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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2020

Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

36 MATERIALS SCIENCE↗
NASA NTRS1989

Accurate quantum chemical calculations

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

Bauschlicher, Charles W., Jr.↗
NASA NTRS1994

Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution

The crystal structure of d(C3T), solved at 1.4 angstroms resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.

Non-NASA Center↗
DOE OSTI2024

Understanding the Chemical Complexity of Multicomponent Systems: Uranium Polyoxometalates as Nanosorbents

The overarching objective of this project was to develop a molecular-scale understanding of chemical interactions of the transuranic (TRU) elements with uranyl-based polyoxometalate nanoclusters (UPOMs). The specific goals that supported this overarching objective were to: (i) quantify TRU interactions with UPOMs as a function of TRU, carbonate, and UPOM concentration, pH, and temperature; (ii) examine the molecular-level bonding environment of TRU-UPOM complexes; and (iii) develop a rate expression capable of describing the sorption and reduction of TRU by UPOMs. The published literature suggests several potential interactions can occur in TRU-UPOM systems: (i) encapsulation of TRU and coordination with the internal ‘-yl’ oxygens of the UPOM, (ii) coordination of TRU with the external ‘-yl’ oxygens of the UPOM, and (iii) coordination of TRU with the bridging ligands (e.g., peroxo, hydroxo, oxalate) of the UPOM. The latter two may induce aggregation of the UPOMs. The concept of encapsulation is demonstrated by the X-ray diffraction structure of crystallized U 20 , which reveals a Na + cation under each pentagonal face (Sigmon et al., 2009). Computational modeling shows that, while the negative charge of U 20 is spread among all the oxygen atoms, the internal ‘-yl’ oxygens host the most negative charge (Miro and Bo, 2012). This negative charge is reduced through the complexation of the templating sodium ions in the interior of the UPOM. Furthermore, Nyman et al. (2011) shows that cesium can exit through the pentagonal window of U 28 in the aqueous phase, suggesting that the TRU elements, which are smaller than cesium, may be capable of entering a UPOM through these windows in an exchange reaction. Under this project, we focused on hafnium, neptunium, and plutonium interactions with UPOMs.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

Vacuum bag bonding with a high temperature adhesive

A novel controlled molecular weight form of LARC-TPI polymide that exhibits an exceptionally high degree of melt flow in the 340-360 C temperature range has been developed. This material has been evaluated as a high-temperature adhesive, and because of its flow, cost-effective vacuum bag/oven processing can be used. Comparison of adhesive performance with higher molecular weight forms bonded at higher pressures shows this novel material to be equal in mechanical strength.

Progar, Donald J.↗
NASA NTRS1980

Modified Iterative Extended Hueckel. 1: Theory

Iterative Extended Huekel is modified by inclusion of explicit effective internuclear and electronic interactions. The one electron energies are shown to obey a variational principle because of the form of the effective electronic interactions. The modifications permit mimicking of aspects of valence bond theory with the additional feature that the energies associated with valence bond type structures are explicitly calculated. In turn, a hybrid molecular, orbital valence, bond scheme is introduced which incorporates variant total molecular electronic density distributions similar to the way that Iterative Extended Hueckel incorporates atoms.

Aronowitz, S.↗
NASA NTRSDate not supplied

Fracture Prediction of Epoxy Resin using Morse Bond Potential Embedded in GAFF using Molecular Dynamics Simulations

A generic method is developed to investigate the fracture behavior of an epoxy resin using atomistic molecular (MD) dynamics simulations. The epoxy system consisted of the stoichiometric mixture of tetra-/tri-functional epoxies and di-functional hardener molecules and was cured with a step-growth crosslinking algorithm. A hybrid force field (hFF) in which Morse bond function were added in second generation-general Amber Force Field (GAFF2) was used to capture bond breaking of the crosslinked epoxy system under uniaxial deformation. The Morse bond parameters for covalent bonds in the crosslinked backbone were fit to dissociation curves computed by CASPT2/6-311+G**. After the systems in various crosslink densities were obtained and equilibrated, the full length of stress-strain (𝜎-𝜀) curve was produced including initial elastic regime, yielding, plastic flow, strain hardening, and progressive failure. We found that the hFF was effective in studying the dissociation of crosslinked polymers and understanding the failure mechanism. In the results, the hFF delivered the same elastic property obtained from the unmodified force field GAFF. The stress-strain curve, however, began to be distinct in the plastic regime due to broken covalent bonds capable of altering the tensile behavior. Once the stress reached maximum, it progressively decreased until the ultimate failure (𝜎=0). Since hFF employed the existing GAFF functions with including a minimal change of its bond potential, this approach is easier to perform and computationally more efficient for unveiling the fracture behavior of polymer materials at the molecular level than other approaches with reactive force fields. We expect this approach will be utilized to accelerate the material-by-design process for thermosets by incorporate data from molecular models.

Changwoon Jang↗
DOE OSTI2024

Dynamic metal-linker bonds in metal–organic frameworks

Metal-linker bonds serve as the “glue” that binds metal ions to multitopic organic ligands in the porous materials known as metal–organic frameworks (MOFs). Despite ample evidence of bond lability in molecular and polymeric coordination compounds, the metal-linker bonds of MOFs were long assumed to be rigid and static. Given the importance of ligand fields in determining the behaviour of metal species, labile bonding in MOFs would help explain outstanding questions about MOF behaviour, while providing a design tool for controlling dynamic and stimuli-responsive optoelectronic, magnetic, catalytic, and mechanical phenomena. Here, in this work, we present emerging evidence that MOF metal-linker bonds exist in dynamic equilibria between weakly and tightly bond conformations, and that these equilibria respond to guest–host chemistry, drive phase change behavior, and exhibit size-dependence in MOF nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗