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At least 451 records · Page 25

All sources NASA NTRS DOE OSTI

NASA NTRS1998

Determining the Molecular Packing Arrangements on Protein Crystal Faces by Atomic Force Microscopy

Periodic Bond Chain (PBC) analysis of the packing of tetragonal lysozyme crystals have revealed that there are two possible molecular packing arrangements for the crystal faces. The analysis also predicted that only one of these, involving the formation of helices about the 4(sub 3) axes, would prevail during crystal growth. In this study high resolution atomic force microscopy (AFM) was employed to verify these predictions for the (110) crystal face. A computer program was developed which constructs the expected AFM image for a given tip shape for each possible molecular packing arrangement. By comparing the actual AFM image with the predicted images the correct packing arrangement was determined. The prediction of an arrangement involving 4(sub 3) helices was confirmed in this manner,"while the alternate arrangement was not observed. The investigation also showed the protein molecules were packed slightly closer about the 4(sub 3) axes than in the crystallographic arrangement of the crystal interior. This study demonstrates a new approach for determining the molecular packing arrangements on protein crystal faces. It also shows the power of combining a theoretical PBC analysis with experimental high resolution AFM techniques in probing protein crystal growth processes at the molecular level.

Li, Huayu↗

DOE OSTI2021

BETO 2021 Peer Review - Biochemical Process Modeling and Simulation (BPMS)

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Biochemical Process Modeling and Simulation (BPMS)

The Biochemical Process Modeling and Simulation project aims to reduce the cost and time of research by applying theory, modeling, and simulation to the most relevant bottlenecks in the biochemical process. We use molecular modeling, quantum mechanics, metabolic modeling, fluid dynamics, and reaction-diffusion methods in close collaboration with pretreatment, hydrolysis, upgrading, and TEA. The project's outcomes are increased yields and efficiency of the biochemical process, added value to products, and reduced price of fuels by specifically targeting catalytic efficiency, reactor design, enzyme efficiency, and microbial design. We work closely with experimental projects to identify problems and iterate with experiments to find and refine solutions. By working with experimentalists, we decide on problems that can be solved with simulation that could otherwise not be solved or would take too long with experiment alone to reach BETO's targets. Over the years, we have produced solutions that have resulted in determining the most likely fatty-acid derivative for passive transport out of bacteria that upgrade biomass, and we have also designed enzyme mutations for enhanced lignin upgrading. Metabolic models have been developed to tune the activity of 2,3 butanediol production for the 2030 target. A computational method to deliver understanding of how complex omics data can be interpreted in the metabolic pathways of organisms used in the Agile Biofoundry. We have found methods to overcome specific barriers and continue to develop those methods. Our reactor studies have guided the design of both the microbes and reactors for aerobic and micro-aerobic production at all scales and have been instrumental in improving the accuracy of techno-economic analysis models. This project is essential in the process of selecting the final processes for 2030 SAF production targets. More specifically, recently, we have: 1) Predicted the strength of the basic structural interactions in commodity plastics to provide guidance for plastics upcycling strategies. 2) Developed computational tool to improve the characterization of lignin-derived compounds 3) Developed new methodologies to enable Machine Learning-based Directed Evolution for protein engineering. 4) Developed Machine Learning methods to predict protein promiscuity and mutations to further improve microbial and enzymatic driven processes and demonstrated the utility of ML approaches to engineering proteins from sparse experimental datasets. 5) Developed new methods to enable high-fidelity simulation of aerobic fermentation at industrial scale and resolving mismatch of time scales through subcycling/operator splitting 7) Identified the difficulty in preventing local high-oxygen conditions in industrial bubble columns, which leads to less-desirable acetoin production, suggesting future research directions in alternative reactor configurations (e.g loop reactors, shallow-channel reactors).

BIOMASS FUELS↗

DOE OSTI2023

Parallel Implementation of Nonadditive Gaussian Process Potentials for Monte Carlo Simulations

A strategy is presented to implement Gaussian process potentials in molecular simulations through parallel programming. Attention is focused on the three-body nonadditive energy, though all algorithms extend straightforwardly to the additive energy. The method to distribute pairs and triplets between processes is general to all potentials. Results are presented for a simulation box of argon, including full box and atom displacement calculations, which are relevant to Monte Carlo simulation. Data on speed-up are presented for up to 120 processes across four nodes. A 4-fold speed-up is observed over five processes, extending to 20-fold over 40 processes and 30-fold over 120 processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A Unified Mechanism on the Formation of Acenes, Helicenes, and Phenacenes in the Gas Phase

Abstract A unified low‐temperature reaction mechanism on the formation of acenes, phenacenes, and helicenes—polycyclic aromatic hydrocarbons (PAHs) that are distinct via the linear, zigzag, and ortho ‐condensed arrangements of fused benzene rings—is revealed. This mechanism is mediated through a barrierless, vinylacetylene mediated gas‐phase chemistry utilizing tetracene, [4]phenacene, and [4]helicene as benchmarks contesting established ideas that molecular mass growth processes to PAHs transpire at elevated temperatures. This mechanism opens up an isomer‐selective route to aromatic structures involving submerged reaction barriers, resonantly stabilized free‐radical intermediates, and systematic ring annulation potentially yielding molecular wires along with racemic mixtures of helicenes in deep space. Connecting helicene templates to the Origins of Life ultimately changes our hypothesis on interstellar carbon chemistry.

Zhao, Long↗

NASA NTRS2019

Deciphering the Effects of Microgravity Cell by Cell

Forces generated by gravity have a profound impact on the behavior of cells in tissues affecting the course of the cell cycle and differentiation fate of progenitors in mammalian tissues. These cells are contributing to normal tissue regenerative health and defence against disease. In Human space exploration context, it is extremely important to determine spaceflight provoked changes in tissue's regenerational capabilities. Microgravity experienced during spaceflight causes unloading and mechanical disuse on all orthostatic support tissues, therefore impacting stem cell fate and lineage commitment decisions. Investigating how ESCs respond to mechanical stimulation is a platform for fundamental developmental and regeneration research applicable for spaceflight. However, the gene expression programs associatiated with early committment stem cell pathways in response to physical stimulation are not readily known. Single-cell RNA-seq technologies have recently revolutionized the world of molecular biology by providing the capability to assess gene expression pattern within a single cell. Our method isolates and separately barcodes mRNAs from thousands of single cells and sequences their expressomes. Understanding regenerative processes on a molecular level would not only help reduce long-term spaceflight impact on health, but also may enable the development of novel tissue regenerative approaches to tissue degeneration on Earth.

Single cell sequencing↗

DOE OSTI2019

A Unified Mechanism on the Formation of Acenes, Helicenes, and Phenacenes in the Gas Phase

A unified low-temperature reaction mechanism on the formation of acenes, phenacenes, and helicenes—polycyclic aromatic hydrocarbons (PAHs) that are distinct via the linear, zigzag, and ortho-condensed arrangements of fused benzene rings—is illustrated. This mechanism is mediated through a barrierless, vinylacetylene mediated gas-phase chemistry utilizing tetracene, [4]phenacene, and [4]helicene as benchmarks contesting established ideas that molecular mass growth processes to PAHs transpire at elevated temperatures. This mechanism opens up an isomer-selective route to aromatic structures involving submerged reaction barriers, resonantly stabilized free-radical intermediates, and systematic ring annulation potentially yielding molecular wires along with racemic mixtures of helicenes in deep space. Thus, connecting helicene templates to the Origins of Life ultimately changes our hypothesis on interstellar carbon chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A chemical dynamics study on the gas-phase formation of triplet and singlet C 5 H 2 carbenes

Significance Carbenes represent key reactive intermediates in molecular mass growth processes leading to carbonaceous nanostructures in the interstellar medium and in combustion systems. However, due to their short lifetimes and tendency for dimerization, carbenes represent one of the foremost obscured classes of reactive intermediates, with the preparation of carbenes in the gas phase remaining largely elusive. By merging molecular beams with electronic structure and quasi-classical trajectory calculations and exploiting triplet pentadiynylidene (HCCCCCH) and singlet ethynylcyclopropenylidene (c-C 5 H 2 ) carbene as benchmarks, we present a versatile protocol to unravel the dynamics leading to exotic carbenes under single-collision conditions. These elementary mechanisms are of significance to our understanding of the fundamental processes leading to unsaturated organic transients in extreme, hydrocarbon-rich environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

A multi-stage single photochrome system for controlled photoswitching responses

The ability of molecular photoswitches to convert on/off responses into large macroscale property change is fundamental to light-responsive materials. However, moving beyond simple binary responses necessitates the introduction of new elements that control the chemistry of the photoswitching process at the molecular scale. To achieve this goal, we designed, synthesized and developed a single photochrome, based on a modified donor–acceptor Stenhouse adduct (DASA), capable of independently addressing multiple molecular states. The multi-stage photoswitch enables complex switching phenomena. To demonstrate this, we show spatial control of the transformation of a three-stage photoswitch by tuning the population of intermediates along the multi-step reaction pathway of the DASAs without interfering with either the first or final stage. This allows for a photonic three-stage logic gate where the secondary wavelength solely negates the input of the primary wavelength. Finally, these results provide a new strategy to move beyond traditional on/off binary photochromic systems and enable the design of future molecular logic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1992

The molecular hydrogen emission around L1551 IRS 5 - Shock-heated molecular gas at the base of the molecular outflow

Spatially resolved observations of the v = 1-0 S(1) molecular hydrogen emission toward L1551 IRS 5 using the grating spectrometer at KPNO are presented. The S(1) emission consists of a ridge component extending toward west along the optical jet from its peak on IRS 5 and a diffuse component which traces the innermost region of the cavity enclosed by the molecular outflow. The ridge component represents shock-heated molecular gas at the root of the optical jet. The diffuse component is too bright to be of scattered origin; it most likely arises from shock-heated gas within the cavity and could represent an acceleration process of the molecular outflow.

Yamashita, Takuya↗

NASA NTRS1987

The physics of interstellar shock waves

This review discusses the observations and theoretical models of interstellar shock waves, in both diffuse cloud and molecular cloud environments. It summarizes the relevant gas dynamics, atomic, molecular and grain processes, radiative transfer, and physics of radiative and magnetic precursors in shock models. It then describes the importance of shocks for observations, diagnostics, and global interstellar dynamics. It concludes with current research problems and data needs for atomic, molecular and grain physics.

Shull, J. Michael↗

DOE OSTI2025

Dissociative electron recombination and rotational cooling of the deuterated triatomic hydrogen ions H 2 ⁡D + and D 2 ⁢H +

We have measured the dissociative recombination (DR) of the deuterated triatomic hydrogen ions H 2 ⁡D + and D 2 ⁢H + as a function of storage time at the Cryogenic Storage Ring (CSR). Both molecular ions were stored for up to 1000 s inside the cryogenic vacuum of the CSR prior to the electron recombination measurements, allowing them to cool to their lowest rotational states. We implement a comprehensive model for all relevant processes to predict the internal state evolution of the ions during storage inside the CSR, employing calculated radiative transition strengths and state-selective rate coefficients for electron collisions. Our DR rate coefficient measurements with deuterated triatomic hydrogen ions in defined quantum states allow for meaningful comparisons with state-of-the-art theoretical calculations, paving the way for a better understanding of the complex DR process for polyatomic molecular ions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

A unified reaction network on the formation of five-membered ringed polycyclic aromatic hydrocarbons (PAHs) and their role in ring expansion processes through radical–radical reactions

Exploiting a chemical microreactor in combination with an isomer-selective product identification through fragment-free photoionization utilizing tunable vacuum ultraviolet (VUV) light in tandem with the detection of the ionized molecules by a high resolution reflection time-of-flight mass spectrometer (Re-TOF-MS), the present investigation reveals molecular mass growth processes to four distinct polycyclic aromatic hydrocarbons carrying two six- and one five-membered ring (C 13 H 10 ): 3H-cyclopenta[a]naphthalene, 1H-cyclopenta[b]naphthalene, 1H-cyclopenta[a]naphthalene, and fluorene in the gas phase. Temperatures of 973 and 1023 K simulating conditions in combustion settings along with circumstellar envelopes of carbon-rich stars and planetary nebulae. These reactions highlight the importance of methyl-substituted aromatic reactants (biphenyl, naphthalene) which can be converted to the methylene (–CH 2 ˙) motive by hydrogen abstraction or photolysis. Upon reaction with acetylene, methylene-substituted aromatics carrying a hydrogen atom at the ortho position of the ring can be then converted to cyclopentadiene-annulated aromatics thus providing a versatile pathway to five-membered ring aromatics at elevated temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Tetrahydrofuran Processable Organic Solar Cells with 19.45% Efficiency Realized by Introducing High Molecular Dipole Unit Into the Terpolymer

Developing organic solar cells (OSCs) processable with halogen‐free, non‐aromatic solvents is crucial for practical applications, yet challenging due to the limited solubility of most photoactive materials. Here, this study introduces high‐performance terpolymers processable in tetrahydrofuran (THF) by incorporating dithienophthalimide (DPI) into the PM6 backbone. DPI extends the absorption band, lowers HOMO levels, and improves THF solubility and film crystallinity through its large dipole moment effect. Optimal PBD‐10:L8‐BO devices processed with THF achieved a competitive power conversion efficiency (PCE) of 18.79%, approaching chloroform‐processed devices (19.04%). By introducing PBTz‐F as a second donor, ternary OSCs reached an impressive 19.45% PCE when processed with THF. This improvement stems from enhanced photon generation, improved morphology, better charge transport, longer exciton lifetimes, efficient charge dissociation and collection, and suppressed recombination. These PCEs of 18.79% and 19.45% for binary and ternary blend OSCs, respectively, represent the highest reported efficiencies for OSCs processed with halogen‐free, non‐aromatic solvents. This work demonstrates significant progress in eco‐friendly OSC fabrication, paving the way for more sustainable and commercially viable organic photovoltaic technologies.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Techno-Economic Analysis of a Carbon Molecular Sieve-Based Xylene Isomer Purification Process

Not Available

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

VUV Photoionization Dynamics and Reactivity of Heterogeneous Water Clusters

This feature focuses on bridging isolated water and bulk water studies. It assembles experiments and theory on water clusters, mainly probed by vacuum ultraviolet (VUV) radiation, and summarizes what the effects are of intermolecular interactions on both the spectroscopy and the VUV-induced processes in water. In particular, it highlights studies of heterogeneous water clusters─those incorporating other molecular species such as naphthalene, methane, formic acid, and glycerol─which serve as model systems to investigate the fundamental roles of water in hydrogen bonding networks, proton transfer, and astrochemical processes. These mixed clusters provide a platform to revisit the stability of protonated water clusters and compile observations of ionization-induced structural rearrangements and fragmentation, especially in systems involving hydroxyl-rich cosolvents. This feature then explores energy transfer mechanisms in molecular clusters, following VUV photoexcitation. It concludes with potential future directions. First, we investigate excited-state dynamics in molecular clusters through direct probing, complementing the synchrotron studies discussed here. Second, exploring gas-phase molecule evaporation from confined spaces and interfaces using advanced spectroscopic techniques sheds light on these ubiquitous, yet currently debated, molecular processes.

Cluster chemistry↗

NASA NTRS1993

Processible Polyazomethines

Processibility enhanced by incorporating trifluoromethylbenzene units into molecules. Results of two unexpected properties: high solubility in common organic solvents and lack of crystallinity. Properties coupled with ability of this class of polymers to undergo exchange reactions at elevated temperatures allow these materials to moderate their molecular weights during processing, which affects resulting mechanical properties after processing. Fluorinated polyazomethines form amorphous films that have excellent mechanical properties. Used in moisture-free environments as electronic semiconducting films and adhesives, and as matrix resins for advanced structural composites.

Bryant, Robert G.↗

DOE OSTI2024

Unconventional gas-phase synthesis of biphenyl and its atropisomeric methyl-substituted derivatives

The biphenyl molecule (C 12 H 10 ) acts as a fundamental molecular backbone in the stereoselective synthesis of organic materials due to its inherent twist angle causing atropisomerism in substituted derivatives and in molecular mass growth processes in circumstellar environments and combustion systems. Here, we reveal an unconventional low-temperature phenylethynyl addition–cyclization–aromatization mechanism for the gas-phase preparation of biphenyl (C 12 H 10 ) along with ortho-, meta-, and para-substituted methylbiphenyl (C 13 H 12 ) derivatives through crossed molecular beams and computational studies providing compelling evidence on their formation via bimolecular gas-phase reactions of phenylethynyl radicals (C 6 H 5 CC, X 2 A 1 ) with 1,3-butadiene-d 6 (C 4 D 6 ), isoprene (CH 2 C(CH 3 )CHCH 2 ), and 1,3-pentadiene (CH 2 CHCHCHCH 3 ). The dynamics involve de-facto barrierless phenylethynyl radical additions via submerged barriers followed by facile cyclization and hydrogen shift prior to hydrogen atom emission and aromatization to racemic mixtures (ortho, meta) of biphenyls in overall exoergic reactions. Furthermore, these findings not only challenge our current perception of biphenyls as high temperature markers in combustion systems and astrophysical environments, but also identify biphenyls as fundamental building blocks of complex polycyclic aromatic hydrocarbons (PAHs) such as coronene (C 24 H 12 ) eventually leading to carbonaceous nanoparticles (soot, grains) in combustion systems and in deep space thus affording critical insight into the low-temperature hydrocarbon chemistry in our universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗