Search NASA⌕ Search

SEARCH · Search NASA

Results for “Chemical tools”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗
DOE OSTI2022

Chasing protons in lithium-ion batteries

Parasitic reactions between delithiated cathode materials and non-aqueous electrolytes have been a major barrier that limits the upper cutoff potential of cathode materials. It is of great importance to suppress such parasitic reactions to unleash the high-energy-density potential of high voltage cathode materials. Although major effort has been made to identify the chemical composition of the cathode electrolyte interface using various cutting edge characterization tools, the chemical nature of parasitic reactions remains a puzzle. This severely hinders the rational development of stable high voltage cathode/electrolyte pairs for high-energy density lithium-ion batteries. This report highlights our latest effort in understanding the chemical/electrochemical role of the cathode electrolyte interface using protons as a chemical tracer for parasitic reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Systematic Bandgap Engineering of a 2D Organic–Inorganic Chalcogenide Semiconductor via Ligand Modification

Hybrid organic–inorganic semiconductors present new opportunities for optoelectronic materials design not available in all-organic or all-inorganic materials. One example is silver phenylselenide (AgSePh) – or “mithrene” – a blue-emitting 2D organic–inorganic semiconductor exhibiting strong optical and electronic anisotropy. Here, we show that the bandgap of mithrene can be systematically tuned by introducing electron-donating and electron-withdrawing groups to the phenyl ligands. We synthesized nine mithrene variants, eight of which formed 2D van der Waals crystals analogous to those of AgSePh. Density functional theory calculations reveal that these 2D mithrene variants are direct-gap or nearly direct gap semiconductors. Furthermore, we identify correlations between the optical gap and three experimental observables – the Hammett constant, 77 Se chemical shift, and selenium partial charge – offering predictive power for bandgap tuning. These findings highlight new opportunities for applying the tools of chemical synthesis to semiconductor materials design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

X-ray absorption spectra of f-element complexes: insight from relativistic multiconfigurational wavefunction theory

X-ray absorption near edge structure (XANES) spectroscopy, coupled with ab initio calculations, has emerged as the state-of-the-art tool for elucidating the metal-ligand bonding in f-element complexes. Furthermore, this highlight presents recent efforts in calculating XANES spectra of lanthanide and actinide compounds with relativistic multiconfiguration wavefunction approaches that account for differences in donation bonding in the ground state (GS) versus a core-excited state (ES), multiplet effects, and spin-orbit-coupling. With the GS and ES wavefunctions available, including spin-orbit effects, an arsenal of chemical bonding tools that are popular among chemists can be applied to rationalize the observed intensities in terms of covalent bonding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Mechanical properties of zeolite-templated carbons from approximate density functional theory calculations

Zeolite-templated carbon (ZTC) is a unique porous carbonaceous material whose structure is ordered at the nanometre scale, enabling a representative periodic description at the atomistic level. Utilizing an existing, well-defined reference model for ZTCs, a structural library of varying compositions was developed by refinement using density-functional tight-binding (DFTB) potentials parameterized for materials science applications. We first determined the quantum chemical-refined structures of models with CH, CHO, CHON, CHOB, and CHOBN compositions with various degrees of heteroatom substitution. These structural models comprise the characteristic morphological features of highly porous carbon materials, such as open-blade surfaces, edges, saddles, and closed-strut formations, spanning a range of curvatures and characteristic sizes. Second, we carried out alternating compression and expansion of the CHO model unit cell to determine the lowest energy structure as well as to obtain its bulk modulus in order to demonstrate a close connection between macroscopic observations and atomic-scale structures. Further, the agreement between experimental measurements and the computational model is remarkable and demonstrates the power of approximate density functional theory as a cost-effective computational tool with chemical accuracy for the investigation of structure/property relationships in real-world carbon-based solids.

03 NATURAL GAS↗
DOE OSTI2020

Liquid ToF-SIMS revealing the oil, water, and surfactant interface evolution

Bilge water from ships is regarded as a major pollutant in the marine environment. Bilge water exists in a stable oil-in-water (O/W) emulsion form. However, little is known about the O/W liquid–liquid (l–l) interface. Traditional bulk characterization approaches are not capable of capturing the chemical changes at the O/W l–l interface. Although surfactants are deemed essential in droplet formation, their roles in bilge water stabilization have not been fully revealed. We have utilized novel in situ chemical imaging tools including in situ scanning electron microscopy (SEM) and in situ time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study the evolving O/W interface using a NAVY bilge model for the first time. The droplet size distribution (DSD) does not change significantly without the addition of X-100 surfactants under static or rocking conditions. Both the oil components and the water clusters are shown to evolve over time at the O/W droplet interface by in situ liquid SIMS imaging. Of particular interest to droplet stabilization, the contribution of surfactants to the aged bilge droplets becomes more significant as the droplet size increases. The higher mass surfactant component does not appear on the droplet surface immediately while many lower mass surfactants are solvated inside the droplet. We have provided the first three-dimensional images of the evolving O/W interface and demonstrated that in situ surface chemical mapping is powerful enough to reveal the complex and dynamic l–l interface in the liquid state. Our observational insights suggest that surfactants are important in mediating droplet growth and facilitating effective separation of bilge water emulsion.

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

Diamond surface functionalization via visible light–driven C–H activation for nanoscale quantum sensing

Nitrogen-vacancy (NV) centers in diamond are a promising platform for nanoscale NMR sensing. Despite significant progress toward using NV centers to detect and localize nuclear spins down to the single spin level, NV-based spectroscopy of individual, intact, arbitrary target molecules remains elusive. Such sensing requires that target molecules are immobilized within nanometers of NV centers with long spin coherence. The inert nature of diamond typically requires harsh functionalization techniques such as thermal annealing or plasma processing, limiting the scope of functional groups that can be attached to the surface. Solution-phase chemical methods can be readily generalized to install diverse functional groups, but they have not been widely explored for single-crystal diamond surfaces. Moreover, realizing shallow NV centers with long spin coherence times requires highly ordered single-crystal surfaces, and solution-phase functionalization has not yet been shown with such demanding conditions. In this work, we report a versatile strategy to directly functionalize C–H bonds on single-crystal diamond surfaces under ambient conditions using visible light, forming C–F, C–Cl, C–S, and C–N bonds at the surface. This method is compatible with NV centers within 10 nm of the surface with spin coherence times comparable to the state of the art. As a proof-of-principle demonstration, we use shallow ensembles of NV centers to detect nuclear spins from surface-bound functional groups. Our approach to surface functionalization opens the door to deploying NV centers as a tool for chemical sensing and single-molecule spectroscopy.

Science & Technology - Other Topics↗
DOE OSTI2021

Computation-guided optimization of split protein systems

Splitting bioactive proteins into conditionally reconstituting fragments is a powerful strategy for building tools to study and control biological systems. However, split proteins often exhibit a high propensity to reconstitute, even without the conditional trigger, limiting their utility. Current approaches for tuning reconstitution propensity are laborious, context-specific or often ineffective. Here, we report a computational design strategy grounded in fundamental protein biophysics to guide experimental evaluation of a sparse set of mutants to identify an optimal functional window. We hypothesized that testing a limited set of mutants would direct subsequent mutagenesis efforts by predicting desirable mutant combinations from a vast mutational landscape. This strategy varies the degree of interfacial destabilization while preserving stability and catalytic activity. We validate our method by solving two distinct split protein design challenges, generating both design and mechanistic insights. Furthermore, this new technology will streamline the generation and use of split protein systems for diverse applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Harnessing Nanobodies for Precision Targeting of Proteoforms: Opportunities and Challenges in Therapeutics and Diagnostics

Proteoforms are biologically distinct yet structurally similar proteins that play key roles in driving disease progression but are rarely accounted for in the development of therapeutics and diagnostics. Nanobodies (Nbs) have emerged as a therapeutic and diagnostic “silver bullet” as they possess unique structural and functional attributes that offer advantages over traditional antibodies. One of the most profound advantages of Nbs is the heightened sensitivity and ability to distinguish subtle changes in the conformation of a given protein. Thus, Nbs have significant potential as therapeutic and diagnostic agents that can identify and distinguish specific pathological proteoforms that underlie a given disease. However, there remain significant challenges in obtaining sufficient quantities and purities of specific proteoform antigens that are required for engineering proteoform-specific Nbs. Recent advancements in chemical biology tools for precision proteoform synthesis have made this task feasible for the first time. In this perspective, we discuss the advantages and challenges associated with developing proteoform-specific Nbs and how success in this endeavor will significantly advance the fields of therapeutics and diagnostics.

Antigens↗
DOE OSTI2020

TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics

TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Here, electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Biocatalytic Synthesis of α-Amino Esters via Nitrene C–H Insertion

α-Amino esters are precursors to noncanonical amino acids used in developing small-molecule therapeutics, biologics, and tools in chemical biology. α-C–H amination of abundant and inexpensive carboxylic acid esters through nitrene transfer presents a direct approach to α-amino esters. Methods for nitrene-mediated amination of the protic α-C–H bonds in carboxylic acid esters, however, are underdeveloped. This gap arises because hydrogen atom abstraction (HAA) of protic C–H bonds by electrophilic metal-nitrenoids is slow: metal-nitrenoids preferentially react with polarity-matched, hydridic C–H bonds, even when weaker protic C–H bonds are present. This study describes the discovery and evolution of highly stable protoglobin nitrene transferases that catalyze the enantioselective intermolecular amination of the α-C–H bonds in carboxylic acid esters. We developed a high-throughput assay to evaluate the activity and enantioselectivity of mutant enzymes together with their sequences using the Every Variant Sequencing (evSeq) method. Furthermore, the assay enabled the identification of enantiodivergent enzymes that function at ambient conditions in Escherichia coli whole cells and whose activities can be enhanced by directed evolution for the amination of a range of substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Functional genetic encoding of sulfotyrosine in mammalian cells

Protein tyrosine O -sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate relevant studies, a generally applicable method is needed to enable efficient expression of sulfoproteins with defined sulfation sites in live mammalian cells. Here we report the engineering, in vitro biochemical characterization, structural study, and in vivo functional verification of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells. We further apply this chemical biology tool to cell-based studies on the role of a sulfation site in the activation of chemokine receptor CXCR4 by its ligand. Our work will not only facilitate cellular studies of PTS, but also paves the way for economical production of sulfated proteins as therapeutic agents in mammalian systems.

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

Long-term super-resolution inner mitochondrial membrane imaging with a lipid probe

The inner mitochondrial membrane (IMM) generates power to drive cell function, and its dynamics control mitochondrial health and cellular homeostasis. Here, we describe the cell-permeant, lipid-like small molecule MAO-N 3 and use it to assemble high-density environmentally sensitive (HIDE) probes that selectively label and image the IMM in live cells and multiple cell states. MAO-N 3 pairs with strain-promoted azide–alkyne click chemistry-reactive fluorophores to support HIDE imaging using confocal, structured illumination, single-molecule localization and stimulated emission depletion microscopy, all with significantly improved resistance to photobleaching. These probes generate images with excellent spatial and temporal resolution, require no genetic manipulations, are non-toxic in model cell lines and primary cardiomyocytes (even under conditions that amplify the effects of mitochondrial toxins) and can visualize mitochondrial dynamics for 12.5 h. This probe will enable comprehensive studies of IMM dynamics with high temporal and spatial resolution.

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

Structural basis for intermodular communication in assembly-line polyketide biosynthesis

Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. Here, to investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain–domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High-precision chemical quantum sensing in flowing monodisperse microdroplets

A method is presented for high-precision chemical detection that integrates quantum sensing with droplet microfluidics. Using nanodiamonds (ND) with fluorescent nitrogen-vacancy (NV) centers as quantum sensors, rapidly flowing microdroplets containing analyte molecules are analyzed. A noise-suppressed mode of optically detected magnetic resonance is enabled by pairing controllable flow with microwave control of NV electronic spins, to detect analyte-induced signals of a few hundredths of a percent of the ND fluorescence. Using this method, paramagnetic ions in droplets are detected with low limit-of-detection using small analyte volumes, with exceptional measurement stability over >10 3 s. In addition, these droplets are used as microconfinement chambers by co-encapsulating ND quantum sensors with various analytes such as single cells, suggesting wide-ranging applications including single-cell metabolomics and real-time intracellular measurements from bioreactors. Important advances are enabled by this work, including portable chemical testing devices, amplification-free chemical assays, and chemical imaging tools for probing reactions within microenvironments.

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

Integration of Experimental Hydroprocessing and FCC Data with Process (Aspen Plus) and Refinery Optimization (Aspen PIMS) Models

NREL's Economic, Sustainability, and Market Analysis (ESMA) team develops process models in Aspen Plus to support techno-economic analysis (TEA) and life-cycle assessment (LCA) of conversion pathways from renewable and circular resources to fuels and chemicals. These tools are being applied to assess probable operational constraints or bottlenecks associated with refinery co-processing and repurposing opportunities. The team also utilizes optimizable refinery models to quantify opportunities for biofuel and bioproduct pathways through integration with existing refining infrastructure. The goals of analysis are to model the transition of refineries to renewable and circular feedstocks and quantify the costs production and CO2 abatement through utilization of existing refineries. At the core of the ESMA team's work is the process data derived from conversion experiments on hydroprocessing and fluid catalytic cracking performed at NREL. The objective of this presentation is to highlight new analysis approaches and capabilities in pathway analysis and refinery optimization modeling with specific emphasis on integration of experimental data.

BIOMASS FUELS,ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

The Chemical Management System (CMS): A Useful Tool for Inventory Management

Comprehensive inventory management is central to the efficient operation of any facility that uses and stores chemicals. There are numerous software packages available that perform this function satisfactorily. Most commercially available inventory management software is regulatory or procurement focused and usually comes with upfront or monthly fees. Finally, this report describes freely downloadable software developed at Sandia National Laboratories that delivers an effective inventory management system with an additional focus on chemical security.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗