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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 OSTI2016

Metal-organic and supramolecular networks driven by 5-chloronicotinic acid: Hydrothermal self-assembly synthesis, structural diversity, luminescent and magnetic properties

Four new crystalline solids, namely [Co{sub 2}(µ{sub 2}-5-Clnic){sub 2}(µ{sub 3}-5-Clnic){sub 2}(µ{sub 2}-H{sub 2}O)]{sub n} (1), [Co(5-Clnic){sub 2}(H{sub 2}O){sub 4}]·2(5-ClnicH) (2), [Pb(µ{sub 2}-5-Clnic){sub 2}(phen)]{sub n} (3), and [Cd(5-Clnic){sub 2}(phen){sub 2}]·3H{sub 2}O (4) were generated by hydrothermal self-assembly methods from the corresponding metal(II) chlorides, 5-chloronicotinic acid (5-ClnicH) as a principal building block, and 1,10-phenanthroline (phen) as an ancillary ligand (optional). All the products 1–4 were characterized by IR spectroscopy, elemental analysis, thermogravimetric (TGA), powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. Their structures range from an intricate 3D metal-organic network 1 with the 3,6T7 topology to a ladder-like 1D coordination polymer 3 with the 2C1 topology, whereas compounds 2 and 4 are the discrete 0D monomers. The structures of 2 and 4 are further extended (0D→2D or 0D→3D) by hydrogen bonds, generating supramolecular networks with the 3,8L18 and ins topologies, respectively. Synthetic aspects, structural features, thermal stability, magnetic (for 1) and luminescent (for 3 and 4) properties were also investigated and discussed. - Graphical abstract: A new series of crystalline solids was self-assembled and fully characterized; their structural, topological, luminescent and magnetic features were investigated. Display Omitted.

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

Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery

Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.

3D structural interaction fingerprints↗
DOE OSTI2025

New Phosphoranylideneketenes and Phosphoranylidenethioketenes‐Synthesis, Structure, Spectroscopy, and Lewis Base Properties

Posphoranylideneketene Ph 3 PCCO and its sulfur analogue, Ph 3 PCCS, are cumulated ylides that exhibit diverse reactivity and distinct structural features. Herein, we present the first systematic study of substituent effects on the structures and bonding of a series of aryl- and alkyl-substituted phosphoranylideneketenes, R 3 PCCO [R = Et, cyclohexyl, NMe 2 , 4-Me 2 N-C 6 H 4 , 4-MeO-C 6 H 4 , 4-CF 3 -C 6 H 4 , 3,5-(CF 3 ) 2 -C 6 H 3 ], prepared from the corresponding phosphonium salts, [R 3 PCH 2 COOEt]X (X = Br, I) and two equivalents of Na[N(SiMe 3 ) 2 ]. Multinuclear NMR and IR spectroscopy, supported by single-crystal X-ray diffraction, revealed that the bond strength within the central P═C═C═O fragment increases with the electron-deficiency of the aryl substituents at phosphorus. The corresponding phosphoranylidenethioketenes, R 3 PCCS (R = Et, cyclohexyl, NMe 2 , 4-Me 2 N-C 6 H 4 , 4-MeO-C 6 H 4 , 4-CF 3 -C 6 H 4 ), were obtained by reactions of R 3 PCCO with CS 2 . Here, the rate of conversion of R 3 PCCO into R 3 PCCS decreases with increasing electron deficiency at phosphorus. Both R 3 PCCO and R 3 PCCS act as relatively weak ambidentate Lewis donors, yet they form stable acid-base adducts with strong Lewis acids such as B(C 6 F 5 ) 3 and Al(C 6 F 5 ) 3 .

Lewis acid-base adduct↗
DOE OSTI2021

Predicting CaO-(MgO)-Al2O3-SiO2 glass reactivity in alkaline environments from force field molecular dynamics simulations

In this investigation, force field-based molecular dynamics (MD) simulations have been employed to generate detailed structural representations for a range of amorphous quaternary CaO-MgO-Al{sub 2}O{sub 3}-SiO{sub 2} (CMAS) and ternary CaO-Al{sub 2}O{sub 3}-SiO{sub 2} (CAS) glasses. Comparison of the simulation results with select experimental X-ray and neutron total scattering and literature data reveals that the MD-generated structures have captured the key structural features of these CMAS and CAS glasses. Based on the MD-generated structural representations, we have developed two structural descriptors, specifically (i) average metal oxide dissociation energy (AMODE) and (ii) average self-diffusion coefficient (ASDC) of all the atoms at melting. Both structural descriptors are seen to more accurately predict the relative glass reactivity than the commonly used degree of depolymerization parameter, especially for the eight synthetic CAS glasses that span a wide compositional range. Hence these descriptors hold great promise for predicting CMAS and CAS glass reactivity in alkaline environments from compositional information.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Vapor-Deposited Glass Structure Determined by Deposition Rate–Substrate Temperature Superposition Principle

In this article, we show that deposition rate substantially affects the anisotropic structure of thin glassy films produced by physical vapor deposition. Itraconazole, a glass-forming liquid crystal, was deposited at rates spanning 3 orders of magnitude over a 25 K range of substrate temperatures, and structure was characterized by ellipsometry and X-ray scattering. Both the molecular orientation and the spacing of the smectic layers obey deposition rate–substrate temperature superposition, such that lowering the deposition rate is equivalent to raising the substrate temperature. We identify two different surface relaxations that are responsible for structural order in the vapor-deposited glasses and find that the process controlling molecular orientation is accelerated by more than 3 orders of magnitude at the surface relative to the bulk. Finally, the identification of distinct surface processes responsible for anisotropic structural features in vapor-deposited glasses will enable more precise control over the structure of glassy materials used in organic electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2022

HIV-1 CD4-binding site germline antibody–Env structures inform vaccine design

BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we report 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures reveal critical Env contacts by BG24 iGL and identify antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24 iGL variants bound to Envs with CD4bs glycans present provide insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276 gp120 glycan. Together, these findings reveal Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Dynamic structural determinants in bacterial microcompartment shells

Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO 2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein–protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Separation of Light Hydrocarbons through Selective Molecular Exclusion by a Microporous Metal–Organic Framework

Abstract [Zn 2 (sdc) 2 (bpe)] (compound 1 , sdc=4,4′‐stilbenedicarboxylate, bpe=1,2‐bis(4‐pyridyl)ethane)), a doubly interpenetrated, pillared‐layer microporous metal–organic framework has been solvothermally synthesized and structurally characterized by single‐crystal X‐ray diffraction. The structure features a common Zn 2 (COO) 4 paddle‐wheel building unit. Compound 1 undergoes structural change upon solvent removal. The activated phase (compound 2 ) displays permanent porosity, excellent thermal/moisture stability, and interesting hydrocarbon adsorption properties. Gas adsorption experiments show that compound 1 selectively adsorbs saturated/unsaturated C 2 hydrocarbons but excludes C 3 and C 4 hydrocarbons at room temperature. We have collected single‐component adsorption isotherms of six light hydrocarbons and calculated adsorption selectivities of various binary hydrocarbon mixtures by ideal adsorbed solution theory (IAST). The results show that compound 1 possesses remarkably high selectivity towards C 2 over C 3 /C 4 hydrocarbons and the separation is achieved by selective molecular exclusion.

Wang, Hao↗
DOE OSTI2014

Crystal structure of product-bound complex of UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

Highlights: • Determined the structure of UDP-D-ManNAcADH to a resolution of 1.55 Å. • First complex structure of PhUDP-D-ManNAcADH with UDP-D-ManMAcA. • The monomeric structure consists of three distinct domains. • Cys258 acting as catalytic nucleophilic and Lys204 acts as acid/base catalyst. • Oligomeric state plays an important role for the catalytic function. - Abstract: UDP-N-acetyl-D-mannosamine dehydrogenase (UDP-D-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-D-mannosamine (UDP-D-ManNAc) to Uridine-diphospho-N-acetyl-D-mannosaminuronic acid (UDP-D-ManNAcA) through twofold oxidation of NAD{sup +}. In order to reveal the structural features of the Pyrococcus horikoshii UDP-D-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55 Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-D-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Luminescent lanthanide coordination polymers synthesized via in-situ hydrolysis of dimethyl-3,4-furandicarboxylate

Dimethyl-3,4-furandicarboxylate undergoes hydrolysis under hydrothermal conditions with lanthanide (Ln) ions to form two-dimensional coordination polymers, [Ln(C{sub 6}H{sub 2}O{sub 5})(C{sub 6}H{sub 3}O{sub 5})(H{sub 2}O)]{sub n} (Ln=Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu). The resulting materials exhibit luminescent properties with quantum yields and lifetimes for the Eu(III) and Tb(III) compounds of 1.1±0.3% and 0.387±0.0001 ms, and 3.3±0.8% and 0.769±0.006 ms, respectively. Energy values for the singlet and triplet states were determined for dimethyl-3,4-furandicarboxylate and 3,4-furandicarboxylic acid. Excited state dynamics and structural features are examined to explicate the reported quantum yields. A series of other FDC structures is briefly presented. - Graphical abstract: A new two-dimensional coordination polymer derived from the in-situ hydrolysis of a furan dimethyl ester with lanthanide(III) ions was obtained in order to study its photophysical behavior when constructed from trivalent Eu and Tb. Quantum yields, lifetime measurements, and singlet/triplet state energies values were obtained. The nature of the material's excited state dynamics is examined and correlated to its structure in order to explain the overall luminescent efficiency of the system. - Highlights: • A new lanthanide–furandicarboxylate coordination polymer is presented. • Eu and Tb compounds display luminescent properties, albeit with low quantum yields. • Photophysical behavior explained through the compound's triplet state and structure. • Nonradiative deactivation of luminescence through high-energy oscillators was noted. • Molecular modeling of the organic moiety was conducted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Synthetic Chlorins, Possible Surrogates for Chlorophylls, Prepared by Derivatization of Porphyrins

Chlorophylls make Earth green, are the central constituents in the engine of photosynthesis, and not surprisingly have garnered extensive attention. A chlorin, the core chromophore of a chlorophyll, is a dihydroporphyrin macrocycle that contains one pyrroline ring and three pyrrole rings. The dominant method for the synthesis of chlorins has entailed the derivatization of porphyrins. The present review covers the ostensibly simple conversion of porphyrins, regardless of synthetic or biological origin, to chlorins. The period covered encompasses the entire history since the beginnings of chlorin synthetic chemistry in the early 20th century through 2015. Representative transformations include hydrogenation, cycloaddition, annulation, and diverse “breaking and mending” approaches. Altogether, the synthesis of >1000 chlorins or chlorin-like compounds (containing >50 distinct pyrroline motifs) is described. Such diversity animates the question “what structural features are essential for a chlorin to resemble chlorophyll?” To begin to address the structure–spectrum relationship, > 250 absorption spectra are provided for representative structures. The synthesis and spectral properties of the vast collection of compounds described herein are expected to illuminate the scope to which synthetic chlorins can serve as surrogates for chlorophylls and be exploited in diverse ways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Polarization dependent formation of femtosecond laser-induced periodic surface structures near stepped features

Laser-induced periodic surface structures (LIPSS) are formed near 110 nm-tall Au microstructured edges on Si substrates after single-pulse femtosecond irradiation with a 150 fs pulse centered near a 780 nm wavelength. We investigate the contributions of Fresnel diffraction from step-edges and surface plasmon polariton (SPP) excitation to LIPSS formation on Au and Si surfaces. For certain laser polarization vector orientations, LIPSS formation is dominated by SPP excitation; however, when SPP excitation is minimized, Fresnel diffraction dominates. The LIPSS orientation and period distributions are shown to depend on which mechanism is activated. These results support previous observations of the laser polarization vector influencing LIPSS formation on bulk surfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Chemometric modeling of power conversion efficiency of organic dyes in dye sensitized solar cells for the future renewable energy

The present study reports chemometric modeling of power conversion efficiency (PCE) of dye sensitized solar cells (DSSCs) using the biggest available data set till date which comprises around 1200 dyes covering 7 chemical classes. To extract the best structural features required for higher PCE, we have developed multiple partial least squares (PLS) quantitative structure-property relationship (QSPR) models for the Triphenylamine, Phenothiazine, Indoline, Porphyrin, Coumarin, Carbazole and Diphenylamine chemical classes using descriptors derived from the best subset selection method followed by selection of best five models in each dataset based on the Mean Absolute Error (MAE) values. The models were validated both internally and externally followed by the consensus predictions employing “Intelligent Consensus Predictor” tool to examine whether the quality of predictions can be improved with the “intelligent” selection of multiple PLS models. The quality of predictions for the respective external sets showed that the consensus models (CM) are better than the individual models (IM) in most of the cases. From the insights of the developed models, we concluded that attributes like a packed structure toward higher conductivity of electrons, auxiliary donor fragment of aromatic tertiary amines, number of thiophenes inducing the bathochromic shift and augmenting the absorption, presence of additional electron donors, enhancement of electron-donating abilities, number of non-aromatic conjugated C(sp 2 ) which helps as conjugation extension units to broaden the absorption and highly conjugated $π$-systems exert positive contributions to the PCE. On the contrary, features negatively contributing to PCE are the followings: fragments which lower the tendency of localized $π–π*$ transition, fragments related to larger volume and surface area of dyes along with hydrophobicity resulting in poor adhesion, fragment RC = N causing dye hydrolysis, steric hindrance for π electronic mobility, fragments enhancing polarity, etc. Finally, the identified features from the best QSPR model of the coumarin dataset was employed in designing of ten more efficient coumarin dyes (predicted %PCE ranging from 8.93 to 10.62) than the existing ones.

14 SOLAR ENERGY↗
DOE OSTI2015

RFe{sub 2}Mg{sub x}Al{sub 8−x} (R=La–Nd and Sm; x≈0.8): Flux synthesis, structure, magnetic and electrical properties

Single crystals of Mg-substituted CeFe{sub 2}Al{sub 8} type intermetallics RFe{sub 2}Mg{sub x}Al{sub 8–x} (R=La–Nd and Sm; x≤1) were grown by reacting iron and rare earth metals in 1:1 Mg/Al mixed flux. The structure features mono-capped and bi-capped trigonal prismatic FeAl{sub 6} units. Electronic structure calculations indicate that magnesium substitution reduces the valence electron count, shifting the Fermi level away from a pseudo-gap. This changes the electronic nature of the cerium analog; the previously reported ternary CeFe{sub 2}Al{sub 8} shows strong hybridization between the cerium states and the conduction electrons, resulting in no magnetic moment on Ce atoms. On the other hand, magnetic susceptibility measurements on CeFe{sub 2}Mg{sub x}Al{sub 8–x} indicates a localized moment on cerium. The newly synthesized Pr, Nd and Sm analogs exhibit antiferromagnetic ordering at 2.8 K, 7.8 K and 12 K respectively. Solid state {sup 27}Al NMR of LaFe{sub 2}Mg{sub x}Al{sub 8–x} exhibits a broad Knight shift at ~1200 ppm, consistent with the metallic behavior shown by electrical resistivity data. - Graphical abstract: Mg substitution into CeFe{sub 2}Al{sub 8} modifies cerium valence due to changing valence electron count. - Highlights: • RFe{sub 2}Mg{sub x}Al{sub 8−x} (R=La–Nd, Sm) grow as large crystals from reactions in Mg/Al flux. • Products are magnesium-substituted variants of CeFe{sub 2}Al{sub 8}, with CaCo{sub 2}Al{sub 8} structure. • Ce magnetic moment in CeFe{sub 2}Mg{sub x}Al{sub 8−x} varies from that in CeFe{sub 2}Al{sub 8} due to VEC change. • Antiferromagnetic ordering observed for Pr, Nd, Sm analogs of RFe{sub 2}Mg{sub x}Al{sub 8−x}.

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

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗