Search NASA⌕ Search

SEARCH · Search NASA

Results for “small molecule”

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 OSTI2023

Catching the Killer: Dynamic Disorder Design Rules for Small–Molecule Organic Semiconductors

Small-molecule organic semiconductors are promising materials for applications ranging from solar cells to medical sensors. Their nearly infinite design space means that, in theory, it is possible to tailor the material to the exact specifications of a particular application. In reality; however, design rules to improve mobility (μ) remain elusive because of the complex calculations required to understand its limiters. Transient localization theory posits that charge carriers are slowed down by the collective phonon motions, called dynamic disorder, which localize charge carriers temporarily. Traditionally, a mode-by-mode analysis is performed to try and identify “killer” modes. Herein, the flaws are demonstrated with this analysis and present a streamlined simulation workflow that simplifies simulation of dynamic disorder and enables engineering of new molecular structures based on phonon dynamics. This workflow is combined with a novel visualization technique that enables per-atom insights into how μ is limited. Furthermore, this workflow is applied and analyzed to a series of -acenes and a series of BTBT-based molecules. Then design rules are identified in each series that identify possible ways to improve the μ beyond current experimental limits using phonon engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Small molecule biosensors

Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Biosensors are produced based on a ligand-binding domain (LBD) using a method that, in principle, can be applied for any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. The power of this method is illustrated by developing biosensors for digoxin and progesterone. Addition of ligand to cells expressing a biosensor activates transcription in yeast, mammalian cells and plants, with a dynamic range of up to about 100-fold or more. The biosensors are used to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules.

Mandell, Daniel J.↗
DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗
DOE OSTI2022

High performance polymerized small molecule acceptor by synergistic optimization on $\pi$-bridge linker and side chain

The polymerized small-molecule acceptors have attracted great attention for application as polymer acceptor in all-polymer solar cells recently. The modification of small molecule acceptor building block and the π-bridge linker is an effective strategy to improve the photovoltaic performance of the polymer acceptors. In this work, we synthesized a new polymer acceptor PG-IT2F which is a modification of the representative polymer acceptor PY-IT by replacing its upper linear alkyl side chains on the small molecule building block with branched alkyl chains and attaching difluorene substituents on its thiophene π-bridge linker. Through this synergistic optimization, PG-IT2F possesses more suitable phase separation, increased charge transportation, better exciton dissociation, lower bimolecular recombination, and longer charge transfer state lifetime than PY-IT in their polymer solar cells with PM6 as polymer donor. Therefore, the devices based on PM6:PG-IT2F demonstrated a high power conversion efficiency of 17.24%, which is one of the highest efficiency reported for the binary all polymer solar cells to date. This work indicates that the synergistic regulation of small molecule acceptor building block and π-bridge linker plays a key role in designing and developing highly efficient polymer acceptors.

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

Statistically-driven Experimental Design to Improve Reference-free Quantification of Small Molecules by Liquid Chromatography-Mass Spectrometry

Non-targeted analysis of small molecules and metabolites in unknown, complex samples using liquid chromatography-tandem mass spectrometry remains challenging. One of the main bottlenecks is the extensive unannotated regions of metabolomics mass spectrometry data, resulting in knowledge gaps. Small molecule annotation in mass spectrometry data has conventionally relied on reference standards and libraries for compound identification and confirmation, which can constrain compound identification to those molecules already known, thus limiting the ability to discover new knowledge and new markers. Retention time prediction can facilitate and expedite unknown compound identification in non-targeted analysis of complex metabolomics samples. Additionally, accurate retention time predictions can also inform sample mixture design for LC-MS/MS analyses. However, current machine learning-based methods for retention time prediction are typically developed for specific chromatographic platforms and are not generalizable across scales. And while technologies and methods to improve reference-free metabolite identification for more comprehensive annotation of unknowns has received much attention, development of the same for quantitation without reference standards has been much more limited, despite its importance in toxicological, environmental, food safety, forensics, and clinical applications. We believe that a reference-free quantitation strategy that exploits mass spectrometry data already collected for reference-free identification can provide much more insight on unknowns, and move the metabolomics field for more complete unknowns characterization. As such, we pursue two efforts to improve upon current state-of-the-art methods in non-targeted analysis: (1) machine learning-based retention time prediction and (2) statistical design of experiments framework for reference-free quantitation. In this work, we develop and demonstrate (1) a generalizable retention time prediction capability across chromatographic conditions and scales, and (2) a statistical design-based framework for response factor contribution elucidation and reference-free quantitation. Evaluation of our retention time prediction model, PrediToR, showed approximately 24% improvement over current models, and we observed approximately 10X improvement in concentration estimation accuracy from our statistical design-based response factor model over a primarily ionization efficiency-based model. We expect that future efforts to improve upon these new capabilities will further advance non-targeted analysis of small molecules towards truly reference-free metabolomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

The METLIN small molecule dataset for machine learning-based retention time prediction

Machine learning has been extensively applied in small molecule analysis to predict a wide range of molecular properties and processes including mass spectrometry fragmentation or chromatographic retention time. However, current approaches for retention time prediction lack sufficient accuracy due to limited available experimental data. Here we introduce the METLIN small molecule retention time (SMRT) dataset, an experimentally acquired reverse-phase chromatography retention time dataset covering up to 80,038 small molecules. To demonstrate the utility of this dataset, we deployed a deep learning model for retention time prediction applied to small molecule annotation. Results showed that in 70% of the cases, the correct molecular identity was ranked among the top 3 candidates based on their predicted retention time. We anticipate that this dataset will enable the community to apply machine learning or first principles strategies to generate better models for retention time prediction.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Separation of isobaric Amino Acids and Small Molecule Metabolites Using Multipass Ion Mobility Analysis

Amino acids along with small molecule metabolites are important biomarkers for the study and detection of diseases that are initially analyzed in untargeted omics fashion. Amino acids and many metabolites are isomeric, and their specific form can have a significant impact on biological function. Chromatographic separation of isomers is challenging, and they cannot be resolved by mass spectrometry alone. Ion mobility is a technique that allows the separation of ions based on their size, shape, and charge. Here we present the results of the separation of isobaric amino acids and small molecule metabolites using a system that allows for multi-pass ion mobility separation which, in turn, enhances the ion mobility resolution of the separation. Amino acid standards and small molecule metabolites commercially available were infused directly into a SELECT SERIES™ Cyclic™ IMS system. Solutions of individual and mixture of the isobaric species were used and the mobility conditions were optimized for multiple passes for each corresponding set of isobaric species. Both ionization polarities and various solvent adducts were tested to provide the best signal intensity and separation. Amino acids such as leucine and isoleucine have previously been separated with ion mobility in a system with lower ion mobility resolution (SYNAPT™ G2 mass spectrometer) rendering about 90% of valley and mobility resolution of around 40 Ω/ΔΩ. With the enhanced ion mobility resolution using the cyclic IMS technique we have obtained almost complete separation of those amino acids rendering a valley of about 10% after 15 passes. For this case, the mobility resolution is around 250 Ω/ΔΩ. Another example is the separation of glucose-6-phosphate from glucose-1-phosphate, and fructose-6phosphate which were separated after 10 passes. For this case, the mobility resolution is around 205 Ω/ΔΩ.

Hernando J Olivos↗
DOE OSTI2020

Charge generation mechanism tuned via film morphology in small molecule bulk-heterojunction photovoltaic materials

Small organic molecules have emerged as promising component materials for organic photovoltaic devices. Compared to most conjugated polymers for the same application, small molecules have unique morphologies that promote electronic processes relevant to organic solar cell (OSC) function that can be significantly different from those of conjugated polymeric materials. Here we investigate constituent loading-dependent effects on OSC morphology and function using the classical fullerene acceptor, PC 61 BM, in a heterojunction blend with the small molecule donor, NDT (thiophene-capped diketopyrrolopyrrole naphthodithiophene). The evolution of active layer morphology as well as exciton speciation and dynamics as a function of the PC 61 BM content are examined in combined structural studies using GIWAXS and spectroscopic studies using transient absorption spectroscopy. We observe evidence for three types of coexisting excitons and details of the interplay between them determines the yield of charge separated states that afford sustained device efficiency.

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

Catalyst design for small molecule activation of energy consequence

This project targets the conversion of ubiquitous small molecules (e.g. NO, CO, H 2 O) into viable precursors to synthetic fuels. Current state of the art catalyst design has not directly targeted transition metal complexes capable of mediating the multi-electron redox processes necessary to reduce the overpotential (energy loss) required achieve efficient activation of small molecule substrates. In this vein, a new strategy has been developed for the assembly of polynuclear architectures; allowing for the construction of tunable polymetallic centers that assemble easily within a pre-organized template (conferring stability, selectivity and tunability) that can effect multi-electron redox processes for reactions. Catalyst development has commenced with the following target design elements: (1) catalysts featuring multiple transition metal ions in the same reaction space to greatly expand accessible molecular redox capabilities; (2) catalysts are assembled in a polynucleating ligand framework that permits control over the cluster morphology as well as the local steric and electronic environment of the transition metal ions within the cluster. The high-tunability of the catalyst composition (metal content) and geometric flexibility has permitted a rigorous assessment of electronic-structure-to-function relationship to be developed, further guiding synthetic efforts to realize more potent catalysts. The numerous permutations possible showcase the high degree of generality to this approach with many synthetic handles to tune redox and reaction chemistry. Trinuclear complexes have been synthesized featuring homo- and hetero-trinuclear cores featuring a variety of first row transition metal ions (Cr→Ni). The molecular clusters have been shown to successfully mediate multi-electron redox processes in a cooperative fashion without requiring strong chemical reductants or oxidants. The reactive molecular complexes are being utilized to activate and breakdown the robust bonds within typical waste stream small molecules (e.g., greenhouse gases) and convert them into value-added commodity chemicals. Ultimately, the catalysts developed by this approach will be required to convert energy acquired via renewable resources (e.g., solar or wind) into synthetic fuels as an energy storage mechanism.

10 SYNTHETIC FUELS↗
DOE OSTI2026

Plutonium(III) versus uranium(III) and samarium(III) in small molecule activation chemistry

We report the PuIII complex, [PuIII(CpMe4)3] (1-Pu), and demonstrate its differences in small molecule reactivity compared to the UIII and SmIII analogs, [UIII(CpMe4)3] (1-U) and [SmIII(CpMe4)3] (1-Sm), respectively. 1-Pu reductively cleaves the small molecule (PhS)2, affording a PuIII complex, [{PuIII(CpMe4)2}2(μ-SPh)2] (2-Pu), while retaining the PuIII center and eliminating (CpMe4)2 as a by-product, a fingerprint of a sterically induced reduction (SIR) reaction. Sm is often used as a surrogate for Pu, but the analogous [SmIII(CpMe4)3], (1-Sm), is unreactive. The (PhS)2 cleavage by 1-U proceeds solely via a metal-based oxidation (i.e., UIII → UIV), to form [UIV(CpMe4)3(SPh)] (3-U). Only 1-U reacts with (PhHN)2, affording the reductive cleavage product, [UIV(CpMe4)3(NHPh)] (4-U). The difference in reactivity of 1-Pu compared to complexes 1-Sm and 1-U was unexpected, and since SIR chemistry can enable complexes to participate in otherwise impossible reductive transformation of substrates, this reinforces the importance of studying small molecule reactivity with the transuranic elements.

Keener, Megan↗
DOE OSTI2020

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of “undruggability” for an intracellular target. Structural studies reveal extensive protein–WDB002 and protein–protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise “undruggable” targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Proton-enabled biomimetic stabilization of small-molecule organic cathode in aqueous zinc-ion batteries

Small-molecule organic cathode materials offer flexible structural design features, high capacity and sustainable production. Nonetheless, the stability decrease due to the high solubility of the electrode materials especially under electrochemical cycling conditions limits their wide-range applications in energy storage technologies. Here we describe a nature-inspired strategy to address cathode stability via introduction of transient vinylogous amide hydrogen bond networks into the small-molecule organic electrode material hexaazatrianthranylene (HATA) embedded quinone (HATAQ). Thanks to the proton-enabled biomimetic mechanism, HATAQ exhibits unparalleled cycling stability, ultra-high capacity and rate capability in aqueous zinc-ion batteries, delivering 492 mA h g -1 at 50 mA g -1 and a reversible capacity of 199 mA h g -1 , corresponding to 99% retention at 20 A g -1 after 1000 cycles.

25 ENERGY STORAGE↗
DOE OSTI2025

Combining MicroED and native mass spectrometry for structural discovery of enzyme–small molecule complexes

With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.

MicroED↗
DOE OSTI2022

Small Molecule Sorting: A Fluorescence Study of Microemulsions

The application of microemulsions to a wide range of industries relies on their ability to solubilize small molecules with vastly different structures. Herein, we use multiple fluorescence techniques to probe ionic (rhodamine 6g, r6g), polar (coumarin 153, c153), nonpolar (diphenylanthracene, DPA), and amphiphilic (laurdan) small molecules in a nonionic, bicontinuous microemulsion of varying hydration. All fluorophores investigated were found to associate with the surfactant region despite their different structures and properties. The hydration of the surfactant layer was found to increase linearly with water addition, but while this initially increases the fluidity of the surfactant layer, fluorescence anisotropy of c153 and r6g indicates a stiffening of the surfactant at water content >60%. This stiffening of the surfactant layer at higher water content correlates with a morphological change in the microemulsion from a bicontinuous structure to droplets. In contrast, the nonpolar DPA shows a change in partitioning as hydration changes, increasing its association with the oil domain. Altogether, these studies elucidate not only the capability of these microemulsions to host a range of small molecules in the surfactant layer with tunable position but also the ability to probe the driving force of bulk structural changes in these heterogeneous fluids.

25 ENERGY STORAGE↗
DOE OSTI2025

An Integral Activity-Based Protein Profiling Method for Higher Throughput Determination of Protein Target Sensitivity to Small Molecules

Activity-based protein profiling (ABPP) is a chemoproteomic technique that uses small molecule probes to label active enzymes selectively and covalently in complex proteomes. Competitive ABPP, which involves treatment of the active proteome with an analyte of interest, is especially powerful for profiling how small molecules impact specific protein activities. Advances in higher throughput workflows have made it possible to generate extensive competitive ABPP data across diverse biological samples, making this approach highly appealing for characterizing shared and unique proteins affected by perturbations such as drug or chemical exposures. To use the competitive ABPP approach effectively to understand potential adverse effects of chemicals of concern (CoC), a wide range of concentrations may be needed, particularly for chemicals that lack potency or toxicity data. In this work, we present an integral competitive ABPP method that enables target sensitivity determination for different organophosphate (OP) pesticides as model toxicants. Using previously developed OP-ABPs, we optimized conditions for tandem mass tag (TMT) multiplexing of ABPP samples and compared conventional competitive ABPP involving samples at discrete paraoxon concentrations to pooled samples across that same concentration range. We then expanded our approach to compare protein target sensitivities toward two additional OP pesticides, chlorpyrifos oxon and malaoxon. The results showed that differences in integral intensities for the pooled competition sample can be used to evaluate the relative sensitivity of specific proteins without increasing the overall number of samples. For 8 CoC concentrations of interest, this strategy reduced the number of TMT plexes and the corresponding number of LC–MS/MS analyses 3-fold. In conclusion, we envision the integral ABPP (IABPP) method will provide a means to screen diverse chemicals more rapidly to identify both high and low sensitivity protein targets.

activity-based probes↗
DOE OSTI2025

Discovery of Signaling Small Molecules (e.g. quorum sensing molecules) from the Microbiome

Microbial communities are shaped through the interactions between their microbial members and the environment (microbe-microbe and host-microbe interactions). Signal transduction pathways in the microbiome are often modulated through the small molecule products of microbial biosynthetic gene clusters (BGCs). Advances in 16S rRNA profiling and shotgun metagenomics have revolutionized our understanding about the microbial composition of various communities and their BGCs. Environmental metagenomes contain thousands of BGCs with uncharacterized small molecule products that potentially play roles in signal transduction. The overarching aim of this proposal was to develop computational techniques for discovering these small molecules and characterizing their bioactivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules

Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promoter function. To facilitate identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.

Biochemistry & Molecular Biology↗
DOE OSTI2024

A Difluoro‐Methoxylated Ending‐Group Asymmetric Small Molecule Acceptor Lead Efficient Binary Organic Photovoltaic Blend

Abstract Developing a new end group for synthesizing asymmetric small molecule acceptors (SMAs) is crucial for achieving high‐performance organic photovoltaics (OPVs). Herein, an asymmetric small molecule acceptor, BTP‐BO‐4FO, featuring a new difluoro‐methoxylated end‐group is reported. Compared to its symmetric counterpart L8‐BO, BTP‐BO‐4FO exhibits an upshifted energy level, larger dipole moment, and more sequential crystallinity. By adopting two representative and widely available solvent additives (1‐chloronaphthalene (CN) and 1,8‐diiodooctane (DIO)), the device based on PM6:BTP‐BO‐4FO (CN) photovoltaic blend demonstrates a power conversion efficiency (PCE) of 18.62% with an excellent open‐circuit voltage (V OC ) of 0.933 V, which surpasses the optimal result of L8‐BO. The PCE of 18.62% realizes the best efficiencies for binary OPVs based on SMAs with asymmetric end groups. A series of investigations reveal that optimized PM6:BTP‐BO‐4FO film demonstrates similar molecular packing motif and fibrillar phase distribution as PM6:L8‐BO (DIO) does, resulting in comparable recombination dynamics, thus, similar fill factor. Besides, it is found PM6:BTP‐BO‐4FO possesses more efficient charge generation, which yields betterV OC –J SC balance. This study provides a new ending group that enables a cutting‐edge efficiency in asymmetric SMA‐based OPVs, enriching the material library and shed light on further design ideas.

Chemistry↗