SEARCH · Engineering Papers
Results for “Neal”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
High-Field Magnetoelectric and Spin-Phonon Coupling in Multiferroic (NH 4 ) 2 [FeCl 5 ·(H 2 O)]
We combine high field polarization, magneto-infrared spectroscopy, and lattice dynamics calculations with prior magnetization to explore the properties of (NH 4 ) 2 [FeCl 5 ·(H 2 O)]-a type II molecular multiferroic in which the mixing between charge, structure, and magnetism is controlled by intermolecular hydrogen and halogen bonds. Electric polarization is sensitive to the series of field-induced spin reorientations, increasing linearly with the field and reaching a maximum before collapsing to zero across the quasi-collinear to collinear-sinusoidal reorientation due to the restoration of inversion symmetry. Magnetoelectric coupling is on the order of 1.2 ps/m for the P∥c, H∥c configuration between 5 and 25 T at 1.5 K. In this range, the coupling takes place via an orbital hybridization mechanism. Other forms of mixing are active in (NH 4 ) 2 [FeCl 5 ·(H 2 O)] as well. Magneto-infrared spectroscopy reveals that all of the vibrational modes below 600 cm –1 are sensitive to the field-induced transition to the fully saturated magnetic state at 30 T. We analyze these local lattice distortions and use frequency shifts to extract spin-phonon coupling constants for the Fe–O stretch, Fe–OH 2 rock, and NH 4 + libration. Inspection also reveals subtle symmetry breaking of the ammonium counterions across the ferroelectric transition. Here, the coexistence of such varied mixing processes in a platform with intermolecular hydrogen- and halogen-bonding opens the door to greater understanding of multiferroics and magnetoelectrics governed by through-space interactions.
Pressure–Temperature Phase Diagram Reveals Spin–Lattice Interactions in Co[N(CN) 2 ] 2
Diamond anvil cell techniques, synchrotron-based infrared and Raman spectroscopies, and lattice dynamics calculations are combined with prior magnetic property work to reveal the pressure–temperature phase diagram of Co[N(CN)2]2. The second-order structural boundaries converge on key areas of activity involving the spin state exposing how the pressure-induced local lattice distortions trigger the ferromagnetic → antiferromagnetic transition in this quantum material.
U(IV) Aqueous Speciation from the Monomer to UO 2 Nanoparticles: Two Levels of Control from Zwitterionic Glycine Ligands
The fate of U(IV)O 2 in the environment in a colloidal form and its dissolution and growth in controlled environments is influenced by organic ligation and redox processes, where both affect solubility, speciation, and transport. Here we investigate U(IV) aqueous speciation from pH 0 to 3 with the glycine (Gly) ligand, the smallest amino acid. We document evolution of the monomeric to the hexameric form from pH 0 to 3 via UV–vis spectroscopy and small-angle X-ray scattering (SAXS). Crystals of the hexamer [U 6 O 4 (OH) 4 (H 2 O) 6 (HGly) 12 ]·12Cl–·12(H 2 O) (U 6 ) were isolated at pH 2.15. The structure of U 6 is a hexanuclear oxo/hydroxo cluster U 6 O 4 (OH) 4 decorated by 12 glycine ligands and 6 water molecules. The effect of pH and temperature on U 6 conversion to UO 2 nanoparticles, or simply reversible aggregation, is detailed by transmission electron microscopy imaging, in addition to SAXS and UV-spectroscopy. Because of the zwitterion behavior of glycine, pH and temperature control over U(IV) speciation is complex. Unexpectedly, stability of the polynuclear cluster actually increases with increased pH. Speciation is sensitive to not only metal-oxo hydrolysis but also ligand lability and hydrophobic ligand–ligand interactions.
Resolving Confined 7 Li Dynamics of Uranyl Peroxide Capsule U 24
Here, we obtained a kerosene-soluble form of the lithium salt [UO 2 (O 2 )(OH) 2 ] 24 phase (Li-U 24 ), by adding cetyltrimethylammonium bromide surfactant to aqueous Li-U 24 . Interestingly, its variable-temperature solution 7 Li NMR spectroscopy resolves two narrowly spaced resonances down to –10 °C, which shift upfield with increasing temperature, and finally coalesce at temperatures > 85 °C. Comparison with solid-state NMR demonstrates that the Li dynamics in the Li-U 24 -CTA phase involves only exchange between different local encapsulated environments. This behavior is distinct from the rapid Li exchange dynamics observed between encapsulated and external Li environments for Li-U 24 in both the aqueous and the solid-state phases. Density functional theory calculations suggest that the two experimental 7 Li NMR chemical shifts are due to Li cations coordinated within the square and hexagonal faces of the U 24 cage, and they can undergo exchange within the confined environment, as the solution is heated. Very different than U 24 in aqueous media, there is no evidence that the Li cations exit the cage, and therefore, this represents a truly confined space.
Frustration and Glasslike Character in RIn 1–x Mn x O 3 (R = Tb, Dy, Gd)
Here, we bring together ac susceptibility and dc magnetization to uncover the rich magnetic field-temperature behavior of a series of rare earth indium oxides, RInO 3 (R = Tb, Dy, and Gd). The degree of frustration is much larger than expected, particularly in TbInO 3 , and the ground states are glasslike with antiferromagnetic tendencies. The activation energy for spin reorientation is low. Chemical substitution with Mn 3+ ions to form TbIn 1–x Mn x O 3 (x ≤ 0.01) relieves much of the frustration that characterizes the parent compound and slightly enhances the short-range antiferromagnetic order. The phase diagrams developed from this work reveal the rich competition between spin orders and provide an opportunity to compare the dynamics in the RInO 3 and Mn-substituted systems. Finally, these structure–property relations may be useful for understanding magnetism in other geometrically frustrated multiferroics.
Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. In this work, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (~98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ~1.5 million atoms is discussed in the context of MuMMI.
Peptide Bond Isomerization in High-Temperature Simulations
Explore the source record for details and available documents.
Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field
Whether lipid rafts are present in the membranes of living cells remains hotly disputed despite their incontrovertible existence in liposomes at 298 K. In attempts to resolve this debate, molecular dynamics (MD) simulations have been extensively used to study lipid phase separation at high resolution. However, computation has been of limited utility in this respect because the experimental distributions of phases in lamellar lipid mixtures are poorly reproduced by simulations. In particular, all-atom (AA) approaches suffer from restrictions on accessible time scales and system sizes whereas the more efficient coarse-grained (CG) force fields remain insufficiently accurate to achieve correspondence with experiment. We refine the CG Martini parameters for the high- and low-melting temperature (T m ) lipids 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC). Our approach involves the modification of bonded Martini parameters based on fitting to atomistic simulations conducted with the CHARMM36 lipid force field. The resulting CG parameters reproduce experimental structural and thermodynamic properties of homogeneous lipid membranes while concurrently improving simulation fidelity to experimental phase diagrams of DPPC, DOPC, and cholesterol lipid mixtures. Importantly, the refined parameters provide much better phase accuracy for regions near the critical point that mimic the lipid concentrations under physiological conditions.
Toward the Validation of Maternal Embryonic Leucine Zipper Kinase: Discovery, Optimization of Highly Potent and Selective Inhibitors, and Preliminary Biology Insight
MELK kinase has been implicated in playing an important role in tumorigenesis. Our previous studies suggested that MELK is involved in the regulation of cell cycle and its genetic depletion leads to growth inhibition in a subset of high MELK-expressing basal-like breast cancer cell lines. Herein we describe the discovery and optimization of novel MELK inhibitors 8a and 8b that recapitulate the cellular effects observed by short hairpin ribonucleic acid (shRNA)-mediated MELK knockdown in cellular models. We also discovered a novel fluorine-induced hydrophobic collapse that locked the ligand in its bioactive conformation and led to a 20-fold gain in potency. Here, these novel pharmacological inhibitors achieved high exposure in vivo and were well tolerated, which may allow further in vivo evaluation.
Discovery of N -((3 R ,4 R )-4-Fluoro-1-(6-((3-methoxy-1-methyl-1 H -pyrazol-4-yl)amino)-9-methyl-9 H -purin-2-yl)pyrrolidine-3-yl)acrylamide (PF-06747775) through Structure-Based Drug Design: A High Affinity Irreversible Inhibitor Targeting Oncogenic EGFR Mutants with Selectivity over Wild-Type EGFR
Abstract not provided
Optimization of Orally Bioavailable Enhancer of Zeste Homolog 2 (EZH2) Inhibitors Using Ligand and Property-Based Design Strategies: Identification of Development Candidate (R)-5,8-Dichloro-7-(methoxy(oxetan-3-yl)methyl)-2-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-3,4-dihydroisoquinolin-1(2H)-one (PF-06821497)
Abstract not provided
CpFe(CO) 2 Radical Generated from Dinuclear [CpFe(CO) 2 ] 2 and Mononuclear (Cp)(CO) 2 Fe(H): Density Functional Theory Is Accurate for One, But Not Both
Density functional theory (DFT) methods remain the most practical approach to calculating properties and reaction mechanisms of transition metal complexes. While the accuracy of DFT methods has been evaluated for some properties of mononuclear organometallic complexes there has been a general lack of evaluation for dinuclear organometallic complexes, in particular bonding changes related to reaction mechanisms. Here, this work evaluated DFT and coupled cluster methods for the accuracy of calculating the CpFe(CO) 2 radical (Fp•) generated from dinuclear [CpFe(CO) 2 ] 2 (Fp 2 ) and mononuclear [(Cp)(CO) 2 Fe(H)] (Fp-H). This transition metal radical fragment was evaluated because dinuclear complexes built with it have recently shown a variety of unique reactions but has proven challenging to accurately calculate with DFT methods. Here we show that DFT methods provide a surprising wide range of fragmentation energies for Fp 2 and lower and mid rung DFT methods as well as DLPNO–CCSD(T) perform well for this dissociation energy. The highest rung double-hybrid methods have a large range in the Fp 2 dissociation energy, and the energy greatly depends on the amount of MP2 correlation energy included. For generating Fp• from Fp-H the lower and mid rung methods that worked well for Fp 2 showed significant error. Double-hybrid methods unfortunately are only accurate for the Fe–H bond if they are very inaccurate for the Fp 2 dissociation energy. While DLPNO–CCSD(T) is not perfect, and not close to chemically accurate for the Fe–H bond, it does provide reasonable accuracy for both Fp 2 and Fp-H dissociation energies.