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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images

High resolution non-contact atomic force microscopy measurements characterize assemblies of trimesic acid molecules on Cu(111) and the link group interactions, providing the first fingerprints utilizing CO-based probes for this widely studied paradigm for hydrogen bond driven molecular self assembly. The enhanced submolecular resolution offered by this technique uniquely reveals key aspects of the competing interactions. Accurate comparison between full-density-based modeled images and experiment allows to identify key structural elements in the assembly in terms of the electron-withdrawing character of the carboxylic groups, interactions of those groups with Cu atoms in the surface, and the valence electron density in the intermolecular region of the hydrogen bonds. This study of trimesic acid assemblies on Cu(111) combining high resolution atomic force microscopy measurements with theory and simulation forges clear connections between fundamental chemical properties of molecules and key features imprinted in force images with submolecular resolution.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Leveraging peptide–cellulose interactions to tailor the hierarchy and mechanics of peptide–polymer hybrids

Inspired by spider silk's hierarchical diversity, we leveraged peptide motifs with the capability to tune structural arrangement for controlling the mechanical properties of a conventional polymer framework. The addition of nanofiller with hydrogen bonding sites was used as another pathway towards hierarchical tuning via matrix–filler interactions. Specifically, peptide–polyurea hybrids (PPUs) were combined with cellulose nanocrystals (CNCs) to develop mechanically-tunable nanocomposites via tailored matrix–filler interactions (or peptide–cellulose interactions). In this material platform, we explored the effect of these matrix–filler interactions on the secondary structure, hierarchical ordering, and mechanical properties of the peptide hybrid nanocomposites. Interactions between the peptide matrix and CNCs occur in all of the PPU/CNC nanocomposites, preventing α-helical ordering, but promoting inter-molecular hydrogen bonded β-sheet formation. Depending on peptide and CNC content, the Young's modulus varies from 10 to 150 MPa. Unlike conventional cellulose-reinforced polymer nanocomposites, the mechanical properties of these composite materials are dictated by a balance of CNC reinforcement, peptidic ordering, and microphase-separated morphology. This research highlights that leveraging peptide–cellulose interactions is a strategy to create materials with targeted mechanical properties for a specific application using a limited selection of building blocks.

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

Electronic structure, dimer physics, orbital-selective behavior, and magnetic tendencies in the bilayer nickelate superconductor $\mathrm{La_3Ni_2O_7}$under pressure

Motivated by the recently reported high-temperature superconductivity in the bilayer La 3 Ni 2 O 7 (LNO) under pressure, we comprehensively study this system using ab initio techniques. The Ni 3d orbitals have a large bandwidth at ambient pressure, increasing by ~22% at 29.5 GPa. Without electronic interactions, the Ni d 3z 2 -r 2 orbitals form a bonding-antibonding molecular orbital state via the O p z inducing a “dimer” lattice in the LNO bilayers. The Fermi surface consists of two-electron sheets with mixed e g orbitals and a hole pocket defined by the d 3z 2 -r 2 orbital, suggesting a Ni two-orbital minimum model. Different from the infinite-layer nickelate, we obtained a large interorbital hopping between d 3z 2 -r 2 and d x 2 -y 2 states in LNO, caused by the ligand “bridge” of in-plane O p x or p y orbitals connecting those two orbitals, inducing d-p σ-bonding characteristics. The competition between the intraorbital and interorbital hoppings leads to an interesting dominant spin stripe (π,0) order because of bond ferromagnetic tendencies via the recently discussed “half-empty” mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Deprotonated sulfamic acid and its homodimers: Does sulfamic acid adopt zwitterion during cluster growth?

Here we present a joint experimental and computational study on the geometric and electronic structures of deprotonated sulfamic acid (SA) clusters [(SA) n –H] – (n = 1, 2) employing negative ion photoelectron spectroscopy and high-level ab initio calculations. The photoelectron spectra provide the vertical/adiabatic detachment energy (VDE/ADE) of the sulfamate anion (SM – ) H 2 N•SO 3 – at 4.85 ± 0.05 and 4.58 ± 0.08 eV, respectively, and the VDE and ADE of the SM – •SA dimer at 6.41 ± 0.05 and 5.87 ± 0.08 eV, respectively. The significantly increased electron binding energies of the dimer confirm the enhanced electronic stability upon the addition of one SA molecule. The CCSD(T)-predicted VDEs/ADEs agree excellently with the experimental data, confirming the identified structures as the most stable ones. Two types of dimer isomers possessing different hydrogen bonding (HB) motifs are identified, corresponding to SM – binding to a zwitterionic SA (SM – •SA z ) and a canonical SA (SM – •SA c ), respectively. Two N–H$\cdots$O HBs and one superior O–H$\cdots$O HB are formed in the lowest-lying SM – •SA c , while SM – •SA z has three moderate N–H$\cdots$O HBs, with the former being 4.71 kcal/mol more stable. Further theoretical analyses reveal that the binding strength advantage of SM – •SA c over SM – •SA z arises from its significant contributions of orbital interactions between fragments, illustrating that sulfamate strongly interacts with its parent SA acid and preferably chooses the canonical SA in the subsequent cluster formations. Given the prominent presence of SA, this study provides the first evidence that the canonical dimer model of sulfamic acid should exist as a superior configuration during cluster growth.

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

Proton-detected 15 N- 1 H dipolar coupling/ 1 H chemical shift correlation experiment for the measurement of NH distances in biological solids under fast MAS solid-state NMR

Measurement of distances from dipolar couplings is essential for structural characterization, refinement and validation using the solid-state nuclear magnetic resonance (ssNMR) spectroscopy. Particularly, knowledge about NH dipolar interactions in biological solids is important for understanding the hydrogen (H)-bonding interactions, molecular geometry and spin dynamics. In this regard, we have proposed a proton-detected two-dimensional (2D) 15 N- 1 H dipolar coupling/ 1 H chemical shift correlation experiment using the C-symmetry based windowless recoupling of chemical shift anisotropy (ROCSA) in combination with the DIPSHIFT pulse-based method for the measurement of short NH distances in the isotopically labeled and naturally abundant biological solids at fast magic angle spinning (MAS) rates (40–70 kHz). Our proposed method results in undistorted recoupled 15 N- 1 H dipolar coupling powder lineshapes that are free from the recoupled 1 H CSA contributions under the 15 N evolution, a feature that is essential for the measurement of NH distances with improved accuracy (± 500 Hz in terms of the NH dipolar couplings). The pulse sequence developed in the present study is also insensitive to the 1H–1H homonuclear dipolar interactions, relaxation effects owing to its constant-time implementation, and t1-noise from the fluctuations in the MAS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

A High Energy X-ray Diffraction Study of Amorphous Indomethacin

Amorphous pharmaceuticals often possess a wide range of molecular conformations and bonding arrangements. The x-ray pair distribution function (PDF) method is a powerful technique for the characterization of variations in both intra-molecular and inter-molecular packing arrangements. Here, the x-ray PDF of amorphous Indomethacin is shown to be particularly sensitive to the preferred orientations of the chlorobenzyl ring found in isomers in the crystalline state. In some cases, the chlorobenzyl ring has no preferred torsional angle in the amorphous form, while in others evidence of distinct isomer orientations are observed. Amorphous samples with no preferred torsion angles of the chlorobenzyl ring are found to favor enhanced inter-molecular hydrogen bonding, and this is reflected in the intensity of the first sharp diffraction peak. These significant variations in structure rule out amorphous Indomethacin as a possible standard for x-ray PDF measurements. At high humidity, time resolved PDF's for >40 h reveal water molecules forming hydrogen bonds with Indomethacin molecules. Finally, a simple linear hydrogen bond model indicates that water molecules in the wet amorphous form have similar hydrogen bond strengths to those found between Indomethacin dimers or chains in the dry amorphous form.

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

Insights into Molecular Magnetism in Metal–Metal Bonded Systems as Revealed by a Spectroscopic and Computational Analysis of Diiron Complexes

A pair of bimetallic compounds featuring Fe–Fe bonds, [Fe( i PrNPPh 2 ) 3 FeR] (R = PMe 3 , ≡N t Bu), have been investigated using High-Frequency Electron Paramagnetic Resonance (HFEPR) as well as field- and temperature-dependent 57 Fe nuclear γ resonance (Mössbauer) spectroscopy. To gain insight into the local site electronic structure, we have concurrently studied a compound containing a single Fe(II) in a geometry analogous to that of one of the dimer sites. Our spectroscopic studies have allowed for the assessment of the electronic structure via the determination of the zero-field splitting and 57 Fe hyperfine parameters for the entire series. We also report on our efforts to correlate structure with physical properties in metal–metal bonded systems using ligand field theory guided by quantum chemical calculations. Through the insight gained in this study, we discuss strategies for the design of single-molecule magnets based on polymetallic compounds linked via direct metal–metal bonds.

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

Electron–Ion Covariance Reveals Geometry-Resolved Inner-Shell Spectra in CS 2 Photodissociation

The chemical shifts of inner-shell atomic orbitals are highly sensitive to chemical bonding and molecular structure. In evolving systems, however, the spectra of distinct molecular species and geometries overlap, obscuring the underlying chemical dynamics. Here we demonstrate the use of electron–ion covariance analysis to combine the structural sensitivity of Coulomb explosion imaging with inner-shell spectroscopy, yielding geometry-specific spectra of transient and product species. We apply this approach to the excited state dynamics of CS 2 probed by ionization above the S 2p edge. Electron–ion covariance with time- and momentum-selected S + and S 2+ ions isolates distinct S 2p photoelectron spectra for ground-state CS 2 , bent photoexcited CS 2 , the CS photoproduct, and bare atomic sulfur ─ species whose spectra overlap strongly in the channel-averaged measurement. Clear chemical shifts are observed in the covariance photoelectron spectrum for each of these species, all of which are consistent with high-level calculations. Here, by extracting the atomic S contribution to the photoelectron spectrum in a finely time-resolved manner we can disentangle this contribution to the overall time-resolved photoelectron spectrum as the photodissociation proceeds. These results demonstrate the promise of electron–ion covariance as a general approach to geometry-resolved inner-shell spectroscopy, opening a route to tracking structural evolution through chemical shifts in complex photoexcited molecules.

Ionization↗
DOE OSTI2024

Reactivity of [Tism Pr i Benz ]MgH and [Tism Pr i Benz ]MgMe towards Carbonyl Compounds: Access to Terminal Alkoxide and Enolate Complexes

The hydride and methyl compounds [Tism Pr i Benz ]MgH and [Tism Pr i Benz ]MgMe undergo insertion of the carbonyl moieties of non-enolizable aldehydes and ketones such as PhCHO and Ph 2 CO into the Mg–H and Mg–Me bonds to form alkoxide compounds, namely [Tism Pr i Benz ]MgOCH 2 Ph, [Tism Pr i Benz ]MgOCHPh 2 , [Tism Pr i Benz ]MgMOCH(Me)Ph and [Tism Pr i Benz ]MgOCMePh 2 . In contrast to the insertion of the carbonyl moiety, the reactions of the enolizable ketones Me 2 CO and PhC(O)Me with [Tism Pr i Benz ]MgMe afford the enolate complexes, [Tism Pr i Benz ]MgOC(Me)=CH 2 and [Tism Pr i Benz ]MgOC(Ph)=CH 2 . The formation of [Tism Pr i Benz ]MgOC(Me)=CH 2 is of note because methyl Grignard reagents preferentially react with acetone to form t-butoxide derivatives. The hydride compound, [Tism Pr i Benz ]MgH, also reacts with acetone to yield the enolate compound, [Tism Pr i Benz ]MgOC(Me)=CH 2 , but while the overall transformation is similar to that of the methyl derivative, [Tism Pr i Benz ]MgMe, the enolate compound is not the initially formed product. Specifically, acetone undergoes preferential insertion into the Mg–H bond to generate the corresponding alkoxide, [Tism Pr i Benz ]MgOPr i , which subsequently converts to the respective enolate in the presence of excess acetone. Furthermore, the relative ability of the hydride and methyl compounds to undergo insertion of carbonyl compounds into the Mg–H and Mg–Me bonds has been addressed computationally, which indicates that the barrier for insertion of the carbonyl group into the Mg–H bond is lower than that for insertion into the Mg–Me bond. The molecular structures of [Tism Pr i Benz ]MgOCH 2 Ph, [Tism Pr i Benz ]MgOCHPh 2 , [Tism Pr i Benz ]MgOCMePh 2 , [Tism Pr i Benz ]MgOC(Me)=CH 2 and [Tism Pr i Benz ]MgOC(Ph)=CH 2 have been determined by X-ray diffraction.

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

Metastability of diamond ramp-compressed to 2 terapascals

Carbon is the fourth-most prevalent element in the Universe and essential for all known life. In the elemental form it is found in multiple allotropes, including graphite, diamond and fullerenes, and it has long been predicted that even more structures can exist at pressures greater than those at Earth’s core. Several phases have been predicted to exist in the multi-terapascal regime, which is important for accurate modelling of the interiors of carbon-rich exoplanets. By compressing solid carbon to 2 terapascals (20 million atmospheres; more than five times the pressure at Earth’s core) using ramp-shaped laser pulses and simultaneously measuring nanosecond-duration time-resolved X-ray diffraction, we found that solid carbon retains the diamond structure far beyond its regime of predicted stability. The results confirm predictions that the strength of the tetrahedral molecular orbital bonds in diamond persists under enormous pressure, resulting in large energy barriers that hinder conversion to more-stable high-pressure allotropes, just as graphite formation from metastable diamond is kinetically hindered at atmospheric pressure. In conclusion, this work nearly doubles the highest pressure at which X-ray diffraction has been recorded on any material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Dynamical electron correlation and the chemical bond. II. Recoupled pair bonds in the $a$ 4 Σ - states of CH and CF

We extended our studies of the effect of dynamical electron correlation on the covalent bonds in the AH and AF series (A = B–F) to the recoupled pair bonds in the excited $a$ 4 Σ - states of the CH and CF molecules. Dynamical correlation is energetically less important in the $a$ 4 Σ - states than in the corresponding X 2 Π states for both molecules, which is reflected in smaller changes in bond energies ($D$ e ). Changes in the equilibrium bond distance ($R$ e ) and vibrational frequency ($ω$ e ), on the other hand, are influenced by the changes in the slope and curvature of the dynamical electron correlation energy as a function of the internuclear distance $R$, $E$ DEC ($R$). In the CH($a$ 4 Σ - ) state, these changes are much smaller than in the CH(X 2 Π) state, but in the CF($a$ 4 Σ - ) state, they are larger, reflecting a significant difference in the shapes of $E$ DEC ($R$) curves. At large $R$, the shape of $E$ DEC ($R$) curves for covalent and recoupled pair bonds is similar although different in magnitude. For the CH($a$ 4 Σ - ) state, $E$ DEC ($R$) has a minimum at $R$ = $R$ e + 0.72 Å as the orbitals associated with the formation of the recoupled pair bond switch places. $E$ DEC (R) for the CF($a$ 4 Σ - ) state decreases continuously throughout the bound region of the potential energy curve because the dynamical correlation energy associated with the electrons in the lone pair orbitals is increasing. In conclusion, these results support our earlier conclusion that we still have much to learn about the nature of dynamical electron correlation in molecules.

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

Vibrational relaxation dynamics in layered perovskite quantum wells

Significance Halide perovskites, especially layered perovskites, offer a number of advantages to creating bright and efficient light-emitting devices and other optoelectronic applications. The organic–inorganic hybrid layered perovskite features complex lattice dynamics due to the ionic character of the crystal and the softness arising from noncovalent bonds between molecular moieties and the inorganic network. Especially, the packing geometry of the organic barriers leads to a structural deformation of inorganic octahedral, which strongly affects the properties that are crucial for device applications. In this work, we use high-resolution resonant impulsive stimulated Raman spectroscopy of a variety of ligand substitutions in layered perovskites. We find the composition of organic ligands can substantially change the dephasing rate of optical phonons and their temperature dependence, due to varying degrees of anharmonicity in the lattice and dynamic structural disorder.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Identification and structural analysis of a thermophilic β-1,3-glucanase from compost

β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thiourea-Derived Chelating Ligands and Their Organometallic Compounds: Investigations into Their Anticancer Activity

Thiones have been investigated as ligands in metal complexes with catalytic and biological activity. We report the synthesis, characterization, and biological evaluation of a series of MII/III complexes of the general formulae [M II (cym)(L)Cl]X (cym = η 6 -p-cymene) or [M III (Cp*)(L)Cl]X (Cp* = η 5 -pentamethylcyclopentadienyl), where X = Cl - or PF 6 - , and L represents heterocyclic derivatives of thiourea. The thiones feature a benzyl-triazolyl pendant and they act as bidentate ligands via N,S-coordination to the metal centers. Several derivatives have been investigated by single-crystal X-ray diffraction analysis. NMR investigations showed a counterion-dependent shift of several protons due to the interaction with the counterions. These NMR investigations were complemented with X-ray diffraction analysis data and the effects of different counterions on the secondary coordination sphere were also investigated by DFT calculations. In biological studies, the Ir benzimidazole derivative was found to accumulate in the cytoplasm and it was the most cytotoxic derivative investigated.

60 APPLIED LIFE SCIENCES↗