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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Charge Transport in Solvated Donor–Acceptor Functionalized Peptoids: Molecular Dynamics and Rate Theory

Scalable solar-energy conversion requires photoactive materials that combine the efficiency of natural photosynthetic systems with the stability and processability needed for practical applications. Achieving reliable charge transport in soft, self-assembled organic materials remains challenging, as structural fluctuations and environmental effects strongly influence charge-transfer (CT) rates. Here, we present a broadly applicable computational framework for evaluating CT rates in the condensed phase, combining Fermi’s golden rule rate theory with inputs from all-atom molecular dynamics (MD) simulations and first-principles electronic-structure calculations. The approach does not rely on system-specific parametrization and is applicable to a wide range of soft and disordered materials. We demonstrate the applicability and usefulness of the framework on redox-active peptoids functionalized with iron–porphyrin (Fe–P) complexes, a bioinspired platform with programmable donor–acceptor units and tunable three-dimensional organization. The calculated CT rates exhibit strong sensitivity to molecular conformation, with variations spanning several orders of magnitude. This dependence is shown to arise from the pronounced variation in diabatic electronic coupling with the relative orientations and separations of the Fe–P complexes across the conformational ensemble. The framework provides a consistent route for connecting atomistic structure to CT kinetics in the condensed phase and enables analysis of structure–rate relations in organic semiconducting systems.

Charge transfer↗
DOE OSTI2025

Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction

We describe the design, synthesis, and single-molecule junction conductance of π-electron molecules bearing both radial and linear π-conjugation pathways, whereby cycloparaphenylene (CPP) radial cores are π-extended linearly with aryl alkyne substituents as models for previously reported CPP-arylene ethynylene conjugated polymers. Although radially and linearly conjugated molecules have been studied previously in isolation as junction-bridging molecular electronic units, this is the first study to examine molecules where both topologies are operative. Our results reveal that the presence of radial CPP components within the junction-spanning pathway leads to a reduction in the conductance of the backbone compared to model linear phenyl substituents. Through tight-binding and DFT-based calculations, we attribute this conductance change to intramolecular van der Waals (vdW) interactions between the CPP ring and the junction-spanning arylene-ethynylene molecular backbone. These interactions induce changes in the dihedral angles of the backbone, leading to a reduced overlap of π orbitals within the molecular junction.

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

High-Resolution Imaging of Unstained Polymer Materials

Electron microscopy has played an important role in polymer characterization. Traditionally, electron diffraction is used to study crystalline polymers while transmission electron microscopy is used to study microphase separation in stained block copolymers and other multiphase systems. We describe developments that eliminate the barrier between these two approaches - it is now possible to image polymer crystals with atomic resolution. The focus of this Review is on high-resolution imaging (30 Å and smaller) of unstained polymers. Recent advances in hardware allow for capturing numerous (as many as 105) low-dose images from an unperturbed specimen; beam damage is a significant barrier to high-resolution electron microscopy of polymers. Machine-learning-based software is then used to sort and average the images to retrieve pristine structural information from a collection of noisy images. Acknowledging the heterogeneity in polymer samples prior to averaging is essential. Molecular conformations in a wide range of amphiphilic block copolymers, polymerized ionic liquids, and conjugated polymers can be gleaned from two-dimensional projections (2D), three-dimensional (3D) tomograms, and four-dimensional (4D) scanning transmission electron microscopy (STEM) data sets where 2D diffraction patterns are taken as a function of position. Some methods such as phase contrast STEM have been used to image closely related materials such as metal-organic frameworks but not polymers. With improvements in hardware and software, such methods may soon be applied to polymers. Our goal is to provide a comprehensive understanding of the strategies toward the high-resolution imaging of radiation sensitive polymer materials at different length scales.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay

The papain-like protease (PL pro ) of SARS-CoV-2 is a validated antiviral drug target. Through a fluorescence resonance energy transfer-based high-throughput screening and subsequent lead optimization, we identified several PL pro inhibitors including Jun9-72-2 and Jun9-75-4 with improved enzymatic inhibition and antiviral activity compared to GRL0617, which was reported as a SARS-CoV PL pro inhibitor. Significantly, we developed a cell-based FlipGFP assay that can be applied to predict the cellular antiviral activity of PL pro inhibitors in the BSL-2 setting. X-ray crystal structure of PL pro in complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to a more closed conformation. Molecular dynamics simulations showed that Jun9-72-2 and Jun9-75-4 engaged in more extensive interactions than GRL0617. Overall, the PL pro inhibitors identified in this study represent promising candidates for further development as SARS-CoV-2 antivirals, and the FlipGFP-PL pro assay is a suitable surrogate for screening PL pro inhibitors in the BSL-2 setting.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Mechanical-Bond-Enabled Highly Efficient Charge Separation in a Light-Harvesting Hetero[2]Catenane

Photodriven charge separation is a key process for converting solar energy into chemical energy. However, it remains a challenge to develop artificial light-harvesting materials that can simultaneously achieve ultrafast charge separation and a long-lived charge-separated state with low energy loss. In contrast to conventional strategies based on covalent or noncovalent interactions, we employed a mechanical bond to forcibly assemble two strongly electron-deficient cationic chromophores (TTzBo x4+ and PDI-C 2+ ), which have very similar reduction potentials and exhibit limited noncovalent interactions, into a hetero[2]catenane (TTzPCat 6+ ). This design provides efficient π electronic couplings, enabling ultrafast charge separation (<2.3 ps) even with a low driving force (|ΔG CS | ≈ 160 meV). Furthermore, the adaptive molecular conformation of TTzPCat 6+ , in combination with the Marcus inverted region effect, successfully prolongs the charge-separated state lifetime (k CS /k CR > 1000), surpassing the conventional trade-off between driving force and charge separation efficiency in heterogeneous donor–acceptor systems. The photocatalytic system based on TTzPCat 6+ exhibits an over 2-fold enhancement in selective oxidation of aryl sulfides under mild conditions, demonstrating the potential of mechanical bonding for preparing photocatalytic materials. This investigation not only highlights a strategy for achieving highly efficient charge separation with low energy loss but also offers fresh insights into developing efficient solar energy conversion systems.

Charge transfer↗
DOE OSTI2023

Interplay of molecular dynamics and radiative decay of a TADF emitter in a glass-forming liquid

Herein we investigate the role of molecular dynamics in the luminescent properties of a prototypical thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, in solution using a combination of temperature dependent time-resolved photoluminescence and absorption spectroscopies. We use a glass forming liquid, 2-methylfuran, to introduce an abrupt change in the temperature dependent diffusion dynamics of the solvent and examine the influence this has on the emission intensity of NAI-DMAC molecules. Comparison of experiment with first principles molecular dynamics simulations reveals that the emission intensity of NAI-DMAC molecules follows the temperature-dependent self-diffusion dynamics of the solvent. A marked reduction of emission intensity is observed as the temperature decreases toward the glass transition because the rate at which NAI-DMAC molecules can access emissive molecular conformations is greatly reduced. Below the glass transition, the diffusion dynamics of the solvent changes more slowly with temperature, which causes the emission intensity to decrease more slowly as well. The combination of experiment and computation suggests a pathway by which TADF emitters may transiently access a distribution of conformational states and avoid the need for an average conformation that strikes a balance between lower singlet–triplet energy splittings versus higher emission probabilities.

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

The primary gas phase hydration shell of hydroxide

The number of water molecules in hydroxide’s primary hydration shell has been long debated to be three from the interpretation of experimental data and four from theoretical studies. Here, we provide direct evidence for the presence of a fourth water molecule in hydroxide’s primary hydration shell from a combined study based on high-resolution cryogenic experimental photoelectron spectroscopy and high-level quantum chemical computations. Well-defined spectra of OH - (H 2 O) n clusters (n = 2 to 5) yield accurate electron binding energies, which are, in turn, used as key signatures of the underlying molecular conformations. Although the smaller OH - (H 2 O) 3 and OH - (H 2 O) 4 clusters adopt close-lying conformations with similar electron binding energies that are hard to distinguish, the OH - (H 2 O) 5 cluster clearly has a predominant conformation with a four-coordinated hydroxide binding motif, a finding that unambiguously determines the gas phase coordination number of hydroxide to be four.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Stochastic equilibrium Raman spectroscopy (STERS)

In this manuscript, we propose a new method for cavity- and surface-enhanced Raman spectroscopy (SERS) with improved temporal resolution in the measurement of stochastic Raman spectral fluctuations. Our approach combines Fourier spectroscopy and photon correlation to decouple the integration time from the temporal resolution. Using statistical optics Monte Carlo simulations, we establish the relationship between time resolution and Raman signal strength, revealing that typical Raman spectral fluctuations, commensurate with molecular conformational dynamics, can theoretically be resolved on micro- to millisecond timescales. The method can further extract average single-molecule dynamics from small sub-ensembles, thereby potentially mitigating challenges in achieving strictly single-molecule isolation on SERS substrates.

Cobb-Bruno, Colburn [University of California, Ber↗
NASA NTRS1998

X-Ray Diffraction Analysis of NLO Crystals: Traditional Applications and More New Opportunities

Single crystal X-ray diffraction analysis is one of the more important methods for the molecular and crystal structure determination of matter and therefore it has a great importance in material science including design and engineering of different compounds with non-linear optical (NLO) properties. It was shown in our previous publications that this method provides unique information about molecular structure of NLO compounds, their crystal symmetry and crystal packing arrays, molecular conformation and geometries and many other structural and electronic characteristics that are important for understanding the nature of NLO properties of solids. A very new application of the X-ray diffraction method is related to analysis of the electron density distribution p(r) in crystals and some of its characteristics (atomic and group charges, dipole and higher multipole moments, etc.), that may be obtained directly form the diffraction measurements. In the present work, we will discuss our preliminary low temperature high-resolution X-ray data for the m-nitroaniline (mNA) single crystal (VI). This is one of the "classical" organic NLO materials and electron density distribution analysis in this simple compound has a great scientific interest.

Antipin, Mikhail Yu.↗
NASA NTRS2005

Protein Crystallization

Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

Chernov, Alexander A.↗
DOE OSTI2022

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

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

Polarized Resonant X-ray Scattering to Measure Molecular Orientation and Conformation in Organic Nanostructures

The ordering of organic (carbon-based) molecules into nanostructures drives useful materials properties for applications such as organic light emitting diodes, flexible batteries, and polymer nanocarriers. However, there is a current lack of techniques to measure this ordering. X-ray scattering techniques involving molecular resonances have shown promise in identifying molecular types, locations, and orientation. However, resonant soft X-ray scattering (RSoXS) techniques have not been developed even lacking basic optical models. The objectives achieved by this research were the development of methods, models, and analysis techniques that harness these resonant phenomena in X-ray scattering measurements to quantitatively probe ordering of organic molecules within devices and nanostructures. This award resulted in 11 peer reviewed publications with two others soon to be submitted. New physical models for X-ray scattering that accurately describe these complex molecular resonances enable measurements of how molecules assemble, orient and conform at the nanometer scale. These new techniques were applied to both organic electronic devices and aqueous nanoparticles being developed for hydrocarbon sequestration. This new measurement capability will enable characterization of structure-property relationships that lead to disruptive technologies of printable, stretchable, and biocompatible devices based on organic materials.

14 SOLAR ENERGY↗
NASA NTRS1990

Molecular arrangements and conformations of liquid n-tridecane chains confined between two hard walls

Monte Carlo simulations based on united CH2 atoms linked with fixed bond lengths and angles, and continuously varying torsional angles subject to appropriate interaction energies, were used to study liquid n-tridecane chains confined between two parallel hard walls with 5 mm separation. The molecules located in the central region are noted to be in very close agreement with ideal unperturbed chains. Nearly all the chain units in the first segmental layer adjacent to the walls belong to two-dimensional chains, and exhibit considerable orientational correlations between neighboring segments of different chains.

Vacatello, Michele↗
DOE OSTI2025

Functional protein mining with conformal guarantees

Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model. Our method (1) lets users select many biologically-relevant loss metrics (i.e. false discovery rate) and assigns reliable functional probabilities for annotating genes of unknown function; (2) achieves state-of-the-art performance in enzyme classification without training new models; and (3) robustly and rapidly pre-filters proteins for computationally intensive structural alignment algorithms. Our framework enhances the reliability of protein homology detection and enables the discovery of uncharacterized proteins with likely desirable functional properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations

Abstract Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE‐allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen‐binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIαtransgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%–89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIαtransgenic mouse model. In summary, the structures of Can f 1‐hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Amphiphile conformation impacts aggregate morphology and solution structure across multiple lengthscales

Although the self-assembly of amphiphiles is well-studied in aqueous solutions, much less is understood about the fundamental driving forces and structure property relationships in non-polar media. In recent work [Journal of Physical Chemistry B, 2020, 124, 10822.] the authors have studied a series of malonomide-based amphiphiles that are relevant to liquid-liquid extraction. That work demonstrated that aggregation is largely driven by local dipole-dipole interactions between molecules. Here, we build upon this observation to develop a more detailed understanding of how the balance of dipole-dipole interactions (controlled by conformation) and molecular architecture influences the morphology of the aggregates across lengthscales. Using constrained molecular dynamics about key degrees of freedom, we demonstrate that the conformation of N,N-dimethyl,N,N-dioctylhexylethoxy malonamide (DMDOHEMA) and N,N-dimethyl,N,N-dibutyltetradecyl malonamide (DMDBTDMA) has a significant impact upon self-association - where appropriate conformational sampling is essential. To quantify the aggregate morphology, several graph theoretic and persistent homology based properties are determined. The former examines the patterns of intermolecular interactions within clusters, while the latter examines the 3-dimensional spatial distribution. Based upon these analyses, we find that the morphology of aggregates, particularly at higher malonamide concentration, depends on a balance of dipole alignment and alkyl tail sterics. Dipole alignment encourages linear patterns of the intermolecular interactions within aggregates, while the alkyl tail steric interactions between the malonamide result in noticeably less linear aggregates for DMDOHEMA than DMDBTDMA. This is reflected in the spatial distribution, where more holes or voids exist between extractants within the DMDOHEMA that distribute within the solution in more of a "swiss cheese" arrangement as opposed to the more filamentous distribution of DMBDTDMA. This study links conformation and molecular structure to the morphology of amphiphile assemblies, and serves as a basis for ongoing study of multicomponent amphiphile solutions with polar and other solutes, and how these impact aggregation phenomena.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗