

Pulse shaping has long been employed for tailoring femtosecond laser pulses to study and control the fragmentation of polyatomic molecules. In many cases, a physical explanation connecting the properties of the field to the observed control is difficult to ascertain. We utilized 80 bit binary spectral phase functions to parametrize and map the search space, gaining insight into which pulse parameters most impact the ion yield and fragmentation pattern for the relatively large triethylamine [N(C 2 H 5 ) 3 ] molecule. Pulse structures used to control the m/z 86 branching ratio beyond a simple intensity dependence are identified and compared to pump–probe results. All of these findings are explained in terms of control via a dissociative Rydberg state in the neutral molecule. This methodology may be used to discover new control mechanisms and shed light onto which pulse parameters most influence the interaction between strong field lasers and matter.

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

Minimization of Disorder as a Key Design Principle for Natural Sizes of Light Harvesting 2 Complexes

The light harvesting 2 (LH2) complex of purple bacteria has excellent energy conversion efficiency. Clarifying the design principle behind such efficiency at the atomistic level is crucial for understanding its structure–function relationship and can be utilized for the design of artificial light harvesting systems. To this end, we conducted comprehensive computational investigation of the dynamical and statistical nature of electronic excited states of pigment molecules in a natural LH2 complex with 9-fold symmetry and its two non-natural in silico analogues with 6- and 12-fold symmetries. To ensure reliable and efficient all-atomistic molecular dynamics simulations, we combined a well established interpolation approach for the construction of the potential energy surface with a neural network machine learning approach. Outcomes of these calculations clarify that non-natural forms of LH2-type complexes have significantly larger quasistatic disorder than those for the natural one. In addition, non-natural systems have more disruptions of the hydrogen bonding, underscoring its crucial role for reducing the disorder. On the other hand, local environmental dynamics are relatively insensitive to the structural changes although there is moderate enhancement in the anharmonic or interatomic components for the synthetic ones. These findings based on all-atomistic simulations provide direct computational evidence that the structure and sizes of natural LH2 complexes are designed to minimize the energetic disorder. We analyze quantitative implications of these for the energy transferring capability of the LH2 complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗