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At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Bimolecular Reductive Elimination of Ethane from Pyridine(diimine) Iron Methyl Complexes: Mechanism, Electronic Structure, and Entry into [2+2] Cycloaddition Catalysis

The application of bimolecular reductive elimination to the activation of iron catalysts for alkene–diene cycloaddition is described. Key to this approach was the synthesis, characterization, electronic structure determination, and ultimately solution stability of a family of pyridine(diimine) iron methyl complexes with diverse steric properties and electronic ground states. Both the aryl-substituted, ( Me PDI)FeCH 3 and ( Et PDI)FeCH 3 ( R PDI = 2,6-(2,6-R 2 -C 6 H 3 N=CMe) 2 C 5 H 3 N), and the alkyl-substituted examples, ( Cy APDI)FeCH 3 ( Cy APDI = 2,6-(C 6 H 11 N=CMe) 2 C 5 H 3 N), have molecular structures significantly distorted from planarity and S = 3/2 ground states. The related N-arylated derivative bearing 2,6-di-isopropyl aryl substituents, ( iPr PDI)FeCH 3 , has an idealized planar geometry and exhibits spin crossover behavior from S = 1/2 to S = 3/2 states. At 23 °C under an N 2 atmosphere, both ( Me PDI)FeCH 3 and ( Et PDI)FeCH 3 underwent reductive elimination of ethane to form the iron dinitrogen precatalysts, [( Me PDI)Fe(N 2 )] 2 (μ-N 2 ) and [( Et PDI)Fe(N 2 )] 2 (μ-N 2 ), respectively, while ( iPr PDI)FeCH 3 proved inert to C–C bond formation. By contrast, addition of butadiene to all three iron methyl complexes induced ethane formation and generated the corresponding iron butadiene complexes, ( R PDI)Fe(η 4 -C 4 H 6 ) (R = Me, Et, i Pr), known precatalysts for the [2+2] cycloaddition of olefins and dienes. Kinetic, crossover experiments, and structural studies were combined with magnetic measurements and Mössbauer spectroscopy to elucidate the electronic and steric features of the iron complexes that enable this unusual reductive elimination and precatalyst activation pathway. Furthermore, transmetalation of methyl groups between iron centers was fast at ambient temperature and independent of steric environment or spin state, while the intermediate dimer underwent the sterically controlled rate-determining reaction with either N 2 or butadiene to access a catalytically active iron compound.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structure, magnetic and complex impedance analysis of (1-x)BaTiO{sub 3}- xMgFe{sub 2}O{sub 4} composite

MgFe{sub 2}O{sub 4} was synthesized by using sol-gel auto-combustion technique and coupled with BaTiO{sub 3} using the conventional solid state reaction method with different weight fraction of x = 0.00, 0.02, 0.04, 0.06 and 0.08 to form (1-x)BaTiO{sub 3} - xMgFe{sub 2}O{sub 4} composite. The structure, magnetic properties and complex impedance analysis of the composite samples were studied using X-ray diffraction technique (XRD), scanning electron microscopy (SEM) and vibrating sample magnetometer (VSM) and High-frequency response analyzer (HFRA) respectively. XRD patterns showed a single phase tetragonal BaTiO{sub 3} for each composition due to the very small amount of MgFe{sub 2}O{sub 4}. The hysteresis loop confirmed that the composite has soft magnetic properties by addition of MgFe{sub 2}O{sub 4}. Small coercive field, HC has been recorded and it decreased with the increasing of MgFe{sub 2}O{sub 4} weight fraction. However, magnetization increased when the amount of MgFe{sub 2}O{sub 4} is increased. Impedance analysis conducted in range of 0.1 Hz to 10 MHz showed two depressed semicircle arcs for samples with MgFe{sub 2}O{sub 4} due to the resistive and capacitive behavior of the bulk and grain boundaries of the samples.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Pnictogen Bonding at the Core of a Carbene-Stiborane-Gold Complex: Impact on Structure and Reactivity

Our interest in the design of ambiphilic ligands and their coordination to gold has led us to synthesize an indazol-3-ylidene gold chloride complex functionalized at the 4-position of the indazole backbone by a stibine functionality. The antimony center of this new complex cleanly reacts with o-chloranil to afford the corresponding stiborane derivative. Structural analysis indicates that the stiborane coordination environment is best described as a distorted square pyramid whose open face is oriented toward the gold center, allowing for the formation of a long donor–acceptor, or pnictogen, Au → Sb bonding interaction. The presence of this interaction, which has been probed computationally, is also manifested in the enhanced catalytic activity of this complex in the cyclization of N-propargyl-4-fluorobenzamide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A , which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K + , Zn 2+ , Pb 2+ ) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic–inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm –1 for Pb(II) and ca. 1580 cm –1 for Zn(II) are consistent with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. These complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble

During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-Å resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the σ factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural Evaluation of Complex Subcomponents Manufactured by Large Scale Extrusion Deposition of Carbon Fiber Reinforced ABS

The large scale extrusion deposition process has recently been commercialized in the form of additive manufacturing machines such as the BAAM from Cincinnati Inc., which enables layered production of chopped fiber reinforced thermoplastic polymer systems. The application of this process to the automotive market is being pursued by Local Motors to enable rapid design to market cycles and build on-demand capability for a wide range of vehicle styles from a distributed network of micro-factories. This endeavor will require an understanding of the structural performance of components with complex geometries, where the properties are known to vary as a function of printing conditions, as well as orientation and shape. In order to rapidly build a database of structural performance, a beam specimen with outer dimensions of 914 x 305 x 64 mm3 was selected to be subjected to bending, torsion, and shear loading with full field displacement measurement by digital image correlation (DIC). A total of 25 different specimen configurations were designed including variation of print geometry, reinforcement by foam filling, and overwrapping with advanced composites. This work documents the results of the study and presents the relative performance of the structures in addition to the approach to simulation that is being initiated to serve as a framework for efficient design of structures manufactured in this way. The results are presented as a table of structural efficiency including stiffness and strength as functions of mass for each design. Additional results will also be provided in the form of surface displacements from DIC; future work will utilize this data to better optimize simulations for predicting structural performance of articles manufactured by this process.

Bedsole, Robert↗
DOE OSTI2014

Modeling and Algorithmic Approaches to Constitutively-Complex, Micro-structured Fluids

The team for this Project made significant progress on modeling and algorithmic approaches to hydrodynamics of fluids with complex microstructure. Our advances are broken down into modeling and algorithmic approaches. In experiments a driven magnetic bead in a complex fluid accelerates out of the Stokes regime and settles into another apparent linear response regime. The modeling explains the take-off as a deformation of entanglements, and the longtime behavior is a nonlinear, far-from-equilibrium property. Furthermore, the model has predictive value, as we can tune microstructural properties relative to the magnetic force applied to the bead to exhibit all possible behaviors. Wave-theoretic probes of complex fluids have been extended in two significant directions, to small volumes and the nonlinear regime. Heterogeneous stress and strain features that lie beyond experimental capability were studied. It was shown that nonlinear penetration of boundary stress in confined viscoelastic fluids is not monotone, indicating the possibility of interlacing layers of linear and nonlinear behavior, and thus layers of variable viscosity. Models, algorithms, and codes were developed and simulations performed leading to phase diagrams of nanorod dispersion hydrodynamics in parallel shear cells and confined cavities representative of film and membrane processing conditions. Hydrodynamic codes for polymeric fluids are extended to include coupling between microscopic and macroscopic models, and to the strongly nonlinear regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

A complex approach to assessing porous structure of structured ceramics obtained by SPS technique

Highlights: • A complex approach to microstructural analysis of nanostructured SPS ceramics was presented. • A bunch of gas, intrusion and microscopic methods were applied for open/closed porosity determination in nanoceramics. • Kinetic TPR analysis for structural changes in nanoceramic was carried out. • 3D pore visualization for nanoceramics was provided via SEM/FIB tomography • Porosity calculations were performed via BET, BJH, t-plot, Washburn equation, FEI Avizo 9.1 software results. - Abstract: Spark plasma sintering (SPS) is a highly prospective technology providing rapid consolidation of nano-disperse compositions into structured ceramics with complex structural organization. Characterizing pore structure of such systems remains a challenge due to different types, size and shape of the pores as well as structural defects occurring in the material, thus requiring special methods to quantify certain porosity type. The paper presents a complex approach to studying structure of SPS hematite-based structured ceramics. The method involves a number of gas, intrusion and electron microscopy probing techniques to characterize open and closed pores in the ceramics bulk. Low temperature nitrogen sorption has been implemented to estimate open micro- and mesoporosity in the size range 0.7–50 nm using BET, BJH and t-plot methods to process experimental data. Additionally, structural peculiarities of consolidated structured ceramics have been studied using temperature-programmed reduction (TPR) with the kinetic analysis of the results being carried out. Volume of macropores sized above 50 nm has been measured with mercury intrusion. Closed pores and structural defects have been quantified with SEM and FIB/SEM tomography. By comparing experimental and estimated results we have shown that addressing all porosity types provides a highly precise structural characterization of the material.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Synthesis and structures of zirconium complexes [Et{sub 2}H{sub 2}N]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–}, [Me{sub 3}NCH{sub 2}Ph]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–}•MeCN, [Ph{sub 3}PC{sub 6}H{sub 4}(CHPh{sub 2}-4)]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–}•2 MeCN, and [Ph{sub 4}Sb]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–}

The complexes [Et{sub 2}H{sub 2}N]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–} (1), [Me{sub 3}NCH{sub 2}Ph]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–}•MeCN (2), [Ph{sub 3}PC{sub 6}H{sub 4}(CHPh{sub 2}-4)]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–}•2 MeCN (3), and [Ph{sub 4}Sb]{sup +}{sub 2}[ZrCl{sub 6}]{sup 2–} (4) were synthesized by the reaction of zirconium tetrachloride with tetraorganylammonium, -phosphonium, and -stibonium chlorides in acetonitrile and structurally characterized. The nitrogen, phosphorus, and antimony atoms in the cations have a distorted tetrahedral geometry. The Zr–Cl distances in the centrosymmetric octahedral [ZrCl{sub 6}]{sup 2−} anions of complexes 1–4 have similar values, the longest bonds being observed in the anion of complex 4. Acetonitrile molecules are involved in the structural organization of the crystals of complex 3via weak hydrogen bonding with phenyl hydrogen atoms of the organylphosphonium cations. In the crystal of 2, no hydrogen bonds between the cations and solvent molecules are observed; acetonitrile molecules fill the cavities formed by cations and anions.

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

Structural study of complexes formed by acidic and neutral organophosphorus reagents

The coordination of the trivalent 4f ions, Ln = La 3+ , Dy 3+ , and Lu 3+ , with neutral and acidic organophosphorus reagents, both individually and combined, was studied by use of X-ray absorption spectroscopy. These studies provide metrical information about the interatomic interactions between these cations and the ligands tri- n -butyl phosphate (TBP) and di- n -butyl phosphoric acid (HDBP), whose behavior are of practical importance to chemical separation processes that are currently used on an industrial scale. Previous studies have suggested the existence of complexes involving a mixture of ligands, accounting for extraction synergy. Through systematic variation of the aqueous phase acidity and extractant concentration and combination, we have found that complexes with Ln and TBP : HDBP at any mixture and HDBP alone involve direct Ln–O interactions involving 6 oxygen atoms and distant Ln–P interactions involving on average 3–5 phosphorus atoms per Ln ion. It was also found that Ln complexes formed by TBP alone seem to favor eight oxygen coordination, though we were unable to obtain metrical results regarding the distant Ln–P interactions due to the low signal attributed to a lower concentration of Ln ions in the organic phases. Our study does not support the existence of mixed Ln–TBP–HDBP complexes but, rather, indicates that the lanthanides are extracted as either Ln–HDBP complexes or Ln–TBP complexes and that these complexes exist in different ratios depending on the conditions of the extraction system. Furthermore, this fundamental structural information offers insight into the solvent extraction processes that are taking place and are of particular importance to issues arising from the separation and disposal of radioactive materials from used nuclear fuel.

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

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

Wasmuth, Elizabeth V.↗
DOE OSTI2014

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2016

Influence of Copper Oxidation State on the Bonding and Electronic Structure of Cobalt-Copper Complexes

Heterobimetallic complexes that pair cobalt and copper were synthesized and characterized by a suite of physical methods, including X-ray diffraction, X-ray anomalous scattering, cyclic voltammetry, magnetometry, electronic absorption spectroscopy, electron paramagnetic resonance, and quantum chemical methods. Both Cu(II) and Cu(I) reagents were independently added to a Co(II) metalloligand to provide (py 3 tren)CoCuCl (1-Cl) and (py 3 tren)CoCu(CH 3 CN) (2-CH 3 CN), respectively, where py3tren is the triply deprotonated form of N,N,N-tris(2-(2-pyridylamino)ethyl)amine. Complex 2-CH 3 CN can lose the acetonitrile ligand to generate a coordination polymer consistent with the formula “(py3tren)CoCu” (2). One-electron chemical oxidation of 2-CH 3 CN with AgOTf generated (py 3 tren)CoCuOTf (1-OTf). The Cu(II)/Cu(I) redox couple for 1-OTf and 2-CH 3 CN is reversible at -0.56 and -0.33 V vs Fc + /Fc, respectively. The copper oxidation state impacts the electronic structure of the heterobimetallic core, as well as the nature of the Co–Cu interaction. Quantum chemical calculations showed modest electron delocalization in the (CoCu) +4 state via a Co–Cu σ bond that is weakened by partial population of the Co–Cu σ antibonding orbital. By contrast, no covalent Co–Cu bonding is predicted for the (CoCu) +3 analogue, and the d-electrons are fully localized at individual metals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗