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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Ship-in-a-Bottle Synthesis of High Concentration of N2 Molecules in a Cage-Structured Electride

We report the formation of neutral nitrogen molecules in the cages of [Ca12Al14O32]2+ (C12A7) framework compensated by extra-framework anions. NH3 treatment of C12A7 electride (C12A7:e–) at 800 °C leads to the formation of N2 and NH2– species in the C12A7 cages. N2 and NHx species in the cages are identified using the Raman spectroscopy of 14NH3 and 15NH3-treated C12A7:e–. The concentration of H and N in the C12A7 cages after NH3 treatment is ~1021 cm–3. We propose a two-step mechanism, supported by density functional theory (DFT) modeling, of N2 incorporation into the C12A7 cages: incorporation of NH2– formed from decomposition of NH3 at C12A7:e– surface followed by the NH2- species reacting to form N2 molecules. Encapsulation of neutral molecules, as opposed to negatively charged species reported in C12A7 previously, offers new opportunities for trapping and storing gaseous substances in nano-porous materials.

Nakao, Takuya↗
DOE OSTI2024

Coercive Fields Exceeding 30 T in the Mixed-Valence Single-Molecule Magnet (Cp iPr5 ) 2 Ho 2 I 3

Mixed-valence dilanthanide complexes of the type (Cp iPr5 ) 2 Ln 2 I 3 (Cp iPr5 = pentaisopropylcyclopentadienyl; Ln = Gd, Tb, Dy) featuring a direct Ln–Ln σ-bonding interaction have been shown to exhibit well-isolated high-spin ground states and, in the case of the Tb and Dy variants, a strong axial magnetic anisotropy that gives rise to a large magnetic coercivity. Here, we report the synthesis and characterization of two new mixed-valence dilanthanide compounds in this series, (Cp iPr5 ) 2 Ln 2 I 3 (1-Ln; Ln = Ho, Er). Both compounds feature a Ln–Ln bonding interaction, the first such interaction in any molecular compounds of Ho or Er. Like the Tb and Dy congeners, both complexes exhibit high-spin ground states arising from strong spin–spin coupling between the lanthanide 4f electrons and a single σ-type lanthanide–lanthanide bonding electron. Beyond these similarities, however, the magnetic properties of the two compounds diverge. In particular, 1-Er does not exhibit observable magnetic blocking or slow magnetic relaxation, while 1-Ho exhibits magnetic blocking below 28 K, which is the highest temperature among Ho-based single-molecule magnets, and a spin reversal barrier of 556(4) cm –1 . Additionally, variable-field magnetization data collected for 1-Ho reveal a coercive field of greater than 32 T below 8 K, more than 6-fold higher than observed for the bulk magnets SmCo 5 and Nd 2 Fe 14 B, and the highest coercive field reported to date for any single-molecule magnet or molecule-based magnetic material. Multiconfigurational calculations, supported by far-infrared magnetospectroscopy data, reveal that the stark differences in magnetic properties of 1-Ho and 1-Er arise from differences in the local magnetic anisotropy of the lanthanide centers.

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

An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering

The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1—autoinhibited for chromatin binding—that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Small molecule BLVRB redox inhibitor promotes megakaryocytopoiesis and stress thrombopoiesis in vivo

Biliverdin IXβ reductase (BLVRB) is an NADPH-dependent enzyme previously implicated in a redox-regulated mechanism of thrombopoiesis distinct from the thrombopoietin (TPO)/c-MPL axis. Here, we apply computational modeling to inform molecule design, followed by de novo syntheses and screening of unique small molecules retaining the capacity for selective BLVRB inhibition as a novel platelet-enhancing strategy. Two distinct classes of molecules are identified, and NMR spectroscopy and co-crystallization studies confirm binding modes within the BLVRB active site and ring stacking between the nicotinamide moiety of the NADP+ cofactor. A diazabicyclo derivative displaying minimal off-target promiscuity and excellent bioavailability characteristics promotes megakaryocyte speciation in biphenotypic (erythro/megakaryocyte) cellular models and synergizes with TPO-dependent megakaryocyte formation in hematopoietic stem cells. Upon oral delivery into mice, this inhibitor expands platelet recovery in stress thrombopoietic models with no adverse effects. In this work, we identify and validate a cellular redox inhibitor retaining the potential to selectively promote megakaryocytopoiesis and enhance stress-associated platelet formation in vivo distinct from TPO receptor agonists.

36 MATERIALS SCIENCE↗
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 OSTI2024

Decoupling excitons from high-frequency vibrations in organic molecules

The coupling of excitons in π-conjugated molecules to high-frequency vibrational modes, particularly carbon–carbon stretch modes (1,000–1,600 cm -1 ) has been thought to be unavoidable. These high-frequency modes accelerate non-radiative losses and limit the performance of light-emitting diodes, fluorescent biomarkers and photovoltaic devices. Here, by combining broadband impulsive vibrational spectroscopy, first-principles modelling and synthetic chemistry, we explore exciton–vibration coupling in a range of π-conjugated molecules. We uncover two design rules that decouple excitons from high-frequency vibrations. First, when the exciton wavefunction has a substantial charge-transfer character with spatially disjoint electron and hole densities, we find that high-frequency modes can be localized to either the donor or acceptor moiety, so that they do not significantly perturb the exciton energy or its spatial distribution. Second, it is possible to select materials such that the participating molecular orbitals have a symmetry-imposed non-bonding character and are, thus, decoupled from the high-frequency vibrational modes that modulate the π-bond order. We exemplify both these design rules by creating a series of spin radical systems that have very efficient near-infrared emission (680–800 nm) from charge-transfer excitons. We show that these systems have substantial coupling to vibrational modes only below 250 cm -1 , frequencies that are too low to allow fast non-radiative decay. This enables non-radiative decay rates to be suppressed by nearly two orders of magnitude in comparison to π-conjugated molecules with similar bandgaps. Our results show that losses due to coupling to high-frequency modes need not be a fundamental property of these systems.

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

Discovery of potent small-molecule inhibitors of lipoprotein(a) formation

Lipoprotein(a) (Lp(a)), an independent, causal cardiovascular risk factor, is a lipoprotein particle that is formed by the interaction of a low-density lipoprotein (LDL) particle and apolipoprotein(a) (apo(a)). Apo(a) first binds to lysine residues of apolipoprotein B-100 (apoB-100) on LDL through the Kringle IV (K IV ) 7 and 8 domains, before a disulfide bond forms between apo(a) and apoB-100 to create Lp(a). Here we show that the first step of Lp(a) formation can be inhibited through small-molecule interactions with apo(a) K IV 7–8. We identify compounds that bind to apo(a) K IV 7–8, and, through chemical optimization and further application of multivalency, we create compounds with subnanomolar potency that inhibit the formation of Lp(a). Oral doses of prototype compounds and a potent, multivalent disruptor, LY3473329 (muvalaplin), reduced the levels of Lp(a) in transgenic mice and in cynomolgus monkeys. Although multivalent molecules bind to the Kringle domains of rat plasminogen and reduce plasmin activity, species-selective differences in plasminogen sequences suggest that inhibitor molecules will reduce the levels of Lp(a), but not those of plasminogen, in humans. These data support the clinical development of LY3473329—which is already in phase 2 studies—as a potent and specific orally administered agent for reducing the levels of Lp(a).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules

We introduce QM7-X, a comprehensive dataset of 42 physicochemical properties for ≈4.2 million equilibrium and non-equilibrium structures of small organic molecules with up to seven non-hydrogen (C, N, O, S, Cl) atoms. To span this fundamentally important region of chemical compound space (CCS), QM7-X includes an exhaustive sampling of (meta-)stable equilibrium structures—comprised of constitutional/structural isomers and stereoisomers, e.g., enantiomers and diastereomers (including cis-/trans- and conformational isomers)—as well as 100 non-equilibrium structural variations thereof to reach a total of ≈4.2 million molecular structures. Computed at the tightly converged quantum-mechanical PBE0+MBD level of theory, QM7-X contains global (molecular) and local (atom-in-a-molecule) properties ranging from ground state quantities (such as atomization energies and dipole moments) to response quantities (such as polarizability tensors and dispersion coefficients). By providing a systematic, extensive, and tightly-converged dataset of quantum-mechanically computed physicochemical properties, we expect that QM7-X will play a critical role in the development of next-generation machine-learning based models for exploring greater swaths of CCS and performing in silico design of molecules with targeted properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1

Acid-sensing ion channels (ASICs) are proton-gated cation channels critical for neuronal functions. Studies of ASIC1, a major ASIC isoform and proton sensor, have identified acidic pocket, an extracellular region enriched in acidic residues, as a key participant in channel gating. While binding to this region by the venom peptide psalmotoxin modulates channel gating, molecular and structural mechanisms of ASIC gating modulation by small molecules are poorly understood. Here, combining functional, crystallographic, computational and mutational approaches, we show that two structurally distinct small molecules potently and allosterically inhibit channel activation and desensitization by binding at the acidic pocket and stabilizing the closed state of rat/chicken ASIC1. Our work identifies a previously unidentified binding site, elucidates a molecular mechanism of small molecule modulation of ASIC gating, and demonstrates directly the structural basis of such modulation, providing mechanistic and structural insight into ASIC gating, modulation and therapeutic targeting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Excited state dynamics of azanaphthalenes reveal opportunities for the rational design of photoactive molecules

Abstract Various photoactive molecules contain motifs built on aza-aromatic heterocycles, although a detailed understanding of the excited state photophysics and photochemistry in such systems is not fully developed. To help address this issue, the non-adiabatic dynamics operating in azanaphthalenes under hexane solvation was studied following 267 nm excitation using ultrafast transient absorption spectroscopy. Specifically, the species quinoline, isoquinoline, quinazoline, quinoxaline, 1,6-naphthyridine, and 1,8-naphthyridine were investigated, providing a systematic variation in the relative positioning of nitrogen heteroatom centres within a bicyclic aromatic structure. Our results indicate considerable differences in excited state lifetimes, and in the propensity for intersystem crossingvsinternal conversion across the molecular series. The overall pattern of behaviour can be explained in terms of potential energy barriers and spin-orbit coupling effects, as demonstrated by extensive quantum chemistry calculations undertaken at the SCS-ADC(2) level of theory. The fact that quantum chemistry calculations can achieve such detailed and nuanced agreement with experimental data across a full set of six molecules exhibiting subtle variations in their composition provides an excellent example of the current state-of-the-art and is indicative of future opportunities for rational design of photoactive molecules.

Chemistry↗
DOE OSTI2024

Rotation in attosecond vibronic coherence spectroscopy for molecules

Abstract Excitation or ionization of a molecule by ultrafast laser pulses can create a superposition of electronic states, whose dynamics is influenced by the interplay of electronic coherence and nuclear motion, resulting in charge migration and possibly charge transfer. Probing the vibronic coherence is therefore vital to monitoring electronic dynamics and controlling chemical reactivity, as recently demonstrated in molecules via attosecond transient absorption spectroscopy (ATAS). However, theories supporting the interpretation of ATAS experiments neglect the effects of molecular rotation, often leading to inaccurate interpretation of experimental data. Here, we develop a comprehensive theory for ATAS of molecules encompassing the entire pump-probe process. Applying the theory to N 2 , we demonstrate that the emergence of coherent signals critically depends on the consideration of molecular rotation. This work contributes to close the gap between theory and ATAS experiments, paving the way for monitoring electronic motion and controlling chemical reactivity in diverse molecular systems.

Physics↗
DOE OSTI2026

Radioactive molecules as laboratories of fundamental physics

Radioactive molecules provide a new platform in the search for new physics, at energy scales complementary to those probed by high-energy particle colliders. Here, by combining enhancements from nuclear properties with the sensitivity and control offered by molecular structure, experiments with radioactive molecules offer great reach in the search for physics beyond the standard model. Progress in this field is being driven by advances in the production and control of radioactive molecules, alongside the development of new experimental tools and theoretical techniques. In this Perspective, we discuss the current status and future prospects of this rapidly developing, interdisciplinary field at the intersection of nuclear physics, atomic and molecular physics and particle physics.

Jadbabaie, A. [Massachusetts Institute of Technolo↗
DOE OSTI2020

Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study

Splitting of molecular hydrogen (H 2 ) into bridging and terminal hydrides is a common step in transition metal chemistry. In this paper, we propose a novel organometallic platform for cleavage of multiple H 2 molecules, which combines metal centers capable of stabilizing multiple oxidation states, and ligands bearing positioned pendant basic groups. Using quantum chemical modeling, we show that low-valent, early transition metal diniobium(II) complexes with diphosphine ligands featuring pendant amines can favorably uptake up to 8 hydrogen atoms, and that the energetics are favored by the formation of intramolecular dihydrogen bonds. This result suggests new possible strategies for the development of hydrogen scavenger molecules that are able to perform reversible splitting of multiple H 2 molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2021

Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model on electrostatic interaction, the nonpolar interaction contribution of solvent and the conformational entropy of solute in solvation free energy, three data sets with implicit or explicit water solvent models, and contribution of conformational entropy of solute are tested. We demonstrate that our ML model can predict the solvation free energy of molecules at chemical accuracy with a mean absolute error of less than 1 kcal/mol for subsets of the QM9 dataset and the Freesolv database. To solve the general data scarcity problem for a graph-based ML model, we propose a dimension reduction algorithm based on the distance between molecular graphs, which can be used to examine the diversity of the molecular data set. It provides a promising way to build a minimum training set to improve prediction for certain test sets where the space of molecular structures is predetermined.

25 ENERGY STORAGE↗
DOE OSTI2024

Confinement-induced clustering of H 2 and CO 2 gas molecules in hydrated nanopores

Gas molecule clustering within nanopores holds significance in the fields of nanofluidics, biology, gas adsorption/desorption, and geological gas storage. However, the intricate roles of nanoconfinement and surface chemistry that govern the formation of gas clusters remain inadequately explored. In this study, through free energy calculation in molecular simulations, we systematically compared the tendencies of H 2 and CO 2 molecules to aggregate within hydrated hydrophobic pyrophyllite and hydrophilic gibbsite nanopores. The results indicate that nanoconfinement enhances gas dimer formation in the nanopores, irrespective of surface chemistry. However, surface hydrophilicity prohibits the formation of gas clusters larger than dimers, while large gas clusters form easily in hydrophobic nanopores. Despite H 2 and CO 2 both being non-polar, the larger quadrupole moment of CO 2 leads to a stronger preference for dimer/cluster formation compared to H 2 . Here, our results also indicate that gases prefer to enter the nanopores as individual molecules, but exit the nanopores as dimers/clusters. This investigation provides a mechanistic understanding of gas cluster formation within nanopores, which is relevant to various applications, including geological gas storage.

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

Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa

Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialylated glycans displayed on human platelets. Despite their important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel small molecule effectors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. The screening successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to Hsa. Furthermore, hierarchical clustering based on the MACCS fingerprints showed that eight of these small molecules do not share a common scaffold with the native ligand. This study indicates that SRR family of adhesin proteins can be inhibited by diverse small molecules and thus prevent the interaction of the protein with the sialoglycans. This opens new avenues for discovering potential drugs against IE.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

All-electron ab initio Bethe-Salpeter equation approach to neutral excitations in molecules with numeric atom-centered orbitals

The Bethe-Salpeter equation (BSE) based on GW quasiparticle levels is a successful approach for calculating the optical gaps and spectra of solids and also for predicting the neutral excitations of small molecules. We here present an all-electron implementation of the GW+BSE formalism for molecules, using numeric atom-centered orbital (NAO) basis sets. We present benchmarks for low-lying excitation energies for a set of small organic molecules, denoted in the literature as “Thiel’s set.” Literature reference data based on Gaussian-type orbitals are reproduced to about one millielectron-volt precision for the molecular benchmark set, when using the same GW quasiparticle energies and basis sets as the input to the BSE calculations. For valence correlation consistent NAO basis sets, as well as for standard NAO basis sets for ground state density-functional theory with extended augmentation functions, we demonstrate excellent convergence of the predicted low-lying excitations to the complete basis set limit. A simple and affordable augmented NAO basis set denoted “tier2+aug2” is recommended as a particularly efficient formulation for production calculations. We finally demonstrate that the same convergence properties also apply to linear-response time-dependent density functional theory within the NAO formalism.

Liu, Chi↗