Spectroscopic and computational insight into the activation of O2 by the mononuclear Cu center in polysaccharide monooxygenases.

PubMed

Kjaergaard, Christian H; Qayyum, Munzarin F; Wong, Shaun D; Xu, Feng; Hemsworth, Glyn R; Walton, Daniel J; Young, Nigel A; Davies, Gideon J; Walton, Paul H; Johansen, Katja Salomon; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

2014-06-17

Strategies for O2 activation by copper enzymes were recently expanded to include mononuclear Cu sites, with the discovery of the copper-dependent polysaccharide monooxygenases, also classified as auxiliary-activity enzymes 9-11 (AA9-11). These enzymes are finding considerable use in industrial biofuel production. Crystal structures of polysaccharide monooxygenases have emerged, but experimental studies are yet to determine the solution structure of the Cu site and how this relates to reactivity. From X-ray absorption near edge structure and extended X-ray absorption fine structure spectroscopies, we observed a change from four-coordinate Cu(II) to three-coordinate Cu(I) of the active site in solution, where three protein-derived nitrogen ligands coordinate the Cu in both redox states, and a labile hydroxide ligand is lost upon reduction. The spectroscopic data allowed for density functional theory calculations of an enzyme active site model, where the optimized Cu(I) and (II) structures were consistent with the experimental data. The O2 reactivity of the Cu(I) site was probed by EPR and stopped-flow absorption spectroscopies, and a rapid one-electron reduction of O2 and regeneration of the resting Cu(II) enzyme were observed. This reactivity was evaluated computationally, and by calibration to Cu-superoxide model complexes, formation of an end-on Cu-AA9-superoxide species was found to be thermodynamically favored. We discuss how this thermodynamically difficult one-electron reduction of O2 is enabled by the unique protein structure where two nitrogen ligands from His1 dictate formation of a T-shaped Cu(I) site, which provides an open coordination position for strong O2 binding with very little reorganization energy.

Synthesis and crystal structure of the coordination compound of pyridoxine with manganese sulfate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Furmanova, N. G., E-mail: furm@ns.crys.ras.ru; Verin, I. A.; Shyityeva, N.

2011-11-15

The reaction of pyridoxine with manganese sulfate in an aqueous solution gave the coordination compound MnSO{sub 4} {center_dot} 2C{sub 8}H{sub 11}O{sub 3}N {center_dot} 2H{sub 2}O (I). The structure of I was determined from single-crystal X-ray diffraction data. In the centrosymmetric complex (sp. gr. P1-bar, Z = 1), the Mn atom is coordinated by two pyridoxine molecules and two water molecules, thus adopting an octahedral coordination. The sulfate anion is also at a center of symmetry and, consequently, is disordered. The pyridoxine molecules are coordinated to the metal atom through the oxygen atoms of the deprotonated hydroxyl group and the CH{submore » 2}OH group that retains the hydrogen atom. The nitrogen atom is protonated in such a way that the heterocycle assumes a pyridinium character. The crystal structure also contains six water molecules of crystallization. A thermogravimetric study showed that the decomposition of I occurs in several successive steps, such as dehydration, the combustion of organic ligands, and the formation of an inorganic residue.« less

Mechanism for chelated sulfate formation from SO2 and bis (triphenylphosphine) platinum

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1985-01-01

Structure and energy surface calculations using the atom superposition and electron delocalization molecular orbital theory show that the first step in the reaction between SO2 and the dioxygen complex (PPh3)2PtO2 is the coordination of SO2 with one oxygen atom of the complex, followed by metal-oxygen bond breaking and reorientation, leading to a five-membered cyclic structure. This then rearranges to form the bidentate coordinated sulfate. Alternative pathways are considered and are found to be less favorable.

Structural Characterization of a Human-Type Corrinoid Adenosyltransferase Confirms That Coenzyme B[subscript 12] Is Synthesized through a Four-Coordinate Intermediate

DOE Office of Scientific and Technical Information (OSTI.GOV)

St. Maurice, Martin; Mera, Paola; Park, Kiyoung

ATP:cob(I)alamin adenosyltransferases (ACAs) catalyze the transfer of the 5{prime}-deoxyadenosyl moiety from ATP to the upper axial ligand position of cobalamin in the synthesis of coenzyme B{sub 12}. For the ACA-catalyzed reaction to proceed, cob(II)alamin must be reduced to cob(I)alamin in the enzyme active site. This reduction is facilitated through the generation of a four-coordinate cob(II)alamin intermediate on the enzyme. We have determined the high-resolution crystal structure of a human-type ACA from Lactobacillus reuteri with a four-coordinate cob(II)alamin bound in the enzyme active site and with the product, adenosylcobalamin, partially occupied in the active site. The assembled structures represent snapshots ofmore » the steps in the ACA-catalyzed formation of the cobalt-carbon bond of coenzyme B{sub 12}. The structures define the corrinoid binding site and provide visual evidence for a base-off, four-coordinate cob(II)alamin intermediate. The complete structural description of ACA-mediated catalysis reveals the molecular features of four-coordinate cob(II)alamin stabilization and provides additional insights into the molecular basis for dysfunction in human patients suffering from methylmalonic aciduria.« less

A General Model of Sensitized Luminescence in Lanthanide-Based Coordination Polymers and Metal-Organic Framework Materials.

PubMed

Einkauf, Jeffrey D; Clark, Jessica M; Paulive, Alec; Tanner, Garrett P; de Lill, Daniel T

2017-05-15

Luminescent lanthanides containing coordination polymers and metal-organic frameworks hold great potential in many applications due to their distinctive spectroscopic properties. While the ability to design coordination polymers for specific functions is often mentioned as a major benefit bestowed on these compounds, the lack of a meaningful understanding of the luminescence in lanthanide coordination polymers remains a significant challenge toward functional design. Currently, the study of these compounds is based on the antenna effect as derived from molecular systems, where organic antennae are used to facilitate lanthanide-centered luminescence. This molecular-based approach does not take into account the unique features of extended network solids, particularly the formation of band structure. While guidelines for the antenna effect are well established, they require modification before being applied to coordination polymers. A series of nine coordination polymers with varying topologies and organic linkers were studied to investigate the accuracy of the antenna effect in coordination polymer systems. By comparing a molecular-based approach to a band-based one, it was determined that the band structure that occurs in aggregated organic solids needs to be considered when evaluating the luminescence of lanthanide coordination polymers.

A novel function of WAVE in lamellipodia: WAVE1 is required for stabilization of lamellipodial protrusions during cell spreading.

PubMed

Yamazaki, Daisuke; Fujiwara, Takashi; Suetsugu, Shiro; Takenawa, Tadaomi

2005-05-01

When a cell spreads and moves, reorganization of the actin cytoskeleton pushes the cell membrane, and the resulting membrane protrusions create new points of contact with the substrate and generate the locomotive force. Membrane extension and adhesion to a substrate must be tightly coordinated for effective cell movement, but little is known about the mechanisms underlying these processes. WAVEs are critical regulators of Rac-induced actin reorganization. WAVE2 is essential for formation of lamellipodial structures at the cell periphery stimulated by growth factors, but it is thought that WAVE1 is dispensable for such processes in mouse embryonic fibroblasts (MEFs). Here we show a novel function of WAVE in lamellipodial protrusions during cell spreading. During spreading on fibronectin (FN), MEFs with knockouts (KOs) of WAVE1 and WAVE2 showed different membrane dynamics, suggesting that these molecules have distinct roles in lamellipodium formation. Formation of lamellipodial structures on FN was inhibited in WAVE2 KO MEFs. In contrast, WAVE1 is not essential for extension of lamellipodial protrusions but is required for stabilization of such structures. WAVE1-deficiency decreased the density of actin filaments and increased the speed of membrane extension, causing deformation of focal complex at the tip of spreading edges. Thus, at the tip of the lamellipodial protrusion, WAVE2 generates the membrane protrusive structures containing actin filaments, and modification by WAVE1 stabilizes these structures through cell-substrate adhesion. Coordination of WAVE1 and WAVE2 activities appears to be necessary for formation of proper actin structures in stable lamellipodia.

Influence of conformational changes on spin crossover properties and superstructure formation in 2D coordination polymers [Fe(hbtz)2(RCN)2](ClO4)2.

PubMed

Książek, Maria; Kusz, Joachim; Białońska, Agata; Bronisz, Robert; Weselski, Marek

2015-11-14

2D structurally related iron(ii) coordination networks {[Fe(hbtz)2(RCN)2](ClO4)2}∞ featuring, besides tetrazol-2-yl rings in the first coordination sphere, also axially coordinated propionitrile or allyl cyanide molecules (R = C3H5-, 1; R = C2H5-, 2) were synthesized. Thermally induced spin crossover (SCO) in 1 takes place in two poorly resolved stages (T(1)1/2(↓) = T(1)1/2(↑) = 198 K, T(2)1/2(↓) = 170 K, T(2)1/2(↑) = 171 K) whereas in 2 complete and relatively gradual one step SCO (T1/2(↓) = T1/2(↑) = 160 K) occurs. Diversification of the SCO properties of the complexes originates from the ability of coordinated allyl cyanide in 1 to undergo conformational alterations, which is not observed for propionitrile molecules in 2. SCO in 1 is accompanied by a non-monotonic change of the contribution of allyl cyanide conformers which is related to reconstruction of the network of intermolecular contacts established between polymeric layers. The coordination network 1 exhibits extraordinary elasticity and in the second stage SCO, accompanied by conformational changes of allyl cyanide, triggers a crystallographic phase transition which leads to the formation of a superstructure. What is important, the formation of the superstructure is not caused by long range ordering of HS and LS iron(ii) ions. The structural alteration is associated with corrugation of the polymeric skeleton and disappearance of nitrile disorder. Irradiation of a single crystal of 1 at 15 K with laser light (520 nm) allowed producing a novel low temperature HS phase of 1 in which, contrary to the high temperature HS phase, disordering of anion and allyl cyanide molecules is not observed and the corrugated nature of the polymeric layer, characteristic of the LS phase, is preserved.

Implementing the Cognitive Orientation to daily Occupational Performance (CO-OP) approach in a group format with children living with motor coordination difficulties.

PubMed

Anderson, Leanne; Wilson, Jessie; Carmichael, Kaity

2018-05-28

Children with developmental coordination disorder demonstrate limited participation in daily occupations which negatively impacts on their physical and psycho-social wellbeing. Literature is emerging supporting the use of the Cognitive Orientation to daily Occupational Performance (CO-OP) within a group format. The purpose of this study was to explore the feasibility of the CO-OP approach in a group format for children with motor coordination difficulties. A single group mixed-method approach was employed. Four children with motor coordination difficulties between seven-to-nine years of age and their mothers, participated in a CO-OP group intervention once a week over 10 weeks. The study examined performance (perceived and actual) and satisfaction of family-chosen goals, gross and fine motor functioning and parental experience of participating in the intervention. Improvements in performance (perceived) and satisfaction ratings of family-chosen goals bordered on achieving statistical significance. Fine and gross motor functioning and performance (actual) improved, however, the change in performance was variable between participants and among the overarching goals. Semi-structured interviews were thematically analysed. Themes included: formation of the group, moving from disenabling to enabling, belonging and the importance of small successes. CO-OP offers a feasible intervention approach when delivered in a group format. Parental perceptions are valuable in shaping the delivery of the CO-OP in future studies. More research is needed to support these findings and contribute to evidence-based practice. © 2018 Occupational Therapy Australia.

Anillin acts as a bifunctional linker coordinating midbody ring biogenesis during cytokinesis

PubMed Central

Kechad, Amel; Jananji, Silvana; Ruella, Yvonne; Hickson, Gilles R. X.

2013-01-01

Summary Animal cell cytokinesis proceeds via constriction of an actomyosin-based contractile ring (CR) [1, 2]. Upon reaching a diameter of ~1 μm [3], a midbody ring (MR) forms to stabilize the intercellular bridge until abscission [4-6]. How MR formation is coupled to CR closure and how plasma membrane anchoring is maintained at this key transition is unknown. Time-lapse microscopy of Drosophila S2 cells depleted of the scaffold protein, Anillin [7-9], revealed that Anillin is required for complete closure of the CR and formation of the MR. Truncation analysis revealed that Anillin N-termini connected with the actomyosin CR and supported formation of stable MR-like structures, but these could not maintain anchoring of the plasma membrane. Conversely, Anillin C-termini failed to connect with the CR or MR but recruited the septin, Peanut, to ectopic structures at the equatorial cortex. Peanut depletion mimicked truncation of the Anillin C-terminus, resulting in MR-like structures that failed to anchor the membrane. These data demonstrate that Anillin coordinates the transition from CR to MR, and that it does so by linking two distinct cortical cytoskeletal elements. One apparently acts as the core structural template for MR assembly, while the other ensures stable anchoring of the plasma membrane beyond the CR stage. PMID:22226749

Six-coordinate manganese(3+) in catalysis by yeast manganese superoxide dismutase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Yuewei; Gralla, Edith Butler; Schumacher, Mikhail

Reduction of superoxide (O{sub 2}{sup -}) by manganese-containing superoxide dismutase occurs through either a 'prompt protonation' pathway, or an 'inner-sphere' pathway, with the latter leading to formation of an observable Mn-peroxo complex. We recently reported that wild-type (WT) manganese superoxide dismutases (MnSODs) from Saccharomyces cerevisiae and Candida albicans are more gated toward the 'prompt protonation' pathway than human and bacterial MnSODs and suggested that this could result from small structural changes in the second coordination sphere of manganese. We report here that substitution of a second-sphere residue, Tyr34, by phenylalanine (Y34F) causes the MnSOD from S. cerevisiae to react exclusivelymore » through the 'inner-sphere' pathway. At neutral pH, we have a surprising observation that protonation of the Mn-peroxo complex in the mutant yeast enzyme occurs through a fast pathway, leading to a putative six-coordinate Mn3+ species, which actively oxidizes O{sub 2}{sup -} in the catalytic cycle. Upon increasing pH, the fast pathway is gradually replaced by a slow proton-transfer pathway, leading to the well-characterized five-coordinate Mn{sup 3+}. We here propose and compare two hypothetical mechanisms for the mutant yeast enzyme, diffeeing in the structure of the Mn-peroxo complex yet both involving formation of the active six-coordinate Mn{sup 3+} and proton transfer from a second-sphere water molecule, which has substituted for the -OH of Tyr34, to the Mn-peroxo complex. Because WT and the mutant yeast MnSOD both rest in the 2+ state and become six-coordinate when oxidized up from Mn{sup 2+}, six-coordinate Mn{sup 3+} species could also actively function in the mechanism of WT yeast MnSODs.« less

Case study of how successful coordination was achieved between a mental health and social care service in Sweden.

PubMed

Hansson, Johan; Øvretveit, John; Brommels, Mats

2012-01-01

This paper summarises the findings from an empirical longitudinal study of a health and social care consortium for people with mental health problems in one area in Stockholm. The aim was to describe the formation and structure of coordination within the consortium, and to assess the intermediate impact on care processes and client outcomes. A multiple-method case study design, theoretically informed by the Pettigrew and Whipp model of strategic change (1993) was applied. Data was gathered from interviews with informants from different organisations at different times in the development of the consortium, and from administrative documents, plans and service statistics showing some of the intermediate changes and client outcomes. The findings revealed activities and factors both helping and hindering the formation of coordination arrangements. One of the most significant hindering factors was the central county purchasing organisation focusing more on volume and costs, with payments for specific units and services, and with less emphasis on quality of the services. Few studies have described implementation of changes to improve coordination with reference to context over a long period of time, as well as assessing different results. This study contributes to knowledge about improved methods for this type of research, as well as knowledge about developing coordination between public health and welfare services. One lesson for the current policy is that, where full structural integration is not possible, then client-level coordination roles in each sector are useful to connect sector services for shared clients. Copyright © 2011 John Wiley & Sons, Ltd.

Synthesis, crystal structure, and luminescent properties of two coordination polymers based on 1,4-phenylenediacetic acid

NASA Astrophysics Data System (ADS)

Zhang, Meili; Ren, Yixia; Ma, Zhenzhen; Qiao, Lei

2017-06-01

Two coordination polymers, [Zn(pda)(bib)]n (1) and [Cd(pda)0.5(bib)Cl]n (2)]. (H2pda = 1,4-phenylenediacetic acid, bib = 1,2-bis(imidazol-1-ylmethyl)benzene), have been synthesized by using Zn(II)/Cd(II) salts with two flexible ligands pda and bib under hydrothermal conditions. Their structures have been characterized by elemental analysis, IR spectroscopy, single-crystal X-ray crystallography and powder X-ray diffraction (PXRD) analysis. Due to the coordination geometry around the metal ions and the diverse coordination modes of the flexible ligands, the obtained complex show diverse structures. In the structure of 1, a pair of bib ligands connect two Zn(II) atoms give rise a 22-membered ring, which is further extended by pda ligands in bidentate coordination mode leading a ring-containing 2D layer. In 2, bib ligands join [Cd2Cl2]2+ dimmers generate 1D polymeric ribbon, the pda ligands further extend such ribbon forming a 2D layer network containing rectangular windows, which discovers the effect of the central metal ions on the formation of metal-organic frameworks. In additional, luminescent properties of two complexes have also been studied, they could be potential fluorescence materials.

DOTA analogues with a phosphinate-iminodiacetate pendant arm: modification of the complex formation rate with a strongly chelating pendant.

PubMed

Procházková, Soňa; Kubíček, Vojtěch; Böhmová, Zuzana; Holá, Kateřina; Kotek, Jan; Hermann, Petr

2017-08-08

The new ligand H 6 do3aP ida combines the macrocyclic DOTA-like cavity and the open-chain iminodiacetate group connected through a coordinating phosphinate spacer. Its acid-base and coordination properties in solution were studied by potentiometry. Thermodynamic coordination characteristics of both chelating units are similar to those reported for H 4 dota and iminodiacetic acid themselves, respectively, so, macrocyclic and iminodiacetate units behave independently. The formation kinetics of the Ce(iii)-H 6 do3aP ida complex was studied by UV-Vis spectrophotometry. Various out-of-cage intermediates were identified with 1 : 1, 1 : 2 and 2 : 1 ligand-to-metal ratios. The presence of the strongly coordinating iminodiacetate group significantly slows down the metal ion transfer into the macrocyclic cavity and, so, the formation of the in-cage complex is two orders of magnitude slower than that reported for the Ce(iii)-H 4 dota system. The kinetic inertness of the [Ce(do3aP ida )] 3- complex towards acid-assisted dissociation is comparable to that of the [Ce(dota)] - complex. The coordination modes of the ligand are demonstrated in the solid-state structure of [Cu 4 (do3aP ida )(OH)(H 2 O) 4 ]Cl·7.5H 2 O.

Hydrodynamical Aspects of the Formation of Spiral-Vortical Structures in Rotating Gaseous Disks

NASA Astrophysics Data System (ADS)

Elizarova, T. G.; Zlotnik, A. A.; Istomina, M. A.

2018-01-01

This paper is dedicated to numerical simulations of spiral-vortical structures in rotating gaseous disks using a simple model based on two-dimensional, non-stationary, barotropic Euler equations with a body force. The results suggest the possibility of a purely hydrodynamical basis for the formation and evolution of such structures. New, axially symmetric, stationary solutions of these equations are derived that modify known approximate solutions. These solutions with added small perturbations are used as initial data in the non-stationary problem, whose solution demonstrates the formation of density arms with bifurcation. The associated redistribution of angular momentum is analyzed. The correctness of laboratory experiments using shallow water to describe the formation of large-scale vortical structures in thin gaseous disks is confirmed. The computations are based on a special quasi-gas-dynamical regularization of the Euler equations in polar coordinates.

The molecular basis of induction and formation of tunneling nanotubes.

PubMed

Kimura, Shunsuke; Hase, Koji; Ohno, Hiroshi

2013-04-01

Tunneling nanotubes (TNTs) and associated structures are recently recognized structures for intercellular communication. They are F-actin-containing thin protrusions of the plasma membrane of a cell and allow a direct physical connection to the plasma membranes of remote cells. TNTs and associated structures serve as mediators for intercellular transfer of organelles as well as membrane components and cytoplasmic molecules. Moreover, several pathogens have been shown to exploit these structures to spread among cells. Because of their contribution to normal cellular functions and importance in pathological conditions, studies on TNTs and related structures have accelerated over the past few years. These studies have revealed key molecules for their induction and/or formation; HIV Nef and M-Sec can induce the formation of TNTs in coordination with the remodeling of the actin cytoskeleton and vesicle trafficking.

Carbohydrate-mediated responses during zygotic and early somatic embryogenesis in the endangered conifer, Araucaria angustifolia

PubMed Central

Elbl, Paula; De Souza, Amanda P.; Jardim, Vinicius; de Oliveira, Leandro F.; Macedo, Amanda F.; dos Santos, André L. W.; Buckeridge, Marcos S.; Floh, Eny I. S.

2017-01-01

Three zygotic developmental stages and two somatic Araucaria angustifolia cell lines with contrasting embryogenic potential were analyzed to identify the carbohydrate-mediated responses associated with embryo formation. Using a comparison between zygotic and somatic embryogenesis systems, the non-structural carbohydrate content, cell wall sugar composition and expression of genes involved in sugar sensing were analyzed, and a network analysis was used to identify coordinated features during embryogenesis. We observed that carbohydrate-mediated responses occur mainly during the early stages of zygotic embryo formation, and that during seed development there are coordinated changes that affect the development of the different structures (embryo and megagametophyte). Furthermore, sucrose and starch accumulation were associated with the responsiveness of the cell lines. This study sheds light on how carbohydrate metabolism is influenced during zygotic and somatic embryogenesis in the endangered conifer species, A. angustifolia. PMID:28678868

Mutually Exclusive Formation of G-Quadruplex and i-Motif Is a General Phenomenon Governed by Steric Hindrance in Duplex DNA.

PubMed

Cui, Yunxi; Kong, Deming; Ghimire, Chiran; Xu, Cuixia; Mao, Hanbin

2016-04-19

G-Quadruplex and i-motif are tetraplex structures that may form in opposite strands at the same location of a duplex DNA. Recent discoveries have indicated that the two tetraplex structures can have conflicting biological activities, which poses a challenge for cells to coordinate. Here, by performing innovative population analysis on mechanical unfolding profiles of tetraplex structures in double-stranded DNA, we found that formations of G-quadruplex and i-motif in the two complementary strands are mutually exclusive in a variety of DNA templates, which include human telomere and promoter fragments of hINS and hTERT genes. To explain this behavior, we placed G-quadruplex- and i-motif-hosting sequences in an offset fashion in the two complementary telomeric DNA strands. We found simultaneous formation of the G-quadruplex and i-motif in opposite strands, suggesting that mutual exclusivity between the two tetraplexes is controlled by steric hindrance. This conclusion was corroborated in the BCL-2 promoter sequence, in which simultaneous formation of two tetraplexes was observed due to possible offset arrangements between G-quadruplex and i-motif in opposite strands. The mutual exclusivity revealed here sets a molecular basis for cells to efficiently coordinate opposite biological activities of G-quadruplex and i-motif at the same dsDNA location.

Reading PDB: perception of molecules from 3D atomic coordinates.

PubMed

Urbaczek, Sascha; Kolodzik, Adrian; Groth, Inken; Heuser, Stefan; Rarey, Matthias

2013-01-28

The analysis of small molecule crystal structures is a common way to gather valuable information for drug development. The necessary structural data is usually provided in specific file formats containing only element identities and three-dimensional atomic coordinates as reliable chemical information. Consequently, the automated perception of molecular structures from atomic coordinates has become a standard task in cheminformatics. The molecules generated by such methods must be both chemically valid and reasonable to provide a reliable basis for subsequent calculations. This can be a difficult task since the provided coordinates may deviate from ideal molecular geometries due to experimental uncertainties or low resolution. Additionally, the quality of the input data often differs significantly thus making it difficult to distinguish between actual structural features and mere geometric distortions. We present a method for the generation of molecular structures from atomic coordinates based on the recently published NAOMI model. By making use of this consistent chemical description, our method is able to generate reliable results even with input data of low quality. Molecules from 363 Protein Data Bank (PDB) entries could be perceived with a success rate of 98%, a result which could not be achieved with previously described methods. The robustness of our approach has been assessed by processing all small molecules from the PDB and comparing them to reference structures. The complete data set can be processed in less than 3 min, thus showing that our approach is suitable for large scale applications.

Coordination of eye and head components of movements evoked by stimulation of the paramedian pontine reticular formation.

PubMed

Gandhi, Neeraj J; Barton, Ellen J; Sparks, David L

2008-07-01

Constant frequency microstimulation of the paramedian pontine reticular formation (PPRF) in head-restrained monkeys evokes a constant velocity eye movement. Since the PPRF receives significant projections from structures that control coordinated eye-head movements, we asked whether stimulation of the pontine reticular formation in the head-unrestrained animal generates a combined eye-head movement or only an eye movement. Microstimulation of most sites yielded a constant-velocity gaze shift executed as a coordinated eye-head movement, although eye-only movements were evoked from some sites. The eye and head contributions to the stimulation-evoked movements varied across stimulation sites and were drastically different from the lawful relationship observed for visually-guided gaze shifts. These results indicate that the microstimulation activated elements that issued movement commands to the extraocular and, for most sites, neck motoneurons. In addition, the stimulation-evoked changes in gaze were similar in the head-restrained and head-unrestrained conditions despite the assortment of eye and head contributions, suggesting that the vestibulo-ocular reflex (VOR) gain must be near unity during the coordinated eye-head movements evoked by stimulation of the PPRF. These findings contrast the attenuation of VOR gain associated with visually-guided gaze shifts and suggest that the vestibulo-ocular pathway processes volitional and PPRF stimulation-evoked gaze shifts differently.

Electron-beam induced amorphization of stishovite: Silicon-coordination change observed using Si K-edge extended electron energy-loss fine structure

NASA Astrophysics Data System (ADS)

van Aken, P. A.; Sharp, T. G.; Seifert, F.

The analysis of the extended energy-loss fine structure (EXELFS) of the Si K-edge for sixfold-coordinated Si in synthetic stishovite and fourfold-coordinated Si in natural α-quartz is reported by using electron energy-loss spectroscopy (EELS) in combination with transmission electron microscopy (TEM). The stishovite Si K-edge EXELFS spectra were measured as a time-dependent series to document irradiation-induced amorphization. The amorphization was also investigated through the change in Si K- and O K-edge energy-loss near edge structure (ELNES). For α-quartz, in contrast to stishovite, electron irradiation-induced vitrification, verified by selected area electron diffraction (SAED), produced no detectable changes of the EXELFS. The Si K-edge EXELFS were analysed with the classical extended X-ray absorption fine structure (EXAFS) treatment and compared to ab initio curve-waved multiple-scattering (MS) calculations of EXAFS spectra for stishovite and α-quartz. Highly accurate information on the local atomic environment of the silicon atoms during the irradiation-induced amorphization of stishovite is obtained from the EXELFS structure parameters (Si-O bond distances, coordination numbers and Debye-Waller factors). The mean Si-O bond distance R and mean Si coordination number N changes from R=0.1775 nm and N=6 for stishovite through a disordered intermediate state (R 0.172 nm and N 5) to R 0.167 nm and N 4.5 for a nearly amorphous state similar to α-quartz (R=0.1609 nm and N=4). During the amorphization process, the Debye-Waller factor (DWF) passes through a maximum value of as it changes from for sixfold to for fourfold coordination of Si. This increase in Debye-Waller factor indicates an increase in mean-square relative displacement (MSRD) between the central silicon atom and its oxygen neighbours that is consistent with the presence of an intermediate structural state with fivefold coordination of Si. The distribution of coordination states can be estimated by modelling the amorphization as a decay process. Using the EXELFS data for amorphization, a new method is developed to derive the relative amounts of Si coordinations in high-pressure minerals with mixed coordination. For the radiation-induced amorphization process of stishovite the formation of a transitory structure with Si largely in fivefold coordination is deduced.

Kinetic control of intralayer cobalt coordination in layered hydroxides: Co(1-0.5x)(oct) Co(x)(tet) (OH)2 (Cl)x (H2O)n.

PubMed

Neilson, James R; Schwenzer, Birgit; Seshadri, Ram; Morse, Daniel E

2009-12-07

We report the synthesis and characterization of new structural variants of the isotypic compound with the generic chemical formula, Co(1-0.5x)(oct) Co(x)(tet) (OH)2 (Cl)x (H2O)n, all modifications of an alpha-Co(OH)2 lattice. We show that the occupancy of tetrahedrally coordinated cobalt sites and associated chloride ligands, x, is modulated by the rate of formation of the respective layered hydroxide salts from kinetically controlled aqueous hydrolysis at an air-water interface. This new level of structural control is uniquely enabled by the slow diffusion of a hydrolytic catalyst, a simple technique. Independent structural characterizations of the compounds separately describe various attributes of the materials on different length scales, revealing details hidden by the disordered average structures. The precise control over the population of distinct octahedrally and tetrahedrally coordinated cobalt ions in the lattice provides a gentle, generic method for modulating the coordination geometry of cobalt in the material without disturbing the lattice or using additional reagents. A mechanism is proposed to reconcile the observation of the kinetic control of the structure with competing interactions during the initial stages of hydrolysis and condensation.

Temperature-dependent self-assembly of NC–Ph{sub 5}–CN molecules on Cu(111)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pivetta, Marina, E-mail: marina.pivetta@epfl.ch; Pacchioni, Giulia E.; Fernandes, Edgar

2015-03-14

We present the results of temperature-dependent self-assembly of dicarbonitrile-pentaphenyl molecules (NC–Ph{sub 5}–CN) on Cu(111). Our low-temperature scanning tunneling microscopy study reveals the formation of metal-organic and purely organic structures, depending on the substrate temperature during deposition (160–300 K), which determines the availability of Cu adatoms at the surface. We use tip functionalization with CO to obtain submolecular resolution and image the coordination atoms, enabling unequivocal identification of metal-coordinated nodes and purely organic ones. Moreover, we discuss the somewhat surprising structure obtained for deposition and measurement at 300 K.

Solvent extraction: the coordination chemistry behind extractive metallurgy.

PubMed

Wilson, A Matthew; Bailey, Phillip J; Tasker, Peter A; Turkington, Jennifer R; Grant, Richard A; Love, Jason B

2014-01-07

The modes of action of the commercial solvent extractants used in extractive hydrometallurgy are classified according to whether the recovery process involves the transport of metal cations, M(n+), metalate anions, MXx(n-), or metal salts, MXx into a water-immiscible solvent. Well-established principles of coordination chemistry provide an explanation for the remarkable strengths and selectivities shown by most of these extractants. Reagents which achieve high selectivity when transporting metal cations or metal salts into a water-immiscible solvent usually operate in the inner coordination sphere of the metal and provide donor atom types or dispositions which favour the formation of particularly stable neutral complexes that have high solubility in the hydrocarbons commonly used in recovery processes. In the extraction of metalates, the structures of the neutral assemblies formed in the water-immiscible phase are usually not well defined and the cationic reagents can be assumed to operate in the outer coordination spheres. The formation of secondary bonds in the outer sphere using, for example, electrostatic or H-bonding interactions are favoured by the low polarity of the water-immiscible solvents.

One-step assembly of coordination complexes for versatile film and particle engineering.

PubMed

Ejima, Hirotaka; Richardson, Joseph J; Liang, Kang; Best, James P; van Koeverden, Martin P; Such, Georgina K; Cui, Jiwei; Caruso, Frank

2013-07-12

The development of facile and versatile strategies for thin-film and particle engineering is of immense scientific interest. However, few methods can conformally coat substrates of different composition, size, shape, and structure. We report the one-step coating of various interfaces using coordination complexes of natural polyphenols and Fe(III) ions. Film formation is initiated by the adsorption of the polyphenol and directed by pH-dependent, multivalent coordination bonding. Aqueous deposition is performed on a range of planar as well as inorganic, organic, and biological particle templates, demonstrating an extremely rapid technique for producing structurally diverse, thin films and capsules that can disassemble. The ease, low cost, and scalability of the assembly process, combined with pH responsiveness and negligible cytotoxicity, makes these films potential candidates for biomedical and environmental applications.

Wounding coordinately induces cell wall protein, cell cycle and pectin methyl esterase genes involved in tuber closing layer and wound periderm development.

PubMed

Neubauer, Jonathan D; Lulai, Edward C; Thompson, Asunta L; Suttle, Jeffrey C; Bolton, Melvin D

2012-04-15

Little is known about the coordinate induction of genes that may be involved in agriculturally important wound-healing events. In this study, wound-healing events were determined together with wound-induced expression profiles of selected cell cycle, cell wall protein, and pectin methyl esterase genes using two diverse potato genotypes and two harvests (NDTX4271-5R and Russet Burbank tubers; 2008 and 2009 harvests). By 5 d after wounding, the closing layer and a nascent phellogen had formed. Phellogen cell divisions generated phellem layers until cessation of cell division at 28 d after wounding for both genotypes and harvests. Cell cycle genes encoding epidermal growth factor binding protein (StEBP), cyclin-dependent kinase B (StCDKB) and cyclin-dependent kinase regulatory subunit (StCKS1At) were induced by 1 d after wounding; these expressions coordinated with related phellogen formation and the induction and cessation of phellem cell formation. Genes encoding the structural cell wall proteins extensin (StExt1) and extensin-like (StExtlk) were dramatically up-regulated by 1-5 d after wounding, suggesting involvement with closing layer and later phellem cell layer formation. Wounding up-regulated pectin methyl esterase genes (StPME and StPrePME); StPME expression increased during closing layer and phellem cell formation, whereas maximum expression of StPrePME occurred at 5-14 d after wounding, implicating involvement in later modifications for closing layer and phellem cell formation. The coordinate induction and expression profile of StTLRP, a gene encoding a cell wall strengthening "tyrosine-and lysine-rich protein," suggested a role in the formation of the closing layer followed by phellem cell generation and maturation. Collectively, the genes monitored were wound-inducible and their expression profiles markedly coordinated with closing layer formation and the index for phellogen layer meristematic activity during wound periderm development; results were more influenced by harvest than genotype. Importantly, StTLRP was the only gene examined that may be involved in phellogen cell wall thickening after cessation of phellogen cell division. Published by Elsevier GmbH.

Structure-based barcoding of proteins.

PubMed

Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

2014-01-01

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

Porphyrin framework solids. Synthesis and structure of hybrid coordination polymers of tetra(carboxyphenyl)porphyrins and lanthanide-bridging ions.

PubMed

Muniappan, Sankar; Lipstman, Sophia; George, Sumod; Goldberg, Israel

2007-07-09

New types of porphyrin-based framework solids were constructed by reacting meso-tetra(3-carboxyphenyl)porphyrin and meso-tetra(4-carboxyphenyl)metalloporphyrins with common salts of lanthanide metal ions. The large size, high coordination numbers and strong affinity for oxo ligands of the latter, combined with favorable hydrothermal reaction conditions, allowed the formation of open three-dimensional single-framework architectures by coordination polymerization, in which the tetradentate porphyrin units are intercoordinated by multinuclear assemblies of the bridging metal ions. The latter serve as construction pillars of the supramolecular arrays, affording stable structures. Several modes of coordination polymerization were revealed by single-crystal X-ray diffraction. They differ by the spatial functionality of the porphyrin building blocks, the coordination patterns of the lanthanide-carboxylate assemblies, and the topology of the resulting frameworks. The seven new reported structures exhibit periodically spaced 0.4-0.6 nm wide channel voids that perforate the respective crystalline polymeric architectures and are accessible to solvent components. Materials based on the m-carboxyphenyl derivative reveal smaller channels than those based on the p-carboxyphenyl analogues. An additional complex of the former with a smaller third-row transition metal (Co) is characterized by coordination connectivity in two dimensions only. Thermal and powder-diffraction analyses confirm the stability of the lanthanide-TmCPP (TmCPP=tetra(m-carboxyphenyl)porphyrin) frameworks.

Zinc complexes of the biomimetic N,N,O ligand family of substituted 3,3-bis(1-alkylimidazol-2-yl)propionates: the formation of oxalate from pyruvate

PubMed Central

Bruijnincx, Pieter C. A.; Lutz, Martin; den Breejen, Johan P.; van Koten, Gerard

2007-01-01

The coordination chemistry of the 2-His-1-carboxylate facial triad mimics 3,3-bis(1-methylimidazol-2-yl)propionate (MIm2Pr) and 3,3-bis(1-ethyl-4-isopropylimidazol-2-yl) propionate (iPrEtIm2Pr) towards ZnCl2 was studied both in solution and in the solid state. Different coordination modes were found depending both on the stoichiometry and on the ligand that was employed. In the 2:1 ligand-to-metal complex [Zn(MIm2Pr)2], the ligand coordinates in a tridentate, tripodal N,N,O fashion similar to the 2-His-1-carboxylate facial triad. However, the 1:1 ligand-to-metal complexes [Zn(MIm2Pr)Cl(H2O)] and [Zn(iPrEtIm2Pr)Cl] were crystallographically characterized and found to be polymeric in nature. A new, bridging coordination mode of the ligands was observed in both structures comprising N,N-bidentate coordination of the ligand to one zinc atom and O-monodentate coordination to a zinc second atom. A rather unique transformation of pyruvate into oxalate was found with [Zn(MIm2Pr)Cl], which resulted in the isolation of the new, oxalato bridged zinc coordination polymer [Zn2(MIm2Pr)2(ox)]·6H2O, the structure of which was established by X-ray crystal structure determination. PMID:17828423

Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.

PubMed

Steinbacher, Stefan; Schiffmann, Susanne; Richter, Gerald; Huber, Robert; Bacher, Adelbert; Fischer, Markus

2003-10-24

Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

PubMed Central

Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.

2010-01-01

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads. PMID:19746468

Bismuth-, Tin-, and Lead-Containing Metal-Organic Materials: Synthesis, Structure, Photoluminescence, Second Harmonic Generation, and Ferroelectric Properties

NASA Astrophysics Data System (ADS)

Wibowo, Arief Cahyo

Metal-Organic Materials (MOMs) contain metal moieties and organic ligands that combine to form discrete (e.g. metal-organic polyhedra, spheres or nanoballs, metal-organic polygons) or polymeric structures with one-, two-, or three-dimensional periodicities that can exhibit a variety of properties resulting from the presence of the metal moieties and/or ligand connectors in the structure. To date, MOMs with a range of functional attributes have been prepared, including record-breaking porosity, catalytic properties, molecular magnetism, chemical separations and sensing ability, luminescence and NLO properties, multiferroic, ferroelectric, and switchable molecular dielectric properties. We are interested in synthesizing non-centrosymmetric MOM single crystals possessing one of the ten polar space groups required for non-linear optical properties (such as second harmonic generation) and ferroelectric applications. This thesis is divided into two main parts: materials with optical properties, such as photoluminescence and materials for targeted applications such as second harmonic generation and ferroelectric properties. This thesis starts with an introduction describing material having centrosymmetric, non-polar space groups, single crystals structures and their photoluminescence properties. These crystals exhibit very interesting and rare structures as well as interesting photoluminescence properties. Chapters 2-5 of this thesis focus on photoluminescent properties of new MOMs, and detail the exploratory research involving the comparatively rare bismuth, lead, and tin coordination polymers. Specifically, the formation of single white-light emitting phosphors based on the combination of bismuth or lead with pyridine-2,5-dicarboxylate is discussed (Chapter 2). The observation of a new Bi2O2 layer and a new Bi4O 3 chain in bismuth terephthalate-based coordination polymers is presented in Chapter 3, while the formation of diverse structures of tin-based coordination polymer ranging from 1D supramolecular structures to true 3D coordination polymers is covered in Chapter 4. The observation of a new 2D Kagome lattice and unique layered perovskite-type bismuth-based coordination polymers and their photoluminescence properties is the focus of Chapter 5. In chapters 6 and 7, a successful approach to implement our novel hybrid strategy for synthesizing enantiomerically pure single crystals consisting of Second Order Jahn Teller (SOJT)-possessing main group metal cations, specifically bismuth and tin, and homochiral ligands or unsymmetric ligands is discussed. The new MOMs with polar space groups exhibit second harmonic generation and have potential for ferroelectric properties.

Pressure-induced Structural Transformations in LanthanideTitanates: La2TiO5 and Nd2TiO5

DOE Office of Scientific and Technical Information (OSTI.GOV)

F Zhang; J Wang; M Lang

The structure of orthorhombic rare earth titanates of La{sub 2}TiO{sub 5} and Nd{sub 2}TiO{sub 5}, where Ti cations are in five-fold coordination with oxygen, has been studied at high pressures by X-ray diffraction (XRD), Raman scattering measurements, and quantum mechanical calculations. Both XRD and Raman results indicated two pressure-induced phase transitions during the process. An orthorhombic super cell (a x b x 2c) formed at a pressure between 6 and 10 GPa, and then transformed to a hexagonal high-pressure phase accompanied by partial decomposition. The hexagonal high-pressure phase is quenchable. Detailed structural analysis indicated that the five-coordinated TiO{sub 5} polyhedramore » remain during the formation of super cell, but the orthorhombic-to-hexagonal phase transition at high pressures is a reconstructive process, and the five-fold Ti-O coordination increased to more than 6. This phase transition sequence was verified by quantum mechanical calculations.« less

New 3D coordination polymers constructed from pillared metal-formate Kagomé layers exhibiting spin canting only in the nickel(II) complex.

PubMed

Li, Zuo-Xi; Zhao, Jiong-Peng; Sañudo, E C; Ma, Hong; Pan, Zhong-Da; Zeng, Yong-Fei; Bu, Xian-He

2009-12-21

Sparked by the strategy of pillared-layer MOFs, three formate coordination polymers, {[Ni(2)(HCO(2))(3)(L)(2)](NO(3)).2H(2)O}(infinity) (1), {[Co(2)(HCO(2))(3)(L)(2)](HCO(2)).2H(2)O}(infinity) (2), and {[Cu(2)(HCO(2))(3)(L)(2)](HCO(2)).2H(2)O}(infinity) (3), have been synthesized by employing the rodlike ligand 4,4'-bis(imidazol-1-yl)biphenyl (L) as the pillar. Structural analysis indicates that the title complexes 1-3 are isostructural compounds, which possess metal-formate 2D layers perpendicularly pillared by the ligand L to afford a 3D open framework. This is an interesting example of a Kagome lattice based on the formate mediator. Moreover, the formate anion of this 2D Kagome layer exhibits various bridging modes: anti-anti, syn-anti, and 3.21 modes. Their magnetic measurements reveals that only complex 1 presents the spin canting phenomenon, while its isostructural Co(II) and Cu(II) complexes are simply paramagnets with antiferromagnetic coupling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Bhadbhade, Mohan; Karatchevtseva, Inna

Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5more » Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.« less

Isostructural 1D coordination polymers of Zn(II), Cd(II) and Cu(II) with phenylpropynoic acid and DABCO as organic linkers

NASA Astrophysics Data System (ADS)

Saravanakumar, Rajendran; Varghese, Babu; Sankararaman, Sethuraman

2014-11-01

Using phenylpropynoic acid (PPA) and 1,4-diazabicyclo[2.2.2]octane (DABCO) as organic spacers, isostructural coordination polymers of Zn(II), Cd(II) and Cu(II) were synthesized by solvothermal method and structurally characterized using single crystal XRD, powder XRD, 13C CP-MAS NMR spectroscopy. Single crystal XRD data revealed four PPA units coordinating with two metal ions forming a paddle wheel secondary building unit (SBU). The paddle wheel units are connected through coordination of DABCO nitrogen to the metal centers from the axial positions leading to the formation of the 1D coordination polymers along the c axis. Intermolecular π stacking and Csbnd H…π interactions between the adjacent polymer chains convert the 1D coordination polymer into an interesting 3D network with the Csbnd H…π bonds running along the crystallographic a and b axes. Thermal and nitrogen adsorption studies of these coordination polymers are reported.

Composition-dependent structural and transport properties of amorphous transparent conducting oxides

NASA Astrophysics Data System (ADS)

Khanal, Rabi; Buchholz, D. Bruce; Chang, Robert P. H.; Medvedeva, Julia E.

2015-05-01

Structural properties of amorphous In-based oxides, In -X -O with X =Zn , Ga, Sn, or Ge, are investigated using ab initio molecular dynamics liquid-quench simulations. The results reveal that indium retains its average coordination of 5.0 upon 20% X fractional substitution for In, whereas X cations satisfy their natural coordination with oxygen atoms. This finding suggests that the carrier generation is primarily governed by In atoms, in accord with the observed carrier concentration in amorphous In-O and In -X -O . At the same time, the presence of X affects the number of six-coordinated In atoms as well as the oxygen sharing between the InO6 polyhedra. Based on the obtained interconnectivity and spatial distribution of the InO6 and XO x polyhedra in amorphous In -X -O , composition-dependent structural models of the amorphous oxides are derived. The results help explain our Hall mobility measurements in In -X -O thin films grown by pulsed-laser deposition and highlight the importance of long-range structural correlations in the formation of amorphous oxides and their transport properties.

Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals.

PubMed

Gao, Juehan; Berden, Giel; Rodgers, M T; Oomens, Jos

2016-03-14

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Competing supramolecular interactions give a new twist to terpyridyl chemistry: anion- and solvent-induced formation of spiral arrays in silver(I) complexes of a simple terpyridine.

PubMed

Hannon, Michael J; Painting, Claire L; Plummer, Edward A; Childs, Laura J; Alcock, Nathaniel W

2002-05-17

Multiple competing molecular interactions (metal-ligand, pi-stacking and hydrogen-bonding) in the silver(I) complexes of 4'-thiomethyl-2,2':6',2"-terpyridine give rise to a range of different molecular architectures, in which the metal-ligand coordination requirements are satisfied in quite different ways. Polynuclear supramolecular spirals, aggregated mononuclear and aggregated dinuclear units are all structurally characterised. The metallo-supramolecular architecture obtained displays a remarkable dependence both on the choice of non-coordinated anion and the type of solvent used (coordinating or non-coordinating). The anion dependence is particularly surprising, since the anions are not integrated into the centre of the supramolecular structure. The solution behaviour is also solvent and anion dependent, with aggregation of planar mononuclear cations observed in acetonitrile, but oligonuclear spiral species implicated in nitromethane. The extraordinarily variable geometries of these systems suggest that they provide a novel example of the "frustration" principle, in which opposing tendencies cannot simultaneously be satisfied and identify an alternative approach to the design of metallo-supramolecular systems whose structure is responsive to external agents.

Syntheses, crystal structures, and properties of new metal-5-bromonicotinate coordination polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wenjie; Li, Guoting; Lv, Lulu

2015-05-15

Four metal–5-bromonicotinate (Brnic) coordination polymers [Fe(Brnic){sub 2}(H{sub 2}O){sub 2}]{sub n} (1), [Ni(Brnic){sub 2}]{sub n} (2), [Ni(Brnic)(bpy)(H{sub 2}O){sub 2}]{sub n}·n(Brnic)·4.5nH{sub 2}O (3), and [Co{sub 2}(Brnic){sub 3}(bpy){sub 2}(OH)]{sub n}·nH{sub 2}O (4) have been synthesized and structurally characterized (bpy=4,4′-bipyridine). Complex 1 has corrugated (4,4) sheets formed by μ-Brnic ligands and planar nodes Fe(II). As for 2–4, they all built up from Brnic-bridged dinuclear subunits, but have very different structure features. Complex 2 is a twin-like polymer with (4,4) layers formed by twin paddle-wheel [Ni{sub 2}(Brnic){sub 4}] subunits. Through the bridge coordination of bpy ligands with dinuclear rings [Ni{sub 2}(Brnic){sub 2}] and trigons [Co{submore » 2}(Brnic){sub 3}(OH)], 6{sup 3}-topological cationic layers with nanosized grids of 3 and chiral ladder-type double chains of 4 formed, respectively. Notably, halogen-related interactions play an important role in the formation of 3D metallosupermolecules 1–4. The thermostabilities of all compounds have been discussed in detail. Moreover, the magnetic investigations of 2 and 4 indicate that there exist antiferromagnetic interactions in the paddle-wheel [Ni{sub 2}(Brnic){sub 4}] and trigon [Co{sub 2}(Brnic){sub 3}(OH)] cores, respectively. - Highlights: • Four novel metal–5-bromonicotinate coordination polymers have been synthesized. • Notably, halogen-related interactions play an important role in the formation of 3D metallosupermolecules. • Antiferromagnetic interactions in nickel(II) paddle-wheel and cobalt(II) trigon cores were observed.« less

Lanthanide-binding peptides with two pendant aminodiacetate arms: impact of the sequence on chelation.

PubMed

Niedźwiecka, Agnieszka; Cisnetti, Federico; Lebrun, Colette; Gateau, Christelle; Delangle, Pascale

2012-03-21

Lanthanide complexes with a series of hexapeptides-incorporating two unnatural chelating amino acids with aminodiacetate groups, Ada(1) and Ada(2)-have been examined in terms of their speciation, structure, stability and luminescence properties. Whereas Ada(2) acts as a tridentate donor in all cases, Ada(1) may act as a tetradentate donor thanks to the coordination of the amide carbonyl function assisted by the formation of a six-membered chelate ring. The position of the Ada(1) residue in the sequence is demonstrated to be critical for the lanthanide complex speciation and structure. Ada(1) promotes the coordination of the backbone amide function to afford a highly dehydrated Ln complex and an S-shape structure of the peptide backbone, only when found in position 2.

Social identity and cooperation in cultural evolution.

PubMed

Smaldino, Paul E

2017-12-06

I discuss the function of social identity signaling in facilitating cooperative group formation, and how the nature of that function changes with the structure of social organization. I propose that signals of social identity facilitate assortment for successful coordination in large-scale societies, and that the multidimensional, context-dependent nature of social identity is crucial for successful coordination when individuals have to cooperate in different contexts. Furthermore, the structure of social identity is tied to the structure of society, so that as societies grow larger and more interconnected, the landscape of social identities grows more heterogeneous. This discussion bears directly on the need to articulate the dynamics of emergent, ephemeral groups as a major factor in human cultural evolution. Copyright © 2017 The Author. Published by Elsevier B.V. All rights reserved.

In situ spectroscopic study of the plastic deformation of amorphous silicon under non-hydrostatic conditions induced by indentation

PubMed Central

Gerbig, Y.B; Michaels, C.A.; Bradby, J.E.; Haberl, B.; Cook, R.F.

2016-01-01

Indentation-induced plastic deformation of amorphous silicon (a-Si) thin films was studied by in situ Raman imaging of the deformed contact region of an indented sample, employing a Raman spectroscopy-enhanced instrumented indentation technique. Quantitative analyses of the generated in situ Raman maps provide unique, new insight into the phase behavior of as-implanted a-Si. In particular, the occurrence and evolving spatial distribution of changes in the a-Si structure caused by processes, such as polyamorphization and crystallization, induced by indentation loading were measured. The experimental results are linked with previously published work on the plastic deformation of a-Si under hydrostatic compression and shear deformation to establish a sequence for the development of deformation of a-Si under indentation loading. The sequence involves three distinct deformation mechanisms of a-Si: (1) reversible deformation, (2) increase in coordination defects (onset of plastic deformation), and (3) phase transformation. Estimated conditions for the occurrence of these mechanisms are given with respect to relevant intrinsic and extrinsic parameters, such as indentation stress, volumetric strain, and bond angle distribution (a measure for the structural order of the amorphous network). The induced volumetric strains are accommodated solely by reversible deformation of the tetrahedral network when exposed to small indentation stresses. At greater indentation stresses, the increased volumetric strains in the tetrahedral network lead to the formation of predominately five-fold coordination defects, which seems to mark the onset of irreversible or plastic deformation of the a-Si thin film. Further increase in the indentation stress appears to initiate the formation of six-fold coordinated atomic arrangements. These six-fold coordinated arrangements may maintain their amorphous tetrahedral structure with a high density of coordination defects or nucleate as a new crystalline β-tin phase within the a-Si network. PMID:26924926

Colloidal alloys with preassembled clusters and spheres.

PubMed

Ducrot, Étienne; He, Mingxin; Yi, Gi-Ra; Pine, David J

2017-06-01

Self-assembly is a powerful approach for constructing colloidal crystals, where spheres, rods or faceted particles can build up a myriad of structures. Nevertheless, many complex or low-coordination architectures, such as diamond, pyrochlore and other sought-after lattices, have eluded self-assembly. Here we introduce a new design principle based on preassembled components of the desired superstructure and programmed nearest-neighbour DNA-mediated interactions, which allows the formation of otherwise unattainable structures. We demonstrate the approach using preassembled colloidal tetrahedra and spheres, obtaining a class of colloidal superstructures, including cubic and tetragonal colloidal crystals, with no known atomic analogues, as well as percolating low-coordination diamond and pyrochlore sublattices never assembled before.

True and masked three-coordinate T-shaped platinum(II) intermediates.

PubMed

Ortuño, Manuel A; Conejero, Salvador; Lledós, Agustí

2013-01-01

Although four-coordinate square-planar geometries, with a formally 16-electron counting, are absolutely dominant in isolated Pt(II) complexes, three-coordinate, 14-electron Pt(II) complexes are believed to be key intermediates in a number of platinum-mediated organometallic transformations. Although very few authenticated three-coordinate Pt(II) complexes have been characterized, a much larger number of complexes can be described as operationally three-coordinate in a kinetic sense. In these compounds, which we have called masked T-shaped complexes, the fourth position is occupied by a very weak ligand (agostic bond, solvent molecule or counteranion), which can be easily displaced. This review summarizes the structural features of the true and masked T-shaped Pt(II) complexes reported so far and describes synthetic strategies employed for their formation. Moreover, recent experimental and theoretical reports are analyzed, which suggest the involvement of such intermediates in reaction mechanisms, particularly C-H bond-activation processes.

The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation.

PubMed

Suzuki, K; Kirisako, T; Kamada, Y; Mizushima, N; Noda, T; Ohsumi, Y

2001-11-01

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Several key reactions performed by these proteins have been described, but a comprehensive understanding of the overall network is still lacking. Based on Apg protein localization, we have identified a novel structure that functions in autophagosome formation. This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. Analysis of apg mutants revealed that the formation of both a phosphatidylethanolamine-conjugated Aut7p and an Apg12p- Apg5p conjugate is essential for the localization of Aut7p to the pre-autophagosomal structure. Vps30p/Apg6p and Apg14p, components of an autophagy- specific phosphatidylinositol 3-kinase complex, Apg9p and Apg16p are all required for the localization of Apg5p and Aut7p to the structure. The Apg1p protein kinase complex functions in the late stage of autophagosome formation. Here, we present the classification of Apg proteins into three groups that reflect each step of autophagosome formation.

The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation

PubMed Central

Suzuki, Kuninori; Kirisako, Takayoshi; Kamada, Yoshiaki; Mizushima, Noboru; Noda, Takeshi; Ohsumi, Yoshinori

2001-01-01

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Several key reactions performed by these proteins have been described, but a comprehensive understanding of the overall network is still lacking. Based on Apg protein localization, we have identified a novel structure that functions in autophagosome formation. This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. Analysis of apg mutants revealed that the formation of both a phosphatidylethanolamine-conjugated Aut7p and an Apg12p– Apg5p conjugate is essential for the localization of Aut7p to the pre-autophagosomal structure. Vps30p/Apg6p and Apg14p, components of an autophagy- specific phosphatidylinositol 3-kinase complex, Apg9p and Apg16p are all required for the localization of Apg5p and Aut7p to the structure. The Apg1p protein kinase complex functions in the late stage of autophagosome formation. Here, we present the classification of Apg proteins into three groups that reflect each step of autophagosome formation. PMID:11689437

Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei.

PubMed

Vergara, Alessandro; Franzese, Marisa; Merlino, Antonello; Vitagliano, Luigi; Verde, Cinzia; di Prisco, Guido; Lee, H Caroline; Peisach, Jack; Mazzarella, Lelio

2007-10-15

Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarctic fish species Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, as well as the x-ray crystal structure of oxidized Trematomus bernacchii Hb, redetermined at high resolution. The oxidation of these Hbs leads to formation of states that were not usually detected in previous analyses of tetrameric Hbs. In addition to the commonly found aquo-met and hydroxy-met species, EPR analyses show that two distinct hemichromes coexist at physiological pH, referred to as hemichromes I and II, respectively. Together with the high-resolution crystal structure (1.5 A) of T. bernacchii and a survey of data available for other heme proteins, hemichrome I was assigned by x-ray crystallography and by EPR as a bis-His complex with a distorted geometry, whereas hemichrome II is a less constrained (cytochrome b5-like) bis-His complex. In four of the five Antartic fish Hbs examined, hemichrome I is the major form. EPR shows that for HbCTn, the amount of hemichrome I is substantially reduced. In addition, the concomitant presence of a penta-coordinated high-spin Fe (III) species, to our knowledge never reported before for a wild-type tetrameric Hb, was detected. A molecular modeling investigation demonstrates that the presence of the bulkier Ile in position 67beta in HbCTn in place of Val as in the other four Hbs impairs the formation of hemichrome I, thus favoring the formation of the ferric penta-coordinated species. Altogether the data show that ferric states commonly associated with monomeric and dimeric Hbs are also found in tetrameric Hbs.

Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases.

PubMed

Ohta, Takehiro; Chakrabarty, Sarmistha; Lipscomb, John D; Solomon, Edward I

2008-02-06

Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.

In Silico Docking of Small-Molecule Inhibitors to the Escherichia coli Type III Secretion System EscN ATPase

DTIC Science & Technology

2014-07-01

coordinates of the EscN protein (Zarivach et al., 2007) were downloaded in pdb file format from the Research Collaboratory for Structural Biology...catalytic activity. Two structurally related compounds were observed to adopt extended conformations in the active-site cleft and essentially...adopt a very compact conformation that occupied only one side of the cleft. Our goal was to determine the three-dimensional structures of the

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

PubMed

Lounnas, V; Vriend, G

2012-02-27

Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The AsteriX Web server is freely available at http://swift.cmbi.ru.nl/bitmapb/.

Diverse CdII coordination complexes derived from bromide isophthalic acid binding with auxiliary N-donor ligands

NASA Astrophysics Data System (ADS)

Tang, Meng; Dong, Bao-Xia; Wu, Yi-Chen; Yang, Fang; Liu, Wen-Long; Teng, Yun-Lei

2016-12-01

The coordination characteristics of 4-bromoisophthalic acid (4-Br-H2ip) have been investigated in a series of CdII-based frameworks. Hydrothermal reactions of CdII salts and 4-Br-H2ip together with flexible or semiflexible N-donor auxiliary ligands resulted in the formation of four three-dimensional coordination complexes with diverse structures: {Cd(bix)0.5(bix)0.5(4-Br-ip)]·H2O}n (1), [Cd(bbi)0.5(bbi)0.5(4-Br-ip)]n (2), {[Cd(btx)0.5(4-Br-ip)(H2O)]·0.5CH3OH·H2O}n (3) and {[Cd(bbt)0.5(4-Br-ip)(H2O)]·3·5H2O}n (4). These compounds were characterized by elemental analyses, IR spectra, single-crystal and powder X-ray diffraction. They displayed diverse structures depending on the configuration of the 4-connected metal node, the coordination mode of the 4-Br-H2ip, the coordination ability and conformationally flexibility of the N-donor auxiliary. Compound 1 exhibits 3-fold interpenetrated 66 topology and compound 2 has a 412 topology. Compounds 3-4 have similar 3D pillar-layered structures based on 3,4-connected binodal net with the Schläfli symbol of (4·38). The thermal stabilities and photoluminescence properties of them were discussed in detail.

Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from Density Functional Theory (DFT) Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Ujjal; Zhang, Guanghui; Hu, Bo

2015-10-28

Amorphous silica (SiO 2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure andmore » activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. In conclusion, the molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.« less

Syntheses, structures, photoluminescence of four dicarboxylate-controlled Zn(II) coordination complexes incorporating flexible 1-(4-pyridylmethyl)-benzimidazole ligand

NASA Astrophysics Data System (ADS)

Hao, Hong-Jun; Du, Ming-Yue; Wang, Dan-Feng; Sun, Cheng-Jie; Wang, Zhan-Hui; Huang, Rong-Bin; Zheng, Lan-Sun

2013-09-01

Four Zn(II) coordination complexes, namely {[Zn(pmbm)2(tpa)]·H2O}n (1), {[Zn(pmbm)(phda)]·2(H2O)}n (2), [Zn(pmbm)(aze)]n (3), {[Zn(pmbm)(1,4-ndc)]·2(CH3OH)}n (4) [pmbm = 1-(4-pyridylmethyl)-benzimidazole, H2tpa = terephthalic acid, H2phda = phenylenediacetic acid, H2aze = azelaic acid, 1,4-ndcH2 = 1,4-naphthalenedicarboxylic acid] have been synthesized by solution phase ultrasonic reactions of Zn(AC)2·2H2O with pmbm and various dicarboxylates ligands under the ammoniacal condition. All the complexes have been characterized by elemental analyses, IR spectra and X-ray diffraction. Complexes 1 and 2 exhibit one-dimensional chains structure and complex 3 and 4 are two-dimensional sheets structure with (4,4) topology. Complexes 1-4 spanning from one-dimensional chains to two-dimensional sheets suggest that dicarboxylates play significant roles in the formation of such coordination architectures. The photoluminescences of the complexes were also investigated in the solid state at room temperature.

FRS Geospatial Return File Format

EPA Pesticide Factsheets

The Geospatial Return File Format describes format that needs to be used to submit latitude and longitude coordinates for use in Envirofacts mapping applications. These coordinates are stored in the Geospatail Reference Tables.

Charge Effect on the Formation of Polyoxometalate-Based Supramolecular Polygons Driven by Metal Coordination.

PubMed

Piot, Madeleine; Hupin, Sébastien; Lavanant, Hélène; Afonso, Carlos; Bouteiller, Laurent; Proust, Anna; Izzet, Guillaume

2017-07-17

The metal-driven self-assembly of a Keggin-based hybrid bearing two remote pyridine units was investigated. The resulting supramolecular species were identified by combination of 2D diffusion NMR spectroscopy (DOSY) and electrospray ionization mass spectrometry (ESI-MS) as a mixture of molecular triangles and squares. This behavior is different from that of the structural analogue Dawson-based hybrid displaying a higher charge, which only led to the formation of molecular triangles. This study highlights the decisive effect of the charge of the POMs in their self-assembly processes that disfavors the formation of large assemblies. An isothermal titration calorimetry (ITC) experiment confirmed the stronger binding in the case of the Keggin hybrids. A correlation between the diffusion coefficient D and the molecular mass M of the POM-based building block and its coordination oligomers was also observed. We show that the diffusion coefficient of these compounds is mainly determined by their occupied volume rather than by their shape.

High-Order Ca(II)-Chloro Complexes in Mixed CaCl2-LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations.

PubMed

Wang, Yu-Lin; Wang, Ying; Yi, Hai-Bo

2016-07-21

In this study, the structural characteristics of high-coordinated Ca-Cl complexes present in mixed CaCl2-LiCl aqueous solution were investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The DFT results show that [CaClx](2-x) (x = 4-6) clusters are quite unstable in the gas phase, but these clusters become metastable when hydration is considered. The MD simulations show that high-coordinated Ca-chloro complexes are possible transient species that exist for up to nanoseconds in concentrated (11.10 mol·kg(-1)) Cl(-) solution at 273 and 298 K. As the temperature increases to 423 K, these high-coordinated structures tend to disassociate and convert into smaller clusters and single free ions. The presence of high-order Ca-Cl species in concentrated LiCl solution can be attributed to their enhanced hydration shell and the inadequate hydration of ions. The probability of the [CaClx](2-x)aq (x = 4-6) species being present in concentrated LiCl solution decreases greatly with increasing temperature, which also indicates that the formation of the high-coordinated Ca-Cl structure is related to its hydration characteristics.

THE REBOUND CONDITION OF DUST AGGREGATES REVEALED BY NUMERICAL SIMULATION OF THEIR COLLISIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wada, Koji; Tanaka, Hidekazu; Yamamoto, Tetsuo

2011-08-10

Collisional growth of dust aggregates is a plausible root of planetesimals forming in protoplanetary disks. However, a rebound of colliding dust aggregates prevents dust from growing into planetesimals. In fact, rebounding aggregates are observed in laboratory experiments but not in previous numerical simulations. Therefore, the condition of rebound between dust aggregates should be clarified to better understand the processes of dust growth and planetesimal formation. We have carried out numerical simulations of aggregate collisions for various types of aggregates and succeeded in reproducing a rebound of colliding aggregates under specific conditions. Our finding is that in the rebound process, themore » key factor of the aggregate structure is the coordination number, namely, the number of particles in contact with a particle. A rebound is governed by the energy dissipation along with restructuring of the aggregates and a large coordination number inhibits the restructuring at collisions. Results of our numerical simulation for various aggregates indicate that they stick to each other when the mean coordination number is less than 6, regardless of their materials and structures, as long as their collision velocity is less than the critical velocity for fragmentation. This criterion of the coordination number would correspond to a filling factor of {approx}0.3, which is somewhat larger than that reported in laboratory experiments. In protoplanetary disks, dust aggregates are expected to have low bulk densities (<0.1 g cm{sup -3}) during their growth, which would prevent dust aggregates from rebounding. This result supports the formation of planetesimals with direct dust growth in protoplanetary disks.« less

UNICON: A Powerful and Easy-to-Use Compound Library Converter.

PubMed

Sommer, Kai; Friedrich, Nils-Ole; Bietz, Stefan; Hilbig, Matthias; Inhester, Therese; Rarey, Matthias

2016-06-27

The accurate handling of different chemical file formats and the consistent conversion between them play important roles for calculations in complex cheminformatics workflows. Working with different cheminformatic tools often makes the conversion between file formats a mandatory step. Such a conversion might become a difficult task in cases where the information content substantially differs. This paper describes UNICON, an easy-to-use software tool for this task. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, PDB, and PDBx/mmCIF via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states, and conformer ensembles. For this purpose, UNICON bundles the key elements of the previously described NAOMI library in a single, easy-to-use command line tool.

Computational study of the electronic structure and magnetic properties of the Ni-C state in [NiFe] hydrogenases including the second coordination sphere.

PubMed

Kampa, Mario; Lubitz, Wolfgang; van Gastel, Maurice; Neese, Frank

2012-12-01

[NiFe] hydrogenases catalyze the reversible formation of H(2). The [NiFe] heterobimetallic active site is rich in redox states. Here, we investigate the key catalytic state Ni-C of Desulfovibrio vulgaris Miyazaki F hydrogenase using a cluster model that includes the truncated amino acids of the entire second coordination sphere of the enzyme. The optimized geometries, computed g tensors, hyperfine coupling constants, and IR stretching frequencies all agree well with experimental values. For the hydride in the bridging position, only a single minimum on the potential energy surface is found, indicating that the hydride bridges and binds to both nickel and iron. The influence of the second coordination sphere on the electronic structure is investigated by comparing results from the large cluster models with truncated models. The largest interactions of the second coordination sphere with the active site concern the hydrogen bonds with the cyanide ligands, which modulate the bond between iron and these ligands. Secondly, the electronic structure of the active site is found to be sensitive to the protonation state of His88. This residue forms a hydrogen bond with the spin-carrying sulfur atom of Cys549, which in turn tunes the spin density at the nickel and coordinating sulfur atoms. In addition, the unequal distribution of spin density over the equatorial cysteine residues results from different orientations of the cysteine side chains, which are kept in their particular orientation by the secondary structure of the protein.

Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export

PubMed Central

2018-01-01

The bacterial flagellum is a supramolecular motility machine. Flagellar assembly begins with the basal body, followed by the hook and finally the filament. A carboxyl-terminal cytoplasmic domain of FlhA (FlhAC) forms a nonameric ring structure in the flagellar type III protein export apparatus and coordinates flagellar protein export with assembly. However, the mechanism of this process remains unknown. We report that a flexible linker of FlhAC (FlhAL) is required not only for FlhAC ring formation but also for substrate specificity switching of the protein export apparatus from the hook protein to the filament protein upon completion of the hook structure. FlhAL was required for cooperative ring formation of FlhAC. Alanine substitutions of residues involved in FlhAC ring formation interfered with the substrate specificity switching, thereby inhibiting filament assembly at the hook tip. These observations lead us to propose a mechanistic model for export switching involving structural remodeling of FlhAC. PMID:29707633

PDB explorer -- a web based algorithm for protein annotation viewer and 3D visualization.

PubMed

Nayarisseri, Anuraj; Shardiwal, Rakesh Kumar; Yadav, Mukesh; Kanungo, Neha; Singh, Pooja; Shah, Pratik; Ahmed, Sheaza

2014-12-01

The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which therefore can be described in the PDB format and have been deposited in PDB database. PDB is a machine generated file, it's not human readable format, to read this file we need any computational tool to understand it. The objective of our present study is to develop a free online software for retrieval, visualization and reading of annotation of a protein 3D structure which is available in PDB database. Main aim is to create PDB file in human readable format, i.e., the information in PDB file is converted in readable sentences. It displays all possible information from a PDB file including 3D structure of that file. Programming languages and scripting languages like Perl, CSS, Javascript, Ajax, and HTML have been used for the development of PDB Explorer. The PDB Explorer directly parses the PDB file, calling methods for parsed element secondary structure element, atoms, coordinates etc. PDB Explorer is freely available at http://www.pdbexplorer.eminentbio.com/home with no requirement of log-in.

Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory NolR

USDA-ARS?s Scientific Manuscript database

The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory...

The Indiana Statewide Plan for Continuing Education in Nursing. Formative Evaluation.

ERIC Educational Resources Information Center

McKenzie, Leon R.; Puetz, Belinda E.

The Indiana Statewide Plan for Continuing Education in Nursing (ISPCEN) was implemented to establish a structure for coordinating resources, data, and personnel which would provide quality continuing education for registered and licensed practical nurses in Indiana at the regional level, ultimately leading to the opportunity for nurses in every…

Effect of lattice-gas atoms on the adsorption behaviour of thioether molecules.

PubMed

Pan, Yi; Yang, Bing; Hulot, Catherine; Blechert, Siegfried; Nilius, Niklas; Freund, Hans-Joachim

2012-08-21

Using STM topographic imaging and spectroscopy, we have investigated the adsorption of two thioether molecules, 1,2-bis(phenylthio)benzene and (bis(3-phenylthio)-phenyl)sulfane, on noble and transition metal surfaces. The two substrates show nearly antipodal behaviour. Whereas complexes with one or two protruding centres are observed on Au(111), only flat and uniform ad-structures are found on NiAl(110). The difference is ascribed to the possibility of the thioethers to form metal-organic complexes by coordinating lattice-gas atoms on the Au(111), while only the pristine molecules adsorb on the alloy surface. The metal coordination in the first case is driven by the formation of strong Au-S bonds and enables the formation of characteristic monomer, dimer and chain-like structures of the thioethers, using the Au atoms as linkers. A similar mechanism is not available on the NiAl, because no lattice gas develops at this surface at room temperature. Our work demonstrates how surface properties, i.e. the availability of mobile ad-species, determine the interaction of organic molecules with metallic substrates.

Formation of ferric oxides from aqueous solutions: A polyhedral approach by X-ray absorption spectroscopy. I. Hydrolysis and formation of ferric gels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Combes, J.M.; Manceau, A.; Calas, G.

1989-03-01

X-ray absorption spectroscopy (XAS) was used to follow the evolution of local structural environments around ferric ions during the formation of ferric hydrous oxide gels from 1 M chloride and 0.1 M nitrate solutions. Fe K-XANES and EXAFS confirm that ferric ions remain 6-fold coordinated during this evolution. With increasing OH availability in the solution, Cl{sup {minus}} anions tend gradually to be exchanged for (O, OH, OH{sub 2}) ligands. Below OH/Fe = 1, no structural order is detected beyond the first coordination sphere. Above this ratio, two Fe-Fe distances at 3.05 {angstrom} and 3.44 {angstrom} are observed and correspond tomore » the presence of edge- and vertex-sharing Fe-octahedra. XAS results show that ferric gels and highly polymerized aqueous species are short-range ordered. The main contribution to disorder in the gels arises from the small size of coherently scattering domains also responsible for their X-ray amorphous character. From the initial to the final stage of hydrolysis, particles possess a nearly spherical shape with a minimum average diameter ranging from 10-30 {angstrom} for polymers formed from chloride and nitrate solutions. As polymerization proceeds, the local order extends to several tens of angstroms and the particle structures becomes progressively closer to that of akaganeite ({beta}-FeOOH) or goethite ({alpha}-FeOOH). This local structure is distinct from that of the lepidocrocite ({gamma}-FeOOH)-like structure of ferric gels precipitated after oxidation of divalent Fe solutions. The growth of the crystalline Fe-oxyhydroxides from gels takes place by the progressive long-range ordering in the ferric polymers without modifying the short-range order around Fe.« less

Diorganotin-based coordination polymers derived from sulfonate/phosphonate/phosphonocarboxylate ligands.

PubMed

Shankar, Ravi; Jain, Archana; Kociok-Köhn, Gabriele; Molloy, Kieran C

2011-02-21

The reactions of diorganotin precursors [R(2)Sn(OR(1))(OSO(2)R(1))](n) [R = R(1) = Me (1); R = Me, R(1) = Et (2)] with an equimolar amount of t-butylphosphonic acid (RT, 8-10 h) in methanol result in the formation of identical products, of composition [(Me(2)Sn)(3)(O(3)PBu(t))(2)(O(2)P(OH)Bu(t))(2)](n) (3). On the other hand, a similar reaction of 2, when carried out in dichloromethane, affords [(Me(2)Sn)(3)(O(3)PBu(t))(2)(OSO(2)Et)(2)·MeOH](n) (4). A plausible mechanism implicating the role of solvent in the formation of these compounds has been put forward. In addition, the synthesis of [(Me(2)Sn)(3)(O(3)PCH(2)CH(2)COOMe)(2)(OSO(2)Me)(2)](n) (5) and [R(2)Sn(O(2)P(OH)CH(2)CH(2)COOMe)(OSO(2)R(1))](n) [R = Et, R(1) = Me (6); R = (n)Bu, R(1) = Et (7)] has been achieved by reacting 1 and related diorganotin(alkoxy)alkanesulfonates with 3-phosphonopropionic acid in methanol. The formation of a methylpropionate functionality on the phosphorus center in these structural frameworks results from in situ esterification of the carboxylic group. X-ray crystallographic studies of 1-7 are presented. The structures of 1 and 2 represent one-dimensional (1D) coordination polymers composed of alternate [Sn-O](2) and [Sn-O-S-O](2) cyclic rings formed by μ(2)-alkoxo and sulfonate ligands, respectively. For 3-5 and 7, variable bonding modes of phosphonate and/or sulfonate ligands afford the construction of two- and three-dimensional self-assemblies that are comprised of trinuclear tin entities with an Sn(3)P(2)O(6) core as well as [Sn-O-P-O](2) and/or [Sn-O-S-O](2) rings. The formation of a 1D coordination polymer in 6 is unique in terms of repeating eight-membered cyclic rings containing Sn, O, P, and S heteroatoms. The contribution from hydrogen-bonding interactions is also found to be significant in these structures.

Synthesis, structure, and luminescence property of a series of Ag–Ln coordination polymers with the N-heterocyclic carboxylato ligand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Jing, E-mail: jinjing_crystal@126.com; Chen, Chong; Gao, Yan

Six Ln–Ag coordination polymers {[LnAg_2(IN)_4(H_2O)_5]·NO_3·2H_2O}{sub n} (Ln=Ho (1) and Tb (2), HIN=isonicotinic acid), {[PrAg_2(IN)_4(H_2O)_2]·NO_3·H_2O}{sub n} (3), [LnAg(pdc){sub 2}]{sub n} (Ln=Eu(4) and Pr (5), H{sub 2}pdc=3,4-pyridine-dicarboxylic acid) and [NdAg(bidc){sub 2}(H{sub 2}O){sub 4}]{sub n} (6) (H{sub 2}bidc=benzimidazole-5,6-dicarboxylic acid) have been hydrothermally synthesized and characterized by single crystal X-ray diffraction, elemental analysis, IR, UV–vis-NIR absorption spectra, fluorescence spectra and thermogravimetric analysis. Structural analyses reveal that the six polymers exhibit 0D (polymer (1)), 1D (polymer (2)), 2D (polymers (3) and (5)) and 3D (polymers (4) and (6)) infinite structures, respectively. Polymers (1)–(6) exhibit the Ln(III) characteristic emission in the near-infrared (NIR) region or inmore » the visible region. Especially, the NIR emission bands of polymers 1, 5 and 6 evidently present shift or splitting due to formation of the Ln–Ag coordination polymers. This can be attributed to the tune of inner levels in Ln–Ag system caused by the interact and influence between the 4d orbital of the Ag(I) ion and the 4f orbital of the Ln(III) ion, which can be confirmed by the UV–vis-NIR absorption spectra of the polymers. In addition, the distortion of coordination geometry as well as difference of the coordination number around the Ag(I) ion affect the structure framework. - Graphical abstract: Six Ag–Ln coordination polymers have been hydrothermally synthesized and characterized. The photoluminescence properties were studied. The distortion of coordination geometry of Ag(I) ion affect structure framework. Introduction of Ag(I) cause wonderful changes to the NIR emission of Ln(III) ions. - Highlights: • Six Ln–Ag polymers have been synthesized and characterized. • The distortion of coordination geometry of Ag(I) ion affect structure framework. • Introduction of Ag(I) cause wonderful changes to the NIR emission of Ln(III) ions.« less

Facial and meridional isomers of holmium-nitrate N-tert-butylacetamide complexes

NASA Astrophysics Data System (ADS)

Chang, Ye-Di; Xue, Jun-Hui; Kang, Xiao-Yan; Yang, Li-Min; Li, Wei-Hong; Xu, Yi-Zhuang; Zhao, Guo-Zhong; Zhang, Gao-Hui; Liu, Ke-Xin; Chen, Jia-Er; Wu, Jin-Guang

2018-06-01

Two Ho(C6H13NO)3(NO3)3 complexes formed by holmium nitrate and N-tert-butylacetamide (NtBA) (Ho-NtBA(I) in a Cc space group, and Ho-NtBA(II) in a P21/c space group) are reported here to investigate the coordination of lanthanide ions with amide groups. Using X-ray single crystal diffraction, FTIR, Raman, FIR and THz methods the structures of the two complexes were identified, in which Ho3+ is 9-coordinated to three carbonyl oxygen atoms provided by three NtBA ligands and three bidentate nitrate ions to form the "facial" and "meridional" isomers. Their FTIR and Raman spectra indicate the formation of two holmium complexes, the variations of NtBA after holmium coordination and the spectra are similar for the isomers in some extent. Their FIR and THz spectroscopic results show the coordination of holmium ions and THz maybe more sensitive to isomers. The results demonstrate the coordination behaviors of holmium ions and NtBA ligand.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Ning; Guo, Wei-Ying; Song, Hui-Hua, E-mail: songhuihua@mail.hebtu.edu.cn

Five new Cd(II) coordination polymers with N-benzoyl-L-glutamic acid (H{sub 2}bzgluO) and different N-donor ligands, [Cd(bzgluO)(2,2′-bipy)(H{sub 2}O)]{sub n} (1), [Cd(bzgluO)(2,4′-bipy){sub 2}(H{sub 2}O)·3H{sub 2}O]{sub n} (2), [Cd(bzgluO)(phen)·H{sub 2}O]{sub n} (3), [Cd(bzgluO)(4,4′-bipy)(H{sub 2}O)]{sub n} (4), [Cd(bzgluO)(bpp)(H{sub 2}O)·2H{sub 2}O]{sub n} (5) were synthesized (2,2′-bipy=2,2′-bipyridine, 2,4′-bipy=2,4′-bipyridine, phen=1,10-phenanthroline, 4,4′-bipy=4,4′-bipyridine, bpp=1,3-di(4-pyridyl)propane). Compounds 1–2 exhibit a 1D single-chain structure. Compound 1 generates a 2D supramolecular structure via π–π stacking and hydrogen bonding, 3D architecture of compound 2 is formed by hydrogen bonding. Compound 3 features a 1D double-chain structure, which are linked by π–π interactions into a 2D supramolecular layer. Compounds 4-5 display a 2D network structure. Neighboringmore » layers of 4 are extended into a 3D supramolecular architecture through hydrogen bonding. The structural diversity of these compounds is attributed to the effect of ancillary N-donor ligands and coordination modes of H{sub 2}bzgluO. Luminescent properties of 1–5 were studied at room temperature. Circular dichroism of compounds 1, 2 and 5 were investigated. - Graphical abstract: Five new Cd(II) metal coordination compounds with H{sub 2}bzgluO and different N-donor ligands were synthesized and characterized. Compounds 1, 2 and 3 present 1D structures, compounds 4 and 5 display 2D networks. Results indicate that auxiliary ligands and coordination modes of H{sub 2}bzgluO play an important role in governing the formation of final frameworks, and the hydrogen-bonding and π–π stacking interactions contribute the formation of the diverse supramolecular architectures. Furthermore, the different crystal structures influence the emission spectra significantly. - Highlights: • It is rarely reported that complexes prepared with N-benzoyl-L-glutamic acid. • Each complex displays diverse structures and different supramolecular interactions. • Results indicate that N-donor ligands play a crucial role in the final structures. • The different crystal structures influence the emission spectra significantly.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A {sm_bullet} U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg{sup 2+} ions, which in turn are octahedrallymore » coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.« less

Scientific Visualization to Study Flux Transfer Events at the Community Coordinated Modeling Center

NASA Technical Reports Server (NTRS)

Rastatter, Lutz; Kuznetsova, Maria M.; Sibeck, David G.; Berrios, David H.

2011-01-01

In this paper we present results of modeling of reconnection at the dayside magnetopause with subsequent development of flux transfer event signatures. The tools used include new methods that have been added to the suite of visualization methods that are used at the Community Coordinated Modeling Center (CCMC). Flux transfer events result from localized reconnection that connect magnetosheath magnetic field and plasma with magnetospheric fields and plasma and results in flux rope structures that span the dayside magnetopause. The onset of flux rope formation and the three-dimensional structure of flux ropes are studied as they have been modeled by high-resolution magnetohydrodynamic simulations of the dayside magnetosphere of the Earth. We show that flux transfer events are complex three-dimensional structures that require modern visualization and analysis techniques. Two suites of visualization methods are presented and we demonstrate the usefulness of those methods through the CCMC web site to the general science user.

Synthesis of branched metal nanostructures with controlled architecture and composition

NASA Astrophysics Data System (ADS)

Ortiz, Nancy

On account of their small size, metal nanoparticles are proven to be outstanding catalysts for numerous chemical transformations and represent promising platforms for applications in the fields of electronics, chemical sensing, medicine, and beyond. Many properties of metal nanoparticles are size-dependent and can be further manipulated through their shape and architecture (e.g., spherical vs. branched). Achieving morphology control of nanoparticles through solution-based techniques has proven challenging due to limited knowledge of morphology development in nanosyntheses. To overcome these complications, a systematic examination of the local ligand environment of metal precursors on nanostructure formation was undertaken to evaluate its contribution to nanoparticle nucleation rate and subsequent growth processes. Specifically, this thesis will provide evidence from ex situ studies---Transmission Electron Microscopy (TEM) and UV-visible spectroscopy (UV-Vis)---that support the hypothesis that strongly coordinated ligands delay burst-like nucleation to generate spherical metal nanoparticles and ligands with intermediate binding affinity regulate the gradual reduction of metal precursors to promote aggregated assembly of nanodendrites. These ex situ studies were coupled with a new in situ perspective, providing detailed understanding of metal precursor transformation, its direct relation to nanoparticle morphology development, and the ligand influence towards the formation of structurally complex metal nanostructures, using in situ synchrotron X-ray Diffraction (XRD) and Ultra Small-Angle X-ray Scattering (USAXS). The principles extracted from the study of monometallic nanostructure formation were also found to be generally applicable to the synthesis of bimetallic nanostructures, e.g., Pd-Pt architectures, with either core-shell or alloyed structures that were readily achieved by ligand selection. These outcomes provide a direct connection between fundamental principles of coordination chemistry and nanoparticle formation, with a stronger foundation for the predictive synthesis of future nanomaterials with controllable structural features.

Cations Modulate Actin Bundle Mechanics, Assembly Dynamics, and Structure.

PubMed

Castaneda, Nicholas; Zheng, Tianyu; Rivera-Jacquez, Hector J; Lee, Hyun-Ju; Hyun, Jaekyung; Balaeff, Alexander; Huo, Qun; Kang, Hyeran

2018-04-12

Actin bundles are key factors in the mechanical support and dynamic reorganization of the cytoskeleton. High concentrations of multivalent counterions promote bundle formation through electrostatic attraction between actin filaments that are negatively charged polyelectrolytes. In this study, we evaluate how physiologically relevant divalent cations affect the mechanical, dynamic, and structural properties of actin bundles. Using a combination of total internal reflection fluorescence microscopy, transmission electron microscopy, and dynamic light scattering, we demonstrate that divalent cations modulate bundle stiffness, length distribution, and lateral growth. Molecular dynamics simulations of an all-atom model of the actin bundle reveal specific actin residues coordinate cation-binding sites that promote the bundle formation. Our work suggests that specific cation interactions may play a fundamental role in the assembly, structure, and mechanical properties of actin bundles.

A new 1D manganese(II) coordination polymer with end-to-end azide bridge and isonicotinoylhydrazone Schiff base ligand: Crystal structure, Hirshfeld surface, NBO and thermal analyses

NASA Astrophysics Data System (ADS)

Khani, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

2018-02-01

A new manganese (II) coordination polymer, [MnL2 (μ-1,3-N3)2]n, with co-ligands including azide anion and Schiff base based on isonicotinoylhydrazone has been synthesized and characterized. The crystal structure determination shows that the azide ligand acts as end-to-end (EE) bridging ligand and generates a one-dimensional coordination polymer. In this compound, each manganes (II) metal center is hexa-coordinated by four azide nitrogens and two pyridinic nitrogens for the formation of octahedral geometry. The analysis of crystal packing indicates that the 1D chain of [MnL2 (μ-1,3-N3)2]n, is stabilized as a 3D supramolecular network by intra- and inter-chain intermolecular interactions of X-H···Y (X = N and C, Y = O and N). Hirshfeld surface analysis and 2D fingerprint plots have been used for a more detailed investigation of intermolecular interactions. Also, natural bond orbital (NBO) analysis was performed to get information about atomic charge distributions, hybridizations and the strength of interactions. Finally, thermal analysis of compound showed its complete decomposition during three thermal steps.

Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na+ coupling

NASA Astrophysics Data System (ADS)

Perez, Camilo; Faust, Belinda; Mehdipour, Ahmad Reza; Francesconi, Kevin A.; Forrest, Lucy R.; Ziegler, Christine

2014-07-01

The Na+-coupled betaine symporter BetP shares a highly conserved fold with other sequence unrelated secondary transporters, for example, with neurotransmitter symporters. Recently, we obtained atomic structures of BetP in distinct conformational states, which elucidated parts of its alternating-access mechanism. Here, we report a structure of BetP in a new outward-open state in complex with an anomalous scattering substrate, adding a fundamental piece to an unprecedented set of structural snapshots for a secondary transporter. In combination with molecular dynamics simulations these structural data highlight important features of the sequential formation of the substrate and sodium-binding sites, in which coordinating water molecules play a crucial role. We observe a strictly interdependent binding of betaine and sodium ions during the coupling process. All three sites undergo progressive reshaping and dehydration during the alternating-access cycle, with the most optimal coordination of all substrates found in the closed state.

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

Dysprosium complexes with mono-/di-carboxylate ligands-From simple dimers to 2D and 3D frameworks

NASA Astrophysics Data System (ADS)

Zhang, Yingjie; Bhadbhade, Mohan; Scales, Nicholas; Karatchevtseva, Inna; Price, Jason R.; Lu, Kim; Lumpkin, Gregory R.

2014-11-01

Four dysprosium (Dy) single carboxylates, a formate, a propionate, a butyrate and an oxalate have been synthesized and structurally characterized. The structure of Dy(HCO2)3 (1) contains nine-fold coordinated Dy polyhedra in perfect tricapped trigonal prisms. They are linked through trigonal O atoms forming 1D pillars which are further linked together through tricapped O atoms into a 3D pillared metal organic framework. The network structure is stable up to 360 °C. The structure of [Dy2(C2O4)3(H2O)6]·2.5H2O (2) contains nine-fold coordinated Dy polyhedra linking together through μ2-bridging oxalate anions into a 2D hexagonal layered structure. Both [Dy2(Pr)6(H2O)4]·(HPr)0.5 (3) [Pr=(C2H5CO2)-1] and [Dy2(Bu)6(H2O)4] (4) [Bu=(C3H7CO2)-1] have similar di-nuclear structures. The Raman vibration modes of the complexes have been investigated.

IRE/F Structure Analysis in Student Expositions during Nursing Practices with SDIS-GSEQ

ERIC Educational Resources Information Center

Ruiz Carrillo, Edgardo; Bravo Sánchez, Luisa; Meraz Martínez, Samuel; Cruz González, José Luiz

2017-01-01

Introduction: In clinical nursing practices where a student presents a class topic, the way in which discourse takes place has a complex formation that places him in an active subject position, but always under the coordination of the teacher. Presentations and activities carried out by the presenter in practice involve discourse-guided…

Effect of hydration on the stability of fullerene-like silica molecules

NASA Astrophysics Data System (ADS)

Filonenko, O. V.; Lobanov, V. V.

2011-05-01

The hydration of fullerene-like silica molecules was studied by the density functional method (exchange-correlation functional B3LYP, basis set 6-31G**). It was demonstrated that completely coordinated structures transform to more stable hydroxylated ones during hydrolysis. These in turn react with H2O molecules with the formation of hydrogen bonds.

Computer simulation of formation and decomposition of Au13 nanoparticles

NASA Astrophysics Data System (ADS)

Stishenko, P.; Svalova, A.

2017-08-01

To study the Ostwald ripening process of Au13 nanoparticles a two-scale model is constructed: analytical approximation of average nanoparticle energy as function of nanoparticle size and structural motive, and the Monte Carlo model of 1000 particles ensemble. Simulation results show different behavior of particles of different structural motives. The change of the distributions of atom coordination numbers during the Ostwald ripening process was observed. The nanoparticles of the equal size and shape with the face-centered cubic structure of the largest sizes appeared to be the most stable.

Ab initio calculations of ionic hydrocarbon compounds with heptacoordinate carbon.

PubMed

Wang, George; Rahman, A K Fazlur; Wang, Bin

2018-04-25

Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C 6 (CH 3 ) 6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C 7 H 7 ) 3+ , in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C 8 H 8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage. Graphical abstract Possible structural transformations of stable configurations of (C 7 H 7 ) 3+ , which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

Extracting numeric measurements and temporal coordinates from Japanese radiological reports

NASA Astrophysics Data System (ADS)

Imai, Takeshi; Onogi, Yuzo

2004-04-01

Medical records are written mainly, in natural language. The focus of this study is narrative radiological reports written in natural Japanese. These reports cannot be used for advanced retrieval, data mining, and so on, unless they are stored, using a structured format such as DICOM-SR. The goal is to structure narrative reports progressively, using natural language processing (NLP). Structure has many different levels, for example, DICOM-SR has three established levels -- basic text, enhanced and comprehensive. At the enhanced level, it is necessary to use numerical measurements and spatial & temporal coordinates. In this study, the wording used in the reports was first standardized, dictionaries were organized, and morphological analysis performed. Next, numerical measurements and temporal coordinates were extracted, and the objects to which they referred, analyzed. 10,000 CT and MR reports were separated into 82,122 sentences, and 34,269 of the 36,444 numerical descriptions were tagged. Periods, slashes, hyphens, and parentheses are ambiguously used in the description of enumerated lists, dates, image numbers, and anatomical names, as well as at the end of sentences; to resolve this ambiguity, descriptions were processed, according to the order -- date, size, unit, enumerated list, and abbreviation -- then, the tagged reports were separated into sentences.

Crystal structure of cis-aqua­chlorido­bis­(1,10-phenanthroline-κ2 N,N′)chromium(III) tetra­chlorido­zincate monohydrate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [CrCl(C12H8N2)2(H2O)][ZnCl4]·H2O, has been determined from synchrotron data. The CrIII ion is bonded to four N atoms from two 1,10-phenanthroline (phen) ligands, one water mol­ecule and a Cl atom in a cis arrangement, displaying an overall distorted octa­hedral coordination environment. The Cr—N(phen) bond lengths are in the range of 2.0495 (18) to 2.0831 (18) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2734 (7) and 1.9986 (17) Å, respectively. The tetra­hedral [ZnCl4]2− anion is slightly distorted owing to its involvement in O—H⋯Cl hydrogen bonding with coordinating and non-coordinating water mol­ecules. The two types of water mol­ecules also inter­act through O—H⋯O hydrogen bonds. The observed hydrogen-bonding pattern leads to the formation of a three-dimensional network structure. PMID:25844190

Dysprosium complexes with mono-/di-carboxylate ligands—From simple dimers to 2D and 3D frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Bhadbhade, Mohan; Scales, Nicholas

2014-11-15

Four dysprosium (Dy) single carboxylates, a formate, a propionate, a butyrate and an oxalate have been synthesized and structurally characterized. The structure of Dy(HCO{sub 2}){sub 3} (1) contains nine-fold coordinated Dy polyhedra in perfect tricapped trigonal prisms. They are linked through trigonal O atoms forming 1D pillars which are further linked together through tricapped O atoms into a 3D pillared metal organic framework. The network structure is stable up to 360 °C. The structure of [Dy{sub 2}(C{sub 2}O{sub 4}){sub 3}(H{sub 2}O){sub 6}]·2.5H{sub 2}O (2) contains nine-fold coordinated Dy polyhedra linking together through μ{sub 2}-bridging oxalate anions into a 2D hexagonalmore » layered structure. Both [Dy{sub 2}(Pr){sub 6}(H{sub 2}O){sub 4}]·(HPr){sub 0.5} (3) [Pr=(C{sub 2}H{sub 5}CO{sub 2}){sup −1}] and [Dy{sub 2}(Bu){sub 6}(H{sub 2}O){sub 4}] (4) [Bu=(C{sub 3}H{sub 7}CO{sub 2}){sup −1}] have similar di-nuclear structures. The Raman vibration modes of the complexes have been investigated. - Graphical abstract: Four dysprosium (Dy) complexes with formate, propionate, butyrate and oxalate ligands have been synthesized and characterized. The Dy formato complex has a 3D pillared metal organic framework and the structure is stable up to 360 °C whilst the complexes with longer alkyl chained mono-carboxylates possess similar di-nuclear structures. The Dy oxalato complex has a 2D hexagonal (honeycomb-type) structure. Their Raman vibration modes have been investigated. - Highlights: • New Dysprosium complexes with formate, propionate, butyrate and oxalate ligands. • Crystal structures range from dimers to two and three dimensional frameworks. • Vibrational modes have been investigated and correlated to the structures. • The complexes are thermal robust and stable to over 300 °C.« less

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.

PubMed

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M; Montelione, Gaetano T

2013-08-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

PDBStat: A Universal Restraint Converter and Restraint Analysis Software Package for Protein NMR

PubMed Central

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M.; Montelione, Gaetano T

2013-01-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data. PMID:23897031

Structural Characterization of Ferric Hemoglobins from Three Antarctic Fish Species of the Suborder Notothenioidei

PubMed Central

Vergara, Alessandro; Franzese, Marisa; Merlino, Antonello; Vitagliano, Luigi; Verde, Cinzia; di Prisco, Guido; Lee, H. Caroline; Peisach, Jack; Mazzarella, Lelio

2007-01-01

Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarctic fish species Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, as well as the x-ray crystal structure of oxidized Trematomus bernacchii Hb, redetermined at high resolution. The oxidation of these Hbs leads to formation of states that were not usually detected in previous analyses of tetrameric Hbs. In addition to the commonly found aquo-met and hydroxy-met species, EPR analyses show that two distinct hemichromes coexist at physiological pH, referred to as hemichromes I and II, respectively. Together with the high-resolution crystal structure (1.5 Å) of T. bernacchii and a survey of data available for other heme proteins, hemichrome I was assigned by x-ray crystallography and by EPR as a bis-His complex with a distorted geometry, whereas hemichrome II is a less constrained (cytochrome b5-like) bis-His complex. In four of the five Antartic fish Hbs examined, hemichrome I is the major form. EPR shows that for HbCTn, the amount of hemichrome I is substantially reduced. In addition, the concomitant presence of a penta-coordinated high-spin Fe (III) species, to our knowledge never reported before for a wild-type tetrameric Hb, was detected. A molecular modeling investigation demonstrates that the presence of the bulkier Ile in position 67β in HbCTn in place of Val as in the other four Hbs impairs the formation of hemichrome I, thus favoring the formation of the ferric penta-coordinated species. Altogether the data show that ferric states commonly associated with monomeric and dimeric Hbs are also found in tetrameric Hbs. PMID:17545238

Diverse Cd{sup II} coordination complexes derived from bromide isophthalic acid binding with auxiliary N-donor ligands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Meng; Dong, Bao-Xia, E-mail: bxdong@yzu.edu.cn; Wu, Yi-Chen

The coordination characteristics of 4-bromoisophthalic acid (4-Br-H{sub 2}ip) have been investigated in a series of Cd{sup II}-based frameworks. Hydrothermal reactions of Cd{sup II} salts and 4-Br-H{sub 2}ip together with flexible or semiflexible N-donor auxiliary ligands resulted in the formation of four three-dimensional coordination complexes with diverse structures: (Cd(bix){sub 0.5}(bix){sub 0.5}(4-Br-ip)]·H{sub 2}O){sub n} (1), [Cd(bbi){sub 0.5}(bbi){sub 0.5}(4-Br-ip)]{sub n} (2), ([Cd(btx){sub 0.5}(4-Br-ip)(H{sub 2}O)]·0.5CH{sub 3}OH·H{sub 2}O){sub n} (3) and ([Cd(bbt){sub 0.5}(4-Br-ip)(H{sub 2}O)]·3·5H{sub 2}O){sub n} (4). These compounds were characterized by elemental analyses, IR spectra, single-crystal and powder X-ray diffraction. They displayed diverse structures depending on the configuration of the 4-connected metal node, themore » coordination mode of the 4-Br-H{sub 2}ip, the coordination ability and conformationally flexibility of the N-donor auxiliary. Compound 1 exhibits 3-fold interpenetrated 6{sup 6} topology and compound 2 has a 4{sup 12} topology. Compounds 3–4 have similar 3D pillar-layered structures based on 3,4-connected binodal net with the Schläfli symbol of (4·3{sup 8}). The thermal stabilities and photoluminescence properties of them were discussed in detail. - Graphical abstract: Four 3D Cd{sup II} coordination complexes on the basis of 4-bromoisophthalic acid (4-Br-H{sub 2}ip) and two types of flexible (bbi, bbt) and semiflexible (bix, btx) N-donor ligands are prepared. They displayed diverse topology structures of 6{sup 6} (1), 4{sup 12} (2) and 4·3{sup 8} (3−4), depending on the configuration of the 4-connected metal node, the coordination mode of the 4-Br-H{sub 2}ip, the coordination ability and conformationally flexibility of the N-donor auxiliary ligand. - Highlights: • Four 3D Cd{sup II} coordination complexes based on 4-Br-H{sub 2}ip and flexible/semiflexible N-donor ligands have been synthesized. • They displayed diverse topology structures of 6{sup 6} for 1, 4{sup 12} for 2 and 4·3{sup 8} for 3–4. • The structural diversity depends on the configuration of 4-Br-H{sub 2}ip and the coordination behaviors of the auxiliary ligand.« less

High-Temperature Formation Phases and Crystal Structure of Hot-Pressed Thermoelectric CuGaTe2 with Chalcopyrite-Type Structure

NASA Astrophysics Data System (ADS)

Fujii, Yosuke; Kosuga, Atsuko

2017-11-01

Polycrystalline CuGaTe2 with a chalcopyrite-type structure consolidated by hot-pressing is a potential candidate as a medium-temperature thermoelectric (TE) material. However, its high-temperature formation phases have rarely been reported to date. Here, we investigated the temperature-dependent formation phases and crystal structure at 300-800 K of hot-pressed CuGaTe2. From synchrotron x-ray diffraction data and crystal structure analysis of the heating and cooling processes, it was clarified that a certain amount of impurity phases, such as Te and CuTe, precipitated from the CuGaTe2 matrix when the temperature was increased (to 500-650 K). This is the temperature range where CuGaTe2 has been reported to show high TE performance. After CuGaTe2 was heated to 800 K, such impurity phases remained, even when cooled to room temperature. They also affected the tetragonal distortion and the x-coordinate of Te in the CuGaTe2 matrix, probably due to deficiencies of Cu and Te in the matrix. Our results reveal detailed information on the formation phases of CuGaTe2 at high temperature and thus provide insight for evaluation of its high-temperature stability and transport properties.

High-Temperature Formation Phases and Crystal Structure of Hot-Pressed Thermoelectric CuGaTe2 with Chalcopyrite-Type Structure

NASA Astrophysics Data System (ADS)

Fujii, Yosuke; Kosuga, Atsuko

2018-06-01

Polycrystalline CuGaTe2 with a chalcopyrite-type structure consolidated by hot-pressing is a potential candidate as a medium-temperature thermoelectric (TE) material. However, its high-temperature formation phases have rarely been reported to date. Here, we investigated the temperature-dependent formation phases and crystal structure at 300-800 K of hot-pressed CuGaTe2. From synchrotron x-ray diffraction data and crystal structure analysis of the heating and cooling processes, it was clarified that a certain amount of impurity phases, such as Te and CuTe, precipitated from the CuGaTe2 matrix when the temperature was increased (to 500-650 K). This is the temperature range where CuGaTe2 has been reported to show high TE performance. After CuGaTe2 was heated to 800 K, such impurity phases remained, even when cooled to room temperature. They also affected the tetragonal distortion and the x-coordinate of Te in the CuGaTe2 matrix, probably due to deficiencies of Cu and Te in the matrix. Our results reveal detailed information on the formation phases of CuGaTe2 at high temperature and thus provide insight for evaluation of its high-temperature stability and transport properties.

Causal Structure around Spinning 5-DIMENSIONAL Cosmic Strings

NASA Astrophysics Data System (ADS)

Slagter, Reinoud Jan

2008-09-01

We present a numerical solution of a stationary 5-dimensional spinning cosmic string in the Einstein-Yang-Mills (EYM) model, where the extra bulk coordinate ψ is periodic. It turns out that when gψψ approaches zero, i.e., a closed time-like curve (CTC) would appear, the solution becomes singular. We also investigated the geometrical structure of the static 5D cosmic string. Two opposite moving 5D strings could, in contrast with the 4D case, fulfil the Gott condition for CTC formation.

Two novel copper(II) complexes constructed from dicarboxylate ligands with different spacer lengths and 2-phenylimidazo[4,5- f]1,10-phenanthroline (PIP): Synthesis, structures and properties

NASA Astrophysics Data System (ADS)

Wang, X.-L.; Chen, Yongqiang; Liu, Guocheng; Lin, Hongyan; Zhang, Jinxia

2009-09-01

Two novel metal-organic coordination polymers [Cu(PIP)(bpea)(H 2O)]·H 2O ( 1) and [Cu(PIP)(1,4-bdc)] ( 2) have been obtained from hydrothermal reaction of copper(II) with the mixed ligands [biphenylethene-4,4'-dicarboxylic acid (bpea) for 1, benzene-1,4-dicarboxylic acid (1,4-H 2bdc) for 2, and 2-phenylimidazo[4,5- f]1,10-phenanthroline (PIP)]. Both complexes have been structurally characterized by elemental analyses, IR and single-crystal X-ray diffraction analyses. Structural analyses reveal that complex 1 possesses infinite one-dimensional zigzag chain, 2 exhibits a two-dimensional (4,4) network, both of which are extended into three-dimensional supramolecular network by weak interactions. The different structures of the title complexes illustrate the influence of the flexibility (the spacer length of carboxyl groups and the structural rigidity of the spacer) of organic dicarboxylate ligands on the formation of such coordination architectures. Moreover, the thermal properties and the voltammetric behavior of complexes 1 and 2 have been reported.

Aqua(pentahydrogennitrilotris(methylenephosphonato))lithium hydrate [Li(H{sub 2}O)(N(CH{sub 2}PO{sub 3}){sub 3}H{sub 5})] • H{sub 2}O: Synthesis and structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somov, N. V., E-mail: somov@phys.unn.ru; Chausov, F. F., E-mail: xps@ftiudm.ru; Zakirova, R. M., E-mail: ftt@udsu.ru

Aqua(pentahydrogennitrilotris(methylenephosphonato))lithium hydrate is a linear coordination polymer. Its crystal structure is described in space group P{sup –}1, Z = 2; a = 5.5732(2), b = 7.0106(2), and c = 16.9010(5) Å; α = 97.515(2)°, β = 94.551(2)°, and γ = 95.123(2)°. The tetrahedral coordination of the Li atom includes two oxygen atoms of a phosphonate ligand, one oxygen atom of another phosphonate ligand, and a water molecule. Complex formation is accompanied by closing of the eight-membered Li–O–P–C–N–C–P–O chelate ring. Polymeric chains run along the [100] direction. The chains are connected by hydrogen bonds.

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

PubMed

Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

2007-07-01

We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

Reactivity of molecular dioxygen towards a series of isostructural dichloroiron(III) complexes with tripodal tetraamine ligands: general access to mu-oxodiiron(III) complexes and effect of alpha-fluorination on the reaction kinetics.

PubMed

Thallaj, Nasser K; Rotthaus, Olaf; Benhamou, Leila; Humbert, Nicolas; Elhabiri, Mourad; Lachkar, Mohammed; Welter, Richard; Albrecht-Gary, Anne-Marie; Mandon, Dominique

2008-01-01

We have synthesized the mono, di-, and tri-alpha-fluoro ligands in the tris(2-pyridylmethyl)amine (TPA) series, namely, FTPA, F(2)TPA and F(3)TPA, respectively. Fluorination at the alpha-position of these nitrogen-containing tripods shifts the oxidation potential of the ligand by 45-70 mV per added fluorine atom. The crystal structures of the dichloroiron(II) complexes with FTPA and F(2)TPA reveal that the iron center lies in a distorted octahedral geometry comparable to that already found in TPAFeCl(2). All spectroscopic data indicate that the geometry is retained in solution. These three isostructural complexes all react with molecular dioxygen to yield stable mu-oxodiiron(III) complexes. Crystal structure analyses are reported for each of these three mu-oxo compounds. With TPA, a symmetrical structure is obtained for a dicationic compound with the tripod coordinated in the kappa(4)N coordination mode. With FTPA, the compound is a neutral mu-oxodiiron(III) complex with a kappa(3)N coordination mode of the ligand. Oxygenation of the F(2)TPA complex gave a neutral unsymmetrical compound, the structure of which is reminiscent of that already found with the trifluorinated ligand. On reduction, all mu-oxodiiron(III) complexes revert to the starting iron(II) species. The oxygenation reaction parallels the well-known formation of mu-oxo derivatives from dioxygen in the chemistry of porphyrins reported almost three decades ago. The striking feature of the series of iron(II) precursors is the effect of the ligand on the kinetics of oxygenation of the complexes. Whereas the parent complex undergoes 90 % conversion over 40 h, the monofluorinated ligand provides a complex that has fully reacted after 30 h, whereas the reaction time for the complex with the difluorinated ligand is only 10 h. Analysis of the spectroscopic data reveals that formation of the mu-oxo complexes proceeds in two distinct reversible kinetic steps with k(1) approximately 10 k(2). For TPAFeCl(2) and FTPAFeCl(2) only small variations in the k(1) and k(2) values are observed. By contrast, F(2)TPAFeCl(2) exhibits k(1) and k(2) values that are ten times higher. These differences in kinetics are interpreted in the light of structural and electronic effects, especially the Lewis acidity at the metal center. Our results suggest coordination of dioxygen as an initial step in the process leading to formation of mu-oxodiiron(III) compounds, by contrast with an unlikely outer-sphere reduction of dioxygen, which generally occurs at negative potentials.

Evolution of Iodoplumbate Complexes in Methylammonium Lead Iodide Perovskite Precursor Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharenko, Alexander; Mackeen, Cameron; Jewell, Leila

Here in this study we investigate the local structure present in single-step precursor solutions of methylammonium lead iodide (MAPbI 3) perovskite as a function of organic and inorganic precursor ratio, as well as with hydriodic acid (HI), using X-ray absorption spectroscopy. An excess of organic precursor as well as the use of HI as a processing additive has been shown to lead to the formation of smooth, continuous, pinhole free MAPbI 3 films, whereas films produced from precursor solutions containing molar equivalents of methylammonium iodide (MAI) and PbI 2 lead to the formation of a discontinuous, needlelike morphology. We nowmore » show that as the amount of excess MAI in the precursor solution is increased, the iodide coordination of iodoplumbate complexes present in solution increases. The use of HI results in a similar increase in iodide coordination. We therefore offer insight into how solution chemistry can be used to control MAPbI 3 thin film morphology by revealing a strong correlation between the lead coordination chemistry in precursor solutions and the surface coverage and morphology of the resulting MAPbI 3 film.« less

Evolution of Iodoplumbate Complexes in Methylammonium Lead Iodide Perovskite Precursor Solutions

DOE PAGES

Sharenko, Alexander; Mackeen, Cameron; Jewell, Leila; ...

2017-02-02

Here in this study we investigate the local structure present in single-step precursor solutions of methylammonium lead iodide (MAPbI 3) perovskite as a function of organic and inorganic precursor ratio, as well as with hydriodic acid (HI), using X-ray absorption spectroscopy. An excess of organic precursor as well as the use of HI as a processing additive has been shown to lead to the formation of smooth, continuous, pinhole free MAPbI 3 films, whereas films produced from precursor solutions containing molar equivalents of methylammonium iodide (MAI) and PbI 2 lead to the formation of a discontinuous, needlelike morphology. We nowmore » show that as the amount of excess MAI in the precursor solution is increased, the iodide coordination of iodoplumbate complexes present in solution increases. The use of HI results in a similar increase in iodide coordination. We therefore offer insight into how solution chemistry can be used to control MAPbI 3 thin film morphology by revealing a strong correlation between the lead coordination chemistry in precursor solutions and the surface coverage and morphology of the resulting MAPbI 3 film.« less

Observation of gold sub-nanocluster nucleation within a crystalline protein cage

NASA Astrophysics Data System (ADS)

Maity, Basudev; Abe, Satoshi; Ueno, Takafumi

2017-03-01

Protein scaffolds provide unique metal coordination environments that promote biomineralization processes. It is expected that protein scaffolds can be developed to prepare inorganic nanomaterials with important biomedical and material applications. Despite many promising applications, it remains challenging to elucidate the detailed mechanisms of formation of metal nanoparticles in protein environments. In the present work, we describe a crystalline protein cage constructed by crosslinking treatment of a single crystal of apo-ferritin for structural characterization of the formation of sub-nanocluster with reduction reaction. The crystal structure analysis shows the gradual movement of the Au ions towards the centre of the three-fold symmetric channels of the protein cage to form a sub-nanocluster with accompanying significant conformational changes of the amino-acid residues bound to Au ions during the process. These results contribute to our understanding of metal core formation as well as interactions of the metal core with the protein environment.

A framework for evaluating the formation, implementation, and performance of accountable care organizations.

PubMed

Fisher, Elliott S; Shortell, Stephen M; Kreindler, Sara A; Van Citters, Aricca D; Larson, Bridget K

2012-11-01

The implementation of accountable care organizations (ACOs), a new health care payment and delivery model designed to improve care and lower costs, is proceeding rapidly. We build on our experience tracking early ACOs to identify the major factors-such as contract characteristics; structure, capabilities, and activities; and local context-that would be likely to influence ACO formation, implementation, and performance. We then propose how an ACO evaluation program could be structured to guide policy makers and payers in improving the design of ACO contracts, while providing insights for providers on approaches to care transformation that are most likely to be successful in different contexts. We also propose key activities to support evaluation of ACOs in the near term, including tracking their formation, developing a set of performance measures across all ACOs and payers, aggregating those performance data, conducting qualitative and quantitative research, and coordinating different evaluation activities.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Syntheses, structures and luminescent properties of a series of 3D lanthanide coordination polymers with tripodal semirigid ligand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin Junsheng; Department of Applied Chemistry, Jilin Institute of Chemical Technology, Jilin 132022; Du Dongying

2011-02-15

Reactions of the tripodal bridging ligand 5-(4-carboxy-phenoxy)-isophthalic acid (abbreviated as H{sub 3}cpia) with lanthanide salts lead to the formation of a family of different coordination polymers, that is, [Ln(cpia)(H{sub 2}O){sub 2}]{sub n}.nH{sub 2}O (Ln=Ce (1), Pr (2), Nd (3), Sm (4), Eu (5), Gd (6), Dy (7), Er (8), Tm (9) and Y (10)) in the presence of formic acid or diethylamine, which are characterized by elemental analysis, IR spectrum, thermogravimetric analysis (TGA), XRPD spectrum and single-crystal X-ray diffraction. Compounds 1-10 are isostructural and exhibit three-dimensional microporous frameworks. Furthermore, the photoluminescent properties of 4, 5 and 7 have been studiedmore » in detail. -- Graphical abstract: Reactions of the tripodal bridging ligand (H{sub 3}cpia) with lanthanide ions lead to the formation of a series of coordination polymers in the presence of formic acid or diethylamine. Display Omitted Research Highlights: {yields} Ten new lanthanides-based coordination polymers (1-10) have been synthesized. {yields} 1-10 exhibit 3D (4,8)-connected fluorite topology networks with 1D channel parallel to the b-axis. {yields} Compounds 4, 5 and 7 exhibit characteristic luminescence of Sm{sup 3+}, Eu{sup 3+} and Dy{sup 3+} ions, respectively.« less

High-Pressure Behavior of Difluorides: The Case of SrF2

NASA Astrophysics Data System (ADS)

Swadba, K. E.; Stan, C. V.; Dutta, R.; Prakapenka, V.; Duffy, T. S.

2016-12-01

The high-pressure behavior of compounds in the AX2 family has attracted much attention due to their extensive polymorphism, highly coordinated structures, and diverse transformation pathways. The canonical transformation sequence for alkaline earth difluorides is from the fluorite-type structure (8 coordinated) to cotunnite (9 coordinated) to Ni2In (11 coordinated). Lead Fluoride, on the other hand, undergoes an unusual isosymmetric transition from cotunnite to a Co2Si-type structure (10 coordinated) at high pressures, during which it exhibits highly anisotropic lattice parameter trends (Haines et al, 1998; Stan et al 2016). Sr has a similar ionic radius as Pb, and is thus a good candidate for further exploring the compressional anisotropy in alkaline earth fluorides. In this study, we report a detailed examination of the compressional behavior of SrF2 to identify whether an intermediate phase occurs in this system prior to transformation to the Ni2In structure. Raman spectroscopy and x-ray diffraction experiments, performed at Princeton University and the Advanced Photon Source GSECARS beamline, respectively, were carried out on SrF2 up to 63 GPa using a diamond anvil cell. From Raman spectroscopy, we observed evidence for a high-pressure phase transition between 38.9 and 51.0 GPa. The x-ray diffraction data in this region show evidence for highly anisotropic compression, most notably a strong negative compressibility in the b direction, in the pressure region from 45.2 to 51.6 GPa. Comparison of our data with lattice parameter systematics for AX2 phases indicates that our results are consistent with the formation of the Co2Si phase in this region, along with a sluggish transformation to the Ni2In-type structure. Our findings contribute to a broader understanding of AX2 compounds and their phase transition pathways.

Coordination chemistry of 6-thioguanine derivatives with cobalt: toward formation of electrical conductive one-dimensional coordination polymers.

PubMed

Amo-Ochoa, Pilar; Alexandre, Simone S; Hribesh, Samira; Galindo, Miguel A; Castillo, Oscar; Gómez-García, Carlos J; Pike, Andrew R; Soler, José M; Houlton, Andrew; Zamora, Félix; Harrington, Ross W; Clegg, William

2013-05-06

In this work we have synthetized and characterized by X-ray diffraction five cobalt complexes with 6-thioguanine (6-ThioGH), 6-thioguanosine (6-ThioGuoH), or 2'-deoxy-6-thioguanosine (2'-d-6-ThioGuoH) ligands. In all cases, these ligands coordinate to cobalt via N7 and S6 forming a chelate ring. However, independently of reagents ratio, 6-ThioGH provided monodimensional cobalt(II) coordination polymers, in which the 6-ThioG(-) acts as bridging ligand. However, for 2'-d-6-ThioGuoH and 6-ThioGuoH, the structure directing effect of the sugar residue gives rise to mononuclear cobalt complexes which form extensive H-bond interactions to generate 3D supramolecular networks. Furthermore, with 2'-d-6-ThioGuoH the cobalt ion remains in the divalent state, whereas with 6-ThioGuoH oxidation occurs and Co(III) is found. The electrical and magnetic properties of the coordination polymers isolated have been studied and the results discussed with the aid of DFT calculations, in the context of molecular wires.

Theoretical study of the coordination behavior of formate and formamidoximate with dioxovanadium( v ) cation: implications for selectivity towards uranyl

DOE PAGES

Mehio, Nada; Johnson, J. Casey; Dai, Sheng; ...

2015-10-28

Poly(acrylamidoxime)-based fibers bearing random mixtures of carboxylate and amidoxime groups are the most widely utilized materials for extracting uranium from seawater. However, the competition between uranyl (UO 2 2+) and vanadium ions poses a significant challenge to the industrial mining of uranium from seawater using the current generation of adsorbents. To design more selective adsorbents, a detailed understanding of how major competing ions interact with carboxylate and amidoxime ligands is required. In this work, we employ density functional theory (DFT) and wave-function methods to investigate potential binding motifs of the dioxovanadium ion, VO 2 +, with water, formate, and formamidoximatemore » ligands. Employing higher level of theory calculations (CCSD(T)) resolve the existing controversy between the experimental results and previous DFT calculations for the structure of the hydrated VO 2 + ion. Consistent with the EXAFS data, CCSD(T) calculations predict higher stability of the distorted octahedral geometry of VO 2 +(H 2O) 4 compared to the five-coordinate complex with a single water molecule in the second hydration shell, while all seven tested DFT methods yield the reverse stability of the two conformations. Analysis of the relative stabilities of formate-VO 2 + complexes indicates that both monodentate and bidentate forms may coexist in thermodynamic equilibrium in solution, with the equilibrium balance leaning more towards the formation of monodentate species. Investigations of VO 2 + coordination with the formamidoximate anion has revealed the existence of seven possible binding motifs, four of which are within ~ 4.0 kcal/mol of each other. Calculations establish that the most stable binding motif entails the coordination of oxime oxygen and amide nitrogen atoms via a tautomeric rearrangement of amidoxime to imino hydroxylamine. Lastly, the difference in the most stable VO 2 + and UO 2 2+ binding conformation has important implications for the design of more selective UO 2 2+ ligands.« less

Electrical characteristics of rocks in fractured and caved reservoirs

NASA Astrophysics Data System (ADS)

Tang, Tianzhi; Lu, Tao; Zhang, Haining; Jiang, Liming; Liu, Tangyan; Meng, He; Wang, Feifei

2017-12-01

The conductive paths formed by fractures and cave in complex reservoirs differ from those formed by pores and throats in clastic rocks. In this paper, a new formation model based on fractured and caved reservoirs is established, and the electrical characteristics of rocks are analyzed with different pore structures using resistance law to understand their effects on rock resistivity. The ratio of fracture width to cave radius (C e value) and fracture dip are employed to depict pore structure in this model. Our research shows that the electrical characteristics of rocks in fractured and caved reservoirs are strongly affected by pore structure and porous fluid distribution. Although the rock electrical properties associated with simple pore structure agree well with Archie formulae, the relationships between F and φ or between I and S w , in more complicated pore structures, are nonlinear in double logarithmic coordinates. The parameters in Archie formulae are not constant and they depend on porosity and fluid saturation. Our calculations suggest that the inclined fracture may lead to resistivity anisotropy in the formation. The bigger dip the inclining fracture has, the more anisotropy the formation resistivity has. All of these studies own practical sense for the evaluation of oil saturation using resistivity logging data.

Unanticipated coordination of tris buffer to the Radical SAM cluster of the RimO methylthiotransferase.

PubMed

Molle, Thibaut; Clémancey, Martin; Latour, Jean-Marc; Kathirvelu, Velavan; Sicoli, Giuseppe; Forouhar, Farhad; Mulliez, Etienne; Gambarelli, Serge; Atta, Mohamed

2016-07-01

Radical SAM enzymes generally contain a [4Fe-4S](2+/1+) (RS cluster) cluster bound to the protein via the three cysteines of a canonical motif CxxxCxxC. The non-cysteinyl iron is used to coordinate SAM via its amino-carboxylate moiety. The coordination-induced proximity between the cluster acting as an electron donor and the adenosyl-sulfonium bond of SAM allows for the homolytic cleavage of the latter leading to the formation of the reactive 5'-deoxyadenosyl radical used for substrate activation. Most of the structures of Radical SAM enzymes have been obtained in the presence of SAM, and therefore, little is known about the situation when SAM is not present. In this report, we show that RimO, a methylthiotransferase belonging to the radical SAM superfamily, binds a Tris molecule in the absence of SAM leading to specific spectroscopic signatures both in Mössbauer and pulsed EPR spectroscopies. These data provide a cautionary note for researchers who work with coordinative unsaturated iron sulfur clusters.

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid-Complex Tauto-Conformers.

PubMed

Schäfer, Bernhard; Greisch, Jean-François; Faus, Isabelle; Bodenstein, Tilmann; Šalitroš, Ivan; Fuhr, Olaf; Fink, Karin; Schünemann, Volker; Kappes, Manfred M; Ruben, Mario

2016-08-26

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism-driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe(II) 4 L4 ](8+) complexes were determined by X-ray diffraction, and the distinctness of the products was confirmed by ion-mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe(II) spin crossover vs. a blocked Fe(II) high-spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

On-Surface Synthesis and Reactivity of Functional Organic and Metal-Organic Adsorbates at Metal Surfaces by Vibrational Spectroscopy

NASA Astrophysics Data System (ADS)

Williams, Christopher Glen

Surface self-assembly is a promising way to introduce functionality to a surface through design at the molecular level. These self-assembled species allow for new on-surface type reactions to be observed and studied. The experiments described in this thesis demonstrate that the molecules used in self-assembly can potentially lead to interesting synthesis pathways and can be used to explore previously under-researched reaction pathways and surface molecular architecture activity or stability. Alkanes are an unreactive species typically used for driving molecular assembly in surface structures. However, with molecular design, alkanes are capable of reacting on surfaces not typically associated with alkane reactivity. Utilizing high-resolution electron energy loss spectroscopy (HREELS) and octaethylporphyrin, we could observe that dehydrogenation is possible on Cu(100) and Ag(111) surfaces at 500 and 610 K respectively. HREELS revealed that after the dehydrogenation, the molecule undergoes an intramolecular C-C bond formation leading to a tetrabenzo-porphyrin structure. Controls with deposited tetrabenzo-porphyrin were performed to verify the structure. This work provides the first example of dehydrocyclization on Cu(100) and Ag(111) to be analyzed by vibrational spectroscopy. Alkyl species in the 1,3,5-tris-(3,5-diethylphenyl)benzene molecule also undergo a dehydrogenation on Cu(100) and Au(111) at 450 and 500 K. The design of this molecule does not let the intramolecular dehydrocyclization reaction take place, but instead the dehydrogenation leads to intermolecular C-C bond formation between molecular species as noted by the formation of extended structure across the surface. Controls with triphenyl-benzene were done to help characterize the peaks in the spectra and observe varying reactivity when the ethyl groups are absent. The fabrication of uniform single-site metal centers at surfaces is important for higher selectivity in next-generation heterogeneous catalysts. We accomplished this by metal coordination to redox non-innocent dipyridyl-tetrazine ligands. We utilize HREELS to observe a surface confined redox process of dipyridyl-tetrazine with V, Fe, Ag, and Pt. With the formation of the V-dipyridyl-tetrazine species, we are able to see that oxygen exposures to the surface results in a more selective vanadyl species formation as opposed to the multiple binding conformations observed with metallic vanadium nanoparticles. This thesis also reveals that the metal substrate used does not play a passive role with the metal-organic complex. Instead, we are the first to characterize a replacement of the coordinating metal species with atoms from the Ag(111) substrate. This replacement results in the redox reaction between the coordinating metal species and the substrate metal.

Synthesis and characterization of crystalline structures based on phenylboronate ligands bound to alkaline earth cations.

PubMed

Reinholdt, Marc; Croissant, Jonas; Di Carlo, Lidia; Granier, Dominique; Gaveau, Philippe; Bégu, Sylvie; Devoisselle, Jean-Marie; Mutin, P Hubert; Smith, Mark E; Bonhomme, Christian; Gervais, Christel; van der Lee, Arie; Laurencin, Danielle

2011-08-15

We describe the preparation of the first crystalline compounds based on arylboronate ligands PhB(OH)(3)(-) coordinated to metal cations: [Ca(PhB(OH)(3))(2)], [Sr(PhB(OH)(3))(2)]·H(2)O, and [Ba(PhB(OH)(3))(2)]. The calcium and strontium structures were solved using powder and single-crystal X-ray diffraction, respectively. In both cases, the structures are composed of chains of cations connected through phenylboronate ligands, which interact one with each other to form a 2D lamellar structure. The temperature and pH conditions necessary for the formation of phase-pure compounds were investigated: changes in temperature were found to mainly affect the morphology of the crystallites, whereas strong variations in pH were found to affect the formation of pure phases. All three compounds were characterized using a wide range of analytical techniques (TGA, IR, Raman, XRD, and high resolution (1)H, (11)B, and (13)C solid-state NMR), and the different coordination modes of phenylboronate ligands were analyzed. Two different kinds of hydroxyl groups were identified in the structures: those involved in hydrogen bonds, and those that are effectively "free" and not involved in hydrogen bonds of any significant strength. To position precisely the OH protons within the structures, an NMR-crystallography approach was used: the comparison of experimental and calculated NMR parameters (determined using the Gauge Including Projector Augmented Wave method, GIPAW) allowed the most accurate positions to be identified. In the case of the calcium compound, it was found that it is the (43)Ca NMR data that are critical to help identify the best model of the structure. © 2011 American Chemical Society

Polarization-correlation diagnostics and differentiation of cholelithiasis in patients with chronic cholecystitis combined with diabetes mellitus type 2

NASA Astrophysics Data System (ADS)

Marchuk, Yu F.; Fediv, O. I.; Ivashchuk, I. O.; Andriychuk, D. R.

2011-09-01

The principles of optical modeling of human bile polycrystalline structure are described. The main types of polycrystalline structures are detailed. It has been proposed and founded the scenarios of formation of bile microscopic images polarization structure in coherent radiation. The results of investigating the interrelation between statistical moments of the 1st-4th order are presented that characterize the coordinate distributions of intensity of laser images of bile smears of cholelithiasis patients in combination with other pathologies. The diagnostic criteria of the cholelithiasis nascency and its severity degree differentiation are determined.

Polarization-correlation diagnostics and differentiation of cholelithiasis in patients with chronic cholecystitis combined with diabetes mellitus type 2

NASA Astrophysics Data System (ADS)

Marchuk, Yu F.; Fediv, O. I.; Ivashchuk, I. O.; Andriychuk, D. R.

2012-01-01

The principles of optical modeling of human bile polycrystalline structure are described. The main types of polycrystalline structures are detailed. It has been proposed and founded the scenarios of formation of bile microscopic images polarization structure in coherent radiation. The results of investigating the interrelation between statistical moments of the 1st-4th order are presented that characterize the coordinate distributions of intensity of laser images of bile smears of cholelithiasis patients in combination with other pathologies. The diagnostic criteria of the cholelithiasis nascency and its severity degree differentiation are determined.

Symmetry and topology code of the cluster self-assembly of framework MT structures of alumophosphates AlPO4(H2O)2 (metavariscite and variscite) and Al2(PO4)2(H2O)3 (APC)

NASA Astrophysics Data System (ADS)

Ilyushin, G. D.; Blatov, V. A.

2017-03-01

The supramolecular chemistry of alumophosphates, which form framework 3D MT structures from polyhedral AlO4(H2O)2 clusters with octahedral O coordination (of M polyhedra) and PO4 and AlO4 with tetrahedral O coordination (of T polyhedra), is considered. A combinatorial-topological modeling of the formation of possible types of linear (six types) and ring (two types) tetrapolyhedral cluster precursors M2T2 from MT monomers is carried out. Different versions of chain formation from linked (MT)2 rings (six types) are considered. The model, which has a universal character, has been used to simulate the cluster selfassembly of the crystal structure of AlPO4(H2O)2 minerals (metavariscite, m-VAR, and variscite, VAR) and zeolite [Al2(PO4)2(H2O)2] · H2O (APC). A tetrapolyhedral linear precursor is established for m-VAR and a ring precursor (MT)2 is established for VAR and APC. The symmetry and topology code of the processes of crystal structure self-assembly from cluster precursors is completely reconstructed. The functional role of the O-H···O hydrogen bonds is considered for the first time. The cluster self-assembly model explains the specific features of the morphogenesis of single crystals: m-VAR prisms, flattened VAR octahedra, and needleshaped APC square-base prisms.

Live-cell imaging for the assessment of the dynamics of autophagosome formation: focus on early steps.

PubMed

Karanasios, Eleftherios; Ktistakis, Nicholas T

2015-03-01

Autophagy is a cytosolic degradative pathway, which through a series of complicated membrane rearrangements leads to the formation of a unique double membrane vesicle, the autophagosome. The use of fluorescent proteins has allowed visualizing the autophagosome formation in live cells and in real time, almost 40 years after electron microscopy studies observed these structures for the first time. In the last decade, live-cell imaging has been extensively used to study the dynamics of autophagosome formation in cultured mammalian cells. Hereby we will discuss how the live-cell imaging studies have tried to settle the debate about the origin of the autophagosome membrane and how they have described the way different autophagy proteins coordinate in space and time in order to drive autophagosome formation. Copyright © 2014 Elsevier Inc. All rights reserved.

[Formative evaluation: experience of the Catalonian family and community medicine teaching units].

PubMed

Ezquerra Lezcano, Matilde; Bundo Vidiella, Magda; Descarrega Queralt, Ramón; Martín Zurro, Amando; Fores García, Dolores; Fornells Vallès, Josep Maria

2010-04-01

The purpose of this article is to report on the experience in formative evaluation that was carried out in the Catalonian family and community medicine teaching units during the years 2001-2007. This formative evaluation project included the use of several evaluation tools such as, self-listening, video-recording, structured observation of clinical practice, cases by computer and simulated patients. Different resident intakes have participated in the development of the project, as well as their teaching unit tutors and coordinators. This accumulated experience has allowed it to progress into the field of formative evaluation, and to adapt and integrate the activities that were being carried out in a resident portfolio, which in our opinion is the best tool for the formative evaluation of the family medicine resident. Copyright 2009 Elsevier España, S.L. All rights reserved.

Fluoride ion encapsulation by Mg2+ and phosphates in a fluoride riboswitch

PubMed Central

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

2012-01-01

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswicthes, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A•U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg2+ ions, which in turn are octahedrally coordinated to waters and five inwardly-pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state defines how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch most likely functions in gene regulation through a transcription termination mechanism. PMID:22678284

Structural diversity in Ni II cluster chemistry: Ni 5, Ni 6, and {NiNa 2} n complexes bearing the Schiff-base ligand N-naphthalidene-2-amino-5-chlorobenzoic acid

DOE PAGES

Perlepe, Panagiota S.; Cunha-Silva, Luis; Bekiari, Vlasoula; ...

2016-05-23

The employment of the fluorescent bridging and chelating ligand N-naphthalidene-2-amino-5-chlorobenzoic acid (nacbH 2) in Ni II cluster chemistry has led to a series of pentanuclear and hexanuclear compounds with different structural motifs, magnetic and optical properties, as well as an interesting 1-D coordination polymer. Synthetic parameters such as the inorganic anion present in the NiX 2 starting materials (X = ClO 4 - or Cl -), the reaction solvent and the nature of the organic base employed for the deprotonation of nacbH 2 were also proved to be structure-directing components. Undoubtedly, the reported results demonstrate the rich coordination chemistry ofmore » nacbH 2 in the presence of Ni II metal ions and the ability of this chelate to adopt a variety of different modes, thus fostering the formation of high-nuclearity molecules with many physical properties.« less

Time-Varying Expression of the Formation Flying along Circular Trajectories

NASA Technical Reports Server (NTRS)

Kawaguchi, Jun'ichiro

2007-01-01

Usually, the formation flying associated with circular orbits is discussed through the well-known Hill s or C-W equations of motion. This paper dares to present and discuss the coordinates that may contain time-varying coefficients. The discussion presents how the controller s performance is affected by the selection of coordinates, and also looks at the special coordinate suitable for designating a target bin to which each spacecraft in the formation has only to be guided. It is revealed that the latter strategy may incorporate the J2 disturbance automatically.

Crystal structure and solution species of Ce(III) and Ce(IV) formates: from mononuclear to hexanuclear complexes.

PubMed

Hennig, Christoph; Ikeda-Ohno, Atsushi; Kraus, Werner; Weiss, Stephan; Pattison, Philip; Emerich, Hermann; Abdala, Paula M; Scheinost, Andreas C

2013-10-21

Cerium(III) and cerium(IV) both form formate complexes. However, their species in aqueous solution and the solid-state structures are surprisingly different. The species in aqueous solutions were investigated with Ce K-edge EXAFS spectroscopy. Ce(III) formate shows only mononuclear complexes, which is in agreement with the predicted mononuclear species of Ce(HCOO)(2+) and Ce(HCOO)2(+). In contrast, Ce(IV) formate forms in aqueous solution a stable hexanuclear complex of [Ce6(μ3-O)4(μ3-OH)4(HCOO)x(NO3)y](12-x-y). The structural differences reflect the different influence of hydrolysis, which is weak for Ce(III) and strong for Ce(IV). Hydrolysis of Ce(IV) ions causes initial polymerization while complexation through HCOO(-) results in 12 chelate rings stabilizing the hexanuclear Ce(IV) complex. Crystals were grown from the above-mentioned solutions. Two crystal structures of Ce(IV) formate were determined. Both form a hexanuclear complex with a [Ce6(μ3-O)4(μ3-OH)4](12+) core in aqueous HNO3/HCOOH solution. The pH titration with NaOH resulted in a structure with the composition [Ce6(μ3-O)4(μ3-OH)4(HCOO)10(NO3)2(H2O)3]·(H2O)9.5, while the pH adjustment with NH3 resulted in [Ce6(μ3-O)4(μ3-OH)4(HCOO)10(NO3)4]·(NO3)3(NH4)5(H2O)5. Furthermore, the crystal structure of Ce(III) formate, Ce(HCOO)3, was determined. The coordination polyhedron is a tricapped trigonal prism which is formed exclusively by nine HCOO(-) ligands. The hexanuclear Ce(IV) formate species from aqueous solution is widely preserved in the crystal structure, whereas the mononuclear solution species of Ce(III) formate undergoes a polymerization during the crystallization process.

Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

PubMed

Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

2016-09-21

The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO 2 ) 57.5 -(B 2 O 3 ) 10 -(Na 2 O) 15 -(CaO) 15 -(MoO 3 ) 2.5 and (SiO 2 ) 57.3 -(B 2 O 3 ) 20 -(Na 2 O) 6.8 -(Li 2 O) 13.4 -(MoO 3 ) 2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na 2 MoO 4 and CaMoO 4 ). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

Two New Families of Lanthanide Mixed-Ligand Complexes, Oxalate-Carbonate and Oxalate-Formate: Synthesis and Structure of [Ce(H 2O)] 2(C 2O 4) 2(CO 3)·2.5 H 2O and Ce(C 2O 4)(HCO 2)

NASA Astrophysics Data System (ADS)

Romero, S.; Mosset, A.; Trombe, J. C.

1996-12-01

Two new families of lanthanide complexes associating the ligands oxalate and carbonate or oxalate and formate have been prepared under autogenous pressure at 200°C using a pseudo-hydrothermal method. The two families have been extended to some lanthanides ( Ln): oxalate-carbonate Ln= Ce, Pr, Nd, and Eu; oxalate-formate Ln= La, Ce, and Sm. The starting suspension contains either oxalate or a mixture of oxalate and oxalic acid. The structures have been solved for the element cerium. In both cases, the structure is built up from cerium atoms sharing all their oxygen atoms with oxalate and carbonate or oxalate and formate ligands, thus forming a three-dimensional network. The cerium polyhedra share either faces or edges or corners. The coordination scheme of the oxalate ligands is variable: bischelating, bischelating and monodentate, or bischelating and bismonodentate. The carbonate group acts as a bischelating and bismonodentate ligand while the formate group is chelating and monodentate. The characterization of these two original families by infrared spectra and thermal behavior is presented for some pure phases. A tentative explanation of the synthesis of these two phases will be emphasized.

The Effect of Team Training Strategies on Team Mental Model Formation and Team Performance under Routine and Non-Routine Environmental Conditions

ERIC Educational Resources Information Center

Hamilton, Katherine L.

2009-01-01

The current study examined how the type of training a team receives (team coordination training vs. cross-training) influences the type of team mental model structures that form and how those mental models in turn impact team performance under different environmental condition (routine vs. non-routine). Three-hundred and fifty-two undergraduate…

Studies on the structural, optical and dielectric properties of samarium coordinated with salicylic acid single crystal

NASA Astrophysics Data System (ADS)

Singh, Harjinder; Slathia, Goldy; Gupta, Rashmi; Bamzai, K. K.

2018-04-01

Samarium coordinated with salicylic acid was successfully grown as a single crystal by low temperature solution technique using mixed solvent of methanol and water in equal ratio. Structural characterization was carried out by single crystal X-ray diffraction analysis and it crystallizes in centrosymmetric space group P121/c1. FTIR and UV-Vis-NIR spectroscopy confirmed the compound formation and help to determine the mode of binding of the ligand to the rare earth-metal ion. Dielectric constant and dielectric loss have been measured over the frequency range 100 Hz - 30MHz. The decrease in dielectric constant with increases in frequency is due to the transition from interfacial polarization to dipolar polarization. The small value of dielectric constant at higher frequency ensures that the crystal is good candidate for NLO devices. Dielectric loss represents the resistive nature of the material.

Synthesis, structure, and magnetic properties of two 1-D helical coordination polymeric Cu(II) complexes

NASA Astrophysics Data System (ADS)

Bian, He-Dong; Yang, Xiao-E.; Yu, Qing; Chen, Zi-Lu; Liang, Hong; Yan, Shi-Ping; Liao, Dai-Zheng

2008-01-01

Two helical coordination polymeric copper(II) complexes bearing amino acid Schiff bases HL or HL', which are condensed from 2-hydroxy-1-naphthaldehyde with 2-aminobenzoic acid or L-valine, respectively, have been prepared and characterised by X-ray crystallography. In [CuL] n ( 1) the copper(II) atoms are bridged by syn- anti carboxylate groups giving infinite 1-D right-handed helical chains which are further connected by weak C-H⋯Cu interactions to build a 2-D network. While in [CuL'] n ( 2) the carboxylate group acts as a rare monatomic bridge to connect the adjacent copper(II) atoms leading to the formation of a left-handed helical chain. Magnetic susceptibility measurements indicate that 1 exhibits weak ferromagnetic interactions whereas an antiferromagnetic coupling is established for 2. The magnetic behavior can be satisfactorily explained on the basis of the structural data.

Local structure and charge distribution in the UO(2)-U(4)O(9) system.

PubMed

Conradson, Steven D; Manara, Dario; Wastin, Franck; Clark, David L; Lander, Gerard H; Morales, Luis A; Rebizant, Jean; Rondinella, Vincenzo V

2004-11-01

Analysis of X-ray absorption fine structure spectra of UO(2+x) for x = 0-0.20 (UO(2)--U(4)O(9)) reveals that the adventitious O atoms are incorporated as oxo groups with U--O distances of 1.74 A, most likely associated with U(VI), that occur in clusters so that the UO(2) fraction of the material largely remains intact. In addition to the formation of some additional longer U--O bonds, the U sublattice consists of an ordered portion that displays the original U--U distance and a spectroscopically silent, glassy part. This is very different from previous models derived from neutron diffraction that maintained long U--O distances and high U--O coordination numbers. UO(2+x) also differs from PuO(2+x) in its substantially shorter An-oxo distances and no sign of stable coordination with H(2)O and its hydrolysis products.

Reactions of Copper and Silver Cations with Carbon Dioxide: An Infrared Photodissociation Spectroscopic and Theoretical Study.

PubMed

Zhao, Zhi; Kong, Xiangtao; Yang, Dong; Yuan, Qinqin; Xie, Hua; Fan, Hongjun; Zhao, Jijun; Jiang, Ling

2017-05-04

The reaction of copper and silver cations with carbon dioxide was studied by mass-selected infrared photodissociation spectroscopy. Quantum chemical calculations were performed on these products, which aided the experimental assignments of the infrared spectra and helped to elucidate the geometrical and electronic structures. The Cu + and Ag + cations bind to an oxygen atom of CO 2 in an end-on configuration via a charge-quadrupole electrostatic interaction in the [M(CO 2 ) n ] + complexes. The formation of oxide-carbonyl and carbonyl-carbonate structures is not favored for the interaction of CO 2 with Cu + and Ag + . For n = 3 and 4, the n + 0 structure is preferred. [Note on the nomenclature: Using i + j, i denotes the number of CO 2 molecules in the first coordination shell, and j denotes the number of CO 2 molecules in the second coordination shell.] The two nearly energy-identical n + 0 and (n - 1) + 1 structures coexist in n = 5 and 6. While the six-coordinated structure is favored for [Cu(CO 2 ) n=7,8 ] + , the n + 0 configuration is dominated in [Ag(CO 2 ) n=7,8 ] + . The reaction of CO 2 with the cationic metal atoms has been compared to that with the neutral and anionic metal atoms, which would have important implications for understanding the interaction of CO 2 with reduction catalysts and rationally designing catalysts for CO 2 reduction based on cost-effective transition metals.

Syntheses, structures and properties of four Cd(II) coordination polymers induced by the pH regulator

NASA Astrophysics Data System (ADS)

Xu, Yun; Ding, Fang; Liu, Dong; Yang, Pei-Pei; Zhu, Li-Li

2018-03-01

Four new coordination polymers [Cd2(CHDC)2(APYZ)(H2O)2](H2O) (1), [Cd(HCHDC)2(APYZ) (H2O)] (2), [Cd2(CHDC)2(PYZ)(H2O)2](H2O) (3), and [Cd(HCHDC)2(PYZ)(H2O)] (4) (H2CHDC = 1,4-cyclohexanedicarboxylic acid, APYZ = 2-aminopyrazine, PYZ = pyrazine) have been synthesized under the hydrothermal conditions by changing the pH regulator and the N-containing ligands. The pH regulator impacted on the degree of deprotonation of the 1,4-cyclohexanedicarboxylic acid ligand and resulted in the formation of the two pairs of different networks. Polymers 1 and 3 crystallize in monoclinic, space group P21/c, exhibit two dimensional 63 net, which further formed three-dimensional supramolecular structure by the Csbnd H⋯O hydrogen bond interactions. While polymers 2 and 4 possess one dimensional chain structures and further link into two dimensional layered supramolecular structures by intermolecular hydrogen bonding interactions. From all three conformers of H2CHDC, e,a-cis is consistently present in the Cd coordination polymers. Furthermore, photoluminescence properties of four polymers are also investigated, the luminescent intensity of polymer 1 (or 2) with amino group in pyrazine is dramatically stronger than that of the similar structure of polymer 3 (or 4) without amino group in pyrazine, the results shown that the presence of the amino group from 2-aminopyrazine play a key role in increasing the luminescence properties.

Crystal structures of Ca(ClO4)2·4H2O and Ca(ClO4)2·6H2O

PubMed Central

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

The title compounds, calcium perchlorate tetra­hydrate and calcium perchlorate hexa­hydrate, were crystallized at low temperatures according to the solid–liquid phase diagram. The structure of the tetra­hydrate consists of one Ca2+ cation eightfold coordinated in a square-anti­prismatic fashion by four water mol­ecules and four O atoms of four perchlorate tetra­hedra, forming chains parallel to [01-1] by sharing corners of the ClO4 tetra­hedra. The structure of the hexa­hydrate contains two different Ca2+ cations, each coordinated by six water mol­ecules and two O atoms of two perchlorate tetra­hedra, forming [Ca(H2O)6(ClO4)]2 dimers by sharing two ClO4 tetra­hedra. The dimers are arranged in sheets parallel (001) and alternate with layers of non-coordinating ClO4 tetra­hedra. O—H⋯O hydrogen bonds between the water mol­ecules as donor and ClO4 tetra­hedra and water mol­ecules as acceptor groups lead to the formation of a three-dimensional network in the two structures. Ca(ClO4)2·6H2O was refined as a two-component inversion twin, with an approximate twin component ratio of 1:1 in each of the two structures. PMID:25552974

Cluster self-organization of TR-containing germanate systems: Suprapolyhedral precursors and self-assembly of the crystal structures of the LiNdGeO{sub 4} and CeGeO{sub 4} compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ilyushin, G. D., E-mail: ilyushin@nc.cryst.ras.ru; Dem'yanets, L. N.

2007-07-15

A combinatorial-topological analysis of the orthogermanates LiNdGeO{sub 4} (space group Pbcn) and CeGeO{sub 4} (space group I 4{sub 1}/a, the scheelite structure type), which have MT frameworks composed of polyhedral structural units in the form of M dodecahedra (NdO{sub 8} and CeO{sub 8}) and T tetrahedra (GeO{sub 4}), is performed using the method of coordination sequences with the TOPOS program package. It is established that the structures of both orthogermanates are characterized by equivalent crystal-forming nets 4444. The cluster precursors of the M{sub 2}T{sub 2} cyclic type are identified by the method of two-color decomposition. The local symmetry of four-polyhedralmore » clusters corresponds to the point group 2. In the precursor of the LiNdGeO{sub 4} orthogermanate, the Li atom is located above the M{sub 2}T{sub 2} ring. The number of Li-O bonds in this precursor is 4. The cluster precursors M{sub 2}T{sub 2} and LiM{sub 2}T{sub 2} are responsible for the formation of crystal-forming clusters of a higher level according to the mechanism of matrix self-assembly. The coordination numbers of the cluster precursors in two-dimensional nets for these structures are found to be equal to 4. The equivalent bilayer TR,Ge stacks that consist of eight cluster precursors are revealed in the structures under investigation. It is demonstrated that there exist three types of translational interlayer arrangements of cluster precursors upon the formation of macrostructures of the orthogermanates.« less

Speciation of aqueous Ni(II)-carboxylate and Ni(II)-fulvic acid solutions: Combined ATR-FTIR and XAFS analysis

NASA Astrophysics Data System (ADS)

Strathmann, Timothy J.; Myneni, Satish C. B.

2004-09-01

Aqueous solutions containing Ni(II) and a series of structurally related carboxylic acids were analyzed using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and Ni K-edge X-ray absorption fine structure spectroscopy (XAFS). XAFS spectra were also collected for solutions containing Ni 2+ and chelating ligands (ethylenediaminetetraacetic acid, nitrilotriacetic acid (NTA)) as well as soil fulvic acid. Limited spectral changes are observed for aqueous Ni(II) complexes with monocarboxylates (formate, acetate) and long-chain polycarboxylates (succinate, tricarballylate), where individual donor groups are separated by multiple bridging methylene groups. These spectral changes indicate weak interactions between Ni(II) and carboxylates, and the trends are similar to some earlier reports for crystalline Ni(II)-acetate solids, for which X-ray crystallography studies have indicated monodentate Ni(II)-carboxylate coordination. Nonetheless, electrostatic or outer-sphere coordination cannot be ruled out for these complexes. However, spectral changes observed for short-chain dicarboxylates (oxalate, malonate) and carboxylates that contain an alcohol donor group adjacent to one of the carboxylate groups (lactate, malate, citrate) demonstrate inner-sphere metal coordination by multiple donor groups. XAFS spectral fits of Ni(II) solutions containing soil fulvic acid are consistent with inner-sphere Ni(II) coordination by one or more carboxylate groups, but spectra are noisy and outer-sphere modes of coordination cannot be ruled out. These molecular studies refine our understanding of the interactions between carboxylates and weakly complexing divalent transition metals, such as Ni(II).

Interphase centrosome organization by the PLP-Cnn scaffold is required for centrosome function

PubMed Central

Lerit, Dorothy A.; Jordan, Holly A.; Poulton, John S.; Fagerstrom, Carey J.; Galletta, Brian J.; Peifer, Mark

2015-01-01

Pericentriolar material (PCM) mediates the microtubule (MT) nucleation and anchoring activity of centrosomes. A scaffold organized by Centrosomin (Cnn) serves to ensure proper PCM architecture and functional changes in centrosome activity with each cell cycle. Here, we investigate the mechanisms that spatially restrict and temporally coordinate centrosome scaffold formation. Focusing on the mitotic-to-interphase transition in Drosophila melanogaster embryos, we show that the elaboration of the interphase Cnn scaffold defines a major structural rearrangement of the centrosome. We identify an unprecedented role for Pericentrin-like protein (PLP), which localizes to the tips of extended Cnn flares, to maintain robust interphase centrosome activity and promote the formation of interphase MT asters required for normal nuclear spacing, centrosome segregation, and compartmentalization of the syncytial embryo. Our data reveal that Cnn and PLP directly interact at two defined sites to coordinate the cell cycle–dependent rearrangement and scaffolding activity of the centrosome to permit normal centrosome organization, cell division, and embryonic viability. PMID:26150390

Interphase centrosome organization by the PLP-Cnn scaffold is required for centrosome function.

PubMed

Lerit, Dorothy A; Jordan, Holly A; Poulton, John S; Fagerstrom, Carey J; Galletta, Brian J; Peifer, Mark; Rusan, Nasser M

2015-07-06

Pericentriolar material (PCM) mediates the microtubule (MT) nucleation and anchoring activity of centrosomes. A scaffold organized by Centrosomin (Cnn) serves to ensure proper PCM architecture and functional changes in centrosome activity with each cell cycle. Here, we investigate the mechanisms that spatially restrict and temporally coordinate centrosome scaffold formation. Focusing on the mitotic-to-interphase transition in Drosophila melanogaster embryos, we show that the elaboration of the interphase Cnn scaffold defines a major structural rearrangement of the centrosome. We identify an unprecedented role for Pericentrin-like protein (PLP), which localizes to the tips of extended Cnn flares, to maintain robust interphase centrosome activity and promote the formation of interphase MT asters required for normal nuclear spacing, centrosome segregation, and compartmentalization of the syncytial embryo. Our data reveal that Cnn and PLP directly interact at two defined sites to coordinate the cell cycle-dependent rearrangement and scaffolding activity of the centrosome to permit normal centrosome organization, cell division, and embryonic viability.

Synthesis of sodium polyhydrides at high pressures

NASA Astrophysics Data System (ADS)

Struzhkin, Viktor V.; Kim, Duck Young; Stavrou, Elissaios; Muramatsu, Takaki; Mao, Ho-Kwang; Pickard, Chris J.; Needs, Richard J.; Prakapenka, Vitali B.; Goncharov, Alexander F.

2016-07-01

The only known compound of sodium and hydrogen is archetypal ionic NaH. Application of high pressure is known to promote states with higher atomic coordination, but extensive searches for polyhydrides with unusual stoichiometry have had only limited success in spite of several theoretical predictions. Here we report the first observation of the formation of polyhydrides of Na (NaH3 and NaH7) above 40 GPa and 2,000 K. We combine synchrotron X-ray diffraction and Raman spectroscopy in a laser-heated diamond anvil cell and theoretical random structure searching, which both agree on the stable structures and compositions. Our results support the formation of multicenter bonding in a material with unusual stoichiometry. These results are applicable to the design of new energetic solids and high-temperature superconductors based on hydrogen-rich materials.

Studies of the structural and magnetic properties of an unsymmetrical ligand 1,2,4-benzenetricarboxylic acid based chiral 3-D trinickel coordination polymer as an alkali base-influenced hydrothermal reaction product

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Yi-Ru; Chien, Po-Hsiu; Chung, Huey-Ting

2014-04-01

The reaction of 1,2,4-benzenetricarboxylic acid (H{sub 3}btc), as a ligand, under pH-controlled hydrothermal conditions with nickel salts leads to the formation of a coordination polymer of (CsNi{sub 3}(OH)(H{sub 2}O){sub 3}[C{sub 6}H{sub 3}(CO{sub 2}){sub 3}]{sub 2}·3H{sub 2}O){sub n} (1). The subunit of compound 1 contains a hydroxide- and carboxylate-bridged trinickel clusters that are linked by an unsymmetrical organic carboxylate spacer to form a chiral three-dimensional anionic framework, in which cesium cations and guest water molecules are located in one-dimensional channels. The presence of a hydroxide ion serves both as a deprotonation agent and a cation source during the hydrothermal reaction, thusmore » permitting the extent of deprotonation of the unsymmetrical ligand H{sub 3}btc to be controlled, which is essential for the successful formation of compound 1. The magnetic properties of compound 1 were analyzed. Both dc and ac magnetic susceptibility as well as reduced magnetization measurements confirmed the spin-frustration nature of 1. - Graphical abstract: A chiral three-dimension MOF compound and its magnetic properties are described. - Highlights: • A new chiral three-dimension coordination polymer were made. • An un-symmetric bridging ligand was used. • Alkali metal ion Cs{sup +} was incorporated in the structure. • Magnetic properties were studied.« less

Reverse lyotropic liquid crystals from europium nitrate and P123 with enhanced luminescence efficiency.

PubMed

Yi, Sijing; Li, Qintang; Liu, Hongguo; Chen, Xiao

2014-10-02

Fabrication of lyotropic aggregates containing the lanthanide ions is becoming a preferable way to prepare novel functional materials. Here, the lyotropic liquid crystals (LLCs) of reverse hexagonal, reverse bicontinuous cubic, and lamellar phases have been constructed in sequence directly from the mixtures of Eu(NO3)3·6H2O and Pluronic P123 amphiphilc block copolymer with increasing the salt proportion. Their phase types and structural characteristics were analyzed using polarized optical microscopy (POM) and small-angle X-ray scattering (SAXS) measurements. The driving forces of reverse LLC phase formation were investigated using Fourier-transformed infrared spectroscopy (FTIR) and rheological measurements. The hydrated europium salt was found to act not only as a solvent here, but also as the bridge to form hydrogen bonding between coordinated water molecules and PEO blocks, which played a key role in the reverse LLCs formation. Compared to those in aqueous solutions and solid state, the enhanced luminescence quantum yields and prolonged excited state lifetimes were observed in two europium containing reverse mesophases. The luminescence quenching effect of lanthanide ions was efficiently suppressed, probably due to the substitution of coordinated water molecules by oxyethyl groups of P123 and ordered phase structures of LLCs, where the coordinated europium ions were confined and isolated by PEO blocks. The optimum luminescence performance was then found to exist in the reverse hexagonal phase. The obtained results on such lanthanide-induced reverse LLCs should be referable for designing new luminescent soft materials construction to expand their application fields.

Embryo as an active granular fluid: stress-coordinated cellular constriction chains

NASA Astrophysics Data System (ADS)

Holcomb, Michael; Gao, Guo-Jie; Thomas, Jeffrey; Blawzdziewicz, Jerzy

2016-11-01

Mechanical stress plays an intricate role in gene expression in individual cells and sculpting of developing tissues. Motivated by our observation of the cellular constriction chains (CCCs) during the initial phase of ventral furrow formation in the Drosophila melanogaster embryo, we propose an active granular fluid (AGF) model that provides valuable insights into cellular coordination in the apical constriction process. In our model, cells are treated as circular particles connected by a predefined force network, and they undergo a random constriction process in which the particle constriction probability P is a function of the stress exerted on the particle by its neighbors. We find that when P favors tensile stress, constricted particles tend to form chain-like structures. In contrast, constricted particles tend to form compact clusters when P favors compression. A remarkable similarity of constricted-particle chains and CCCs observed in vivo provides indirect evidence that tensile-stress feedback coordinates the apical constriction activity.

Mesoporous nitrogen-doped carbon microfibers derived from Mg-biquinoline-dicarboxy compound for efficient oxygen electroreduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kong, Aiguo, E-mail: agkong@chem.ecnu.edu.cn; Fan, Xiaohong; Chen, Aoling

An in-situ MgO-templating synthesis route was introduced to obtain the mesoporous nitrogen-doped carbon microfibers by thermal conversion of new Mg-2,2′-biquinoline 4,4-dicarboxy acid coordination compound (Mg-DCA) microfibers. The investigated crystal structure of Mg-DCA testified that the assembling of Mg{sup 2+} and DCA through Mg-O coordination bond and hydrogen bond contributed to the formation of one-dimensional (1D) crystalline Mg-DCA microfibers. The nitrogen-doped carbons derived from the pyrolysis of Mg-DCA showed the well-defined microfiber morphology with high mesopore-surface area. Such mesoporous microfibers exhibited the efficient catalytic activity for oxygen reduction reaction (ORR) in alkaline solutions with better stability and methanol-tolerance performance. - Graphicalmore » abstract: Mesoporous nitrogen-doped carbon microfibers with efficient oxygen electroreduction activity were prepared by thermal conversion of new Mg-biquinoline-based coordination compound microfibers.« less

Keratitis-associated fungi form biofilms with reduced antifungal drug susceptibility.

PubMed

Zhang, Xiaoyan; Sun, Xuguang; Wang, Zhiqun; Zhang, Yang; Hou, Wenbo

2012-11-21

To investigate the biofilm-forming capacity of Fusarium solani, Cladosporium sphaerospermum, and Acremonium implicatum, and the activities of antifungal agents against the three keratitis-associated fungi. The architecture of biofilms was analyzed using scanning electron microscopy and confocal scanning laser microscopy (CSLM). Susceptibility against six antifungal drugs was measured using the CLSI M38-A method and XTT reduction assay. Time course analyses of CSLM revealed that biofilm formation occurred in an organized fashion through four distinct developmental phases: adhesion, germling formation, microcolony formation, and biofilm maturation. Scanning electron microscopy revealed that mature biofilms displayed a complex three-dimensional structure, consisting of coordinated network of hyphal structures glued by the extracellular matrix (ECM). The antifungal susceptibility testing demonstrated a time-dependent decrease in efficacy for all six antifungal agents as the complexity of fungal hyphal structures developed. Natamycin (NAT), amphotericin B (AMB), and NAT were the most effective against F. solani, C. sphaerospermum, and A. implicatum biofilm, respectively. Corneal isolates of F. solani, C. sphaerospermum, and A. implicatum could produce biofilms that were resistant to antifungal agents in vitro.

Enhanced CO2 electroreduction efficiency through secondary coordination effects on a pincer iridium catalyst.

PubMed

Ahn, Steven T; Bielinski, Elizabeth A; Lane, Elizabeth M; Chen, Yanqiao; Bernskoetter, Wesley H; Hazari, Nilay; Palmore, G Tayhas R

2015-04-07

An iridium(III) trihydride complex supported by a pincer ligand with a hydrogen bond donor in the secondary coordination sphere promotes the electrocatalytic reduction of CO2 to formate in water/acetonitrile with excellent Faradaic efficiency and low overpotential. Preliminary mechanistic experiments indicate formate formation is facile while product release is a kinetically difficult step.

Hybrid materials based on novel 2D lanthanide coordination polymers covalently bonded to amine-modified SBA-15 and MCM-41: assembly, characterization, structural features, thermal and luminescence properties.

PubMed

Wang, Jun; Dou, Wei; Kirillov, Alexander M; Liu, Weisheng; Xu, Cailing; Fang, Ran; Yang, Lizi

2016-11-22

Three novel 2D coordination polymers [Tb 2 (μ 4 -L) 2 (μ-HL)(μ-HCOO)(DEF)] n (Tb-L), [Eu(μ 4 -L)(L)(H 2 O) 2 ] n (Eu-L), and [Nd(μ 4 -L)(L)(H 2 O) 2 ] n (Nd-L) were assembled from the corresponding lanthanide(iii) nitrates and 5 methoxy-(4-benzaldehyde)-1,3-benzenedicarboxylic acid (H 2 L) as a main multifunctional building block bearing carboxylate and aldehyde functional groups, using H 2 O/DEF {DEF = N,N-diethylformamide} as a reaction medium. The obtained coordination polymers were isolated as stable microcrystalline solids and fully characterized by elemental analysis, FT-IR spectroscopy, TGA, BET, PXRD, and single-crystal X-ray diffraction methods. Their structures feature intricate 2D metal-organic networks, which were topologically classified as underlying layers with the 4,6L26 (for Tb-L) or sql (for Eu-L and Nd-L) topologies. Besides, a novel series of mesoporous hybrid materials wherein the Tb-L, Eu-L, or Nd-L coordination polymers are covalently grafted into the amine-functionalized SBA-15-NH 2 or MCM-41-NH 2 matrices (via the formation of Schiff-base groups) was also synthesized and fully characterized. These hybrid materials show high thermal and photoluminescence stability, as well as remarkable chemical resistance to boiling water, and acidic or alkaline medium. Luminescent properties of the parent coordination polymers and derived hybrid materials are investigated in detail, showing that the latter combine the luminescent characteristics (intense green or red emissions and excellent stability) of lanthanide coordination polymers and structural features of ordered mesoporous silica molecular sieves. Moreover, light emitting devices were assembled, by coating the hybrid materials onto the surface of UV-LED bulbs, and showed excellent light emitting properties.

Novel 3D Compression Methods for Geometry, Connectivity and Texture

NASA Astrophysics Data System (ADS)

Siddeq, M. M.; Rodrigues, M. A.

2016-06-01

A large number of applications in medical visualization, games, engineering design, entertainment, heritage, e-commerce and so on require the transmission of 3D models over the Internet or over local networks. 3D data compression is an important requirement for fast data storage, access and transmission within bandwidth limitations. The Wavefront OBJ (object) file format is commonly used to share models due to its clear simple design. Normally each OBJ file contains a large amount of data (e.g. vertices and triangulated faces, normals, texture coordinates and other parameters) describing the mesh surface. In this paper we introduce a new method to compress geometry, connectivity and texture coordinates by a novel Geometry Minimization Algorithm (GM-Algorithm) in connection with arithmetic coding. First, each vertex ( x, y, z) coordinates are encoded to a single value by the GM-Algorithm. Second, triangle faces are encoded by computing the differences between two adjacent vertex locations, which are compressed by arithmetic coding together with texture coordinates. We demonstrate the method on large data sets achieving compression ratios between 87 and 99 % without reduction in the number of reconstructed vertices and triangle faces. The decompression step is based on a Parallel Fast Matching Search Algorithm (Parallel-FMS) to recover the structure of the 3D mesh. A comparative analysis of compression ratios is provided with a number of commonly used 3D file formats such as VRML, OpenCTM and STL highlighting the performance and effectiveness of the proposed method.

Electron core ionization in compressed alkali metal cesium

NASA Astrophysics Data System (ADS)

Degtyareva, V. F.

2018-01-01

Elements of groups I and II in the periodic table have valence electrons of s-type and are usually considered as simple metals. Crystal structures of these elements at ambient pressure are close-packed and high-symmetry of bcc and fcc-types, defined by electrostatic (Madelung) energy. Diverse structures were found under high pressure with decrease of the coordination number, packing fraction and symmetry. Formation of complex structures can be understood within the model of Fermi sphere-Brillouin zone interactions and supported by Hume-Rothery arguments. With the volume decrease there is a gain of band structure energy accompanied by a formation of many-faced Brillouin zone polyhedra. Under compression to less than a half of the initial volume the interatomic distances become close to or smaller than the ionic radius which should lead to the electron core ionization. At strong compression it is necessary to assume that for alkali metals the valence electron band overlaps with the upper core electrons, which increases the valence electron count under compression.

Pentasubstituted ferrocene and dirhodium(II) tetracarboxylate as building blocks for discrete fullerene-like and extended supramolecular structures.

PubMed

Tong, Lok H; Guénée, Laure; Williams, Alan F

2011-03-21

The synthesis of a penta(1-methylpyrazole)ferrocenyl phosphine oxide ligand (1) [Fe(C(5)(C(3)H(2)N(2)CH(3))(5))(C(5)H(4)PO(t-C(4)H(9))(2))] is reported together with its X-ray crystal structure. Its self-assembly behavior with a dirhodium(II) tetraoctanoate linker (2) [Rh(2)(O(2)CC(7)H(15))(4)] was investigated for construction of fullerene-like assemblies of composition [(ligand)(12)(linker)(30)]. Reaction between 1 and 2 in acetonitrile resulted in the formation of a light purple precipitate (3). Evidence for the ligand-to-linker ratio of 1:2.5 expected for a fullerene-like structure [Fe(C(5)(C(3)H(2)N(2)CH(3))(5))(C(5)H(4)PO(t-C(4)H(9))(2))](12)[Rh(2)(O(2)CC(7)H(15))(4)](30) was obtained from (1)H NMR and elemental analysis. IR and Raman studies confirmed the diaxially bound coordination environment of the dirhodium linker by comparing the stretching frequencies of the carboxylate group and the rhodium-rhodium bond with those in model compound (5), [Rh(2)(O(2)CC(7)H(15))(4)](C(3)H(3)N(2)CH(3))(2), the bis-adduct of linker 2 with 1-methylpyrazole. X-ray powder diffraction and molecular modeling studies provide additional support for the formation of a spherical molecule topologically identical to fullerene with a diameter of approximately 38 Å and a molecular formula of [(1)(12)(2)(30)]. Dissolution of 3 in tetrahydrofuran (THF) followed by layering with acetonitrile afforded purple crystals of [(1)(2)(2)](∞) (6) [Fe(C(5)(C(3)H(2)N(2)CH(3))(5))(C(5)H(4)PO(t-C(4)H(9))(2))][Rh(2)(O(2)CC(7)H(15))(4)](2) with a two-dimensional polymeric structure determined by X-ray crystallography. The dirhodium linkers link ferrocenyl units by coordination to the pyrazoles but only four of the five pyrazole moieties of the pentapyrazole ligand are coordinated. The ligand-to-linker ratio of 1:2 in 6 was confirmed by (1)H NMR spectroscopy and elemental analysis, while results from IR and Raman are in agreement with the diaxially coordinated environment of the linker observed in the solid state.

Homochiral coordination polymers constructed from aminocarboxylate derivates: Effect of bipyridine on the amidation reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen Jianshan; Sheng Tianlu; Hu Shengmin

2012-08-15

Using aminocarboxylate derivates (S)-N-(4-cyanobenzoic)-glutamic acid (denoted as cbg, 1a) and (S)-N-(4-nitrobenzoic)-glutamic acid (denoted as nbg, 1b) as chiral ligands, five new homochiral coordination polymers formulated as [Cu(cbg)(H{sub 2}O){sub 2}]{sub n} (3), [Cu(cbop){sub 2}(4,4 Prime -bipy)(H{sub 2}O)]{sub n} (4) (cbop=(S)-N-(4-cyanobenzoic)-5-oxoproline, 4,4 Prime -bipy=4,4 Prime -bipyridine), {l_brace}[Cu(nbop){sub 2}(4,4 Prime -bipy)]{center_dot}4H{sub 2}O{r_brace}{sub n} (5) (nbop=(S)-N-(4-nitrobenzoic)-5-oxoproline), {l_brace}[Cd(nbop){sub 2}(4,4 Prime -bipy)]{center_dot}2H{sub 2}O{r_brace}{sub n} (6), and [Ni(nbop){sub 2}(4,4 Prime -bipy)(H{sub 2}O){sub 2}]{sub n} (7) have been hydrothermally synthesized and structurally characterized. Single-crystal X-ray diffraction study reveals that the original chirality of aminocarboxylate derivates is maintained in all these complexes. Complexes 3, 4, and 7 are one-dimensionalmore » infinite chain coordination polymers, while complexes 5 and 6 possess two-dimensional network structures. In situ cyclization of 1a and 1b was taken place in the formation of complexes 4-7, which may be due to the competition of 4,4 Prime -bipyridine with chiral ligands during the coordination process. Preliminary optical behavior investigation indicates that ligands 1a, 1b, and complexes 6, 7 are nonlinear optical active. - Graphical abstract: Using aminocarboxylate derivates as chiral ligands, five new homochiral coordination polymers possessing second harmonic generation activities have been hydrothermally synthesized. Highlights: Black-Right-Pointing-Pointer Two new chiral aminocarboxylate derivates were firstly synthesized. Black-Right-Pointing-Pointer Five new homochiral metal organic complexes were obtained hydrothermally based on these ligands. Black-Right-Pointing-Pointer Intramolecular amidation was taken place on the aminocarboxylate derivates during the formation of these complexes. Black-Right-Pointing-Pointer In situ amidation may be due to the impact of 4,4 Prime -bipyridine. Black-Right-Pointing-Pointer The homochiral complexes are nonlinear optical active.« less

Crystal structures of ZnCl2·2.5H2O, ZnCl2·3H2O and ZnCl2·4.5H2O

PubMed Central

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

The formation of different complexes in aqueous solutions is an important step in understanding the behavior of zinc chloride in water. The structure of concentrated ZnCl2 solutions is governed by coordination competition of Cl− and H2O around Zn2+. According to the solid–liquid phase diagram, the title compounds were crystallized below room temperature. The structure of ZnCl2·2.5H2O contains Zn2+ both in a tetra­hedral coordination with Cl− and in an octa­hedral environment defined by five water mol­ecules and one Cl− shared with the [ZnCl4]2− unit. Thus, these two different types of Zn2+ cations form isolated units with composition [Zn2Cl4(H2O)5] (penta­aqua-μ-chlorido-tri­chlorido­di­zinc). The trihydrate {hexa­aqua­zinc tetra­chlorido­zinc, [Zn(H2O)6][ZnCl4]}, consists of three different Zn2+ cations, one of which is tetra­hedrally coordinated by four Cl− anions. The two other Zn2+ cations are each located on an inversion centre and are octa­hedrally surrounded by water mol­ecules. The [ZnCl4] tetra­hedra and [Zn(H2O)6] octa­hedra are arranged in alternating rows parallel to [001]. The structure of the 4.5-hydrate {hexa­aqua­zinc tetra­chlorido­zinc trihydrate, [Zn(H2O)6][ZnCl4]·3H2O}, consists of isolated octa­hedral [Zn(H2O)6] and tetra­hedral [ZnCl4] units, as well as additional lattice water mol­ecules. O—H⋯O hydrogen bonds between the water mol­ecules as donor and ZnCl4 tetra­hedra and water mol­ecules as acceptor groups leads to the formation of a three-dimensional network in each of the three structures. PMID:25552980

The structure of MgO-SiO2 glasses at elevated pressure.

PubMed

Wilding, Martin; Guthrie, Malcolm; Kohara, Shinji; Bull, Craig L; Akola, Jaakko; Tucker, Matt G

2012-06-06

The magnesium silicate system is an important geophysical analogue and neutron diffraction data from glasses formed in this system may also provide an initial framework for understanding the structure-dependent properties of related liquids that are important during planetary formation. Neutron diffraction data collected in situ for a single composition (38 mol% SiO(2)) magnesium silicate glass sample shows local changes in structure as pressure is increased from ambient conditions to 8.6 GPa at ambient temperature. A method for obtaining the fully corrected, total structure factor, S(Q), has been developed that allows accurate structural characterization as this weakly scattering glass sample is compressed. The measured S(Q) data indicate changes in chemical ordering with pressure and the real-space transforms show an increase in Mg-O coordination number and a distortion of the local environment around magnesium ions. We have used reverse Monte Carlo methods to compare the high pressure and ambient pressure structures and also compare the high pressure form with a more silica-poor glass (Mg(2)SiO(4)) that represents the approach to a more dense, void-free and topologically ordered structure. The Mg-O coordination number increases with pressure and we also find that the degree of continuous connectivity of Si-O bonds increases via a collapse of interstices.

Development of modular control software for construction 3D-printer

NASA Astrophysics Data System (ADS)

Bazhanov, A.; Yudin, D.; Porkhalo, V.

2018-03-01

This article discusses the approach to developing modular software for real-time control of an industrial construction 3D printer. The proposed structure of a two-level software solution is implemented for a robotic system that moves in a Cartesian coordinate system with multi-axis interpolation. An algorithm for the formation and analysis of a path is considered to enable the most effective control of printing through dynamic programming.

Formation, expansion, and interconversion of metallarings in a sulfur-bridged Au(I) Co(III) coordination system.

PubMed

Oji, Katsuya; Igashira-Kamiyama, Asako; Yoshinari, Nobuto; Konno, Takumi

2014-02-10

A novel Au(I) Co(III) coordination system that is derived from the newly prepared [Co(D-nmp)2 ](-) (1(-) ; D-nmp=N-methyl-D-penicillaminate) and a gold(I) precursor Au(I) is reported. Complex 1(-) acts as a sulfur-donating metallaligand and reacts with the gold(I) precursor to give [Au2 Co2 (D-nmp)4 ] (2), which has an eight-membered Au(I) 2 Co(III) 2 metallaring. Treatment of 2 with [Au2 (dppe)2 ](2+) (dppe=1,2-bis(diphenylphosphino)ethane) leads to the formation of [Au4 Co2 (dppe)2 (D-nmp)4 ](2+) (3(2+) ), which consists of an 18-membered Au(I) 4 Co(III) 2 metallaring that accommodates a tetrahedral anion (BF4 (-) , ClO4 (-) , ReO4 (-) ). In solution, the metallaring structure of 3(2+) is readily interconvertible with the nine-membered Au(I) 2 Co(III) metallaring structure of [Au2 Co(dppe)(D-nmp)2 ](+) (4(+) ); this process depends on external factors, such as solvent, concentration, and nature of the counteranion. These results reveal the lability of the AuS and AuP bonds, which is essential for metallaring expansion and contraction. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zinc(II)-methimazole complexes: synthesis and reactivity.

PubMed

Isaia, Francesco; Aragoni, Maria Carla; Arca, Massimiliano; Bettoschi, Alexandre; Caltagirone, Claudia; Castellano, Carlo; Demartin, Francesco; Lippolis, Vito; Pivetta, Tiziana; Valletta, Elisa

2015-06-07

The tetrahedral S-coordinated complex [Zn(MeImHS)4](ClO4)2, synthesised from the reaction of [Zn(ClO4)2] with methimazole (1-methyl-3H-imidazole-2-thione, MeImHS), reacts with triethylamine to yield the homoleptic complex [Zn(MeImS)2] (MeImS = anion methimazole). ESI-MS and MAS (13)C-NMR experiments supported MeImS acting as a (N,S)-chelating ligand. The DFT-optimised structure of [Zn(MeImS)2] is also reported and the main bond lengths compared to those of related Zn-methimazole complexes. The complex [Zn(MeImS)2] reacts under mild conditions with methyl iodide and separates the novel complex [Zn(MeImSMe)2I2] (MeImSMe = S-methylmethimazole). X-ray diffraction analysis of the complex shows a ZnI2N2 core, with the methyl thioethers uncoordinated to zinc. Conversely, the reaction of [Zn(MeImS)2] with hydroiodic acid led to the formation of the complex [Zn(MeImHS)2I2] having a ZnI2S2 core with the neutral methimazole units S-coordinating the metal centre. The Zn-coordinated methimazole can markedly modify the coordination environment when changing from its thione to thionate form and vice versa. The study of the interaction of the drug methimazole with the complex [Zn(MeIm)4](2+) (MeIm = 1-methylimidazole) - as a model for Zn-enzymes containing a N4 donor set from histidine residues - shows that methimazole displaces only one of the coordinated MeIm molecules; the formation constant of the mixed complex [Zn(MeIm)3(MeImHS)](2+) was determined.

Co-ordinated action between youth-care and sports: facilitators and barriers.

PubMed

Hermens, Niels; de Langen, Lisanne; Verkooijen, Kirsten T; Koelen, Maria A

2017-07-01

In the Netherlands, youth-care organisations and community sports clubs are collaborating to increase socially vulnerable youths' participation in sport. This is rooted in the idea that sports clubs are settings for youth development. As not much is known about co-ordinated action involving professional care organisations and community sports clubs, this study aims to generate insight into facilitators of and barriers to successful co-ordinated action between these two organisations. A cross-sectional study was conducted using in-depth semi-structured qualitative interview data. In total, 23 interviews were held at five locations where co-ordinated action between youth-care and sports takes place. Interviewees were youth-care workers, representatives from community sports clubs, and Care Sport Connectors who were assigned to encourage and manage the co-ordinated action. Using inductive coding procedures, this study shows that existing and good relationships, a boundary spanner, care workers' attitudes, knowledge and competences of the participants, organisational policies and ambitions, and some elements external to the co-ordinated action were reported to be facilitators or barriers. In addition, the participants reported that the different facilitators and barriers influenced the success of the co-ordinated action at different stages of the co-ordinated action. Future research is recommended to further explore the role of boundary spanners in co-ordinated action involving social care organisations and community sports clubs, and to identify what external elements (e.g. events, processes, national policies) are turning points in the formation, implementation and continuation of such co-ordinated action. © 2017 John Wiley & Sons Ltd.

Redox-active porous coordination polymer based on trinuclear pivalate: Temperature-dependent crystal rearrangement and redox-behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lytvynenko, Anton S.; Kiskin, Mikhail A., E-mail: mkiskin@igic.ras.ru; Dorofeeva, Victoria N.

2015-03-15

Linking of trinuclear pivalate Fe{sub 2}NiO(Piv){sub 6} (Piv=O{sub 2}CC(CH{sub 3}){sub 3}) by 2,6-bis(4-pyridyl)-4-(1-naphthyl)pyridine (L) resulted in formation of 1D-porous coordination polymer Fe{sub 2}NiO(Piv){sub 6}(L)·Solv, which was characterized in two forms: DMSO solvate Fe{sub 2}NiO(Piv){sub 6}(L)(DMSO)·2.5DMSO (1) or water solvate Fe{sub 2}NiO(Piv){sub 6}(L)(H{sub 2}O) (2). X-ray structure of 1 was determined. Crystal lattice of 1 at 160 K contained open channels, filled by captured solvent, while temperature growth to 296 K led to the crystal lattice rearrangement and formation of closed voids. Redox-behavior of 2 was studied by cyclic voltammetry for a solid compound, deposited on glassy-carbon electrode. Redox-activity of Lmore » preserved upon incorporation in the coordination polymer. The presence of pores in desolvated sample Fe{sub 2}NiO(Piv){sub 6}(L) was confirmed by the measurements of N{sub 2} and H{sub 2} adsorption at 77 K. Potential barriers of the different molecules diffusion through pores were estimated by the means of molecular mechanics. - Graphical abstract: Redox-behavior of 1D-porous coordination polymer Fe{sub 2}NiO(Piv){sub 6}(L)(H{sub 2}O) was studied by cyclic voltammetry in thin film, deposited on glassy-carbon electrode. Redox-activity of L preserved upon incorporation in the coordination polymer. Potential barriers of different molecules diffusion through pores were estimated by the means of molecular mechanics. - Highlights: • Porous 1D coordination polymer was synthesized. • Temperature growth led to pores closing due to crystal lattice rearrangement. • Redox-activity of ligand preserved upon incorporation into coordination polymer. • Redox-properties of solid coordination polymer were studied in thin film. • Diffusion barriers were evaluated by molecular mechanics.« less

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100-x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-03-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Cobalt ion-coordinated self-assembly synthesis of nitrogen-doped ordered mesoporous carbon nanosheets for efficiently catalyzing oxygen reduction.

PubMed

Wang, Haitao; Wang, Wei; Asif, Muhammad; Yu, Yang; Wang, Zhengyun; Wang, Junlei; Liu, Hongfang; Xiao, Junwu

2017-10-19

The design and synthesis of a promising porous carbon-based electrocatalyst with an ordered and uninterrupted porous structure for oxygen reduction reaction (ORR) is still a significant challenge. Herein, an efficient catalyst based on cobalt-embedded nitrogen-doped ordered mesoporous carbon nanosheets (Co/N-OMCNS) is successfully prepared through a two-step procedure (cobalt ion-coordinated self-assembly and carbonization process) using 3-aminophenol as a nitrogen source, cobalt acetate as a cobalt source and Pluronic F127 as a mesoporous template. This work indicates that the formation of a two dimensional nanosheet structure is directly related to the extent of the cobalt ion coordination interaction. Moreover, the critical roles of pyrolysis temperature in nitrogen doping and ORR catalytic activity are also investigated. Benefiting from the high surface area and graphitic degree, high contents of graphitic N and pyridinic N, ordered interconnected mesoporous carbon framework, as well as synergetic interaction between the cobalt nanoparticles and protective nitrogen doped graphitic carbon layer, the resultant optimal catalyst Co/N-OMCNS-800 (pyrolyzed at 800 °C) exhibits comparable ORR catalytic activity to Pt/C, superior tolerance to methanol crossover and stability.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100- x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-06-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Further insights into the metal ion binding abilities and the metalation pathway of a plant metallothionein from Musa acuminata

PubMed Central

Cabral, Augusto C. S.; Jakovleska, Jovana; Deb, Aniruddha; Penner-Hahn, James E.; Pecoraro, Vincent L.

2017-01-01

The superfamily of metallothioneins (MTs) combines a diverse group of metalloproteins, sharing the characteristics of rather low molecular weight and high cysteine content. The latter provides MTs with the capability to coordinate thiophilic metal ions, in particular those with a d10 electron configuration. The sub-family of plant MT3 proteins is only poorly characterized and there is a complete lack of three-dimensional structure information. Building upon our previous results on the Musa acuminata MT3 (musMT3) protein, the focus of the present work is to understand the metal cluster formation process, the role of the single histidine residue present in musMT3, and the metal ion binding affinity. We concentrate our efforts on the coordination of ZnII and CdII ions, using CoII as a spectroscopic probe for ZnII binding. The overall protein-fold is analysed with a combination of limited proteolytic digestion, mass spectrometry, and dynamic light scattering. Histidine coordination of metal ions is probed with extended X-ray absorption fine structure spectroscopy and CoII titration experiments. Initial experiments with isothermal titration calorimetry provide insights into the thermodynamics of metal ion binding. PMID:29218632

Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Shuyan; Sun, Cancan; Tan, Kemin

Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystalmore » structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.« less

Structure and thermodynamics of uranium-containing iron garnets

NASA Astrophysics Data System (ADS)

Guo, Xiaofeng; Navrotsky, Alexandra; Kukkadapu, Ravi K.; Engelhard, Mark H.; Lanzirotti, Antonio; Newville, Matthew; Ilton, Eugene S.; Sutton, Stephen R.; Xu, Hongwu

2016-09-01

Use of crystalline garnet as a waste form phase appears to be advantageous for accommodating actinides from nuclear waste. Previous studies show that large amounts of uranium (U) and its analogues such as cerium (Ce) and thorium (Th) can be incorporated into the garnet structure. In this study, we synthesized U loaded garnet phases, Ca3UxZr2-xFe3O12 (x = 0.5-0.7), along with the endmember phase, Ca3(Zr2)SiFe3+2O12, for comparison. The oxidation states of U were determined by X-ray photoelectron and absorption spectroscopies, revealing the presence of mixed pentavalent and hexavalent uranium in the phases with x = 0.6 and 0.7. The oxidation states and coordination environments of Fe were measured using transmission 57Fe-Mössbauer spectroscopy, which shows that all iron is tetrahedrally coordinated Fe3+. U substitution had a significant effect on local environments, the extent of U substitution within this range had a minimal effect on the structure, and unlike in the x = 0 sample, Fe exists in two different environments in the substituted garnets. The enthalpies of formation of garnet phases from constituent oxides and elements were first time determined by high temperature oxide melt solution calorimetry. The results indicate that these substituted garnets are thermodynamically stable under reducing conditions. Our structural and thermodynamic analysis further provides explanation for the formation of natural uranium garnet, elbrusite-(Zr), and supports the potential use of Ca3UxZr2-xFe3O12 as viable waste form phases for U and other actinides.

The Copper Active Site of CBM33 Polysaccharide Oxygenases

PubMed Central

2013-01-01

The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme’s three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

Structure and lifetimes in ionic liquids and their mixtures.

PubMed

Gehrke, Sascha; von Domaros, Michael; Clark, Ryan; Hollóczki, Oldamur; Brehm, Martin; Welton, Tom; Luzar, Alenka; Kirchner, Barbara

2018-01-01

With the aid of molecular dynamics simulations, we study the structure and dynamics of different ionic liquid systems, with focus on hydrogen bond, ion pair and ion cage formation. To do so, we report radial distribution functions, their number integrals, and various time-correlation functions, from which we extract well-defined lifetimes by means of the reactive flux formalism. We explore the influence of polarizable force fields vs. non-polarizable ones with downscaled charges (±0.8) for the example of 1-butyl-3-methylimidazolium bromide. Furthermore, we use 1-butyl-3-methylimidazolium trifluoromethanesulfonate to investigate the impact of temperature and mixing with water as well as with the chloride ionic liquid. Smaller coordination numbers, larger distances, and tremendously accelerated dynamics are observed when the polarizable force field is applied. The same trends are found with increasing temperature. Adding water decreases the ion-ion coordination numbers whereas the water-ion and water-water coordination is enhanced. A domain analysis reveals that the nonpolar parts of the ions are dispersed and when more water is added the water clusters increase in size. The dynamics accelerate in general upon addition of water. In the ionic liquid mixture, the coordination number around the cation changes between the two anions, but the number integrals of the cation around the anions remain constant and the dynamics slow down with increasing content of the chloride ionic liquid.

Attitude coordination of multi-HUG formation based on multibody system theory

NASA Astrophysics Data System (ADS)

Xue, Dong-yang; Wu, Zhi-liang; Qi, Er-mai; Wang, Yan-hui; Wang, Shu-xin

2017-04-01

Application of multiple hybrid underwater gliders (HUGs) is a promising method for large scale, long-term ocean survey. Attitude coordination has become a requisite for task execution of multi-HUG formation. In this paper, a multibody model is presented for attitude coordination among agents in the HUG formation. The HUG formation is regarded as a multi-rigid body system. The interaction between agents in the formation is described by artificial potential field (APF) approach. Attitude control torque is composed of a conservative torque generated by orientation potential field and a dissipative term related with angular velocity. Dynamic modeling of the multibody system is presented to analyze the dynamic process of the HUG formation. Numerical calculation is carried out to simulate attitude synchronization with two kinds of formation topologies. Results show that attitude synchronization can be fulfilled based on the multibody method described in this paper. It is also indicated that different topologies affect attitude control quality with respect to energy consumption and adjusting time. Low level topology should be adopted during formation control scheme design to achieve a better control effect.

Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

NASA Astrophysics Data System (ADS)

Paul, Avijit Kumar

2018-04-01

One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

Coordinating properties of uridine 5'-monophosphate with selected Ln(3+) ions in ionic micellar media.

PubMed

Sudhiranjan Singh, M; Homendra, Naorem; Lonibala, R K

2012-12-01

Coordinating properties of uridine 5'-monophosphate (UMP) towards trivalent La, Pr, Nd, Sm, Eu and Gd ions in presence of cationic and anionic micelles have been investigated by potentiometric pH-titration and spectroscopic methods. Stability constants of the 2:1 complexes have been determined and the change in free energy, enthalpy and entropy associated with the complexation are also calculated. Nd(III) complexes isolated from aqueous and aqueous-micellar media do not show any significant structural difference. Formation of Ln(III) complexes in all cases completes below pH 7.5 showing that UMP best interacts with Ln(3+) ions at the physiological pH range 7.3-7.5. The nucleobase is not involved in the complexation and the metal ion coordination of UMP is through the phosphate moiety only. Coordinating tendency of UMP with lanthanides, Nd(III) ion in particular, at different pH is also discussed. Luminescent properties of Eu(III) complex and its decay lifetime are also presented. This information may prove helpful regarding the use of lanthanides as biological probes for calcium/magnesium ions.

Quantum anharmonic oscillator plus delta-function potential: a molecular view of pairing formation and breaking in the coordinate space

NASA Astrophysics Data System (ADS)

Sumaryada, Tony; Maha Putra, Bima; Pramudito, Sidikrubadi

2017-05-01

We propose an alternative way to describe the pairing formation and breaking via a quantum anharmonic oscillator with a delta-function potential model. Unlike BCS theory, which describes the pairing formation in the momentum space, this model works in the coordinate space and is able to give a molecular view of pairing formation and breaking in the coordinate space. By exploring the dynamical interplay between the intrinsic factor (dissociation energy) and external factor (pairing strength) of this system additional information was gained, including the critical pairing strength and critical scattering length, which might relate to the BCS-BEC crossover phenomena and halo state formation. Although only the energetic aspect of pairing is described by this model, its simplicity and pedagogical steps might help undergraduate students to understand the pairing problem in a simple way.

An OpenEarth Framework (OEF) for Integrating and Visualizing Earth Science Data

NASA Astrophysics Data System (ADS)

Moreland, J. L.; Nadeau, D. R.; Baru, C.; Crosby, C. J.

2009-12-01

The integration of data is essential to make transformative progress in understanding the complex processes operating at the Earth’s surface and within its interior. While our current ability to collect massive amounts of data, develop structural models, and generate high-resolution dynamics models is well developed, our ability to quantitatively integrate these data and models into holistic interpretations of Earth systems is poorly developed. We lack the basic tools to realize a first-order goal in Earth science of developing integrated 4D models of Earth structure and processes using a complete range of available constraints, at a time when the research agenda of major efforts such as EarthScope demand such a capability. Among the challenges to 3D data integration are data that may be in different coordinate spaces, units, value ranges, file formats, and data structures. While several file format standards exist, they are infrequently or incorrectly used. Metadata is often missing, misleading, or relegated to README text files along side the data. This leaves much of the work to integrate data bogged down by simple data management tasks. The OpenEarth Framework (OEF) being developed by GEON addresses these data management difficulties. The software incorporates file format parsers, data interpretation heuristics, user interfaces to prompt for missing information, and visualization techniques to merge data into a common visual model. The OEF’s data access libraries parse formal and de facto standard file formats and map their data into a common data model. The software handles file format quirks, storage details, caching, local and remote file access, and web service protocol handling. Heuristics are used to determine coordinate spaces, units, and other key data features. Where multiple data structure, naming, and file organization conventions exist, those heuristics check for each convention’s use to find a high confidence interpretation of the data. When no convention or embedded data yields a suitable answer, the user is prompted to fill in the blanks. The OEF’s interaction libraries assist in the construction of user interfaces for data management. These libraries support data import, data prompting, data introspection, the management of the contents of a common data model, and the creation of derived data to support visualization. Finally, visualization libraries provide interactive visualization using an extended version of NASA WorldWind. The OEF viewer supports visualization of terrains, point clouds, 3D volumes, imagery, cutting planes, isosurfaces, and more. Data may be color coded, shaded, and displayed above, or below the terrain, and always registered into a common coordinate space. The OEF architecture is open and cross-platform software libraries are available separately for use with other software projects, while modules from other projects may be integrated into the OEF to extend its features. The OEF is currently being used to visualize data from EarthScope-related research in the Western US.

Structure of 1:1 complex of 1-naphthylmethyl ester of monensin A with sodium perchlorate studied by X-ray, FT-IR and ab initio methods

NASA Astrophysics Data System (ADS)

Huczyński, Adam; Janczak, Jan; Brzezinski, Bogumil

2012-12-01

A new crystalline complex formed between 1-naphthylmethyl ester of the naturally occurring antibiotic - monensin A (MON8) with sodium perchlorate has been obtained and studied using X-ray crystallography and FT-IR spectroscopy. The X-ray data of the complex show that MON8 forms a pseudo-cyclic structure stabilised by one weak intramolecular hydrogen bond and the sodium cation co-ordinated by two oxygen atoms of hydroxyl groups and four etheric oxygen atoms in the hydrophilic sphere. Within this structure the oxygen atoms of the ester groups are not involved in the coordination of sodium cation. In contrast to the solid state structure of the complex, in acetonitrile solution an equilibrium between two structures, in which the oxygen atom of the carbonyl ester group is either involved or not involved in the complexation of the sodium cation, is found. In acetonitrile this equilibrium is shifted towards the latter structure i.e. the structure existing in the solid state. The gas-phase structure of [MON8sbnd Na]+ cation as shown the ab initio MO calculations is comparable with the crystal one. Three-dimensional molecular electrostatic potential calculated for the neutral MON8 and [MON8sbnd Na]+ molecules is helpful for understanding the structural aspects of the sodium complex formation.

Synthesis of sodium polyhydrides at high pressures

DOE PAGES

Struzhkin, Viktor V.; Kim, Duck Young; Stavrou, Elissaios; ...

2016-07-28

Archetypal ionic NaH is the only known compound of sodium and hydrogen. Application of high pressure is known to promote states with higher atomic coordination, but extensive searches for polyhydrides with unusual stoichiometry have had only limited success in spite of several theoretical predictions. Here we report the first observation of the formation of polyhydrides of Na (NaH 3 and NaH 7) above 40 GPa and 2,000 K. Moreover, we combine synchrotron X-ray diffraction and Raman spectroscopy in a laser-heated diamond anvil cell and theoretical random structure searching, which both agree on the stable structures and compositions. Our results supportmore » the formation of multicenter bonding in a material with unusual stoichiometry. These results are applicable to the design of new energetic solids and high-temperature superconductors based on hydrogen-rich materials.« less

On the genetic control of planar growth during tissue morphogenesis in plants.

PubMed

Enugutti, Balaji; Kirchhelle, Charlotte; Schneitz, Kay

2013-06-01

Tissue morphogenesis requires extensive intercellular communication. Plant organs are composites of distinct radial cell layers. A typical layer, such as the epidermis, is propagated by stereotypic anticlinal cell divisions. It is presently unclear what mechanisms coordinate cell divisions relative to the plane of a layer, resulting in planar growth and maintenance of the layer structure. Failure in the regulation of coordinated growth across a tissue may result in spatially restricted abnormal growth and the formation of a tumor-like protrusion. Therefore, one way to approach planar growth control is to look for genetic mutants that exhibit localized tumor-like outgrowths. Interestingly, plants appear to have evolved quite robust genetic mechanisms that govern these aspects of tissue morphogenesis. Here we provide a short summary of the current knowledge about the genetics of tumor formation in plants and relate it to the known control of coordinated cell behavior within a tissue layer. We further portray the integuments of Arabidopsis thaliana as an excellent model system to study the regulation of planar growth. The value of examining this process in integuments was established by the recent identification of the Arabidopsis AGC VIII kinase UNICORN as a novel growth suppressor involved in the regulation of planar growth and the inhibition of localized ectopic growth in integuments and other floral organs. An emerging insight is that misregulation of central determinants of adaxial-abaxial tissue polarity can lead to the formation of spatially restricted multicellular outgrowths in several tissues. Thus, there may exist a link between the mechanisms regulating adaxial-abaxial tissue polarity and planar growth in plants.

Alkaline earth-based coordination polymers derived from a cyclotriphosphazene-functionalized hexacarboxylate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ling, Yajing; Bai, Dongjie; Feng, Yunlong

Combination of hexakis(4-carboxylatephenoxy)cyclotriphosphazene with alkaline earth ions of increasing ionic radii (Mg{sup 2+}, Ca{sup 2+} and Ba{sup 2+}) under different solvothermal conditions yielded three new coordination polymers, and their crystal structures were determined by single-crystal X-ray diffraction analysis. The magnesium compound displays a three dimensional (3D) network structure constructed from the deprotonated ligand and the secondary building block Mg(COO){sub 4}, which can be rationalized as a (4,6)-connected topological net with the Schläfli symbol of (4{sup 4}·6{sup 2}){sub 3}(4{sup 9}·6{sup 6}){sub 2}. The calcium compound consists of 1D infinite “Ca-O” inorganic chains connected by the deprotonated ligands to from a 3Dmore » framework. The barium compound exhibits a 3D framework in which 1D “Ba-O” inorganic chains are connected together by the deprotonated organic linkers. Due to the semi-rigid nature, the ligand adopts distinctly different conformations in the three compounds. The metal ions’ influence exerted on the final structure of the resulting coordination polymers is also discussed. When the radii of alkaline earth ions increases descending down the group from Mg(II) to Ba(II), the coordination number becomes larger and more versatile: from 6 in the magnesium compound, to 6,7 and 10 in the calcium compound, and to 8 and 9 in the barium compound, thus substantially influencing the resulting final framework structures. Also, the photophysical properties were investigated systematically, revealing that the three compounds are photoluminscent in the solid state at room temperature. This work demonstrates that although the multiplicity of conformation in the hexacarboxylate ligand based on the inorganic scaffold cyclotriphosphazene makes it difficult to predict how this ligand will form extended network, but provides unique opportunities for the formation of diverse inorganic-organic hybrids exhibiting rich structural topologies. - Graphical abstract: Three alkaline earth-based coordination polymers were constructed from a semirigid cyclotriphosphazene-functionalized hexacarboxylate exhibiting different inorganic nodes as well as distinct ligand conformations relying on the metal ions, which presents the first example of such a ligand incorporated into alkaline earth–based coordination polymers. - Highlights: • Three alkaline earth-based coordination polymers were synthesized. • The three compounds exhibit different inorganic nodes and ligand conformations. • The three compounds are photoluminscent in the solid state.« less

Rutile (β-)MnO2 surfaces and vacancy formation for high electrochemical and catalytic performance.

PubMed

Tompsett, David A; Parker, Stephen C; Islam, M Saiful

2014-01-29

MnO2 is a technologically important material for energy storage and catalysis. Recent investigations have demonstrated the success of nanostructuring for improving the performance of rutile MnO2 in Li-ion batteries and supercapacitors and as a catalyst. Motivated by this we have investigated the stability and electronic structure of rutile (β-)MnO2 surfaces using density functional theory. A Wulff construction from relaxed surface energies indicates a rod-like equilibrium morphology that is elongated along the c-axis, and is consistent with the large number of nanowire-type structures that are obtainable experimentally. The (110) surface dominates the crystallite surface area. Moreover, higher index surfaces than considered in previous work, for instance the (211) and (311) surfaces, are also expressed to cap the rod-like morphology. Broken coordinations at the surface result in enhanced magnetic moments at Mn sites that may play a role in catalytic activity. The calculated formation energies of oxygen vacancy defects and Mn reduction at key surfaces indicate facile formation at surfaces expressed in the equilibrium morphology. The formation energies are considerably lower than for comparable structures such as rutile TiO2 and are likely to be important to the high catalytic activity of rutile MnO2.

First-principles study of the solid solution of hydrogen in lanthanum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schoellhammer, Gunther; Herzig, Peter; Wolf, Walter

2011-09-01

Results from first-principles investigations of the energetical, structural, electronic, and vibrational properties of model structures probing the metal-rich region of the lanthanum-hydrogen system, i.e., the region of the solid solution of hydrogen in lanthanum, are presented. We have studied the site preference and the ordering tendency of hydrogen atoms interstitially bonded in close-packed lanthanum. Spatially separated hydrogen atoms have turned out to exhibit an energetical preference for the occupation of octahedral interstitial sites at low temperature. Indications for a reversal of the site preference in favor of the occupation of tetrahedral interstitial sites at elevated temperature have been found. Linearmore » arrangements consisting of pairs of octahedrally and/or tetrahedrally coordinated hydrogen atoms collinearly bonded to a central lanthanum atom have turned out to be energetically favorable structure elements. Further stabilization is achieved if such hydrogen pairs are in turn linked together so that extended chains of La-H bonds are formed. Pair formation and chain linking counteract the energetical preference for octahedral coordination observed for separated hydrogen atoms.« less

Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions† †Electronic supplementary information (ESI) available: Characterization data and additional tables and figures. CCDC 1515722 and 1515723. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04070a

PubMed Central

Yang, Linlin; Jing, Xu; An, Bowen; Yang, Yang

2017-01-01

By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system. PMID:29675152

Structures of nitrato-(2-hydroxybenzaldehydo) (2,2 Prime -bipyridyl)copper and nitrato-(2-hydroxy-5-nitrobenzaldehydo)(2,2 Prime -bipyridyl)copper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chumakov, Yu. M.; Paladi, L. G.; Antosyak, B. Ya.

2011-03-15

Nitrato-(2-hydroxy-5-nitrobenzaldehydo)(2,2 Prime -bipyridyl)copper (I) and nitrato-(2-hydroxybenzaldehydo)(2,2 Prime -bipyridyl)copper (II) were synthesized and characterized by X-ray diffraction. The coordination polyhedron of the central copper atom in complex I can be described as a distorted tetragonal pyramid whose base is formed by the phenol and carbonyl oxygen atoms of the monodeprotonated 2-hydroxy-5nitrobenzaldehyde molecule and the nitrogen atoms of the 2,2 Prime -bipyridyl ligand and whose apex is occupied by the oxygen atom of the nitrato group. In the crystal structure, complexes I are linked by the acido ligands and the NO{sub 2} groups of the aldehyde molecule into infinite chains. In complexmore » II, the central copper atom is coordinated by 2-hydroxybenzaldehyde, 2,2 Prime -bipyridyl, and the nitrato group, resulting in the formation of centrosymmetric dimers. The coordination polyhedron of the central copper atom can be described as a bipyramid (4 + 1 + 1) with the same base as in complex I. The axial vertices of the bipyramid are occupied by the oxygen atom of the nitrato group and the bridging phenol oxygen atom of the adjacent complex related to the initial complex by a center of symmetry. In the crystal structure, complexes II are hydrogen bonded into infinite chains.« less

Synthesis and characterization of two new zinc(II) coordination polymers with bidentate flexible ligands: Formation of a 2D structure with (44.62)-sql topology

NASA Astrophysics Data System (ADS)

Lalegani, Arash; Khaledi Sardashti, Mohammad; Gajda, Roman; Woźniak, Krzysztof

2017-12-01

Zinc(II) coordination polymers [Zn(bip)2(NCS)2]n (1) and [Zn(μ-bbd)(N3)2]n (2) were synthesized by using the neutral flexible bidentate N-donor ligands 1,4-bis(3,5-dimethylpyrazolyl)butane (bbd) and 1,3-bis(imidazolyl)propane (bip), mono-anionic NCS- or N3-ligand and zinc(II) chloride salts. The results of the X-ray analyses demonstrate that in the structure of 1, the zinc(II) ion is located on an inversion center and exhibits an ZnN6 octahedral arrangement while, in the structure of 2, the zinc(II) ion adopts an ZnN4 tetrahedral geometry. In the polymer 1, the NCS groups are terminally N-bonded to the metal center and the each bip with anti-gauche conformation acts as bridging connecting four zinc(II) ions to form a two-dimensional network with a sql [point symbol (44.62)] topology while, in the polymer 1, the N3 groups are terminally bonded to the metal center and each bbd with anti-anti-anti conformation acts as bridging ligand connecting two zinc(II) ions to form a one-dimensional zig-zag chain. Coordination compounds 1 and 2 have been characterized by infrared spectroscopy, elemental analyses and single-crystal X-ray diffraction. Thermal analyses of polymers were also presented.

Syntheses, crystal structures, and properties of new metal--5-bromonicotinate coordination polymers

NASA Astrophysics Data System (ADS)

Li, Wenjie; Li, Guoting; Lv, Lulu; Zhao, Hong; Wu, Benlai

2015-05-01

Four metal-5-bromonicotinate (Brnic) coordination polymers [Fe(Brnic)2(H2O)2]n (1), [Ni(Brnic)2]n (2), [Ni(Brnic)(bpy)(H2O)2]n·n(Brnic)·4.5nH2O (3), and [Co2(Brnic)3(bpy)2(OH)]n·nH2O (4) have been synthesized and structurally characterized (bpy=4,4‧-bipyridine). Complex 1 has corrugated (4,4) sheets formed by μ-Brnic ligands and planar nodes Fe(II). As for 2-4, they all built up from Brnic-bridged dinuclear subunits, but have very different structure features. Complex 2 is a twin-like polymer with (4,4) layers formed by twin paddle-wheel [Ni2(Brnic)4] subunits. Through the bridge coordination of bpy ligands with dinuclear rings [Ni2(Brnic)2] and trigons [Co2(Brnic)3(OH)], 63-topological cationic layers with nanosized grids of 3 and chiral ladder-type double chains of 4 formed, respectively. Notably, halogen-related interactions play an important role in the formation of 3D metallosupermolecules 1-4. The thermostabilities of all compounds have been discussed in detail. Moreover, the magnetic investigations of 2 and 4 indicate that there exist antiferromagnetic interactions in the paddle-wheel [Ni2(Brnic)4] and trigon [Co2(Brnic)3(OH)] cores, respectively.

Identification of O-rich structures on platinum(111)-supported ultrathin iron oxide films

DOE PAGES

Merte, Lindsay R.; Bai, Yunhai; Zeuthen, Helene; ...

2016-01-06

Using high-resolution scanning tunneling microscopy (STM) we have studied the oxidation of ultrathin FeO films grown on Pt(111). At the initial stage of the FeO film oxidation by atomic oxygen exposure, we identified three distinct types of line defects, all of which form boundaries between FeO domains of opposite orientation. Two types of line defects appearing bright ( type-i) and dark ( type-ii) in the STM images at typical scanning parameters are “metallic”, whereas the third line defect exhibits nonmetallic behavior ( type-iii). Atomic-scale structure models of these line defects are proposed, with type-i defects exhibiting 4-fold coordinated Fe atoms,more » type-ii exhibiting 2-fold coordinated O atoms, and type-iii exhibiting tetrahedrally-coordinated Fe atoms. In addition, FeO 2 trilayer islands are formed upon oxidation, which appear at FCC-type domains of the moiré structure. At high scanning bias, distinct protrusions on the trilayer islands are observed over surface O ions, which are assigned to H adatoms. The experimental data are supported by density functional theory (DFT) calculations, in which bare and hydroxylated FeO 2 trilayer islands are compared. Finally, we compare the formation of O-rich features on continuous FeO films using atomic oxygen with the oxidation of Pt(111)-supported FeO islands accomplished by O 2 exposure.« less

Nanoparticulate mackinawite formation; a stopped and continuous flow XANES and EXAFS investigation

NASA Astrophysics Data System (ADS)

Butler, I. B.; Bell, A. M.; Charnock, J. M.; Rickard, D.; Vaughan, D. J.; Oldroyd, A.

2009-12-01

The sequestration of sulfur and iron within sedimentary iron sulfides, and ultimately as pyrite, is a major sink in global biogeochemical cycles of those elements and has impacts on global carbon and oxygen cycles. The formation of the metastable black iron (II) monosulfide mackinawite is a key process because mackinawite forms in aqueous solutions where the Fe(II) and S(-II) IAP exceeds mackinawite’s Ksp. Mackinawite is the first formed iron sulfide phase, a consequence of Ostwald’s step rule and is a reactant phase during the formation of thermodynamically stable sedimentary iron sulfide minerals such as pyrite. The reaction of dissolved Fe(II) and sulfide is extremely fast and reactions in the environmentally significant near-neutral pH range tend to completion in <1 second. We have combined stopped and continuous flow techniques with X-ray absorption spectroscopy to evaluate the products of the fast precipitation kinetics of mackinawite over millisecond timescales. EXAFS spectra and data collected during flow experiments were compared with those from a well characterised freeze-dried nanoparticulate mackinawite standard and with published data. Published work has used Rietveld crystal structure refinement to determine bond distances of 2.2558 and 2.5976Å for Fe-S and Fe-Fe respectively. In our experiments Fe K edge XANES is consistent with tetrahedrally coordinated Fe in the precipitated sulfide phase. EXAFS data show that local Fe-S and Fe-Fe coordination and interatomic distances (Fe-S = 2.24Å; Fe-Fe = 2.57Å) are consistent with those determined for the standard mackinawite and published data. The coordination and spacing are developed in the precipitated phase after <10ms reaction at pH5, and considerably faster in experiments at near neutral to alkaline pH. No evidence for phases structurally intermediate between hexaqua Fe(II) and precipitated mackinawite was observed. Aqueous FeS° cluster complexes previously identified as intermediates during mackinawite formation and iron sulfide mineral transformations did not contribute significantly to the EXAFS spectra collected. For environmental, geological and biogeochemical applications, the precipitation of the mineral mackinawite can be considered to proceed rapidly from aqueous Fe(II) and S(-II) ions to the nanoparticulate crystalline mineral. The materials labelled “disordered mackinawite”, or “amorphous FeS” phase which have been widely quoted in the iron sulfide literature do not form at any stage of the precipitation of mackinawite from aqueous solutions. Physical and chemical properties previously ascribed to an amorphous or disordered structure are a consequence of the nanoparticulate form of the first precipitated solid.

Crystal structures of Sr(ClO4)2·3H2O, Sr(ClO4)2·4H2O and Sr(ClO4)2·9H2O

PubMed Central

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

The title compounds, strontium perchlorate trihydrate {di-μ-aqua-aquadi-μ-perchlorato-strontium, [Sr(ClO4)2(H2O)3]n}, strontium perchlorate tetra­hydrate {di-μ-aqua-bis­(tri­aqua­diperchloratostrontium), [Sr2(ClO4)4(H2O)8]} and strontium perchlorate nona­hydrate {hepta­aqua­diperchloratostrontium dihydrate, [Sr(ClO4)2(H2O)7]·2H2O}, were crystallized at low temperatures according to the solid–liquid phase diagram. The structures of the tri- and tetra­hydrate consist of Sr2+ cations coordinated by five water mol­ecules and four O atoms of four perchlorate tetra­hedra in a distorted tricapped trigonal–prismatic coordination mode. The asymmetric unit of the trihydrate contains two formula units. Two [SrO9] polyhedra in the trihydrate are connected by sharing water mol­ecules and thus forming chains parallel to [100]. In the tetra­hydrate, dimers of two [SrO9] polyhedra connected by two sharing water mol­ecules are formed. The structure of the nona­hydrate contains one Sr2+ cation coordinated by seven water mol­ecules and by two O atoms of two perchlorate tetra­hedra (point group symmetry ..m), forming a tricapped trigonal prism (point group symmetry m2m). The structure contains additional non-coordinating water mol­ecules, which are located on twofold rotation axes. O—H⋯O hydrogen bonds between the water mol­ecules as donor and ClO4 tetra­hedra and water mol­ecules as acceptor groups lead to the formation of a three-dimensional network in each of the three structures. PMID:25552979

Consensus seeking, formation keeping, and trajectory tracking in multiple vehicle cooperative control

NASA Astrophysics Data System (ADS)

Ren, Wei

Cooperative control problems for multiple vehicle systems can be categorized as either formation control problems with applications to mobile robots, unmanned air vehicles, autonomous underwater vehicles, satellites, aircraft, spacecraft, and automated highway systems, or non-formation control problems such as task assignment, cooperative transport, cooperative role assignment, air traffic control, cooperative timing, and cooperative search. The cooperative control of multiple vehicle systems poses significant theoretical and practical challenges. For cooperative control strategies to be successful, numerous issues must be addressed. We consider three important and correlated issues: consensus seeking, formation keeping, and trajectory tracking. For consensus seeking, we investigate algorithms and protocols so that a team of vehicles can reach consensus on the values of the coordination data in the presence of imperfect sensors, communication dropout, sparse communication topologies, and noisy and unreliable communication links. The main contribution of this dissertation in this area is that we show necessary and/or sufficient conditions for consensus seeking with limited, unidirectional, and unreliable information exchange under fixed and switching interaction topologies (through either communication or sensing). For formation keeping, we apply a so-called "virtual structure" approach to spacecraft formation flying and multi-vehicle formation maneuvers. As a result, single vehicle path planning and trajectory generation techniques can be employed for the virtual structure while trajectory tracking strategies can be employed for each vehicle. The main contribution of this dissertation in this area is that we propose a decentralized architecture for multiple spacecraft formation flying in deep space with formation feedback introduced. This architecture ensures the necessary precision in the presence of actuator saturation, internal and external disturbances, and stringent inter-vehicle communication limitations. A constructive approach based on the satisficing control paradigm is also applied to multi-robot coordination in hardware. For trajectory tracking, we investigate nonlinear tracking controllers for fixed wing unmanned air vehicles and nonholonomic mobile robots with velocity and heading rate constraints. The main contribution of this dissertation in this area is that our proposed tracking controllers are shown to be robust to input uncertainties and measurement noise, and are computationally simple and can be implemented with low-cost, low-power microcontrollers. In addition, our approach allows piecewise continuous reference velocity and heading rate and can be extended to derive a variety of other trajectory tracking strategies.

Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly.

PubMed

Xu, Kai; Chan, Yee-Peng; Bradel-Tretheway, Birgit; Akyol-Ataman, Zeynep; Zhu, Yongqun; Dutta, Somnath; Yan, Lianying; Feng, YanRu; Wang, Lin-Fa; Skiniotis, Georgios; Lee, Benhur; Zhou, Z Hong; Broder, Christopher C; Aguilar, Hector C; Nikolov, Dimitar B

2015-12-01

Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein.

Unique behaviour of dinitrogen-bridged dimolybdenum complexes bearing pincer ligand towards catalytic formation of ammonia.

PubMed

Tanaka, Hiromasa; Arashiba, Kazuya; Kuriyama, Shogo; Sasada, Akira; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

2014-04-28

It is vital to design effective nitrogen fixation systems that operate under mild conditions, and to this end we recently reported an example of the catalytic formation of ammonia using a dinitrogen-bridged dimolybdenum complex bearing a pincer ligand, where up to twenty three equivalents of ammonia were produced based on the catalyst. Here we study the origin of the catalytic behaviour of the dinitrogen-bridged dimolybdenum complex bearing the pincer ligand with density functional theory calculations, based on stoichiometric and catalytic formation of ammonia from molecular dinitrogen under ambient conditions. Comparison of di- and mono-molybdenum systems shows that the dinitrogen-bridged dimolybdenum core structure plays a critical role in the protonation of the coordinated molecular dinitrogen in the catalytic cycle.

Local structural order and relaxation effects in metal-chalcogenide glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saleh, Z.M.

1990-01-01

Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) have been employed to study the local structural order and the relaxation mechanisms in metal-arsenic-chalcogenide glasses for metal concentrations within the glass forming region. The glass forming region in the Cu-As-S and Cu-As-se glassy systems extends approximately to 6 and 25 at. % copper, respectively. In the composition Cu[sub x](As[sub 2/5]Ch[sub 3/5])[sub 1[minus]x], where Ch = S or Se, there is evidence of dramatic changes in the local structure as copper is added to the system. One important change is the formation of As-As bonds which are absent in As[sub 2]Ch[submore » 3]. The [sup 75]As NQR measurements indicate that the density of these bonds increases with copper concentration x. These results are consistent with the predictions of a model proposed recently to explain the local structural order in glassy metal chalcogenides. While NQR data show that arsenic atoms are threefold coordinated, EXAFs measurements have shown that copper is fourfold coordinated within the glass forming ranges in both systems. The NMR measurements confirm this result and quantitatively determine the local environment around the copper nuclei. For the naturally occurring mineral luzonite (Cu[sub 3]AsS[sub 4]) copper is fourfold coordinated. The known structure of this mineral has been used as a guide to understanding the local structure in the glasses. Copper and arsenic nuclear relaxation measurements were used to study the dynamics of these systems. The temperature and frequency dependence of the spin-lattice and spin-spin relaxation times have been carefully measured to determine the relaxation mechanisms.« less

Part I. Student success in intensive versus traditional introductory chemistry courses. Part II. Synthesis of salts of the weakly coordinating trisphat anion

NASA Astrophysics Data System (ADS)

Hall, Mildred V.

Part I. Intensive courses have been shown to be associated with equal or greater student success than traditional-length courses in a wide variety of disciplines and education levels. Student records from intensive and traditional-length introductory general chemistry courses were analyzed to determine the effects, of the course format, the level of academic experience, life experience (age), GPA, academic major and gender on student success in the course. Pretest scores, GPA and ACT composite scores were used as measures of academic ability and prior knowledge; t-tests comparing the means of these variables were used to establish that the populations were comparable prior to the course. Final exam scores, total course points and pretest-posttest differences were used as measures of student success; t-tests were used to determine if differences existed between the populations. ANCOVA analyses revealed that student GPA, pretest scores and course format were the only variables tested that were significant in accounting for the variance of the academic success measures. In general, the results indicate that students achieved greater academic success in the intensive-format course, regardless of the level of academic experience, life experience, academic major or gender. Part II. Weakly coordinating anions have many important applications, one of which is to function as co-catalysts in the polymerization of olefins by zirconocene. The structure of tris(tetrachlorobenzenedialato) phosphate(V) or "trisphat" anion suggests that it might be an outstanding example of a weakly coordinating anion. Trisphat acid was synthesized and immediately used to prepare the stable tributylammonium trisphat, which was further reacted to produce trisphat salts of Group I metal cations in high yields. Results of the 35Cl NQR analysis of these trisphat salts indicate only very weak coordination between the metal cations and the chlorine atoms of the trisphat anion.

A coordination theory for intelligent machines

NASA Technical Reports Server (NTRS)

Wang, Fei-Yue; Saridis, George N.

1990-01-01

A formal model for the coordination level of intelligent machines is established. The framework of the coordination level investigated consists of one dispatcher and a number of coordinators. The model called coordination structure has been used to describe analytically the information structure and information flow for the coordination activities in the coordination level. Specifically, the coordination structure offers a formalism to (1) describe the task translation of the dispatcher and coordinators; (2) represent the individual process within the dispatcher and coordinators; (3) specify the cooperation and connection among the dispatcher and coordinators; (4) perform the process analysis and evaluation; and (5) provide a control and communication mechanism for the real-time monitor or simulation of the coordination process. A simple procedure for the task scheduling in the coordination structure is presented. The task translation is achieved by a stochastic learning algorithm. The learning process is measured with entropy and its convergence is guaranteed. Finally, a case study of the coordination structure with three coordinators and one dispatcher for a simple intelligent manipulator system illustrates the proposed model and the simulation of the task processes performed on the model verifies the soundness of the theory.

DFT study of uranyl peroxo complexes with H2O, F-, OH-, CO3(2-), and NO3(-).

PubMed

Odoh, Samuel O; Schreckenbach, Georg

2013-05-06

The structural and electronic properties of monoperoxo and diperoxo uranyl complexes with aquo, fluoride, hydroxo, carbonate, and nitrate ligands have been studied using scalar relativistic density functional theory (DFT). Only the complexes in which the peroxo ligands are coordinated to the uranyl moiety in a bidentate mode were considered. The calculated binding energies confirm that the affinity of the peroxo ligand for the uranyl group far exceeds that of the F(-), OH(-), CO3(2-), NO3(-), and H2O ligands. The formation of the monoperoxo complexes from UO2(H2O)5(2+) and HO2(-) were found to be exothermic in solution. In contrast, the formation of the monouranyl-diperoxo, UO2(O2)2X2(4-) or UO2(O2)2X(4-/3-) (where X is any of F(-), OH(-), CO3(2-), or NO3(-)), complexes were all found to be endothermic in aqueous solution. This suggests that the monoperoxo species are the terminal monouranyl peroxo complexes in solution, in agreement with recent experimental work. Overall, we find that the properties of the uranyl-peroxo complexes conform to well-known trends: the coordination of the peroxo ligand weakens the U-O(yl) bonds, stabilizes the σ(d) orbitals and causes a mixing between the uranyl π- and peroxo σ- and π-orbitals. The weakening of the U-O(yl) bonds upon peroxide coordination results in uranyl stretching vibrational frequencies that are much lower than those obtained after the coordination of carbonato or hydroxo ligands.

Relative position finite-time coordinated tracking control of spacecraft formation without velocity measurements.

PubMed

Hu, Qinglei; Zhang, Jian

2015-01-01

This paper investigates finite-time relative position coordinated tracking problem by output feedback for spacecraft formation flying without velocity measurement. By employing homogeneous system theory, a finite-time relative position coordinated tracking controller by state feedback is firstly developed, where the desired time-varying trajectory given in advance can be tracked by the formation. Then, to address the problem of lack of velocity measurements, a finite-time output feedback controller is proposed by involving a novel filter to recover unknown velocity information in a finite time. Rigorous proof shows that the proposed control law ensures global stability and guarantees the position of spacecraft formation to track a time-varying reference in finite time. Finally, simulation results are presented to illustrate the performance of the proposed controller. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

Network topology for the formation of solvated electrons in binary CaO–Al2O3 composition glasses

PubMed Central

Akola, Jaakko; Kohara, Shinji; Ohara, Koji; Fujiwara, Akihiko; Watanabe, Yasuhiro; Masuno, Atsunobu; Usuki, Takeshi; Kubo, Takashi; Nakahira, Atsushi; Nitta, Kiyofumi; Uruga, Tomoya; Weber, J. K. Richard; Benmore, Chris J.

2013-01-01

Glass formation in the CaO–Al2O3 system represents an important phenomenon because it does not contain typical network-forming cations. We have produced structural models of CaO–Al2O3 glasses using combined density functional theory–reverse Monte Carlo simulations and obtained structures that reproduce experiments (X-ray and neutron diffraction, extended X-ray absorption fine structure) and result in cohesive energies close to the crystalline ground states. The O–Ca and O–Al coordination numbers are similar in the eutectic 64 mol % CaO (64CaO) glass [comparable to 12CaO·7Al2O3 (C12A7)], and the glass structure comprises a topologically disordered cage network with large-sized rings. This topologically disordered network is the signature of the high glass-forming ability of 64CaO glass and high viscosity in the melt. Analysis of the electronic structure reveals that the atomic charges for Al are comparable to those for Ca, and the bond strength of Al–O is stronger than that of Ca–O, indicating that oxygen is more weakly bound by cations in CaO-rich glass. The analysis shows that the lowest unoccupied molecular orbitals occurs in cavity sites, suggesting that the C12A7 electride glass [Kim SW, Shimoyama T, Hosono H (2011) Science 333(6038):71–74] synthesized from a strongly reduced high-temperature melt can host solvated electrons and bipolarons. Calculations of 64CaO glass structures with few subtracted oxygen atoms (additional electrons) confirm this observation. The comparable atomic charges and coordination of the cations promote more efficient elemental mixing, and this is the origin of the extended cage structure and hosted solvated (trapped) electrons in the C12A7 glass. PMID:23723350

Network topology for the formation of solvated electrons in binary CaO-Al2O3 composition glasses.

PubMed

Akola, Jaakko; Kohara, Shinji; Ohara, Koji; Fujiwara, Akihiko; Watanabe, Yasuhiro; Masuno, Atsunobu; Usuki, Takeshi; Kubo, Takashi; Nakahira, Atsushi; Nitta, Kiyofumi; Uruga, Tomoya; Weber, J K Richard; Benmore, Chris J

2013-06-18

Glass formation in the CaO-Al2O3 system represents an important phenomenon because it does not contain typical network-forming cations. We have produced structural models of CaO-Al2O3 glasses using combined density functional theory-reverse Monte Carlo simulations and obtained structures that reproduce experiments (X-ray and neutron diffraction, extended X-ray absorption fine structure) and result in cohesive energies close to the crystalline ground states. The O-Ca and O-Al coordination numbers are similar in the eutectic 64 mol % CaO (64CaO) glass [comparable to 12CaO·7Al2O3 (C12A7)], and the glass structure comprises a topologically disordered cage network with large-sized rings. This topologically disordered network is the signature of the high glass-forming ability of 64CaO glass and high viscosity in the melt. Analysis of the electronic structure reveals that the atomic charges for Al are comparable to those for Ca, and the bond strength of Al-O is stronger than that of Ca-O, indicating that oxygen is more weakly bound by cations in CaO-rich glass. The analysis shows that the lowest unoccupied molecular orbitals occurs in cavity sites, suggesting that the C12A7 electride glass [Kim SW, Shimoyama T, Hosono H (2011) Science 333(6038):71-74] synthesized from a strongly reduced high-temperature melt can host solvated electrons and bipolarons. Calculations of 64CaO glass structures with few subtracted oxygen atoms (additional electrons) confirm this observation. The comparable atomic charges and coordination of the cations promote more efficient elemental mixing, and this is the origin of the extended cage structure and hosted solvated (trapped) electrons in the C12A7 glass.

Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes

PubMed Central

Voigt, Oliver; Adamska, Maja; Adamski, Marcin; Kittelmann, André; Wencker, Lukardis; Wörheide, Gert

2017-01-01

The ability to form mineral structures under biological control is widespread among animals. In several species, specific proteins have been shown to be involved in biomineralization, but it is uncertain how they influence the shape of the growing biomineral and the resulting skeleton. Calcareous sponges are the only sponges that form calcitic spicules, which, based on the number of rays (actines) are distinguished in diactines, triactines and tetractines. Each actine is formed by only two cells, called sclerocytes. Little is known about biomineralization proteins in calcareous sponges, other than that specific carbonic anhydrases (CAs) have been identified, and that uncharacterized Asx-rich proteins have been isolated from calcitic spicules. By RNA-Seq and RNA in situ hybridization (ISH), we identified five additional biomineralization genes in Sycon ciliatum: two bicarbonate transporters (BCTs) and three Asx-rich extracellular matrix proteins (ARPs). We show that these biomineralization genes are expressed in a coordinated pattern during spicule formation. Furthermore, two of the ARPs are spicule-type specific for triactines and tetractines (ARP1 or SciTriactinin) or diactines (ARP2 or SciDiactinin). Our results suggest that spicule formation is controlled by defined temporal and spatial expression of spicule-type specific sets of biomineralization genes. PMID:28406140

Sphingosine 1-Phosphate (S1P) Receptors 1 and 2 Coordinately Induce Mesenchymal Cell Migration through S1P Activation of Complementary Kinase Pathways*

PubMed Central

Quint, Patrick; Ruan, Ming; Pederson, Larry; Kassem, Moustapha; Westendorf, Jennifer J.; Khosla, Sundeep; Oursler, Merry Jo

2013-01-01

Normal bone turnover requires tight coupling of bone resorption and bone formation to preserve bone quantity and structure. With aging and during several pathological conditions, this coupling breaks down, leading to either net bone loss or excess bone formation. To preserve or restore normal bone metabolism, it is crucial to determine the mechanisms by which osteoclasts and osteoblast precursors interact and contribute to coupling. We showed that osteoclasts produce the chemokine sphingosine 1-phosphate (S1P), which stimulates osteoblast migration. Thus, osteoclast-derived S1P may recruit osteoblasts to sites of bone resorption as an initial step in replacing lost bone. In this study we investigated the mechanisms by which S1P stimulates mesenchymal (skeletal) cell chemotaxis. S1P treatment of mesenchymal (skeletal) cells activated RhoA GTPase, but this small G protein did not contribute to migration. Rather, two S1P receptors, S1PR1 and S1PR2, coordinately promoted migration through activation of the JAK/STAT3 and FAK/PI3K/AKT signaling pathways, respectively. These data demonstrate that the chemokine S1P couples bone formation to bone resorption through activation of kinase signaling pathways. PMID:23300082

Harnessing redox activity for the formation of uranium tris(imido) compounds

NASA Astrophysics Data System (ADS)

Anderson, Nickolas H.; Odoh, Samuel O.; Yao, Yiyi; Williams, Ursula J.; Schaefer, Brian A.; Kiernicki, John J.; Lewis, Andrew J.; Goshert, Mitchell D.; Fanwick, Phillip E.; Schelter, Eric J.; Walensky, Justin R.; Gagliardi, Laura; Bart, Suzanne C.

2014-10-01

Classically, late transition-metal organometallic compounds promote multielectron processes solely through the change in oxidation state of the metal centre. In contrast, uranium typically undergoes single-electron chemistry. However, using redox-active ligands can engage multielectron reactivity at this metal in analogy to transition metals. Here we show that a redox-flexible pyridine(diimine) ligand can stabilize a series of highly reduced uranium coordination complexes by storing one, two or three electrons in the ligand. These species reduce organoazides easily to form uranium-nitrogen multiple bonds with the release of dinitrogen. The extent of ligand reduction dictates the formation of uranium mono-, bis- and tris(imido) products. Spectroscopic and structural characterization of these compounds supports the idea that electrons are stored in the ligand framework and used in subsequent reactivity. Computational analyses of the uranium imido products probed their molecular and electronic structures, which facilitated a comparison between the bonding in the tris(imido) structure and its tris(oxo) analogue.

Artificial photosynthesis: understanding water splitting in nature

PubMed Central

Cox, Nicholas; Pantazis, Dimitrios A.; Neese, Frank; Lubitz, Wolfgang

2015-01-01

In the context of a global artificial photosynthesis (GAP) project, we review our current work on nature's water splitting catalyst. In a recent report (Cox et al. 2014 Science 345, 804–808 (doi:10.1126/science.1254910)), we showed that the catalyst—a Mn4O5Ca cofactor—converts into an ‘activated’ form immediately prior to the O–O bond formation step. This activated state, which represents an all MnIV complex, is similar to the structure observed by X-ray crystallography but requires the coordination of an additional water molecule. Such a structure locates two oxygens, both derived from water, in close proximity, which probably come together to form the product O2 molecule. We speculate that formation of the activated catalyst state requires inherent structural flexibility. These features represent new design criteria for the development of biomimetic and bioinspired model systems for water splitting catalysts using first-row transition metals with the aim of delivering globally deployable artificial photosynthesis technologies. PMID:26052426

Metal-Assisted Channel Stabilization: Disposition of a Single Histidine on the N-terminus of Alamethicin Yields Channels with Extraordinarily Long Lifetimes

PubMed Central

Noshiro, Daisuke; Asami, Koji; Futaki, Shiroh

2010-01-01

Abstract Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn2+, suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination. PMID:20441743

Regioselectivity of H Cluster Oxidation

PubMed Central

2011-01-01

The H2-evolving potential of [FeFe] hydrogenases is severely limited by the oxygen sensitivity of this class of enzymes. Recent experimental studies on hydrogenase from C. reinhardtii point to O2-induced structural changes in the [Fe4S4] subsite of the H cluster. Here, we investigate the mechanistic basis of this observation by means of density functional theory. Unexpectedly, we find that the isolated H cluster shows a pathological catalytic activity for the formation of reactive oxygen species such as O2– and HO2–. After protonation of O2–, an OOH radical may coordinate to the Fe atoms of the cubane, whereas H2O2 specifically reacts with the S atoms of the cubane-coordinating cysteine residues. Both pathways are accompanied by significant structural distortions that compromise cluster integrity and thus catalytic activity. These results explain the experimental observation that O2-induced inhibition is accompanied by distortions of the [Fe4S4] moiety and account for the irreversibility of this process. PMID:22106822

Synthesis, spectral, thermal and structural characterization of two complexes containing [N-(2-hydroxyethyl)-ethylenediamine] with carboxylate

NASA Astrophysics Data System (ADS)

Aycan, Tuǧba; Paşaoǧlu, Hümeyra

2018-02-01

Compounds based on the [Zn(hydet-en)2].(tpht).(H2O) (1) (tpht=dianion of terephthalic acid, hydet-en=N-(2-hydroxyethyl)ethylenediamine) has been synthesized which is characterized by single crystal X-ray determination, IR and thermal analysis. In 1, the Zinc(II) ion is six-coordinated that sandwiched by two hydet-en ligands which lies each hydeten ligand adopts a tripodal conformation and acts as tridentate ligand, carboxylate is uncoordinated. The coordination monomer is connected by C(13) chains and linear chains are connected by O-H...O H-bonds formed by DA:AD type 4 organization of aqua ligands and tpa2- ions resulting in R44(12 ) synthons to 3D structure. The FT-IR investigation of the complex were performed within the mid-IR region, mainly focusing on the characteristic vibrations of its free state and ligand behaviour in the case of complex formation. Thermal behaviours of 1 were followed using TG, DTA and DTG techniques.

The StreamCat Dataset: Accumulated Attributes for NHDPlusV2 Catchments Riparian Buffer (Version 2.1) for the Conterminous United States: Wildland Fire Perimeters By Year 2000 - 2010

EPA Pesticide Factsheets

This dataset represents the historical fire perimeters within individual local NHDPlusV2 catchments and upstream, contributing watersheds riparian buffers based on the GeoMAC (Geospatial Multi-Agency Coordination) mapping tool (See Supplementary Info for Glossary of Terms). Fire perimeters contain data as they are submitted by field offices to GeoMAC (Geospatial Multi-Agency Coordination) in a polygon format. Fire perimeter data is based on input from incident intelligence sources, GPS data, infrared (IR) imagery from fixed wing and satellite platforms. Polygons are selected by year and then converted into a binary raster format where values of 1 represent fire perimeters of the given year and 0 describes the remaining areas across the CONUS, leaving No Data to be anything outside the CONUS border. The wildland fire characteristics (% forest loss to fire) were summarized by year to produce local catchment-level and watershed-level metrics as a continuous data type (see Data Structure and Attribute Information for a description).

The StreamCat Dataset: Accumulated Attributes for NHDPlusV2 Catchments (Version 2.1) for the Conterminous United States: Wildland Fire Perimeters By Year 2000 - 2010

EPA Pesticide Factsheets

This dataset represents the historical fire perimeters within individual local NHDPlusV2 catchments and upstream, contributing watersheds based on the GeoMAC (Geospatial Multi-Agency Coordination) mapping tool (See Supplementary Info for Glossary of Terms). Fire perimeters contain data as they are submitted by field offices to GeoMAC (Geospatial Multi-Agency Coordination) in a polygon format. Fire perimeter data is based on input from incident intelligence sources, GPS data, infrared (IR) imagery from fixed wing and satellite platforms. Polygons are selected by year and then converted into a binary raster format where values of 1 represent fire perimeters of the given year and 0 describes the remaining areas across the CONUS, leaving No Data to be anything outside the CONUS border. The wildland fire characteristics (% forest loss to fire) were summarized by year to produce local catchment-level and watershed-level metrics as a continuous data type (see Data Structure and Attribute Information for a description).

Solvent induced rapid modulation of micro/nano structures of metal carboxylates coordination polymers: mechanism and morphology dependent magnetism.

PubMed

Liu, Kun; Shen, Zhu-Rui; Li, Yue; Han, Song-De; Hu, Tong-Liang; Zhang, Da-Shuai; Bu, Xian-He; Ruan, Wen-Juan

2014-08-12

Rational modulation of morphology is very important for functional coordination polymers (CPs) micro/nanostructures, and new strategies are still desired to achieve this challenging target. Herein, organic solvents have been established as the capping agents for rapid modulating the growth of metal-carboxylates CPs in organic solvent/water mixtures at ambient conditions. Co-3,5-pyridinedicarboxylate (pydc) CPs was studied here as the example. During the reaction, the organic solvents exhibited three types of modulation effect: anisotropic growth, anisotropic growth/formation of new crystalline phase and the formation of new crystalline phase solely, which was due to the variation of their binding ability with metal cations. The following study revealed that the binding ability was critically affected by their functional groups and molecular size. Moreover, their modulation effect could be finely tuned by changing volume ratios of solvent mixtures. Furthermore, they could be applied for modulating other metal-carboxylates CPs: Co-1,3,5-benzenetricarboxylic (BTC), Zn-pydc and Eu-pydc etc. Additionally, the as-prepared Co-pydc CPs showed a fascinating morphology-dependent antiferromagnetic behavior.

Solvent induced rapid modulation of micro/nano structures of metal carboxylates coordination polymers: mechanism and morphology dependent magnetism

NASA Astrophysics Data System (ADS)

Liu, Kun; Shen, Zhu-Rui; Li, Yue; Han, Song-De; Hu, Tong-Liang; Zhang, Da-Shuai; Bu, Xian-He; Ruan, Wen-Juan

2014-08-01

Rational modulation of morphology is very important for functional coordination polymers (CPs) micro/nanostructures, and new strategies are still desired to achieve this challenging target. Herein, organic solvents have been established as the capping agents for rapid modulating the growth of metal-carboxylates CPs in organic solvent/water mixtures at ambient conditions. Co-3,5-pyridinedicarboxylate (pydc) CPs was studied here as the example. During the reaction, the organic solvents exhibited three types of modulation effect: anisotropic growth, anisotropic growth/formation of new crystalline phase and the formation of new crystalline phase solely, which was due to the variation of their binding ability with metal cations. The following study revealed that the binding ability was critically affected by their functional groups and molecular size. Moreover, their modulation effect could be finely tuned by changing volume ratios of solvent mixtures. Furthermore, they could be applied for modulating other metal-carboxylates CPs: Co-1,3,5-benzenetricarboxylic (BTC), Zn-pydc and Eu-pydc etc. Additionally, the as-prepared Co-pydc CPs showed a fascinating morphology-dependent antiferromagnetic behavior.

Solvent induced rapid modulation of micro/nano structures of metal carboxylates coordination polymers: mechanism and morphology dependent magnetism

PubMed Central

Liu, Kun; Shen, Zhu-Rui; Li, Yue; Han, Song-De; Hu, Tong-Liang; Zhang, Da-Shuai; Bu, Xian-He; Ruan, Wen-Juan

2014-01-01

Rational modulation of morphology is very important for functional coordination polymers (CPs) micro/nanostructures, and new strategies are still desired to achieve this challenging target. Herein, organic solvents have been established as the capping agents for rapid modulating the growth of metal-carboxylates CPs in organic solvent/water mixtures at ambient conditions. Co-3,5-pyridinedicarboxylate (pydc) CPs was studied here as the example. During the reaction, the organic solvents exhibited three types of modulation effect: anisotropic growth, anisotropic growth/formation of new crystalline phase and the formation of new crystalline phase solely, which was due to the variation of their binding ability with metal cations. The following study revealed that the binding ability was critically affected by their functional groups and molecular size. Moreover, their modulation effect could be finely tuned by changing volume ratios of solvent mixtures. Furthermore, they could be applied for modulating other metal-carboxylates CPs: Co-1,3,5-benzenetricarboxylic (BTC), Zn-pydc and Eu-pydc etc. Additionally, the as-prepared Co-pydc CPs showed a fascinating morphology-dependent antiferromagnetic behavior. PMID:25113225

Coordination-driven self-assembly of a novel carbonato-bridged heteromolecular neutral nickel(II) triangle by atmospheric CO2 fixation.

PubMed

Mukherjee, Pampa; Drew, Michael G B; Estrader, Marta; Ghosh, Ashutosh

2008-09-01

Formation of a quasi-symmetrical mu 3-carbonato-bridged self-assembled heteromolecular triangle of Ni(II), [(mu 3-CO 3){Ni 2(salmeNH) 2(NCS) 2}{Ni(salmeNH 2) 2].Et 2O.H 2O (HsalmeNH = 2-[(3-methylamino-propylimino)-methyl]-phenol) involves atmospheric CO 2 uptake in a neutral medium, by spontaneous self-reorganization of the starting mononuclear Ni(II)-Schiff-base complex, [Ni(salmeNH) 2]. The environment around Ni(II) in two of the subunits is different from the third one. The starting complex, [Ni(salmeNH) 2], and one of the possible intermediate species, [Ni(salmeNH 2) 2(NCS) 2], which has a very similar coordination environment to that in the third Ni(II) center, have been characterized structurally. A plausible mechanism for the formation of such a triangle has also been proposed. The compound shows a very strong antiferromagnetic coupling. Fit as a regular triangular arrangement gave J = -53.1, g = 2.24, and R = 1.5 x 10 (-4).

[The formation of the self-maintenance skills in the pre-school children presenting with locomotor and coordination disorders].

PubMed

Poletaeva-Dubrovina, N A; Burkova, A M

2016-01-01

The Ministry of Health of the Russian Federation acknowledges the sharp rise in the prevalence of congenital malformation in this country during the past 30 years. In 2010-2011, this pathology was estimated to occur in 3% of the children. It includes a variety of locomotor and coordination disorders of which the most widespread are infantile cerebral paralysis, ataxia, consequences of perinatal lesions of the central nervous system, etc. This article contains a detailed description of these locomotor and coordination disorders. The objective of the present work was to elaborate and evaluate the program for the formation of the self-maintenance skills in the pre-school children presenting with locomotor and coordination disorders under conditions of family guidance and education. The study was carried out from September 2013 till May 2014 based at MUP DOD "Semeiny klub Nadezhda" ("The Hope Family Club", Municipal unitary facility for children's additional education) and supported by B.N. El'tsin Ural Federal University. It included 10 children suffering from locomotor and coordination disorders of different severity and members of their families. The following methods were used: the self-service skills scorecard , monitoring formation of the motor skills, and Wilcoxon's T-test. The use of the program based on the cooperation with the children's families allowed to achieve positive dynamics in the patients' conditions. Moreover, 30% of them acquired the full scope of the self-maintenance skills. The most pronounced changes in the motor abilities were apparent in the movements of the upper and lower extremitis, walking, and motion in space. The proposed program for the formation of the self-maintenance skills in the pre-school children presenting with locomotor and coordination disorders proved to be highly efficacious. The study has demonstrated the importance of the parents' involvement in the process of formation of the self-maintenance skills and motor abilities. It is concluded that the formation of the self-maintenance skills and locomotor abilities are two interdependent processes.

Mesostructure of Ordered Corneal Nano-nipple Arrays: The Role of 5-7 Coordination Defects

NASA Astrophysics Data System (ADS)

Lee, Ken C.; Yu, Qi; Erb, Uwe

2016-06-01

Corneal nano-nipple structures consisting of hexagonally arranged protrusions with diameters around 200 nm have long been known for their antireflection capability and have served as biological blueprint for solar cell, optical lens and other surface designs. However, little is known about the global arrangement of these nipples on the ommatidial surface and their growth during the eye development. This study provides new insights based on the analysis of nano-nipple arrangements on the mesoscale across entire ommatidia, which has never been done before. The most important feature in the nipple structures are topological 5- and 7-fold coordination defects, which align to form dislocations and interconnected networks of grain boundaries that divide the ommatidia into crystalline domains in different orientations. Furthermore, the domain size distribution might be log-normal, and the domains demonstrate no preference in crystal orientation. Both observations suggest that the nipple growth process may be similar to the nucleation and growth mechanisms during the formation of other crystal structures. Our results are also consistent with the most recently proposed Turing-type reaction-diffusion process. In fact, we were able to produce the key structural characteristics of the nipple arrangements using Turing analysis from the nucleation to the final structure development.

MaROS Strategic Relay Planning and Coordination Interfaces

NASA Technical Reports Server (NTRS)

Allard, Daniel A.

2010-01-01

The Mars Relay Operations Service (MaROS) is designed to provide planning and analysis tools in support of ongoing Mars Network relay operations. Strategic relay planning requires coordination between lander and orbiter mission ground data system (GDS) teams to schedule and execute relay communications passes. MaROS centralizes this process, correlating all data relevant to relay coordination to provide a cohesive picture of the relay state. Service users interact with the system through thin-layer command line and web user interface client applications. Users provide and utilize data such as lander view periods of orbiters, Deep Space Network (DSN) antenna tracks, and reports of relay pass performance. Users upload and download relevant relay data via formally defined and documented file structures including some described in Extensible Markup Language (XML). Clients interface with the system via an http-based Representational State Transfer (ReST) pattern using Javascript Object Notation (JSON) formats. This paper will provide a general overview of the service architecture and detail the software interfaces and considerations for interface design.

Mercury coordination polymers with flexible ethane-1,2-diyl-bis-(pyridyl-3-carboxylate): Synthesis, structures, thermal and luminescent properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vallejos, Javier; Brito, Iván, E-mail: ivanbritob@yahoo.com; Cárdenas, Alejandro

2015-03-15

The reaction of the flexible ligand, ethane-1,2-diyl-bis-(pyridyl-3-carboxylate), (L) with HgI{sub 2} and HgBr{sub 2} salts under the same experimental conditions leads to the formation of two coordination polymers with different motifs: ([Hg(L)(Br{sub 2})]){sub n}(1) and ([Hg(L)(I{sub 2})]){sub n}(2). In both compounds, the ligand, (L) acts in a μ2-N:N′-bidentate fashion to link HgBr{sub 2} and HgI{sub 2} units to form a linear and helical chain motif, along [1 0 0] for (1) and [0 0 1] for (2). The ethylene moiety of (L) has gauche and trans conformation in compounds (1) and (2), respectively. The flexible conformation of L produces differencesmore » in the optical and crystal properties of the two compounds. - Graphical abstract: This work demonstrates how the HgX{sub 2} units are coordinates by bi-dentate ligand forming polymeric coordination complexes by self-assembly of both chemical units.- Highlights: • News 1-D d{sup 10} transition metal coordination polymers. • The photoluminescent properties have been measured. • The thermal properties have been measured.« less

Synthesis of CuO by Cu-CPPs with the determination of Cu(II) coordination modes from a novel complex of [Cu(terpyOH){sub 2}]·(HBTC)·2H{sub 2}O

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yu, E-mail: wangyu1012@hit.edu.cn; Chen, Gang, E-mail: gchen@hit.edu.cn; Han, Li

2013-10-15

In this study, we investigated the synthesis of CuO microrods by simple calcination of copper-based coordination polymer particles (Cu-CPPs) at high temperature in air. The photocatalytic activity of the CuO microrods was tested by the decomposition of aqueous solution of RhB, which was completely decomposed by irradiation with light. To analyze the relationship of metal ions and ligands in the Cu-CPPs, the single crystal of [Cu(terpyOH){sub 2}]∙(HBTC)∙2H{sub 2}O (1) (terpyOH=4′-hydroxy-2,2′:6′,2″-terpyridine, BTC=1,3,5-benzene tricarboxylate) was first prepared and characterized by X-ray single crystal structural analysis. A variety of hydrogen bonds constructing the 3D complex structure in [Cu(terpyOH){sub 2}]∙(HBTC)∙2H{sub 2}O (1) were observed.more » - Graphical abstract: Demonstrating a general method to synthesize CuO microrods via simple calcination of Cu-CPPs and Cu(II) coordination modes from a novel complex of [Cu(terpyOH){sub 2}]∙(HBTC)·2H{sub 2}O constructed by hydrogen bonding. Display Omitted - Highlights: • The formation of microrods CuO from thermal treatment of Cu-CPPs through an “escape-by-crafty-scheme” strategy has been studied. • Determination of Cu(II) coordination modes in Cu-CPPs from a novel complex of [Cu(terpyOH){sub 2}]∙(HBTC) 2H{sub 2}O. • Invested the behave of hydrogen bonding to construct the 3D complex structure. • Commendable photodegradation performance was observed.« less

Short-range structure and cation bonding in calcium-aluminum metaphosphate glasses.

PubMed

Schneider, J; Oliveira, S L; Nunes, L A O; Bonk, F; Panepucci, H

2005-01-24

Comprehension of short- and medium-range order of phosphate glasses is a topic of interest, due to the close relation between network structure and mechanical, thermal, and optical properties. In this work, the short-range structure of glasses (1 - x)Ca(PO(3))(2).xAl(PO(3))(3) with 0 < or = x < or = 0.47 was studied using solid-state nuclear magnetic resonance spectroscopy, Raman spectroscopy, density measurements, and differential scanning calorimetry. The bonding between a network modifier species, Al, and the network forming phosphate groups was probed using high-resolution nuclear magnetic resonance spectroscopy of (27)Al and (31)P. Changes in the compositional behavior of the density, glass transition temperature, PO(2) symmetric vibrations, and Al coordination number were verified at around x = 0.30. (31)P NMR spectra show the presence of phosphorus in Q(2) sites with nonbridging oxygens (NBOs) coordinated by Ca ions and also Q(2) sites with one NBO coordinated by Al (namely, Q(2)(1Al)). The changes in the properties as a function of x can be understood by considering the mean coordination number measured for Al and the formation of only Q(2) and Q(2)(1Al) species. It is possible to calculate that a network formed only by Q(2)(1Al) phosphates can just exist up to the upper limit of x = 0.48. Above this value, Q(2)(2Al) species should appear, imposing a major reorganization of the network. Above x = 0.30 the network undergoes a progressive reorganization to incorporate Al ions, maintaining the condition that only Q(2)(1Al) species are formed. These observations support the idea that bonding principles for cationic species inferred originally in binary phosphate glasses can also be extended to ternary systems.

Structure and thermodynamics of uranium-containing iron garnets

DOE PAGES

Guo, Xiaofeng; Navrotsky, Alexandra; Kukkadapu, Ravi K.; ...

2016-09-15

Use of crystalline garnet as a waste form phase appears to be advantageous for accommodating actinides from nuclear waste. Previous studies show that large amounts of uranium (U) and its analogues such as cerium (Ce) and thorium (Th) can be incorporated into the garnet structure. In this study, we synthesized U loaded garnet phases, Ca 3U xZr 2–xFe 3O 12 (x = 0.5–0.7), along with the endmember phase, Ca 3(Zr 2)SiFe 3+ 2O 12, for comparison. The oxidation states of U were determined by X-ray photoelectron and absorption spectroscopies, revealing the presence of mixed pentavalent and hexavalent uranium in themore » phases with x = 0.6 and 0.7. The oxidation states and coordination environments of Fe were measured using transmission 57Fe-Mössbauer spectroscopy, which shows that all iron is tetrahedrally coordinated Fe 3+. U substitution had a significant effect on local environments, the extent of U substitution within this range had a minimal effect on the structure, and unlike in the x = 0 sample, Fe exists in two different environments in the substituted garnets. The enthalpies of formation of garnet phases from constituent oxides and elements were first time determined by high temperature oxide melt solution calorimetry. The results indicate that these substituted garnets are thermodynamically stable under reducing conditions. Furthermore, our structural and thermodynamic analysis further provides explanation for the formation of natural uranium garnet, elbrusite-(Zr), and supports the potential use of Ca 3U xZr 2–xFe 3O 12 as viable waste form phases for U and other actinides.« less

Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

USGS Publications Warehouse

Blackwell, C.D.

1988-01-01

Codes for the unique identification of public and private organizations listed in computerized data systems are presented. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), National Cartographic Information Center (NCIC), and Office of Water Data Coordination (OWDC). The format structure of the codes is discussed and instructions are given for requesting new books. (Author 's abstract)

Studying Venus using a GIS database

NASA Technical Reports Server (NTRS)

Price, Maribeth; Suppe, John

1993-01-01

A Geographic Information System (GIS) can significantly enhance geological studies on Venus because it facilitates concurrent analysis of many sources of data, as demonstrated by our work on topographic and deformation characteristics of tesserae. We are creating a database of structures referenced to real-world coordinates to encourage the archival of Venusian studies in digital format and to foster quantitative analysis of many combinations of data. Contributions to this database from all aspects of Venusian science are welcome.

Porphyrin coordination polymer nanospheres and nanorods

DOEpatents

Wang, Zhongchun; Shelnutt, John A.; Medforth, Craig J.

2012-12-04

A porphyrin coordination polymer nanostructure comprising a network of pyridyl porphyrin molecules and coordinating metal ions coordinatively bound through the pyridyl groups. In some embodiments, the porphyrins are metalloporphyrins. A variety of nanostructures are formed by the network polymer, including nanospheres, polygonal nanostructures, nanorods, and nanofibers, depending on a variety of factors including coordination metal ion, porphyrin type, metal of the metalloporphyrin, and degree of agitation during nanostructure formation. Reduction of coordinating metal ions may be used to form metal nanoparticles on the coordination polymer nanostructure.

Porphyrin coordination polymer nanospheres and nanorods

DOEpatents

Wang, Zhongchun; Shelnutt, John A.; Medforth, Craig J.

2013-09-10

A porphyrin coordination polymer nanostructure comprising a network of pyridyl porphyrin molecules and coordinating metal ions coordinatively bound through the pyridyl groups. In some embodiments, the porphyrins are metalloporphyrins. A variety of nanostructures are formed by the network polymer, including nanospheres, polygonal nanostructures, nanorods, and nanofibers, depending on a variety of factors including coordination metal ion, porphyrin type, metal of the metalloporphyrin, and degree of agitation during nanostructure formation. Reduction of coordinating metal ions may be used to form metal nanoparticles on the coordination polymer nanostructure.

Curriculum renewal in child psychiatry.

PubMed

Hanson, M; Tiberius, R; Charach, A; Ulzen, T; Sackin, D; Jain, U; Reiter, S; Shomair, G

1999-11-01

To ensure uniform design and evaluation of a clerkship curriculum for child and adolescent psychiatry teaching common disorders and problems in an efficient manner across 5 teaching sites and to include structures for continuous improvement. The curriculum committee selected for course inclusion disorders and problems of child psychiatry that were commonly encountered by primary care physicians. Instruction methods that encouraged active student learning were selected. Course coordination across sites was encouraged by several methods: involving faculty, adopting a centralized examination format, and aligning teaching methods with examination format. Quantitative and qualitative methods were used to measure students' perceptions of the course's value. These evaluative results were reviewed, and course modifications were implemented and reevaluated. The average adjusted student return rate for course evaluation questionnaires for the 3-year study period was 63%. Clerks' ratings of course learning value demonstrated that the course improved significantly and continually across all sites, according to a Scheffé post-hoc analysis. Analysis of student statements from focus-group transcripts contributed to course modifications, such as the Brief Focused Interview (BFI). Our curriculum in child psychiatry, which focused on common problems and used active learning methods, was viewed as a valuable learning experience by clinical clerks. Curriculum coordination across multiple teaching sites was accomplished by including faculty in the process and by using specific teaching and examination strategies. Structures for continuous course improvement were effective.

Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs.

PubMed

Santamaría-Díaz, Noelia; Méndez-Arriaga, José M; Salas, Juan M; Galindo, Miguel A

2016-05-17

The oligonucleotide d(TX)9 , which consists of an octadecamer sequence with alternating non-canonical 7-deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double-stranded DNA through the formation of hydrogen-bonded Watson-Crick base pairs. dsDNA with metal-mediated base pairs was then obtained by selectively replacing W-C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag(+) ions, and its stability is significantly enhanced in the presence of Ag(+) ions while its double-helix structure is retained. Temperature-dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)-mediated base pairs. This strategy could become useful for preparing stable metallo-DNA-based nanostructures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molybdenum Valence in Basaltic Silicate Melts: Effects of Temperature and Pressure

NASA Technical Reports Server (NTRS)

Danielson, L. R.; Righter, K.; Newville, M.; Sutton, S.; Choi, Y.; Pando, K.

2011-01-01

The metal-silicate partitioning behavior of molybdenum has been used as a test for equilibrium core formation hypotheses [for example, 1-6]. However, current models that apply experimental data to equilibrium core-mantle differentiation infer the oxidation state of molybdenum from solubility data or from multivariable coefficients from metal-silicate partitioning data [1,3,7]. Molybdenum, a multi-valent element with a valence transition near the fO2 of interest for core formation (approx.IW-2) will be sensitive to changes in fO2 of the system and silicate melt structure. In a silicate melt, Mo can occur in either 4+ or 6+ valence state, and Mo(6+) can be either octahedrally or tetrahedrally coordinated. Here we present X-ray absorption near edge structure (XANES) measurements of Mo valence in basaltic run products at a range of P, T, and fO2 and further quantify the valence transition of Mo.

Acenaphthenequinone thiosemicarbazone and its transition metal complexes: synthesis, structure, and biological activity.

PubMed

Rodriguez-Argüelles, M C; Belicchi Ferrari, M; Gasparri Fava, G; Pelizzi, C; Pelosi, G; Albertini, R; Bonati, A; Dall'Aglio, P P; Lunghi, P; Pinelli, S

1997-04-01

The reaction of iron, nickel, copper, and zinc chlorides or acetates with acenaphthenequinone thiosemicarbazone, Haqtsc leads to the formation of novel complexes that have been characterized by spectroscopic studies (NMR, IR) and biological properties. The crystal structures of the free ligand Haqtsc 1 and of the compound [Ni(aqtsc)2].DMF 2, have also been determined by X-ray methods from diffractometer data. In 1, the conformation of the two nonequivalent molecules is governed by intramolecular hydrogen bonds, while an intermolecular hydrogen bond is responsible for dimer-like groups formation. In 2, the coordination geometry about nickel is distorted octahedral, and the two ligand molecules are terdentate monodeprotonated. Biological studies have shown that, for the first time at least up the used doses, a free ligand is active both in the inhibition of cell proliferation and in the induced differentiation on Friend erythroleukemia cells (FLC).

ORPC RivGen Hydrokinetic Turbine Wake Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomson, Jim; Guerra, Maricarmen

Field measurements of mean flow and turbulence parameters at the Kvichak river prior to and after the deployment of ORPC's RivGen hydrokinetic turbine. Data description and turbine wake analysis are presented in the attached manuscript "Wake measurements from a hydrokinetic river turbine" by Guerra and Thomson (recently submitted to Renewable Energy). There are three data sets: NoTurbine (prior to deployment), Not_Operational_Turbine (turbine underwater, but not operational), and Operational_Turbine. The data has been quality controlled and organized into a three-dimensional grid using a local coordinate system described in the paper. All data sets are in Matlab format (.mat). Variables available inmore » the data sets are: qx: X coordinate matrix (m) qy: Y coordinate matrix (m) z : z coordinate vector (m) lat : grid cell latitude (degrees) lon: grid cell longitude (degrees) U : velocity magnitude (m/s) Ux: x velocity (m/s) Vy: y velocity (m/s) W: vertical velocity (m/s) Pseudo_beam.b_i: pseudo-along beam velocities (i = 1 to 4) (m/s) (structure with raw data within each grid cell) beam5.b5: 5th-beam velocity (m/s) (structure with raw data within each grid cell) tke: turbulent kinetic energy (m2/s2) epsilon: TKE dissipation rate (m2/s3) Reynolds stresses: uu, vv, ww, uw, vw (m2/s2) Variables from the Not Operational Turbine data set are identified with _T Variables from the Operational Turbine data set are identified with _TO« less

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

A quasi-hexagonal prism-shaped carbon nitride for photoreduction of carbon dioxide under visible light.

PubMed

He, Zhiqiao; Wang, Danfen; Tang, Juntao; Song, Shuang; Chen, Jianmeng; Tao, Xinyong

2017-03-01

A quasi-hexagonal prism-shaped carbon nitride (H-C 3 N 4 ) was synthesized from urea-derived C 3 N 4 (U-C 3 N 4 ) using an alkaline hydrothermal process. U-C 3 N 4 decomposition followed by hydrogen bond rearrangement of hydrolyzed products leads to the formation of a quasi-hexagonal prism-shaped structure. The H-C 3 N 4 catalysts displayed superior activity in the photoreduction of CO 2 with H 2 O compared to U-C 3 N 4 . The enhanced photocatalytic activities can be attributed to the promotion of incompletely coordinated nitrogen atom formation in the C 3 N 4 molecules. Graphical abstract ᅟ.

Bacterial surface adaptation

NASA Astrophysics Data System (ADS)

Utada, Andrew

2014-03-01

Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

Synthesis and Visible-Light Photocatalytic Activity of CeO₂ Nanoboxes Based on Pearson’s Principle.

PubMed

Ge, Shengsong; Bao, Liwei; Shao, Qian; Zhang, Qiaoxia; Liu, Zingyun

2017-01-01

The CeO₂ nanoboxes with well-defined hollow structure were fabricated by template-engaged coordinating etching of Cu₂O cubes based on Pearson’s hard and soft acid-base principle. The morphologically uniform CeO₂ nanoboxes have an average edge length of 400 nm and shell thickness of around 60 nm. The strong chemical affinity between Cu+ and S₂O(2− 3) was the driving force for the etching of Cu₂O templates and the formation of shells. A possible formation mechanism of CeO₂ nanoboxes was proposed. The synthesized CeO₂ nanoboxes exhibit good photocatalytic activity for photodegradation of acid orange 7 (AO 7) under visible light irradiation.

Polarization-phase diagnostics of latent course of cholelithiasis in patients with chronic cholecystitis combined with diabetes mellitus type 2

NASA Astrophysics Data System (ADS)

Fediv, O. I.; Ivashchuk, O. I.; Marchuk, Yu. F.; Andriychuk, D. R.

2011-09-01

The principles of optical model of human bile polycrystalline structure are described. The three optical levels - isotropic, liquid-crystal and solid-crystal have been proposed. It has been introduced and proposed the scenarios of phase distribution formation in the boundary field of laser radiation, transformed by bile layers. The experimental scheme of direct measurement of coordinate phase distributions has been presented. The results of investigating the interrelation between the values of correlation and fractal parameters are presented. They characterize the coordinate distributions of phase shifts between the orthogonal components of the amplitude in the points of laser images of bile smears of cholelithiasis patients in combination with other pathologies. The diagnostic criteria of the cholelithiasis nascency and its severity degree differentiation are determined.

A new heterometallic hybrid based on polymeric iodoplumbate and lanthanide metal-carboxylic coordination polycation

NASA Astrophysics Data System (ADS)

Gong, An-Weng; Wu, Hong-Yan; Lian, Zhao-Xun; Dong, Hai-Jun; Li, Hao-Hong; Chen, Zhi-Rong

2013-03-01

A 3-D supramolecular hybrid {[La(EPC)3(H2O)3]2(Pb6I18)}n (EPC+ = N-ethyl-pyridium-4-carboxylate) (1) has been structurally determined, which assume significance for its incorporating lanthanide metal-carboxylic coordination polycation into polymeric iodoplumbate to get heterometallics. 1 consists of 1-D (PbI)n6n- zigzag-like anion chains with lanthanide metalcarboxylic [La(EPC)3(HO)3]n3n+ polycations, which arrange in a criss-cross configuration. C-H⋯I and C-H⋯O hydrogen bonds among inorganic anions and polycations contribute to the formation of a 3-D supramolecular framework. Moreover, the framework displays an absorption edge at 2.46 eV which is comparable to PbI2's absorption edge.

Ti K-edge EXAFS and XANES study on tektites from different strewnfields

NASA Astrophysics Data System (ADS)

Wang, L.; Furuta, T.; Okube, M.; Yoshiasa, A.

2011-12-01

The concentration and local structure of each element may have various kinds of information about the asteroid impact and mass extinction. Farges and Brown have discussed about the Ti local structure by XANES, and concluded that Ti in tektite occupies 4-coordinated site. EXAFS can be analyzed to give precise information about the distance from Ti to near neighbors. The XAFS measurement of Ti local structure was preformed at the beamline 9C of the Photon Factory in KEK, Tsukuba, Japan. The specimens of tektites are from different strewnfields, they are: indochinite, bediasite, hainanite, philippinite, australite and moldavite. Sample for comparison are Libya desert glass and suevite. The k3χ(k) function was transformed into the radial structure function (RSF) for Ti K-edge of six tektites. The RSF for the Ti atom in indochinite and bediasite are similar; hainanite, australite and philippinite are similar; and moldavite is discriminated from others. It indicates that they have the same local atomic environmental around the Ti atoms and extended structure respectively. Coordination numbers and radial structure function are determined by EXAFS analyses (Table 1). We classified the tektites in three types: in indochinite and bediasite, Ti occupies 4-coordinated tetrahedral site and Ti-O distances are 1.84-1.81 Å; in hainanite, australite and philippinite, Ti occupies 5-coordinated trigonal bi-pyramidal or tetragonal pyramidal site and Ti-O distances are 1.92-1.87 Å; in moldavite, Ti occupies the 6-coordinated octahedral site and Ti-O distance is 2.00-1.96 Å. Formation of tektites is related to the impact process. It is generally recognized that tektites were formed under higher temperature and high pressure. But through this study, local structures of Ti are differing in three strewnfields and even different locations of the same strewnfield. What caused the various local structures will be another topic of tektite studies. Local structure of Ti may be changed in the impact event and the following stage. Tektites splashed to the space and travel in several kinds of processes and routes, which lead to different temperature and pressure history. Local structure of Ti should be related with the temperature, pressure, quenching rate, sizes of impact meteorite and size of falling melts. [1] Koeberl. Ann.Rev.Earth Planet.Sci. 14, 323-350 (1986) [2] François Farges & Gordon E. Brown Jr Geochim. Cosmo. Acta.61, 1863-1870 (1997). [3]Paris, E., Dingwell, D., Seifert, F., Mottana, A. & Romano, C. (1994). Phys. Chem. Miner. 21, 520-525.
Table 1 Structure parameters determined by EXAFS

Structure of liquid tricalcium aluminate

NASA Astrophysics Data System (ADS)

Drewitt, James W. E.; Barnes, Adrian C.; Jahn, Sandro; Kohn, Simon C.; Walter, Michael J.; Novikov, Alexey N.; Neuville, Daniel R.; Fischer, Henry E.; Hennet, Louis

2017-02-01

The atomic-scale structure of aerodynamically levitated and laser-heated liquid tricalcium aluminate (Ca3Al2O6 ) was measured at 2073(30) K by using the method of neutron diffraction with Ca isotope substitution (NDIS). The results enable the detailed resolution of the local coordination environment around calcium and aluminum atoms, including the direct determination of the liquid partial structure factor, SCaCa(Q ) , and partial pair distribution function, gCaCa(r ) . Molecular dynamics (MD) simulation and reverse Monte Carlo (RMC) refinement methods were employed to obtain a detailed atomistic model of the liquid structure. The composition Ca3Al2O6 lies at the CaO-rich limit of the CaO:Al2O3 glass-forming system. Our results show that, although significantly depolymerized, liquid Ca3Al2O6 is largely composed of AlO4 tetrahedra forming an infinite network with a slightly higher fraction of bridging oxygen atoms than expected for the composition. Calcium-centered polyhedra exhibit a wide distribution of four- to sevenfold coordinated sites, with higher coordinated calcium preferentially bonding to bridging oxygens. Analysis of the MD configuration reveals the presence of ˜10 % unconnected AlO4 monomers and Al2O7 dimers in the liquid. As the CaO concentration increases, the number of these isolated units increases, such that the upper value for the glass-forming composition of CaO:Al2O3 liquids could be described in terms of a percolation threshold at which the glass can no longer support the formation of an infinitely connected AlO4 network.

Coordination Covalent Frameworks: A New Route for Synthesis and Expansion of Functional Porous Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elsaidi, Sameh K.; Mohamed, Mona H.; Loring, John S.

The synthetic approaches for fine-tuning the structural properties of coordination polymers or metal organic frameworks have exponentially grown during the last decade. This is due to the control over the properties of the resulting structures such as stability, pore size, pore chemis-try and surface area for myriad possible applications. Herein, we present a new class of porous materials called Covalent Coordination Frameworks (CCFs) that were designed and effectively synthesized using a two-step reticular chemistry approach. During the first step, trigonal prismatic molecular building block was isolated using 4-aminobenazoic acid and Cr (III) salt, subsequently in the second step the polymerizationmore » of the isolated molecular building blocks (MBBs) takes place by the formation of strong covalent bonds where small organic molecules can connect the MBBs forming extended porous CCF materials. All the isolated CCFs were found to be permanently porous while the discrete MBB were non-porous. This approach would inevitably open a feasible path for the applications of reticular chemistry and the synthesis of novel porous materials with various topologies under ambient conditions using simple organic molecules and versatile MBBs with different functionalities which would not be possible using the traditional one step approach« less

Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase.

PubMed

Shomura, Yasuhito; Yoon, Ki-Seok; Nishihara, Hirofumi; Higuchi, Yoshiki

2011-10-16

Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2) → 2H(+) + 2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32 Å. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme.

Four-coordinate, 14-electron Ru(II) complexes: unusual trigonal pyramidal geometry enforced by bis(phosphino)silyl ligation.

PubMed

MacInnis, Morgan C; McDonald, Robert; Ferguson, Michael J; Tobisch, Sven; Turculet, Laura

2011-08-31

Unprecedented diamagnetic, four-coordinate, formally 14-electron (Cy-PSiP)RuX (Cy-PSiP = [κ(3)-(2-R(2)PC(6)H(4))(2)SiMe](-); X = amido, alkoxo) complexes that do not require agostic stabilization and that adopt a highly unusual trigonal pyramidal coordination geometry are reported. The tertiary silane [(2-Cy(2)PC(6)H(4))(2)SiMe]H ((Cy-PSiP)H) reacted with 0.5 [(p-cymene)RuCl(2)](2) in the presence of Et(3)N and PCy(3) to afford [(Cy-PSiP)RuCl](2) (1) in 74% yield. Treatment of 1 with KO(t)Bu led to the formation of (Cy-PSiP)RuO(t)Bu (2, 97% yield), which was crystallographically characterized and shown to adopt a trigonal pyramidal coordination geometry in the solid state. Treatment of 1 with NaN(SiMe(3))(2) led to the formation of (Cy-PSiP)RuN(SiMe(3))(2) (3, 70% yield), which was also found to adopt a trigonal pyramidal coordination geometry in the solid state. The related anilido complexes (Cy-PSiP)RuNH(2,6-R(2)C(6)H(3)) (4, R = H; 5, R = Me) were also prepared in >90% yields by treating 1 with LiNH(2,6-R(2)C(6)H(3)) (R = H, Me) reagents. The solid state structure of 5 indicates a monomeric trigonal pyramidal complex that features a C-H agostic interaction. Complexes 2 and 3 were found to react readily with 1 equiv of H(2)O to form the dimeric hydroxo-bridged complex [(Cy-PSiP)RuOH](2) (6, 94% yield), which was crystallographically characterized. Complexes 2 and 3 also reacted with 1 equiv of PhOH to form the new 18-electron η(5)-oxocyclohexadienyl complex (Cy-PSiP)Ru(η(5)-C(6)H(5)O) (7, 84% yield). Both amido and alkoxo (Cy-PSiP)RuX complexes reacted with H(3)B·NHRR' reagents to form bis(σ-B-H) complexes of the type (Cy-PSiP)RuH(η(2):η(2)-H(2)BNRR') (8, R = R' = H; 9, R = R' = Me; 10, R = H, R' = (t)Bu), which illustrates that such four-coordinate (Cy-PSiP)RuX (X = amido, alkoxo) complexes are able to undergo multiple E-H (E = main group element) bond activation steps. Computational methods were used to investigate structurally related PCP, PPP, PNP, and PSiP four-coordinate Ru complexes and confirmed the key role of the strongly σ-donating silyl group of the PSiP ligand set in enforcing the unusual trigonal pyramidal coordination geometry featured in complexes 2-5, thus substantiating a new strategy for the synthesis of low-coordinate Ru species. The mechanism of the activation of ammonia-borane by such low-coordinate (R-PSiP)RuX (X = amido, alkoxo) species was also studied computationally and was determined to proceed most likely in a stepwise fashion via intramolecular deprotonation of ammonia and subsequent borane B-H bond oxidative addition steps.

Crystal structure of a looped-chain CoII coordination polymer: catena-poly[[bis-(nitrato-κO)cobalt(II)]bis-[μ-bis-(pyridin-3-ylmeth-yl)sulfane-κ2N:N'

PubMed

Moon, Suk-Hee; Seo, Joobeom; Park, Ki-Min

2017-11-01

The asymmetric unit of the title compound, [Co(NO 3 ) 2 (C 12 H 12 N 2 S) 2 ] n , contains a bis-(pyridin-3-ylmeth-yl)sulfane ( L ) ligand, an NO 3 - anion and half a Co II cation, which lies on an inversion centre. The Co II cation is six-coordinated, being bound to four pyridine N atoms from four symmetry-related L ligands. The remaining coordination sites are occupied by two O atoms from two symmetry-related nitrate anions in a monodentate manner. Thus, the Co II centre adopts a distorted octa-hedral geometry. Two symmetry-related L ligands are connected by two symmetry-related Co II cations, forming a 20-membered cyclic dimer, in which the Co II atoms are separated by 10.2922 (7) Å. The cyclic dimers are connected to each other by sharing Co II atoms, giving rise to the formation of an infinite looped chain propagating along the [101] direction. Inter-molecular C-H⋯π (H⋯ring centroid = 2.89 Å) inter-actions between one pair of corresponding L ligands and C-H⋯O hydrogen bonds between the L ligands and the nitrate anions occur in the looped chain. In the crystal, adjacent looped chains are connected by inter-molecular π-π stacking inter-actions [centroid-to-centroid distance = 3.8859 (14) Å] and C-H⋯π hydrogen bonds (H⋯ring centroid = 2.65 Å), leading to the formation of layers parallel to (101). These layers are further connected through C-H⋯O hydrogen bonds between the layers, resulting in the formation of a three-dimensional supra-molecular architecture.

Synthesis and characterization of two novel chiral-type formate frameworks templated by protonated diethylamine and ammonium cations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mączka, Mirosław, E-mail: m.maczka@int.pan.wroc.pl; Gągor, Anna; Hanuza, Jerzy

2017-01-15

Two novel formate frameworks templated by ammonium and diethylammonium (DEtA{sup +}) cations have been synthesized. Chemical analysis as well as optical, Raman and IR studies showed partial substitution of nickel ions by Cr(III) or Fe(III). X-ray diffraction revealed that these compounds crystallize in the chiral-type structure of P6{sub 3}22 symmetry. The oxygen atoms from formate ligands form octahedral coordination around the metal centers and the octahedra are bridged by the formate groups in the anti-anti mode configuration forming the hexagonal structure with large channels expanding along the c direction. The channels are filled with disordered DEtA{sup +} and NH{sub 4}{supmore » +} ions and they show unusual compression with the c/a ratio of only 0.862 and 0.852 for the iron- and chromium-containing compound, respectively. Magnetic studies revealed that the both compounds order magnetically at low temperatures but the ordering temperature is significantly higher for the iron compound (37 K) compared to the chromium analogue (26 K). - Graphical abstract: Temperature dependence of magnetization M of DEtAFeNi showing magnetic order at 37 K. - Highlights: • Two novel chiral formates of P6{sub 3}22 symmetry were synthesized. • The structures contain strongly compressed hexagonal channels filled with disordered cations. • The obtained compounds exhibit magnetic order at low temperatures. • Raman, IR and absorption spectra prove incorporation of Cr(III) and Fe(III) in the frameworks.« less

System of Monitoring Potential Deceased Organ Donations in Over 200 Hospitals in Poland Using a Web Tool: Implementation and Structure.

PubMed

Danek, T; Protasiuk, R; Mańkowski, M; Brutkiewicz, A; Trześniewski, R; Podlińska, I; Milecka, A; Jonas, M; Danielewicz, R; Czerwiński, J

2016-06-01

In 2010 the formation of the Polish Hospitals Network of Organ Donation Coordinators, originated by Poltransplant, began. One of the goals of this project is to report all deaths in hospital ICUs in which a coordinator is posted. The aim of this strategy is to monitor donation potential, following the recruitment process of potential donors and indicating stages of that process that may be improved to increase effective recruitment. Until the end of 2014 all data were forwarded to Poltransplant as Excel files, but since January 1, 2015, reporting and data collection have been are performed using web tool www.koordynator.net. The aim of the paper is to present the essentials in functioning principles, structure, and usage of the www.koordynator.net system, its technical construction, and to display good practices (know-how) tested by 1 country, for countries such as Poland, that contend with organ insufficiency. The application www.koordynator.net allows for remote addition of individual records with information about deceased patients in hospital ICUs, the forwarding of data about potential and actual organ donors, the generation of complete reports about deceased patients in each hospital monthly, and the introduction of historical data. Introduction of a potential donation monitoring system in 209 hospitals with transplant coordinators increases the number of identified potential and effective actual donors due to self-assessment analysis. Eventually, the www.koordynator.net reporting system allowed for external evaluation by coordinators from other hospitals, regional coordinators, and Poltransplant. The system is a modern tool that improves and increases the quality system in the organ donation field (quality assurance program). Copyright © 2016 Elsevier Inc. All rights reserved.

Crown Ether Complexes of Alkali-Metal Chlorides from SO2.

PubMed

Reuter, Kirsten; Rudel, Stefan S; Buchner, Magnus R; Kraus, Florian; von Hänisch, Carsten

2017-07-18

The structures of alkali-metal chloride SO 2 solvates (Li-Cs) in conjunction with 12-crown-4 or 1,2-disila-12-crown-4 show strong discrepancies, despite the structural similarity of the ligands. Both types of crown ethers form 1:1 complexes with LiCl to give [Li(1,2-disila-12-crown-4)(SO 2 Cl)] (1) and [Li(12-crown-4)Cl]⋅4 SO 2 (2). However, 1,2-disila-12-crown-4 proved unable to coordinate cations too large for the cavity diameter, for example, by the formation of sandwich-type complexes. As a result, 12-crown-4 reacts exclusively with the heavier alkali-metal chlorides NaCl, KCl and RbCl. Compounds [Na(12-crown-4) 2 ]Cl⋅4 SO 2 (3) and [M(12-crown-4) 2 (SO 2 )]Cl⋅4 SO 2 (4: M=K; 5: M=Rb) all showed S-coordination to the chloride ions through four SO 2 molecules. Compounds 4 and 5 additionally exhibit the first crystallographically confirmed non-bridging O,O'-coordination mode of SO 2 . Unexpectedly, the disila-crown ether supports the dissolution of RbCl and CsCl in the solvent and gives the homoleptic SO 2 -solvated alkali-metal chlorides [MCl⋅3 SO 2 ] (6: M=Rb; 7: M=Cs), which incorporate bridging μ-O,O'-coordinating moieties and the unprecedented side-on O,O'-coordination mode. All compounds were characterised by single-crystal X-ray diffraction. The crown ether complexes were additionally studied by using NMR spectroscopy, and the presence of SO 2 at ambient temperature was revealed by IR spectroscopy of the neat compounds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Implementation of Satellite Formation Flight Algorithms Using SPHERES Aboard the International Space Station

NASA Technical Reports Server (NTRS)

Mandy, Christophe P.; Sakamoto, Hiraku; Saenz-Otero, Alvar; Miller, David W.

2007-01-01

The MIT's Space Systems Laboratory developed the Synchronized Position Hold Engage and Reorient Experimental Satellites (SPHERES) as a risk-tolerant spaceborne facility to develop and mature control, estimation, and autonomy algorithms for distributed satellite systems for applications such as satellite formation flight. Tests performed study interferometric mission-type formation flight maneuvers in deep space. These tests consist of having the satellites trace a coordinated trajectory under tight control that would allow simulated apertures to constructively interfere observed light and measure the resulting increase in angular resolution. This paper focuses on formation initialization (establishment of a formation using limited field of view relative sensors), formation coordination (synchronization of the different satellite s motion) and fuel-balancing among the different satellites.

Infrared Multiple-Photon Dissociation spectroscopy of group II metal complexes with salicylate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan P. Dain; Gary Gresham; Gary S. Groenewold

2011-07-01

Ion-trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations were used to characterize singly-charged, 1:1 complexes of Ca2+, Sr2+ and Ba2+ with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO2 and (b) formation of [MOH]+ where M=Ca2+, Sr2+ or Ba2+. DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cationmore » is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 – 1650 cm-1, and the best correlation between theoretical and experimental spectra for the structure that features coordination of the metal ion by phenoxide and the carbonyl group of the carboxylic acid group, consistent with calculated energies for the respective species.« less

Infrared multiple-photon dissociation spectroscopy of group II metal complexes with salicylate.

PubMed

Dain, Ryan P; Gresham, Gary; Groenewold, Gary S; Steill, Jeffrey D; Oomens, Jos; van Stipdonk, Michael J

2011-07-15

Ion trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations, were used to characterize singly charged, 1:1 complexes of Ca(2+), Sr(2+) and Ba(2+) with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO(2) and (b) formation of [MOH](+) where M = Ca(2+), Sr(2+) or Ba(2+). DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cation is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 and 1650 cm(-1), and the best correlation between theoretical and experimental spectra is found for the structure that features coordination of the metal ion by phenoxide and the carbonyl O of the carboxylic acid group, consistent with the calculated energies for the respective species. Copyright © 2011 John Wiley & Sons, Ltd.

Stigmergic construction and topochemical information shape ant nest architecture

PubMed Central

Khuong, Anaïs; Gautrais, Jacques; Perna, Andrea; Sbaï, Chaker; Combe, Maud; Kuntz, Pascale; Jost, Christian; Theraulaz, Guy

2016-01-01

The nests of social insects are not only impressive because of their sheer complexity but also because they are built from individuals whose work is not centrally coordinated. A key question is how groups of insects coordinate their building actions. Here, we use a combination of experimental and modeling approaches to investigate nest construction in the ant Lasius niger. We quantify the construction dynamics and the 3D structures built by ants. Then, we characterize individual behaviors and the interactions of ants with the structures they build. We show that two main interactions are involved in the coordination of building actions: (i) a stigmergic-based interaction that controls the amplification of depositions at some locations and is attributable to a pheromone added by ants to the building material; and (ii) a template-based interaction in which ants use their body size as a cue to control the height at which they start to build a roof from existing pillars. We then develop a 3D stochastic model based on these individual behaviors to analyze the effect of pheromone presence and strength on construction dynamics. We show that the model can quantitatively reproduce key features of construction dynamics, including a large-scale pattern of regularly spaced pillars, the formation and merging of caps over the pillars, and the remodeling of built structures. Finally, our model suggests that the lifetime of the pheromone is a highly influential parameter that controls the growth and form of nest architecture. PMID:26787857

Complexation of NpO2+ with (2-Hydroxyethyl)ethylenediaminetriacetic Acid (HEDTA) in Aqueous Solutions: Thermodynamic Studies and Structural Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xingliang; Zhang, Zhicheng; Martin, Leigh R

Complexation of Np(V) with N-(2-hydroxyethyl)ethylenediaminetriacetic acid (HEDTA) was studied in aqueous solution (I = 1.0 mol L -1 NaClO 4, t = 25 °C) by spectrophotometry, microcalorimetry and Extended X-ray absorption fine structure (EXAFS) spectroscopy. Equilibrium constants for the formation of three complexes, NpO 2L 2-, NpO 2(HL) -, and (NpO 2)2(OH)2L26 -, were determined to be (6.91 ± 0.06), (4.28 ± 0.03) and -(4.93 ± 0.03), respectively. The enthalpies of complexation were determined to be -(8.0 ± 2.0) kJ mol -1 for NpO 2L 2 - and -(2.2 ± 2.0) kJ mol-1 for NpO 2(HL) -. Thermodynamic data ofmore » the complexation of Np(V) with HEDTA were compared to those of Np(V) with other aminopolycarboxylic acids, gaining insight into the possible coordination modes of the complexes. The EXAFS studies provided further structural information on those modes. In both NpO 2L 2 - and NpO 2(HL) - complexes, HEDTA coordinates to Np(V) in a tridentate mode through two oxygens of two carboxylic groups and one nitrogen of the amine group. In the (NpO 2) 2(OH) 2L 2 6- complex, two Np(V) atoms are bridged by two hydroxides and each HEDTA maintains the tridentate coordination mode.« less

Complexation of NpO2+ with (2-Hydroxyethyl)ethylenediaminetriacetic Acid (HEDTA) in Aqueous Solutions: Thermodynamic Studies and Structural Analysis

DOE PAGES

Li, Xingliang; Zhang, Zhicheng; Martin, Leigh R; ...

2016-12-02

Complexation of Np(V) with N-(2-hydroxyethyl)ethylenediaminetriacetic acid (HEDTA) was studied in aqueous solution (I = 1.0 mol L -1 NaClO 4, t = 25 °C) by spectrophotometry, microcalorimetry and Extended X-ray absorption fine structure (EXAFS) spectroscopy. Equilibrium constants for the formation of three complexes, NpO 2L 2-, NpO 2(HL) -, and (NpO 2)2(OH)2L26 -, were determined to be (6.91 ± 0.06), (4.28 ± 0.03) and -(4.93 ± 0.03), respectively. The enthalpies of complexation were determined to be -(8.0 ± 2.0) kJ mol -1 for NpO 2L 2 - and -(2.2 ± 2.0) kJ mol-1 for NpO 2(HL) -. Thermodynamic data ofmore » the complexation of Np(V) with HEDTA were compared to those of Np(V) with other aminopolycarboxylic acids, gaining insight into the possible coordination modes of the complexes. The EXAFS studies provided further structural information on those modes. In both NpO 2L 2 - and NpO 2(HL) - complexes, HEDTA coordinates to Np(V) in a tridentate mode through two oxygens of two carboxylic groups and one nitrogen of the amine group. In the (NpO 2) 2(OH) 2L 2 6- complex, two Np(V) atoms are bridged by two hydroxides and each HEDTA maintains the tridentate coordination mode.« less

Stigmergic construction and topochemical information shape ant nest architecture.

PubMed

Khuong, Anaïs; Gautrais, Jacques; Perna, Andrea; Sbaï, Chaker; Combe, Maud; Kuntz, Pascale; Jost, Christian; Theraulaz, Guy

2016-02-02

The nests of social insects are not only impressive because of their sheer complexity but also because they are built from individuals whose work is not centrally coordinated. A key question is how groups of insects coordinate their building actions. Here, we use a combination of experimental and modeling approaches to investigate nest construction in the ant Lasius niger. We quantify the construction dynamics and the 3D structures built by ants. Then, we characterize individual behaviors and the interactions of ants with the structures they build. We show that two main interactions are involved in the coordination of building actions: (i) a stigmergic-based interaction that controls the amplification of depositions at some locations and is attributable to a pheromone added by ants to the building material; and (ii) a template-based interaction in which ants use their body size as a cue to control the height at which they start to build a roof from existing pillars. We then develop a 3D stochastic model based on these individual behaviors to analyze the effect of pheromone presence and strength on construction dynamics. We show that the model can quantitatively reproduce key features of construction dynamics, including a large-scale pattern of regularly spaced pillars, the formation and merging of caps over the pillars, and the remodeling of built structures. Finally, our model suggests that the lifetime of the pheromone is a highly influential parameter that controls the growth and form of nest architecture.

Developing a MATLAB(registered)-Based Tool for Visualization and Transformation

NASA Technical Reports Server (NTRS)

Anderton, Blake J.

2003-01-01

An important step in the structural design and development of spacecraft is the experimental identification of a structure s modal characteristics, such as its natural frequencies and modes of vibration. These characteristics are vital to developing a representative model of any given structure or analyzing the range of input frequencies that can be handled by a particular structure. When setting up such a representative model of a structure, careful measurements using precision equipment (such as accelerometers and instrumented hammers) must be made on many individual points of the structure in question. The coordinate location of each data point is used to construct a wireframe geometric model of the structure. Response measurements obtained from the accelerometers is used to generate the modal shapes of the particular structure. Graphically, this is displayed as a combination of the ways a structure will ideally respond to a specified force input. Two types of models of the tested structure are often used in modal analysis: an analytic model showing expected behavior of the structure, and an experimental model showing measured results due to observed phenomena. To evaluate the results from the experimental model, a comparison of analytic and experimental results must be made between the two models. However, comparisons between these two models become difficult when the two coordinate orientations differ in a manner such that results are displayed in an unclear fashion. Such a problem proposes the need for a tool that not only communicates a graphical image of a structure s wireframe geometry based on various measurement locations (called nodes), but also allows for a type of transformation of the image s coordinate geometry so that a model s coordinate orientation is made to match the orientation of another model. Such a tool should also be designed so that it is able to construct coordinate geometry based on many different listings of node locations and is able to transform the wireframe coordinate orientation to match almost any possible orientation (i.e. it should not be a problem specific application) if it is to be of much value in modal analysis. Also, since universal files are used to store modal parameters and wireframe geometry, the tool must be able to read and extract information from universal files and use these files to exchange model data.The purpose of this project is to develop such a tool as a computer graphical user interface (GUI) capable of performing the following tasks: 1) Browsing for a particular universal file within the computer directory and displaying the name of this file to the screen; 2) Plotting each of the nodes within the universal file in a useful, descriptive, and easily understood figure; 3) Reading the node numbers from the selected file and listing these node numbers to the user for selection in an easily accessible format; 4) Allowing for user selection of a new model orientation defined by three selected nodes; and 5) Allowing the user to specify a directory to which the transformed model s node locations will be saved, and saving the transformed node locations to the specified file.

Structural and spectroscopic investigation of new luminescent hybrid materials based on calix[4]arene-tetracarboxylate and Ln3+ ions (Ln = Gd, Tb or Eu)

NASA Astrophysics Data System (ADS)

Viana, R. S.; Oliveira, C. A. F.; Chojnacki, J.; Barros, B. S.; Alves-Jr, S.; Kulesza, J.

2017-07-01

Lanthanide-calixarene hybrid materials are of particular interest due to the combination of the interesting properties of the ligand cavity-like structure and the luminescent features of lanthanides. The aim of this study was to synthesize and investigate the photophysical properties of Eu3+, Tb3+ and Gd3+ hybrids based on calix[4]arene-tetracarboxylate. The preparation of two structurally different Tb3+ compounds (calix-TA-SC-Tb and calix-TA-Tb) was dictated by the ligand to metal molar ratio and the synthesis time. Analysis of calix-TA-SC-Tb monocrystals revealed the formation of a mononuclear complex of C2 symmetry containing Tb3+ coordinated by four calixarene ionized groups and formate anion encapsulated within the upper cavity. Syntheses of other hybrids failed in producing high-quality crystals and the structures could not be solved. The solid-state luminescent properties of hybrids were evaluated, and the structure/property relationship was investigated. Based on the emission and excitation spectra, the energy diagrams for calix-TA-Eu, calix-TA-Tb and calix-TA-Gd were proposed.

Controlling the intermediate structure of an ionic liquid for f-block element separations

DOE PAGES

Abney, Carter W.; Do, Changwoo; Luo, Huimin; ...

2017-04-19

Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separations processes, but nevertheless remains largely unexplored. Here we apply small angle neutron scattering (SANS) and x-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (~150 Å) which we demonstrate can be controlled by judicious selection of counter ion. Mesoscale structural features (> 500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregatemore » structures, similar to those observed in traditional solvent extraction processes, and suggest additional parallels may be drawn from further study. As a result, achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE Office of Scientific and Technical Information (OSTI.GOV)

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE PAGES

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun; ...

2016-11-16

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li-S Battery.

PubMed

See, Kimberly A; Wu, Heng-Liang; Lau, Kah Chun; Shin, Minjeong; Cheng, Lei; Balasubramanian, Mahalingam; Gallagher, Kevin G; Curtiss, Larry A; Gewirth, Andrew A

2016-12-21

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2 -LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2 -LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. The electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.

Variations of structures and solid-state conductivity of isomeric silver(I) coordination polymers having linear and V-shaped thiophene-centered ditriazole ligands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Bin; School of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, 330063; Geng, Jiao

2014-07-01

A pair of new linear and V-shaped acceptor–donor–acceptor (A−D−A) thiophene-centered ditriazole structural isomers, i.e., 2,5-di(1H-1,2,4-triazol-1-yl)thiophene (L{sup 1}) and 3,4-di(1H-1,2,4-triazol-1-yl)thiophene (L{sup 2}), has been synthesized and characterized. They are used as μ{sub 2}-bridging ligands to prepare a pair of silver(I) coordination polymers formulated as [Ag(L{sup 1})(NO{sub 3})]{sub n} (1) and [Ag(L{sup 2})(NO{sub 3})]{sub n} (2), which are also structural isomers at the supramolecular level. X-ray single-crystal diffraction analyses for 1 and 2 reveal that they exhibit the same one-dimensional (1D) coordination polymers but different structural architectures because of the distinguishable shape and configuration of isomeric ligands (L{sup 1} and L{sup 2})more » and the alterations of the coordination numbers. More interestingly, compared with the free ligands, 1D silver(I) polymeric isomers 1 and 2 show significant enhancement of solid-state conductivity to different extents (1.42×10{sup 4} and 2.17×10{sup 3} times), where 6.96 times' enhancement of solid-state conductivity from 1 to 2 has been observed. The formation of Ag–N coordinative bonds and the configurational discrepancy of L{sup 1} and L{sup 2} are believed to play important roles in facilitating the electron transport between molecules, which can also be supported by Density Function Theory calculations of their band gaps. - Graphical abstract: A pair of linear and V-shaped isomeric thiophene-centered ditriazole ligands (L{sup 1}) and L{sup 2} are used to prepare a pair of silver(I) polymeric isomers (1 and 2), where significant enhancement of solid-state conductivity to different extents are observed originating from the distinguishable shape and configuration of isomeric ligands. - Highlights: • A pair of linear and V-shaped thiophene-centered ditriazole structural isomers is prepared. • They are used as µ{sub 2}-bridging ligands to prepare a pair of silver(I) polymeric isomers. • Significant enhancement of solid-state conductivity is observed for each polymeric isomer.« less

Heavy Metals and the Petroleum Industr

DTIC Science & Technology

1993-05-01

460 11 Fat Rendering 220 210 70 460 6 Bakery 150 330 430 280 2 Misc. Foods 350 150 110 1100 6 Brewery 410 60 40 470 5 Soft Drinks/ Flavoring 2040 180...arsenic react with -SH groups and can form coordination complexes and chelates with various compounds and structures in the cell .’ The -SH and...important in the function of the human body. It is present in the circulatory system, and a component in the formation of bones and teeth. Calcium is

Hierarchically-Clustered Structures: Formation During Colloidal Processing and Evolution During Sintering

DTIC Science & Technology

1990-12-04

18) E. Carnal and A Mocellin , " A Topological Model for Plane Sections of Polycrystals," Submitted to Acta. Metal.. 19) S. Fakuda, R. Kikuchi, and I...obtained from his CCD and the perimeter law matched the GSD generated by the Exxon group. Mocellin and his coworkers in Switzerland 32,33 (the Swiss...cellular networks," Phil. Mag B52(3), 795 (1985). 32). M. Blanc, A. Mocellin , "Grain coordination in plane sections of polycrystals," Acta Metall. 27

Grain boundaries at the surface of consolidated MgO nanocrystals and acid-base functionality.

PubMed

Vingurt, Dima; Fuks, David; Landau, Miron V; Vidruk, Roxana; Herskowitz, Moti

2013-09-21

The increase of the surface basicity-acidity of MgO material by factors of 1.8-3.0 due to consolidation of its nanocrystals was demonstrated by the indicator titration. It was shown that the parallel increase of surface acidity and basicity is attributed to the formation of grain boundaries (GB) after MgO aerogel densification. A simple model predicting the increase of surface acidity-basicity of MgO that correlates with the results of direct measurements was proposed. The model is based on the study of the fine atomic structure at GB surface areas in consolidated MgO nanocrystals in the framework of Density Functional Theory. It is found that the displacements of coordinatively unsaturated surface ions near the GB are significant at the distances ~3-4 atomic layers from the geometrical contact plane between nanocrystals. The detailed analysis of atomic positions inside GB demonstrated the coordination deficiency of surface atoms at the GB areas leading to the formation of stretched bonds and to creation of low coordinated surface ions due to splitting of coordination numbers of surface atoms belonging to GB areas. Density of states for electrons shows the existence of additional states in the band gap close to the bottom of the conduction band. The adsorption energy of CO2 molecules atop oxygen atoms exposed at surface GB areas is of the same order of magnitude as that reported for oxygen atoms at crystallographic edges and corners of MgO crystals. It provides additional options for bonding of molecules at the surface of nanocrystalline MgO increasing the adsorption capacity and catalytic activity.

Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck.

PubMed

Stanishneva-Konovalova, Tatiana B; Kelley, Charlotte F; Eskin, Tania L; Messelaar, Emily M; Wasserman, Steven A; Sokolova, Olga S; Rodal, Avital A

2016-09-20

Membrane remodeling by Fes/Cip4 homology-Bin/Amphiphysin/Rvs167 (F-BAR) proteins is regulated by autoinhibitory interactions between their SRC homology 3 (SH3) and F-BAR domains. The structural basis of autoregulation, and whether it affects interactions of SH3 domains with other cellular ligands, remain unclear. Here we used single-particle electron microscopy to determine the structure of the F-BAR protein Nervous Wreck (Nwk) in both soluble and membrane-bound states. On membrane binding, Nwk SH3 domains do not completely dissociate from the F-BAR dimer, but instead shift from its concave surface to positions on either side of the dimer. Unexpectedly, along with controlling membrane binding, these autoregulatory interactions inhibit the ability of Nwk-SH3a to activate Wiskott-Aldrich syndrome protein (WASp)/actin related protein (Arp) 2/3-dependent actin filament assembly. In Drosophila neurons, Nwk autoregulation restricts SH3a domain-dependent synaptopod formation, synaptic growth, and actin organization. Our results define structural rearrangements in Nwk that control F-BAR-membrane interactions as well as SH3 domain activities, and suggest that these two functions are tightly coordinated in vitro and in vivo.

Synthesis and characterization of the tetranuclear iron(III) complex of a new asymmetric multidentate ligand. A structural model for purple acid phosphatases.

PubMed

Boudalis, Athanassios K; Aston, Robyn E; Smith, Sarah J; Mirams, Ruth E; Riley, Mark J; Schenk, Gerhard; Blackman, Allan G; Hanton, Lyall R; Gahan, Lawrence R

2007-11-28

The ligand, 2-((2-hydroxy-5-methyl-3-((pyridin-2-ylmethylamino)methyl)benzyl)(2-hydroxybenzyl)amino)acetic acid (H(3)HPBA), which contains a donor atom set that mimics that of the active site of purple acid phosphatase is described. Reaction of H(3)HPBA with iron(III) or iron(II) salts results in formation of the tetranuclear complex, [Fe(4)(HPBA)(2)(OAc)(2)(mu-O)(mu-OH)(OH(2))(2)]ClO(4) x 5H(2)O. X-Ray structural analysis reveals the cation consists of four iron(III) ions, two HPBA(3-) ligands, two bridging acetate ligands, a bridging oxide ion and a bridging hydroxide ion. Each binucleating HPBA(3-) ligand coordinates two structurally distinct hexacoordinate iron(III) ions. The two metal ions coordinated to a HPBA(3-) ligand are linked to the two iron(III) metal ions of a second, similar binuclear unit by intramolecular oxide and hydroxide bridging moieties to form a tetramer. The complex has been further characterised by elemental analysis, mass spectrometry, UV-vis and MCD spectroscopy, X-ray crystallography, magnetic susceptibility measurements and variable-temperature Mössbauer spectroscopy.

Secondary ligand-directed assembly of Co(II) coordination polymers based on a pyridine carboxylate ligand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni

2014-07-01

To investigate the influence of hydrogen bonds and secondary ligands on the structures and properties of the resulting frameworks, five new Co(II) compounds have been synthesized by the reactions of Co(II) salts and 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL) with four rationally selected dicarboxylic acid ligands. Without secondary ligand, we got one compound [CoL{sub 2}(H{sub 2}O){sub 2}]{sub n}·2nH{sub 2}O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H{sub 2}adbc), terephthalic acid (H{sub 2}tpa), thiophene-2,5-dicarboxylic acid (H{sub 2}tdc) and 1,4-benzenedithioacetic acid (H{sub 2}bdtc), four 3D structures [Co{sub 2}L{sub 2}(adbc)]{sub n}·nH{sub 2}O (2), [Co{sub 2}L{sub 2}(tpa)]{sub n}more » (3), [Co{sub 2}L{sub 2}(tdc)]{sub n} (4), [Co{sub 2}L{sub 2}(bdtc)(H{sub 2}O)]{sub n} (5) were obtained, respectively. It can be observed from the architectures of 1–5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions.« less

Formation Flying Control of Multiple Spacecraft

NASA Technical Reports Server (NTRS)

Hadaegh, F. Y.; Lau, Kenneth; Wang, P. K. C.

1997-01-01

The problem of coordination and control of multiple spacecraft (MS) moving in formation is considered. Here, each MS is modeled by a rigid body with fixed center of mass. First, various schemes for generating the desired formation patterns are discussed, Then, explicit control laws for formation-keeping and relative attitude alignment based on nearest neighbor-tracking are derived. The necessary data which must be communicated between the MS to achieve effective control are examined. The time-domain behavior of the feedback-controlled MS formation for typical low-Earth orbits is studied both analytically and via computer simulation. The paper concludes with a discussion of the implementation of the derived control laws, and the integration of the MS formation coordination and control system with a proposed inter-spacecraft communication/computing network.

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae

PubMed Central

Schmidt, Christian; Berninghausen, Otto; Becker, Thomas

2017-01-01

Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resolution, revealing in molecular detail how assembly factors regulate the timely folding of pre-18S rRNA. The structure shows that, rather than sterically blocking 40S translational active sites, the associated assembly factors Tsr1, Enp1, Rio2 and Pno1 collectively preclude their final maturation, thereby preventing untimely tRNA and mRNA binding and error prone translation. Moreover, the structure explains how Pno1 coordinates the 3’end cleavage of the 18S rRNA by Nob1 and how the late factor’s removal in the cytoplasm ensures the structural integrity of the maturing 40S subunit. PMID:29155690

Syntactic Prediction in Language Comprehension: Evidence From Either…or

PubMed Central

Staub, Adrian; Clifton, Charles

2006-01-01

Readers’ eye movements were monitored as they read sentences in which two noun phrases or two independent clauses were connected by the word or (NP-coordination and S-coordination, respectively). The word either could be present or absent earlier in the sentence. When either was present, the material immediately following or was read more quickly, across both sentence types. In addition, there was evidence that readers misanalyzed the S-coordination structure as an NP-coordination structure only when either was absent. The authors interpret the results as indicating that the word either enabled readers to predict the arrival of a coordination structure; this predictive activation facilitated processing of this structure when it ultimately arrived, and in the case of S-coordination sentences, enabled readers to avoid the incorrect NP-coordination analysis. The authors argue that these results support parsing theories according to which the parser can build predictable syntactic structure before encountering the corresponding lexical input. PMID:16569157

Tuning the formations of metal-1,3,5-benzenetricarboxylate frameworks via the assistance of amino acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Xiao-Ping; Lian, Ting-Ting; Chen, Shu-Mei, E-mail: csm@fzu.edu.cn

Seven new metal-1,3,5-benzenetricarboxylate coordination polymers have been synthesized by modification of auxiliary components during the assembly reactions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by XRD and TGA. Interestingly, they show fascinating topological structures. Compounds 1 and 2 possess the undulating layer structure with 3-connected hcb network and (3,6)-connected kgd network. Compound 3 possesses three-dimensional (3D) pillared-layer structure with 3-connected 2-fold interpenetrating srs net. Compound 4 also has the 3D 2-fold interpenetrating pillared-layer structure; however, it has (3,5)-connected hms topology because the Cd(II) center is 5-connected. Compound 5 possess 3D structure through hydrogen bondingmore » interactions between ladder-like layers. Compounds 6 and 7 have the similar 3D frameworks with 4-connected umc net and (3,7)-connected (3.4.5)(3{sup 2}.4{sup 6}.5{sup 5}.6{sup 8}) topology, respectively. The photoluminescent properties of compounds 2–7 were also investigated. - Graphical abstract: Presented here are seven new metal-1,3,5-benzenetricarboxylate coordination polymers with diverse structures from 2D layers to 3D open frameworks. The synthesis and structural diversity of these compounds are determined by the additional amino acids as unusual buffering agents. - Highlights: • Structural diversity of metal-1,3,5-benzenetricarboxylate frameworks. • Tuning structural topologies of MOFs via the assistance of amino acids. • Amino acids as unusual buffering agents for the synthesis of MOFs.« less

Mercury coordination polymers with flexible ethane-1,2-diyl-bis-(pyridyl-3-carboxylate): Synthesis, structures, thermal and luminescent properties

NASA Astrophysics Data System (ADS)

Vallejos, Javier; Brito, Iván; Cárdenas, Alejandro; Llanos, Jaime; Bolte, Michael; López-Rodríguez, Matías

2015-03-01

The reaction of the flexible ligand, ethane-1,2-diyl-bis-(pyridyl-3-carboxylate), (L) with HgI2 and HgBr2 salts under the same experimental conditions leads to the formation of two coordination polymers with different motifs: {[Hg(L)(Br2)]}n(1) and {[Hg(L)(I2)]}n(2). In both compounds, the ligand, (L) acts in a μ2-N:N‧-bidentate fashion to link HgBr2 and HgI2 units to form a linear and helical chain motif, along [1 0 0] for (1) and [0 0 1] for (2). The ethylene moiety of (L) has gauche and trans conformation in compounds (1) and (2), respectively. The flexible conformation of L produces differences in the optical and crystal properties of the two compounds.

CfRadial - CF NetCDF for Radar and Lidar Data in Polar Coordinates.

NASA Astrophysics Data System (ADS)

Dixon, M. J.; Lee, W. C.; Michelson, D.; Curtis, M.

2016-12-01

Since 1990, NCAR has supported over 20 different data formats for radar and lidar data in polar coordinates. Researchers, students and operational users spend unnecessary time handling a multitude of unique formats. CfRadial grew out of the need to simplify the use of these data and thereby to improve efficiency in research and operations. CfRadial adopts the well-known NetCDF framework, along with the Climate and Forecasting (CF) conventions such that data and metadata are accurately represented. Mobile platforms are also supported. The first major release, CfRadial version 1.1, occurred in February 2011, followed by minor updates. CfRadial has been adopted by NCAR as well as other agencies in the US and the UK. CfRadial development was boosted in 2015 through a two-year NSF EarthCube grant to improve CF in general. Version 1.4 was agreed upon in May 2016, adding explicit support for quality control fields and spectra. In Europe and Australia, EUMETNET OPERA's HDF5-based ODIM_H5 standard has been rapidly embraced as the modern standard for exchanging weather radar data for operations. ODIM_H5 exploits data groups, hierarchies, and built-in compression, characteristics that have been added to NetCDF4. A meeting of the WMO Task Team on Weather Radar Data Exchange (TT-WRDE) was held at NCAR in Boulder in July 2016, with a goal of identifying a single global standard for radar and lidar data in polar coordinates. CfRadial and ODIM_H5 were considered alongside the older and more rigid table-driven WMO BUFR and GRIB2 formats. TT-WRDE recommended that CfRadial 1.4 be merged with the sweep-oriented structure of ODIM_H5, making use of NetCDF groups, to produce a single format that will encompass the best ideas of both formats. That has led to the emergence of the CfRadial 2.0 standard. This format should meet the objectives of both the NSF EarthCube CF 2.0 initiative and the WMO TT-WRDE. It has the added benefit of improving data exchange between operational and research users, making operational data more readily available to researchers, and research algorithms more accessible to operational agencies.

The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana

PubMed Central

Tekleyohans, Dawit G.; Wittkop, Benjamin; Snowdon, Rod J.

2016-01-01

Seed formation is a pivotal process in plant reproduction and dispersal. It begins with megagametophyte development in the ovule, followed by fertilization and subsequently coordinated development of embryo, endosperm, and maternal seed coat. Two closely related MADS-box genes, SHATTERPROOF 1 and 2 (SHP1 and SHP2) are involved in specifying ovule integument identity in Arabidopsis thaliana. The MADS box gene ARABIDOPSIS BSISTER (ABS or TT16) is required, together with SEEDSTICK (STK) for the formation of endothelium, part of the seed coat and innermost tissue layer formed by the maternal plant. Little is known about the genetic interaction of SHP1 and SHP2 with ABS and the coordination of endosperm and seed coat development. In this work, mutant and expression analysis shed light on this aspect of concerted development. Triple tt16 shp1 shp2 mutants produce malformed seedlings, seed coat formation defects, fewer seeds, and mucilage reduction. While shp1 shp2 mutants fail to coordinate the timely development of ovules, tt16 mutants show less peripheral endosperm after fertilization. Failure in coordinated division of the innermost integument layer in early ovule stages leads to inner seed coat defects in tt16 and tt16 shp1 shp2 triple mutant seeds. An antagonistic action of ABS and SHP1/SHP2 is observed in inner seed coat layer formation. Expression analysis also indicates that ABS represses SHP1, SHP2, and FRUITFUL expression. Our work shows that the evolutionary conserved Bsister genes are required not only for endothelium but also for endosperm development and genetically interact with SHP1 and SHP2 in a partially antagonistic manner. PMID:27776173

Coordination-Driven Dimerization of Zinc Chlorophyll Derivatives Possessing a Dialkylamino Group.

PubMed

Watanabe, Hiroaki; Kamatani, Yusuke; Tamiaki, Hitoshi

2017-04-04

Zinc chlorophyll derivatives Zn-1-3 possessing a tertiary amino group at the C3 1 position have been synthesized through reductive amination of methyl pyropheophorbide-d obtained from naturally occurring chlorophyll-a. In a dilute CH 2 Cl 2 solution as well as in a dilute 10 %(v/v) CH 2 Cl 2 /hexane solution, Zn-1 possessing a dimethylamino group at the C3 1 position showed red-shifted UV/Vis absorption and intensified exciton-coupling circular dichroism (CD) spectra at room temperature owing to its dimer formation via coordination to the central zinc by the 3 1 -N atom of the dimethylamino group. However, Zn-2/3 bearing 3 1 -ethylmethylamino/diethylamino groups did not. The difference was dependent on the steric factor of the substituents in the tertiary amino group, where an increase of the carbon numbers on the N atom reduced the intermolecular N⋅⋅⋅Zn coordination. UV/Vis, CD, and 1 H NMR spectroscopic analyses including DOSY measurements revealed that Zn-1 formed closed-type dimers via an opened dimer by single-to-double axial coordination with an increase in concentration and a temperature decrease in CH 2 Cl 2 , while Zn-2/3 gave open and flexible dimers in a concentrated CH 2 Cl 2 solution at low temperature. The supramolecular closed dimer structures of Zn-1 were estimated by molecular modelling calculations, which showed these structures were promising models for the chlorophyll dimer in a photosynthetic reaction center. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coordinated prefrontal-hippocampal activity and navigation strategy-related prefrontal firing during spatial memory formation.

PubMed

Negrón-Oyarzo, Ignacio; Espinosa, Nelson; Aguilar, Marcelo; Fuenzalida, Marco; Aboitiz, Francisco; Fuentealba, Pablo

2018-06-18

Learning the location of relevant places in the environment is crucial for survival. Such capacity is supported by a distributed network comprising the prefrontal cortex and hippocampus, yet it is not fully understood how these structures cooperate during spatial reference memory formation. Hence, we examined neural activity in the prefrontal-hippocampal circuit in mice during acquisition of spatial reference memory. We found that interregional oscillatory coupling increased with learning, specifically in the slow-gamma frequency (20 to 40 Hz) band during spatial navigation. In addition, mice used both spatial and nonspatial strategies to navigate and solve the task, yet prefrontal neuronal spiking and oscillatory phase coupling were selectively enhanced in the spatial navigation strategy. Lastly, a representation of the behavioral goal emerged in prefrontal spiking patterns exclusively in the spatial navigation strategy. These results suggest that reference memory formation is supported by enhanced cortical connectivity and evolving prefrontal spiking representations of behavioral goals.

Efficient CO2 capture by tertiary amine-functionalized ionic liquids through Li+-stabilized zwitterionic adduct formation

PubMed Central

Yang, Zhen-Zhen

2014-01-01

Summary Highly efficient CO2 absorption was realized through formation of zwitterionic adducts, combining synthetic strategies to ionic liquids (ILs) and coordination. The essence of our strategy is to make use of multidentate cation coordination between Li+ and an organic base. Also PEG-functionalized organic bases were employed to enhance the CO2-philicity. The ILs were reacted with CO2 to form the zwitterionic adduct. Coordination effects between various lithium salts and neutral ligands, as well as the CO2 capacity of the chelated ILs obtained were investigated. For example, the CO2 capacity of PEG150MeBu2N increased steadily from 0.10 to 0.66 (mol CO2 absorbed per mol of base) through the formation of zwitterionic adducts being stabilized by Li+. PMID:25246955

Synthon preference in the cocrystal of 3,4,5-trifluorophenylboronic acid with urea.

PubMed

Kopczyńska, Karolina; Marek, Paulina H; Banaś, Bartłomiej; Madura, Izabela D

2017-11-01

The comprehensive description of the crystal structure of a novel 1:1 cocrystal of 3,4,5-trifluorophenylboronic acid with urea, C 6 H 4 BF 3 O 2 ·CH 4 N 2 O, is presented. Both components are good candidates for crystal engineering as they can create a variety of supramolecular synthons. The preference for the formation of different hetrosynthons is verified based on theoretical calculations. The syn-anti conformation of boronic acid has been found to be the most favourable in the formation of intermolecular interactions with urea. Moreover, the distortions present in the boron coordination sphere have been described quantitatively based on experimental data according to bond-valence vector model calculations. The results revealed that the deformation of the sphere is typical for a syn-anti conformation of boronic acids. The supramolecular structure of the cocrystal is composed of large synthons in the form of layers made up of O-H...O and N-H...O hydrogen bonds. The layers are joined via N-H...F hydrogen bonds which are unusual for urea cocrystal structures.

[Ortho/para spin-isomers of H2O molecules as a factor responsible for formation of two structural motifs in water].

PubMed

Zakharov, S D

2013-01-01

According to the last results obtained by small-angle X-ray scattering and X-ray spectroscopy it was suggested that water within the nanometer scale represents a fluctuating mixture of clusters with tetrahedral structure and a subphase with partially broken hydrogen bonds whereas the nuclear configuration of the H20 molecule corresponds to single tetrahedral coordination. The basic reason of such structural partition is not clear until now. Here we show that it can be associated with the existence of two nuclear H2O spin-isomers which have different probability to be in one or another subphase. The para-molecule can transfer an excess of its rotational energy to the environment up to the complete stopping of rotation because its rotational quantum number J = 0 in the basic state. This property is favorable for the formation of clusters with closed H-bonds. Ortho-molecules with odd-numbered J states lack for this property and thus should be predominantly present in the surrounding with distorted bonds.

Silver(I) coordination polymers assembled from flexible cyclotriphosphazene ligand: structures, topologies and investigation of the counteranion effects.

PubMed

Davarcı, Derya; Gür, Rüştü; Beşli, Serap; Şenkuytu, Elif; Zorlu, Yunus

2016-06-01

The reactions of a flexible ligand hexakis(3-pyridyloxy)cyclotriphosphazene (HPCP) with a variety of silver(I) salts (AgX; X = NO3(-), PF6(-), ClO4(-), CH3PhSO3(-), BF4(-) and CF3SO3(-)) afforded six silver(I) coordination polymers, namely {[Ag2(HPCP)]·(NO3)2·H2O}n (1), {[Ag2(HPCP)(CH3CN)]·(PF6)2}n (2), {[Ag2(HPCP)(CH3CN)]·(ClO4)2}n (3), [Ag3(HPCP)(CH3PhSO3)3]n (4), [Ag2(HPCP)(CH3CN)(BF4)2]n (5) and {[Ag(HPCP)]·(CF3SO3)}n (6). All of the isolated crystalline compounds were structurally determined by X-ray crystallography. Changing the counteranions in the reactions, which were conducted under similar conditions of M/L ratio (1:1), temperature and solvent, resulted in structures with different types of topologies. In complexes (1)-(6), the ligand HPCP shows different coordination modes with Ag(I) ions giving two-dimensional layered structures and three-dimensional frameworks with different topologies. Complex (1) displays a new three-dimensional framework adopting a (3,3,6)-connected 3-nodal net with point symbol {4.6(2)}2{4(2).6(10).8(3)}. Complexes (2) and (3) are isomorphous and have a two-dimensional layered structure showing the same 3,6L60 topology with point symbol {4.2(6)}2{4(8).6(6).8}. Complex (4) is a two-dimensional structure incorporating short Ag...Ag argentophilic interactions and has a uninodal 4-connected sql/Shubnikov tetragonal plane net with {4(4).6(2)} topology. Complex (5) exhibits a novel three-dimensional framework and more suprisingly contains twofold interpenetrated honeycomb-like networks, in which the single net has a trinodal (2,3,5)-connected 3-nodal net with point symbol {6(3).8(6).12}{6(3)}{8}. Complex (6) crystallizes in a trigonal crystal system with the space group R\\bar 3 and possesses a three-dimensional polymeric structure showing a binodal (4,6)-connected fsh net with the point symbol (4(3).6(3))2.(4(6).6(6).8(3)). The effect of the counteranions on the formation of coordination polymers is discussed in this study.

Investigation of Supramolecular Coordination Self-Assembly and Polymerization Confined on Metal Surfaces Using Scanning Tunneling Microscopy

NASA Astrophysics Data System (ADS)

Lin, Tao

Organic molecules are envisioned as the building blocks for design and fabrication of functional devices in future, owing to their versatility, low cost and flexibility. Although some devices such as organic light-emitting diode (OLED) have been already applied in our daily lives, the field is still in its infancy and numerous challenges still remain. In particular, fundamental understanding of the process of organic material fabrication at a molecular level is highly desirable. This thesis focuses on the design and fabrication of supramolecular and macromolecular nanostructures on a Au(111) surface through self-assembly, polymerization and a combination of two. We used scanning tunneling microscopy (STM) as an experimental tool and Monte Carlo (MC) and kinetic Monte Carlo (KMC) simulations as theoretical tools to characterize the structures of these systems and to investigate the mechanisms of the self-assembly and polymerization processes at a single-molecular level. The results of this thesis consist of four parts as below: Part I addresses the mechanisms of two-dimensional multicomponent supramolecular self-assembly via pyridyl-Fe-terpyridyl coordination. Firstly, we studied four types of self-assembled metal-organic systems exhibiting different dimensionalities using specifically-designed molecular building blocks. We found that the two-dimensional system is under thermodynamic controls while the systems of lower dimension are under kinetic controls. Secondly, we studied the self-assembly of a series of cyclic supramolecular polygons. Our results indicate that the yield of on-surface cyclic polygon structures is very low independent of temperature and concentration and this phenomenon can be attributed to a subtle competition between kinetic and thermodynamic controls. These results shed light on thermodynamic and kinetic controls in on-surface coordination self-assembly. Part II addresses the two-dimensional supramolecular self-assembly of porphyrin derivatives. Firstly, we investigated the coordination self-assembly of a series of peripheral bromo-phenyl and pyridyl substituted porphyrins with Fe. The self-assembly of the porphyrin derivatives in which phenyl groups are substituted by bromo-phenyl results in coordination networks exhibiting identical structures to that of the parent compounds, but contained nanopores that are functionalized by bromine substitutes. Secondly, we studied a two-dimensional coordination networks formed by 5,10,15,20-tetra(4-pyridyl)porphyrin and Fe. We discovered a novel coordination motif in which a pair of vertically aligned Fe atoms is ligated by four equatorial pyridyl groups. Lateral manipulation, vertical manipulation and tunneling spectroscopy were employed to characterize the networks. These novel coordination networks decorated with Br or vertically aligned Fe atoms may provide potential functions as nano-receptor, molecular magnetism or catalyst. Part III addresses the mechanism of on-surface Ullmann coupling reaction. We studied Pd- and Cu-catalyzed Ullmann coupling reactions between phenyl bromide functionalized porphyrin derivatives. We discovered that the reactions catalyzed by Pd or Cu can be described as a two-phase process that involves an initial activation followed by C-C bond formation. Analysis of rate constants of the Pd-catalyzed reactions allowed us to determine its activation energy as (0.41 +/- 0.03) eV. These results provide a quantitative understanding of on-surface Ullmann coupling reaction. Part IV addresses the on-surface self-assembly driven by a combination of coordination bonds and covalent bonds. Firstly, we utilized metal-directed template to control the on-surface polymerization process. Taking advantage of efficient topochemical enhancement owing to the conformation flexibility of the Cu-pyridyl bonds, macromolecular porphyrin structures that exhibit a narrow size distribution were synthesized. The results reveal that the polymerization process profited from the rich chemistry of Cu which catalyzed the C-C bond formation, controlled the size of the macromolecular products, and organized the macromolecules in a highly ordered manner on the surface. Secondly, we demonstrated a two-step approach for assembling metal-organic coordination network exhibiting very large pores. The first step involves obtaining one kind of building blocks via on-surface Ullmann coupling and the second step is coordination self-assembly. Moreover, the modulation of the surface-state electrons in the network was studied. These results provide new approaches to design and fabricate on-surface nanostructures. In summary, we resolved the structures and studied the on-surface assembly and reaction mechanisms of supramolecular and macromolecular nanostructures at a sub-molecular level. These fundamental studies may shed lights on design and fabrication of low-dimensional organic materials.

The effect of cerium (III) on the chlorophyll formation in spinach.

PubMed

Fashui, Hong; Ling, Wang; Xiangxuan, Meng; Zheng, Wei; Guiwen, Zhao

2002-12-01

The effect of Ce(3+) on the chlorophyll (chl) of spinach was studied in pot culture experiments. The results showed that Ce(3+) could obviously stimulate the growth of spinach and increase its chlorophyll contents and photosynthetic rate. It could also improve the PSII formation and enhance its electron transport rate of PSII as well. By inductively coupled plasma-mass spectroscopy and atom absorption spectroscopy methods, it was revealed that the rare-earth-element (REE) distribution pattern in the Ce(3+)-treated spinach was leaf > root > shoot in Ce(3+) contents. The spinach leaves easily absorbed REEs. The Ce(3+) contents of chloroplast and chlorophyll of the Ce(3+)-treated spinach were higher than that of any other rare earth and were much higher than that of the control; it was also suggested that Ce(3+) could enter the chloroplast and bind easily to chlorophyll and might replace magnesium to form Ce-chlorophyll. By ultraviolet-visible, Fourier transform infrared, and extended X-ray absorption fine structure (EXAFS) methods, Ce(3+)-coordinated nitrogen of porphyrin rings with eight coordination numbers and average length of the Ce-N bond of 0.251 nm.

The innovative rehabilitation team: an experiment in team building.

PubMed

Halstead, L S; Rintala, D H; Kanellos, M; Griffin, B; Higgins, L; Rheinecker, S; Whiteside, W; Healy, J E

1986-06-01

This article describes an effort by one rehabilitation team to create innovative approaches to team care in a medical rehabilitation hospital. The major arena for implementing change was the weekly patient rounds. We worked to increase patient involvement, developed a rounds coordinator role, used a structured format, and tried to integrate research findings into team decision making. Other innovations included use of a preadmission questionnaire, a discharge check list, and a rounds evaluation questionnaire. The impact of these changes was evaluated using the Group Environment Scale and by analyzing participation in rounds based on verbatim transcripts obtained prior to and 20 months after formation of the Innovative Rehabilitation Team (IRT). The results showed decreased participation by medical personnel during rounds, and increased participation by patients. The rounds coordinator role increased participation rates of staff from all disciplines and the group environment improved within the IRT. These data are compared with similar evaluations made of two other groups, which served as control teams. The problems inherent in making effective, lasting changes in interdisciplinary rehabilitation teams are reviewed, and a plea is made for other teams to explore additional ways to use the collective creativity and resources latent in the team membership.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Satish, Rohit; Lim, Kipil; Bucher, Nicolas

Lithium rich layered materials are an interesting class of materials which exploit both anionic and cationic redox reactions to store energy upwards of 250 mA h g –1. This paper aims to understand the nature of the redox reactions taking place in these compounds. Li 2RuO 3 was used as the base compound, which is then compared with compounds generated by partially substituting Ru with Ti and Fe respectively. Electrochemical tests indicate that Fe substitution in the sample leads to an improvement in capacity, cycle life and reduction of potential decay. To elucidate the reason for this improvement in operandomore » diffraction experiments were carried out, highlighting the formation of a secondary de-lithiated phase. The distortion of the pristine structure eventually induces frontier orbital reorganization leading to the oxygen redox reaction resulting in extra capacity. Local changes at Fe and Ru ions are recorded using in operando X-ray absorption spectroscopy (XAS). It was noted that while Ru undergoes a reversible redox reaction, Fe undergoes a significant irreversible change in its coordination environment during cycling. In conclusion, the changes in the coordination environment of oxygen and formation of O 2 n– type species were probed in situ using soft X-rays.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolyniuk, Juli-Anna; Zaikina, Julia V.; Kaseman, Derrick C.

A new clathrate type has been discovered in the Ba/Cu/Zn/P system. The crystal structure of the Ba 8M 24P 28+δ (M=Cu/Zn) clathrate is composed of the pentagonal dodecahedra common to clathrates along with a unique 22-vertex polyhedron with two hexagonal faces capped by additional partially occupied phosphorus sites. This is the first example of a clathrate compound where the framework atoms are not in tetrahedral or trigonal-pyramidal coordination. In Ba 8M 24P 28+δ a majority of the framework atoms are five- and six-coordinated, a feature more common to electron-rich intermetallics. The crystal structure of this new clathrate was determined bymore » a combination of X-ray and neutron diffraction and was confirmed with solid-state 31P NMR spectroscopy. Based on chemical bonding analysis, the driving force for the formation of this new clathrate is the excess of electrons generated by a high concentration of Zn atoms in the framework. The rattling of guest atoms in the large cages results in a very low thermal conductivity, a unique feature of the clathrate family of compounds.« less

Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes

PubMed Central

2012-01-01

Background Transcript profiling of differentiating secondary xylem has allowed us to draw a general picture of the genes involved in wood formation. However, our knowledge is still limited about the regulatory mechanisms that coordinate and modulate the different pathways providing substrates during xylogenesis. The development of compression wood in conifers constitutes an exceptional model for these studies. Although differential expression of a few genes in differentiating compression wood compared to normal or opposite wood has been reported, the broad range of features that distinguish this reaction wood suggest that the expression of a larger set of genes would be modified. Results By combining the construction of different cDNA libraries with microarray analyses we have identified a total of 496 genes in maritime pine (Pinus pinaster, Ait.) that change in expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Samples from different provenances collected in different years and geographic locations were integrated into the analyses to mitigate the effects of multiple sources of variability. This strategy allowed us to define a group of genes that are consistently associated with compression wood formation. Correlating with the deposition of a thicker secondary cell wall that characterizes compression wood development, the expression of a number of genes involved in synthesis of cellulose, hemicellulose, lignin and lignans was up-regulated. Further analysis of a set of these genes involved in S-adenosylmethionine metabolism, ammonium recycling, and lignin and lignans biosynthesis showed changes in expression levels in parallel to the levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. Conclusions The comparative transcriptomic analysis reported here have revealed a broad spectrum of coordinated transcriptional modulation of genes involved in biosynthesis of different cell wall polymers associated with within-tree variations in pine wood structure and composition. In particular, we demonstrate the coordinated modulation at transcriptional level of a gene set involved in S-adenosylmethionine synthesis and ammonium assimilation with increased demand for coniferyl alcohol for lignin and lignan synthesis, enabling a better understanding of the metabolic requirements in cells undergoing lignification. PMID:22747794

Formation of an Oxidant-Sensible Pd(II) Coordination Compound and Its [superscript 1]H NMR Specific Characterization: A Preparative and Analytical Challenge in Current Coordination Chemistry

ERIC Educational Resources Information Center

Abraham, Maria L.; Oppel, Iris M.

2014-01-01

A three-part experiment that leads to the synthesis of palladium(II) complex starting from a C[subscript 3]-symmetric triaminoguanidinium-based ligand is presented. In the first part, the preparation of tris-benzylidenetriaminoguanidinium chloride ([H[subscript 6]Br[subscript 3]L]Cl) by an acidic catalyzed 3-fold imine formation reaction of…

Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

DTIC Science & Technology

2015-01-01

Parallel Simulator ( LAMMPS ) is used as the MD simulator [9], the coordinates must be formatted for use in LAMMPSs. VMD has a set of tools (TopoTools...that can be used to generate a LAMMPS -readable format [6]. 3 Figure 4. Ethylene Monomer Produced From Coordinates in PDB and Rendered Using...where, i and j are the atom subscripts. Simulations are performed using LAMMPS simulation software. Periodic boundary conditions are

Structural studies of the rhombohedral and orthorhombic monouranates: CaUO{sub 4}, α-SrUO{sub 4}, β-SrUO{sub 4} and BaUO{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, Gabriel; Kennedy, Brendan J., E-mail: kennedyb@chem.usyd.edu.au; Johannessen, Bernt

The structures of some AUO{sub 4} (A=Ca, Sr, or Ba) oxides have been determined using a combination of neutron and synchrotron X-ray diffraction, supported by X-ray absorption spectroscopic measurements at the U L{sub 3}-edge. The smaller Ca cation favours a rhombohedral AUO{sub 4} structure with 8-coordinate UO{sub 8} moieties whilst an orthorhombic structure based on UO{sub 6} groups is found for BaUO{sub 4}. Both the rhombohedral and orthorhombic structures can be stabilised for SrUO{sub 4}. The structural studies suggest that the bonding requirements of the A site cation play a significant role in determining which structure is favoured. In themore » rhombohedral structure, Bond Valence Sums demonstrate the A site is invariably overbonded, which, in the case of rhombohedral α-SrUO{sub 4}, is compensated for by the formation of vacancies in the oxygen sub-lattice. The uranium cation, with its flexible oxidation state, is able to accommodate this by inducing vacancies along its equatorial coordination site as demonstrated by neutron powder diffraction. - Graphical abstract: Diffraction studies of AUO{sub 4} (A = Ca, Sr, or Ba) oxides reveal the importance of the bonding requirements of the A site cation in determining whether the structure is rhombohedral or orthorhombic. - Highlights: • Structures of AUO{sub 4} ( A = Ca Sr, Ba) refined against X-ray and Neutron diffraction. • The alkali cations size has a dramatic effect on the crystal structure. • Smaller cations favouring a rhombohedral structure. • Oxygen vacancies to stabilise the rhombohedral structure in SrUO{sub 4}.« less

The characterisation of atomic structure and glass-forming ability of the Zr-Cu-Co metallic glasses studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Celtek, M.; Sengul, S.

2018-03-01

In the present work, the glass formation process and structural properties of Zr50Cu50-xCox (0 ≤ x ≤ 50) bulk metallic glasses were investigated by a molecular dynamics simulation with the many body tight-binding potentials. The evolution of structure and glass formation process with temperature were discussed using the coordination number, the radial distribution functions, the volume-temperature curve, icosahedral short-range order, glass transition temperature, Voronoi analysis, Honeycutt-Andersen pair analysis technique and the distribution of bond-angles. Results indicate that adding Co causes similar responses on the nature of the Zr50Cu50-xCox (0 ≤ x ≤ 50) alloys except for higher glass transition temperature and ideal icosahedral type ordered local atomic environment. Also, the differences of the atomic radii play the key role in influencing the atomic structure of these alloys. Both Cu and Co atoms play a significant role in deciding the chemical and topological short-range orders of the Zr50Cu50-xCox ternary liquids and amorphous alloys. The glass-forming ability of these alloys is supported by the experimental observations reported in the literature up to now.

Caveolae.

PubMed

Parton, Robert G; Tillu, Vikas A; Collins, Brett M

2018-04-23

Caveolae are one of the most abundant and striking features of the plasma membrane of many mammalian cell types. These surface pits have fascinated biologists since their discovery by the pioneers of electron microscopy in the middle of the last century, but we are only just starting to understand their multiple functions. Molecular understanding of caveolar formation is advancing rapidly and we now know that sculpting the membrane to generate the characteristic bulb-shaped caveolar pit involves the coordinated action of integral membrane proteins and peripheral membrane coat proteins in a process dependent on their multiple interactions with membrane lipids. The resulting structure is further stabilised by protein complexes at the caveolar neck. Caveolae can bud to generate an endocytic carrier but can also be disassembled in response to specific stimuli to function as a mechanoprotective device. These structures have also been linked to numerous signalling pathways. Here, we will briefly summarise the current molecular and structural understanding of caveolar formation and dynamics, discuss how the crucial structural components of caveolae work together to generate a dynamic sensing domain, and discuss the implications of recent studies on the diverse roles proposed for caveolae in different cells and tissues. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.

PubMed

Lee, Soon Goo; Krishnan, Hari B; Jez, Joseph M

2014-04-29

The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.

A Coordination Network with Ligand-Centered Redox Activity Based on facial-[CrIII (2-mercaptophenolato)3 ]3- Metalloligands.

PubMed

Wakizaka, Masanori; Matsumoto, Takeshi; Kobayashi, Atsushi; Kato, Masako; Chang, Ho-Chol

2017-07-21

The design of redox-active metal-organic frameworks and coordination networks (CNs), which exhibit metal- and/or ligand-centered redox activity, has recently received increased attention. In this study, the redox-active metalloligand (RML) [Me 4 N] 3 fac-[Cr III (mp) 3 ] (1) (mp=2-mercaptophenolato) was synthesized and characterized by single-crystal X-ray diffraction analysis, and its reversible ligand-centered one-electron oxidation was examined by cyclic voltammetry and spectroelectrochemical measurements. Since complex 1 contains O/S coordination sites in three directions, complexation with K + ions led to the formation of the two-dimensional honeycomb sheet-structured [K 3 fac-{Cr III (mp) 3 }(H 2 O) 6 ] n (2⋅6 H 2 O), which is the first example of a redox-active CN constructed from a RML with o-disubstituted benzene ligands. Herein, we unambiguously demonstrate the ligand-centered redox activity of the RML within the CN 2⋅6 H 2 O in the solid state. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facile solid-state synthesis of Ni@C nanosheet-assembled hierarchical network for high-performance lithium storage

NASA Astrophysics Data System (ADS)

Gu, Jinghe; Li, Qiyun; Zeng, Pan; Meng, Yulin; Zhang, Xiukui; Wu, Ping; Zhou, Yiming

2017-08-01

Micro/nano-architectured transition-metal@C hybrids possess unique structural and compositional features toward lithium storage, and are thus expected to manifest ideal anodic performances in advanced lithium-ion batteries (LIBs). Herein, we propose a facile and scalable solid-state coordination and subsequent pyrolysis route for the formation of a novel type of micro/nano-architectured transition-metal@C hybrid (i.e., Ni@C nanosheet-assembled hierarchical network, Ni@C network). Moreover, this coordination-pyrolysis route has also been applied for the construction of bare carbon network using zinc salts instead of nickel salts as precursors. When applied as potential anodic materials in LIBs, the Ni@C network exhibits Ni-content-dependent electrochemical performances, and the partially-etched Ni@C network manifests markedly enhanced Li-storage performances in terms of specific capacities, cycle life, and rate capability than the pristine Ni@C network and carbon network. The proposed solid-state coordination and pyrolysis strategy would open up new opportunities for constructing micro/nano-architectured transition-metal@C hybrids as advanced anode materials for LIBs.

Coordination-Enabled One-Step Assembly of Ultrathin, Hybrid Microcapsules with Weak pH-Response.

PubMed

Yang, Chen; Wu, Hong; Yang, Xiao; Shi, Jiafu; Wang, Xiaoli; Zhang, Shaohua; Jiang, Zhongyi

2015-05-06

In this study, an ultrathin, hybrid microcapsule is prepared though coordination-enabled one-step assembly of tannic acid (TA) and titanium(IV) bis(ammonium lactate) dihydroxide (Ti-BALDH) upon a hard-templating method. Briefly, the PSS-doped CaCO3 microspheres with a diameter of 5-8 μm were synthesized and utilized as the sacrificial templates. Then, TA-Ti(IV) coatings were formed on the surface of the PSS-doped CaCO3 templates through soaking in TA and Ti-BALDH aqueous solutions under mild conditions. After removing the template by EDTA treatment, the TA-Ti(IV) microcapsules with a capsule wall thickness of 15 ± 3 nm were obtained. The strong coordination bond between polyphenol and Ti(IV) conferred the TA-Ti(IV) microcapsules high structural stability in the range of pH values 3.0-11.0. Accordingly, the enzyme-immobilized TA-Ti(IV) microcapsules exhibited superior pH and thermal stabilities. This study discloses the formation of TA-Ti(IV) microcapsules that are suitable for use as supports in catalysis due to their extensive pH and thermal stabilities.

Quantum mechanics/molecular mechanics study of the catalytic cycle of water splitting in photosystem II.

PubMed

Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

2008-03-19

This paper investigates the mechanism of water splitting in photosystem II (PSII) as described by chemically sensible models of the oxygen-evolving complex (OEC) in the S0-S4 states. The reaction is the paradigm for engineering direct solar fuel production systems since it is driven by solar light and the catalyst involves inexpensive and abundant metals (calcium and manganese). Molecular models of the OEC Mn3CaO4Mn catalytic cluster are constructed by explicitly considering the perturbational influence of the surrounding protein environment according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, in conjunction with the X-ray diffraction (XRD) structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The resulting models are validated through direct comparisons with high-resolution extended X-ray absorption fine structure spectroscopic data. Structures of the S3, S4, and S0 states include an additional mu-oxo bridge between Mn(3) and Mn(4), not present in XRD structures, found to be essential for the deprotonation of substrate water molecules. The structures of reaction intermediates suggest a detailed mechanism of dioxygen evolution based on changes in oxidization and protonation states and structural rearrangements of the oxomanganese cluster and surrounding water molecules. The catalytic reaction is consistent with substrate water molecules coordinated as terminal ligands to Mn(4) and calcium and requires the formation of an oxyl radical by deprotonation of the substrate water molecule ligated to Mn(4) and the accumulation of four oxidizing equivalents. The oxyl radical is susceptible to nucleophilic attack by a substrate water molecule initially coordinated to calcium and activated by two basic species, including CP43-R357 and the mu-oxo bridge between Mn(3) and Mn(4). The reaction is concerted with water ligand exchange, swapping the activated water by a water molecule in the second coordination shell of calcium.

Structural investigation of oxovanadium(IV) Schiff base complexes: X-ray crystallography, electrochemistry and kinetic of thermal decomposition.

PubMed

Asadi, Mozaffar; Asadi, Zahra; Savaripoor, Nooshin; Dusek, Michal; Eigner, Vaclav; Shorkaei, Mohammad Ranjkesh; Sedaghat, Moslem

2015-02-05

A series of new VO(IV) complexes of tetradentate N2O2 Schiff base ligands (L(1)-L(4)), were synthesized and characterized by FT-IR, UV-vis and elemental analysis. The structure of the complex VOL(1)⋅DMF was also investigated by X-ray crystallography which revealed a vanadyl center with distorted octahedral coordination where the 2-aza and 2-oxo coordinating sites of the ligand were perpendicular to the "-yl" oxygen. The electrochemical properties of the vanadyl complexes were investigated by cyclic voltammetry. A good correlation was observed between the oxidation potentials and the electron withdrawing character of the substituents on the Schiff base ligands, showing the following trend: MeO5-H>5-Br>5-Cl. Furthermore, the kinetic parameters of thermal decomposition were calculated by using the Coats-Redfern equation. According to the Coats-Redfern plots the kinetics of thermal decomposition of studied complexes is of the first-order in all stages, the free energy of activation for each following stage is larger than the previous one and the complexes have good thermal stability. The preparation of VOL(1)⋅DMF yielded also another compound, one kind of vanadium oxide [VO]X, with different habitus of crystals, (platelet instead of prisma) and without L(1) ligand, consisting of a V10O28 cage, diaminium moiety and dimethylamonium as a counter ions. Because its crystal structure was also new, we reported it along with the targeted complex. Copyright © 2014 Elsevier B.V. All rights reserved.

Mechanism of Pd(NHC)-catalyzed transfer hydrogenation of alkynes.

PubMed

Hauwert, Peter; Boerleider, Romilda; Warsink, Stefan; Weigand, Jan J; Elsevier, Cornelis J

2010-12-01

The transfer semihydrogenation of alkynes to (Z)-alkenes shows excellent chemo- and stereoselectivity when using a zerovalent palladium(NHC)(maleic anhydride)-complex as precatalyst and triethylammonium formate as hydrogen donor. Studies on the kinetics under reaction conditions showed a broken positive order in substrate and first order in catalyst and hydrogen donor. Deuterium-labeling studies on the hydrogen donor showed that both hydrogens of formic acid display a primary kinetic isotope effect, indicating that proton and hydride transfers are separate rate-determining steps. By monitoring the reaction with NMR, we observed the presence of a coordinated formate anion and found that part of the maleic anhydride remains coordinated during the reaction. From these observations, we propose a mechanism in which hydrogen transfer from coordinated formate anion to zerovalent palladium(NHC)(MA)(alkyne)-complex is followed by migratory insertion of hydride, after which the product alkene is liberated by proton transfer from the triethylammonium cation. The explanation for the high selectivity observed lies in the competition between strongly coordinating solvent and alkyne for a Pd(alkene)-intermediate.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Jinhee; Chen, Ying-Pin; Perry, Zachary

A series of molybdenum- and copper-based MOPs were synthesized through coordination-driven process of a bridging ligand (3,3 -PDBAD, L1) and dimetal paddlewheel clusters. Three conformers of the ligand exist with an ideal bridging angle between the two carboxylate groups of 0° (H2α-L1), 120° (H2β-L1), and of 90° (H2γ-L1), respectively. At ambient or lower temperature, H2L1 and Mo2(OAc)4 or Cu2(OAc)4 were crystallized into a molecular square with γ-L1 and Mo2/Cu2 units. With proper temperature elevation, not only the molecular square with γ-L1 but also a lantern-shaped cage with α-L1 formed simultaneously. Similar to how Watson–Crick pairs stabilize the helical structure ofmore » duplex DNA, the core–shell molecular assembly possesses favorable H-bonding interaction sites. This is dictated by the ligand conformation in the shell, coding for the formation and providing stabilization of the central lantern shaped core, which was not observed without this complementary interaction. On the basis of the crystallographic implications, a heterobimetallic cage was obtained through a postsynthetic metal ion metathesis, showing different reactivity of coordination bonds in the core and shell. As an innovative synthetic strategy, the site-selective metathesis broadens the structural diversity and properties of coordination assemblies.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, J; Chen, YP; Perry, Z

A series of molybdenum- and copper-based MOPs were synthesized through coordination-driven process of a bridging ligand (3,3'-PDBAD, L-1) and dimetal paddlewheel clusters. Three conformers of the ligand exist with an ideal bridging angle between the two carboxylate groups of 0 degrees (H-2 zeta-L(1)), 120 degrees (H-2 beta-L-1), and of 90 degrees (H-2 beta-L-1), respectively. At ambient or lower temperature, (HL1)-L-2 and Mo-2(OAc)(4) or Cu-2(OAc)(4) were crystallized into a molecular square with ?-L-1 and Mo-2/Cu-2 units. With proper temperature elevation, not only the molecular square with ?-L-1 but also a lantern-shaped cage with a-L-1 formed simultaneously. Similar to how Watson-Crick pairsmore » stabilize the helical structure of duplex DNA, the core-shell molecular assembly possesses favorable H-bonding interaction sites. This is dictated by the ligand conformation in the shell, coding for the formation and providing stabilization of the central lantern shaped core, which was not observed without this complementary interaction. On the basis of the crystallographic implications, a heterobimetallic cage was obtained through a postsynthetic metal ion metathesis, showing different reactivity of coordination bonds in the core and shell. As an innovative synthetic strategy, the site-selective metathesis broadens the structural diversity and properties of coordination assemblies.« less

Interaction of NaOH solutions with silica surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rimsza, Jessica M.; Jones, Reese E.; Criscenti, Louise J.

Sodium adsorption on silica surfaces depends on the solution counter-ion. Here, we use NaOH solutions to investigate basic environments. Sodium adsorption on hydroxylated silica surfaces from NaOH solutions were investigated through molecular dynamics with a dissociative force field, allowing for the development of secondary molecular species. Furthermore, across the NaOH concentrations (0.01 M – 1.0 M), ~50% of the Na + ions were concentrated in the surface region, developing silica surface charges between –0.01 C/m 2 (0.01 M NaOH) and –0.76 C/m 2 (1.0 M NaOH) due to surface site deprotonation. Five inner-sphere adsorption complexes were identified, including monodentate, bidentate,more » and tridentate configurations and two additional structures, with Na + ions coordinated by bridging oxygen and hydroxyl groups or water molecules. Coordination of Na + ions by bridging oxygen atoms indicates partial or complete incorporation of Na + ions into the silica surface. Residence time analysis identified that Na + ions coordinated by bridging oxygen atoms stayed adsorbed onto the surface four times longer than the mono/bi/tridentate species, indicating formation of relatively stable and persistent Na + ion adsorption structures. Such inner-sphere complexes form only at NaOH concentrations of > 0.5 M. Na + adsorption and lifetimes have implications for the stability of silica surfaces.« less

Interaction of NaOH solutions with silica surfaces

DOE PAGES

Rimsza, Jessica M.; Jones, Reese E.; Criscenti, Louise J.

2018-01-16

Sodium adsorption on silica surfaces depends on the solution counter-ion. Here, we use NaOH solutions to investigate basic environments. Sodium adsorption on hydroxylated silica surfaces from NaOH solutions were investigated through molecular dynamics with a dissociative force field, allowing for the development of secondary molecular species. Furthermore, across the NaOH concentrations (0.01 M – 1.0 M), ~50% of the Na + ions were concentrated in the surface region, developing silica surface charges between –0.01 C/m 2 (0.01 M NaOH) and –0.76 C/m 2 (1.0 M NaOH) due to surface site deprotonation. Five inner-sphere adsorption complexes were identified, including monodentate, bidentate,more » and tridentate configurations and two additional structures, with Na + ions coordinated by bridging oxygen and hydroxyl groups or water molecules. Coordination of Na + ions by bridging oxygen atoms indicates partial or complete incorporation of Na + ions into the silica surface. Residence time analysis identified that Na + ions coordinated by bridging oxygen atoms stayed adsorbed onto the surface four times longer than the mono/bi/tridentate species, indicating formation of relatively stable and persistent Na + ion adsorption structures. Such inner-sphere complexes form only at NaOH concentrations of > 0.5 M. Na + adsorption and lifetimes have implications for the stability of silica surfaces.« less

Trinuclear Lanthanoid Complexes of 1,3,5-Triamino-1,3,5-trideoxy-cis-inositol with a Unique, Sandwich-Type Cage Structure(1).

PubMed

Hedinger, Roman; Ghisletta, Michele; Hegetschweiler, Kaspar; Tóth, Eva; Merbach, André E.; Sessoli, Roberta; Gatteschi, Dante; Gramlich, Volker

1998-12-28

A variety of trinuclear complexes [M(3)(H(-)(3)L)(2)](3+) [M = Y, La, Eu, Gd, Dy; L = 1,3,5-triamino-1,3,5-trideoxy-cis-inositol (taci) and 1,3,5-trideoxy-1,3,5-tris(dimethylamino)-cis-inositol (tdci)] was prepared as solid materials of the composition M(3)(H(-)(3)L)(2)X(3).pH(2)O.qEtOH (X = Cl, NO(3); 2.5

Bending nanofibers into nanospirals: coordination chemistry as a tool for shaping hydrophobic assemblies.

PubMed

Kossoy, Elizaveta; Weissman, Haim; Rybtchinski, Boris

2015-01-02

In the current work, we demonstrate how coordination chemistry can be employed to direct self-assembly based on strong hydrophobic interactions. To investigate the influence of coordination sphere geometry on aqueous self-assembly, we synthesized complexes of the amphiphilic perylene diimide terpyridine ligand with the first-row transition-metal centers (zinc, cobalt, and nickel). In aqueous medium, aggregation of these complexes is induced by hydrophobic interactions between the ligands. However, the final shapes of the resulting assemblies depend on the preferred geometry of the coordination spheres typical for the particular metal center. The self-assembly process was characterized by UV/Vis spectroscopy, zeta potential measurements, and cryogenic transmission electron microscopy (cryo-TEM). Coordination of zinc(II) and cobalt(II) leads to the formation of unique nanospiral assemblies, whereas complexation of nickel(II) leads to the formation of straight nanofibers. Notably, coordination bonds are utilized not as connectors between elementary building blocks, but as directing interactions, enabling control over supramolecular geometry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of indirect readout mechanism in TATA box binding protein-DNA interaction.

PubMed

Mondal, Manas; Choudhury, Devapriya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay

2015-03-01

Gene expression generally initiates from recognition of TATA-box binding protein (TBP) to the minor groove of DNA of TATA box sequence where the DNA structure is significantly different from B-DNA. We have carried out molecular dynamics simulation studies of TBP-DNA system to understand how the DNA structure alters for efficient binding. We observed rigid nature of the protein while the DNA of TATA box sequence has an inherent flexibility in terms of bending and minor groove widening. The bending analysis of the free DNA and the TBP bound DNA systems indicate presence of some similar structures. Principal coordinate ordination analysis also indicates some structural features of the protein bound and free DNA are similar. Thus we suggest that the DNA of TATA box sequence regularly oscillates between several alternate structures and the one suitable for TBP binding is induced further by the protein for proper complex formation.

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

DOE PAGES

Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi; ...

2016-03-19

The S 3 state of the Mn 4CaO 5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S 2 to S 3 transition that becomes a substrate water, we examined if the water insertion is essential for the S 3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S 3 stage. The novel S 3 state structure consisting of only short 2.7–2.8 Å MnMn distances was discussed.

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi

The S 3 state of the Mn 4CaO 5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S 2 to S 3 transition that becomes a substrate water, we examined if the water insertion is essential for the S 3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S 3 stage. The novel S 3 state structure consisting of only short 2.7–2.8 Å MnMn distances was discussed.

Formation Energies and Electronic Properties of Vanadium Carbides Found in High Strength Steel Alloys

NASA Astrophysics Data System (ADS)

Limmer, Krista; Medvedeva, Julia

2013-03-01

Carbide formation and stabilization in steels is of great interest owing to its effect on the microstructure and properties of the Fe-based alloys. The appearance of carbides with different metal/C ratios strongly depends on the carbon concentration, alloy composition as well as the heat treatment. Strong carbide-forming elements such as Ti, V, and Nb have been used in microalloyed steels; with VC showing an increased solubility in the iron matrix as compared with TiC and NbC. This allows for dissolution of the VC into the steel during heating and fine precipitation during cooling. In addition to VC, the primary vanadium carbide with cubic structure, a wide range of non-stoichiometric compositions VCy with y varying from 0.72 to 0.88, has been observed. This range includes two ordered compounds, V8C7 and V6C5. In this study, first-principles density functional theory (DFT) is employed to examine the stability of the binary carbides by calculating their formation energies. We compare the local structures (atomic coordination, bond distances and angles) and the density of states in optimized geometries of the carbides. Further, the effect of alloying additions, such as niobium and titanium, on the carbide stabilization is investigated. We determine the energetically preferable substitutional atom location in each carbide and study the impurity distribution as well as its role in the carbide formation energy and electronic structure.

New coordination features; a bridging pyridine and the forced shortest non-covalent distance between two CO3 2– species† †Electronic supplementary information (ESI) available: Mass Spectrometry and BVS analysis CCDC 996546–996548. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc02491e Click here for additional data file. Click here for additional data file.

PubMed Central

Velasco, V.; Aguilà, D.; Barrios, L. A.; Borilovic, I.; Roubeau, O.; Ribas-Ariño, J.; Fumanal, M.; Teat, S. J.

2015-01-01

The aerobic reaction of the multidentate ligand 2,6-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-pyridine, H4L, with Co(ii) salts in strong basic conditions produces the clusters [Co4(L)2(OH)(py)7]NO3 (1) and [Co8Na4(L)4(OH)2(CO3)2(py)10](BF4)2 (2). Analysis of their structure unveils unusual coordination features including a very rare bridging pyridine ligand or two trapped carbonate anions within one coordination cage, forced to stay at an extremely close distance (d O···O = 1.946 Å). This unprecedented non-bonding proximity represents a meeting point between long covalent interactions and “intermolecular” contacts. These original motifs have been analysed here through DFT calculations, which have yielded interaction energies and the reduced repulsion energy experimented by both CO3 2– anions when located in close proximity inside the coordination cage. PMID:28616127

Amorphous Metal Polysulfides: Electrode Materials with Unique Insertion/Extraction Reactions.

PubMed

Sakuda, Atsushi; Ohara, Koji; Fukuda, Katsutoshi; Nakanishi, Koji; Kawaguchi, Tomoya; Arai, Hajime; Uchimoto, Yoshiharu; Ohta, Toshiaki; Matsubara, Eiichiro; Ogumi, Zempachi; Okumura, Toyoki; Kobayashi, Hironori; Kageyama, Hiroyuki; Shikano, Masahiro; Sakaebe, Hikari; Takeuchi, Tomonari

2017-07-05

A unique charge/discharge mechanism of amorphous TiS 4 is reported. Amorphous transition metal polysulfide electrodes exhibit anomalous charge/discharge performance and should have a unique charge/discharge mechanism: neither the typical intercalation/deintercalation mechanism nor the conversion-type one, but a mixture of the two. Analyzing the mechanism of such electrodes has been a challenge because fewer tools are available to examine the "amorphous" structure. It is revealed that the electrode undergoes two distinct structural changes: (i) the deformation and formation of S-S disulfide bonds and (ii) changes in the coordination number of titanium. These structural changes proceed continuously and concertedly for Li insertion/extraction. The results of this study provide a novel and unique model of amorphous electrode materials with significantly larger capacities.

HEME-HEME COMUNICATION DURING THE ALKALINE INDUCED STRUCTURAL TRANSITION IN CYTOCROME C OXIDASE

PubMed Central

Ji, Hong; Rousseau, Denis L.; Yeh, Syun-Ru

2009-01-01

Alkaline induced conformational changes at pH 12.0 in the oxidized as well as the reduced state of cytochrome c oxidase have been systematically studied with time-resolved optical absorption and resonance Raman spectroscopies. In the reduced state, the heme a3 first converts from the native five-coordinate configuration to a six-coordinate bis-histidine intermediate as a result of the coordination of one of the CuB ligands, H290 or H291, to the heme iron. The coordination state change in the heme a3 causes the alteration in the microenvironment of the formyl group of the heme a3 and the disruption of the H-bond between R38 and the formyl group of the heme a. This structural transition, which occurs within 1 minute following the initiation of the pH jump, is followed by a slower reaction, in which Schiff base linkages are formed between the formyl groups of the two hemes and their nearby amino acid residues, presumably R38 and R302 for the heme a and a3, respectively. In the oxidized enzyme, a similar Schiff base modification on heme a and a3 was observed but it is triggered by the coordination of the H290 or H291 to heme a3 followed by the breakage of the native proximal H378-iron and H376-iron bonds in heme a and a3, respectively. In both oxidation states, the synchronous formation of the Schiff base linkages in heme a and a3 relies on the structural communication between the two hemes via the H-bonding network involving R438 and R439 and the propionate groups of the two hemes as well as the helix X housing the two proximal ligands, H378 and H376, of the hemes. The heme-heme communication mechanism revealed in this work may be important in controlling the coupling of the oxygen and redox chemistry in the heme sites to proton pumping during the enzymatic turnover of CcO. PMID:18187199

40 CFR 300.205 - Planning and coordination structure.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 29 2013-07-01 2013-07-01 false Planning and coordination structure... POLLUTION CONTINGENCY PLAN Planning and Preparedness § 300.205 Planning and coordination structure. (a... assure pre-planning of joint response efforts, including appropriate procedures for mechanical recovery...

40 CFR 300.205 - Planning and coordination structure.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 28 2014-07-01 2014-07-01 false Planning and coordination structure... POLLUTION CONTINGENCY PLAN Planning and Preparedness § 300.205 Planning and coordination structure. (a... assure pre-planning of joint response efforts, including appropriate procedures for mechanical recovery...

40 CFR 300.205 - Planning and coordination structure.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 28 2011-07-01 2011-07-01 false Planning and coordination structure... POLLUTION CONTINGENCY PLAN Planning and Preparedness § 300.205 Planning and coordination structure. (a... assure pre-planning of joint response efforts, including appropriate procedures for mechanical recovery...

40 CFR 300.205 - Planning and coordination structure.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 29 2012-07-01 2012-07-01 false Planning and coordination structure... POLLUTION CONTINGENCY PLAN Planning and Preparedness § 300.205 Planning and coordination structure. (a... assure pre-planning of joint response efforts, including appropriate procedures for mechanical recovery...

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

PubMed

Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

2018-02-01

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

Relative position coordinated control for spacecraft formation flying with communication delays

NASA Astrophysics Data System (ADS)

Ran, Dechao; Chen, Xiaoqian; Misra, Arun K.; Xiao, Bing

2017-08-01

This study addresses a relative position coordinated control problem for spacecraft formation flying subject to directed communication topology. Two different kinds of communication delay cases, including time-varying delays and arbitrarily bounded delays are investigated. Using the backstepping control technique, two virtual velocity control inputs are firstly designed to achieve coordinated position tracking for the kinematic subsystem. Furthermore, a hyperbolic tangent function is introduced to guarantee the boundedness of the virtual controller. Then, a finite-time control algorithm is designed for the dynamic subsystem. It can guarantee that the virtual velocity can be followed by the real velocity after finite time. It is theoretically proved that the proposed control scheme can asymptotically stabilize the closed-loop system. Numerical simulations are further presented that not only highlight closed-loop performance benefiting from the proposed control scheme, but also illustrate its superiority in comparison with conventional formation control schemes.

Coordination-Driven Syntheses of Compact Supramolecular Metallacycles toward Extended Metallo-organic Stacked Supramolecular Assemblies.

PubMed

Lescop, Christophe

2017-04-18

One important concept associated with supramolecular chemistry is supramolecular self-assembly, which deals with the way discrete individual components interact via intermolecular interactions in order to build, upon their spontaneous association, high order functional assemblies. The accumulation of these very simple and localized noncovalent interactions (such as H-bonding, dipole-dipole, hydrophobic/hydrophilic, van der Waals, π-π, π-CH, etc.) is ubiquitous in the complexity of natural systems (such as DNA, proteins, membranes, micelles, etc.). It can also be transposed to the directed synthesis of intricate artificial scaffolds, which have anticipated geometries and properties. Among the synthetic strategies based on this concept, coordination-driven supramolecular chemistry uses the robust, reversible, and directional metal-to-ligand coordinative bond to build discrete metallo-supramolecular architectures. Within the last two decades, coordination-driven supramolecular chemistry has proved to be one of the most powerful contemporary synthetic approaches and has provided a significant number of increasingly complex supramolecular assemblies, which have predetermined sizes and geometries. While much focus has been devoted to architectures bearing internal cavities for host-guest chemistry or to generate specific reactivity, particular attention can also be paid to compact supramolecular assemblies given that their specific structures are characterized by peculiar synthetic guiding rules as well as by alternative long-range self-assembling properties. This Account describes how a preassembled Cu I bimetallic clip bearing short intermetallic distances can be used as a U-shaped molecular clip to give general and versatile access to a large variety of original compact supramolecular metallacycles. When this Cu I precursor is reacted with various cyano-capped ditopic linkers that have increasing lengths and complexities, specific effects guiding the selective and straightforward syntheses of such compact supramolecular objects are highlighted. Whereas a subtle compromise between the length of the ditopic linkers and the steric bulk of the molecular clip appears to be a purely stereogeometric preliminary parameter to master, lateral interlinker interactions (π-π stacking interactions or aurophilic interactions depending on the nature of the internal cores of the linkers) can circumvent these constraints regardless of the length of the linkers and allow the selective formation of new compact supramolecular structures. Generally, such derivatives presented a strong tendency to self-assemble in the solid state due to inter-supramolecule interactions. This approach thus opens a new door toward molecular materials having an attractive solid state structure for potential applications related to charge carrier mobility and luminescence properties. These compact supramolecular assemblies can therefore be considered as original secondary binding units directing the predictive preparation of such extended networks. The on-purpose design of original building blocks bearing specific cores allowed the formation of new compact supramolecular metallacycles such as "U-shaped" π-stacked assemblies or "pseudodouble paracyclophanes". Similarly, the control of the secondary structure of one-dimensional coordination polymers alternating π-stacked compact supramolecular metallacycles was also conducted. The results that are discussed in this Account illustrate how the rational design of both preassembled polymetallic precursors bearing short intermetallic distances and ditopic linkers able to induce cumulative lateral weak interactions can implement the general synthetic guiding rules of coordination driven supramolecular chemistry. This opens perspectives to use such compact supramolecular assemblies as secondary building blocks for the design of long-range organized functional molecular materials that have predictable architectures and targeted properties.

Processing Coordination Ambiguity

ERIC Educational Resources Information Center

Engelhardt, Paul E.; Ferreira, Fernanda

2010-01-01

We examined temporarily ambiguous coordination structures such as "put the butter in the bowl and the pan on the towel." Minimal Attachment predicts that the ambiguous noun phrase "the pan" will be interpreted as a noun-phrase coordination structure because it is syntactically simpler than clausal coordination. Constraint-based…

Transcriptional Modulation of Genes Encoding Structural Characteristics of Differentiating Enterocytes During Development of a Polarized Epithelium In Vitro

PubMed Central

Halbleib, Jennifer M.; Sääf, Annika M.

2007-01-01

Although there is considerable evidence implicating posttranslational mechanisms in the development of epithelial cell polarity, little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized the temporal program of gene expression during cell–cell adhesion–initiated polarization of human Caco-2 cells in tissue culture, which develop structural and functional polarity similar to that of enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts between neighboring cells. Expression of genes involved in cell proliferation was down-regulated concomitant with induction of genes necessary for functional specialization of polarized epithelial cells. Transcriptional up-regulation of these latter genes correlated with formation of important structural and functional features in enterocyte differentiation and establishment of structural and functional cell polarity; components of the apical microvilli were induced as the brush border formed during polarization; as barrier function was established, expression of tight junction transmembrane proteins peaked; transcripts encoding components of the apical, but not the basal-lateral trafficking machinery were increased during polarization. Coordinated expression of genes encoding components of functional cell structures were often observed indicating temporal control of expression and assembly of multiprotein complexes. PMID:17699590

DOE Office of Scientific and Technical Information (OSTI.GOV)

NSTec Environmental Restoration

Homeland Security Presidential Directive HSPD-5 requires all federal departments and agencies to adopt a National Incident Management System (NIMS)/Incident Command System (ICS) and use it in their individual domestic incident management and emergency prevention, preparedness, response, recovery, and mitigation programs and activities, as well as in support of those actions taken to assist state and local entities. This system provides a consistent nationwide template to enable federal, state, local, and tribal governments, private-sector, and nongovernmental organizations to work together effectively and efficiently to prepare for, prevent, respond to, and recover from domestic incidents, regardless of cause, size, or complexity, includingmore » acts of catastrophic terrorism. This document identifies the operational concepts of the Federal Radiological Monitoring and Assessment Center's (FRMAC) implementation of the NIMS/ICS response structure under the National Response Plan (NRP). The construct identified here defines the basic response template to be tailored to the incident-specific response requirements. FRMAC's mission to facilitate interagency environmental data management, monitoring, sampling, analysis, and assessment and link this information to the planning and decision staff clearly places the FRMAC in the Planning Section. FRMAC is not a mitigating resource for radiological contamination but is present to conduct radiological impact assessment for public dose avoidance. Field monitoring is a fact-finding mission to support this effort directly. Decisions based on the assessed data will drive public protection and operational requirements. This organizational structure under NIMS is focused by the mission responsibilities and interface requirements following the premise to provide emergency responders with a flexible yet standardized structure for incident response activities. The coordination responsibilities outlined in the NRP are based on the NIMS/ICS construct and Unified Command (UC) for management of a domestic incident. The NRP Nuclear/Radiological Incident Annex (NUC) further provides requirements and protocols for coordinating federal government capabilities to respond to nuclear/radiological Incidents of National Significance (INS) and other radiological incidents. When a FRMAC is established, it operates under the parameters of NIMS as defined in the NRP. FRMAC and its operations have been modified to reflect NIMS/ICS concepts and principles and to facilitate working in a Unified Command structure. FRMAC is established at or near the scene of the incident to coordinate radiological monitoring and assessment and is established in coordination with the U.S. Department of Homeland Security (DHS); the coordinating agency; other federal agencies; and state, local, and tribal authorities. However, regardless of the coordinating agency designation, U.S. Department of Energy (DOE) coordinates radiological monitoring and assessment activities for the initial phases of the offsite federal incident response through the Radiological Assistance Program (RAP) and FRMAC assets. Monitoring and assessment data are managed by FRMAC in an accountable, secure, and retrievable format. Monitoring data interpretations, including exposure rate contours, dose projections, and any requested radiological assessments are to be provided to the DHS; to the coordinating agency; and to state, local, and tribal government agencies.« less

Formation of nano-laminated structures in a dry sliding wear-induced layer under different wear mechanisms of 20CrNi2Mo steel

NASA Astrophysics Data System (ADS)

Yin, Cun-hong; Liang, Yi-long; Jiang, Yun; Yang, Ming; Long, Shao-lei

2017-11-01

The microstructures of 20CrNi2Mo steel underneath the contact surface were examined after dry sliding. Scanning Electronic Microscopy (SEM), Transmission Electron Microscopy (TEM), Electron Backscattered Diffraction (EBSD) and an ultra-micro-hardness tester were used to characterize the worn surface and dry sliding wear-induced layer. Martensite laths were ultra-refined due to cumulative strains and a large strain gradient that occurred during cyclic loading in wear near the surface. The microstructure evolution in dominant abrasive wear differs from that in adhesive wear. In dominant abrasive wear, only bent martensite laths with high-density deformation dislocations were observed. In contrast, in dominant adhesive wear, gradient structures were formed along the depth from the wear surface. Cross-sectional TEM foils were prepared in a focused ion beam (FIB) to observe the gradient structures in a dry sliding wear-induced layer at depths of approximately 1-5 μm and 5-20 μm. The gradient structures contained nano-laminated structures with an average thickness of 30-50 nm and bent martensite laths. We found that the original martensite laths coordinated with the strain energy and provided origin boundaries for the formation of gradient structures. Geometrically necessary boundaries (GNBs) and isolated dislocation boundaries (IDBs) play important roles in forming the nano-laminated structures.

Oriented Attachment Is a Major Control Mechanism To Form Nail-like Mn-Doped ZnO Nanocrystals.

PubMed

Patterson, Samuel; Arora, Priyanka; Price, Paige; Dittmar, Jasper W; Das, Vijay Kumar; Pink, Maren; Stein, Barry; Morgan, David Gene; Losovyj, Yaroslav; Koczkur, Kallum M; Skrabalak, Sara E; Bronstein, Lyudmila M

2017-12-26

Here, we present a controlled synthesis of Mn-doped ZnO nanoparticles (NPs) with predominantly nail-like shapes, whose formation occurs via tip-to-base-oriented attachment of initially formed nanopyramids, followed by leveling of sharp edges that lead to smooth single-crystalline "nails". This shape is prevalent in noncoordinating solvents such as octadecene and octadecane. Yet, the double bond in the former promotes oriented attachment. By contrast, Mn-doped ZnO NP synthesis in a weakly coordinating solvent, benzyl ether, results in dendritic structures because of random attachment of initial NPs. Mn-doped ZnO NPs possess a hexagonal wurtzite structure, and in the majority of cases, the NP surface is enriched with Mn, indicating a migration of Mn 2+ ions to the NP surface during the NP formation. When the NP formation is carried out without the addition of octadecyl alcohol, which serves as a surfactant and a reaction initiator, large, concave pyramid dimers are formed whose attachment takes place via basal planes. UV-vis and photoluminescence spectra of these NPs confirm the utility of controlling the NP shape to tune electro-optical properties.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

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 consistentmore » 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. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

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 consistentmore » 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.« less

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

DOE PAGES

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.; ...

2016-09-07

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 consistentmore » 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. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Computational Study of the Adsorption of Dimethyl Methylphosphonate (DMMP) on the (010) Surface of Anatase TiO2 With and Without Faceting

DTIC Science & Technology

2009-12-05

surface area of anatase nanocrystals [6] and to be es- pecially active in photocatalysis [7]. Recent work by Dzwigaj et al. [8] has clearly shown that the...two-fold-coordinated (O2c) sites can also be involved in hydrogen bond (H-bond) formation. The effects, on the structure of the (100) and other...To reduce the computational cost , geometry optimization was done at the restricted Hartree Fock (RHF) level. This has previously been shown [36,37

Structure and Properties of Modified and Charge-Compensated Chalcogenide Glasses in the Na/Ba-Ga-Ge Selenide System

NASA Astrophysics Data System (ADS)

Mao, Alvin W.

Chalcogenide glasses exhibit unique optical properties such as infrared transparency owing to the low-phonon energies, optical non-linearity, and photo-induced effects that have important consequences for a wide range of technological applications. However, to fully utilize these properties, it is necessary to better understand the atomic-scale structure and structure-property relationships in this important class of materials. Of particular interest in this regard are glasses in the stoichiometric system Na2Se/BaSe--Ga 2Se3--GeSe2 as they are isoelectronic with the well-studied, oxide glasses of the type M2O(M'O)--Al 2O3--SiO2 (M = alkali, M' = alkaline earth). This dissertation investigates the structure of stoichiometric Na 2Se/BaSe--Ga2Se3--GeSe2 and off-stoichiometric BaSe--Ga2Se3--GeSe 2+/-Se glasses using a combination of Fourier-transform Raman and solid state nuclear magnetic resonance (NMR) spectroscopies. The spectroscopic data is then compared to composition-dependent trends in physical properties such as density, optical band gap, glass transition temperature, and melt fragility to develop predictive structural models of the short- and intermediate-range order in the glass network. These models significantly improve our current understanding of the effects of modifier addition on the structure and properties of chalcogenide glasses, and thus enable a more efficient engineering of these highly functional materials for applications as solid electrolytes in batteries or as optical components in infrared photonics. In general, the underlying stoichiometric Ga2Se3--GeSe 2 network consists primarily of corner-sharing (Ga/Ge)Se4 tetrahedra, where the coordination numbers of Ga, Ge, and Se are 4, 4, and 2, respectively. Some edge-sharing exists, but this configuration is relatively unstable and its concentration tends to decrease with any deviation from the GeSe2 composition. Due to the tetrahedral coordination of Ga, the initial addition of Se-deficient Ga2Se3 to GeSe 2 results in the preferential formation of Ge-Ge bonds, which are distributed such that the clustering of ethane-like (Se3)Ge-Ge(Se3) units is avoided to the maximum extent. This behavior is entirely consistent with the continuously-alloyed structural scenario of chalcogenide glasses. However, for contents of Ga2Se3 greater than about 25--30 mol%, the avoidance of Ga-Ga and mixed Ga-Ge bonds results in the appearance of three-coordinated Se as an alternate mechanism to accommodate the Se deficiency. The addition of either Na2Se or BaSe to Ga2Se 3--GeSe2 glasses introduces an ionic bonding character to an otherwise largely covalently bonded network. As a result, the structure responds by adopting characteristics of the charge-compensated structural scenario of oxide glasses. In the stoichiometric Na2Se/BaSe--Ga 2Se3--GeSe2 glasses, the ratio of Na 2Se/BaSe:Ga2Se3 = 1 serves as a chemical threshold, where the network consists predominantly of corner-sharing (Ga/Ge)e4 tetrahedra, and the charge on the Na(Ba) cations is balanced by the GaSe4- tetrahedra. For glasses with Na 2Se/BaSe:Ga2Se3 < 1, the addition of Se-deficient Ga2Se3 induces the formation of Ge-Ge bonds. However, for glasses with Na2Se/BaSe:Ga2Se3 > 1, the addition of Na2Se/BaSe results in the formation of non-bridging Se atoms, which break up the connectivity of the glassy network. The major difference between the modifying elements Na and Ba is that the high field strength of the Ba cation induces a higher degree of chemical disorder in the glass network. This conclusion is evidenced by the presence of some Ge-Ge bonds in BaSe--Ga2Se3--GeSe2 glasses even at the chemical threshold composition of BaSe:Ga2Se3 = 1. The structural duality of the Na2Se/BaSe--Ga2Se 3--GeSe2 system is best observed in the off-stoichiometric BaSe--Ga2Se3--GeSe2+/-Se glasses. Here, the removal of Se from a stoichiometric glass with BaSe:Ga2Se 3 > 1 results in Ge-Ge bonds, while its addition in excess of stoichiometry forms Se-Se bonds. Although such behavior is consistent with the continuously-alloyed structural model, it should be contrasted with the response of the network to the removal or addition of BaSe. In the latter case especially, the network responds with the formation of non-bridging Se atoms, which is reminiscent of the charge-compensated structural scenario. The aforementioned structural conclusions are supported by trends in physical properties. Of all the properties measured, the glass transition temperature Tg responds most predictably to changes in glass structure in the sense that the removal of heteropolar (Ga/Ge)-Se bonds from the glassy network consistently results in a decrease in Tg. Indeed, Tg is observed to be maximized around chemical threshold compositions that are expected to have a fully-connected network of (Ga/Ge)Se¬4 tetrahedra. The formation of homopolar Ge-Ge bonds causes Tg to drop by ~40--80 °C, while the formation of Se-Se and/or non-bridging Se causes Tg to decrease by at least 120 °C. Trends in density reflect both the packing efficiency of the structural units within the glassy network as well as the masses of the constituent elements, and are generally observed to increase or decrease monotonically. As a result, an increase in density is associated with: 1) the removal of inefficiently packed structural units such as edge-sharing tetrahedra, 2) the formation of efficiently packed units such as three-coordinated Se atoms, 3) the removal of lighter elements like Na, and 4) the addition of heavier elements like Ba. Optical band gap is related to the bonding character within the glassy network, and tends to decrease as the bonding character becomes increasingly metallic. Therefore, a decrease in optical band gap is observed with the formation of homopolar Ge-Ge bonds when Ga2Se3 is added to GeSe2. However, the stoichiometric BaSe--Ga2Se 3--GeSe2 glasses show an anomaly in this regard because optical band gap decreases with the addition of BaSe, and consequently the removal of Ge-Ge bonds. This observation was ascribed instead to the formation of Ba-Se bonds, which are associated with a lower bandgap compared to the (Ga/Ge)-Se bonds that they replace. Finally, there is no straightforward structural explanation for trends in fragility, because it is related to the number of structural configurations dynamically available to the supercooled liquid. In the binary Ga2Se3--GeSe2 glasses, the fragility tends to increase with the formation of homopolar Ge-Ge bonds, which is consistent with other chalcogenide systems in which fragility increases with the removal of heteropolar bonds within corner-sharing tetrahedra and pyramids. In the stoichiometric BaSe--Ga2Se3--GeSe2 glasses on the other hand, a shift in trend near the compositions where BaSe:Ga 2Se3 = 1 coincides with a structural shift between the formation of Ge-Ge bonds and Se-Se/non-bridging Se.

Four thiophene-pyridyl-amide-based Zn{sup II}/Cd{sup II} coordination polymers: Assembly, structures, photocatalytic properties and fluorescent recognition for Fe{sup 3+}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiu-Li; Wu, Xiao-Mei; Liu, Guo-Cheng

By tuning metal ions and combining with different dicarboxylates, four new semi-rigid thiophene-bis-pyridyl-bis-amide-based coordination polymers, namely, [Zn(3-bptpa)(1,3-BDC)]·DMA·2H{sub 2}O (1), [Zn(3-bptpa)(5-MIP)] (2), [Cd(3-bptpa)(1,3-BDC)]·2H{sub 2}O (3) and [Cd(3-bptpa)(5-MIP)]·4H{sub 2}O (4) (3-bptpa=N,N′-bis(pyridine-3-yl)thiophene-2,5-dicarboxamide, 1,3-H{sub 2}BDC=1,3-benzenedicarboxylic acid, 5-H{sub 2}MIP=5-methylisophthalic acid, DMA=N,N-dimethylacetamide), were solvothermally/hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction analyses, IR spectra, UV–vis diffuse-reflectance spectra (DRS), powder X-ray diffraction (PXRD) and thermal gravimetric analyses (TG). The structural analysis reveals that Zn-complexes 1 and 2 are similar 2D networks. While Cd-complexes 3 and 4 exhibit similar 2-fold interpenetrating 3D α-Po frameworks with the (4{sup 12}·6{sup 3}) topology. The photocatalytic properties for the degradation ofmore » methylene blue (MB) under ultraviolet light irradiation of the title complexes have been investigated in detail. Furthermore, the luminescent sensing behaviors for metal cations of 1–4 have been studied, the results indicate that 3 is an excellent fluorescent probe, with high sensitivity, selectivity, and simple regeneration, for environmentally relevant Fe{sup 3+} ions. - Graphical abstract: Four Zn{sup II}/Cd{sup II} coordination polymers with a thiophene-pyridyl-amide ligand have been prepared. The photocatalytic activities and fluorescent sensing properties for metal ions of the title complexes have been investigated. - Highlights: • Four coordination polymers with thiophene-pyridyl-amide ligands have been obtained. • The central metal ions play an important role in the formation of the frameworks. • The photoluminescent sensing and the photocatalytic properties have been investigated.« less

Modular syntheses of H₄octapa and H₂dedpa, and yttrium coordination chemistry relevant to ⁸⁶Y/⁹⁰Y radiopharmaceuticals.

PubMed

Price, Eric W; Cawthray, Jacqueline F; Adam, Michael J; Orvig, Chris

2014-05-21

The ligands H2dedpa, H4octapa, p-SCN-Bn-H2dedpa, and p-SCN-Bn-H4octapa were synthesized using a new protection chemistry approach, with labile tert-butyl esters replacing the previously used methyl esters as protecting groups for picolinic acid moieties. Additionally, the ligands H2dedpa and p-SCN-Bn-H2dedpa were synthesized using nosyl protection chemistry for the first time. The use of tert-butyl esters allows for deprotection at room temperature in trifluoroacetic acid (TFA), which compares favorably to the harsh conditions of refluxing HCl (6 M) or LiOH that were previously required for methyl ester cleavage. H4octapa has recently been shown to be a very promising (111)In and (177)Lu ligand for radiopharmaceutical applications; therefore, coordination chemistry studies with Y(3+) are described to assess its potential for use with (86)Y/(90)Y. The solution chemistry of H4octapa with Y(3+) is shown to be suitable via solution NMR studies of the [Y(octapa)](-) complex and density functional theory (DFT) calculations of the predicted structure, suggesting properties similar to those of the analogous In(3+) and Lu(3+) complexes. The molecular electrostatic potential (MEP) was mapped onto the molecular surface of the DFT-calculated coordination structures, suggesting very similar and even charge distributions between both the Lu(3+) and Y(3+) complexes of octapa(4-), and coordinate structures between 8 (ligand only) and 9 (ligand and one H2O). Potentiometric titrations determined H4octapa to have a formation constant (log K(ML)) with Y(3+) of 18.3 ± 0.1, revealing high thermodynamic stability. This preliminary work suggests that H4octapa may be a competent ligand for future (86)Y/(90)Y radiopharmaceutical applications.

(ZrO 2) 0.85( REO 1.5) 0.15 ( RE=Sc, Y) solid solutions prepared via three Pechini-type gel routes: 1—gel formation and calcination behaviors

NASA Astrophysics Data System (ADS)

Zhang, Yawen; Li, Ang; Yan, Zhengguang; Xu, Gang; Liao, Chunsheng; Yan, Chunhua

2003-02-01

(ZrO2)0.85(REO1.5)0.15 (RE=Sc, Y) nanoparticles with pure cubic fluorite structure have been synthesized by three Pechini-type gel routes, viz. poly(vinyl alcohol) containing-process (route I), poly(ethylene glycol) and formic acid-containing process (route II), and in situ polymerizable complex method (route III). The coordination modes between metal ions and polymers in the gels are shown to be highly correlative with the synthesis route used. The gels prepared by route III have the strongest coordination throughout their network and therefore the best chemical homogeneity. The altered variety of polymer and cross-linking within the gels adopted by these three routes has made the as-synthesized samples show appreciable differences in thermal behavior, powder reactivity and nanoparticle properties.

Neural crest development and craniofacial morphogenesis is coordinated by nitric oxide and histone acetylation

PubMed Central

Kong, Yawei; Grimaldi, Michael; Curtin, Eugene; Dougherty, Max; Kaufman, Charles; White, Richard M.; Zon, Leonard I.; Liao, Eric C.

2015-01-01

Cranial neural crest (CNC) cells are patterned and coalesce to facial prominences that undergo convergence and extension to generate the craniofacial form. We applied a chemical genetics approach to identify pathways that regulate craniofacial development during embryogenesis. Treatment with the nitric oxide synthase inhibitor TRIM abrogated first pharyngeal arch structures and induced ectopic ceratobranchial formation. TRIM promoted a progenitor CNC fate and inhibited chondrogenic differentiation, which were mediated through impaired nitric oxide (NO) production without appreciable effect on global protein S-nitrosylation. Instead, TRIM perturbed hox gene patterning and caused histone hypoacetylation. Rescue of TRIM phenotype was achieved with over-expression of histone acetyltransferase kat6a, inhibition of histone deacetylase, and complimentary NO. These studies demonstrate that NO signaling and histone acetylation are coordinated mechanisms that regulate CNC patterning, differentiation and convergence during craniofacial morphogenesis. PMID:24684905

Uncovering the Local Magnesium Environment in the Metal–Organic Framework Mg 2 (dobpdc) Using 25 Mg NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Jun; Blaakmeer, E. S. Merijn; Lipton, Andrew S.

The incorporation of N,N'-dimethylethylenediamine into an expanded MOF-74 framework has yielded a material (mmen-Mg2(dobpdc)) exhibiting “step-shaped” CO2 adsorption isotherms. The coordination of mmen at the Mg open metal center is essential for the unique cooperative adsorption mechanism elucidated for this material. Despite its importance for carbon capture, there is as yet no experimental structure determination available for the underlying metal– organic framework Mg2(dobpdc). Our 25Mg solid-state NMR data unravel the local Mg environments in several Mg2(dobpdc) samples, unambiguously confirming the formation of fivecoordinate Mg centers in the activated material and six-coordinate Mg centers in the solvent- or diamine-loaded samples, suchmore » as mmen-Mg2(dobpdc). A fraction of the Mg centers are locally disordered due to the framework deformation accompanied by the guest distributions and dynamics.« less

Common Data Format (CDF) and Coordinated Data Analysis Web (CDAWeb)

NASA Technical Reports Server (NTRS)

Candey, Robert M.

2010-01-01

The Coordinated Data Analysis Web (CDAWeb) data browsing system provides plotting, listing and open access v ia FTP, HTTP, and web services (REST, SOAP, OPeNDAP) for data from mo st NASA Heliophysics missions and is heavily used by the community. C ombining data from many instruments and missions enables broad resear ch analysis and correlation and coordination with other experiments a nd missions. Crucial to its effectiveness is the use of a standard se lf-describing data format, in this case, the Common Data Format (CDF) , also developed at the Space Physics Data facility , and the use of metadata standa rds (easily edited with SKTeditor ). CDAweb is based on a set of IDL routines, CDAWlib . . The CDF project also maintains soft ware and services for translating between many standard formats (CDF. netCDF, HDF, FITS, XML) .

Phosphorus-supported ligands for the assembly of multimetal architectures.

PubMed

Chandrasekhar, Vadapalli; Murugesapandian, Balasubramanian

2009-08-18

Modeled after boron-based scorpionate ligands, acyclic and cyclic phosphorus-containing compounds possessing reactive groups can serve as excellent precursors for the assembly of novel phosphorus-supported ligands that can coordinate multiple sites. In such ligands, the phosphorus atom does not have any role in coordination but is used as a structural support to assemble one or more coordination platforms. In this Account, we describe the utility of inorganic heterocyclic rings such as cyclophosphazenes and carbophosphazenes as well as acyclic phosphorus-containing compounds such as (S)PCl(3), RP(O)Cl(2), and R(2)P(O)Cl for building such multisite coordination platforms. We can modulate the number and orientation of such coordination platforms through the choice of the phosphorus-containing precursor. This methodology is quite general and modular and allows the creation of well-defined libraries of multisite coordination ligands. Phosphorus-supported pyrazolyl ligands are quite useful for building multimetallic architectures. Some of these ligands are prone to P-N bond hydrolysis upon metalation, but we have exploited the P-N bond sensitivity to generate hydrolyzed ligands in situ, which are useful to build multimetal assemblies. In addition, the intimate relationship between small molecule cyclophosphazenes and the corresponding pendant cyclophosphazene-containing polymer systems facilitated our design of polymer-supported catalysts for phosphate ester hydrolysis, plasmid DNA modification, and C-C bond formation reactions. Phosphorus hydrazides containing reactive amine groups are ideal precursors for integration into more complex ligand systems. The ligand (S)P[N(Me)N=CH-C(6)H(4)-2-OH](3) (LH(3)) contains six coordination sites, and its coordination response depends upon the oxidation state of the metal ion employed. LH(3) reacts with divalent transition metal ions to afford neutral trimetallic derivatives L(2)M(3), where the three metal ions are arranged in a perfectly linear manner in many cases. Incorporating an additional methoxy group into LH(3) affords the ligand (S)P[N(Me)N=CH-C(6)H(3)-2-OH-3-OMe](3) (L'H(3)), which contains nine coordination sites: three imino nitrogen atoms, three phenolate oxygen atoms, and three methoxy oxygen atoms. The reaction of L'H(3) with transition metal salts in 1:1 ratio leads to the in situ formation of a metalloligand (L'M), which on further treatment with lanthanide salts gives heterobimetallic trinuclear cationic complexes [L'(2)M(2)Ln](+) containing a M-Ln-M linear array (M = transition metal ion in a +2 oxidation state). Many of these 3d-4f compounds behave as single-molecule magnets at low temperatures. Although challenges remain in the development of synthetic methods and in the architectural control of the coordination platforms, we see opportunities for further research into coordination platforms supported by main group elements such as phosphorus. As we have shown in this Account, one potential disadvantage, sensitivity of P-N bonds to hydrolysis, can be used successfully to build larger assemblies.

Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

PubMed

Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling

2016-05-01

Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

2,6-diacetylpyridine bis(thiosemicarbazones) zinc complexes: synthesis, structure, and biological activity.

PubMed

Rodriguez-Argüelles, M C; Belicchi Ferrari, M; Gasparri Fava, G; Pelizzi, C; Tarasconi, P; Albertini, R; Dall'Aglio, P P; Lunghi, P; Pinelli, S

1995-05-15

The reaction of zinc chloride, acetate, or perchlorate with two bis(thiosemicarbazones) of 2,6-diacetylpyridine [H2daptsc = 2,6-diacetylpyridine bis(thiosemicarbazone) and H2dapipt = 2,6-diacetylpyridine bis(hydrazinopyruvoylthiosemicarbazone)] leads to the formation of four novel complexes that have been characterized by spectroscopic studies (NMR, IR) and biological properties. The crystal structures of the two compounds--[Zn(daptsc)]2.2DMF (1) and [Zn(H2dapipt)(OH2)2](CIO4)2.3H2O (2)--also have been determined by x-ray methods from diffractometer data. Compound (1) is dimeric and the two zinc atoms have a distorted octahedral coordination. The ligand is deprotonated. In compound (2), the coordination geometry about zinc is pentagonal--bipyramidal and the ligand is in the neutral form. The molecular structure of (2) consists of cations [Zn(H2dapipt)(OH2)]2+, CIO4- disordered anions, and three water molecules of solvation. Biological studies have shown that the ligands and the complexes Zn(daptsc).1/2EtOH and Zn(H2daptsc)Cl2 have an effect in vitro on cell proliferation and differentiation (inhibition); both are concentration dependent. [Zn(daptsc)]2.2DMF (1) shows the effects at lower concentration values with respect to other compounds.

Molecular dynamics of bacteriorhodopsin.

PubMed

Lupo, J A; Pachter, R

1997-02-01

A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.

Reorganization of the human central nervous system.

PubMed

Schalow, G; Zäch, G A

2000-10-01

The key strategies on which the discovery of the functional organization of the central nervous system (CNS) under physiologic and pathophysiologic conditions have been based included (1) our measurements of phase and frequency coordination between the firings of alpha- and gamma-motoneurons and secondary muscle spindle afferents in the human spinal cord, (2) knowledge on CNS reorganization derived upon the improvement of the functions of the lesioned CNS in our patients in the short-term memory and the long-term memory (reorganization), and (3) the dynamic pattern approach for re-learning rhythmic coordinated behavior. The theory of self-organization and pattern formation in nonequilibrium systems is explicitly related to our measurements of the natural firing patterns of sets of identified single neurons in the human spinal premotor network and re-learned coordinated movements following spinal cord and brain lesions. Therapy induced cell proliferation, and maybe, neurogenesis seem to contribute to the host of structural changes during the process of re-learning of the lesioned CNS. So far, coordinated functions like movements could substantially be improved in every of the more than 100 patients with a CNS lesion by applying coordination dynamic therapy. As suggested by the data of our patients on re-learning, the human CNS seems to have a second integrative strategy for learning, re-learning, storing and recalling, which makes an essential contribution of the functional plasticity following a CNS lesion. A method has been developed by us for the simultaneous recording with wire electrodes of extracellular action potentials from single human afferent and efferent nerve fibres of undamaged sacral nerve roots. A classification scheme of the nerve fibres in the human peripheral nervous system (PNS) could be set up in which the individual classes of nerve fibres are characterized by group conduction velocities and group nerve fibre diameters. Natural impulse patterns of several identified single afferent and efferent nerve fibres (motoneuron axons) were extracted from multi-unit impulse patterns, and human CNS functions could be analyzed under physiologic and pathophysiologic conditions. With our discovery of premotor spinal oscillators it became possible to judge upon CNS neuronal network organization based on the firing patterns of these spinal oscillators and their driving afferents. Since motoneurons fire occasionally for low activation and oscillatory for high activation, the coherent organization of subnetworks to generate macroscopic function is very complex and for the time being, may be best described by the theory of coordination dynamics. Since oscillatory firing has also been observed by us in single motor unit firing patterns measured electromyographically, it seems possible to follow up therapeutic intervention in patients with spinal cord and brain lesions not only based on the activity levels and phases of motor programs during locomotion but also based on the physiologic and pathophysiologic firing patterns and recruitment of spinal oscillators. The improvement of the coordination dynamics of the CNS can be partly measured directly by rhythmicity upon the patient performing rhythmic movements coordinated up to milliseconds. Since rhythmic dynamic, coordinated, stereotyped movements are mainly located in the spinal cord and only little supraspinal drive is necessary to initiate, maintain, and terminate them, rhythmic, dynamic, coordinated movements were used in therapy to enforce reorganization of the lesioned CNS by improving the self-organization and relative coordination of spinal oscillators (and their interactions with occasionally firing motoneurons) which became pathologic in their firing following CNS lesion. Paraparetic, tetraparetic spinal cord and brain-lesioned patients re-learned running and other movements by an oscillator formation and coordination dynamic therapy. Our development in neurorehabilitation is in accordance with those of theoretical and computational neurosciences which deal with the self-organization of neuronal networks. In particular, jumping on a springboard 'in-phase' and in 'anti-phase' to re-learn phase relations of oscillator coupling can be understood in the framework of the Haken-Kelso-Bunz coordination dynamic model. By introducing broken symmetry, intention, learning and spasticity in the landscape of the potential function of the integrated CNS activity, the change in self-organization becomes understandable. Movement patterns re-learned by oscillator formation and coordination dynamic therapy evolve from reorganization and regeneration of the lesioned CNS by cooperative and competitive interplay between intrinsic coordination dynamics, extrinsic therapy related inputs with physiologic re-afferent input, including intention, motivation, supervised learning, interpersonal coordination, and genetic constraints including neurogenesis. (ABSTRACT TRUNCATED)

EFFECTS OF LASER RADIATION ON MATTER: Influence of fluctuations of the size and number of surface microdefects on the thresholds of laser plasma formation

NASA Astrophysics Data System (ADS)

Borets-Pervak, I. Yu; Vorob'ev, V. S.

1990-08-01

An analysis is made of the influence of the statistical scatter of the size of thermally insulated microdefects and of their number in the focusing spot on the threshold energies of plasma formation by microsecond laser pulses interacting with metal surfaces. The coordinates of the laser pulse intensity and the surface density of the laser energy are used in constructing plasma formation regions corresponding to different numbers of microdefects within the focusing spot area; the same coordinates are used to represent laser pulses. Various threshold and nonthreshold plasma formation mechanisms are discussed. The sizes of microdefects and their statistical characteristics deduced from limited experimental data provide a consistent description of the characteristics of plasma formation near polished and nonpolished surfaces.

Acetylene hydratase: a non-redox enzyme with tungsten and iron-sulfur centers at the active site.

PubMed

Kroneck, Peter M H

2016-03-01

In living systems, tungsten is exclusively found in microbial enzymes coordinated by the pyranopterin cofactor, with additional metal coordination provided by oxygen and/or sulfur, and/or selenium atoms in diverse arrangements. Prominent examples are formate dehydrogenase, formylmethanofuran dehydrogenase, and aldehyde oxidoreductase all of which catalyze redox reactions. The bacterial enzyme acetylene hydratase (AH) stands out of its class as it catalyzes the conversion of acetylene to acetaldehyde, clearly a non-redox reaction and a reaction distinct from the reduction of acetylene to ethylene by nitrogenase. AH harbors two pyranopterins bound to W, and a [4Fe-4S] cluster. W is coordinated by four dithiolene sulfur atoms, one cysteine sulfur, and one oxygen ligand. AH activity requires a strong reductant suggesting W(IV) as the active oxidation state. Two different types of reaction pathways have been proposed. The 1.26 Å structure reveals a water molecule coordinated to W which could gain a partially positive net charge by the adjacent protonated Asp-13, enabling a direct attack of C2H2. To access the W-Asp site, a substrate channel was evolved distant from where it is found in other members of the DMSOR family. Computational studies of this second shell mechanism led to unrealistically high energy barriers, and alternative pathways were proposed where C2H2 binds directly to W. The architecture of the catalytic cavity, the specificity for C2H2 and the results from site-directed mutagenesis do not support this first shell mechanism. More investigations including structural information on the binding of C2H2 are needed to present a conclusive answer.

Insight into the coordination and the binding sites of Cu(2+) by the histidyl-6-tag using experimental and computational tools.

PubMed

Watly, Joanna; Simonovsky, Eyal; Wieczorek, Robert; Barbosa, Nuno; Miller, Yifat; Kozlowski, Henryk

2014-07-07

His-tags are specific sequences containing six to nine subsequent histydyl residues, and they are used for purification of recombinant proteins by use of IMAC chromatography. Such polyhistydyl tags, often used in molecular biology, can be also found in nature. Proteins containing histidine-rich domains play a critical role in many life functions in both prokaryote and eukaryote organisms. Binding mode and the thermodynamic properties of the system depend on the specific metal ion and the histidine sequence. Despite the wide application of the His-tag for purification of proteins, little is known about the properties of metal-binding to such tag domains. This inspired us to undertake detailed studies on the coordination of Cu(2+) ion to hexa-His-tag. Experiments were performed using the potentiometric, UV-visible, CD, and EPR techniques. In addition, molecular dynamics (MD) simulations and density functional theory (DFT) calculations were applied. The experimental studies have shown that the Cu(2+) ion binds most likely to two imidazoles and one, two, or three amide nitrogens, depending on the pH. The structures and stabilities of the complexes for the Cu(2+)-Ac-(His)6-NH2 system using experimental and computational tools were established. Polymorphic binding states are suggested, with a possibility of the formation of α-helix structure induced by metal ion coordination. Metal ion is bound to various pairs of imidazole moieties derived from the tag with different efficiencies. The coordination sphere around the metal ion is completed by molecules of water. Finally, the Cu(2+) binding by Ac-(His)6-NH2 is much more efficient compared to other multihistidine protein domains.

Molecular tectonics: hierarchical organization of heterobimetallic coordination networks into heterotrimetallic core-shell crystals.

PubMed

Zhang, Fan; Adolf, Cyril R R; Zigon, Nicolas; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais

2017-03-23

Combinations of a neutral Pt(ii) organometallic tecton bearing two triphenylphosphine and two 3-ethynylpyridyl coordinating moieties in trans positions with MX 2 complexes (M = Co(ii) and X = Cl - or Br - and M = Zn(ii) and X = Cl - ) lead to the formation of isostructural 1D heterobimetallic coordination compounds. By 3D epitaxial growth processes, using coordination bonding, heterotrimetallic core-shell crystals are generated by the growth of crystalline layers on seed crystals.

Solvent-coordinate free-energy landscape view of water-mediated ion-pair dissociation

NASA Astrophysics Data System (ADS)

Yonetani, Yoshiteru

2017-12-01

Water-mediated ion-pair dissociation is studied by molecular dynamics simulations of NaCl in water. Multidimensional free-energy analysis clarifies the relation between two essential solvent coordinates: the water coordination number and water-bridge formation. These two are related in a complex way. Both are necessary to describe ion-pair dissociation. The mechanism constructed with both solvent variables clearly shows the individual roles. The water coordination number is critical for starting ion-pair dissociation. Water-bridge formation is also important because it increases the likelihood of ion-pair dissociation by reducing the dissociation free-energy barrier. Additional Ca-Cl and NH4-Cl calculations show that these conclusions are unaffected by changes in the ion charge and shape. The present results will contribute to future explorations of many other molecular events such as surface water exchange and protein-ligand dissociation because the same mechanism is involved in such events.

Final Project Report for ER15351 “A Study of New Actinide Zintl Ion Materials”

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peter K. Dorhout

2007-11-12

The structural chemistry of actinide main-group metal materials provides the fundamental basis for the understanding of structural coordination chemistry and the formation of materials with desired or predicted structural features. The main-group metal building blocks, comprising sulfur-group, phosphorous-group, or silicon-group elements, have shown versatility in oxidation state, coordination, and bonding preferences. These building blocks have allowed us to elucidate a series of structures that are unique to the actinide elements, although we can find structural relationships to transition metal and 4f-element materials. In the past year, we investigated controlled metathesis and self-propagating reactions between actinide metal halides and alkali metalmore » salts of main-group metal chalcogenides such as K-P-S salts. Ternary plutonium thiophosphates have resulted from these reactions at low temperature in sealed ampules. we have also focused efforts to examine reactions of Th, U, and Pu halide salts with other alkali metal salts such as Na-Ge-S and Na-Si-Se and copper chloride to identify if self-propagating reactions may be used as a viable reaction to prepare new actinide materials and we prepared a series of U and Th copper chalcogenide materials. Magnetic measurements continued to be a focus of actinide materials prepared in our laboratory. We also contributed to the XANES work at Los Alamos by preparing materials for study and for comparison with environmental samples.« less

76 FR 12358 - Common Formats for Patient Safety Data Collection and Event Reporting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-07

... HHS, AHRQ coordinates the development of a set of common definitions and reporting formats (Common... unsafe conditions that increase risks and hazards to patients. Definitions and other details about PSOs... hospitals and skilled nursing facilities. Definition of Common Formats The term ``Common Formats'' refers to...

Wet formation and structural characterization of quasi-hexagonal monolayers.

PubMed

Batys, Piotr; Weroński, Paweł; Nosek, Magdalena

2016-01-01

We have presented a simple and efficient method for producing dense particle monolayers with controlled surface coverage. The method is based on particle sedimentation, manipulation of the particle-substrate electrostatic interaction, and gentle mechanical vibration of the system. It allows for obtaining quasi-hexagonal structures under wet conditions. Using this method, we have produced a monolayer of 3 μm silica particles on a glassy carbon substrate. By optical microscopy, we have determined the coordinates of the particles and surface coverage of the obtained structure to be 0.82. We have characterized the monolayer structure by means of the pair-correlation function and power spectrum. We have also compared the results with those for a 2D hexagonal monolayer and monolayer generated by random sequential adsorption at the coverage 0.50. We have found the surface fractal dimension to be 2.5, independently of the monolayer surface coverage. Copyright © 2015 Elsevier Inc. All rights reserved.

Sulfur Donor Atom Effects on Copper(I)/O2 Chemistry with Thioanisole Containing Tetradentate N3S Ligand Leading to μ-1,2-Peroxo-Dicopper(II) species

PubMed Central

Lee, Yunho; Lee, Dong-Heon; Park, Ga Young; Lucas, Heather R.; Sarjeant, Amy A. Narducci; Kieber-Emmons, Matthew T.; Vance, Michael A.; Milligan, Ashley E.; Solomon, Edward I.; Karlin, Kenneth D.

2010-01-01

To better understand the effect of thioether coordination in copper-O2 chemistry, the tetradentate N3S ligand LASM (2-(methylthio)-N,N-bis((pyridin-2-yl)methyl)benzenamine) and related alkylether ligand LEOE (2-ethoxy-N,N-bis((pyridin-2-yl)methyl)ethanamine) have been studied. The corresponding copper(I) complexes, [(LASM)CuI]+ (1a) and [(LEOE)CuI]+ (3a) were studies as were the related compound [(LESE)CuI]+ (2a, LESE = (2-ethylthio-N,N-bis((pyridin-2-yl)methyl)ethanamine). The X-ray structure of 1a and its solution conductivity reveal a monomeric molecular structure possessing thioether coordination which persists in solution. In contrast, the C-O stretching frequencies of the derivative Cu(I)-CO complexes reveal that for these complexes, the modulated ligand arms, whether arylthioether, alkylthioether or ether, are not coordinated to the cuprous ion. Electrochemical data for 1a and 2a in CH3CN and DMF show the thioanisole moiety to be a poor electron donor compared to alkylthioether (1a is ~ 200 mV more positive than 2a). The structures of [(LASM)CuII(CH3OH)]2+ (1c) and [(LESE)CuII(CH3OH)]2+ (2c) have also been obtained and indicate nearly identical copper coordination environments. Oxygenation of 1a at reduced temperature gives a characteristic deep blue colored intermediate [{(LASM)CuII}2(O22−)]2+ (1bP) with absorption features at 442 (1,500 M−1cm−1), 530 (8,600 M−1cm−1) and 605 nm (10,400 M−1cm−1); these values compare well to the LMCT transitions previously reported for [{(LESE)CuII}2(O22−)]2+ (2bP). Resonance Raman data for [{(LASM)CuII}2(O22−)]2+ (1bP) support the formation of μ-1,2-peroxo species (ν(O-O) = 828 cm−1 (Δ(18O2) = 48), νsym(Cu-O) = 547 cm−1 (Δ(18O2) = 23) and νasym(Cu-O) = 497 cm−1 (Δ(18O2) = 22) and suggest the LASM ligand is a poorer electron donor to copper than is LESE. In contrast, the oxygenation of [(LEOE)CuI]+ (3a), possessing an ether donor as an analogue of the thioether in LESE, led to the formation of a bis(μ-oxo) species [{(LEOE)CuIII}2(O2−)2]2+ (3bO; 380 nm, ε ~ 10,000 M−1cm−1). This result provides further support for the sulfur influence in 1bP and 2bP, in particular coordination of the sulfur to the Cu. Thermal decomposition of 1bP is accompanied by ligand sulfoxidation. The structure of [{(LEOE)CuII(Cl)}2]+ (3c) generated from the reductive dehalogenation of organic chlorides suggests that the ether moiety is weakly bound to the cupric ion. A detailed discussion of the spectroscopic and structural characteristics of 1bP, 2bP and 3bO is presented. PMID:20822156

Room-temperature polar order in [NH4][Cd(HCOO)3]--a hybrid inorganic-organic compound with a unique perovskite architecture.

PubMed

Gómez-Aguirre, L C; Pato-Doldán, B; Stroppa, A; Yáñez-Vilar, S; Bayarjargal, L; Winkler, B; Castro-García, S; Mira, J; Sánchez-Andújar, M; Señarís-Rodríguez, M A

2015-03-02

We report on the hybrid inorganic-organic ammonium compound [NH4][Cd(HCOO)3], which displays a most unusual framework structure: instead of the expected 4(9)·6(6) topology, it shows an ABX3 perovskite architecture with the peculiarity and uniqueness (among all the up-to-date reported hybrid metal formates) that the Cd ions are connected only by syn-anti formate bridges, instead of anti-anti ones. This change of the coordination mode of the formate ligand is thus another variable that can provide new possibilities for tuning the properties of these versatile functional metal-organic framework materials. The room-temperature crystal structure of [NH4][Cd(HCOO)3] is noncentrosymmetric (S.G.: Pna21) and displays a polar axis. DFT calculations and symmetry mode analysis show that the rather large polarization arising from the off-center shift of the ammonium cations in the cavities (4.33 μC/cm(2)) is partially canceled by the antiparallel polarization coming from the [Cd(HCOO)3](-) framework, thus resulting in a net polarization of 1.35 μC/cm(2). As shown by second harmonic generation studies, this net polarization can be greatly increased by applying pressure (Pmax = 14 GPa), an external stimulus that, in turn, induces the appearance of new structural phases, as confirmed by Raman spectroscopy.

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

Copper coordination polymers from cavitand ligands: hierarchical spaces from cage and capsule motifs, and other topologies† †Electronic supplementary information (ESI) available: Further details of crystallographic studies, thermogravimetric analyses, Raman spectroscopy. CCDC 1401250–1401256. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01801c Click here for additional data file. Click here for additional data file.

PubMed Central

Thorp-Greenwood, Flora L.; Ronson, Tanya K.

2015-01-01

The cyclotriveratrylene-type ligands (±)-tris(iso-nicotinoyl)cyclotriguaiacylene L1 (±)-tris(4-pyridylmethyl)cyclotriguaiacylene L2 and (±)-tris{4-(4-pyridyl)benzyl}cyclotriguaiacylene L3 all feature 4-pyridyl donor groups and all form coordination polymers with CuI and/or CuII cations that show a remarkable range of framework topologies and structures. Complex [CuI 4CuII 1.5(L1)3(CN)6]·CN·n(DMF) 1 features a novel 3,4-connected framework of cyano-linked hexagonal metallo-cages. In complexes [Cu3(L2)4(H2O)3]·6(OTf)·n(DMSO) 2 and [Cu2(L3)2Br2(H2O)(DMSO)]·2Br·n(DMSO) 3 capsule-like metallo-cryptophane motifs are formed which linked through their metal vertices into a hexagonal 2D network of (43.123)(42.122) topology or a coordination chain. Complex [Cu2(L1)2(OTf)2(NMP)2(H2O)2]·2(OTf)·2NMP 4 has an interpenetrating 2D 3,4-connected framework of (4.62.8)(62.8)(4.62.82) topology with tubular channels. Complex [Cu(L1)(NCMe)]·BF4·2(CH3CN)·H2O 5 features a 2D network of 63 topology while the CuII analogue [Cu2(L1)2(NMP)(H2O)]·4BF4·12NMP·1.5H2O 6 has an interpenetrating (10,3)-b type structure and complex [Cu2(L2)2Br3(DMSO)]·Br·n(DMSO) 7 has a 2D network of 4.82 topology. Strategies for formation of coordination polymers with hierarchical spaces emerge in this work and complex 2 is shown to absorb fullerene-C60 through soaking the crystals in a toluene solution. PMID:28791086

Formation of nanocolloidal metacinnabar in mercury-DOM-sulfide systems

USGS Publications Warehouse

Gerbig, Chase A.; Kim, Christopher S.; Stegemeier, John P.; Ryan, Joseph N.; Aiken, George R.

2011-01-01

Direct determination of mercury (Hg) speciation in sulfide-containing environments is confounded by low mercury concentrations and poor analytical sensitivity. Here we report the results of experiments designed to assess mercury speciation at environmentally relevant ratios of mercury to dissolved organic matter (DOM) (i.e., <4 nmol Hg (mg DOM)−1) by combining solid phase extraction using C18 resin with extended X-ray absorption fine structure (EXAFS) spectroscopy. Aqueous Hg(II) and a DOM isolate were equilibrated in the presence and absence of 100 μM total sulfide. In the absence of sulfide, mercury adsorption to the resin increased as the Hg:DOM ratio decreased and as the strength of Hg-DOM binding increased. EXAFS analysis indicated that in the absence of sulfide, mercury bonds with an average of 2.4 ± 0.2 sulfur atoms with a bond length typical of mercury-organic thiol ligands (2.35 Å). In the presence of sulfide, mercury showed greater affinity for the C18 resin, and its chromatographic behavior was independent of Hg:DOM ratio. EXAFS analysis showed mercury–sulfur bonds with a longer interatomic distance (2.51–2.53 Å) similar to the mercury–sulfur bond distance in metacinnabar (2.53 Å) regardless of the Hg:DOM ratio. For all samples containing sulfide, the sulfur coordination number was below the ideal four-coordinate structure of metacinnabar. At a low Hg:DOM ratio where strong binding DOM sites may control mercury speciation (1.9 nmol mg–1) mercury was coordinated by 2.3 ± 0.2 sulfur atoms, and the coordination number rose with increasing Hg:DOM ratio. The less-than-ideal coordination numbers indicate metacinnabar-like species on the nanometer scale, and the positive correlation between Hg:DOM ratio and sulfur coordination number suggests progressively increasing particle size or crystalline order with increasing abundance of mercury with respect to DOM. In DOM-containing sulfidic systems nanocolloidal metacinnabar-like species may form, and these species need to be considered when addressing mercury biogeochemistry.

Self-assembled via axial coordination magnesium porphyrin-imidazole appended fullerene dyad: spectroscopic, electrochemical, computational, and photochemical studies.

PubMed

D'Souza, Francis; El-Khouly, Mohamed E; Gadde, Suresh; McCarty, Amy L; Karr, Paul A; Zandler, Melvin E; Araki, Yasuyaki; Ito, Osamu

2005-05-26

Spectroscopic, redox, and electron transfer reactions of a self-assembled donor-acceptor dyad formed by axial coordination of magnesium meso-tetraphenylporphyrin (MgTPP) and fulleropyrrolidine appended with an imidazole coordinating ligand (C(60)Im) were investigated. Spectroscopic studies revealed the formation of a 1:1 C(60)Im:MgTPP supramolecular complex, and the anticipated 1:2 complex could not be observed because of the needed large amounts of the axial coordinating ligand. The formation constant, K(1), for the 1:1 complex was found to be (1.5 +/- 0.3) x 10(4) M(-1), suggesting fairly stable complex formation. The geometric and electronic structures of the dyads were probed by ab initio B3LYP/3-21G() methods. The majority of the highest occupied frontier molecular orbital (HOMO) was found to be located on the MgTPP entity, while the lowest unoccupied molecular orbital (LUMO) was on the fullerene entity, suggesting that the charge-separated state of the supramolecular complex is C(60)Im(*-):MgTPP(*+). Redox titrations involving MgTPP and C(60)Im allowed accurate determination of the oxidation and reduction potentials of the donor and acceptor entities in the supramolecular complex. These studies revealed more difficult oxidation, by about 100 mV, for MgTPP in the pentacoordinated C(60)Im:MgTPP compared to pristine MgTPP in o-dichlorobenzene. A total of six one-electron redox processes corresponding to the oxidation and reduction of the zinc porphyrin ring and the reduction of fullerene entities was observed within the accessible potential window of the solvent. The excited state events were monitored by both steady state and time-resolved emission as well as transient absorption techniques. In o-dichlorobenzene, upon coordination of C(60)Im to MgTPP, the main quenching pathway involved electron transfer from the singlet excited MgTPP to the C(60)Im moiety. The rate of forward electron transfer, k(CS), calculated from the picosecond time-resolved emission studies was found to be 1.1 x 10(10) s(-1) with a quantum yield, Phi(CS), of 0.99, indicating fast and efficient charge separation. The rate of charge recombination, k(CR), evaluated from nanosecond transient absorption studies, was found to be 8.3 x 10(7) s(-1). A comparison between k(CS) and k(CR) suggested an excellent opportunity to utilize the charge-separated state for further electron-mediating processes.

Experimental and ab initio studies of the reactive processes in gas phase i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH collisions with potassium ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

López, E.; Lucas, J. M.; Andrés, J. de

2014-10-28

Collisions between potassium ions and neutral i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH, all in their electronic ground state, have been studied in the 0.10–10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K{sup +} + i-C{sub 3}H{sub 7}Br collisions KHBr{sup +} formation was observed and quantified, while the analogous KH{sub 2}O{sup +} formation in K{sup +} + i-C{sub 3}H{sub 7}OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C{sub 3}H{sub 7}{sup +} and either KBr or KOH, respectively, have been observed. For all these processes, absolutemore » cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr{sup +} formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.« less

Formation of graphene on BN substrate by vapor deposition method and size effects on its structure

NASA Astrophysics Data System (ADS)

Giang, Nguyen Hoang; Hanh, Tran Thi Thu; Ngoc, Le Nhu; Nga, Nguyen To; Van Hoang, Vo

2018-04-01

We report MD simulation of the growth of graphene by the vapor deposition on a two-dimensional hBN substrate. The systems (containing carbon vapor and hBN substrate) are relaxed at high temperature (1500 K), and then it is cooled down to room one (300 K). Carbon atoms interact with the substrate via the Lennard-Jones potential while the interaction between carbon atoms is computed via the Tersoff potential. Depending on the size of the model, different crystalline honeycomb structures have been found. Structural properties of the graphene obtained at 300 K are studied by analyzing radial distribution functions (RDFs), coordination numbers, ring statistics, interatomic distances, bond-angle distributions and 2D visualization of atomic configurations. We find that the models containing various numbers of atoms have a honeycomb structure. Besides, differences in structural properties of graphene formed by the vapor deposition on the substrate and free standing one are found. Moreover, the size effect on the structure is significant.

The research of statistical properties of colorimetric features of screens with a three-component color formation principle

NASA Astrophysics Data System (ADS)

Zharinov, I. O.; Zharinov, O. O.

2017-12-01

The problem of the research is concerned with quantitative analysis of influence of technological variation of the screen color profile parameters on chromaticity coordinates of the displayed image. Some mathematical expressions which approximate the two-dimensional distribution of chromaticity coordinates of an image, which is displayed on the screen with a three-component color formation principle were proposed. Proposed mathematical expressions show the way to development of correction techniques to improve reproducibility of the colorimetric features of displays.

Structural Peculiarities of Ion-Conductive Organic-Inorganic Polymer Composites Based on Aliphatic Epoxy Resin and Salt of Lithium Perchlorate.

PubMed

Matkovska, Liubov; Iurzhenko, Maksym; Mamunya, Yevgen; Tkachenko, Igor; Demchenko, Valeriy; Synyuk, Volodymyr; Shadrin, Andriy; Boiteux, Gisele

2017-12-01

The article is concerned with hybrid amorphous polymers synthesized basing on epoxy oligomer of diglycide aliphatic ester of polyethylene glycol that was cured by polyethylene polyamine and lithium perchlorate salt. Structural peculiarities of organic-inorganic polymer composites were studied by differential scanning calorimetry, wide-angle X-ray spectra, infrared spectroscopic, scanning electron microscopy, elemental analysis, and transmission and reflective optical microscopy. On the one hand, the results showed that the introduction of LiClO 4 salt into epoxy polymer leads to formation of the coordinative metal-polymer complexes of donor-acceptor type between central Li + ion and ligand. On the other hand, the appearance of amorphous microinclusions, probably of inorganic nature, was also found.

Endothelial cell motility, coordination and pattern formation during vasculogenesis.

PubMed

Czirok, Andras

2013-01-01

How vascular networks assemble is a fundamental problem of developmental biology that also has medical importance. To explain the organizational principles behind vascular patterning, we must understand how can tissue level structures be controlled through cell behavior patterns like motility and adhesion that, in turn, are determined by biochemical signal transduction processes? We discuss the various ideas that have been proposed as mechanisms for vascular network assembly: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and multicellular sprouting guided by cell-cell contacts. All of these processes yield emergent patterns, thus endothelial cells can form an interconnected structure autonomously, without guidance from an external pre-pattern. © 2013 Wiley Periodicals, Inc.

Toward Exploring the Structure of Monolayer to Few-layer TaS2 by Efficient Ultrasound-free Exfoliation

NASA Astrophysics Data System (ADS)

Hu, Yiwei; Hao, Qiaoyan; Zhu, Baichuan; Li, Biao; Gao, Zhan; Wang, Yan; Tang, Kaibin

2018-01-01

Tantalum disulfide nanosheets have attracted great interest due to its electronic properties and device applications. Traditional solution-ased ultrasonic process is limited by ultrasound which may cause the disintegration into submicron-sized flake. Here, an efficient multi-step intercalation and ultrasound-free process has been successfully used to exfoliate 1T-TaS2. The obtained TaS2 nanosheets reveal an average thickness of 3 nm and several micrometers in size. The formation of few-layer TaS2 nanosheets as well as monolayer TaS2 sheets is further confirmed by atomic force microscopy images. The few-layer TaS2 nanosheets remain the 1T structure, whereas monolayer TaS2 sheets show lattice distortion and may adopt the 1H-like structure with trigonal prism coordination.

[Zn(C 7H 3O 5N)] n · nH 2O: A third-order NLO Zn coordination polymer with spiroconjugated structure

NASA Astrophysics Data System (ADS)

Zhou, Guo-Wei; Lan, You-Zhao; Zheng, Fa-Kun; Zhang, Xin; Lin, Meng-Hai; Guo, Guo-Cong; Huang, Jin-Shun

2006-08-01

[Zn(C 7H 3O 5N)] n · nH 2O ( 1) possesses an anticlockwise windmill-like framework structure and formats spiroconjugation over the infinite molecular layer that is predicted to have large static third-order polarizability and the convergence value of γxxxx reaches 6.86 × 10 -33 esu in the case of zero input photon energy. The third-order NLO properties of 1 were investigated via Z-scan techniques at wavelength of 532 nm. It showed strong third-order NLO absorptive properties, and its n2 value was calculated to be 4.15 × 10 -11 esu. The relationship between the spiroconjugated structure and the NLO property has been discussed, which supposed to be more valuable for the NLO research.

Utilizing semantic networks to database and retrieve generalized stochastic colored Petri nets

NASA Technical Reports Server (NTRS)

Farah, Jeffrey J.; Kelley, Robert B.

1992-01-01

Previous work has introduced the Planning Coordinator (PCOORD), a coordinator functioning within the hierarchy of the Intelligent Machine Mode. Within the structure of the Planning Coordinator resides the Primitive Structure Database (PSDB) functioning to provide the primitive structures utilized by the Planning Coordinator in the establishing of error recovery or on-line path plans. This report further explores the Primitive Structure Database and establishes the potential of utilizing semantic networks as a means of efficiently storing and retrieving the Generalized Stochastic Colored Petri Nets from which the error recovery plans are derived.

Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations

DOE PAGES

Ziatdinov, Maxim; Dyck, Ondrej; Maksov, Artem; ...

2017-12-07

Recent advances in scanning transmission electron and scanning probe microscopies have opened unprecedented opportunities in probing the materials structural parameters and various functional properties in real space with an angstrom-level precision. This progress has been accompanied by exponential increase in the size and quality of datasets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large datasets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extracting informationmore » from atomically resolved images including location of the atomic species and type of defects. We develop a “weakly-supervised” approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular “rotor”. In conclusion, this deep learning based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.« less

Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ziatdinov, Maxim; Dyck, Ondrej; Maksov, Artem

Recent advances in scanning transmission electron and scanning probe microscopies have opened unprecedented opportunities in probing the materials structural parameters and various functional properties in real space with an angstrom-level precision. This progress has been accompanied by exponential increase in the size and quality of datasets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large datasets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extracting informationmore » from atomically resolved images including location of the atomic species and type of defects. We develop a “weakly-supervised” approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular “rotor”. In conclusion, this deep learning based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.« less

Crystal structure of tris­(trans-1,2-cyclo­hexa­ne­diamine-κ2 N,N′)chromium(III) tetra­chlorido­zincate chloride trihydrate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2016-01-01

The structure of the title double salt, [Cr(rac-chxn)3][ZnCl4]Cl·3H2O (chxn is trans-1,2-cyclo­hexa­nedi­amine; C6H14N2), has been determined from synchrotron data. The CrIII ion is coordinated by six N atoms of three chelating chxn ligands, displaying a slightly distorted octa­hedral coordination environment. The distorted tetra­hedral [ZnCl4]2− anion, the isolated Cl− anion and three lattice water mol­ecules remain outside the coordination sphere. The Cr—N(chxn) bond lengths are in a narrow range between 2.0737 (12) and 2.0928 (12) Å; the mean N—Cr—N bite angle is 82.1 (4)°. The crystal packing is stabilized by hydrogen-bonding inter­actions between the amino groups of the chxn ligands and the water mol­ecules as donor groups, and O atoms of the water mol­ecules, chloride anions and Cl atoms of the [ZnCl4]2− anions as acceptor groups, leading to the formation of a three-dimensional network. The [ZnCl4]2− anion is disordered over two sets of sites with an occupancy ratio of 0.94:0.06. PMID:27308016

Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations.

PubMed

Ziatdinov, Maxim; Dyck, Ondrej; Maksov, Artem; Li, Xufan; Sang, Xiahan; Xiao, Kai; Unocic, Raymond R; Vasudevan, Rama; Jesse, Stephen; Kalinin, Sergei V

2017-12-26

Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of data sets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large data sets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extract information from atomically resolved images including location of the atomic species and type of defects. We develop a "weakly supervised" approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular "rotor". This deep learning-based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.

(N-Benzyl-N-isopropyl-dithio-carbamato)chloridodiphenyl-tin(IV).

PubMed

Abdul Muthalib, Amirah Faizah; Baba, Ibrahim; Mohamed Tahir, Mohamed Ibrahim; Ng, Seik Weng; Tiekink, Edward R T

2010-08-11

The Sn(IV) atom in the title organotin dithio-carbamate, [Sn(C(6)H(5))(2)(C(11)H(14)NS(2))Cl], is penta-coordinated by an asymmetrically coordinating dithio-carbamate ligand, a Cl and two ispo-C atoms of the Sn-bound phenyl groups. The resulting C(2)ClS(2) donor set defines a coordination geometry inter-mediate between square-pyramidal and trigonal-bipyramidal with a slight tendency towards the latter. The formation of close intra-molecular C-H⋯Cl and C-H⋯S contacts precludes the Cl and S atoms from forming significant inter-molecular contacts. The presence of C-H⋯π contacts leads to the formation of supra-molecular arrays that stack along the b axis.

Defects in doped LaGaO3 anionic conductors: linking NMR spectral features, local environments, and defect thermodynamics.

PubMed

Blanc, Frédéric; Middlemiss, Derek S; Gan, Zhehong; Grey, Clare P

2011-11-09

Doped lanthanum gallate perovskites (LaGaO(3)) constitute some of the most promising electrolyte materials for solid oxide fuel cells operating in the intermediate temperature regime. Here, an approach combining experimental multinuclear NMR spectroscopy with density functional theory total energy and GIPAW NMR calculations yields a comprehensive understanding of the structural and defect chemistries of Sr- and Mg-doped LaGaO(3) anionic conductors. The DFT energetics demonstrate that Ga-V(O)-Ga (V(O) = oxygen vacancy) environments are favored (vs Ga-V(O)-Mg, Mg-V(O)-Mg and Mg-O-Mg-V(O)-Ga) across a range y = 0.0625, 0.125, and 0.25 of fractional Mg contents in LaGa(1-y)Mg(y)O(3-y/2). The results are interpreted in terms of doping and mean phase formation energies (relative to binary oxides) and are compared with previous calculations and experimental calorimetry data. Experimental multinuclear NMR data reveal that while Mg sites remain six-fold coordinated across the range of phase stoichiometries, albeit with significant structural disorder, a stoichiometry-dependent minority of the Ga sites resonate at a shift consistent with Ga(V) coordination, demonstrating that O vacancies preferentially locate in the first anion coordination shell of Ga. The strong Mg-V(O) binding inferred by previous studies is not observed here. The (17)O NMR spectra reveal distinct resonances that can be assigned by using the GIPAW NMR calculations to anions occupying equatorial and axial positions with respect to the Ga(V)-V(O) axis. The disparate shifts displayed by these sites are due to the nature and extent of the structural distortions caused by the O vacancies.

Mechanochemical synthesis of low-fluorine doped aluminum hydroxide fluorides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scalise, V.; Scholz, G., E-mail: gudrun.scholz@rz.hu-berlin.de; Kemnitz, E., E-mail: erhard.kemnitz@chemie.hu-berlin.de

2016-11-15

Different aluminum hydroxide fluorides with varying Al/F molar ratios from 1:1.5 up to 1:0.05 were successfully synthesized by mechanochemical reactions. The characterization of the products by XRD, {sup 27}Al and {sup 19}F MAS NMR, thermal analysis, nitrogen adsorption and zeta potential techniques allows a detailed understanding of the structure and surface properties of the products. Using γ-Al(OH){sub 3} and β-AlF{sub 3}·3H{sub 2}O as OH- and F-sources, respectively, strongly disordered products were obtained with an Al: F molar ratio higher than 1:0.25. The fluorination degree has affected the amount of 4- and 5-fold coordinated Al sites, not present in the reactants.more » An evolution of the sub-coordinated Al-species has been detected also as a consequence of annealing processes. Obviously, these species affect the phase transition to alumina, by decreasing the transition temperature of the formation of α-Al{sub 2}O{sub 3}. Synthesis conditions (milling time, fluorination degree) play a crucial role for the product composition. - Graphical abstract: The impact of the combined action of the milling and the different fluorine doping on the structure of new aluminum hydroxide fluorides was followed by {sup 27}Al and {sup 19}F NMR and by other complementary techniques. - Highlights: • Low F-doped Al-hydroxide fluorides can be successfully prepared by mechanosynthesis. • Both F-doping and mechanochemical synthesis introduce a high number of defects in the structure. • The fluorination degree affects the amount of 4- and 5-fold coordinated Al sites as well as the transition temperature to corundum.« less

Two novel mixed-ligand complexes containing organosulfonate ligands.

PubMed

Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

2008-07-01

The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

A copper(II) paddle-wheel structure of tranexamic acid: di-chloro-tetra-kis-[μ-4-(ammonio-meth-yl)cyclo-hexane-1-carboxyl-ato-O,O']dicopper(II) dichloride hexa-hydrate.

PubMed

Altaf, Muhammad; Stoeckli-Evans, Helen

2017-10-01

Tranexamic acid [systematic name: trans -4-(amino-meth-yl)cyclo-hexane-1-carb-oxy-lic acid], is an anti-fibrinolytic amino acid that exists as a zwitterion [ trans -4-(ammonio-meth-yl)cyclo-hexane-1-carboxyl-ate] in the solid state. Its reaction with copper chloride leads to the formation of a compound with a copper(II) paddle-wheel structure that crystallizes as a hexa-hydrate, [Cu 2 Cl 2 (C 8 H 15 NO 2 ) 4 ] 2+ ·2Cl - ·6H 2 O. The asymmetric unit is composed of a copper(II) cation, two zwitterionic tranexamic acid units, a coordinating Cl - anion and a free Cl - anion, together with three water mol-ecules of crystallization. The whole structure is generated by inversion symmetry, with the Cu⋯Cu axle of the paddle-wheel dication being located about a center of symmetry. The cyclo-hexane rings of the zwitterionic tranexamic acid units have chair conformations. The carboxyl-ate groups that bridge the two copper(II) cations are inclined to one another by 88.4 (8)°. The copper(II) cation is ligated by four carboxyl-ate O atoms in the equatorial plane and by a Cl - ion in the axial position. Hence, it has a fivefold O 4 Cl coordination sphere with a perfect square-pyramidal geometry and a τ 5 index of zero. In the crystal, the paddle-wheel dications are linked by a series of N-H⋯Cl hydrogen bonds, involving the coordinating and free Cl - ions, forming a three-dimensional network. This network is strengthened by a series of N-H⋯O water , O water -H⋯Cl and O water -H⋯O hydrogen bonds.

Carbonate-mediated Mars-van Krevelen mechanism for CO oxidation on cobalt-doped ceria catalysts: facet-dependence and coordination-dependence.

PubMed

Liu, Bing; Li, Wenping; Song, Weiyu; Liu, Jian

2018-06-13

Carbonate intermediates have been reported to play an active role in CO oxidation over ceria-based catalysts in recent experimental studies. However, the detailed CO oxidation mechanism involving carbonate intermediates over ceria-based catalysts remains obscure. In this work, we carried out systematic density functional theory calculations corrected by on-site Coulomb interactions (DFT+U) to investigate the complete CO oxidation mechanism involving carbonate intermediates over cobalt-doped CeO2 catalysts, aiming to unravel how the carbonate participates in CO oxidation and shed light on the underlying factors that control the carbonate-mediated reaction mechanism. A novel carbonate-mediated Mars-van Krevelen (M-vK) mechanism was proposed, in which the carbonate acts as an active intermediate rather than a spectator and can react with CO to form CO2. This carbonate-mediated M-vK mechanism is facet-dependent because it is predominant on the (110) surface whereas the conventional M-vK mechanism is more favorable on (111) and (100) surfaces. The origin of facet-dependence was discussed by analyzing the geometric and electronic structures. It is found that the negatively charged bent CO2- intermediate formed on the (110) surface plays a critical role in the carbonate-mediated M-vK mechanism, whereas the formation of a neutral linear CO2 intermediate on (111) and (100) surfaces hinders the carbonate-mediated M-vK mechanism. The surface oxygen vacancy hinders the formation of carbonate intermediates, indicating that the carbonate-mediated M-vK mechanism is also vacancy-dependent. The formation of carbonate intermediates on different metal (Ti, V, W, Mo and Re) doped CeO2(110) surfaces was studied and the results indicate that the coordination environment of the dopant species is a key factor that determines the carbonate-mediated M-vK mechanism. This study provides atomic-scale insights into the reaction mechanism involving carbonate intermediates and the structure-mechanism relationship for CO oxidation over cobalt-ceria catalysts.

Reaction mechanism of molybdoenzyme formate dehydrogenase.

PubMed

Leopoldini, Monica; Chiodo, Sandro G; Toscano, Marirosa; Russo, Nino

2008-01-01

Formate dehydrogenase is a molybdoenzyme of the anaerobic formate hydrogen lyase complex of the Escherichia coli microorganism that catalyzes the oxidation of formate to carbon dioxide. The two proposed mechanisms of reaction, which differ in the occurrence of a direct coordination or not of a SeCys residue to the molybdenum metal during catalysis were analyzed at the density functional level in both vacuum and protein environments. Some DF functionals, in addition to the very popular B3LYP one, were employed to compute barrier heights. Results revealed the role played by the SeCys residue in performing the abstraction of the proton from the formate substrate. The computation of the energetic profiles for both mechanisms indicated that the reaction barriers are higher when the selenium is directly coordinated to the metal, whereas less energy is required when SeCys is not a ligand at the molybdenum site.

Discrete Kalman filtering equations of second-order form for control-structure interaction simulations

NASA Technical Reports Server (NTRS)

Park, K. C.; Alvin, K. F.; Belvin, W. Keith

1991-01-01

A second-order form of discrete Kalman filtering equations is proposed as a candidate state estimator for efficient simulations of control-structure interactions in coupled physical coordinate configurations as opposed to decoupled modal coordinates. The resulting matrix equation of the present state estimator consists of the same symmetric, sparse N x N coupled matrices of the governing structural dynamics equations as opposed to unsymmetric 2N x 2N state space-based estimators. Thus, in addition to substantial computational efficiency improvement, the present estimator can be applied to control-structure design optimization for which the physical coordinates associated with the mass, damping and stiffness matrices of the structure are needed instead of modal coordinates.

48 CFR 952.223-78 - Sustainable acquisition program.

Code of Federal Regulations, 2010 CFR

2010-10-01

... activities with and submit required reports through the Environmental Sustainability Coordinator or... reports through the Environmental Sustainability Coordinator or equivalent position. Reporting under this... prepare and submit performance reports, if required, using prescribed DOE formats, at the end of the...

How precise are reported protein coordinate data?

PubMed

Konagurthu, Arun S; Allison, Lloyd; Abramson, David; Stuckey, Peter J; Lesk, Arthur M

2014-03-01

Atomic coordinates in the Worldwide Protein Data Bank (wwPDB) are generally reported to greater precision than the experimental structure determinations have actually achieved. By using information theory and data compression to study the compressibility of protein atomic coordinates, it is possible to quantify the amount of randomness in the coordinate data and thereby to determine the realistic precision of the reported coordinates. On average, the value of each C(α) coordinate in a set of selected protein structures solved at a variety of resolutions is good to about 0.1 Å.

Theory of Gearing

DTIC Science & Technology

1989-12-01

motion of rigid bodies and their kinematical and dynamic characteristics, which are associated with different coordinate systems. In the theory of...rigidly connected surfaces EF and Ep with respect to gears I and 2 may be represented as the motion of a rigid body . However, we assume that in the... rigid body . Coordinate tran:;formation will be considered for systems with (1) common origin and noncoincident coordinate axes and (2) noncoincident

A Network Analysis Perspective to Implementation: The Example of Health Links to Promote Coordinated Care.

PubMed

Yousefi Nooraie, Reza; Khan, Sobia; Gutberg, Jennifer; Baker, G Ross

2018-01-01

Although implementation models broadly recognize the importance of social relationships, our knowledge about applying social network analysis (SNA) to formative, process, and outcome evaluations of health system interventions is limited. We explored applications of adopting an SNA lens to inform implementation planning, engagement and execution, and evaluation. We used Health Links, a province-wide program in Canada aiming to improve care coordination among multiple providers of high-needs patients, as an example of a health system intervention. At the planning phase, an SNA can depict the structure, network influencers, and composition of clusters at various levels. It can inform the engagement and execution by identifying potential targets (e.g., opinion leaders) and by revealing structural gaps and clusters. It can also be used to assess the outcomes of the intervention, such as its success in increasing network connectivity; changing the position of certain actors; and bridging across specialties, organizations, and sectors. We provided an overview of how an SNA lens can shed light on the complexity of implementation along the entire implementation pathway, by revealing the relational barriers and facilitators, the application of network-informed and network-altering interventions, and testing hypotheses on network consequences of the implementation.

Structural Modulation from 1D Chain to 3D Framework: Improved Thermostability, Insensitivity, and Energies of Two Nitrogen-Rich Energetic Coordination Polymers.

PubMed

Guo, Zhaoqi; Wu, Yunlong; Deng, Chongqing; Yang, Guoping; Zhang, Jiangong; Sun, Zhihua; Ma, Haixia; Gao, Chao; An, Zhongwei

2016-11-07

Two new energetic coordination polymers (CPs) [Pb(BT)(H 2 O) 3 ] n (1) and [Pb 3 (DOBT) 3 (H 2 O) 2 ] n ·(4H 2 O) n (2) with 1D and 3D structures were synthesized by employing two rational designed ligands, 1H,1'H-5,5'-bitetrazole (H 2 BT) and 1H,1'H-[5,5'-bitetrazole]-1,1'-diol ligands (DHBT), respectively. Thermal analyses and sensitivity tests show that the 3D architecture reinforces the network of 2 which has higher thermal stability and lower sensitivity than that of 1. Through oxygen-bomb combustion calorimetry the molar enthalpy of formation of 2 is derived to be much higher than that of 1 as well as the reported CPs. Herein, more importantly, the heats of detonation (ΔH det ) were calculated according to the decomposition products of TG-DSC-MS-FTIR simultaneous analyses for the first time. The calculated results show that ΔH det of 2 is 23% higher than that of 1. This research demonstrates that 3D energetic CP with outstanding energetic properties can be obtained through efficient and reasonable design.

A novel conformation of gel grown biologically active cadmium nicotinate

NASA Astrophysics Data System (ADS)

Nair, Lekshmi P.; Bijini, B. R.; Divya, R.; Nair, Prabitha B.; Eapen, S. M.; Dileep Kumar, B. S.; Nishanth Kumar, S.; Nair, C. M. K.; Deepa, M.; Rajendra Babu, K.

2017-11-01

The elimination of toxic heavy metals by the formation of stable co-ordination compounds with biologically active ligands is applicable in drug designing. A new crystalline complex of cadmium with nicotinic acid is grown at ambient temperature using the single gel diffusion method in which the crystal structure is different from those already reported. Single crystal x-ray diffraction reveals the identity of crystal structure belonging to monoclinic system, P21/c space group with cell dimensions a = 17.220 (2) Å, b = 10.2480 (2) Å, c = 7.229(9) Å, β = 91.829(4)°. Powder x-ray diffraction analysis confirmed the crystallinity of the sample. The unidentate mode of co-ordination between the metal atom and the carboxylate group is supported by the Fourier Transform Infra Red spectral data. Thermal analysis ensures the thermal stability of the complex. Kinetic and thermodynamic parameters are also calculated. The stoichiometry of the complex is confirmed by the elemental analysis. The UV-visible spectral analysis shows the wide transparency window of the complex in the visible region. The band gap of the complex is found to be 3.92 eV. The complex shows excellent antibacterial and antifungal activity.

Different water clusters dependent on long-chain dicarboxylates in two Ag(I) coordination polymers: Synthesis, structure and thermal stability

NASA Astrophysics Data System (ADS)

Sun, Di; Liu, Fu-Jing; Hao, Hong-Jun; Huang, Rong-Bin; Zheng, Lan-Sun

2011-10-01

Two mixed-ligand Ag(I) coordination polymers (CPs), [Ag 2(bipy) 2(sub)·5H 2O] n ( 1), [Ag 2(bipy) 2(aze)·3H 2O] n ( 2), (bipy = 4,4'-bipyridine, H 2sub = suberic acid, H 2aze = azelaic acid) have been synthesized and structurally characterized by elemental analysis, infrared (IR) spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric (TG) analysis, and single crystal X-ray diffraction. Both 1 and 2 are two-dimensional (2D) sheets based on infinite [Ag(bipy)] n double chain incorporating Ag⋯Ag interactions. Interestingly, two different water clusters are encapsulated in the voids between the sheets of 1 and 2. For 1, one water decamer (H 2O) 10 based on a cyclic water tetramer was hydrogen-bonded with the host 2D sheet. While, one water hexamer (H 2O) 6 also based on a cyclic water tetramer was observed in 2. Comparing the experimental results, it is comprehensible that the dicarboxylates play a crucial role in the formation of the different water clusters. Moreover, the thermal stabilities of them were also discussed.

Structural morphology study of Cd2+ induced Langmuir Blodgett multilayer films of arachidic acid

NASA Astrophysics Data System (ADS)

Roy, Dhrubojyoti; Das, Nayan Mani; Gupta, P. S.

2013-04-01

The organization and headgroup co-ordination of Cadmium Arachidate (CdAA) molecule in Langmuir-Blodgett (LB) multilayer films deposited on hydrophilic Glass (SiO2) and Silicon (100) substrate at normal subphase pH (6.8) are studied. X-ray diffraction (XRD) and X-ray reflectivity (XRR) study reveals ordered layer by layer organization with uniform packing of CdAA molecules, and with a small tilt angle of alkyl chain of CdAA molecule equal to 6.8° ± 1.75°. Electron density profiles (EDPs) shows that the coverage of films remains almost constant with increase in bilayer thickness which indicate very little presence of pinhole defects. AFM study for 25 ML shows that coverage of the film remain intact upto 22nd ML and then decreases sharply due to presence of pinhole defects. Fourier transform infrared spectroscopy (FTIR) study is also consistent with XRD and XRR study of ordered deposition of CdAA molecule. FTIR and X-ray photoelectron spectroscopy (XPS) study indicates the formation of unidentate bridging metal-carboxylate coordination type headgroups consistent with one cadmium metal ion between two carboxylate (COO) groups in each headgroup structure.

Embryo as an active granular fluid: stress-coordinated cellular constriction chains

NASA Astrophysics Data System (ADS)

Gao, Guo-Jie Jason; Holcomb, Michael C.; Thomas, Jeffrey H.; Blawzdziewicz, Jerzy

2016-10-01

Mechanical stress plays an intricate role in gene expression in individual cells and sculpting of developing tissues. However, systematic methods of studying how mechanical stress and feedback help to harmonize cellular activities within a tissue have yet to be developed. Motivated by our observation of the cellular constriction chains (CCCs) during the initial phase of ventral furrow formation in the Drosophila melanogaster embryo, we propose an active granular fluid (AGF) model that provides valuable insights into cellular coordination in the apical constriction process. In our model, cells are treated as circular particles connected by a predefined force network, and they undergo a random constriction process in which the particle constriction probability P is a function of the stress exerted on the particle by its neighbors. We find that when P favors tensile stress, constricted particles tend to form chain-like structures. In contrast, constricted particles tend to form compact clusters when P favors compression. A remarkable similarity of constricted-particle chains and CCCs observed in vivo provides indirect evidence that tensile-stress feedback coordinates the apical constriction activity. Our particle-based AGF model will be useful in analyzing mechanical feedback effects in a wide variety of morphogenesis and organogenesis phenomena.

Luminescent Thermochromism of 2D Coordination Polymers Based on Copper(I) Halides with 4-Hydroxythiophenol

PubMed Central

Troyano, Javier; Perles, Josefina; Amo-Ochoa, Pilar; Martínez, Jose Ignacio; Concepción Gimeno, Maria; Fernández-Moreira, Vanesa; Zamora, Félix; Delgado, Salomé

2016-01-01

Solvothermal reactions between copper(I) halides and 4-mercaptophenol give rise to the formation of three coordination polymers with general formula [Cu3X(HT)2]n (X= Cl, 1; Br, 2; and I, 3). The structures of these coordination polymers have been determined by X-ray diffraction at both room temperature and low temperature (110 K), showing a general shortening in Cu-S, Cu-X and Cu···Cu bond distances at low temperatures. 1 and 2 are isostructural consisting of layers in which the halogen ligands act as μ3-bridges joining two Cu1 and one Cu2 atoms whereas in 3 the iodine ligands is as μ4-mode but the layers are quasi-isostructural with 1 or 2. These compounds show a reversible thermochromic luminescence, with strong orange emission for 1 and 2, but weaker for 3 at room temperature, while upon cooling at 77 K 1 and 2 show stronger yellow as well as 3 displays stronger green emission. DFT calculations have been used to rationalise these observations. These results suggest a high potential for this novel and promising stimuli-responsive materials. PMID:27809369

Luminescent Thermochromism of 2D Coordination Polymers Based on Copper(I) Halides with 4-Hydroxythiophenol.

PubMed

Troyano, Javier; Perles, Josefina; Amo-Ochoa, Pilar; Martínez, Jose Ignacio; Concepción Gimeno, Maria; Fernández-Moreira, Vanesa; Zamora, Félix; Delgado, Salomé

2016-12-12

Solvothermal reactions between copper(I) halides and 4-mercaptophenol give rise to the formation of three coordination polymers with general formula [Cu 3 X(HT) 2 ] n (X=Cl, 1; Br, 2; and I, 3). The structures of these coordination polymers have been determined by X-ray diffraction at both room- and low temperature (110 K), showing a general shortening in Cu-S, Cu-X and Cu-Cu bond lengths at low temperatures. 1 and 2 are isostructural, consisting of layers in which the halogen ligands act as μ 3 -bridges joining two Cu1 and one Cu2 atoms whereas in 3 the iodine ligands is as μ 4 -mode but the layers are quasi-isostructural with 1 or 2. These compounds show a reversible thermochromic luminescence, with strong orange emission for 1 and 2, but weaker for 3 at room temperature, whereas upon cooling at 77 K 1 and 2 show stronger yellow emission, and 3 displays stronger green emission. DFT calculations have been used to rationalize these observations. These results suggest a high potential for this novel and promising stimuli-responsive materials. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Individual Differences in Algebraic Cognition: Relation to the Approximate Number and Sematic Memory Systems

PubMed Central

Geary, David C.; Hoard, Mary K.; Nugent, Lara; Rouder, Jeffrey N.

2015-01-01

The relation between performance on measures of algebraic cognition and acuity of the approximate number system (ANS) and memory for addition facts was assessed for 171 (92 girls) 9th graders, controlling parental education, sex, reading achievement, speed of numeral processing, fluency of symbolic number processing, intelligence, and the central executive component of working memory. The algebraic tasks assessed accuracy in placing x,y pairs in the coordinate plane, speed and accuracy of expression evaluation, and schema memory for algebra equations. ANS acuity was related to accuracy of placements in the coordinate plane and expression evaluation, but not schema memory. Frequency of fact-retrieval errors was related to schema memory but not coordinate plane or expression evaluation accuracy. The results suggest the ANS may contribute to or is influenced by spatial-numerical and numerical only quantity judgments in algebraic contexts, whereas difficulties in committing addition facts to long-term memory may presage slow formation of memories for the basic structure of algebra equations. More generally, the results suggest different brain and cognitive systems are engaged during the learning of different components of algebraic competence, controlling demographic and domain general abilities. PMID:26255604

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Interagency Coordination Structures in Stabilization and Reconstruction Operations

DTIC Science & Technology

2010-06-11

poor interagency coordination and lack of unity as significant problems that compromise USG efforts in Afghanistan. This lack of interagency...objectives into consolidated tactical level goals and initiatives. Lack of interagency coordination structures at this level causes a variety of...Iraqi Reconstruction noticed a similar series of issues in an audit of civil police training in Afghanistan and Iraq. The lack of coordination

Preliminary Study for a Tetrahedron Formation: Quality Factors and Visualization

NASA Technical Reports Server (NTRS)

Guzman, Jose J.; Schiff, Conrad; Bauer, Frank (Technical Monitor)

2002-01-01

Spacecraft flying in tetrahedron formations are excellent for electromagnetic and plasma studies. The quality of the science recorded is strongly affected by the tetrahedron evolution. This paper is a preliminary study on the computation of quality factors and visualization for a formation of four or five satellites. Four of the satellites are arranged geometrically in a tetrahedron shape. If a fifth satellite is present, it is arbitrarily initialized at the geometric center of the tetrahedron. The fifth satellite could act as a collector or as a spare spacecraft. Tetrahedron natural coordinates are employed for the initialization. The natural orbit evolution is visualized in geocentric equatorial inertial and in geocentric solar magnetospheric coordinates.

Steric modulation of coordination number and reactivity in the synthesis of lanthanoid(III) formamidinates.

PubMed

Cole, Marcus L; Deacon, Glen B; Forsyth, Craig M; Junk, Peter C; Konstas, Kristina; Wang, Jun

2007-01-01

Reactions of a range of the readily prepared and sterically tunable N,N'-bis(aryl)formamidines with lanthanoid metals and bis(pentafluorophenyl)mercury (Hg(C6F5)2) in THF have given an extensive series of tris(formamidinato)lanthanoid(III) complexes, [Ln(Form)3(thf)n], namely [La(o-TolForm)3(thf)2], [Er(o-TolForm)3(thf)], [La(XylForm)3(thf)], [Sm(XylForm)3], [Ln(MesForm)3] (Ln=La, Nd, Sm and Yb), [Ln(EtForm)3] (Ln=La, Nd, Sm, Ho and Yb), and [Ln(o-PhPhForm)3] (Ln=La, Nd, Sm and Er). [For an explanation of the N,N'-bis(aryl)formamidinate abbreviations used see Scheme 1.] Analogous attempts to prepare [Yb(o-TolForm)3] by this method invariably yielded [{Yb(o-TolForm)2(mu-OH)(thf)}2], but [Yb(o-TolForm)3] was isolated from a metathesis synthesis. X-ray crystal structures show exclusively N,N'-chelation of the Form ligands and a gradation in coordination number with Ln3+ size and with Form ligand bulk. The largest ligands, MesForm, EtForm and o-PhPhForm give solely homoleptic complexes, the first two being six-coordinate, the last having an eta1-pi-Ar--Ln interaction. Reaction of lanthanoid elements and Hg(C6F5)2 with the still bulkier DippFormH in THF resulted in C--F activation and formation of [Ln(DippForm)2F(thf)] (Ln=La, Ce, Nd, Sm and Tm) complexes, and o-HC6F4O(CH2)4DippForm in which the formamidine is functionalised by a ring-opened THF that has trapped tetrafluorobenzyne. Analogous reactions between Ln metals, Hg(o-HC6F4)2 and DippFormH yielded [Ln(DippForm)2F(thf)] (Ln=La, Sm and Nd) and 3,4,5-F3C6H2O(CH2)4DippForm. X-ray crystal structures of the heteroleptic fluorides show six-coordinate monomers with two chelating DippForm ligands and cisoid fluoride and THF ligands in a trigonal prismatic array. The organometallic species [Ln(DippForm)2(C[triple chemical bond]CPh)(thf)] (Ln=Nd or Sm) are obtained from reaction of Nd metal, bis(phenylethynyl)mercury (Hg(C[triple chemical bond]CPh)2) and DippFormH, and the oxidation of [Sm(DippForm)2(thf)2] with Hg(C[triple chemical bond]CPh)2, respectively. The monomeric, six-coordinate, cisoid [Ln(DippForm)2(C[triple chemical bond]CPh)(thf)] complexes have trigonal prismatic geometries and rare (for Ln) terminal C[triple chemical bond]CPh groups with contrasting Ln--C[triple chemical bond]C angles (Ln=Nd, 170.9(4) degrees; Ln=Sm, 142.9(7) degrees). Their formation lends support to the view that [Ln(DippForm)2F(thf)] complexes arise from oxidative formation and C--F activation of [Ln(DippForm)2(C6F5)] intermediates.

On the Plausibility of Pseudosugar Formation in Cometary Ices and Oxygen-rich Tholins

NASA Astrophysics Data System (ADS)

Lavado, Nieves; Ávalos, Martín; Babiano, Reyes; Cintas, Pedro; Light, Mark E.; Jiménez, José Luis; Palacios, Juan C.

2016-03-01

We revisit herein the formation and structure of dihydroxy dioxanes, which can be obtained from prebiotically available precursors and can be regarded as primeval sugar surrogates. Previous studies dealing with the heterogeneous composition of interstellar bodies point to the existence of significant amounts of small polyalcohols along with oxygen-containing oligomers. Even though such derivatives did not give rise to nucleosides and oligonucleotides, nor they were incorporated into subsequent metabolic routes, molecular chimeras based on sugar-like species could be opportunistic scaffolds in pre-evolutionary scenarios. We could figure out that pseudosugars, assembled by hemiacetalic bonds from available precursors in both interstellar and terrestrial scenarios, were presumably more abundant than thought. Moreover, these species share some key features with naturally-occurring sugar rings, such as anomeric preferences, coordinating ability, and the prevalent occurrence of racemic compounds.

Mind-to-mind heteroclinic coordination: Model of sequential episodic memory initiation.

PubMed

Afraimovich, V S; Zaks, M A; Rabinovich, M I

2018-05-01

Retrieval of episodic memory is a dynamical process in the large scale brain networks. In social groups, the neural patterns, associated with specific events directly experienced by single members, are encoded, recalled, and shared by all participants. Here, we construct and study the dynamical model for the formation and maintaining of episodic memory in small ensembles of interacting minds. We prove that the unconventional dynamical attractor of this process-the nonsmooth heteroclinic torus-is structurally stable within the Lotka-Volterra-like sets of equations. Dynamics on this torus combines the absence of chaos with asymptotic instability of every separate trajectory; its adequate quantitative characteristics are length-related Lyapunov exponents. Variation of the coupling strength between the participants results in different types of sequential switching between metastable states; we interpret them as stages in formation and modification of the episodic memory.

Mind-to-mind heteroclinic coordination: Model of sequential episodic memory initiation

NASA Astrophysics Data System (ADS)

Afraimovich, V. S.; Zaks, M. A.; Rabinovich, M. I.

2018-05-01

Retrieval of episodic memory is a dynamical process in the large scale brain networks. In social groups, the neural patterns, associated with specific events directly experienced by single members, are encoded, recalled, and shared by all participants. Here, we construct and study the dynamical model for the formation and maintaining of episodic memory in small ensembles of interacting minds. We prove that the unconventional dynamical attractor of this process—the nonsmooth heteroclinic torus—is structurally stable within the Lotka-Volterra-like sets of equations. Dynamics on this torus combines the absence of chaos with asymptotic instability of every separate trajectory; its adequate quantitative characteristics are length-related Lyapunov exponents. Variation of the coupling strength between the participants results in different types of sequential switching between metastable states; we interpret them as stages in formation and modification of the episodic memory.

Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.

PubMed

Berns, Veronica M; Fredrickson, Daniel C

2014-10-06

Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity.

Crystalline Coordination Networks of Zero-Valent Metal Centers: Formation of a 3-Dimensional Ni(0) Framework with m-Terphenyl Diisocyanides.

PubMed

Agnew, Douglas W; DiMucci, Ida M; Arroyave, Alejandra; Gembicky, Milan; Moore, Curtis E; MacMillan, Samantha N; Rheingold, Arnold L; Lancaster, Kyle M; Figueroa, Joshua S

2017-12-06

A permanently porous, three-dimensional metal-organic material formed from zero-valent metal nodes is presented. Combination of ditopic m-terphenyl diisocyanide, [CNAr Mes2 ] 2 , and the d 10 Ni(0) precursor Ni(COD) 2 , produces a porous metal-organic material featuring tetrahedral [Ni(CNAr Mes2 ) 4 ] n structural sites. X-ray absorption spectroscopy provides firm evidence for the presence of Ni(0) centers, whereas gas-sorption and thermogravimetric analysis reveal the characteristics of a robust network with a microdomain N 2 -adsorption profile.

Crystalline Coordination Networks of Zero-Valent Metal Centers: Formation of a 3-Dimensional Ni(0) Framework with m-Terphenyl Diisocyanides

DOE PAGES

Agnew, Douglas W.; DiMucci, Ida M.; Arroyave, Alejandra; ...

2017-11-13

A permanently porous, three-dimensional metal–organic material formed from zero-valent metal nodes is presented. Combination of ditopic m-terphenyl diisocyanide, [CNAr Mes2] 2, and the d 10 Ni(0) precursor Ni(COD) 2, produces a porous metal–organic material featuring tetrahedral [Ni(CNAr Mes2) 4] n structural sites. X-ray absorption spectroscopy provides firm evidence for the presence of Ni(0) centers, whereas gas-sorption and thermogravimetric analysis reveal the characteristics of a robust network with a microdomain N 2-adsorption profile.

Self-assembly of a [Ni8] carbonate cube incorporating four μ4-carbonato linkers through fixation of atmospheric CO2 by ligated [Ni2] complexes.

PubMed

Ghosh, Aloke Kumar; Pait, Moumita; Shatruk, Michael; Bertolasi, Valerio; Ray, Debashis

2014-02-07

The communication reports the synthesis, characterization, and magnetic behavior of a novel μ4-carbonato supported and imidazole capped ligated nickel cage [Ni8(μ-H2bpmp)4(μ4-CO3)4(ImH)8](NO3)4·2H2O (1) through self-assembly of ligand bound ferromagnetic Ni2 building blocks. Structural analysis indicates newer geometrical features for the coordination cage formation and dominant interdimer antiferromagnetic coupling resulting in a diamagnetic ground state.

Triboluminescence and crystal structure of the complex [Eu(NО3 )3 (HMPA)3 ]: role of cleavage planes.

PubMed

Bukvetskii, B V; Mirochnik, A G; Zhikhareva, P A

2017-05-01

The atomic structure of crystals of the [Eu(NО 3 ) 3 (HMPA) 3 ] [hexamethylphosphotriamide (HMPA)] complex characterized by an intensive luminescence and triboluminescence was determined using X-ray structural analysis. Noncentrosymmetric crystals have a monoclinic syngony: a = 16.0686 (3), b = 11.0853 (2), c = 20.9655 Å (4), β = 93.232° (1), space group P2 1 , Z = 4, ρ calc  = 1.560 g/cm 3 . The crystal structure is represented by individual С 18 Н 54 EuN 12 O 12 P 3 complexes linked through van der Waals interactions with clearly expressed cleavage planes. The Eu(III) atom coordination polyhedron reflected the state of a distorted square antiprism. Structural aspects of the suggested model, including formation of triboluminescence properties, were considered and the role of the cleavage planes was discussed. Copyright © 2016 John Wiley & Sons, Ltd.

Analytical Solution for Low-Thrust Minimum Time Control of a Satellite Formation

DTIC Science & Technology

2004-09-01

The Classical Clohessy - Wiltshire Equations . . . . . . . . . A-1 A.1 Hill’s Rotating Coordinate Frame . . . . . . . . . . . . . . . A-1 A.2 Kinematics...9 A.1. The Clohessy and Wiltshire coordinate frame with x in the radial direction and y in the velocity direction. . . . . . . . . . . . . . . . A-1 B...coordinate system and approx- imations made by Clohessy and Wiltshire , combined with body-fixed thruster control, result in a linearized dynamic system. The

Convergent and divergent two-dimensional coordination networks formed through substrate-activated or quenched alkynyl ligation.

PubMed

Čechal, Jan; Kley, Christopher S; Kumagai, Takashi; Schramm, Frank; Ruben, Mario; Stepanow, Sebastian; Kern, Klaus

2014-09-07

Metal coordination assemblies of the symmetric bi-functional 4,4'-di-(1,4-buta-1,3-diynyl)-benzoic acid are investigated by scanning tunnelling microscopy on metal surfaces. The formation of long-range ordered, short-range disordered and random phases depends on the competition between the convergent and divergent coordination motifs of the individual functional groups and is crucially influenced by the substrate.

Intraformation positioning system

NASA Astrophysics Data System (ADS)

Sheldon, Stuart; Zadzora, Timothy

1996-05-01

The IntraFormation Positioning System is a networked relative navigation system currently being developed for rendezvous, join-up, and formation flight of Air Force helicopters and fixed wing aircraft in instrument meteorological conditions. The system is designed to be integrated into existing aircraft and will display relative positions of all aircraft within a formation, as well as the relative positions of other formations participating in coordinated missions. The system uses a Global Positioning System receiver integrated with the aircraft Inertial Navigation System to generate accurate aircraft position and velocity data. These data are transmitted over a data link to all participating aircraft and displayed as graphic symbols at the relative range and bearing to own aircraft on a situational awareness display format similar to a radar plan position indicator. Flight guidance computation is based on the difference between a desired formation slot position and current aircraft position relative to the formation lead aircraft. This information is presented on the flight director display allowing the pilot to null out position errors. The system is being developed for the Air Force Special Operations Command; however, it is applicable to all aircraft desiring improved formation situational awareness and formation flight coordination.

Silver sulfadoxinate: Synthesis, structural and spectroscopic characterizations, and preliminary antibacterial assays in vitro

NASA Astrophysics Data System (ADS)

Zanvettor, Nina T.; Abbehausen, Camilla; Lustri, Wilton R.; Cuin, Alexandre; Masciocchi, Norberto; Corbi, Pedro P.

2015-02-01

The sulfa drug sulfadoxine (SFX) reacted with Ag+ ions in aqueous solution, affording a new silver(I) complex (AgSFX), which was fully characterized by chemical, spectroscopic and structural methods. Elemental, ESI-TOF mass spectrometric and thermal analyses of AgSFX suggested a [Ag(C12H13N4O2S)] empirical formula. Infrared spectroscopic measurements indicated ligand coordination to Ag(I) through the nitrogen atoms of the (deprotonated) sulfonamide group and by the pyrimidine ring, as well as through oxygen atom(s) of the sulfonamide group. These hypotheses were corroborated by 13C and 15N SS-NMR spectroscopy and by an unconventional structural characterization based on X-ray powder diffraction data. The latter showed that AgSFX crystallizes as centrosymmetric dimers with a strong Ag⋯Ag interaction of 2.7435(6) Å, induced by the presence of exo-bidentate N,N‧ bridging ligands and the formation of an eight-membered ring of [AgNCN]2 sequence, nearly planar. Participation of oxygen atoms of the sulfonamide residues generates in the crystal a 1D coordination polymer, likely responsible for its very limited solubility in all common solvents. Besides the analytical, spectroscopic and structural description, the antibacterial properties of AgSFX were assayed using disc diffusion methods against Escherichia coli and Pseudomonas aeruginosa (Gram-negative), and Staphylococcus aureus (Gram-positive) bacterial strains. The AgSFX complex showed to be active against Gram-positive and Gram-negative bacterial strains, being comparable to the activities of silver sulfadiazine.

Mapping the Dynamics of Shear Stress—Induced Structural Changes in Endothelial Cells

PubMed Central

Mott, Rosalind E.; Helmke, Brian P.

2009-01-01

Hemodynamic shear stress regulates endothelial cell biochemical processes that govern cytoskeletal contractility, focal adhesion dynamics, and extracellular matrix assembly. Since shear stress causes rapid strain focusing at discrete locations in the cytoskeleton, we hypothesized that shear stress coordinately alters structural dynamics in the cytoskeleton, focal adhesion sites, and extracellular matrix on a time scale of minutes. Using multi-wavelength 4-D fluorescence microscopy, we measured the displacement of rhodamine-fibronectin and of GFP-labeled actin, vimentin, paxillin, and/or vinculin in aortic endothelial cells before and after onset of steady unidirectional shear stress. In the cytoskeleton, the onset of shear stress increased actin polymerization into lamellipodia, altered the angle of lateral displacement of actin stress fibers and vimentin filaments, and decreased centripetal remodeling of actin stress fibers in both subconfluent and confluent cell layers. Shear stress induced the formation of new focal complexes and reduced the centripetal remodeling of focal adhesions in regions of new actin polymerization. The structural dynamics of focal adhesions and the fibronectin matrix varied with cell density. In subconfluent cell layers, shear stress onset decreased the displacement of focal adhesions and fibronectin fibrils. In confluent monolayers, the direction of fibronectin and focal adhesion displacement shifted significantly towards the downstream direction within one minute after onset of shear stress. These spatially coordinated rapid changes in the structural dynamics of cytoskeleton, focal adhesions, and extracellular matrix are consistent with focusing of mechanical stress and/or strain near major sites of shear stress-mediated mechanotransduction. PMID:17855768

Electronegativity and hardness as coordinates in structure stability diagrams.

PubMed Central

Shankar, S; Parr, R G

1985-01-01

With electronegativity and hardness of an atom defined as 1/2(I + A) and 1/2(I - A), respectively, where I and A are the ionization potential and electron affinity, electronegativity difference and hardness sum are proposed as coordinates in structure stability diagrams. With these coordinates a successful topological classification of the crystal structures of octet and suboctet binary compounds is obtained, and a clear delineation of the structural classes portraying chemical periodicity is found. PMID:3855552

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Kaushik, E-mail: kaushikdas2089@gmail.com; Kundu, Sarathi

Long chain fatty acid molecules (e.g., stearic and behenic acids) form a monolayer on water surface in the presence of Ba{sup 2+} ions at low subphase pH (≈ 5.5) and remain as a monolayer before collapse generally occurs at higher surface pressure (π{sub c} > 50 mN/m). Monolayer formation is verified from the surface pressure vs. area per molecule (π-A) isotherms and also from the atomic force microscopy (AFM) analysis of the films deposited by single upstroke of hydrophilic Si (001) substrate through the monolayer covered water surface. At high subphase pH (≈ 9.5), barium stearate molecules form multilayer structuremore » at lower surface pressure which is verified from the π-A isotherms and AFM analysis of the film deposited at 25 mN/m. Such monolayer to multilayer structure formation or monolayer collapse at lower surface pressure is unusual as at this surface pressure generally fatty acid salt molecules form a monolayer on the water surface. Formation of bidentate chelate coordination in the metal containing headgroups is the reason for such monolayer to multilayer transition. However, for longer chain barium behenate molecules only monolayer structure is maintained at that high subphase pH (≈ 9.5) due to the presence of relatively more tail-tail hydrophobic interaction.« less

The C( 3P) + NH 3 reaction in interstellar chemistry. I. Investigation of the product formation channels

DOE PAGES

Bourgalais, Jeremy; Capron, Michael; Kailasanathan, Ranjith Kumar Abhinavam; ...

2015-10-13

The product formation channels of ground state carbon atoms, C( 3P), reacting with ammonia, NH3, have been investigated using two complementary experiments and electronic structure calculations. Reaction products are detected in a gas flow tube experiment (330 K, 4 Torr) using tunable vacuum-ultraviolet (VUV) photoionization coupled with time of flight mass spectrometry. Temporal profiles of the species formed and photoionization spectra are used to identify primary products of the C + NH 3 reaction. In addition, H-atom formation is monitored by VUV laser induced fluorescence (LIF) from room temperature to 50 K in a supersonic gas flow generated by themore » Laval nozzle technique. Electronic structure calculations are performed to derive intermediates, transition states, and complexes formed along the reaction coordinate. The combination of photoionization and LIF experiments supported by theoretical calculations indicate that in the temperature and pressure range investigated, the H + H 2CN production channel represents 100% of the product yield for this reaction. As a result, kinetics measurements of the title reaction down to 50 K and the effect of the new rate constants on interstellar nitrogen hydride abundances using a model of dense interstellar clouds are reported in Paper II.« less

Homo- and Heterometallic Bis(Pentafluorobenzoyl)Methanide Complexes of Copper(II) and Cobalt(II)

NASA Astrophysics Data System (ADS)

Crowder, Janell M.

beta-Diketones are well known to form metal complexes with practically every known metal and metalloid. Metal complexes of fluorinated beta-diketones generally exhibit increased volatility and thermal stability compared to the non-fluorinated analogues, and thus are used extensively in various chemical vapor deposition (CVD) processes for the deposition of metal, simple or mixed metal oxides, and fluorine-doped metal oxide thin films. Furthermore, the electron-withdrawing nature of the fluorinated ligand enhances the Lewis acidity of a coordinatively unsaturated metal center which facilitates additional coordination reactions. The physical and structural properties of fluorinated beta-diketonate complexes are discussed in Chapter 1 and a few key application examples are given. The focus of this work is the synthesis and single crystal X-ray structural characterization of unsolvated and coordinatively unsaturated metal complexes of bis(pentafluorobenzoyl)- methanide (L, C6F5COCHCOC 6F5-). In Chapter 2, we present the preparation and isolation of the unsolvated complex [Cu(L)2] in pure crystalline form for the first time. We subsequently investigated the reaction of unsolvated [Cu(L)2] with sodium hexafluoroacetylacetonate [Na(hfac)] in a solvent-free environment. This reaction allowed the isolation of the first heterometallic Na-Cu diketonate [Na2Cu2(L) 4(hfac)2] structurally characterized by single crystal X-ray crystallography. Thermal decomposition of [Na2Cu2(L) 4(hfac)2] was investigated for its potential application in MOCVD processes. In the final chapter, we present the first exploration of the anhydrous synthesis of Co(II) complexed with bis(pentafluorobenzoyl)methanide in order to produce a complex without ligated water. Single crystal X-ray crystallographic investigations revealed the isolation of the ethanol adduct, [Co2(L)4(C2H5OH)2], and following the removal of ethanol, a 1,4-dioxane adduct, [{Co 2(L)4}2(C4H8O2)]. In this work, we have provided the first investigation of the synthesis, isolation and single crystal X-ray structural characterization of unsolvated and coordinatively unsaturated Cu(II) and Co(II) complexes of bis(pentafluorobenzoyl)methanide ligand. These studies demonstrate how the electrophilicity of a coordinatively unsaturated metal complexed to highly-fluorinated â-diketone ligands can be utilized for the formation of new adducts or new and interesting heterometallic complexes. This body of work provides a basis upon which future research into unsolvated and unligated bis(pentafluorobenzoyl)methanide metal complexes can expand.

Neural network-based distributed attitude coordination control for spacecraft formation flying with input saturation.

PubMed

Zou, An-Min; Kumar, Krishna Dev

2012-07-01

This brief considers the attitude coordination control problem for spacecraft formation flying when only a subset of the group members has access to the common reference attitude. A quaternion-based distributed attitude coordination control scheme is proposed with consideration of the input saturation and with the aid of the sliding-mode observer, separation principle theorem, Chebyshev neural networks, smooth projection algorithm, and robust control technique. Using graph theory and a Lyapunov-based approach, it is shown that the distributed controller can guarantee the attitude of all spacecraft to converge to a common time-varying reference attitude when the reference attitude is available only to a portion of the group of spacecraft. Numerical simulations are presented to demonstrate the performance of the proposed distributed controller.

Velocity-free attitude coordinated tracking control for spacecraft formation flying.

PubMed

Hu, Qinglei; Zhang, Jian; Zhang, Youmin

2018-02-01

This article investigates the velocity-free attitude coordinated tracking control scheme for a group of spacecraft with the assumption that the angular velocities of the formation members are not available in control feedback. Initially, an angular velocity observer is constructed based on each individual's attitude quarternion. Then, the distributed attitude coordinated control law is designed by using the observed states, in which adaptive control method is adopted to handle the external disturbances. Stability of the overall closed-loop system is analyzed theoretically, which shows the system trajectory converges to a small set around origin with fast convergence rate. Numerical simulations are performed to demonstrate fast convergence and improved tracking performance of the proposed control strategy. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

(N-Benzyl-N-isopropyl­dithio­carbamato)chloridodiphenyl­tin(IV)

PubMed Central

Abdul Muthalib, Amirah Faizah; Baba, Ibrahim; Mohamed Tahir, Mohamed Ibrahim; Ng, Seik Weng; Tiekink, Edward R. T.

2010-01-01

The SnIV atom in the title organotin dithio­carbamate, [Sn(C6H5)2(C11H14NS2)Cl], is penta-coordinated by an asymmetrically coordinating dithio­carbamate ligand, a Cl and two ispo-C atoms of the Sn-bound phenyl groups. The resulting C2ClS2 donor set defines a coordination geometry inter­mediate between square-pyramidal and trigonal-bipyramidal with a slight tendency towards the latter. The formation of close intra­molecular C–H⋯Cl and C–H⋯S contacts precludes the Cl and S atoms from forming significant inter­molecular contacts. The presence of C–H⋯π contacts leads to the formation of supra­molecular arrays that stack along the b axis. PMID:21588504

The Structure of Liquid and Amorphous Hafnia.

PubMed

Gallington, Leighanne C; Ghadar, Yasaman; Skinner, Lawrie B; Weber, J K Richard; Ushakov, Sergey V; Navrotsky, Alexandra; Vazquez-Mayagoitia, Alvaro; Neuefeind, Joerg C; Stan, Marius; Low, John J; Benmore, Chris J

2017-11-10

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf-O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that show density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf-Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf-Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO 6,7 polyhedra resembling that observed in the monoclinic phase.

Formation of a disordered solid via a shock-induced transition in a dense particle suspension

NASA Astrophysics Data System (ADS)

Petel, Oren E.; Frost, David L.; Higgins, Andrew J.; Ouellet, Simon

2012-02-01

Shock wave propagation in multiphase media is typically dominated by the relative compressibility of the two components of the mixture. The difference in the compressibility of the components results in a shock-induced variation in the effective volume fraction of the suspension tending toward the random-close-packing limit for the system, and a disordered solid can take form within the suspension. The present study uses a Hugoniot-based model to demonstrate this variation in the volume fraction of the solid phase as well as a simple hard-sphere model to investigate the formation of disordered structures within uniaxially compressed model suspensions. Both models are discussed in terms of available experimental plate impact data in dense suspensions. Through coordination number statistics of the mesoscopic hard-sphere model, comparisons are made with the trends of the experimental pressure-volume fraction relationship to illustrate the role of these disordered structures in the bulk properties of the suspensions. A criterion for the dynamic stiffening of suspensions under high-rate dynamic loading is suggested as an analog to quasi-static jamming based on the results of the simulations.

Structural Characterization of Am(III)- and Pu(III)-DOTA Complexes.

PubMed

Audras, Matthieu; Berthon, Laurence; Berthon, Claude; Guillaumont, Dominique; Dumas, Thomas; Illy, Marie-Claire; Martin, Nicolas; Zilbermann, Israel; Moiseev, Yulia; Ben-Eliyahu, Yeshayahu; Bettelheim, Armand; Cammelli, Sebastiano; Hennig, Christoph; Moisy, Philippe

2017-10-16

The complexation of 1,4,7,10-tetrazacyclodecane-1,4,7,10-tetraacetic acid (DOTA) ligand with two trivalent actinides (Am 3+ and Pu 3+ ) was investigated by UV-visible spectrophotometry, NMR spectroscopy, and extended X-ray absorption fine structure in conjunction with computational methods. The complexation process of these two cations is similar to what has been previously observed with lanthanides(III) of similar ionic radius. The complexation takes place in different steps and ends with the formation of a (1:1) complex [(An(III)DOTA)(H 2 O)] - , where the cation is bonded to the nitrogen atoms of the ring, the four carboxylate arms, and a water molecule to complete the coordination sphere. The formation of An(III)-DOTA complexes is faster than the Ln(III)-DOTA systems of equivalent ionic radius. Furthermore, it is found that An-N distances are slightly shorter than Ln-N distances. Theoretical calculations showed that the slightly higher affinity of DOTA toward Am over Nd is correlated with slightly enhanced ligand-to-metal charge donation arising from oxygen and nitrogen atoms.

Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus.

PubMed

Xi, Wang; Song, Dongliang; Sun, Jiayan; Shen, Junhui; Li, Laigeng

2017-03-01

Cellulose biosynthesis is mediated by cellulose synthases (CesAs), which constitute into rosette-like cellulose synthase complexe (CSC) on the plasma membrane. Two types of CSCs in Arabidopsis are believed to be involved in cellulose synthesis in the primary cell wall and secondary cell walls, respectively. In this work, we found that the two type CSCs participated cellulose biosynthesis in differentiating xylem cells undergoing secondary cell wall thickening in Populus. During the cell wall thickening process, expression of one type CSC genes increased while expression of the other type CSC genes decreased. Suppression of different type CSC genes both affected the wall-thickening and disrupted the multilaminar structure of the secondary cell walls. When CesA7A was suppressed, crystalline cellulose content was reduced, which, however, showed an increase when CesA3D was suppressed. The CesA suppression also affected cellulose digestibility of the wood cell walls. The results suggest that two type CSCs are involved in coordinating the cellulose biosynthesis in formation of the multilaminar structure in Populus wood secondary cell walls.

Formation of Ge nanoparticles in SiO xN y by ion implantation and thermal annealing

DOE PAGES

Mirzaei, Sahar; Kremer, F.; Sprouster, D. J.; ...

2015-10-20

Germanium nanoparticles embedded within dielectric matrices hold much promise for applications in optoelectronic and electronic devices. Here we investigate the formation of Ge nanoparticles in amorphous SiO 1.67N 0.14 as a function of implanted atom concentration and thermal annealing temperature. Using x-ray absorption spectroscopy and other complementary techniques, we show Ge nanoparticles exhibit significant finite-size effects such that the coordination number decreases and structural disorder increases as the nanoparticle size decreases. While the composition of SiO 1.67N 0.14 is close to that of SiO 2, we demonstrate that the addition of this small fraction of N yields a much reducedmore » nanoparticle size relative to those formed in SiO 2 under comparable implantation and annealing conditions. We attribute this difference to an increase in an atomic density and a much reduced diffusivity of Ge in the oxynitride matrix. Finally, these results demonstrate the potential for tailoring Ge nanoparticle sizes and structural properties in the SiO xN y matrices by controlling the oxynitride stoichiometry.« less

The Structure of Liquid and Amorphous Hafnia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallington, Leighanne; Ghadar, Yasaman; Skinner, Lawrie

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf–O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that showmore » density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf–Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf–Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO 6,7 polyhedra resembling that observed in the monoclinic phase.« less

The Structure of Liquid and Amorphous Hafnia

DOE PAGES

Gallington, Leighanne; Ghadar, Yasaman; Skinner, Lawrie; ...

2017-11-10

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf–O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that showmore » density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf–Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf–Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO 6,7 polyhedra resembling that observed in the monoclinic phase.« less

Embryonic multipotent progenitors remodel the Drosophila airways during metamorphosis

PubMed Central

Pitsouli, Chrysoula; Perrimon, Norbert

2010-01-01

Adult structures in holometabolous insects such as Drosophila are generated by groups of imaginal cells dedicated to the formation of different organs. Imaginal cells are specified in the embryo and remain quiescent until the larval stages, when they proliferate and differentiate to form organs. The Drosophila tracheal system is extensively remodeled during metamorphosis by a small number of airway progenitors. Among these, the spiracular branch tracheoblasts are responsible for the generation of the pupal and adult abdominal airways. To understand the coordination of proliferation and differentiation during organogenesis of tubular organs, we analyzed the remodeling of Drosophila airways during metamorphosis. We show that the embryonic spiracular branch tracheoblasts are multipotent cells that express the homeobox transcription factor Cut, which is necessary for their survival and normal development. They give rise to three distinct cell populations at the end of larval development, which generate the adult tracheal tubes, the spiracle and the epidermis surrounding the spiracle. Our study establishes the series of events that lead to the formation of an adult tubular structure in Drosophila. PMID:20940225

DSSR-enhanced visualization of nucleic acid structures in Jmol.

PubMed

Hanson, Robert M; Lu, Xiang-Jun

2017-07-03

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Synthesis, crystal structure and DFT studies of a novel dinuclear copper(I) complex with triphenylphosphine and 2-mercaptonicotinic acid

NASA Astrophysics Data System (ADS)

Ahmad, Tayyaba; Mahmood, Rashid; Georgieva, Ivelina; Zahariev, Tsvetan; Tahir, Muhammad Nawaz; Shaheen, Muhammad Ashraf; Gilani, Mazhar Amjad; Ahmad, Saeed

2018-02-01

A novel dinuclear copper(I) complex, {[Cu2(Mnt)2(PPh3)2Cl2].2H2O.CH3CN}2 (1) (Mnt = Mercaptonicotinic acid, PPh3 = triphenylphosphine) was prepared and its structure was determined by X-ray crystallography. The complex 1 consists of two dinuclear molecules and in each molecule, the two copper atoms are bridged by S atoms of N-protonated mercaptonicotinic acid forming a four-membered ring. The planar Cu2S2 core is characterized by significant cuprophilic interactions (Cusbnd Cu distance = 2.7671(8), 2.8471(8) Å). Each copper atom in 1 is coordinated by two sulfur atoms of Mnt, one phosphorus atom of PPh3 and a chloride ion adopting a tetrahedral geometry. The calculated Gibbs energies for reaction in CH3CN supported the experimental structure and predicted more favorable formation of dinuclear Cu(I) complex as compared to the mononuclear Cu(I) complex. The dinuclear complex is stabilized by 65.98 kJ mol-1 by coupling of two mononuclear Cu(I) complexes. The IR spectra of 1 and Mnt ligand were reliably interpreted and the Mnt vibrations, which are sensitive to the ligand coordination to Cu(I) ion in 1 were selected with the help of DFT/ωB97XD calculations.

Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase.

PubMed

Boll, Matthias; Einsle, Oliver; Ermler, Ulrich; Kroneck, Peter M H; Ullmann, G Matthias

2016-01-01

In biology, tungsten (W) is exclusively found in microbial enzymes bound to a bis-pyranopterin cofactor (bis-WPT). Previously known W enzymes catalyze redox oxo/hydroxyl transfer reactions by directly coordinating their substrates or products to the metal. They comprise the W-containing formate/formylmethanofuran dehydrogenases belonging to the dimethyl sulfoxide reductase (DMSOR) family and the aldehyde:ferredoxin oxidoreductase (AOR) families, which form a separate enzyme family within the Mo/W enzymes. In the last decade, initial insights into the structure and function of two unprecedented W enzymes were obtained: the acetaldehyde forming acetylene hydratase (ACH) belongs to the DMSOR and the class II benzoyl-coenzyme A (CoA) reductase (BCR) to the AOR family. The latter catalyzes the reductive dearomatization of benzoyl-CoA to a cyclic diene. Both are key enzymes in the degradation of acetylene (ACH) or aromatic compounds (BCR) in strictly anaerobic bacteria. They are unusual in either catalyzing a nonredox reaction (ACH) or a redox reaction without coordinating the substrate or product to the metal (BCR). In organic chemical synthesis, analogous reactions require totally nonphysiological conditions depending on Hg2+ (acetylene hydration) or alkali metals (benzene ring reduction). The structural insights obtained pave the way for biological or biomimetic approaches to basic reactions in organic chemistry. © 2016 S. Karger AG, Basel.

Size versus electronic factors in transition metal carbide and TCP phase stability

NASA Astrophysics Data System (ADS)

Pettifor, D. G.; Seiser, B.; Margine, E. R.; Kolmogorov, A. N.; Drautz, R.

2013-09-01

The contributions of atomic size and electronic factors to the structural stability of transition metal carbides and topologically close-packed (TCP) phases are investigated. The hard-sphere model that has been used by Cottrell to rationalize the occurrence of the octahedral and trigonal local coordination polyhedra within the transition metal carbides is shown to have limitations in TiC since density functional theory (DFT) predicts that the second most metastable phase closest to the B1 (NaCl) ground state takes the B? (BN) structure type with 5-atom local coordination polyhedra with very short Ti-C bond lengths. The importance of electronic factors in the TCP phases is demonstrated by DFT predictions that the A15, ? and ? phases are stabilized between groups VI and VII of the elemental transition metals, whereas the ? and Laves phases are destabilized. The origin of this difference is related to the bimodal shape parameter of the electronic density of states by using the bond-order potential expansion of the structural energy within a canonical tight-binding model. The importance of the size factor in the TCP phases is illustrated by the DFT heats of formation for the binary systems Mo-Re, Mo-Ru, Nb-Re and Nb-Ru which show that the ? and Laves phases become more and more stable compared to A15, ? and ? as the size factor increases from Mo-Re through to Nb-Ru.

Robust distributed control of spacecraft formation flying with adaptive network topology

NASA Astrophysics Data System (ADS)

Shasti, Behrouz; Alasty, Aria; Assadian, Nima

2017-07-01

In this study, the distributed six degree-of-freedom (6-DOF) coordinated control of spacecraft formation flying in low earth orbit (LEO) has been investigated. For this purpose, an accurate coupled translational and attitude relative dynamics model of the spacecraft with respect to the reference orbit (virtual leader) is presented by considering the most effective perturbation acceleration forces on LEO satellites, i.e. the second zonal harmonic and the atmospheric drag. Subsequently, the 6-DOF coordinated control of spacecraft in formation is studied. During the mission, the spacecraft communicate with each other through a switching network topology in which the weights of its graph Laplacian matrix change adaptively based on a distance-based connectivity function between neighboring agents. Because some of the dynamical system parameters such as spacecraft masses and moments of inertia may vary with time, an adaptive law is developed to estimate the parameter values during the mission. Furthermore, for the case that there is no knowledge of the unknown and time-varying parameters of the system, a robust controller has been developed. It is proved that the stability of the closed-loop system coupled with adaptation in network topology structure and optimality and robustness in control is guaranteed by the robust contraction analysis as an incremental stability method for multiple synchronized systems. The simulation results show the effectiveness of each control method in the presence of uncertainties and parameter variations. The adaptive and robust controllers show their superiority in reducing the state error integral as well as decreasing the control effort and settling time.

Medicaid Managed Care Structures and Care Coordination.

PubMed

Gilchrist-Scott, Douglas H; Feinstein, James A; Agrawal, Rishi

2017-09-01

Child enrollment in Medicaid managed care (MMC) has expanded dramatically, primarily through state mandates. Care coordination is a key metric in MMC evaluation because it drives much of the proposed cost savings and may be associated with improved health outcomes and utilization. We evaluated the relationships between enrollment in 2 MMC structures, primary care case management (PCCM) and health maintenance organization (HMO) and access to and receipt of care coordination by children. Using data from the 2011/2012 National Survey of Children's Health and the Medicaid Statistical Information System state data mart, we conducted a retrospective, cross-sectional analysis of the relationships between fee-for-service, PCCM or HMO enrollment, and access to and receipt of care coordination. State-level univariate analyses and individual and state multilevel multivariable analyses evaluated correlations between MMC enrollment and care coordination, controlling for demographic characteristics and state financing levels. In univariate and multilevel multivariable analyses, the PCCM penetration rate was significantly associated with increased access to care coordination (adjusted odds ratio: 1.23, P = .034) and receipt of care coordination (adjusted odds ratio: 1.37, P = .02). The HMO penetration rate was significantly associated with lower access to care coordination (adjusted odds ratio: 0.85, P = .05) and receipt of care coordination (adjusted odds ratio: 0.71, P < .001). Fee-for-service served as the referent. State utilization of MMC varied widely. These data suggest that care coordination may be more effective in PCCM than HMO structures. States should consider care coordination outcomes when structuring their Medicaid programs. Copyright © 2017 by the American Academy of Pediatrics.

How the guest molecules in nanoporous Zn(II) metal-organic framework can prevent agglomeration of ZnO nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moeinian, Maryam; Akhbari, Kamran, E-mail: akhbari.k@khayam.ut.ac.ir

The host and the apohost framework of [Zn{sub 2}(BDC){sub 2}(H{sub 2}O){sub 2}·(DMF){sub 2}]{sub n} (1·2H{sub 2}O·2DMF), (BDC{sup 2−}=benzene-1,4-dicarboxylate and DMF=N,N-Dimethylformamide), were synthesized and subsequently used for preparation of ZnO nanomaterials. With calcination of the host framework of 1·2H{sub 2}O·2DMF, ZnO nanoparticles were obtained. By the same process on the apohost framework of 1, agglomerated nanoparticles of ZnO were formed. These nano-structures were characterized by X-ray powder diffraction (XRD) and Scanning electron microscopy (SEM). These results indicate that with removal of the guest DMF and coordinated H{sub 2}O molecules from the one-dimensional channels of 1·2H{sub 2}O·2DMF, the tendency of nanoparticles tomore » agglomerate increases and the role of this MOF in preparation of ZnO nanoparticles from this precursor was reduced. - Graphical abstract: Nano-porous zinc(II) MOF with guest DMF and coordinated H{sub 2}O molecules has been synthesized and characterized. The host and the apohost framework of it were used for preparation of ZnO nanomaterials. The role of these species in preparation of ZnO nanoparticles from the host framework is probably similar to the role of polymeric stabilizers in formation of nanoparticles. - Highlights: • Nanoparticles of ZnO were fabricated from nanoporous metal-organic framework. • The effect of guest DMF and coordinated H{sub 2}O molecules on this process was studied. • The effect of them in formation nanoparticle is similar to polymeric stabilizers.« less

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations.

PubMed

Chen, Ying; Bylaska, Eric J; Weare, John H

2017-03-31

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe 3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe 3+ . The water molecules capping surface Fe 3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe 3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe 3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe 3+ , those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe 3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH 2 distances in the DFT calculations it was proposed that the surface Fe 3+ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination. Graphical abstract All first principle calculations, at all practically achievable levels, for the goethite 100 aqueous interface support a long bond and weak interaction between the exposed surface Fe 3+ and water molecules capping the surface. This result is supported by bond valence theory calculations and is indicative that each surface Fe 3+ is coordinated with only 5 neighbors.

Photodeposited Pd Nanoparticles with Disordered Structure for Phenylacetylene Semihydrogenation

PubMed Central

Fan, Qining; He, Sha; Hao, Lin; Liu, Xin; Zhu, Yue; Xu, Sailong; Zhang, Fazhi

2017-01-01

Developing effective heterogeneous metal catalysts with high selectivity and satisfactory activity for chemoselective hydrogenation of alkyne to alkene is of great importance in the chemical industry. Herein, we report our efforts to fabricate TiO2-supported Pd catalysts by a photodeposition method at room temperature for phenylacetylene semihydrogenation to styrene. The resulting Pd/TiO2 catalyst, possessing smaller Pd ensembles with ambiguous lattice fringes and more low coordination Pd sites, exhibits higher styrene selectivity compared to two contrastive Pd/TiO2 samples with larger ensembles and well-organized crystal structure fabricated by deposition-precipitation or photodeposition with subsequent thermal treatment at 300 °C. The sample derived from photodeposition exhibits greatly slow styrene hydrogenation in kinetic evaluation because the disordered structure of Pd particles in photodeposited Pd/TiO2 may prevent the formation of β-hydride phases and probably produce more surface H atoms, which may favor high styrene selectivity. PMID:28176843

Photodeposited Pd Nanoparticles with Disordered Structure for Phenylacetylene Semihydrogenation

NASA Astrophysics Data System (ADS)

Fan, Qining; He, Sha; Hao, Lin; Liu, Xin; Zhu, Yue; Xu, Sailong; Zhang, Fazhi

2017-02-01

Developing effective heterogeneous metal catalysts with high selectivity and satisfactory activity for chemoselective hydrogenation of alkyne to alkene is of great importance in the chemical industry. Herein, we report our efforts to fabricate TiO2-supported Pd catalysts by a photodeposition method at room temperature for phenylacetylene semihydrogenation to styrene. The resulting Pd/TiO2 catalyst, possessing smaller Pd ensembles with ambiguous lattice fringes and more low coordination Pd sites, exhibits higher styrene selectivity compared to two contrastive Pd/TiO2 samples with larger ensembles and well-organized crystal structure fabricated by deposition-precipitation or photodeposition with subsequent thermal treatment at 300 °C. The sample derived from photodeposition exhibits greatly slow styrene hydrogenation in kinetic evaluation because the disordered structure of Pd particles in photodeposited Pd/TiO2 may prevent the formation of β-hydride phases and probably produce more surface H atoms, which may favor high styrene selectivity.

Multi-disciplinary optimization of aeroservoelastic systems

NASA Technical Reports Server (NTRS)

Karpel, Mordechay

1991-01-01

New methods were developed for efficient aeroservoelastic analysis and optimization. The main target was to develop a method for investigating large structural variations using a single set of modal coordinates. This task was accomplished by basing the structural modal coordinates on normal modes calculated with a set of fictitious masses loading the locations of anticipated structural changes. The following subject areas are covered: (1) modal coordinates for aeroelastic analysis with large local structural variations; and (2) time simulation of flutter with large stiffness changes.

The coordination structure of the extracted copper(II) complex with a synergistic mixture containing dinonylnaphthalene sulfonic acid and n-hexyl 3-pyridinecarboxylate ester

NASA Astrophysics Data System (ADS)

Zhu, Shan; Hu, Huiping; Hu, Jiugang; Li, Jiyuan; Hu, Fang; Wang, Yongxi

2017-09-01

In continuation of our interest in the coordination structure of the nickel(II) complex with dinonylnaphthalene sulfonic acid (HDNNS) and 2-ethylhexyl 4-pyridinecarboxylate ester (4PC), it was observed that the coordination sphere was completed by the coordination of two N atoms of pyridine rings in ligands 4PC and four water molecules while no direct interaction between Ni(II) and deprotonated HDNNS was observed. To investigate whether the coordination structure of nickel(II) with the synergistic mixture containing HDNNS and 4PC predominates or not in the copper(II) complex with the synergistic mixtures containing HDNNS and pyridinecarboxylate esters, a copper(II) synergist complex with n-hexyl 3-pyridinecarboxylate ester (L) and naphthalene-2-sulfonic acid (HNS, the short chain analogue of HDNNS), was prepared and studied by X-ray single crystal diffraction, elemental analyses and thermo gravimetric analysis (TGA), respectively. It was shown that the composition of the copper(II) synergist complex was [Cu(H2O)2(L)2(NS)2] and formed a trans-form distorted octahedral coordination structure. Two oxygen atoms of the two coordinated water molecules and two N atoms of the pyridine rings in the ligands L defined the basal plane while two O atoms from two sulfonate anions of the deprotonated HNS ligands occupied the apical positions by direct coordination with Cu(II), which was distinguished from the coordination structure of the nickel(II) synergist complex as reported in our previous work. In the crystal lattice, neighboring molecules [Cu(H2O)2L2(NS)2] were linked through the intermolecular hydrogen bonds between the hydrogen atoms of the coordinated water molecules and the oxygen atoms of the sulfonate anions in the copper(II) synergist complex to form a 2D plane. In order to bridge the gap between the solid state structure of the copper(II) synergist complex and the solution structure of the extracted copper(II) complex with the actual synergistic mixture containing L and HDNNS in the non-polar organic phase, the structures of the two copper(II) complexes were further investigated by Fourier transform infrared spectroscopy (FT-IR) and electrospray ionization mass spectrometry (ESI-MS), and the results indicated that the extracted copper(II) complex in the non-polar organic phase might possess a similar coordination structure as the copper(II) synergist complex.

Computational, electrochemical, and spectroscopic studies of two mononuclear cobaloximes: the influence of an axial pyridine and solvent on the redox behaviour and evidence for pyridine coordination to cobalt(I) and cobalt(II) metal centres†

PubMed Central

Lawrence, Mark A. W.; Celestine, Michael J.; Artis, Edward T.; Joseph, Lorne S.; Esquivel, Deisy L.; Ledbetter, Abram J.; Cropek, Donald M.; Jarrett, William L.; Bayse, Craig A.; Brewer, Matthew I.; Holder, Alvin A.

2018-01-01

[Co(dmgBF2)2(H2O)2] 1 (where dmgBF2 = difluoroboryldimethylglyoximato) was used to synthesize [Co(dmgBF2)2(H2O)(py)]·0.5(CH3)2CO 2 (where py = pyridine) in acetone. The formulation of complex 2 was confirmed by elemental analysis, high resolution MS, and various spectroscopic techniques. The complex [Co(dmgBF2)2(solv)(py)] (where solv = solvent) was readily formed in situ upon the addition of pyridine to complex 1. A spectrophotometric titration involving complex 1 and pyridine proved the formation of such a species, with formation constants, log K = 5.5, 5.1, 5.0, 4.4, and 3.1 in 2-butanone, dichloromethane, acetone, 1,2-difluorobenzene/acetone (4 : 1, v/v), and acetonitrile, respectively, at 20 °C. In strongly coordinating solvents, such as acetonitrile, the lower magnitude of K along with cyclic voltammetry, NMR, and UV-visible spectroscopic measurements indicated extensive dissociation of the axial pyridine. In strongly coordinating solvents, [Co(dmgBF2)2(solv)(py)] can only be distinguished from [Co(dmgBF2)2(solv)2] upon addition of an excess of pyridine, however, in weakly coordinating solvents the distinctions were apparent without the need for excess pyridine. The coordination of pyridine to the cobalt(II) centre diminished the peak current at the Epc value of the CoI/0 redox couple, which was indicative of the relative position of the reaction equilibrium. Herein we report the first experimental and theoretical 59Co NMR spectroscopic data for the formation of Co(I) species of reduced cobaloximes in the presence and absence of py (and its derivatives) in CD3CN. From spectroelectrochemical studies, it was found that pyridine coordination to a cobalt(I) metal centre is more favourable than coordination to a cobalt(II) metal centre as evident by the larger formation constant, log K = 4.6 versus 3.1, respectively, in acetonitrile at 20 °C. The electrosynthesis of hydrogen by complexes 1 and 2 in various solvents demonstrated the dramatic effects of the axial ligand and the solvent on the turnover number of the respective catalyst. PMID:27244471

77 FR 71820 - Meeting Announcement: North American Wetlands Conservation Council

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-04

.... Written statements must be supplied to the Council Coordinator in both of the following formats: One hard copy with original signature, and one electronic copy via email (acceptable file formats are Adobe...

78 FR 33856 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-05

... statements must be supplied to the Council Coordinator in one of the following formats: One hard copy with original signature, and one electronic copy via email (acceptable file formats are Adobe Acrobat PDF, MS...

The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

DOE PAGES

Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; ...

2014-09-25

To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na 7Sn 3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Namore » 9Sn 4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na 14.78Sn 4 (Pnma), better described as Na 16-xSn 4, is Na-richer than cubic Na 15Sn 4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na 7Sn 3 and Na 15Sn 4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.« less

Solvent-induced controllable synthesis, single-crystal to single-crystal transformation and encapsulation of Alq3 for modulated luminescence in (4,8)-connected metal-organic frameworks.

PubMed

Lan, Ya-Qian; Jiang, Hai-Long; Li, Shun-Li; Xu, Qiang

2012-07-16

In this work, for the first time, we have systematically demonstrated that solvent plays crucial roles in both controllable synthesis of metal-organic frameworks (MOFs) and their structural transformation process. With solvent as the only variable, five new MOFs with different structures have been constructed, in which one MOF undergoes solvent-induced single-crystal to single-crystal (SCSC) transformation that involves not only solvent exchange but also the cleavage and formation of coordination bonds. Particularly, a significant crystallographic change has been realized through an unprecedented three-step SCSC transformation process. Furthermore, we have demonstrated that the obtained MOF could be an excellent host for chromophores such as Alq3 for modulated luminescent properties.

Real-Time Processing of Pressure-Sensitive Paint Images

DTIC Science & Technology

2006-12-01

intermediate or final data to the hard disk in 3D grid format. In addition to the pressure or pressure coefficient at every grid point, the saved file may...occurs. Nevertheless, to achieve an accurate mapping between 2D image coordinates and 3D spatial coordinates, additional parameters must be introduced. A...improved mapping between the 2D and 3D coordinates. In a more sophisticated approach, additional terms corresponding to specific deformation modes

Structural analysis of the coordination of dinitrogen to transition metal complexes.

PubMed

Peigné, Benjamin; Aullón, Gabriel

2015-06-01

Transition-metal complexes show a wide variety of coordination modes for the nitrogen molecule. A structural database study has been undertaken for dinitrogen complexes, and geometrical parameters around the L(n)M-N2 unit are retrieved from the Cambridge Structural Database. These data were classified in families of compounds, according to metal properties, to determine the degree of lengthening for the dinitrogen bonding. The importance of the nature of the metal center, such as coordination number and electronic configuration, is reported. Our study reveals poor activation by coordination of dinitrogen in mononuclear complexes, always having end-on coordination. However, partial weakening of nitrogen-nitrogen bonding is found for end-on binuclear complexes, whereas side-on complexes can be completely activated.

Reactive p-block cations stabilized by weakly coordinating anions

PubMed Central

Engesser, Tobias A.; Lichtenthaler, Martin R.; Schleep, Mario

2016-01-01

The chemistry of the p-block elements is a huge playground for fundamental and applied work. With their bonding from electron deficient to hypercoordinate and formally hypervalent, the p-block elements represent an area to find terra incognita. Often, the formation of cations that contain p-block elements as central ingredient is desired, for example to make a compound more Lewis acidic for an application or simply to prove an idea. This review has collected the reactive p-block cations (rPBC) with a comprehensive focus on those that have been published since the year 2000, but including the milestones and key citations of earlier work. We include an overview on the weakly coordinating anions (WCAs) used to stabilize the rPBC and give an overview to WCA selection, ionization strategies for rPBC-formation and finally list the rPBC ordered in their respective group from 13 to 18. However, typical, often more organic ion classes that constitute for example ionic liquids (imidazolium, ammonium, etc.) were omitted, as were those that do not fulfill the – naturally subjective – “reactive”-criterion of the rPBC. As a rule, we only included rPBC with crystal structure and only rarely refer to important cations published without crystal structure. This collection is intended for those who are simply interested what has been done or what is possible, as well as those who seek advice on preparative issues, up to people having a certain application in mind, where the knowledge on the existence of a rPBC that might play a role as an intermediate or active center may be useful. PMID:26612538

HTSeq--a Python framework to work with high-throughput sequencing data.

PubMed

Anders, Simon; Pyl, Paul Theodor; Huber, Wolfgang

2015-01-15

A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. © The Author 2014. Published by Oxford University Press.

XAFS investigation of polyamidoxime-bound uranyl contests the paradigm from small molecule studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayes, Richard T.; Piechowicz, Marek; Lin, Zekai

In this study, limited resource availability and population growth have motivated interest in harvesting valuable metals from unconventional reserves, but developing selective adsorbents for this task requires structural knowledge of metal binding environments. Amidoxime polymers have been identified as the most promising platform for large-scale extraction of uranium from seawater. However, despite more than 30 years of research, the uranyl coordination environment on these adsorbents has not been positively identified. We report the first XAFS investigation of polyamidoxime-bound uranyl, with EXAFS fits suggesting a cooperative chelating model, rather than the tridentate or η 2 motifs proposed by small molecule andmore » computational studies. Samples exposed to environmental seawater also display a feature consistent with a μ 2-oxo-bridged transition metal in the uranyl coordination sphere, suggesting in situ formation of a specific binding site or mineralization of uranium on the polymer surface. These unexpected findings challenge several long-held assumptions and have significant implications for development of polymer adsorbents with high selectivity.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alí-Torres, Jorge; Mirats, Andrea; Maréchal, Jean-Didier

Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu{sup 2+} metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu{sup 2+}-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment ofmore » these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu{sup 2+}-Aβ coordination and build plausible Cu{sup 2+}-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.« less

XAFS investigation of polyamidoxime-bound uranyl contests the paradigm from small molecule studies

DOE PAGES

Mayes, Richard T.; Piechowicz, Marek; Lin, Zekai; ...

2015-11-12

In this study, limited resource availability and population growth have motivated interest in harvesting valuable metals from unconventional reserves, but developing selective adsorbents for this task requires structural knowledge of metal binding environments. Amidoxime polymers have been identified as the most promising platform for large-scale extraction of uranium from seawater. However, despite more than 30 years of research, the uranyl coordination environment on these adsorbents has not been positively identified. We report the first XAFS investigation of polyamidoxime-bound uranyl, with EXAFS fits suggesting a cooperative chelating model, rather than the tridentate or η 2 motifs proposed by small molecule andmore » computational studies. Samples exposed to environmental seawater also display a feature consistent with a μ 2-oxo-bridged transition metal in the uranyl coordination sphere, suggesting in situ formation of a specific binding site or mineralization of uranium on the polymer surface. These unexpected findings challenge several long-held assumptions and have significant implications for development of polymer adsorbents with high selectivity.« less

Specific Cx43 phosphorylation events regulate gap junction turnover in vivo

PubMed Central

Solan, Joell L.; Lampe, Paul D.

2014-01-01

Gap junctions, composed of proteins from the connexin gene family, are highly dynamic structures that are regulated by kinase-mediated signaling pathways and interactions with other proteins. Phosphorylation of Connexin43 (Cx43) at different sites controls gap junction assembly, gap junction size and gap junction turnover. Here we present a model describing how Akt, mitogen activated protein kinase (MAPK) and src kinase coordinate to regulate rapid turnover of gap junctions. Specifically, Akt phosphorylates Cx43 at S373 eliminating interaction with zona occludens-1 (ZO-1) allowing gap junctions to enlarge. Then MAPK and src phosphorylate Cx43 to initiate turnover. We integrate published data with new data to test and refine this model. Finally, we propose that differential coordination of kinase activation and Cx43 phosphorylation controls the specific routes of disassembly, e.g., annular junction formation or gap junctions can potentially “unzip” and be internalized/endocytosed into the cell that produced each connexin. PMID:24508467

Graded levels of FGF protein span the midbrain and can instruct graded induction and repression of neural mapping labels

PubMed Central

Chen, Yao; Mohammadi, Moosa; Flanagan, John G.

2009-01-01

Summary Graded guidance labels are widely used in neural map formation, but it is not well understood which potential strategy leads to their graded expression. In midbrain tectal map development, FGFs can induce an entire midbrain, but their protein distribution is unclear, nor is it known whether they may act instructively to produce graded gene expression. Using a receptor-alkaline phosphatase fusion probe, we find a long-range posterior>anterior FGF protein gradient spanning the midbrain. Heparan sulfate proteoglycan (HSPG) is required for this gradient. To test whether graded FGF concentrations can instruct graded gene expression, a quantitative tectal explant assay was developed. Engrailed-2 and ephrin-As, normally in posterior>anterior tectal gradients, showed graded upregulation. Moreover, EphAs, normally in anterior>posterior countergradients, showed coordinately graded downregulation. These results provide a mechanism to establish graded mapping labels, and more generally provide a developmental strategy to coordinately induce a structure and pattern its cell properties in gradients. PMID:19555646

Combined EXAFS and DFT Structure Calculations Provide Structural Insights into the 1:1 Multi-Histidine Complexes of CuII, CuI and ZnII with the Tandem Octarepeats of the Mammalian Prion Protein

PubMed Central

Pushie, M. Jake; Nienaber, Kurt H.; McDonald, Alex; Millhauser, Glenn L.; George, Graham N.

2014-01-01

The metal coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of copper interaction with PrP just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, and yet the structural details of the various metal coordination modes have not been fully elucidated in some cases. Herein we employ X-ray absorption near edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for CuII, CuI and ZnII with an N-terminal fragment of PrP. The PrP fragment constitutes four tandem repeats representative of the mammalian octarepeat domain, designated OR4, which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations provide additional structural and thermodynamic data, and candidate structures are used to inform EXAFS data analysis. The optimized geometries from DFT calculations are used to identify potential coordination complexes for multi-histidine coordination of CuII, CuI and ZnII in an aqueous medium, modeled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve fitting, using full multiple scattering on candidate structures from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of CuII, CuI and ZnII with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as a square planar [CuII(His)4]2+, digonal [CuI(His)2]+ and tetrahedral [ZnII(His)3(OH2)]2+, respectively. PMID:25042361

Movement Coordination during Conversation

PubMed Central

Latif, Nida; Barbosa, Adriano V.; Vatiokiotis-Bateson, Eric; Castelhano, Monica S.; Munhall, K. G.

2014-01-01

Behavioral coordination and synchrony contribute to a common biological mechanism that maintains communication, cooperation and bonding within many social species, such as primates and birds. Similarly, human language and social systems may also be attuned to coordination to facilitate communication and the formation of relationships. Gross similarities in movement patterns and convergence in the acoustic properties of speech have already been demonstrated between interacting individuals. In the present studies, we investigated how coordinated movements contribute to observers’ perception of affiliation (friends vs. strangers) between two conversing individuals. We used novel computational methods to quantify motor coordination and demonstrated that individuals familiar with each other coordinated their movements more frequently. Observers used coordination to judge affiliation between conversing pairs but only when the perceptual stimuli were restricted to head and face regions. These results suggest that observed movement coordination in humans might contribute to perceptual decisions based on availability of information to perceivers. PMID:25119189

Crystal and electronic structures of magnesium(II), copper(II), and mixed magnesium(II)-copper(II) complexes of the quinoline half of styrylquinoline-type HIV-1 integrase inhibitors.

PubMed

Courcot, B; Firley, D; Fraisse, B; Becker, P; Gillet, J-M; Pattison, P; Chernyshov, D; Sghaier, M; Zouhiri, F; Desmaële, D; d'Angelo, J; Bonhomme, F; Geiger, S; Ghermani, N E

2007-05-31

A new target in AIDS therapy development is HIV-1 integrase (IN). It was proven that HIV-1 IN required divalent metal cations to achieve phosphodiester bond cleavage of DNA. Accordingly, all newly investigated potent IN inhibitors contain chemical fragments possessing a high ability to chelate metal cations. One of the promising leads in the polyhydroxylated styrylquinolines (SQLs) series is (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinoline carboxylic acid (1). The present study focuses on the quinoline-based progenitor (2), which is actually the most probable chelating part of SQLs. Conventional and synchrotron low-temperature X-ray crystallographic studies were used to investigate the chelating power of progenitor 2. Mg2+ and Cu2+ cations were selected for this purpose, and three types of metal complexes of 2 were obtained: Mg(II) complex (4), Cu(II) complex (5) and mixed Mg(II)-Cu(II) complexes (6 and 7). The analysis of the crystal structure of complex 4 indicates that two tridentate ligands coordinate two Mg2+ cations, both in octahedral geometry. The Mg-Mg distance was found equal to 3.221(1) A, in agreement with the metal-metal distance of 3.9 A encountered in the crystal structure of Escherichia coli DNA polymerase I. In 5, the complex is formed by two bidentate ligands coordinating one copper ion in tetrahedral geometry. Both mixed Mg(II)-Cu(II) complexes, 6 and 7 exhibit an original arrangement of four ligands linked to a central heterometallic cluster consisting of three octahedrally coordinated magnesium ions and one tetrahedrally coordinated copper ion. Quantum mechanics calculations were also carried out in order to display the electrostatic potential generated by the dianionic ligand 2 and complex 4 and to quantify the binding energy (BE) during the formation of the magnesium complex of progenitor 2. A comparison of the binding energies of two hypothetical monometallic Mg(II) complexes with that found in the bimetallic magnesium complex 4 was made.

New 3-D coordination polymers based on semi-rigid V-shape tetracarboxylates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jing-Jing; Xu, Wei; Wang, Yan-Ning

Under the hydrothermal conditions, the reactions of transition-metal salts, tetracarboxylic acids and N,N′-donor ligands yielded three new coordination polymers as [Cu{sub 4}(fph){sub 2}(bpe){sub 3}(H{sub 2}O){sub 2}]·2H{sub 2}O (fph=4,4′-(hexafluoroisopropylidene)diphthalate, bpe=1,2-bis(pyridyl)ethylene) 1, [Co{sub 2}(fph)(bpa){sub 2}(H{sub 2}O){sub 2}]·3H{sub 2}O (bpa=1,2-bis(pyridyl)ethylane) 2, and [Ni(H{sub 2}O)(H{sub 2}oph)(bpa)] (oph=4,4′-oxydiphthalate) 3. X-ray single-crystal diffraction analysis revealed that the title three compounds all possess the three-dimensional (3-D) network structures. For compound 1, the fph molecules first link the Cu{sup 2+} ions into a two-dimensional (2-D) wave-like layer with a (4,4) topology. The bpe molecules act as the second linkers, extending the 2-D layers into a 3-D network. Formore » compound 2, the fph molecules still serve as the first connectors, linking the Co{sup 2+} ions into a one-dimensional (1-D) tube-like chain. Then the bpa molecules propagate the chains into a 3-D (4,4,4)-connected network. In the formation of the 3-D network of compound 3, the oph molecule does not play a role. The bpa molecules as well as the water molecules act as a mixed bridge. Only a kind of 4-connected metal node is observed in compound 3. The magnetic properties of compounds 1–3 were investigated and all exhibit the predominant antiferromegnetic magnetic behaviors. - Graphical abstract: Structures of three semi-rigid V-shape tetracarboxylate-based coordination polymers were reported, and their magnetic properties were investigated. - Highlights: • Structures of three tetracarboxylate-based coordination polymers were reported. • Role of organic bases in metal–tetracarboxylate compounds was discussed. • Characters of V-shape and semi-rigidity for tetracarboxylate play a key role in crystal growth. • Their magnetic properties were investigated.« less

The effects of feedback format, and egocentric & allocentric relative phase on coordination stability.

PubMed

Pickavance, John; Azmoodeh, Arianne; Wilson, Andrew D

2018-06-01

The stability of coordinated rhythmic movement is primarily affected by the required mean relative phase. In general, symmetrical coordination is more stable than asymmetrical coordination; however, there are two ways to define relative phase and the associated symmetries. The first is in an egocentric frame of reference, with symmetry defined relative to the sagittal plane down the midline of the body. The second is in an allocentric frame of reference, with symmetry defined in terms of the relative direction of motion. Experiments designed to separate these constraints have shown that both egocentric and allocentric constraints contribute to overall coordination stability, with the former typically showing larger effects. However, separating these constraints has meant comparing movements made either in different planes of motion, or by limbs in different postures. In addition, allocentric information about the coordination is either in the form of the actual limb motion, or a transformed, Lissajous feedback display. These factors limit both the comparisons that can be made and the interpretations of these comparisons. The current study examined the effects of egocentric relative phase, allocentric relative phase, and allocentric feedback format on coordination stability in a single task. We found that while all three independently contributed to stability, the egocentric constraint dominated. This supports previous work. We examine the evidence underpinning theoretical explanations for the egocentric constraint, and describe how it may reflect the haptic perception of relative phase. Copyright © 2018 Elsevier B.V. All rights reserved.

Cobalt(II) and Cobalt(III) Coordination Compounds.

ERIC Educational Resources Information Center

Thomas, Nicholas C.; And Others

1989-01-01

Presents a laboratory experiment which illustrates the formation of tris(phenanthroline)cobalt complexes in the 2+ and 3+ oxidation states, the effect of coordination on reactions of the ligand, and the use of a ligand displacement reaction in recovering the transformed ligand. Uses IR, UV-VIS, conductivity, and NMR. (MVL)

NASA STI Program Coordinating Council Twelfth Meeting: Standards

NASA Technical Reports Server (NTRS)

1994-01-01

The theme of this NASA Scientific and Technical Information Program Coordinating Council Meeting was standards and their formation and application. Topics covered included scientific and technical information architecture, the Open Systems Interconnection Transmission Control Protocol/Internet Protocol, Machine-Readable Cataloging (MARC) open system environment procurement, and the Government Information Locator Service.

77 FR 39252 - Meeting Announcement: North American Wetlands Conservation Council

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-02

... statements must be supplied to the Council Coordinator in both of the following formats: One hard copy with original signature, and one electronic copy via email (acceptable file formats are Adobe Acrobat PDF, MS...

78 FR 53156 - Sport Fishing and Boating Partnership Council; Teleconference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-28

... Council Coordinator in one of the following formats: One hard copy with original signature, and one electronic copy via email (acceptable file formats are Adobe Acrobat PDF, MS Word, MS PowerPoint, or rich...

Gadolinium sulfate modified by formate to obtain optimized magneto-caloric effect.

PubMed

Xu, Long-Yang; Zhao, Jiong-Peng; Liu, Ting; Liu, Fu-Chen

2015-06-01

Three new Gd(III) based coordination polymers [Gd2(C2H6SO)(SO4)3(H2O)2]n (1), {[Gd4(HCOO)2(SO4)5(H2O)6]·H2O}n (2), and [Gd(HCOO)(SO4)(H2O)]n (3) were obtained by modifying gadolinium sulfate. With the gradual increase of the volume ratio of HCOOH and DMSO in synthesis, the formate anions begin to coordinate with metal centers; this results in the coordination numbers of sulfate anion increasing and the contents of water and DMSO molecules decreasing in target complexes. Accordingly, spin densities both per mass and per volume were enhanced step by step, which are beneficial for the magneto-caloric effect (MCE). Magnetic studies reveal that with the more formate anions present, the larger the negative value of magnetic entropy change (-ΔSm) is. Complex 3 exhibits the largest -ΔSm = 49.91 J kg(-1) K(-1) (189.51 mJ cm(-3) K(-1)) for T = 2 K and ΔH = 7 T among three new complexes.

Influence of specific contacts on the stability and structure of proteins. Theory for the perturbation of a harmonic system.

PubMed Central

Jackson, M B

1987-01-01

The question of how specific contacts within a protein influence its stability and structure is examined within a formal theoretical framework. A mathematical model is developed in which the potential energy of a protein is taken as a harmonic expansion of all of its internal or normal coordinates. With classical statistical mechanics the properties of the system can be derived from this potential energy function. A few new contacts are then introduced as additional energy terms, each having a quadratic dependence on a single internal coordinate. These terms are added as perturbations to the original potential energy, and the attendant changes in the properties of the system are obtained. Exact expressions can be derived for changes in the enthalpy, entropy, and for any arbitrary internal degree of freedom. These quantities are expressed in terms of the parameters of the potential energy functions of the new contacts, and the mean square displacements and positional correlation functions of the internal coordinates. These results provide qualitative insights into the role of contacts in stabilizing a particular conformation. Estimates are given for the entropy of formation of a hydrogen bond in a protein. A criterion is proposed for determining whether a contact is essential to the stability of a protein conformation. This model may be applicable to many experimental systems in which mutant or modified proteins are available that differ by one or a few amino acids. The results may also be useful in thermodynamic analyses of computer simulations. PMID:3828463

Two mixed-ligand lanthanide–hydrazone complexes: [Pr(NCS)3(pbh)2]·H2O and [Nd(NCS)(NO3)(pbh)2(H2O)]NO3·2.33H2O [pbh is N′-(pyridin-2-ylmethylidene)benzo­hydrazide, C13H11N3O

PubMed Central

Paschalidis, Damianos G.; Harrison, William T. A.

2016-01-01

The gel-mediated syntheses and crystal structures of [N′-(pyridin-2-ylmethylidene-κN)benzohydrazide-κ2 N′,O]tris(thiocyanato-κN)praseodymium(III) mono­hydrate, [Pr(NCS)3(C13H11N3O)2]·H2O, (I), and aqua(nitrato-κ2 O,O′)[N′-(pyri­din-2-ylmethylidene-κN)benzohydrazide-κ2 N′,O](thiocyanato-κN)neo­dym­ium(III) nitrate 2.33-hydrate, [Nd(NCS)(NO3)(C13H11N3O)2(H2O)]NO3·2.33H2O, (II), are reported. The Pr3+ ion in (I) is coordinated by two N,N,O-tridentate N′-(pyridin-2-ylmethylidene)benzohydrazide (pbh) ligands and three N-bonded thio­cyanate ions to generate an irregular PrN7O2 coordination polyhedron. The Nd3+ ion in (II) is coordinated by two N,N,O-tridentate pbh ligands, an N-bonded thio­cyanate ion, a bidentate nitrate ion and a water mol­ecule to generate a distorted NdN5O5 bicapped square anti­prism. The crystal structures of (I) and (II) feature numerous hydrogen bonds, which lead to the formation of three-dimensional networks in each case. PMID:26958385

Channel characteristics and coordination in three-echelon dual-channel supply chain

NASA Astrophysics Data System (ADS)

Saha, Subrata

2016-02-01

We explore the impact of channel structure on the manufacturer, the distributer, the retailer and the entire supply chain by considering three different channel structures in radiance of with and without coordination. These structures include a traditional retail channel and two manufacturer direct channels with and without consistent pricing. By comparing the performance of the manufacturer, the distributer and the retailer, and the entire supply chain in three different supply chain structures, it is established analytically that, under some conditions, a dual channel can outperform a single retail channel; as a consequence, a coordination mechanism is developed that not only coordinates the dual channel but also outperforms the non-cooperative single retail channel. All the analytical results are further analysed through numerical examples.

76 FR 75898 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... following formats: One hard copy with original signature, and one electronic copy via email (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Please submit your statement to Douglas Hobbs, Council Coordinator (see FOR FURTHER...

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination.

PubMed

Dokmanić, Ivan; Sikić, Mile; Tomić, Sanja

2008-03-01

Metal ions are constituents of many metalloproteins, in which they have either catalytic (metalloenzymes) or structural functions. In this work, the characteristics of various metals were studied (Cu, Zn, Mg, Mn, Fe, Co, Ni, Cd and Ca in proteins with known crystal structure) as well as the specificity of their environments. The analysis was performed on two data sets: the set of protein structures in the Protein Data Bank (PDB) determined with resolution <1.5 A and the set of nonredundant protein structures from the PDB. The former was used to determine the distances between each metal ion and its electron donors and the latter was used to assess the preferred coordination numbers and common combinations of amino-acid residues in the neighbourhood of each metal. Although the metal ions considered predominantly had a valence of two, their preferred coordination number and the type of amino-acid residues that participate in the coordination differed significantly from one metal ion to the next. This study concentrates on finding the specificities of a metal-ion environment, namely the distribution of coordination numbers and the amino-acid residue types that frequently take part in coordination. Furthermore, the correlation between the coordination number and the occurrence of certain amino-acid residues (quartets and triplets) in a metal-ion coordination sphere was analysed. The results obtained are of particular value for the identification and modelling of metal-binding sites in protein structures derived by homology modelling. Knowledge of the geometry and characteristics of the metal-binding sites in metalloproteins of known function can help to more closely determine the biological activity of proteins of unknown function and to aid in design of proteins with specific affinity for certain metals.

Nature of the Active Sites for CO Reduction on Copper Nanoparticles; Suggestions for Optimizing Performance.

PubMed

Cheng, Tao; Xiao, Hai; Goddard, William A

2017-08-30

Recent experiments show that the grain boundaries (GBs) of copper nanoparticles (NPs) lead to an outstanding performance in reducing CO 2 and CO to alcohol products. We report here multiscale simulations that simulate experimental synthesis conditions to predict the structure of a 10 nm Cu NP (158 555 atoms). To identify active sites, we first predict the CO binding at a large number of sites and select four exhibiting CO binding stronger than the (211) step surface. Then, we predict the formation energy of the *OCCOH intermediate as a descriptor for C-C coupling, identifying two active sites, both of which have an under-coordinated surface square site adjacent to a subsurface stacking fault. We then propose a periodic Cu surface (4 by 4 supercell) with a similar site that substantially decreases the formation energy of *OCCOH, by 0.14 eV.

Single and double C-Cl-activation of methylene chloride by P,N-ligand coordinated rhodium complexes.

PubMed

Blank, Benoît; Glatz, Germund; Kempe, Rhett

2009-02-02

Two in one: The simultaneous formation of bimetallic mu-methylene bridged Rh(III) complexes as well as dimeric Rh(III) complexes with terminal chloromethyl groups is observed for P,N-ligand stabilized Rh(I) complexes by C-Cl bond activation of methylene chloride. A mechanistic proposal for the formation of both activation products is also discussed. The synthesis of Rh(I) complexes with P-functionalized aminopyridine ligands is reported as well as the first simultaneous observation of a single and double activation of C-Cl bonds of methylene chloride affording both a dimeric Rh(III) complex bearing terminal CH(2)Cl groups in addition to a binuclear Rh(III) complex with a bridging mu-CH(2) group. The structures of the oxidative addition products were obtained by X-ray diffraction studies and NMR experiments were performed to elucidate some aspects of the reaction pathway.

Molybdenum Valence in Basaltic Silicate Melts

NASA Technical Reports Server (NTRS)

Danielson, L. R.; Righter, K.; Newville, M.; Sutton, S.; Pando, K.

2010-01-01

The moderately siderophile element molybdenum has been used as an indicator in planetary differentiation processes, and is particularly relevant to core formation [for example, 1-6]. However, models that apply experimental data to an equilibrium differentiation scenario infer the oxidation state of molybdenum from solubility data or from multivariable coefficients from metal-silicate partitioning data [1,3,7]. Partitioning behavior of molybdenum, a multivalent element with a transition near the J02 of interest for core formation (IW-2) will be sensitive to changes in JO2 of the system and silicate melt structure. In a silicate melt, Mo can occur in either 4+ or 6+ valence state, and Mo6+ can be either octahedrally or tetrahedrally coordinated. Here we present first XANES measurements of Mo valence in basaltic run products at a range of P, T, and JO2 and further quantify the valence transition of Mo.

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

Cytotoxic T cells use mechanical force to potentiate target cell killing

PubMed Central

Basu, Roshni; Whitlock, Benjamin M.; Husson, Julien; Le Floc’h, Audrey; Jin, Weiyang; Oyler-Yaniv, Alon; Dotiwala, Farokh; Giannone, Gregory; Hivroz, Claire; Biais, Nicolas; Lieberman, Judy; Kam, Lance C.; Huse, Morgan

2016-01-01

SUMMARY The immunological synapse formed between a cytotoxic T lymphocyte (CTL) and an infected or transformed target cell is a physically active structure capable of exerting mechanical force. Here, we investigated whether synaptic forces promote the destruction of target cells. CTLs kill by secreting toxic proteases and the pore forming protein perforin into the synapse. Biophysical experiments revealed a striking correlation between the magnitude of force exertion across the synapse and the speed of perforin pore formation on the target cell, implying that force potentiates cytotoxicity by enhancing perforin activity. Consistent with this interpretation, we found that increasing target cell tension augmented pore formation by perforin and killing by CTLs. Our data also indicate that CTLs coordinate perforin release and force exertion in space and time. These results reveal an unappreciated physical dimension to lymphocyte function and demonstrate that cells use mechanical forces to control the activity of outgoing chemical signals. PMID:26924577

Regulatory Peptides in Plants.

PubMed

Vanyushin, B F; Ashapkin, V V; Aleksandrushkina, N I

2017-02-01

Many different peptides regulating cell differentiation, growth, and development are found in plants. Peptides participate in regulation of plant ontogenesis starting from pollination, pollen tube growth, and the very early stages of embryogenesis, including formation of embryo and endosperm. They direct differentiation of meristematic stem cells, formation of tissues and individual organs, take part in regulation of aging, fruit maturation, and abscission of plant parts associated with apoptosis. Biological activity of peptides is observed at very low concentrations, and it has mainly signal nature and hormonal character. "Mature" peptides appear mainly due to processing of protein precursors with (or without) additional enzymatic modifications. Plant peptides differ in origin, structure, and functional properties. Their specific action is due to binding with respective receptors and interactions with various proteins and other factors. Peptides can also regulate physiological functions by direct peptide-protein interactions. Peptide action is coordinated with the action of known phytohormones (auxins, cytokinins, and others); thus, peptides control phytohormonal signal pathways.

Constitutional Dynamics of Metal-Organic Motifs on a Au(111) Surface.

PubMed

Kong, Huihui; Zhang, Chi; Xie, Lei; Wang, Likun; Xu, Wei

2016-06-13

Constitutional dynamic chemistry (CDC), including both dynamic covalent chemistry and dynamic noncovalent chemistry, relies on reversible formation and breakage of bonds to achieve continuous changes in constitution by reorganization of components. In this regard, CDC is considered to be an efficient and appealing strategy for selective fabrication of surface nanostructures by virtue of dynamic diversity. Although constitutional dynamics of monolayered structures has been recently demonstrated at liquid/solid interfaces, most of molecular reorganization/reaction processes were thought to be irreversible under ultrahigh vacuum (UHV) conditions where CDC is therefore a challenge to be achieved. Here, we have successfully constructed a system that presents constitutional dynamics on a solid surface based on dynamic coordination chemistry, in which selective formation of metal-organic motifs is achieved under UHV conditions. The key to making this reversible switching successful is the molecule-substrate interaction as revealed by DFT calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Portrait of an Enzyme, a Complete Structural Analysis of a Multimodular beta-N-Acetylglucosaminidase from Clostridium perfringens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ficko-Blean, E.; Gregg, K; Adams, J

2009-01-01

Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens ?-toxin, which was determined using a combination of smallmore » angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.« less

Extended x-ray absorption fine structure spectroscopy and x-ray absorption near edge spectroscopy study of aliovalent doped ceria to correlate local structural changes with oxygen vacancies clustering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirbhate, S. C.; Acharya, S. A., E-mail: saha275@yahoo.com; Yadav, A. K.

2016-04-04

This study provides atomic scale insight to understand the role of aliovalent dopants on oxygen vacancies clustering and dissociation mechanism in ceria system in order to enhance the performance of oxy-ion conductor. Dopants induced microscale changes in ceria are probed by extended X-ray absorption fine structure spectroscopy, X-ray absorption near edge spectra, and Raman spectroscopy. The results are explored to establish a correlation between atomic level structural changes (coordination number, interatomic spacing) → formation of dimer and trimer type cation-oxygen vacancies defect complex (intrinsic and extrinsic) → dissociation of oxygen vacancies from defect cluster → ionic conductivity temperature. It ismore » a strategic approach to understand key physics of ionic conductivity mechanism in order to reduce operating temperature of electrolytes for intermediate temperature (300–450 °C) electrochemical devices for the first time.« less

[Implementation of the Mobile Emergency Medical Service in Brazil: action strategies and structural dimension].

PubMed

O'Dwyer, Gisele; Konder, Mariana Teixeira; Reciputti, Luciano Pereira; Macedo, Cesar; Lopes, Monica Guimarães Macau

2017-08-07

The Mobile Emergency Medical Service (SAMU) was the first component of the National Policy for Emergency Care implemented in Brazil in the early 2000. The article analyzed the implementation of mobile pre-hospital emergency care in Brazil. The methods included document analysis, interviews with state emergency care coordinators, and an expert panel. The theoretical reference was the strategic conduct analysis from Giddens' Structuration Theory. The results showed uneven implementation of the SAMU between states and regions of Brazil, identifying six patterns of implementation, considering the states' capacity to expand the population coverage and regionalize the service. Structural difficulties included physician retention, poorly equipped dispatch centers, and shortage of ambulances. The North and Northeast were the country's most heavily affected regions. SAMU is formatted as a structuring strategy in the emergency care network, but its performance suffered the impact of limited participation by primary care in the emergency network and especially the lack of hospital beds.

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

NASA Astrophysics Data System (ADS)

Metere, Alfredo; Oleynikov, Peter; Dzugutov, Mikhail; O'Keeffe, Michael

2014-12-01

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

About the algorithm for construction of coordinated university timetables

NASA Astrophysics Data System (ADS)

Dobrynin, A. S.; Kulakov, S. M.; Taraborina, E. N.

2018-05-01

The factual description of the task and an algorithm for drawing up a coordinated timetable of academic work of the faculty and students at the level of department (local timetable) is presented, as well as the procedure for integrating private schedules, i.e. the formation of a university-wide timetable. Coordination of the latter has not only spatio-temporal in nature, but also takes into account the preferences (interests) of agents (users and performers of works).

Coordination Polymer Gels with Modular Nanomorphologies, Tunable Emissions, and Stimuli-Responsive Behavior Based on an Amphiphilic Tripodal Gelator.

PubMed

Sutar, Papri; Maji, Tapas Kumar

2017-08-21

The recent upsurge in research on coordination polymer gels (CPGs) stems from their synthetic modularity, nanoscale processability, and versatile functionalities. Here we report self-assembly of an amphiphilic, tripodal low-molecular weight gelator (L) that consists of 4,4',4-[1,3,5-phenyl-tri(methoxy)]-tris-benzene core and 2,2':6',2″-terpyridyl termini, with different metal ions toward the formation of CPGs that show controllable nanomorphologies, tunable emission, and stimuli-responsive behaviors. L can also act as a selective chemosensor for Zn II with very low limit of detection (0.18 ppm) in aqueous medium. Coordination-driven self-assembly of L with Zn II in H 2 O/MeOH solvent mixture results in a coordination polymer hydrogel (ZnL) that exhibits sheet like morphology and charge-transfer emission. On the other hand, coordination of L with Tb III and Eu III in CHCl 3 /tetrahydrofuran solvent mixture results in green- and red-emissive CPGs, respectively, with nanotubular morphology. Moreover, precise stoichiometric control of L/Eu III /Tb III ratio leads to the formation of bimetallic CPGs that show emissions over a broad spectral range, including white-light-emission. We also explore the multistimuli responsive properties of the white-light-emitting CPG by exploiting the dynamics of Ln III -tpy coordination.

Multi-disciplinary team meetings in stroke rehabilitation: an observation study and conceptual framework.

PubMed

Tyson, S F; Burton, L; McGovern, A

2014-12-01

To explore how multi-disciplinary team meetings operate in stroke rehabilitation. Non-participant observation of multi-disciplinary team meetings and semi-structured interviews with attending staff. Twelve meetings were observed (at least one at each site) and 18 staff (one psychologist, one social worker; four nurses; four physiotherapists four occupational therapists, two speech and language therapists, one stroke co-ordinator and one stroke ward manager) were interviewed in eight in-patient stroke rehabilitation units. Multi-disciplinary team meetings in stroke rehabilitation were complex, demanding and highly varied. A model emerged which identified the main inputs to influence conduct of the meetings were personal contributions of the members and structure and format of the meetings. These were mediated by the team climate and leadership skills of the chair. The desired outputs; clinical decisions and the attributes of apparently effective meetings were identified by the staff. A notable difference between the meetings that staff considered effective and those that were not, was their structure and format. Successful meetings tended to feature a set agenda, structured documentation; formal use of measurement tools; pre-meeting preparation and skilled chairing. These features were often absent in meetings perceived to be ineffective. The main features of operation of multi-disciplinary team meetings have been identified which will enable assessment tools and interventions to improve effectiveness to be developed. © The Author(s) 2014.

Exploring the influence of iron substitution in lithium rich layered oxides Li 2Ru 1–xFe xO 3: triggering the anionic redox reaction

DOE PAGES

Satish, Rohit; Lim, Kipil; Bucher, Nicolas; ...

2017-06-23

Lithium rich layered materials are an interesting class of materials which exploit both anionic and cationic redox reactions to store energy upwards of 250 mA h g –1. This paper aims to understand the nature of the redox reactions taking place in these compounds. Li 2RuO 3 was used as the base compound, which is then compared with compounds generated by partially substituting Ru with Ti and Fe respectively. Electrochemical tests indicate that Fe substitution in the sample leads to an improvement in capacity, cycle life and reduction of potential decay. To elucidate the reason for this improvement in operandomore » diffraction experiments were carried out, highlighting the formation of a secondary de-lithiated phase. The distortion of the pristine structure eventually induces frontier orbital reorganization leading to the oxygen redox reaction resulting in extra capacity. Local changes at Fe and Ru ions are recorded using in operando X-ray absorption spectroscopy (XAS). It was noted that while Ru undergoes a reversible redox reaction, Fe undergoes a significant irreversible change in its coordination environment during cycling. In conclusion, the changes in the coordination environment of oxygen and formation of O 2 n– type species were probed in situ using soft X-rays.« less

9-Triptycenecarboxylate-Bridged Diiron(II) Complexes

PubMed Central

Friedle, Simone; Kodanko, Jeremy J.; Fornace, Kyrstin L.; Lippard, Stephen J.

2008-01-01

The synthesis and characterization of diiron(II) complexes supported by 9-triptycenecarboxylate ligands (-O2CTrp) is described. The interlocking nature of the triptycenecarboxylates facilitates formation of quadruply bridged diiron(II) complexes of the type [Fe2(μ-O2CTrp)4(L)2] (L = THF, pyridine or imidazole derivative) with a paddlewheel geometry. A systematic lengthening of the Fe-Fe distance occurs with the increase in steric bulk of the neutral donor L, resulting in values of up to 3 Å without disassembly of the paddlewheel structure. Reactions with an excess of water do not lead to decomposition of the diiron(II) core, indicating that these quadruply bridged complexes are of exceptional stability. The red-colored complexes [Fe2(μ-O2CTrp)4(4-AcPy)2] (10) and [Fe2(μ-O2CTrp)4(4-CNPy)2] (11) exhibit solvent-dependent thermochromism in coordinating solvents that was studied by variable temperature UV-vis spectroscopy. Reaction of [Fe2(μ-O2CTrp)4(THF)2] with N,N,N’,N’-tetramethylethylenediamine (TMEDA), tetra-n-butyl ammonium thiocyanate, or excess 2-methylimidazole resulted in the formation of mononuclear complexes [Fe(O2CTrp)2(TMEDA)] (13), (n-Bu4N)2[Fe(O2CTrp)2(SCN)2] (14), and [Fe(O2CTrp)2(2-MeIm)2] (15) having an O4/N2 coordination sphere composition. PMID:19915653

Controls on the Fate and Speciation of Np(V) During Iron (Oxyhydr)oxide Crystallization.

PubMed

Bots, Pieter; Shaw, Samuel; Law, Gareth T W; Marshall, Timothy A; Mosselmans, J Frederick W; Morris, Katherine

2016-04-05

The speciation and fate of neptunium as Np(V)O2(+) during the crystallization of ferrihydrite to hematite and goethite was explored in a range of systems. Adsorption of NpO2(+) to iron(III) (oxyhydr)oxide phases was reversible and, for ferrihydrite, occurred through the formation of mononuclear bidentate surface complexes. By contrast, chemical extractions and X-ray absorption spectroscopy (XAS) analyses showed the incorporation of Np(V) into the structure of hematite during its crystallization from ferrihydrite (pH 10.5). This occurred through direct replacement of octahedrally coordinated Fe(III) by Np(V) in neptunate-like coordination. Subsequent analyses on mixed goethite and hematite crystallization products (pH 9.5 and 11) showed that Np(V) was incorporated during crystallization. Conversely, there was limited evidence for Np(V) incorporation during goethite crystallization at the extreme pH of 13.3. This is likely due to the formation of a Np(V) hydroxide precipitate preventing incorporation into the goethite particles. Overall these data highlight the complex behavior of Np(V) during the crystallization of iron(III) (oxyhydr)oxides, and demonstrate clear evidence for neptunium incorporation into environmentally important mineral phases. This extends our knowledge of the range of geochemical conditions under which there is potential for long-term immobilization of radiotoxic Np in natural and engineered environments.

Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences

NASA Astrophysics Data System (ADS)

Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

2013-07-01

We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing nativelike substructures or “foldons.” Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that nativelike propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the molecular dynamics study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo.

Synthesis and characterization of thorium(IV) sulfates.

PubMed

Knope, Karah E; Wilson, Richard E; Skanthakumar, S; Soderholm, L

2011-09-05

Three Th(IV) sulfates, two new and one previously reported, have been synthesized from aqueous solution. In all of the compounds, the sulfate anions coordinate the Th(4+) metal center(s) in a monodentate manner with Th-S distances of 3.7-3.8 Å. Th(SO(4))(2)(H(2)O)(7)·2(H(2)O) (1; P2(1)/m, a = 7.224(1) Å, b = 12.151(1) Å, c = 7.989(1) Å, ss =98.289(2)°) and Th(4)(SO(4))(7)(H(2)O)(7)(OH)(2)·H(2)O (2; Pnma, a = 18.139(2) Å, b = 11.173(1) Å, c = 14.391(2) Å) each contain 9-coordinate monomeric (1,2) and dimeric (2) Th(IV) cations in monocapped square antiprism geometry. Alternatively, Th(OH)(2)SO(4) (3; Pnma, a = 11.684(1) Å, b = 6.047(1) Å, c = 7.047(1) Å) is built from chains of hydroxo-bridged, 8-coordinate Th(4+) centers. Whereas 1 adopts a molecular structure, 2 and 3 both exhibit 3D architectures. Differences in the dimensionality and the topology of 1-3 are manifested in the local coordination environment about the Th(IV) centers, the formation of oligomeric Th(4+) species, and the extended connectivity of the sulfate ligands. Herein, we report the syntheses and characterization of 1-3 as well as the atomic correlations of 1 in solution, as determined by high-energy X-ray scattering (HEXS).

Crystal structure of tetra­aqua­(5,5′-dimethyl-2,2′-bipyridyl-κ2 N,N′)iron(II) sulfate

PubMed Central

Belamri, Yamine; Setifi, Fatima; Francuski, Bojana M.; Novaković, Sladjana B.; Zouaoui, Setifi

2014-01-01

In the title compound, [Fe(C12H12N2)(H2O)4]SO4, the central FeII ion is coordinated by two N atoms from the 5,5′-dimethyl-2,2′-bi­pyridine ligand and four water O atoms in a distorted octa­hedral geometry. The Fe—O coordination bond lengths vary from 2.080 (3) to 2.110 (3) Å, while the two Fe—N coordination bonds have practically identical lengths [2.175 (3) and 2.177 (3) Å]. The chelating N—Fe—N angle of 75.6 (1)° shows the largest deviation from an ideal octa­hedral geometry; the other coordination angles deviate from ideal values by 0.1 (1) to 9.1 (1)°. O—H⋯O hydrogen bonding between the four aqua ligands of the cationic complex and four O-atom acceptors of the anion leads to the formation of layers parallel to the ab plane. Neighbouring layers further inter­act by means of C—H⋯O and π–π inter­actions involving the laterally positioned bi­pyridine rings. The perpen­dicular distance between π–π inter­acting rings is 3.365 (2) Å, with a centroid–centroid distance of 3.702 (3) Å. PMID:25552988

Stochastic phase of ventral furrow formation in the Drosophila embryo: cellular constriction chains, mechanical feedback, and robustness

NASA Astrophysics Data System (ADS)

Blawzdziewicz, Jerzy; Gao, Guo-Jie J.; Holcomb, Michael C.; Thomas, Jeffrey H.

The key process giving rise to ventral furrow formation (VFF) in Drosophila embryo is apical constriction of cells in the ventral region. The constriction produces negative spontaneous curvature of the cell layer. During the initial slower phase of VFF approximately 40% of cells constrict in a seemingly random order. We show that this initial phase of VFF does not depend on random uncorrelated events. Instead, constricted cell apices form well-defined correlated structures, i.e., cellular constriction chains (CCCs), indicative of strong spatial and directional correlations between the constriction events. We argue that this chain formation is a signature of mechanical signaling that coordinates apical constrictions through tensile stress. To gain insights into the mechanisms involved in this correlated constriction process, we propose an active granular fluid (AGF) model which considers a tissue as a collection of mechanically active, stress-responsive objects. Our AGF molecular dynamics simulations show that cell constriction sensitivity to tensile stress results in formation of CCCs whereas compressive-stress sensitivity leads to compact constricted cell clusters; the CCCs, which can penetrate less-active regions, increase the robustness of the VFF process.

Synthesis of CuInSe2 nanocrystals using a continuous hot-injection microreactor

NASA Astrophysics Data System (ADS)

Jin, Hyung Dae; Chang, Chih-Hung

2012-10-01

A very rapid and simple synthesis of CuInSe2 nanocrystals (NCs) was successfully performed using a continuous hot-injection microreactor with a high throughput per reactor volume. It was found that copper-rich CuInSe2 with a sphalerite structure was formed initially followed by the formation of more ordered CuInSe2 at longer reaction times along with the formation of Cu2Se and In2Se3. Binary syntheses were performed and the results show a much faster formation rate of Cu2Se than In2Se3. The rate limiting step in the formation of CuInSe2 is forming the In2Se3 intermediate. Rapid synthesis of stoichiometric CuInSe2 NCs using a continuous-flow microreactor was accomplished by properly adjusting the Cu/In precursor ratio. Tuning the ratio of coordinating solvents can cause size differences from 2.6 to 4.1 nm, bandgaps from 1.1 to 1.3 eV, and different production yields of NCs. The highest production yield as determined by weight was achieved up to 660 mg/h using a microreactor with a small volume of 3.2 cm3.

Theoretical Prediction of Vibrational Circular Dichroism Spectra of R- Glyceraldehyde, R-Erythrose, and R-Threose. 2. Development of a Procedure to Scale the Force Constant Matrix Expressed in Terms of Internal Coordinates

DTIC Science & Technology

1993-11-01

IS PROGRAM NUMBER 1 OF THE COMPLETE VIBRATIONAL PACKAGE. C C BMAT ... WIL.riON B MATRIX ELDEMETS FOR INTERNAL COORDINATES C iVERSIONO JUL 28, 1977) C...MATRIX ISCAN=ISCAN+ 1 IER=O GO TO 30 210 WRITE(6,1120) STOP 1000 FORMAT(20A4/20A4/214) 1010 FORMAT(’l’,20A4,24X.’ BMAT (VERSIONO JUL 28. 1977)’/1X,20A4

Two-step crystal growth mechanism during crystallization of an undercooled Ni50Al50 alloy

NASA Astrophysics Data System (ADS)

An, Simin; Li, Jiahao; Li, Yang; Li, Shunning; Wang, Qi; Liu, Baixin

2016-08-01

Crystallization processes are always accompanied by the emergence of multiple intermediate states, of which the structures and transition dynamics are far from clarity, since it is difficult to experimentally observe the microscopic pathway. To insight the structural evolution and the crystallization dynamics, we perform large-scale molecular dynamics simulations to investigate the time-dependent crystallization behavior of the NiAl intermetallic upon rapid solidification. The simulation results reveal that the crystallization process occurs via a two-step growth mechanism, involving the formation of initial non-equilibrium long range order (NLRO) regions and of the subsequent equilibrium long range order (ELRO) regions. The formation of the NLRO regions makes the grains rather inhomogeneous, while the rearrangement of the NLRO regions into the ELRO regions makes the grains more ordered and compact. This two-step growth mechanism is actually controlled by the evolution of the coordination polyhedra, which are characterized predominantly by the transformation from five-fold symmetry to four-fold and six-fold symmetry. From liquids to NLRO and further to ELRO, the five-fold symmetry of these polyhedra gradually fades, and finally vanishes when B2 structure is distributed throughout the grain bulk. The energy decrease along the pathway further implies the reliability of the proposed crystallization processes.

Learning structure-property relationship in crystalline materials: A study of lanthanide-transition metal alloys

NASA Astrophysics Data System (ADS)

Pham, Tien-Lam; Nguyen, Nguyen-Duong; Nguyen, Van-Doan; Kino, Hiori; Miyake, Takashi; Dam, Hieu-Chi

2018-05-01

We have developed a descriptor named Orbital Field Matrix (OFM) for representing material structures in datasets of multi-element materials. The descriptor is based on the information regarding atomic valence shell electrons and their coordination. In this work, we develop an extension of OFM called OFM1. We have shown that these descriptors are highly applicable in predicting the physical properties of materials and in providing insights on the materials space by mapping into a low embedded dimensional space. Our experiments with transition metal/lanthanide metal alloys show that the local magnetic moments and formation energies can be accurately reproduced using simple nearest-neighbor regression, thus confirming the relevance of our descriptors. Using kernel ridge regressions, we could accurately reproduce formation energies and local magnetic moments calculated based on first-principles, with mean absolute errors of 0.03 μB and 0.10 eV/atom, respectively. We show that meaningful low-dimensional representations can be extracted from the original descriptor using descriptive learning algorithms. Intuitive prehension on the materials space, qualitative evaluation on the similarities in local structures or crystalline materials, and inference in the designing of new materials by element substitution can be performed effectively based on these low-dimensional representations.

Tripodal polyphosphine ligands as inductors of chelate ring-opening processes in mononuclear palladium(II) and platinum(II) compounds. The X-ray crystal structure of two derivatives containing dangling phosphorus.

PubMed

Fernández-Anca, Damián; García-Seijo, M Inés; García-Fernández, M Esther

2010-03-07

The reaction of NP(3) (tris[2-(diphenylphosphino)ethyl]amine and PP(3) (tris[2-(diphenylphosphino)ethyl]phosphine) with the five-coordinate complexes [PdCl(NP(3))]Cl (1) and [MX(PP(3))]X [M = Pd: X = Cl(2), Br(3), I(4); M = Pt: X = Cl(5), Br(6), I(7)], respectively, followed by (31)P{(1)H}NMR when X = Cl, led to the formation of unprecedented four-coordinate halides in a 1 : 2 metal to ligand ratio, [M(AP(3))(2)]X(2) [A = N, M = Pd: X = Cl(8); A = P, M = Pd: X = Cl(9), Br(10), I(11); A = P, M = Pt: X = Cl(12), Br(13), I (14)], containing reactive dangling phosphorus. Given the non characterised precursors [M(ONO(2))(PP(3))](NO(3))], the interaction between the heteronuclear species [MAg(NO(3))(3)(PP(3))] [M = Pd(15), Pt(16)] and PP(3) was explored. It was found that the addition of 1 equivalent of phosphine afforded [MAg(NO(3))(PP(3))(2)](NO(3))(2) [M = Pd(15*), Pt(16*)] containing Ag(I) bound to two dangling phosphorus while the reaction with 2 equivalents led to the complexes [M(PP(3))(2)](NO(3))(2) [M = Pd (17), Pt (18)] in coexistence with [Ag(2)(mu-PP(3))(2)](NO(3))(2). The fate of Ag(I) on the reaction of the mixed metal compounds with excess PP(3) consisted of preventing dissociation, observed in solution for halides, and acting as an assistant for crystallization. Colourless single crystals of 18 and 10, studied by X-ray diffraction, were afforded by reaction of 16 with 4 equivalents of PP(3) and from solutions of 10 in chloroform coexisting with red crystals of 3, respectively. The structures revealed the presence of dications [M(PP(3))(2)](2+) that show two five-membered chelate rings to M(II) in a square-planar arrangement and four uncoordinated phosphine arms with the counter anions being symmetrically placed at 4.431 (Br(-)) and 13.823 (NO(3)(-)) A from M(II) above and below its coordination, MP(4), plane. Complexes 9 and 12 were shown to undergo an interesting reactivity in solution versus group 11 monocations. The reactions consisted of conversions of the two five-membered chelate rings to M into three (structure I) or two (structure II) fused five-membered chelate rings, formation of species where Pt(II) retained its square-planar environment with the two dangling phosphine arms of each PP(3) bound to Cu(I) or Ag(I) (structure III) and complexes bearing distorted square-planar (P(2)MCl(2)) and presumably tetrahedral (AuP(4)+ P(2)AuCl(2)) arrangements (structure IV). The processes with Ag(I) salts also gave mixtures of I+III (chloride and nitrate) or II+III (nitrate).

Reactivity pathways for nitric oxide and nitrosonium with iron complexes in biologically relevant sulfur coordination spheres.

PubMed

Harrop, Todd C; Song, Datong; Lippard, Stephen J

2007-11-01

The interaction of nitric oxide (NO) with iron-sulfur cluster proteins results in the formation of dinitrosyl iron complexes (DNICs) coordinated by cysteine residues from the peptide backbone or with low molecular weight sulfur-containing molecules like glutathione. Such DNICs are among the modes available in biology to store, transport, and deliver NO to its relevant targets. In order to elucidate the fundamental chemistry underlying the formation of DNICs and to characterize possible intermediates in the process, we have investigated the interaction of NO (g) and NO(+) with iron-sulfur complexes having the formula [Fe(SR)(4)](2-), where R=(t)Bu, Ph, or benzyl, chosen to mimic sulfur-rich iron sites in biology. The reaction of NO (g) with [Fe(S(t)Bu)(4)](2-) or [Fe(SBz)(4)](2-) cleanly affords the mononitrosyl complexes (MNICs), [Fe(S(t)Bu)(3)(NO)](-) (1) and [Fe(SBz)(3)(NO)](-) (3), respectively, by ligand displacement. Mononitrosyl species of this kind were previously unknown. These complexes further react with NO (g) to generate the corresponding DNICs, [Fe(SPh)(2)(NO)(2)](-) (4) and [Fe(SBz)(2)(NO)(2)](-) (5), with concomitant reductive elimination of the coordinated thiolate donors. Reaction of [Fe(SR)(4)](2-) complexes with NO(+) proceeds by a different pathway to yield the corresponding dinitrosyl S-bridged Roussin red ester complexes, [Fe(2)(mu-S(t)Bu)(2)(NO)(4)] (2), [Fe(2)(mu-SPh)(2)(NO)(4)] (7) and [Fe(2)(mu-SBz)(2)(NO)(4)] (8). The NO/NO(+) reactivity of an Fe(II) complex with a mixed nitrogen/sulfur coordination sphere was also investigated. The DNIC and red ester species, [Fe(S-o-NH(2)C(6)H(4))(2)(NO)(2)](-) (6) and [Fe(2)(mu-S-o-NH(2)C(6)H(4))(2)(NO)(4)] (9), were generated. The structures of 8 and 9 were verified by X-ray crystallography. The MNIC complex 1 can efficiently deliver NO to iron-porphyrin complexes like [Fe(TPP)Cl], a reaction that is aided by light. Removal of the coordinated NO ligand of 1 by photolysis and addition of elemental sulfur generates higher nuclearity Fe/S clusters.

Individual differences in algebraic cognition: Relation to the approximate number and semantic memory systems.

PubMed

Geary, David C; Hoard, Mary K; Nugent, Lara; Rouder, Jeffrey N

2015-12-01

The relation between performance on measures of algebraic cognition and acuity of the approximate number system (ANS) and memory for addition facts was assessed for 171 ninth graders (92 girls) while controlling for parental education, sex, reading achievement, speed of numeral processing, fluency of symbolic number processing, intelligence, and the central executive component of working memory. The algebraic tasks assessed accuracy in placing x,y pairs in the coordinate plane, speed and accuracy of expression evaluation, and schema memory for algebra equations. ANS acuity was related to accuracy of placements in the coordinate plane and expression evaluation but not to schema memory. Frequency of fact retrieval errors was related to schema memory but not to coordinate plane or expression evaluation accuracy. The results suggest that the ANS may contribute to or be influenced by spatial-numerical and numerical-only quantity judgments in algebraic contexts, whereas difficulties in committing addition facts to long-term memory may presage slow formation of memories for the basic structure of algebra equations. More generally, the results suggest that different brain and cognitive systems are engaged during the learning of different components of algebraic competence while controlling for demographic and domain general abilities. Copyright © 2015 Elsevier Inc. All rights reserved.

Light-induced charge separation across bio-inorganic interface.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dimitrijevic, N. M.; Rajh, T.; De La Garza, L.

Rational design of hybrid biomolecule - nanoparticulate semiconductor conjugates enables coupling of functionality of biomolecules with the capability of semiconductors for solar energy capture, that can have potential application in energy conversion, sensing and catalysis. The particular challenge is to obtain efficient charge separation analogous to the natural photosynthesis process. The synthesis of axially anisotropic TiO{sub 2} nano-objects such as tubes, rods and bricks, as well as spherical and faceted nanoparticles has been developed in our laboratory. Depending on their size and shape, these nanostructures exhibit different domains of crystallinity, surface areas and aspect ratios. Moreover, in order to accommodatemore » for high curvature in nanoscale regime, the surfaces of TiO{sub 2} nano-objects reconstructs resulting in changes in the coordination of surface Ti atoms from octahedral (D{sub 2d}) to square pyramidal structures (C{sub 4v}). The formation of these coordinatively unsaturated Ti atoms, thus depends strongly on the size and shape of nanocrystallites and affects trapping and reactivity of photogenerated charges. We have exploited these coordinatively unsaturated Ti atoms to coupe electron-donating (such as dopamine) and electron-accepting (pyrroloquinoline quinone) conductive linkers that allow wiring of biomolecules and proteins resulting in enhanced charge separation which increases the yield of ensuing chemical transformations.« less

Impact of Seawater Nonlinearities on Nordic Seas Circulation

NASA Astrophysics Data System (ADS)

Helber, R. W.; Wallcraft, A. J.; Shriver, J. F.

2017-12-01

The Nordic Seas (Greenland, Iceland, and Norwegian Seas) form an ocean basin important for Arctic-mid-latitude climate linkages. Cold fresh water from the Arctic Ocean and warm salty water from the North Atlantic Ocean meet in the Nordic Seas, where a delicate balance between temperature and salinity variability results in deep water formation. Seawater non-linearities are stronger at low temperatures and salinities making high-latitude oceans highly subject to thermbaricity and cabbeling. This presentation highlights and quantifies the impact of seawater non-linearities on the Nordic Seas circulation. We use two layered ocean circulation models, the Hybrid Coordinate Ocean Model (HYOCM) and the Modular Ocean Model version 6 (MOM6), that enable accurate representation of processes along and across density or neutral density surfaces. Different equations-of-state and vertical coordinates are evaluated to clarify the impact of seawater non-linearities. Present Navy systems, however, do not capture some features in the Nrodic Seas vertical structure. For example, observations from the Greenland Sea reveal a subsurface temperature maximum that deepens from approximately 1500 m during 1998 to 1800 m during 2005. We demonstrate that in terms of density, salinity is the largest source of error in Nordic Seas Navy forecasts, regional scale models can represent mesoscale features driven by thermobaricity, vertical coordinates are a critical issue in Nordic Sea circulation modeling.

Two-dimensional replica exchange approach for peptide-peptide interactions

NASA Astrophysics Data System (ADS)

Gee, Jason; Shell, M. Scott

2011-02-01

The replica exchange molecular dynamics (REMD) method has emerged as a standard approach for simulating proteins and peptides with rugged underlying free energy landscapes. We describe an extension to the original methodology—here termed umbrella-sampling REMD (UREMD)—that offers specific advantages in simulating peptide-peptide interactions. This method is based on the use of two dimensions in the replica cascade, one in temperature as in conventional REMD, and one in an umbrella sampling coordinate between the center of mass of the two peptides that aids explicit exploration of the complete association-dissociation reaction coordinate. To mitigate the increased number of replicas required, we pursue an approach in which the temperature and umbrella dimensions are linked at only fully associated and dissociated states. Coupled with the reweighting equations, the UREMD method aids accurate calculations of normalized free energy profiles and structural or energetic measures as a function of interpeptide separation distance. We test the approach on two families of peptides: a series of designed tetrapeptides that serve as minimal models for amyloid fibril formation, and a fragment of a classic leucine zipper peptide and its mutant. The results for these systems are compared to those from conventional REMD simulations, and demonstrate good convergence properties, low statistical errors, and, for the leucine zippers, an ability to sample near-native structures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Streltsov, Victor A.; Titmuss, Stephen J.; Epa, V. Chandana

Neurodegeneration observed in Alzheimer disease (AD) is believed to be related to the toxicity from reactive oxygen species (ROS) produced in the brain by the amyloid-{beta} (A{beta}) protein bound primarily to copper ions. The evidence for an oxidative stress role of A{beta}-Cu redox chemistry is still incomplete. Details of the copper binding site in A{beta} may be critical to the etiology of AD. Here we present the structure determined by combining x-ray absorption spectroscopy (XAS) and density functional theory analysis of A{beta} peptides complexed with Cu{sup 2+} in solution under a range of buffer conditions. Phosphate-buffered saline buffer salt (NaCl)more » concentration does not affect the high-affinity copper binding mode but alters the second coordination sphere. The XAS spectra for truncated and full-length A{beta}-Cu{sup 2+} peptides are similar. The novel distorted six-coordinated (3N3O) geometry around copper in the A{beta}-Cu{sup 2+} complexes include three histidines: glutamic, or/and aspartic acid, and axial water. The structure of the high-affinity Cu{sup 2+} binding site is consistent with the hypothesis that the redox activity of the metal ion bound to A{beta} can lead to the formation of dityrosine-linked dimers found in AD.« less

Cation Distribution and Local Configuration of Fe 2+ Ions in Structurally Nonequivalent Lattice Sites of Heterometallic Fe(II)/ M(II) ( M = Mn, Co, Ni, Cu, Zn) Diaquadiformato Complexes

NASA Astrophysics Data System (ADS)

Devillers, M.; Ladrière, J.

1993-03-01

57Fe Mössbauer investigations are carried out on a wide series of heterometallic diaquadiformato Fe(II)/ M(II) complexes with M = Mn, Co, Ni, Cu, and Zn to provide a local picture of the coordination environment of the 57Fe 2+ ions as a function of (i) the nature of the host cation and (ii) the relative amounts of both metals in the matrix (between 50 and 0.25 at.% Fe). Information is obtained on the quantitative distribution of both metals between the two structurally nonequivalent lattice sites and on the local geometry around the dopant atom in each crystal site. In the mixed Fe-Cu complexes. Fe 2+ ions are preferentially incorporated in the tetrahydrated site; in Cu-rich Fe xCu 1- x(HCO 2) 2· 2H 2O, the 57Fe 2+ ions located in the hexaformato-coordinated site are surrounded by an axially compressed octahedron of formate ligands which contrasts with the elongated configuration observed in the pure iron compound and in the other mixed systems. Semiquantitative estimations of the tetragonal field splitting and of the extent of metal-ligand interactions are proposed from the temperature dependence of the quadrupole splitting values.

Role of second-sphere coordination in anion binding: Synthesis, characterization and X-ray structure of hexaamminecobalt(III) chloride hydrogen phthalate trihydrate and sodium hexaamminecobalt(III) benzoate monohydrate

NASA Astrophysics Data System (ADS)

Sharma, Raj Pal; Bala, Ritu; Sharma, Rajni; Kariuki, B. M.; Rychlewska, Urszula; Warżajtis, Beata

2005-06-01

In an effort to utilize [Co(NH 3) 6] 3+cation as a new host for carboxylate ions, orange coloured crystalline solids of composition [Co(NH 3) 6]Cl(C 8H 5O 4) 2·3H 2O ( 1) and Na[Co(NH 3) 6](C 7H 5O 2) 4·H 2O ( 2) were obtained by reacting hot aqueous solutions of hexaamminecobalt(III) chloride with potassium hydrogen phthalate and sodium benzoate in 1:3 molar ratio, respectively. The title complex salts were characterized by elemental analyses and spectroscopic studies (IR, UV/Visible and NMR). Single crystal X-ray structure determinations revealed the formation of second-sphere coordination complexes based on hydrogen bond interactions. In complex salt 1 only two out of three ionisable chloride ions present in [Co(NH 3) 6]Cl 3 were replaced by two CHO4- ions whereas in complex salt 2 all the three ionisable chloride ions present in [Co(NH 3) 6]Cl 3 were replaced and the final product was an adduct with another mole of sodium benzoate in solid state. The crystal lattice is stabilized by electrostatic forces of attraction and predominantly N-H⋯O interactions.

An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human.

PubMed

Chakrabarti, Bornali; Bairagya, Hridoy R; Mallik, Payel; Mukhopadhyay, Bishnu P; Bera, Asim K

2011-02-01

Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (W(H), W(I) and W(S)) to Zn(c) and one water to Zn(s). The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zn(s) from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Zn(c) - W(H) (W(1))...W(2)....W(3)....H(187) Zn(s)) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Zn(c) ...Zn(s) coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.

Molecular Regulation of Lumen Morphogenesis Review

PubMed Central

Datta, Anirban; Bryant, David M.; Mostov, Keith E.

2013-01-01

The asymmetric polarization of cells allows specialized functions to be performed at discrete subcellular locales. Spatiotemporal coordination of polarization between groups of cells allowed the evolution of metazoa. For instance, coordinated apical-basal polarization of epithelial and endothelial cells allows transport of nutrients and metabolites across cell barriers and tissue microenvironments. The defining feature of such tissues is the presence of a central, interconnected luminal network. Although tubular networks are present in seemingly different organ systems, such as the kidney, lung, and blood vessels, common underlying principles govern their formation. Recent studies using in vivo and in vitro models of lumen formation have shed new light on the molecular networks regulating this fundamental process. We here discuss progress in understanding common design principles underpinning de novo lumen formation and expansion. PMID:21300279

Interaction studies of human prion protein (HuPrP109-111: methionine-lysine-histidine) tripeptide model with transition metal cations.

PubMed

Pitchumani Violet Mary, C; Shankar, R; Vijayakumar, S; Kolandaivel, P

2016-09-01

In the present study, the coordination bonds between the Methionine-Lysine-Histidine (Ac-MKH-NHMe) tripeptide model associated with the fifth metal binding site, which triggers the β-sheet formation of human prion protein and the divalent metal cations such as Mn(2+), Cu(2+) and Zn(2+) were studied using B3LYP and M052X levels of theory with LANL2DZ basis set. For each transition divalent metal cation, three different coordination modes (4N, 3NO, and 2NSO) were analyzed. The present result reveals that overall structural parameters of MKH model tripeptide are altered due to the interaction of divalent metal cations. Among these three coordination modes, the 4N-M(2)(+) and 4N2O-Mn(2+) complexes are found to have the larger interaction energy, MIA and deformation energies. The triply deprotonated coordination mode of the Ac-MKH-NHMe tripeptide transfers more amount of charge to the divalent metal cations than the dually and singly deprotonated complexes. Furthermore, the atoms in molecules (AIM) topological analysis confirm that, the interaction between the metal cations Mn(2+), Cu(2+) and Zn(2+) and Ac-MKH-NHMe tripeptide are electrostatic dominant and the coordination modes with triply deprotonation states possess larger electron density at their BCP corresponding to their coordination bonds. The electrostatic potential difference maps of the most stable 4N-M(2+) (M(2+)=Cu(2+) and Zn(2+)) and 4N2O-Mn(2+) reveals that, as the ionic radii of the metal ion increases, the delocalization charges localized on the metal cations are found to be decreased. The Infra-red stretching frequencies of NH, CH, and CH2 groups of each coordination complexes are observed with shift in their stretching frequencies. From these observations we conclude that, the transition divalent metal cations binding in 4N coordination mode will induce more conformational changes of the Prion protein. Copyright © 2016 Elsevier Inc. All rights reserved.

Bacterial determinants of the social behavior of Bacillus subtilis.

PubMed

Romero, Diego

2013-09-01

Bacteria utilize sophisticated cellular machinery to sense environmental changes and coordinate the most appropriate response. Fine sensors located on cell surfaces recognize a myriad of triggers and initiate genetic cascades leading to activation or repression of certain groups of genes. Structural elements such as pilli, exopolysaccharides and flagella are also exposed at the cell surface and contribute to modulating the intimate interaction with surfaces and host cells. This review will cover the latest advances in our understanding of the biology and functionality of these bacterial determinants within the context of biofilm formation of Bacillus subtilis. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Titanium Insertion into CO Bonds in Anionic Ti-CO2 Complexes.

PubMed

Dodson, Leah G; Thompson, Michael C; Weber, J Mathias

2018-03-22

We explore the structures of [Ti(CO 2 ) y ] - cluster anions using infrared photodissociation spectroscopy and quantum chemistry calculations. The existence of spectral signatures of metal carbonyl CO stretching modes shows that insertion of titanium atoms into C-O bonds represents an important reaction during the formation of these clusters. In addition to carbonyl groups, the infrared spectra show that the titanium center is coordinated to oxalato, carbonato, and oxo ligands, which form along with the metal carbonyls. The presence of a metal oxalato ligand promotes C-O bond insertion in these systems. These results highlight the affinity of titanium for C-O bond insertion processes.