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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Encapsulation Enhances the Quantum Coherence of a Solid‐State Molecular Spin Qubit

Spins within molecules benefit from the atomistic control of synthetic chemistry for the realization of qubits. One advantage is that the quantum superpositions of the spin states encoding the qubit can be coherently manipulated using electromagnetic radiation. The main challenge is the fragility of these superpositions when qubits are to partake of solid-state devices. We address this issue with a supramolecular approach for protecting molecular spin qubits against decoherence. The molecular qubit [Cr(ox)3]3- has been encapsulated inside the diamagnetic triple-stranded helicate [Zn2L3]4+ (L is a bis-pyrazolylpyridine ligand). The quantum coherence of the protected qubit is then analyzed with pulsed EPR spectroscopy and compared with the unprotected qubit, both in solution and in the solid state. Crucially, the spin-spin relaxation in the solid state has been examined within diamagnetic crystal lattices of the isostructural ([Al(ox)3]@[Zn2L3])+ or [Al(ox)3]3- assemblies, respectively, doped with the Cr3+ qubit in two different (<10%) concentrations. The study unveils a surprising increase of the phase memory time of the qubit upon encapsulation only in the solid. Spin-lattice relaxation times also exhibit a significant enhancement, as established from inversion recovery pulse sequences and from slow relaxation of the magnetization of the protected qubit, not featured by the free qubit.

Swain, Abinash↗
DOE OSTI2021

Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen

A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth-inhibiting, lipid-derived plant hormone and mutagenized this line. Students in the CURE cultured the mutagenized plant population and selected and characterized suppressor mutants. They learned to observe phenotypes related to the biosynthesis and perception of the plant hormone and explored the genetic and biochemical basis of these phenotypes. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they were able to translate this knowledge into practice and develop scientific arguments. This CURE was a successful collaboration between the teaching lab and the research lab. It benefited both parties as the students had a real-life, deep learning experience in scientific methodology, while the research lab gathered data and materials for further studies

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

A Hybrid Structural Method for Investigating Low Molecular Weight Oligomeric Structures of Amyloid Beta

Spurred in part by the failure of recent therapeutics targeting amyloid β plaques in Alzheimer's Disease (AD), attention is increasingly turning to the oligomeric forms of this peptide that form early in the aggregation process. However, while numerous amyloid β fibril structures have been characterized, primarily by NMR spectroscopy and cryo-EM, obtaining structural information on the low molecular weight forms of amyloid β that presumably precede and/or seed fibril formation has proved challenging. Furthermore, these transient forms are heterogeneous, and depend heavily on experimental conditions such as buffer, temperature, concentration, and degree of quiescence during measurement. Here, we present the concept for a new approach to delineating structural features of early-stage low molecular weight amyloid β oligomers, using a solvent accessibility assay in conjunction with simultaneous fluorescence measurements.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Metal Phosphide Nanoparticles Generated via a Molecular Precursor Route for Hydrotreatment of Methyl Laurate

Transition metal phosphide nanoparticles supported on silica were used as catalysts to investigate the hydrodeoxygenation of methyl laurate (used as a model compound for vegetable oils). Ni 2 P, Ni 1 Mo 1 P, and Ni 1.6 Mo 0.4 P were synthesized using a molecular precursor route. The nanoparticles were added to the silica support without any changes in their structure or particle size. As a reference and for comparison, MoP/SiO 2 was also prepared by the phosphite method. The prepared catalysts were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, transmission electron microscopy, and chemical analysis. A higher conversion is reached with the MoP/SiO 2 monometallic catalyst, close to that with Ni 1 Mo 1 P/SiO 2 . However, this observation is misleading because the differences in dispersion obscure the result that the intrinsic activity (turnover frequency) of the bimetallic catalyst, prepared by a molecular precursor route, is significantly higher than that of the monometallic catalyst, prepared by the phosphite route, revealing a synergistic effect on the catalytic activity due to the formation of the bimetallic phosphide.

09 BIOMASS FUELS↗
DOE OSTI2021

Molecularly Functionalized Electrodes for Efficient Electrochemical Water Remediation

Here, the development and investigation of materials that leverage unique interfacial effects on electronic structure and redox chemistry are likely to play an outstanding role in advanced technologies for wastewater treatment. Here, the use of surface functionalization of metal oxides with a Ru(II)poly(pyridyl) complex was reported as a way to create hybrid assemblies with optimized electrochemical performance for water remediation, superior to those that could be achieved with the molecular catalyst or metal-oxide electrodes used individually. Mechanistic analysis demonstrated that the molecularly functionalized electrodes could suppress the formation of hydroxyl radicals (i. e., the dominant remediation pathway for bare metal-oxide electrodes), allowing the water remediation to proceed through the highly oxidizing Ru 3+ ions in the surface-bound complexes. Furthermore, the underlying metal-oxide substrates played a crucial role in altering the electronic structure and electrochemical properties of the surface-bound catalyst, such that the competing side reaction (i. e., water splitting) was largely inhibited.

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

Electrolyte Engineering Stabilizes Photoanodes Decorated with Molecular Catalysts

Molecular catalysts are promising oxygen evolution promoters in conjunction with photoanodes for solar water splitting. Maintaining the stability of both photoabsorber and cocatalyst is still a prime challenge, with many efforts tackling this issue through sophisticated material designs. Such approaches often mask the importance of the electrode-electrolyte interface and overlook easily tunable system parameters, such as the electrolyte environment, to improve efficiency. We provide a systematic study on the activity-stability relationship of a prominent Fe 2 O 3 photoanode modified with Ir molecular catalysts using in situ mass spectroscopy. After gaining detailed insights into the dissolution behavior of the Ir cocatalyst, a comprehensive pH study is conducted to probe the impact of the electrolyte on the performance. An inverse trend in Fe and Ir stability is found, with the best activity-stability synergy obtained at pH 9.7. The results bring awareness to the overall photostability and electrolyte engineering when advancing catalysts for solar water splitting.

14 SOLAR ENERGY↗
DOE OSTI2024

On the performance of composite schemes in determining equilibrium molecular structures

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, in this study, the performance of two different ab initio composite approaches for obtaining equilibrium structures, “energy scheme” and “geometry scheme,” is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

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

Multi‐Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi

Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time‐, substrate‐ and species‐specific responses at multi‐omics levels for the tested fungi, highlighting species‐specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings improves our understanding of complex molecular networks underlying FPBC and fungal ecological roles, offering novel insights that can guide future genetic engineering of fungi for valorization of agriculture waste into value‐added bioproducts.

CAZy↗
DOE OSTI2020

Molecular subtyping reveals immune alterations in IDH wild‐type lower‐grade diffuse glioma

Abstract Isocitrate dehydrogenase ( IDH ) wild‐type diffuse lower‐grade glioma (LGG) is usually associated with poor outcome, but there have been disputes over its clinical outcome and classification. We present here a robust gene expression‐based molecular classification of IDH wild‐type diffuse LGG into two subtypes with distinct biological and clinical features. A discovery cohort of 49 IDH wild‐type diffuse LGGs from the Chinese Glioma Genome Atlas (CGGA) was subjected to clustering and function analysis. Seventy‐three tumors from The Cancer Genome Atlas (TCGA) were used to validate our findings. Consensus clustering of transcriptional data uncovered concordant classification of two robust and prognostically significant subtypes of IDH wild‐type LGG. Subtype 1, associated with poorer outcomes, was characterized by significantly higher immune and cytolytic scores, M2 macrophages, and up‐regulation of immune exhaustion markers, while Subtype 2, which had elevated lymphocytes and plasma cells, showed relatively favorable survival. Somatic alteration analysis revealed that Subtype 1 showed more frequently deleted regions, such as the locus of CDKN2A / CDKN2B , DMRTA1 , C9orf53 , and MTAP . Furthermore, we developed and validated a five‐gene signature for better application of this acquired stratification. Our data demonstrate the biological and prognostic heterogeneity within IDH wild‐type diffuse LGGs and deepen our molecular understandi‐g of this tumor entity. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Wu, Fan↗
DOE OSTI2024

Ultra–high molecular weight polyethylene micro–ribbon fibers gel spun using orange terpenes

Toxic, hazardous petrochemical solvents are commonly used for industrial-scale ultra-high molecular weight polyethylene (UHMWPE) fiber production, but orange terpenes, a byproduct of orange fruit production, present a bio-derived, sustainable alternative. In this work, fine UHMWPE fibers were spun using orange terpenes as the spin solvent, hot-drawn at a draw ratio of 5:1, investigated for their morphology, microstructure, and thermal and mechanical properties. The resulting fibers exhibited a flat, micro-ribbon cross-section, which is highly desirable for achieving high fiber volume fractions in UHMWPE-fiber reinforced composites. After drawing, the fibers possessed 4× greater breaking tenacity than any previously published studies on UHMWPE fibers spun using orange terpenes with a tenacity of 8.6 cN/dtex and tensile modulus of 229.2 cN/dtex. Microstructural analysis via differential scanning calorimetry and X-ray diffraction revealed that the hot drawing process significantly increased molecular orientation, but crystallinity decreased due to crystallite melting during drawing. Therefore, the mechanical properties of these fibers may be significantly improved with optimization of the fiber drawing process. As a work, this work establishes the strong potential of orange terpenes as an environmentally-friendly alternative solvent for UHMWPE gel spinning and sets a foundation for future parametric optimization of the spinning and drawing of these fibers.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Sorption-induced polymer rearrangement: approaches from molecular modeling

With the growing need for chemical separation and chemical storage solutions, polymeric adsorbents have emerged as a promising class of candidate materials because of their potentially tunable sorption properties, membrane structure and relatively cost consciousness. Moreover, the developing field of polymeric membrane materials has shown particular success at integrating both experimental and computational studies. However, these material systems are known to suffer from varying degrees of induced membrane structural rearrangement upon adsorbate uptake, and thus many polymeric membrane performance metrics are often considered to degrade with an increasing number of ‘guest’ species. In this mini–review, we highlight methodology tradeoffs and provide insights into atomistic molecular simulations used to study adsorption with flexible frameworks, which have the potential to predict separation, storage or catalytic capabilities a priori to experimental efforts. Specifically, molecular simulation methods that have been applied to provide predictions of polymeric membrane properties that have included consideration for sorbate–induced polymer chain rearrangement, swelling and/or plasticization are reviewed. Here, the examples and methodologies described provide demonstrations of the applicability of simulations as an approach to understand adsorption–based phenomena at an atomistic/molecular level, and as a tool to carry out screening studies aimed at efficiently providing analysis for a diversity of polymeric adsorbent–adsorbate systems.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-D-glucosidic linkages. Modification of cell wall chemistry via RNAi-mediated downregulation of Populus deltoides KOR1 (PdKOR), a endo-β-1,4-glucanase gene, in Populus deltoides has been shown to have functional consequences for the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here we used a LC-MS/MS-based proteome profiling approach to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides were identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of GO categories and specific individual proteins showed differential expression of proteins relevant to plant-microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.

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

Fluorescence Microscopic Investigations of Molecular Dynamics in Self–Assembled Nanostructures

Many analytical methods employ self-assembled nanostructured materials as chemical recognition media. Molecular permeation through these materials exhibits unique selectivity owing to nanoconfinement-induced enhancement of permeant–nanostructure interactions. This Personal Account introduces our efforts to investigate the detailed dynamics of single or a small number of molecules in nanostructured materials. Here, we developed new experimental and analysis approaches built upon laser-based fluorescence microscopy to measure the detailed translational and orientational dynamics of molecules diffusing in horizontally-oriented, cylindrical nanostructures, including surfactant micelles, silica mesopores, block copolymer microdomains, and bolaamphiphile-based organic nanotubes. Our studies clarified nanoscale details on the structural/chemical heterogeneity of the nanostructures, and their impacts on molecular mass transport dynamics.

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

Investigation of Molecular Diffusion at Block Copolymer Thin Films Using Maximum Entropy Method-Based Fluorescence Correlation Spectroscopy and Single Molecule Tracking

Fluorescence correlation spectroscopy (FCS) has been widely used to investigate molecular diffusion behavior in various samples. The use of the maximum entropy method (MEM) for FCS data analysis provides a unique means to determine multiple distinct diffusion coefficients without a priori assumption of their number. Comparison of the MEM-based FCS method (MEM-FCS) with another method will reveal its utility and advantage as an analytical tool to investigate diffusion dynamics. Herein, we measured diffusion of fluorescent probes doped into nanostructured thin films using MEM-FCS, and validated the results with single molecule tracking (SMT) data. The efficacy of the MEM code employed was first demonstrated by analyzing simulated FCS data for systems incorporating one and two diffusion modes with broadly distributed diffusion coefficients. The MEM analysis accurately afforded the number of distinct diffusion modes and their mean diffusion coefficients. These results contrasted with those obtained by fitting the simulated data to conventional two-component and anomalous diffusion models, which yielded inaccurate estimates of the diffusion coefficients. Subsequently, the MEM analysis was applied to FCS data acquired from hydrophilic dye molecules incorporated into microphase-separated polystyrene-block-poly(ethylene oxide) (PS-b-PEO) thin films characterized under a water-saturated nitrogen atmosphere. The MEM analysis revealed distinct fast and slow diffusion components attributable to molecules diffusing on the film surface and inside the film, respectively. SMT studies of the same materials yielded trajectories for mobile molecules that appear to follow the curved PEO microdomains. Diffusion coefficients obtained from the SMT data were consistent with those obtained for the slow diffusion component detected by MEM-FCS. Furthermore, these results highlight the utility of MEM-FCS and SMT for gaining complementary information on molecular diffusion processes in heterogeneous material systems.

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

Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences

Abstract Allophycocyanins are phycobiliproteins that absorb red light and transfer the energy to the reaction centers of oxygenic photosynthesis in cyanobacteria and red algae. Recently, it was shown that some allophycocyanins absorb far-red light and that one subset of these allophycocyanins, comprising subunits from the ApcD4 and ApcB3 subfamilies (FRL-AP), form helical nanotubes. The lowest energy absorbance maximum of the oligomeric ApcD4-ApcB3 complexes occurs at 709 nm, which is unlike allophycocyanin (AP; ApcA-ApcB) and allophycocyanin B (AP-B; ApcD-ApcB) trimers that absorb maximally at ~ 650 nm and ~ 670 nm, respectively. The molecular bases of the different spectra of AP variants are presently unclear. To address this, we structurally compared FRL-AP with AP and AP-B, performed spectroscopic analyses on FRL-AP, and leveraged computational approaches. We show that among AP variants, the α-subunit constrains pyrrole ring A of its phycocyanobilin chromophore to different extents, and the coplanarity of ring A with rings B and C sets a baseline for the absorbance maximum of the chromophore. Upon oligomerization, the α-chromophores of all AP variants exhibit a red shift of the absorbance maximum of ~ 25 to 30 nm and band narrowing. We exclude excitonic coupling in FRL-AP as the basis for this red shift and extend the results to discuss AP and AP-B. Instead, we attribute these spectral changes to a conformational alteration of pyrrole ring D, which becomes more coplanar with rings B and C upon oligomerization. This study expands the molecular understanding of light-harvesting attributes of phycobiliproteins and will aid in designing phycobiliproteins for biotechnological applications.

Gisriel, Christopher J.↗
DOE OSTI2021

Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei : a Molecular Dynamics Approach

Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics

Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent K C modulus for bilayer bending. Our results show a strong correlation with K C values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein

IGHV3-33 -encoded antibodies are prevalent in the human humoral response against the Plasmodium falciparum circumsporozoite protein (PfCSP). Among VH3-33 antibodies, cross-reactivity between PfCSP major repeat (NANP), minor (NVDP), and junctional (NPDP) motifs is associated with high affinity and potent parasite inhibition. However, the molecular basis of antibody cross-reactivity and the relationship with efficacy remain unresolved. Here, we perform an extensive structure-function characterization of 12 VH3-33 anti-PfCSP monoclonal antibodies (mAbs) with varying degrees of cross-reactivity induced by immunization of mice expressing a human immunoglobulin gene repertoire. We identify residues in the antibody paratope that mediate cross-reactive binding and delineate four distinct epitope conformations induced by antibody binding, with one consistently associated with high protective efficacy and another that confers comparably potent inhibition of parasite liver invasion. Our data show a link between molecular features of cross-reactive VH3-33 mAb binding to PfCSP and mAb potency, relevant for the development of antibody-based interventions against malaria.

59 BASIC BIOLOGICAL SCIENCES↗