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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 37 records · Page 2

Molecular Geometry and Electronic Structure of Copper Corroles

Copper corroles are known for their unique multiconfigurational electronic structures in the ground state, which arise from the transfer of electrons from the π orbitals of the corrole to the d-orbital of copper. While density functional theory (DFT) provides reasonably good molecular geometries, the determination of the ground spin state and the associated energetics is heavily influenced by functional choice, particularly the percentage of the Hartree–Fock exchange. Using extended multireference perturbation theory methods (XMS-CASPT2), the functional choice can be assessed. The molecular geometries and electronic structures of both the unsubstituted and the meso-triphenyl copper corroles were investigated. A minimal active space was employed for structural characterization, while larger active spaces are required to examine the electronic structure. The XMS-CASPT2 investigations conclusively identify the ground electronic state as a multiconfigurational singlet (S o ) with three dominant electronic configurations in its lowest energy and characteristic saddled structure. In contrast, the planar geometry corresponds to the triplet state (T o ), which is approximately 5 kcal/mol higher in energy compared to the S o state for both the bare and substituted copper corroles. Notably, the planarity of the T o geometry is reduced in the substituted corrole compared with that in the unsubstituted one. By analyzing the potential energy surface (PES) between the S o and T o geometries using XMS-CASPT2, the multiconfigurational electronic structure is shown to transition toward a single electron configuration as the saddling angle decreases (i.e., as one approaches the planar geometry). Despite the ability of the functionals to reproduce the minimum energy structures, only the TPSSh-D 3 PES is reasonably close to the XMS-CASPT2 surface. Significant deviations along the PES are observed with other functionals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of Hydrogen Bonding and Molecular Chain Flexibility of Substituted n-Alkyldimethylsilanes On Impact Ice Adhesion Shear Strength

The effects of hydrogen bonding and molecular flexibility upon ice adhesion shear strength were investigated using aluminum substrates coated with substituted n-alkyldimethylalkoxysilanes. The location of the chemical group substitution was on the opposing end of the linear n-alkyl chain with respect to silicon. Three hydrogen-bonding characteristics were evaluated: 1) non-hydrogen bonding, 2) donor/acceptor, and 3) acceptor. Varying the length of the n-alkyl chain provided an assessment of molecular chain flexibility. Coated and uncoated aluminum surfaces were characterized by receding water contact angle and surface roughness. Ice adhesion shear strength was determined in the Adverse Environment Rotor Test Stand facility from -16 to -8°C that simulated aircraft in-flight icing conditions within the FAR Part 25/29 Appendix C icing envelope. Surface roughness of the coatings was similar allowing for comparison of the test results. An adhesion reduction factor, based on the ice adhesion shear strength data with respect to uncoated aluminum obtained at the same temperature, was calculated to compare the data. The results revealed complex interactions with impacting supercooled water droplets that were interdependent upon ice accretion temperature, surface energy characteristics of water and ice, hydrogen bonding characteristic of the substituent, and length of the n-alkyl chain. To aid in explaining the results, 1) changes in the surface energy component (i.e., non-polar and polar) values that water undergoes during its’ phase change from liquid to solid that arise from the freezing of impacting supercooled water droplets on the surface depended upon the temperature during accretion were taken into account and 2) the physical properties (i.e., water solubility and melting point) of small compounds analogous to the substituted n-alkyldimethylalkoxysilanes used in this study were compared.

Smith, Joseph G.↗

Comprehensive review of photophysical parameters (ε, Φ f , τ s ) of tetraphenylporphyrin (H 2 TPP) and zinc tetraphenylporphyrin (ZnTPP) – Critical benchmark molecules in photochemistry and photosynthesis

Tetraphenylporphyrin (H 2 TPP) and zinc tetraphenylporphyrin (ZnTPP) are widely used benchmark molecules in diverse photochemical studies given facile synthetic access, rich visible-region spectra, and broad structural analogy to chlorophylls. Yet the literature values for each key photophysical parameter – the molar absorption coefficient (ε), fluorescence quantum yield (Φ f ), and also singlet excited-state lifetime (τ S ) – vary over an astonishing range. Here, a comprehensive literature review (~1940–September 2020) encompassing 871 publications is reported for these essential parameters. Each parameter is determined by measurement with distinct instrumentation and suffers idiosyncratic sources of error. The best values for H 2 TPP are ε = 460,000 cm -1 ·M -1 , Φ f = 0.090, and τ S = 12.8 ns in Ar- purged toluene (Φf = 0.070, τS = 9.9 ns in toluene in air); the best values for ZnTPP are ε = 560,000 cm -1 ·M -1 , Φf = 0.030, and τ S = 2.1 ns in Ar-purged toluene (Φ f = 0.029, τ S = 2.0 ns in toluene in air). The choice of values for such parameters has far-reaching consequences in photochemistry ranging from fluorescence (or Förster) resonance energy transfer (FRET) processes to assessments of molecular brightness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ENVnet provides a global molecular resource of dissolved organic matter

Dissolved organic matter (DOM) is an important component of Earth's carbon cycle and one of the planet's most chemically diverse pools, yet the molecular structures of its constituents remain largely unresolved. This limitation has hindered our ability to link DOM composition to microbial processes and ecosystem function. Here we present ENVnet, a global molecular repository built from tandem mass spectrometry data collected across 13 terrestrial and aquatic environment types, including 419 newly generated samples that expand publicly available DOM metabolomics data and cover previously underrepresented environments. By computationally deconvolving chimeric mass spectra, a longstanding challenge in environmental metabolomics, we recover high-quality fragmentation data for >22,000 distinct molecular features (defined by a specific precursor mass and fragmentation pattern). Using ENVnet, we uncover conserved and environment-specific molecular patterns in DOM composition and underlying biogeochemical processes. We also use molecular features encoded in ENVnet to train predictive models of DOM persistence, allowing molecular-level assessment of microbial turnover in independent systems.

54 ENVIRONMENTAL SCIENCES↗

Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials

The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R 2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C 11 H 16 O 4 , C 18 H 34 O 4 , and C 6 H 15 NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C 6 H 15 NO (assuming it presented as Diethylethanolamine).

59 BASIC BIOLOGICAL SCIENCES↗

Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies

Significance Synthetic biology has entered an era in which reading and writing DNA sequences are no longer rate-limiting steps in microbial strain engineering. Indeed, analytical methods measuring the resulting metabolic outcomes of specific gene edits have lagged behind the ability to generate new recombinant strains. Herein, we report a mass spectrometry strategy to accelerate these analytical workflows by directly analyzing metabolites and molecules produced from engineered microorganisms in a multiplexed process. Using untargeted acquisitions and unsupervised analytics, we assess the molecular features that change across discrete strains including primary target species, secondary products, and species outside the engineered fatty acid biosynthesis pathway.

09 BIOMASS FUELS↗

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗

Environmental DNA as a tool for hydropower impact assessments: current status, special considerations, and future integration

Globally there is an urgent need to find sustainable solutions to balance energy production with the protection of vulnerable species and conservation of biodiversity. This is particularly critical for freshwater ecosystems, habitats, and species that may be impacted by hydropower development and operations needed to meet energy grid demands. Reliable and accurate environmental impact assessments (EIAs) that identify the biological, physical, or social impacts of hydropower are key to ensure biodiversity, ecosystem, and societal sustainability. The analysis of environmental DNA (eDNA) has the potential to transform hydropower EIAs, management and mitigation planning, and decision-making procedures. Further, the incorporation of eDNA surveys into EIAs during both hydropower planning and continued operations may streamline regulatory processes by improving our understanding of potentially impacted biota and habitats and evaluating environmental impacts mitigation. Here, we: (i) highlight current understanding and use of eDNA in freshwater environments; (ii) examine critical considerations for eDNA integration into hydropower EIAs and biological monitoring; (iii) identify knowledge gaps in eDNA analysis and applications unique to hydropower-regulated systems; and (iv) discuss future opportunities to bolster the incorporation of eDNA into hydropower research including regulatory acceptance and public engagement. While we acknowledge that there are several factors that may complicate the broad adoption of eDNA as a tool for assessing the impacts of hydropower, we anticipate that growing confidence in eDNA through hydropower-specific protocols, calibrations, and validations will overcome these inherent uncertainties.

aquatic biodiversity↗

Development of Composite Photocatalyst Materials that are Highly Selective for Solar Hydrogen Production and their Evaluation in Z-Scheme Reactor Designs

The key technology gap preventing a vertically stacked dual-bed particle suspension reactor from achieving the DOE MYRD&D ultimate cost target for H 2 production remains the lack of materials in particle form factor that exhibit ≥10% solar-to-H 2 energy conversion (STH) efficiency as a suspension. Therefore, our project goals centered around strategies to increase the STH efficiency by enhancing photophysical properties of perovskite oxide particles including increased visible-light absorption, increased selectivity for electrocatalysis of the H 2 evolution reaction (HER) and the O 2 evolution reaction (OER) through development of ultrathin oxide coatings, correlating composition and structure to function, and improving understanding of multiscale transport and kinetic processes.

08 HYDROGEN↗

Cancer Detection Using Neural Computing Methodology

This paper describes a novel learning methodology used to analyze bio-materials. The premise of this research is to help pathologists quickly identify anomalous cells in a cost efficient method. Skilled pathologists must methodically, efficiently and carefully analyze manually histopathologic materials for the presence, amount and degree of malignancy and/or other disease states. The prolonged attention required to accomplish this task induces fatigue that may result in a higher rate of diagnostic errors. In addition, automated image analysis systems to date lack a sufficiently intelligent means of identifying even the most general regions of interest in tissue based studies and this shortfall greatly limits their utility. An intelligent data understanding system that could quickly and accurately identify diseased tissues and/or could choose regions of interest would be expected to increase the accuracy of diagnosis and usher in truly automated tissue based image analysis.

liquid crystal tunable filters↗

Cleaning Genesis Solar Wind Collectors with Ultrapure Water: Residual Contaminant Particle Analysis

Additional experience has been gained in removing contaminant particles from the surface of Genesis solar wind collectors fragments by using megasonically activated ultrapure water (UPW)[1]. The curatorial facility has cleaned six of the eight array collector material types to date: silicon (Si), sapphire (SAP), silicon-on-sapphire (SOS), diamond-like carbon-on-silicon (DOS), gold-on-sapphire (AuOS), and germanium (Ge). Here we make estimates of cleaning effectiveness using image analysis of particle size distributions and an SEM/EDS reconnaissance of particle chemistry on the surface of UPW-cleaned silicon fragments (Fig. 1). Other particle removal techniques are reported by [2] and initial assessment of molecular film removal is reported by [3].

Allton, J. H.↗

Genesis Solar Wind Sample Curation: A Progress Report

In the year since the Genesis solar wind collector fragments were returned, early science samples, specimens for cleaning experiments, and science allocations have been distributed. Solar wind samples are stored under nitrogen and handled in an ISO Class 4 (Class 10) laboratory. For array collector fragments, a basic characterization process has been established. This characterization consists of identification of solar wind regime, whole fragment image for identification and surface quality, higher magnification images for contaminant particle density, and assessment of molecular film contaminant thickness via ellipsometry modeling. Compilations of this characterization data for AuOS (gold film on sapphire), and sapphire from the bulk solar wind for fragments greater than 2 cm are available. Removal of contaminant particles using flowing ultrapure water (UPW) energized megasonically is provided as requested.

Allton, Judith H.↗

Spaceflight Causes Increased Virulence of Serratia Marcescens on a Drosophila Melanogaster Host

Drosophila melanogaster, or the fruit fly, has long been an important organism for Earth-based research, and is now increasingly utilized as a model system to understand the biological effects of spaceflight. Studies in Drosophila melanogaster have shown altered immune responses in 3rd instar larvae and adult males following spaceflight, changes similar to those observed in astronauts. In addition, spaceflight has also been shown to affect bacterial physiology, as evidenced by studies describing altered virulence of Salmonella typhimurium following spaceflight and variation in biofilm growth patterns for the opportunistic pathogen Pseudomonas aeruginosa during flight. We recently sent Serratia marcescens Db11, a Drosophila pathogen and an opportunistic human pathogen, to the ISS on SpaceX-5 (Fruit Fly Lab-01). S. marcescens samples were stored at 4degC for 24 days on-orbit and then allowed to grow for 120 hours at ambient station temperature before being returned to Earth. Upon return, bacteria were isolated and preserved in 50% glycerol or RNAlater. Storage, growth, and isolation for ground control samples were performed using the same procedures. Spaceflight and ground samples stored in 50% glycerol were diluted and injected into 5-7-day-old ground-born adult D. melanogaster. Lethality was significantly greater in flies injected with the spaceflight samples compared to those injected with ground bacterial samples. These results indicate a shift in the virulence profile of the spaceflight S. marcescens Db11 and will be further assessed with molecular biological analyses. Our findings strengthen the conclusion that spaceflight impacts the virulence of bacterial pathogens on model host organisms such as the fruit fly. This research was supported by NASA's ISS Program Office (ISSPO) and Space Life and Physical Sciences Research and Applications (SLPSRA).

Serratia marcescens↗

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗

Assessing the effect of regularization on the molecular properties predicted by SCAN and self-interaction corrected SCAN meta-GGA

Recent regularization of the SCAN meta-GGA functional (rSCAN) has simplified the numerical complexities of the SCAN functional, alleviating SCAN's stringent demand on the numerical integration grids to some extent. The regularization of rSCAN, however, results in the breaking of some constraints such as the uniform electron gas limit, the slowly varying density limit, and coordinate scaling of the iso-orbital indicator. Here, we assess the effects of regularization on the electronic, structural, vibrational, and magnetic properties of molecules by comparing the SCAN and rSCAN predictions. The properties studied include atomic energies, atomization energies, ionization potentials, electron affinities, barrier heights, infrared intensities, dissociation and reaction energies, spin moments of molecular magnets, and isomer ordering of water clusters. Our results show that rSCAN requires less dense numerical grids and gives very similar results to those of SCAN for all properties examined with the exception of atomization energies, which are worsened in rSCAN. We also examine the performance of self-interaction-corrected (SIC) rSCAN with respect to SIC-SCAN using the Perdew–Zunger (PZ) SIC method. The PZSIC method uses orbital densities to compute one-electron self-interaction errors and places an even more stringent demand on numerical grids. Our results show that SIC-rSCAN gives marginally better performance than SIC-SCAN for almost all properties studied in this work with numerical grids that are on average half or less as dense as that needed for SIC-SCAN.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube

The effect of the protonation state of glutamic acid on its translocation through cyclic peptide nanotubes (CPNs) was assessed by using molecular dynamics (MD) simulations. Anionic (GLU–), neutral zwitterionic (GLU0), and cationic (GLU+) forms of glutamic acid were selected as three different protonation states for an analysis of energetics and diffusivity for acid transport across a cyclic decapeptide nanotube. Based on the solubility-diffusion model, permeability coefficients for the three protonation states of the acid were calculated and compared with experimental results for CPN-mediated glutamate transport through CPNs. Potential of mean force (PMF) calculations reveal that, due to the cation-selective nature of the lumen of CPNs, GLU–, so-called glutamate, shows significantly high free energy barriers, while GLU+ displays deep energy wells and GLU0 has mild free energy barriers and wells inside the CPN. The considerable energy barriers for GLU– inside CPNs are mainly attributed to unfavorable interactions with DMPC bilayers and CPNs and are reduced by favorable interactions with channel water molecules through attractive electrostatic interactions and hydrogen bonding. Unlike the distinct PMF curves, position-dependent diffusion coefficient profiles exhibit comparable frictional behaviors regardless of the charge status of three protonation states due to similar confined environments imposed by the lumen of the CPN. The calculated permeability coefficients for the three protonation states clearly demonstrate that glutamic acid has a strong protonation state dependence for its transport through CPNs, as determined by the energetics rather than the diffusivity of the protonation state. In addition, the permeability coefficients also imply that GLU– is unlikely to pass through a CPN due to the high energy barriers inside the CPN, which is in disagreement with experimental measurements, where a considerable amount of glutamate permeating through the CPN was detected. To resolve the discrepancy between this work and the experimental observations, several possibilities are proposed, including a large concentration gradient of glutamate between the inside and outside of lipid vesicles and bilayers in the experiments, the glutamate activity difference between our MD simulations and experiments, an overestimation of energy barriers due to the artifacts imposed in MD simulations, and/or finally a transformation of the protonation state from GLU– to GLU0 to reduce the energy barriers. Altogether, our study demonstrates that the protonation state of glutamic acid has a strong effect on the transport of the acid and suggests a possible protonation state change for glutamate permeating through CPNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗