Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.

PubMed

Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J

2017-05-01

Gas-phase hydrogen/deuterium exchange (HDX) using D 2 O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.

Operando XRD studies as a tool for determination of transport parameters of mobile ions in electrode materials

NASA Astrophysics Data System (ADS)

Kondracki, Łukasz; Kulka, Andrzej; Świerczek, Konrad; Ziąbka, Magdalena; Molenda, Janina

2017-11-01

In this work a detailed operando XRD investigations of structural properties of LixMn2O4 manganese spinel are shown to be a complementary, successful method of determination of diffusion coefficient D and surface exchange coefficient k in the working electrode. Kinetics of lithium ions transport are estimated on the basis of rate of structural changes of the cathode material during a relaxation stage after a high current charge, i.e. during structural relaxation of the material. The presented approach seems to be applicable as a complementary method of determination of transport coefficients for all intercalation-type electrode materials.

Highly charged ion based time of flight emission microscope

DOEpatents

Barnes, Alan V.; Schenkel, Thomas; Hamza, Alex V.; Schneider, Dieter H.; Doyle, Barney

2001-01-01

A highly charged ion based time-of-flight emission microscope has been designed, which improves the surface sensitivity of static SIMS measurements because of the higher ionization probability of highly charged ions. Slow, highly charged ions are produced in an electron beam ion trap and are directed to the sample surface. The sputtered secondary ions and electrons pass through a specially designed objective lens to a microchannel plate detector. This new instrument permits high surface sensitivity (10.sup.10 atoms/cm.sup.2), high spatial resolution (100 nm), and chemical structural information due to the high molecular ion yields. The high secondary ion yield permits coincidence counting, which can be used to enhance determination of chemical and topological structure and to correlate specific molecular species.

Complete structural characterization of ceramides as [M – H]− ions by multiple-stage linear ion trap mass spectrometry

PubMed Central

Hsu, Fong-Fu

2016-01-01

Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MSn) towards complete structural determination of ceramides in ten major families characterized as the [M – H]− ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS2 spectrum, while the sequential MS3 and MS4 spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail. PMID:27523779

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

2013-01-01

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana.

PubMed

Kazama, Yusuke; Hirano, Tomonari; Saito, Hiroyuki; Liu, Yang; Ohbu, Sumie; Hayashi, Yoriko; Abe, Tomoko

2011-11-15

Heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. Heavy-ion beams show high linear energy transfer (LET) and thus more effectively induce DNA double-strand breaks than other mutagenic techniques. Previously, we determined the most effective heavy-ion LET (LETmax: 30.0 keV μm(-1)) for Arabidopsis mutagenesis by analysing the effect of LET on mutation induction. However, the molecular structure of mutated DNA induced by heavy ions with LETmax remains unclear. Knowledge of the structure of mutated DNA will contribute to the effective exploitation of heavy-ion beam mutagenesis. Dry Arabidopsis thaliana seeds were irradiated with carbon (C) ions with LETmax at a dose of 400 Gy and with LET of 22.5 keV μm(-1) at doses of 250 Gy or 450 Gy. The effects on mutation frequency and alteration of DNA structure were compared. To characterise the structure of mutated DNA, we screened the well-characterised mutants elongated hypocotyls (hy) and glabrous (gl) and identified mutated DNA among the resulting mutants by high-resolution melting curve, PCR and sequencing analyses. The mutation frequency induced by C ions with LETmax was two-fold higher than that with 22.5 keV μm(-1) and similar to the mutation frequency previously induced by ethyl methane sulfonate. We identified the structure of 22 mutated DNAs. Over 80% of the mutations caused by C ions with both LETs were base substitutions or deletions/insertions of less than 100 bp. The other mutations involved large rearrangements. The C ions with LETmax showed high mutation efficiency and predominantly induced base substitutions or small deletions/insertions, most of which were null mutations. These small alterations can be determined by single-nucleotide polymorphism (SNP) detection systems. Therefore, C ions with LETmax might be useful as a highly efficient reverse genetic system in conjunction with SNP detection systems, and will be beneficial for forward genetics and plant breeding.

Experimental study of copper-alkali ion exchange in glass

NASA Astrophysics Data System (ADS)

Gonella, F.; Caccavale, F.; Bogomolova, L. D.; D'Acapito, F.; Quaranta, A.

1998-02-01

Copper-alkali ion exchange was performed by immersing different silicate glasses (soda-lime and BK7) in different molten eutectic salt baths (CuSO4:Na2SO4 and CuSO4:K2SO4). The obtained optical waveguides were characterized by m-lines spectroscopy for the determination of refractive index profiles, and by secondary ion mass spectrometry for the concentration profiles of the ion species involved in the exchange process. The different oxidation states of copper inside the glass structure were studied by electron paramagnetic resonance and x-ray absorption techniques. Interdiffusion copper coefficients were also determined. The Cu-alkali exchange was observed to give rise to local structural rearrangement of the atoms in the glass matrix. The Cu+ ion was found to mainly govern the exchange process, while competition between Cu-Na and K-Na exchanges occurred when a potassium sulfate bath was used. In this case, significant waveguide modal birefringence was observed.

Multiply Reduced Oligofluorenes: Their Nature and Pairing with THF-Solvated Sodium Ions

DOE PAGES

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet; ...

2016-07-01

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Investigation of the adhesive bonding technology for the insulator structure of EAST neutral beam injector

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

Wei, Jiang-Long, E-mail: jlwei@ipp.ac.cn; Li, Jun; Hu, Chun-Dong

A key issue on the development of EAST ion source was the junction design of insulator structure, which consists of three insulators and four supporting flanges of electrode grid. Because the ion source is installed on the vertical plane, the insulator structure has to withstand large bending and shear stress due to the gravity of whole ion source. Through a mechanical analysis, it was calculated that the maximum bending normal stress was 0.34 MPa and shear stress was 0.23 MPa on the insulator structure. Due to the advantages of simplicity and high strength, the adhesive bonding technology was applied tomore » the junction of insulator structure. A tensile testing campaign of different junction designs between insulator and supporting flange was performed, and a junction design of stainless steel and fiber enhanced epoxy resin with epoxy adhesive was determined. The insulator structure based on the determined design can satisfy both the requirements of high-voltage holding and mechanical strength.« less

Ionic structures and transport properties of hot dense W and U plasmas

NASA Astrophysics Data System (ADS)

Hou, Yong; Yuan, Jianmin

2016-10-01

We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

Modification of the crystal structure of gadolinium gallium garnet by helium ion irradiation

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

Ostafiychuk, B. K.; Yaremiy, I. P., E-mail: yaremiy@rambler.ru; Yaremiy, S. I.

2013-12-15

The structure of gadolinium gallium garnet (GGG) single crystals before and after implantation by He{sup +} ions has been investigated using high-resolution X-ray diffraction methods and the generalized dynamic theory of X-ray scattering. The main types of growth defects in GGG single crystals and radiation-induced defects in the ion-implanted layer have been determined. It is established that the concentration of dislocation loops in the GGG surface layer modified by ion implantation increases and their radius decreases with an increase in the implantation dose.

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

Poletika, T. M., E-mail: poletm@ispms.tsc.ru; Girsova, S. L., E-mail: llm@ispms.tsc.ru; Meisner, L. L., E-mail: girs@ispms.tsc.ru

The structure of the surface and near-surface layers of single crystals of NiTi, differently oriented relative to the direction of ion beam treatment was investigated. The role of the crystallographic orientation in formation of structure of surface layers after ion-plasma alloying was revealed. It was found that the orientation effects of selective sputtering and channeling determine the thickness of the oxide and amorphous layers, the depth of penetration of ions and impurities, the distribution of Ni with depth.

Biological Ion Exchanger Resins

PubMed Central

Damadian, Raymond; Goldsmith, Michael; Zaner, K. S.

1971-01-01

Biological selectivity is shown to vary with medium osmotic strength and temperature. Selectivity reversals occur at 4°C and at an external osmolality of 0.800 indicating that intracellular hydration and endosolvent (intracellular water) structure are important determinants in selectivity. Magnetic resonance measurements of line width by steady-state nuclear magnetic resonance (NMR) indicate a difference in the intracellular water signal of 16 Hz between the K form and Na form of Escherichia coli, providing additional evidence that changes in the ionic composition of cells are accompanied by changes in endosolvent structure. The changes were found to be consistent with the thermodynamic and magnetic resonance properties of aqueous electrolyte solutions. Calculation of the dependence of ion-pairing forces on medium dielectric reinforces the role of endosolvent structure in determining ion exchange selectivity. PMID:4943653

Ab initio calculation of the ion feature in x-ray Thomson scattering.

PubMed

Plagemann, Kai-Uwe; Rüter, Hannes R; Bornath, Thomas; Shihab, Mohammed; Desjarlais, Michael P; Fortmann, Carsten; Glenzer, Siegfried H; Redmer, Ronald

2015-07-01

The spectrum of x-ray Thomson scattering is proportional to the dynamic structure factor. An important contribution is the ion feature which describes elastic scattering of x rays off electrons. We apply an ab initio method for the calculation of the form factor of bound electrons, the slope of the screening cloud of free electrons, and the ion-ion structure factor in warm dense beryllium. With the presented method we can calculate the ion feature from first principles. These results will facilitate a better understanding of x-ray scattering in warm dense matter and an accurate measurement of ion temperatures which would allow determining nonequilibrium conditions, e.g., along shock propagation.

Compositional, structural, and optical changes of polyimide implanted by 1.0 MeV Ni+ ions

NASA Astrophysics Data System (ADS)

Mikšová, R.; Macková, A.; Pupikova, H.; Malinský, P.; Slepička, P.; Švorčík, V.

2017-09-01

The ion irradiation leads to deep structural and compositional changes in the irradiated polymers. Ni+ ions implanted polymers were investigated from the structural and compositional changes point of view and their optical properties were investigated. Polyimide (PI) foils were implanted with 1.0 MeV Ni+ ions at room temperature with fluencies of 1.0 × 1013-1.0 × 1015 cm-2 and two different ion implantation currents densities (3.5 and 7.2 nA/cm2). Rutherford Back-Scattering (RBS) and Elastic Recoil Detection Analysis (ERDA) were used for determination of oxygen and hydrogen escape in implanted PI. Atomic Force Microscopy (AFM) was used to follow surface roughness modification after the ion implantation and UV-Vis spectroscopy was employed to check the optical properties of the implanted PI. The implanted PI structural changes were analysed using Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR-FTIR). High energy Ni-ion implantation causes only a minor release of hydrogen and oxygen close to the polymer sub-surface region in about 60 nm thick layer penetrated by the ion beam; especially at ion fluencies below 1.0 × 1014 cm-2. The mostly pronounced structural changes of the Ni implanted PI were found for the samples implanted above ion fluence 1.0 × 1015 cm-2 and at the ion current density 7.2 nA/cm2, where the optical band gap significantly decreases and the reduction of more complex structural unit of PI monomer was observed.

A cost-effective protocol for the over-expression and purification of fully-functional and more stable Erwinia chrisanthemi ligand-gated ion channel

PubMed Central

Elberson, Benjamin W.; Whisenant, Ty E.; Cortes, D. Marien; Cuello, Luis G.

2017-01-01

The Erwinia chrisanthemi ligand-gated ion channel, ELIC, is considered an excellent structural and functional surrogate for the whole pentameric ligand-gated ion channel family. Despite its simplicity, ELIC is structurally capable of undergoing ligand-dependent activation and a concomitant desensitization process. To determine at the molecular level the structural changes underlying ELIC’s function, it is desirable to produce large quantities of protein. This protein should be properly folded, fully-functional and amenable to structural determinations. In the current paper, we report a completely new protocol for the expression and purification of milligram quantities of fully-functional, more stable and crystallizable ELIC. The use of an autoinduction media and inexpensive detergents during ELIC extraction, in addition to the high-quality and large quantity of the purified channel, are the highlights of this improved biochemical protocol. PMID:28279818

Nonlinear Korteweg-de Vries-Burger equation for ion acoustic shock waves in a weakly relativistic electron-positron-ion plasma with thermal ions

NASA Astrophysics Data System (ADS)

Saeed, R.; Shah, Asif

2010-03-01

The nonlinear propagation of ion acoustic waves in electron-positron-ion plasma comprising of Boltzmannian electrons, positrons, and relativistic thermal ions has been examined. The Korteweg-de Vries-Burger equation has been derived by reductive perturbation technique, and its shock like solution is determined analytically through tangent hyperbolic method. The effect of various plasma parameters on strength and structure of shock wave is investigated. The pert graphical view of the results has been presented for illustration. It is observed that strength and steepness of the shock wave enervate with an increase in the ion temperature, relativistic streaming factor, positron concentrations, electron temperature and they accrue with an increase in coefficient of kinematic viscosity. The convective, dispersive, and dissipative properties of the plasma are also discussed. It is determined that the electron temperature has remarkable influence on the propagation and structure of nonlinear wave in such relativistic plasmas. The numerical analysis has been done based on the typical numerical data from a pulsar magnetosphere.

Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

NASA Astrophysics Data System (ADS)

Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

2015-09-01

The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry.

PubMed

Sugimura, Natsuhiko; Igarashi, Yoko; Aoyama, Reiko; Shibue, Toshimichi

2017-02-01

Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C-C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

Surface topographical and structural analysis of Ag+-implanted polymethylmethacrylate

NASA Astrophysics Data System (ADS)

Arif, Shafaq; Rafique, M. Shahid; Saleemi, Farhat; Naab, Fabian; Toader, Ovidiu; Sagheer, Riffat; Bashir, Shazia; Zia, Rehana; Siraj, Khurram; Iqbal, Saman

2016-08-01

Specimens of polymethylmethacrylate (PMMA) were implanted with 400-keV Ag+ ions at different ion fluences ranging from 1 × 1014 to 5 × 1015 ions/cm2 using a 400-kV NEC ion implanter. The surface topographical features of the implanted PMMA were investigated by a confocal microscope. Modifications in the structural properties of the implanted specimens were analyzed in comparison with pristine PMMA by X-ray diffraction (XRD) and Raman spectroscopy. UV-Visible spectroscopy was applied to determine the effects of ion implantation on optical transmittance of the implanted PMMA. The confocal microscopic images revealed the formation of hillock-like microstructures along the ion track on the implanted PMMA surface. The increase in ion fluence led to more nucleation of hillocks. The XRD pattern confirmed the amorphous nature of pristine and implanted PMMA, while the Raman studies justified the transformation of Ag+-implanted PMMA into amorphous carbon at the ion fluence of ⩾5 × 1014 ions/cm2. Moreover, the decrease in optical transmittance of PMMA is associated with the formation of hillocks and ion-induced structural modifications after implantation.

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

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

PubMed

Mir, Aamir; Golden, Barbara L

2016-02-02

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

Two active site divalent ions in the crystal structure of the hammerhead ribozyme bound to a transition state analogue

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

Mir, Aamir; Golden, Barbara L.

2015-11-09

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the p K A of G12. Finally, on the basis ofmore » this crystal structure as well as a wealth of biochemical studies, in this paper we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.« less

Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.

PubMed

Howard, Rebecca J; Trudell, James R; Harris, R Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

PubMed Central

Trudell, James R.; Harris, R. Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646

Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials.

PubMed

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun; Wang, Bei; Bremer, Peer-Timo; Papka, Michael E; Curtiss, Larry A; Pascucci, Valerio

2016-01-01

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermally annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.

Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials

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

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

2016-01-01

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermallymore » annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.« less

Interstitial and interlayer ion diffusion geometry extraction in graphitic nanosphere battery materials

DOE PAGES

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun; ...

2016-01-31

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermallymore » annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Lastly, our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.« less

COHERENT EVENTS AND SPECTRAL SHAPE AT ION KINETIC SCALES IN THE FAST SOLAR WIND TURBULENCE

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

Lion, Sonny; Alexandrova, Olga; Zaslavsky, Arnaud, E-mail: sonny.lion@obspm.fr

2016-06-10

In this paper we investigate spectral and phase coherence properties of magnetic fluctuations in the vicinity of the spectral transition from large, magnetohydrodynamic to sub-ion scales using in situ measurements of the Wind spacecraft in a fast stream. For the time interval investigated by Leamon et al. (1998) the phase coherence analysis shows the presence of sporadic quasi-parallel Alfvén ion cyclotron (AIC) waves as well as coherent structures in the form of large-amplitude, quasi-perpendicular Alfvén vortex-like structures and current sheets. These waves and structures importantly contribute to the observed power spectrum of magnetic fluctuations around ion scales; AIC waves contributemore » to the spectrum in a narrow frequency range whereas the coherent structures contribute to the spectrum over a wide frequency band from the inertial range to the sub-ion frequency range. We conclude that a particular combination of waves and coherent structures determines the spectral shape of the magnetic field spectrum around ion scales. This phenomenon provides a possible explanation for a high variability of the magnetic power spectra around ion scales observed in the solar wind.« less

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Kinetic feature of dipolarization fronts produced by interchange instability in the magnetotail

NASA Astrophysics Data System (ADS)

Lyu, Haoyu

2017-04-01

A two-dimensional extended MHD simulation is performed to study the kinetic feature of depolarization fronts (DF) in the scale of the ion inertial length / ion Larmor radius. The interchange instability, arising due to the force imbalance between the tailward gradient of thermal pressure and Earthward magnetic curvature force, self-consistently produces the DF in the near-Earth region. Numerical investigations indicate that the DF is a tangential discontinuity, which means that the normal plasma velocity across the DF should be zero in the reference system that is static with the DF structure. The electric system, including electric field and current, is determined by Hall effect arising in the scale of ion inertial length. Hall effect not only mainly contributes on the electric field normal to the tangent plane of the DF, increases the current along the tangent plane of the DF, but also makes the DF structure asymmetric. The drifting motion of the large-scale DF structure is determined by the FLR effect arising in the scale of ion Larmor radius. The ion magnetization velocity induced by the FLR effect is towards to duskward at the subsolar point of the DF, but the y component of velocity in the region after the DF, which dominantly results in the drifting motion of the whole mushroom structure towards the dawn.

g-Factor of heavy ions: a new access to the fine structure constant.

PubMed

Shabaev, V M; Glazov, D A; Oreshkina, N S; Volotka, A V; Plunien, G; Kluge, H-J; Quint, W

2006-06-30

A possibility for a determination of the fine structure constant in experiments on the bound-electron g-factor is examined. It is found that studying a specific difference of the g-factors of B- and H-like ions of the same spinless isotope in the Pb region to the currently accessible experimental accuracy of 7 x 10(-10) would lead to a determination of the fine structure constant to an accuracy which is better than that of the currently accepted value. Further improvements of the experimental and theoretical accuracy could provide a value of the fine structure constant which is several times more precise than the currently accepted one.

Temporal Evolution of Ion Spectral Structures During a Geomagnetic Storm: Observations and Modeling

NASA Astrophysics Data System (ADS)

Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

2018-01-01

Using the Van Allen Probes/Helium, Oxygen, Proton, and Electron mass spectrometer, we perform a case study of the temporal evolution of ion spectral structures observed in the energy range of 1 to 50 keV throughout the geomagnetic storm of 2 October 2013. The ion spectral features are observed near the inner edge of the plasma sheet and are signatures of fresh transport from the plasma sheet into the inner magnetosphere. We find that the characteristics of the ion structures are determined by the intensity of the convection electric field. Prior to the beginning of the storm, the plasma sheet inner edge exhibits narrow nose spectral structures that vary little in energy across L values. Ion access to the inner magnetosphere during these times is limited to the nose energy bands. As convection is enhanced and large amounts of plasma are injected from the plasma sheet during the main phase of the storm, ion access occurs at a wide energy range, as no nose structures are observed. As the magnetosphere recovers from the storm, single noses and then multiple noses are observed once again. We use a model of ion drift and losses due to charge exchange to simulate the ion spectra and gain insight into the main observed features.

Temporal evolution of ion spectral structures during a geomagnetic storm: Observations and modeling

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

Ferradas Alva, Cristian Pablo; Zhang, J.-C.; Spence, H. E.

Using the Van Allen Probes/Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometer, we perform a case study of the temporal evolution of ion spectral structures observed in the energy range of 1- ~50 keV throughout the geomagnetic storm of 2 October 2013. The ion spectral features are observed near the inner edge of the plasma sheet and are signatures of fresh transport from the plasma sheet into the inner magnetosphere. We find that the characteristics of the ion structures are determined by the intensity of the convection electric field. Prior to the beginning of the storm, the plasma sheet innermore » edge exhibits narrow nose spectral structures that vary little in energy across L values. Ion access to the inner magnetosphere during these times is limited to the nose energy bands. As convection is enhanced and large amounts of plasma are injected from the plasma sheet during the main phase of the storm, ion access occurs at a wide energy range, as no nose structures are observed. Here, as the magnetosphere recovers from the storm, single noses and then multiple noses are observed once again. Lastly, we use a model of ion drift and losses due to charge exchange to simulate the ion spectra and gain insight into the main observed features.« less

Temporal evolution of ion spectral structures during a geomagnetic storm: Observations and modeling

DOE PAGES

Ferradas Alva, Cristian Pablo; Zhang, J.-C.; Spence, H. E.; ...

2017-12-13

Using the Van Allen Probes/Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometer, we perform a case study of the temporal evolution of ion spectral structures observed in the energy range of 1- ~50 keV throughout the geomagnetic storm of 2 October 2013. The ion spectral features are observed near the inner edge of the plasma sheet and are signatures of fresh transport from the plasma sheet into the inner magnetosphere. We find that the characteristics of the ion structures are determined by the intensity of the convection electric field. Prior to the beginning of the storm, the plasma sheet innermore » edge exhibits narrow nose spectral structures that vary little in energy across L values. Ion access to the inner magnetosphere during these times is limited to the nose energy bands. As convection is enhanced and large amounts of plasma are injected from the plasma sheet during the main phase of the storm, ion access occurs at a wide energy range, as no nose structures are observed. Here, as the magnetosphere recovers from the storm, single noses and then multiple noses are observed once again. Lastly, we use a model of ion drift and losses due to charge exchange to simulate the ion spectra and gain insight into the main observed features.« less

Combining the Power of Irmpd with Ion-Molecule Reactions: the Structure and Reactivity of Radical Ions of Cysteine and its Derivatives

NASA Astrophysics Data System (ADS)

Lesslie, Michael; Osburn, Sandra; Berden, Giel; Oomens, J.; Ryzhov, Victor

2015-06-01

Most of the work on peptide radical cations has involved protons as the source of charge. Nonetheless, using metal ions as charge sources often offers advantages like stabilization of the structure via multidentate coordination and the elimination of the "mobile proton". Moreover, characterization of metal-bound amino acids is of general interest as the interaction of peptide side chains with metal ions in biological systems is known to occur extensively. In the current study, we generate thiyl radicals of cysteine and homocysteine in the gas phase complexed to alkali metal ions. Subsequently, we utilize infrared multiple-photon dissociation (IRMPD) and ion-molecule reactions (IMR) to characterize the structure and reactivity of these radical ions. Our group has worked extensively with the cysteine-based radical cations and anions, characterizing the gas-phase reactivity and rearrangement of the amino acid and several of its derivatives. In a continuation of this work, we are perusing the effects of metal ions as the charge bearing species on the reactivity of the sulfur radical. Our S-nitroso chemistry can easily be used in conjunction with metal ion coordination to produce initial S-based radicals in peptide radical-metal ion complexes. In all cases we have been able to achieve radical formation with significant yield to study reactivity. Ion-molecule reactions of metallated radicals with allyl iodide, dimethyl disulfide, and allyl bromide have all shown decreasing reactivity going down group 1A. Recently, we determined the experimental IR spectra for the homocysteine radical cation with Li+, Na+, and K+ as the charge bearing species at the FELIX facility. For comparison, the protonated IR spectrum of homocysteine has previously been obtained by our group. A preliminary match of the IR spectra has been confirmed. Finally, calculations are underway to determine the bond distances of all the metal adduct structures.

The influence of Ag content and annealing time on structural and optical properties of SGS antimony-germanate glass doped with Er3+ ions

NASA Astrophysics Data System (ADS)

Zmojda, J.; Kochanowicz, M.; Miluski, P.; Baranowska, A.; Basa, A.; Jadach, R.; Sitarz, M.; Dorosz, D.

2018-05-01

A series of erbium doped SGS antimony-germanate glass embedding silver (Ag0) nanoparticles have been synthesized by a one-step melt-quench thermochemical reduction technique. The effect of NPs concentration and annealing time on the structural and photoluminescent (PL) properties were investigated. The Raman spectra as a function of temperature measured in-situ allow to determine the structural changes in vicinity of Ag+ ions and confirmed thermochemical reduction of Ag+ ions by Sb3+ ions. The surface plasmon resonance absorption band was evidenced near 450 nm. The impact of local field effect generated by Ag0 nanoparticles (NPs) and energy transfer from surface of silver NPs to trivalent erbium ions on near-infrared and up-conversion luminescence was described in terms of enhancement and quench phenomena.

Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.

PubMed

Ehrnstorfer, Ines A; Geertsma, Eric R; Pardon, Els; Steyaert, Jan; Dutzler, Raimund

2014-11-01

Members of the SLC11 (NRAMP) family transport iron and other transition-metal ions across cellular membranes. These membrane proteins are present in all kingdoms of life with a high degree of sequence conservation. To gain insight into the determinants of ion selectivity, we have determined the crystal structure of Staphylococcus capitis DMT (ScaDMT), a close prokaryotic homolog of the family. ScaDMT shows a familiar architecture that was previously identified in the amino acid permease LeuT. The protein adopts an inward-facing conformation with a substrate-binding site located in the center of the transporter. This site is composed of conserved residues, which coordinate Mn2+, Fe2+ and Cd2+ but not Ca2+. Mutations of interacting residues affect ion binding and transport in both ScaDMT and human DMT1. Our study thus reveals a conserved mechanism for transition-metal ion selectivity within the SLC11 family.

Determination of N-linked glycosylation in viral glycoproteins by negative ion mass spectrometry and ion mobility

PubMed Central

Bitto, David; Harvey, David J.; Halldorsson, Steinar; Doores, Katie J.; Pritchard, Laura K.; Huiskonen, Juha T.; Bowden, Thomas A.; Crispin, Max

2016-01-01

Summary Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans. PMID:26169737

Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form

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

Yokoyama, Hideshi, E-mail: h-yokoya@u-shizuoka-ken.ac.jp; Tsuruta, Osamu; Akao, Naoya

2012-06-15

Highlights: Black-Right-Pointing-Pointer Structures of a metal-bound Helicobacter pylori neutrophil-activating protein were determined. Black-Right-Pointing-Pointer Two zinc ions were tetrahedrally coordinated by ferroxidase center (FOC) residues. Black-Right-Pointing-Pointer Two cadmium ions were coordinated in a trigonal-bipyramidal and octahedral manner. Black-Right-Pointing-Pointer The second metal ion was more weakly coordinated than the first at the FOC. Black-Right-Pointing-Pointer A zinc ion was found in one negatively-charged pore suitable as an ion path. -- Abstract: Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn{sup 2+}-more » or Cd{sup 2+}-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.« less

Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS.

PubMed

Eklund, Lars; Hofer, Tomas S; Persson, Ingmar

2015-01-28

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2(-), chlorate, ClO3(-), and perchlorate, ClO4(-). In addition, the structures of the hydrated hypochlorite, ClO(-), bromate, BrO3(-), iodate, IO3(-) and metaperiodate, IO4(-), ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO6(3-), ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01-0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.

Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS

PubMed Central

Eklund, Lars; Hofer, Tomas S.

2014-01-01

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2−, chlorate, ClO3−, and perchlorate, ClO4−. In addition, the structures of the hydrated hypochlorite, ClO−, bromate, BrO3−, iodate, IO3− and metaperiodate, IO4−, ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO63−, ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01–0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5=1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5=2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions. PMID:25473816

Insights into channel dysfunction from modelling and molecular dynamics simulations.

PubMed

Musgaard, Maria; Paramo, Teresa; Domicevica, Laura; Andersen, Ole Juul; Biggin, Philip C

2018-04-01

Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.' Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems.

PubMed

Bostick, David L; Brooks, Charles L

2010-09-29

An influx of experimental and theoretical studies of ion transport protein structure has inspired efforts to understand underlying determinants of ionic selectivity. Design principles for selective ion binding can be effectively isolated and interrogated using simplified models composed of a single ion surrounded by a set of ion-ligating molecular species. While quantum mechanical treatments of such systems naturally incorporate electronic degrees of freedom, their computational overhead typically prohibits thorough dynamic sampling of configurational space and, thus, requires approximations when determining ion-selective free energy. As an alternative, we employ dynamical simulations with a polarizable force field to probe the structure and K(+)/Na(+) selectivity in simple models composed of one central K(+)/Na(+) ion surrounded by 0-8 identical model compounds: N-methylacetamide, formamide, or water. In the absence of external restraints, these models represent gas-phase clusters displaying relaxed coordination structures with low coordination number. Such systems display Na(+) selectivity when composed of more than ∼3 organic carbonyl-containing compounds and always display K(+) selectivity when composed of water molecules. Upon imposing restraints that solely enforce specific coordination numbers, we find all models are K(+)-selective when ∼7-8-fold ion coordination is achieved. However, when models composed of the organic compounds provide ∼4-6-fold coordination, they retain their Na(+) selectivity. From these trends, design principles emerge that are of basic importance in the behavior of K(+) channel selectivity filters and suggest a basis not only for K(+) selectivity but also for modulation of block and closure by smaller ions.

Polymers for Traveling Wave Ion Mobility Spectrometry Calibration

NASA Astrophysics Data System (ADS)

Duez, Quentin; Chirot, Fabien; Liénard, Romain; Josse, Thomas; Choi, ChangMin; Coulembier, Olivier; Dugourd, Philippe; Cornil, Jérôme; Gerbaux, Pascal; De Winter, Julien

2017-07-01

One of the main issues when using traveling wave ion mobility spectrometry (TWIMS) for the determination of collisional cross-section (CCS) concerns the need for a robust calibration procedure built from referent ions of known CCS. Here, we implement synthetic polymer ions as CCS calibrants in positive ion mode. Based on their intrinsic polydispersities, polymers offer in a single sample the opportunity to generate, upon electrospray ionization, numerous ions covering a broad mass range and a large CCS window for different charge states at a time. In addition, the key advantage of polymer ions as CCS calibrants lies in the robustness of their gas-phase structure with respect to the instrumental conditions, making them less prone to collisional-induced unfolding (CIU) than protein ions. In this paper, we present a CCS calibration procedure using sodium cationized polylactide and polyethylene glycol, PLA and PEG, as calibrants with reference CCS determined on a home-made drift tube. Our calibration procedure is further validated by testing the polymer calibration to determine CCS of numerous different ions for which CCS are reported in the literature. [Figure not available: see fulltext.

X-ray structure of acid-sensing ion channel 1-snake toxin complex reveals open state of a Na(+)-selective channel.

PubMed

Baconguis, Isabelle; Bohlen, Christopher J; Goehring, April; Julius, David; Gouaux, Eric

2014-02-13

Acid-sensing ion channels (ASICs) detect extracellular protons produced during inflammation or ischemic injury and belong to the superfamily of degenerin/epithelial sodium channels. Here, we determine the cocrystal structure of chicken ASIC1a with MitTx, a pain-inducing toxin from the Texas coral snake, to define the structure of the open state of ASIC1a. In the MitTx-bound open state and in the previously determined low-pH desensitized state, TM2 is a discontinuous α helix in which the Gly-Ala-Ser selectivity filter adopts an extended, belt-like conformation, swapping the cytoplasmic one-third of TM2 with an adjacent subunit. Gly 443 residues of the selectivity filter provide a ring of three carbonyl oxygen atoms with a radius of ∼3.6 Å, presenting an energetic barrier for hydrated ions. The ASIC1a-MitTx complex illuminates the mechanism of MitTx action, defines the structure of the selectivity filter of voltage-independent, sodium-selective ion channels, and captures the open state of an ASIC. Copyright © 2014 Elsevier Inc. All rights reserved.

Superhyperfine Structure of the EPR Spectra of Nd3+ Impurity Ions in Fluorite CaF2

NASA Astrophysics Data System (ADS)

Aminov, L. K.; Gafurov, M. R.; Kurkin, I. N.; Malkin, B. Z.; Rodionov, A. A.

2018-05-01

EPR spectra of a CaF2 single crystal that was grown from melt containing a small addition of NdF3 were studied. Signals corresponding to tetragonal centers of Nd3+ ions and cubic centers of Er3+ and Yb3+ ions were found. Superhyperfine structure (SHFS) in the spectra of the Nd3+ ions was observed for the first time in this crystal; parameters of the superhyperfine interaction of the Nd3+ ions with the nearest nine fluorine ions were determined. The dependence of the resolution of the Nd3+ EPR spectrum SHFS on the incident microwave power at the temperature of T ≈ 6 K was studied. Obtained results are discussed and compared with the literature data.

X-ray crystal structure and theoretical study of a new dinuclear Cu(II) complex with two different geometry centers bridged with an oxo group

NASA Astrophysics Data System (ADS)

Golbedaghi, Reza; Azimi, Saeid; Molaei, Atefeh; Hatami, Masoud; Notash, Behrouz

2017-10-01

A new Schiff base ligand HL, 1,3-bis(2-((Z)-(2-aminoethylimino)methyl)phenoxy)ethylene di amine, has been synthesized from the reaction of a new aldehyde and ethylenediamine. After preparation the Schiff base, a new dinuclear Cu(II) complex with two different geometry for each metal ion was synthesized. Single crystal X-ray structure analysis of the complex Cu(II) showed that the complex is binuclear and all nitrogen and oxygen atoms of ligand (N4O3) are coordinated to two Cu(II) center ions. The crystal structure studying shows, a perchlorate ion has been coordinated to the two Cu(II) metal centers as bridged and another perchlorate coordinated to the one of Cu(II) ion as terminal. However, two interesting structures square pyramidal and distorted octahedral Cu(II) ions are bridged asymmetrically by a perchlorate ion and oxygen of hydroxyl group of Schiff base ligand. In addition, we had a theoretical study to have a comparison of experimental and theoretical results we determined the HOMO and LUMO orbitals.

The role of SO{sub 4}{sup 2−} surface distribution in arsenic removal by iron oxy-hydroxides

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

Tresintsi, S.; Simeonidis, K., E-mail: ksime@physics.auth.gr; Department of Mechanical Engineering, University of Thessaly, 38334 Volos

2014-05-01

This study investigates the contribution of chemisorbed SO{sub 4}{sup 2−} in improving arsenic removal properties of iron oxy-hydroxides through an ion-exchange mechanism. An analytical methodology was developed for the accurate quantification of sulfate ion (SO{sub 4}{sup 2−}) distribution onto the surface and structural compartments of iron oxy-hydroxides synthesized by FeSO{sub 4} precipitation. The procedure is based on the sequential determination of SO{sub 4}{sup 2−} presence in the diffuse and Stern layers, and the structure of these materials as defined by the sulfate-rich environments during the reaction and the variation in acidity (pH 3–12). Physically sorbed SO{sub 4}{sup 2−}, extracted inmore » distilled water, and physically/chemically adsorbed ions on the oxy-hydroxide's surface leached by a 5 mM NaOH solution, were determined using ion chromatography. Total sulfate content was gravimetrically measured by precipitation as BaSO{sub 4}. To validate the suggested method, results were verified by X-ray photoelectron and Fourier-transformed infrared spectroscopy. Results showed that low precipitation pH-values favor the incorporation of sulfate ions into the structure and the inner double layer, while under alkaline conditions ions shift to the diffuse layer. - Graphical abstract: An analytical methodology for the accurate quantification of sulfate ions (SO{sub 4}{sup 2−}) distribution onto the diffuse layer, the Stern layer and the structure of iron oxy-hydroxides used as arsenic removal agents. - Highlights: • Quantification of sulfate ions presence in FeOOH surface compartments. • Preparation pH defines the distribution of sulfates. • XPS and FTIR verify the presence of SO{sub 4}{sup 2−} in the structure, the Stern layer the diffuse layer of FeOOH. • Chemically adsorbed sulfates control the arsenic removal efficiency of iron oxyhydroxides.« less

Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site.

PubMed

Harata, K; Schubert, W D; Muraki, M

2001-11-01

Ultica dioica agglutinin, a plant lectin from the stinging nettle, consists of a total of seven individual isolectins. One of these structures, isolectin I, was determined at 1.9 A resolution by the X-ray method. The crystals belong to the space group P2(1) and the asymmetric unit contains two molecules related by local twofold symmetry. The molecule consists of two hevein-like chitin-binding domains lacking distinct secondary structure, but four disulfide bonds in each domain maintain the tertiary structure. The backbone structure of the two independent molecules is essentially identical and this is similarly true of the sugar-binding sites. In the crystal, the C-terminal domains bind Zn(2+) ions at the sugar-binding site. Owing to their location near a pseudo-twofold axis, the two zinc ions link the two independent molecules in a tail-to-tail arrangement: thus, His47 of molecule 1 and His67 of molecule 2 coordinate the first zinc ion, while the second zinc ion links Asp75 of molecule 1 and His47 of molecule 2.

Structure of a CLC chloride ion channel by cryo-electron microscopy

PubMed Central

Park, Eunyong; Campbell, Ernest B.; MacKinnon, Roderick

2017-01-01

CLC proteins transport chloride (Cl−) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl− ions passively, whereas others are secondary active transporters that exchange two Cl− ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture based on sequence homology. To solve this puzzle we determined the structure of a mammalian CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl− transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl− passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl−/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl− down its electrochemical gradient. PMID:28002411

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds

PubMed Central

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C.; Orimo, Shin-ichi

2016-01-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures. PMID:27032978

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds.

PubMed

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C; Orimo, Shin-ichi

2016-04-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures.

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

Measurements of ion species separation in strong plasma shocks

NASA Astrophysics Data System (ADS)

Rinderknecht, Hans

2017-10-01

Shocks are important dynamic phenomena in inertial confinement fusion (ICF) and astrophysical plasmas. While the relationship between upstream and downstream plasmas far from the shock front is fully determined by conservation equations, the structure of shock fronts is determined by dynamic kinetic processes. Kinetic theory and simulations predict that the width of a strong (M >2) collisional plasma shock front is on the order of tens of ion mean-free-paths. The shock front structure plays an important role for overall dynamics when the shock front width approaches plasma scale lengths, as in the spherically converging shock in the DT-vapor in an ICF implosion. However, there has been no experimental data benchmarking shock front structure in the plasma phase. The structure of a shock front in a plasma with multiple ion species has been directly measured for the first time using a combination of Thomson scattering and proton radiography in experiments on the OMEGA laser. Thomson scattering of a 263.25 nm probe beam is used to diagnose electron density, electron and ion temperature, ion species concentration, and flow velocity in strong shocks (M 5) propagating through low-density (ρ 0.1 mg/cc) plasmas composed of H(98%) +Ne(2%). Within the shock front, velocity separation of the ion species is observed for the first time: the light species (H) accelerates to of order the shocked fluid velocity (450 microns/ns) before the heavy species (Ne) begins to move. This velocity-space separation implies that the separation of ion species occurs at the shock front, a predicted feature of shocks in multi-species plasmas but never observed experimentally until now. Comparison of experimental data with PIC, Vlasov-Fokker-Planck, and multi-component hydrodynamic simulations will be presented.

The influence of the ion plasma flow on the phase composition and microhardness of carbon coatings doped with metals

NASA Astrophysics Data System (ADS)

Rudenkov, A. S.; Piliptsou, D. G.; Luchnikov, P. A.; Rogachev, A. V.; Jiang, Xiaohong; Fedosenko, N. N.

2018-01-01

The Raman spectroscopy method established that subsequent treatment with ion ions leads to a change in the microstructure of coatings based on carbon and metals. It is established that the structure change is determined by the changes occurring at the interface and depends on the sp3 → sp2 phase transition due to the appearance of local thermal peaks at the end of tracks of nitrogen ions implanted in the coating volume. It is shown that the microhardness of metal-carbon coatings (α-C: Cu, α-C: Ti, α-C:Al) increases after ion-plasma treatment, which is determined by the formation of solid interstitial phases based on CNx and metal carbonitrides.

Paramagnetic resonance of Mn4+ and Mn2+ centers in lanthanum gallate single crystals

NASA Astrophysics Data System (ADS)

Vazhenin, V. A.; Potapov, A. P.; Guseva, V. B.; Artyomov, M. Yu.

2010-03-01

An increase in the manganese concentration in lanthanum gallate in the range 0.5-5.0% has been found to result in a complete replacement of individual Mn4+ ions by Mn2+ ions. The relative concentrations and binding energies of individual Mn4+, Mn3+, and Mn2+ ions have been determined. The spin Hamiltonians of the Mn2+ and Mn4+ centers in the rhombohedral and orthorhombic phases, respectively, have been constructed and the orientation of the principal axes of the fine-structure tensor of Mn4+ at room temperature has been found. The possibility of using electron paramagnetic resonance for determining the rotation angles of oxygen octahedra of lanthanum gallate with respect to the perovskite structure has been discussed.

Never at rest: insights into the conformational dynamics of ion channels from cryo-electron microscopy.

PubMed

Lau, Carus; Hunter, Mark J; Stewart, Alastair; Perozo, Eduardo; Vandenberg, Jamie I

2018-04-01

The tightly regulated opening and closure of ion channels underlies the electrical signals that are vital for a wide range of physiological processes. Two decades ago the first atomic level view of ion channel structures led to a detailed understanding of ion selectivity and conduction. In recent years, spectacular developments in the field of cryo-electron microscopy have resulted in cryo-EM superseding crystallography as the technique of choice for determining near-atomic resolution structures of ion channels. Here, we will review the recent developments in cryo-EM and its specific application to the study of ion channel gating. We will highlight the advantages and disadvantages of the current technology and where the field is likely to head in the next few years. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

Formation of the Electric Double Layer and its Effects on Moving Bodies in a Space Plasma Environment

NASA Technical Reports Server (NTRS)

Yang, Qianli; Wu, S. T.; Stone, N. H.; Li, Xiaoquing

1996-01-01

In this paper we solve the self-consistent Vlasov and Poisson equations by a numerical method to determine the local distribution function of the ion and the electron, within a thin layer near the moving body, respectively. Using these ion and electron distributions, the number density for the ions and electrons are determined, such that, the electric potential is obtained within this thin layer (i.e., measured by Debye length). Numerical results are presented for temporal evolution of the electron and ion density and its corresponding electric potential within the layer which shows the formation of electric double layer and its structures. From these numerical results, we are able to determine the maximum conditions of the electric potential, it may create satellite anomaly.

Enhancement of maximum attainable ion energy in the radiation pressure acceleration regime using a guiding structure

DOE PAGES

Bulanov, S. S.; Esarey, E.; Schroeder, C. B.; ...

2015-03-13

Radiation Pressure Acceleration is a highly efficient mechanism of laser driven ion acceleration, with the laser energy almost totally transferrable to the ions in the relativistic regime. There is a fundamental limit on the maximum attainable ion energy, which is determined by the group velocity of the laser. In the case of a tightly focused laser pulses, which are utilized to get the highest intensity, another factor limiting the maximum ion energy comes into play, the transverse expansion of the target. Transverse expansion makes the target transparent for radiation, thus reducing the effectiveness of acceleration. Utilization of an external guidingmore » structure for the accelerating laser pulse may provide a way of compensating for the group velocity and transverse expansion effects.« less

Novel carbon-ion fuel cells. Quarterly technical report, April--June 1996

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

Cocks, F.H.

1996-11-01

This report presents research to develop a new type of of fuel cell using a solid electrolyte that transports carbon ions. This new class of fuel cell would use solid C dissolved in molten metal (carbide) as a fuel reservoir and anode; thus expensive gas or liquid fuel would not be required. Thermodynamic efficiency of carbon-ion fuel cells is reviewed, as are electrolyte crystal structures (oxide and fluorite carbides). The sequence of laboratory research procedures for developing a solid C-ion electrolyte and to determine the ionic conductivity of C ions therein is outlined; results of the laboratory research to datemore » are summarized, including XRD analysis of crystal structures and transition temperatures of carbides (La, Ce, Be, Al) and SIMS of carbon isotopes.« less

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

Ohshimo, Keijiro; Institute for Excellence in Higher Education, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai 980-8576; Norimasa, Naoya

Geometrical structures of titanium oxide cluster cations and anions have been investigated by ion mobility mass spectrometry and quantum chemical calculations based on density functional theory. Stable cluster compositions with respect to collision induced dissociation were also determined by changing ion injection energy to an ion drift cell for mobility measurements. The Ti{sub n}O{sub 2n−1}{sup +} cations and Ti{sub n}O{sub 2n}{sup −} anions were predominantly observed at high injection energies, in addition to Ti{sub n}O{sub 2n}{sup +} for cations and Ti{sub n}O{sub 2n+1}{sup −} for anions. Collision cross sections of Ti{sub n}O{sub 2n}{sup +} and Ti{sub n}O{sub 2n+1}{sup −} formore » n = 1-7, determined by ion mobility mass spectrometry, were compared with those obtained theoretically as orientation-averaged cross sections for the optimized structures by quantum chemical calculations. All of the geometrical structures thus assigned have three-dimensional structures, which are in marked contrast with other oxides of late transition metals. One-oxygen atom dissociation processes from Ti{sub n}O{sub 2n}{sup +} and Ti{sub n}O{sub 2n+1}{sup −} by collisions were also explained by analysis of spin density distributions.« less

Status and directions of modified tribological surfaces by ion processes

NASA Technical Reports Server (NTRS)

Spalvins, Talivaldis

1988-01-01

An overview is presented of recent advances in modifying contacting surfaces in motion by the various ion assisted surface coating/modification processes to reduce and control tribological failures. The ion assisted coating processes and the surface modification processes offer the greatest potential to custom tailor and optimize the tribological performance. Hard, wear resistant and low shear coatings deposited by the ion assisted processes are discussed. Primarily the recent advances of sputtered MoS2 ion plated Au, Ag, Pb lubricating films and sputtered and ion plated hard, wear resistant TiN, HfN, TiC films are described in terms of structural property performance interrelationships which lead to improved adhesion, cohesion, nucleation, morphological growth, density, film thickness as determined by structural and chemical characterization and frictional and wear behavior. Also, the recent tribological advances using the surface modification processes such as ion implantation, ion beam mixing is discussed with emphasis on the development of lubricous high temperature ceramic surfaces.

Ion nose spectral structures observed by the Van Allen Probes

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

Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.

Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H +, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H + noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

Ion nose spectral structures observed by the Van Allen Probes

DOE PAGES

Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

2016-11-22

Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H +, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H + noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

Ion nose spectral structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

2016-12-01

We present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+ and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses, and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted by using a steady state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge-exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

How ions affect the structure of water.

PubMed

Hribar, Barbara; Southall, Noel T; Vlachy, Vojko; Dill, Ken A

2002-10-16

We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.

Statistical Determinants of Selective Ionic Complexation: Ions in Solvent, Transport Proteins, and Other “Hosts”

PubMed Central

Bostick, David L.; Brooks, Charles L.

2009-01-01

To provide utility in understanding the molecular evolution of ion-selective biomembrane channels/transporters, globular proteins, and ionophoric compounds, as well as in guiding their modification and design, we present a statistical mechanical basis for deconstructing the impact of the coordination structure and chemistry of selective multidentate ionic complexes. The deconstruction augments familiar ideas in liquid structure theory to realize the ionic complex as an open ion-ligated system acting under the influence of an “external field” provided by the host (or surrounding medium). Using considerations derived from this basis, we show that selective complexation arises from exploitation of a particular ion's coordination preferences. These preferences derive from a balance of interactions much like that which dictates the Hofmeister effect. By analyzing the coordination-state space of small family IA and VIIA ions in simulated fluid media, we derive domains of coordinated states that confer selectivity for a given ion upon isolating and constraining particular attributes (order parameters) of a complex comprised of a given type of ligand. We demonstrate that such domains may be used to rationalize the ion-coordinated environments provided by selective ionophores and biological ion channels/transporters of known structure, and that they can serve as a means toward deriving rational design principles for ion-selective hosts. PMID:19486671

Control of the conformations of ion Coulomb crystals in a Penning trap

PubMed Central

Mavadia, Sandeep; Goodwin, Joseph F.; Stutter, Graham; Bharadia, Shailen; Crick, Daniel R.; Segal, Daniel M.; Thompson, Richard C.

2013-01-01

Laser-cooled atomic ions form ordered structures in radiofrequency ion traps and in Penning traps. Here we demonstrate in a Penning trap the creation and manipulation of a wide variety of ion Coulomb crystals formed from small numbers of ions. The configuration can be changed from a linear string, through intermediate geometries, to a planar structure. The transition from a linear string to a zigzag geometry is observed for the first time in a Penning trap. The conformations of the crystals are set by the applied trap potential and the laser parameters, and agree with simulations. These simulations indicate that the rotation frequency of a small crystal is mainly determined by the laser parameters, independent of the number of ions and the axial confinement strength. This system has potential applications for quantum simulation, quantum information processing and tests of fundamental physics models from quantum field theory to cosmology. PMID:24096901

Ion-implanted epitaxially grown ZnSe

NASA Technical Reports Server (NTRS)

Chernow, F.

1975-01-01

The use of ZnSe to obtain efficient, short wavelength injection luminescence was investigated. It was proposed that shorter wavelength emission and higher efficiency be achieved by employing a p-i-n diode structure rather than the normal p-n diode structure. The intervening i layer minimizes concentration quenching effects and the donor-acceptor pair states leading to long wavelength emission. The surface p layer was formed by ion implantation; implantation of the i layer rather than the n substrate permits higher, uncompensated p-type doping. An ion implanted p-n junction in ZnSe is efficiency-limited by high electron injection terminating in nonradiative recombination at the front surface, and by low hole injection resulting from the inability to obtain high conductivity p-type surface layers. While the injection ratio in p-n junctions was determined by the radio of majority carrier concentrations, the injection ratio in p-i-n structures was determined by the mobility ratios and/or space charge neutrality requirements in the i layer.

Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids

PubMed Central

2015-01-01

Density functional tight binding (DFTB), which is ∼100–1000 times faster than full density functional theory (DFT), has been used to simulate the structure and properties of protic ionic liquid (IL) ions, clusters of ions and the bulk liquid. Proton affinities for a wide range of IL cations and anions determined using DFTB generally reproduce G3B3 values to within 5–10 kcal/mol. The structures and thermodynamic stabilities of n-alkyl ammonium nitrate clusters (up to 450 quantum chemical atoms) predicted with DFTB are in excellent agreement with those determined using DFT. The IL bulk structure simulated using DFTB with periodic boundary conditions is in excellent agreement with published neutron diffraction data. PMID:25328497

Refinement of the crystal structure of the high-temperature phase G0 in (NH4)2WO2F4 (powder, x-ray, and neutron scattering)

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

Novak, D. M.; Smirnov, Lev S; Kolesnikov, Alexander I

2013-01-01

The (NH4)2WO2F4 compound undergoes a series of phase transitions: G0 -> 201 K -> G1 -> 160 K -> G2, with a significant change in entropy ( S1 ~ Rln10 at the G0 -> G1 transition), which indicates significant orientational disordering in the G0 phase and the order disorder type of the phase transition. X-ray diffraction is used to identify the crystal structure of the G0 phase as rhombohedral (sp. gr. Cmcm, Z = 4), determine the lattice parameters and the positions of all atoms (except hydrogen), and show that [WO2F4]2 ions can form a superposition of dynamic and staticmore » orientational disorders in the anionic sublattice. A determination of the orientational position of [NH4]+ ions calls for the combined method of elastic and inelastic neutron scattering. Inelastic neutron scattering is used to determine the state of hindered rotation for ammonium ions in the G0 phase. Powder neutron diffraction shows that the orientational disorder of NH4 ions can adequately be described within the free rotation approximation.« less

Gyrotropic Guiding-Center Fluid Theory for the Turbulent Heating of Magnetospheric Ions in Downward Birkeland Current Regions

DTIC Science & Technology

2006-11-20

Doppler -shifted, quasistatic turbulence from the real, time- mogeneous medium,18 we can then estimate that k - k1 and dependent turbulence near the...ground is due to Doppler -shifted, spatially irregular, electric- field structures that are stationary in the ion frame. Sub- we have determined that the...erpnding cn ar ion tepeoratre- 18F J. Crary, M. V. Goldman , R. E. Ergun, and D. L. Newman, Geophys. sented in this paper gives the perpendicular ion

Positive Ion Induced Solidification of He4

NASA Astrophysics Data System (ADS)

Moroshkin, P.; Lebedev, V.; Weis, A.

2009-03-01

We have observed bulk solidification of He4 induced by nucleation on positive alkali ions in pressurized superfluid helium. The ions are extracted into the liquid from alkali-doped solid He by a static electric field. The experiments prove the existence of charged particles in a solid structure composed of doped He that was recently shown to coexist with superfluid helium below the He solidification pressure. This supports our earlier suggestion that the Coulomb interaction of positive ions surrounded by a solid He shell (snowballs) and electrons trapped in spherical cavities (electron bubbles), together with surface tension, is responsible for the stability of that structure against melting. We have determined the density of charges in the sample by two independent methods.

Linear and Nonlinear Coupling of Electrostatic Drift and Acoustic Perturbations in a Nonuniform Bi-Ion Plasma with Non-Maxwellian Electrons

NASA Astrophysics Data System (ADS)

Ali, Gul-e.; Ahmad, Ali; Masood, W.; Mirza, Arshad M.

2017-12-01

Linear and nonlinear coupling of drift and ion acoustic waves are studied in a nonuniform magnetized plasma comprising of Oxygen and Hydrogen ions with nonthermal distribution of electrons. It has been observed that different ratios of ion number densities and kappa and Cairns distributed electrons significantly modify the linear dispersion characteristics of coupled drift-ion acoustic waves. In the nonlinear regime, KdV (for pure drift waves) and KP (for coupled drift-ion acoustic waves) like equations have been derived to study the nonlinear evolution of drift solitary waves in one and two dimensions. The dependence of drift solitary structures on different ratios of ion number densities and nonthermal distribution of electrons has also been explored in detail. It has been found that the ratio of the diamagnetic drift velocity to the velocity of the nonlinear structure determines the existence regimes for the drift solitary waves. The present investigation may be beneficial to understand the formation of solitons in the ionospheric F-region.

Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong

2009-12-01

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree-Fock level has been performed to investigate structural and dynamical parameters of the V(3+) ion in dilute aqueous solution. A distorted octahedral structure with the average V(3+)-O distance of 1.99 A is evaluated from the QM/MM simulation, which is in good agreement with the X-ray data. Several structural parameters such as angular distribution functions, theta- and tilt-angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V(3+). The Jahn-Teller distortions of the V(3+) ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. (c) 2009 Wiley Periodicals, Inc.

Alkali oxide-tantalum, niobium and antimony oxide ionic conductors

NASA Technical Reports Server (NTRS)

Roth, R. S.; Brower, W. S.; Parker, H. S.; Minor, D. B.; Waring, J. L.

1975-01-01

The phase equilibrium relations of four systems were investigated in detail. These consisted of sodium and potassium antimonates with antimony oxide and tantalum and niobium oxide with rubidium oxide as far as the ratio 4Rb2O:llB2O5 (B=Nb, Ta). The ternary system NaSbO3-Sb2O4-NaF was investigated extensively to determine the actual composition of the body centered cubic sodium antimonate. Various other binary and ternary oxide systems involving alkali oxides were examined in lesser detail. The phases synthesized were screened by ion exchange methods to determine mobility of the mobility of the alkali ion within the niobium, tantalum or antimony oxide (fluoride) structural framework. Five structure types warranted further investigation; these structure types are (1) hexagonal tungsten bronze (HTB), (2) pyrochlore, (3) the hybrid HTB-pyrochlore hexagonal ordered phases, (4) body centered cubic antimonates and (5) 2K2O:3Nb2O5. Although all of these phases exhibit good ion exchange properties only the pyrochlore was prepared with Na(+) ions as an equilibrium phase and as a low porosity ceramic. Sb(+3) in the channel interferes with ionic conductivity in this case, although relatively good ionic conductivity was found for the metastable Na(+) ion exchanged analogs of RbTa2O5F and KTaWO6 pyrochlore phases.

Self-consistent Simulation of Microparticle and Ion Wakefield Configuration

NASA Astrophysics Data System (ADS)

Sanford, Dustin; Brooks, Beau; Ellis, Naoki; Matthews, Lorin; Hyde, Truell

2017-10-01

In a complex plasma, positively charged ions often have a directed flow with respect to the negatively charged dust grains. The resulting interaction between the dust and the flowing plasma creates an ion wakefield downstream from the dust particles, with the resulting positive space region modifying the interaction between the grains and contributing to the observed dynamics and equilibrium structure of the system. Here we present a proof of concept method that uses a molecular dynamics simulation to model the ion wakefield allowing the dynamics of the dust particles to be determined self-consistently. The trajectory of each ion is calculated including the forces from all other ions, which are treated as ``Yukawa particles'' and shielded from thermal electrons and the forces of the charged dust particles. Both the dust grain charge and the wakefield structure are also self-consistently determined for various particle configurations. The resultant wakefield potentials are then used to provide dynamic simulations of dust particle pairs. These results will be employed to analyze the formation and dynamics of field-aligned chains in CASPER's PK4 experiment onboard the International Space Station, allowing examination of extended dust chains without the masking force of gravity. This work was supported by the National Science Foundation under Grants PHY-1414523 and PHY-1740203.

Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs

PubMed Central

Hübel, Niklas; Dahlem, Markus A.

2014-01-01

The classical Hodgkin-Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied by the resistance of the ion channels, and by the gating time constants. We study slow dynamics in an extended HH framework that includes time-dependent ion concentrations, pumps, and buffers. Fluxes across the neuronal membrane change intra- and extracellular ion concentrations, whereby the latter can also change through contact to reservoirs in the surroundings. Ion gain and loss of the system is identified as a bifurcation parameter whose essential importance was not realized in earlier studies. Our systematic study of the bifurcation structure and thus the phase space structure helps to understand activation and inhibition of a new excitability in ion homeostasis which emerges in such extended models. Also modulatory mechanisms that regulate the spiking rate can be explained by bifurcations. The dynamics on three distinct slow times scales is determined by the cell volume-to-surface-area ratio and the membrane permeability (seconds), the buffer time constants (tens of seconds), and the slower backward buffering (minutes to hours). The modulatory dynamics and the newly emerging excitable dynamics corresponds to pathological conditions observed in epileptiform burst activity, and spreading depression in migraine aura and stroke, respectively. PMID:25474648

Multilayer photosensitive structures based on porous silicon and rare-earth-element compounds: Study of spectral characteristics

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

Kirsanov, N. Yu.; Latukhina, N. V., E-mail: natalat@yandex.ru; Lizunkova, D. A.

2017-03-15

The spectral characteristics of the specular reflectance, photosensitivity, and photoluminescence (PL) of multilayer structures based on porous silicon with rare-earth-element (REE) ions are investigated. It is shown that the photosensitivity of these structures in the wavelength range of 0.4–1.0 μm is higher than in structures free of REEs. The structures with Er{sup 3+} ions exhibit a luminescence response at room temperature in the spectral range from 1.1 to 1.7 μm. The PL spectrum of the erbium impurity is characterized by a fine line structure, which is determined by the splitting of the {sup 4}I{sub 15/2} multiplet of the Er{sup 3+}more » ion. It is shown that the structures with a porous layer on the working surface have a much lower reflectance in the entire spectral range under study (0.2–1.0 μm).« less

Search for solid conductors of Na(+) and K(+) ions: Five new conductors

NASA Technical Reports Server (NTRS)

Singer, J.; Kautz, H.; Fielder, W. L.; Fordyce, J.

1975-01-01

Five conductors of three structure types were discovered which, as solids, can transport Na(+) or K(+) ions with conductivities of approximately .00001/(omega cm) at 300 K. These compounds are: (1) the pyrochlores NaTaWO6 and NaTa2O5F, both with an activation energy for conduction delta E of 21 kJ/mole; (2) the bodycentered cubic form of NaSbO3, with delta E = 42 kJ/mole; and (3) the niobates 2Na2O with 3Nb2O5 and 2K2O with 3Nb2O5, with the alkali ions probably in open layers of the incompletely determined structure; delta E = 17 kJ/mole. On the basis of approximately 40 structure types, some generalizations were made regarding the relation between structure and ionic transport.

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

Pestehe, S. J., E-mail: sjpest@tabrizu.ac.ir; Mohammadnejad, M.; Research Institute for Applied Physics and Astronomy, University of Tabriz, Tabriz

A theoretical model is developed to study the signals from a typical dynamic Faraday cup, and using this model the output signals from this structure are obtained. A detailed discussion on the signal structure, using different experimental conditions, is also given. It is argued that there is a possibility of determining the total charge of the generated ion pulse, the maximum velocity of the ions, ion velocity distribution, and the number of ion species for mixed working gases, under certain conditions. In addition, the number of different ionization stages, the number of different pinches in one shot, and the numbermore » of different existing acceleration mechanisms can also be determined provided that the mentioned conditions being satisfied. An experiment is carried out on the Filippov type 90 kJ Sahand plasma focus using Ar as the working gas at the pressure of 0.25 Torr. The data from a typical shot are fitted to a signal from the model and the total charge of the related energetic ion pulse is deduced using the values of the obtained fit parameters. Good agreement between the obtained amount of the total charge and the values obtained during other experiments on the same plasma focus device is observed.« less

Tandem mass spectrometry in combination with product ion mobility for the identification of phospholipids

DOE PAGES

Berry, Karin A. Zemski; Barkley, Robert M.; Berry, Joseph J.; ...

2016-11-29

Concerted tandem and traveling wave ion mobility mass spectrometry (CTS analysis) is a unique method that results in a four-dimensional data set including nominal precursor ion mass, product ion mobility, accurate mass of product ion, and ion abundance. This nontargeted lipidomics CTS approach was applied in both positive- and negative-ion mode to phospholipids present in human serum, and the data set was used to evaluate the value of product ion mobility in identifying lipids in a complex mixture. As a result, it was determined that the combination of diagnostic product ions and unique collisional cross-section values of product ions ismore » a powerful tool in the structural identification of lipids in a complex biological sample.« less

Tandem mass spectrometry in combination with product ion mobility for the identification of phospholipids

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

Berry, Karin A. Zemski; Barkley, Robert M.; Berry, Joseph J.

Concerted tandem and traveling wave ion mobility mass spectrometry (CTS analysis) is a unique method that results in a four-dimensional data set including nominal precursor ion mass, product ion mobility, accurate mass of product ion, and ion abundance. This nontargeted lipidomics CTS approach was applied in both positive- and negative-ion mode to phospholipids present in human serum, and the data set was used to evaluate the value of product ion mobility in identifying lipids in a complex mixture. As a result, it was determined that the combination of diagnostic product ions and unique collisional cross-section values of product ions ismore » a powerful tool in the structural identification of lipids in a complex biological sample.« less

High-resolution Measurement of Contact Ion-pair Structures in Aqueous RbCl Solutions from the Simultaneous Corefinement of their Rb and Cl K-edge XAFS and XRD Spectra

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

Pham, Van-Thai; Fulton, John L.

2016-06-21

In concentrated solutions of aqueous RbCl, all of the Rb+ and Cl- ions exist as contact ion pairs. This full structural assessment is derived from the refinement of three independent experimental measurements: the Rb and Cl K-edge x-ray absorption fine structure (XAFS) and the x-ray diffraction spectra (XRD). This simultaneous refinement of the XAFS and XRD data provides high accuracy since each method probes the structure of different local regions about the ions with high sensitivity. At high RbCl concentration (6 m (mol/kg )) the solution is dominated by Rb+ - Cl- contact ion pairs yielding an average of 1.5more » pairs at an Rb-Cl distance of 3.24 Å. Upon formation of these ion pairs, approximately 1.1 waters molecules are displaced from the Rb+ and 1.4 water molecules from Cl-. The hydration shells about both the cation and anion are also determined. These results greatly improve the understanding of monovalent ions and provide a basis for testing the Rb+-Cl- interaction potentials used in molecular dynamics (MD) simulation. This research was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger

PubMed Central

Giladi, Moshe; Almagor, Lior; van Dijk, Liat; Hiller, Reuben; Man, Petr; Forest, Eric; Khananshvili, Daniel

2016-01-01

In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins. PMID:26876271

Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A

PubMed Central

Baştuğ, Turgut; Gray-Weale, Angus; Patra, Swarna M.; Kuyucak, Serdar

2006-01-01

Proteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason—besides the well-known problem with the description of single file pore water—why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model. PMID:16415054

Properties of small Ar sub N-1 K/+/ ionic clusters

NASA Technical Reports Server (NTRS)

Etters, R. D.; Danilowicz, R.; Dugan, J.

1977-01-01

A self-consistent formalism is developed that, based upon a many-body potential, dynamically determines the thermodynamic properties of ionic clusters without an a priori designation of the equilibrium structures. Aggregates consisting of a single closed shell K(+) ion and N-1 isoelectronic argon atoms were studied. The clusters form crystallites at low temperatures, and melting transitions and spontaneous dissociations are indicated. The results confirm experimental evidence that shows that ionic clusters become less stable with increasing N. The crystallite structures formed by four different clusters are isosceles triangle, skewed form, octahedron with ion in the middle, and icosahedron with the ion in the middle.

Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS

DOE PAGES

Eklund, Lars; Hofer, Tomas S.; Persson, Ingmar

2014-11-26

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO 2 –, chlorate, ClO 3 –, and perchlorate, ClO 4 –. In addition, the structures of the hydrated hypochlorite, ClO –, bromate, BrO 3 –, iodate, IO 3 – and metaperiodate, IO 4 –, ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H 2IO 6 3–, ions have been determinedmore » by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl–O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01–0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. Here, the water exchange rate for the perchlorate ion is significantly faster, τ 0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ 0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.« less

An Rf Focused Interdigital Ion Accelerating Structure

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

Swenson, D.A.

2003-08-26

An Rf Focused Interdigital (RFI) ion accelerating structure will be described. It represents an effective combination of the Wideroee (or interdigital) linac structure, used for many low frequency, heavy ion applications, and the rf electric quadrupole focusing used in the RFQ and RFD linac structures. As in the RFD linac structure, rf focusing is introduced into the RFI linac structure by configuring the drift tubes as two independent pieces operating at different electrical potentials as determined by the rf fields of the linac structure. Each piece (or electrode) of the RFI drift tube supports two fingers pointed inwards towards themore » opposite end of the drift tube forming a four-finger geometry that produces an rf quadrupole field along the axis of the linac for focusing the beam. However, because of the differences in the rf field configuration along the axis, the scheme for introducing rf focusing into the interdigital linac structure is quite different from that adopted for the RFD linac structure. The RFI linac structure promises to have significant size, efficiency, performance, and cost advantages over existing linac structures for the acceleration of low energy ion beams of all masses (light to heavy). These advantages will be reviewed. A 'cold model' of this new linac structure has been fabricated and the results of rf cavity measurements on this cold model will be presented.« less

Influence of different metal ions on the ultrastructure, biochemical properties, and protein localization of the K562 cell nuclear matrix.

PubMed

Neri, L M; Bortul, R; Zweyer, M; Tabellini, G; Borgatti, P; Marchisio, M; Bareggi, R; Capitani, S; Martelli, A M

1999-06-01

The higher order of chromatin organization is thought to be determined by the nuclear matrix, a mainly proteinaceous structure that would act as a nucleoskeleton. The matrix is obtained from isolated nuclei by a series of extraction steps involving the use of high salt and nonspecific nucleases, which remove chromatin and other loosely bound components. It is currently under debate whether these structures, isolated in vitro by unphysiological extraction buffers, correspond to a nucleoskeleton existing in vivo. In most cell types investigated, the nuclear matrix does not spontaneously resist these extractions steps; rather, it must be stabilized before the application of extracting agents. In this study nuclei, isolated from K562 human erythroleukemia cells, were stabilized by incubation with different metal ions (Ca2+, Cu2+, Zn2+, Cd2+), and the matrix was obtained by extraction with 2 M NaCl. By means of ultrastructural analysis of the resulting structures, we determined that, except for Ca2+, all the other metals induced a stabilization of the matrix, which retained the inner fibrogranular network and residual nucleoli. The biochemical composition, analyzed by two-dimensional gel electrophoresis separation, exhibited a distinct matrix polypeptide pattern, characteristic of each type of stabilizing ion employed. We also investigated to what extent metal ions could maintain in the final structures the original distribution of three inner matrix components, i.e. NuMA, topoisomerase IIalpha, and RNP. Confocal microscopy analysis showed that only NuMa, and, to a lesser extent, topoisomerase IIalpha, were unaffected by stabilization with divalent ions. On the contrary, the fluorescent RNP patterns detected in the resulting matrices were always disarranged, irrespective of the stabilization procedure. These results indicate that several metal ions are powerful stabilizing agents of the nuclear matrix prepared from K562 erythroleukemia cells and also strengthen the concept that NuMA and topoisomerase IIalpha may act as structural components of the nuclear matrix.

IR spectroscopy study of SBA-15 silicas functionalized with the ethylthiocarbamidepropyl groups and their interactions with Ag(I) and Hg(II) ions

NASA Astrophysics Data System (ADS)

Melnyk, Inna V.; Nazarchuk, Galyna I.; Václavíková, Miroslava; Zub, Yuriy L.

2018-04-01

Mesoporous structure of silica is determined by the type of template, but the introduction of functional groups during the synthesis has additional influence. The structure of SBA-15 may be violated by the introduction of long functions, such as ≡Si(CH2)3NHC(=S)NHC2H5. These ethylthiocarbamidepropyl groups can form complexes with metal ions in thiol or thione tautomeric forms. We determined that the 2D hexagonal p6 mm structure is preserved for SBA-15 with thiourea groups at maximal TEOS:trifunctional silane ratio (mol) = 10:2, which was confirmed by TEM and by the presence of an intense reflex in the small-angle region of diffractograms of the final product. It was shown that the obtained sorbents possess high kinetic characteristics. The experimental data fit pseudo-second-order kinetic equation, but the rate constants depend on the content of functional groups in the surface layer. Template Pluronic P-123 defines the porosity of functional mesoporous silica materials even at increasing content of trifunctional silane in the initial solution. Infrared spectroscopy analysis showed that thione form of thiourea ligand is prevalent on the surface of pores of mesoporous samples. However, during the sorption of silver(I) ions, there are both thione and thiol forms on the surface. Thione form is transformed into thiol with increasing concentration of mercury(II) ions in the sorption solution. Adsorption experiments showed that the SBA-15 silicas functionalized with ethylthiocarbamidepropyl groups had high selectivity for silver(I) ions and could concentrate Ag(I) ions from metal ions mixture at pH 2.

Combining Sequential Extractions and X-ray Absorption Spectroscopy for Quantitative and Qualitative Zinc Speciation in Soil

NASA Astrophysics Data System (ADS)

Bauer, Tatiana; Minkina, Tatiana; Batukaev, Abdulmalik; Nevidomskaya, Dina; Burachevskaya, Marina; Tsitsuashvili, Viktoriya; Urazgildieva, Kamilya

2017-04-01

The combined use of X-ray absorption spectrometry and extractive fractionation is an effective approach for studying the interaction of metal ions with soil compounds and identifying the phases-carriers of metals in soil and their stable fixation. These studies were carried out using the technique of X-ray absorption spectroscopy and chemical extractive fractionation. In a model experiment the samples taken in Calcic Chernozem were artificially contaminated with higher portion of Zn(NO3)2 (2000 mg/kg). The metal were incubated in soil samples for 2 year. The samples of soil mineral and organic phases (calcite, kaolinite, bentonite, humic acids) were saturated with Zn2+ from a solution of nitrate salts of metal. The total content of Zn in soil and soil various phases was determined using the X-ray fluorescence method. Extended X-ray absorption fine structure (EXAFS) Zn was measured at the Structural Materials Science beamline of the Kurchatov Center for Synchrotron Radiation. Sequential fractionation of Zn in soil conducted by Tessier method (Tessier et al., 1979) which determining 5 fractions of metals in soil: exchangeable, bound to Fe-Mn oxide, bound to carbonate, bound to the organic matter, and bound to silicate (residual). This methodology has so far more than 4000 citations (Web of Science), which demonstrates the popularity of this approach. Much Zn compounds are contained in uncontaminated soils in stable primary and secondary silicates inherited from the parental rocks (67% of the total concentrations in all fractions), which is a regional trait of soils in the fore-Caucasian plain. Extracted fractionation of metal compounds in soil samples, artificially contaminated with Zn salts, indicates the priority holding of Zn2+ ions by silicates, carbonates and Fe-Mn oxides. The Zn content significantly increases in the exchangeable fraction. Atomic structure study of the soil various phases saturated with Zn2+ ion by using (XANES) X-ray absorption spectroscopy allowed the determination of mechanism of metal ions interaction with soil phases and the resulting types of chemical bonds. Interaction with soil components modifies the electron structure of the metal ions themselves. The soil contamination with Zn is accompanied by decreasing the stable connection between metal and soil components. Interacting with humic acids in chernozem, the Zn2+ ion is coordinated by functional groups and ligands and forms unstable outer-sphere complexes. Zinc included into octahedral structures of layered minerals and hydro(oxides) can be inner-and outer-sphere adsorbed. The Zn2+ ions enable to replace Ca2+ ions in octahedral positions being coordinated with carbonate ions as ligands, thus forming absorbed complexes at the surface of mineral calcite. This work was supported by grant of the Russian Scientific Foundation № 16-14-10217.

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

DOE PAGES

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.; ...

2017-05-17

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less

Laspartomycin, an acidic lipopeptide antibiotic with a unique peptide core.

PubMed

Borders, Donald B; Leese, Richard A; Jarolmen, Howard; Francis, Noreen D; Fantini, Amadeo A; Falla, Tim; Fiddes, John C; Aumelas, André

2007-03-01

Laspartomycin was originally isolated and characterized in 1968 as a lipopeptide antibiotic related to amphomycin. The molecular weight and structure remained unknown until now. In the present study, laspartomycin was purified by a novel calcium chelate procedure, and the structure of the major component (1) was determined. The structure of laspartomycin C (1) differs from that of amphomycin and all related antibiotics as a result of its peptide region being acidic rather than amphoteric and the amino acid branching into the side chain being diaminopropionic rather than diaminobutyric. In addition, the fatty acid side chain is 2,3-unsaturated compared to 3,4-unsaturated for amphomycin and other related antibiotics. Calcium ion addition to stabilize a particular conformer was found to be important for an enzymatic deacylation of the antibiotic. A peptide resulting from the deacylation was critical for chemical structure determination by NMR studies, which also involved addition of calcium ions to stabilize a conformer.

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

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

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less

Determinants of cation transport selectivity: Equilibrium binding and transport kinetics

PubMed Central

2015-01-01

The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K+-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules. PMID:26078056

Assignment of the Stereochemistry and Anomeric Configuration of Sugars within Oligosaccharides Via Overlapping Disaccharide Ladders Using MSn

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Londry, Frank A.; Bendiak, Brad; Xia, Yu

2014-08-01

A systematic approach is described that can pinpoint the stereo-structures (sugar identity, anomeric configuration, and location) of individual sugar units within linear oligosaccharides. Using a highly modified mass spectrometer, dissociation of linear oligosaccharides in the gas phase was optimized along multiple-stage tandem dissociation pathways (MSn, n = 4 or 5). The instrument was a hybrid triple quadrupole/linear ion trap mass spectrometer capable of high-efficiency bidirectional ion transfer between quadrupole arrays. Different types of collision-induced dissociation (CID), either on-resonance ion trap or beam-type CID could be utilized at any given stage of dissociation, enabling either glycosidic bond cleavages or cross-ring cleavages to be maximized when wanted. The approach first involves optimizing the isolation of disaccharide units as an ordered set of overlapping substructures via glycosidic bond cleavages during early stages of MSn, with explicit intent to minimize cross-ring cleavages. Subsequently, cross-ring cleavages were optimized for individual disaccharides to yield key diagnostic product ions ( m/ z 221). Finally, fingerprint patterns that establish stereochemistry and anomeric configuration were obtained from the diagnostic ions via CID. Model linear oligosaccharides were derivatized at the reducing end, allowing overlapping ladders of disaccharides to be isolated from MSn. High confidence stereo-structural determination was achieved by matching MSn CID of the diagnostic ions to synthetic standards via a spectral matching algorithm. Using this MSn ( n = 4 or 5) approach, the stereo-structures, anomeric configurations, and locations of three individual sugar units within two pentasaccharides were successfully determined.

Ion-binding properties of a K+ channel selectivity filter in different conformations.

PubMed

Liu, Shian; Focke, Paul J; Matulef, Kimberly; Bian, Xuelin; Moënne-Loccoz, Pierre; Valiyaveetil, Francis I; Lockless, Steve W

2015-12-08

K(+) channels are membrane proteins that selectively conduct K(+) ions across lipid bilayers. Many voltage-gated K(+) (KV) channels contain two gates, one at the bundle crossing on the intracellular side of the membrane and another in the selectivity filter. The gate at the bundle crossing is responsible for channel opening in response to a voltage stimulus, whereas the gate at the selectivity filter is responsible for C-type inactivation. Together, these regions determine when the channel conducts ions. The K(+) channel from Streptomyces lividians (KcsA) undergoes an inactivation process that is functionally similar to KV channels, which has led to its use as a practical system to study inactivation. Crystal structures of KcsA channels with an open intracellular gate revealed a selectivity filter in a constricted conformation similar to the structure observed in closed KcsA containing only Na(+) or low [K(+)]. However, recent work using a semisynthetic channel that is unable to adopt a constricted filter but inactivates like WT channels challenges this idea. In this study, we measured the equilibrium ion-binding properties of channels with conductive, inactivated, and constricted filters using isothermal titration calorimetry (ITC). EPR spectroscopy was used to determine the state of the intracellular gate of the channel, which we found can depend on the presence or absence of a lipid bilayer. Overall, we discovered that K(+) ion binding to channels with an inactivated or conductive selectivity filter is different from K(+) ion binding to channels with a constricted filter, suggesting that the structures of these channels are different.

Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

USGS Publications Warehouse

Leenheer, J.A.; Brown, G.K.; MacCarthy, P.; Cabaniss, S.E.

1998-01-01

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The 'metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-1R spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short- chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The `metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

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

Akparov, V. Kh., E-mail: valery@akparov.ru; Timofeev, V. I., E-mail: tostars@mail.ru; Maghsoudi, N. N., E-mail: maghsudi@yahoo.com

2017-03-15

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and themore » acetate ion is different from that reported by Yoshimoto et al.« less

The Structure of the Metal Transporter Tp34 and its Affinity for Divalent Metal Ions

NASA Astrophysics Data System (ADS)

Knutsen, Gregory; Deka, Ranjit; Brautigam, Chad; Tomchick, Diana; Machius, Mischa; Norgard, Michael

2007-10-01

Tp34 is periplasmic membrane protein of the nonculitvatable spirochete Treponema pallidum, the pathogen of syphillis. It was proposed that Tp34 is a divalent metal transporter, but the identity of the preferred metal ion(s) was unclear. In this study we investigated the ability of divalent metal ions to induce rTp34 dimerization using hydrodynamic techniques and determine the crystal structure of metal bound forms. Using analytical ultracentrifugation sedimentation velocity experiments, we determined that cobalt is superior to nickel at inducing the dimerization of rTp34. rTp34 was crystallized and selected crystals were incubated at a pH 7.5 with CuSO4 and NiSO4. Diffraction experiments were conducted and the processed electron density maps showed that copper was bound to the major metal binding site as well as to three additional minor binding sites. By contrast nickel was only bound to the major metal binding site in one monomer and to three additional minor sites. These results along with previous findings support evidence of Tp34 being involved with metal transport and/or iron utilization.

Synthesis of diethylaminoethyl dextran hydrogel and its heavy metal ion adsorption characteristics.

PubMed

Demirbilek, Celile; Dinç, Cemile Özdemir

2012-10-01

Epichlorohydrin-crosslinked diethylaminoethyl dextran (DEAE-D/ECH) hydrogel was synthesized by intermolecular side-chain reaction of DEAE-D hydroxyl groups with monomeric crosslinking agent, ECH. Swelling ability, adsorption capacity and metal removal of the hydrogel were profoundly determined and some structural parameters for the hydrogel such as volume of non-swollen gel, percentages of gellation, swelling ratio and equilibrium water content were evaluated in this study. The ability of removing heavy metal ions from Orontes River by the synthesized hydrogel, thoroughly characterized by photometric spectrometer and the adsorption characteristics of metal ions, was investigated as well as surface morphologies of the hydrogel before and after metal adsorption were examined by SEM. Structure of DEAE-D/ECH gel was analyzed by FTIR, TGA, and DSC. Gellation point of binary system reaction between DEAE-D and ECH was determined via monitoring viscosity changes during reaction. The order of affinity based on amount of metal ion uptake was found as follows: Zn(2+)>Mn(2+)>Pb(2+)>Cd(2+). Copyright © 2012 Elsevier Ltd. All rights reserved.

Irradiation of zinc single crystal with 500 keV singly-charged carbon ions: surface morphology, structure, hardness, and chemical modifications

NASA Astrophysics Data System (ADS)

Waqas Khaliq, M.; Butt, M. Z.; Saleem, Murtaza

2017-07-01

Cylindrical specimens of (1 0 4) oriented zinc single crystal (diameter  =  6 mm and length  =  5 mm) were irradiated with 500 keV C+1 ions with the help of a Pelletron accelerator. Six specimens were irradiated in an ultra-high vacuum (~10‒8 Torr) with different ion doses, namely 3.94  ×  1014, 3.24  ×  1015, 5.33  ×  1015, 7.52  ×  1015, 1.06  ×  1016, and 1.30  ×  1016 ions cm-2. A field emission scanning electron microscope (FESEM) was utilized for the morphological study of the irradiated specimens. Formation of nano- and sub-micron size rods, clusters, flower- and fork-like structures, etc, was observed. Surface roughness of the irradiated specimens showed an increasing trend with the ions dose. Energy dispersive x-ray spectroscopy (EDX) helped to determine chemical modifications in the specimens. It was found that carbon content varied in the range 22.86-31.20 wt.% and that oxygen content was almost constant, with an average value of 10.16 wt.%. The balance content was zinc. Structural parameters, i.e. crystallite size and lattice strain, were determined by Williamson-Hall analysis using x-ray diffraction (XRD) patterns of the irradiated specimens. Both crystallite size and lattice strain showed a decreasing trend with the increasing ions dose. A good linear relationship between crystallite size and lattice strain was observed. Surface hardness depicted a decreasing trend with the ions dose and followed an inverse Hall-Petch relation. FTIR spectra of the specimens revealed that absorption bands gradually diminish as the dose of singly-charged carbon ions is increased from 3.94  ×  1014 ions cm-1 to 1.30  ×  1016 ions cm-1. This indicates progressive deterioration of chemical bonds with the increase in ion dose.

Optical and electrical properties of ion beam textured Kapton and Teflon

NASA Technical Reports Server (NTRS)

Mirtich, M. J.; Sovey, J. S.

1977-01-01

An electron bombardment argon ion source was used to ion etch polyimide (Kapton) and fluorinated ethylene, FEP (Teflon). Samples of polyimide and FEP were exposed to (0.5-1.0) keV Ar ions at ion current densities of (1.0-1/8) mA/sq cm for various exposure times. Changes in the optical and electrical properties of the samples were used to characterize the exposure. Spectral reflectance and transmittance measurements were made between 0.33 and 2.16 micron m using an integrating sphere after each exposure. From these measurements, values of solar absorptance were obtained. Total emittance measurements were also recorded for some samples. Surface resistivity was used to determine changes in the electrical conductivity of the etched samples. A scanning electron microscope recorded surface structure after exposure. Spectral optical data, resistivity measurements, calculated absorptance and emittance measurements are presented along with photomicrographs of the surface structure for the various exposures to Ar ions.

Evaluation of oriented lysozyme immobilized with monoclonal antibody

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Okada, Keigo; Shigyo, Ayako; Man, Naoki; Karen, Akiya

2008-12-01

The orientation of a lysozyme immobilized with a monoclonal antibody was evaluated based on determination of the uppermost surface structure using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Specific peaks of the oriented lysozyme immobilized with monoclonal anti-lysozyme antibody were obtained in comparison with reference samples, non-oriented immobilized lysozyme and immobilized anti-lysozyme antibody. All samples were freeze-dried before TOF-SIMS measurement, and then each sample was measured using TOF-SIMS with a bismuth cluster ion source. TOF-SIMS spectra were analyzed to select peaks specific to the oriented immobilized lysozyme as well as to identify their chemical formula and ensemble of amino acids. The possible chemical formulae of the lysozyme fragments were then investigated with an element matching program and a residue matching program. The results from TOF-SIMS spectra analysis were compared to the amino acid sequence of the lysozyme and its three-dimensional structure registered in the protein data bank. Finally, the fragment-ion-generating regions of the oriented immobilized lysozyme were determined based on the suggested residues and the three-dimensional structure.

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennite -- A Computational Modeling Study

NASA Astrophysics Data System (ADS)

Adebiyi, Babatunde Mattew

Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance, are required. A computational material modeling methodology is investigated and demonstrated for a key cement hydrated component material chemistry structure of Calcium-Silicate-Hydrate (C-S-H) Jennite in this work. The effect of material ion exchanges on the mechanical stiffness properties and shear deformation behavior of hydrated cement material chemistry structure of Calcium Silicate Hydrate (C-S-H) Jennite was studied. Calcium ions were replaced with Magnesium ions in Jennite structure of the C-S-H gel. Different level of substitution of the ions was used. The traditional Jennite structure was obtained from the American Mineralogist Crystal Structure Database and super cells of the structures were created using a Molecular Dynamics Analyzer and Visualizer Material Studio. Molecular dynamics parameters used in the modeling analysis were determined by carrying out initial dynamic studies. 64 unit cell of C-S-H Jennite was used in material modeling analysis studies based on convergence results obtained from the elastic modulus and total energies. NVT forcite dynamics using COMPASS force field based on 200 ps dynamics time was used to determine mechanical modulus of the traditional C-S-H gel and the Magnesium ion modified structures. NVT Discover dynamics using COMPASS forcefield was used in the material modeling studies to investigate the influence of ionic exchange on the shear deformation of the associated material chemistry structures. A prior established quasi-static deformation method to emulate shear deformation of C-S-H material chemistry structure that is based on a triclinic crystal structure was used, by deforming the triclinic crystal structure at 0.2 degree per time step for 75 steps of deformation. It was observed that there is a decrease in the total energies of the systems as the percentage of magnesium ion increases in the C-S-H Jennite molecular structure systems. Investigation of effect of ion exchange on the elastic modulus shows that the elastic stiffness modulus tends to decrease as the amount of Mg in the systems increases, using either COMPASS or universal force field. On the other hand, shear moduli obtained after deforming the structures computed from the stress-strain curve obtained from material modeling increases as the amount of Mg increases in the system. The present investigations also showed that ultimate shear stress obtained from predicted shear stress---strain also increases with amount of Mg in the chemistry structure. Present study clearly demonstrates that computational material modeling following molecular dynamics analysis methodology is an effective way to predict and understand the effective material chemistry and additive changes on the stiffness and deformation characteristics in cementitious materials, and the results suggest that this method can be extended to other materials.

What makes the difference in perovskite titanates?

NASA Astrophysics Data System (ADS)

Bussmann-Holder, Annette; Roleder, Krystian; Ko, Jae-Hyeon

2018-06-01

We have investigated in detail the lattice dynamics of five different perovskite titanates ATiO3 (A = Ca, Sr, Ba, Pb, Eu) where the A sites are occupied by +2 ions. In spite of the largely ionic character of these ions, the properties of these compounds differ substantially. They range from order/disorder like, to displacive ferroelectric, quantum paraelectric, and antiferromagnetic. All compounds crystallize in the cubic structure at high temperature and undergo structural phase transitions to tetragonal symmetry, partly followed by further transitions to lower symmetries. Since the TiO6 moiety is the essential electronic and structural unit, the question arises, what makes the significant difference between them. It is shown that the lattice dynamics of these compounds are very different, and that mode-mode coupling effects give rise to many distinct properties. In addition, the oxygen ion nonlinear polarizability plays a key role since it dominates the anharmonicity of these perovskites and determines the structural instability.

Cyclic performance tests of Sn/MWCNT composite lithium ion battery anodes at different temperatures

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

Tocoglu, U., E-mail: utocoglu@sakarya.edu.tr; Cevher, O.; Akbulut, H.

In this study tin-multi walled carbon nanotube (Sn-MWCNT) lithium ion battery anodes were produced and their electrochemical galvanostatic charge/discharge tests were conducted at various (25 °C, 35 °C, 50 °C) temperatures to determine the cyclic behaviors of anode at different temperatures. Anodes were produced via vacuum filtration and DC magnetron sputtering technique. Tin was sputtered onto buckypapers to form composite structure of anodes. SEM analysis was conducted to determine morphology of buckypapers and Sn-MWCNT composite anodes. Structural and phase analyses were conducted via X-ray diffraction and Raman Spectroscopy technique. CR2016 coin cells were assembled for electrochemical tests. Cyclic voltammetry testmore » were carried out to determine the reversibility of reactions between anodes and reference electrode between 0.01-2.0 V potential window. Galvanostatic charge/discharge tests were performed to determine cycle performance of anodes at different temperatures.« less

The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state.

PubMed

Almog, Orna; González, Ana; Godin, Noa; de Leeuw, Marina; Mekel, Marlene J; Klein, Daniela; Braun, Sergei; Shoham, Gil; Walter, Richard L

2009-02-01

We determine and compare the crystal structure of two proteases belonging to the subtilisin superfamily: S41, a cold-adapted serine protease produced by Antarctic bacilli, at 1.4 A resolution and Sph, a mesophilic serine protease produced by Bacillus sphaericus, at 0.8 A resolution. The purpose of this comparison was to find out whether multiple calcium ion binding is a molecular factor responsible for the adaptation of S41 to extreme low temperatures. We find that these two subtilisins have the same subtilisin fold with a root mean square between the two structures of 0.54 A. The final models for S41 and Sph include a calcium-loaded state of five ions bound to each of these two subtilisin molecules. None of these calcium-binding sites correlate with the high affinity known binding site (site A) found for other subtilisins. Structural analysis of the five calcium-binding sites found in these two crystal structures indicate that three of the binding sites have two side chains of an acidic residue coordinating the calcium ion, whereas the other two binding sites have either a main-chain carbonyl, or only one acidic residue side chain coordinating the calcium ion. Thus, we conclude that three of the sites are of high affinity toward calcium ions, whereas the other two are of low affinity. Because Sph is a mesophilic subtilisin and S41 is a psychrophilic subtilisin, but both crystal structures were found to bind five calcium ions, we suggest that multiple calcium ion binding is not responsible for the adaptation of S41 to low temperatures. Copyright 2008 Wiley-Liss, Inc.

Low energy ion beam induced changes in ETFE polymer

NASA Astrophysics Data System (ADS)

Parada, M. A.; Delalez, N.; de Almeida, A.; Muntele, C.; Muntele, I.; Ila, D.

2006-01-01

Low energy ion beam bombardment of ethylenetetrafluoroethylene (ETFE) modifies the physical and chemical properties of the polymer surface in ways that enhance or compromise applications in the technological and medical physics fields. When a material is exposed to ionizing radiation, its changes depends on the type, energy and intensity of the applied radiation. In order to determine the nature of the induced radiation changes, ETFE films were bombarded with fluences from 1012 up to 1015 ions/cm2 of keV N and protons. The emission of gaseous species during the bombardments was monitored with a residual gas analyser (RGA). The bombarded films were analysed with optical absorption photospectrometry (OAP), Fourier transform infrared (FTIR) and micro-Raman spectrometries that determine the chemical nature of the structural changes caused by ions bombardment.

Ion penetration depth in the plant cell wall

NASA Astrophysics Data System (ADS)

Yu, L. D.; Vilaithong, T.; Phanchaisri, B.; Apavatjrut, P.; Anuntalabhochai, S.; Evans, P.; Brown, I. G.

2003-05-01

This study investigates the depth of ion penetration in plant cell wall material. Based on the biological structure of the plant cell wall, a physical model is proposed which assumes that the wall is composed of randomly orientated layers of cylindrical microfibrils made from cellulose molecules of C 6H 12O 6. With this model, we have determined numerical factors for ion implantation in the plant cell wall to correct values calculated from conventional ion implantation programs. Using these correction factors, it is possible to apply common ion implantation programs to estimate the ion penetration depth in the cell for bioengineering purposes. These estimates are compared with measured data from experiments and good agreement is achieved.

Structural and optical study on antimony-silicate glasses doped with thulium ions.

PubMed

Dorosz, D; Zmojda, J; Kochanowicz, M; Miluski, P; Jelen, P; Sitarz, M

2015-01-05

Structural, spectroscopic and thermal properties of SiO₂-Al₂O₃-Sb₂O₃-Na₂O glass system doped with 0.2 mol% Tm₂O₃ have been presented. Synthesis of antimony-silicate glasses with relatively low phonon energy (600 cm(-1), which implicates a small non-radiative decay rate) was performed by conventional high-temperature melt-quenching methods. The effect of SiO₂/Sb₂O₃ ratio in fabricated Tm(3+) doped glass on thermal, structural and luminescence properties was investigated. On the basis of structural investigations decomposition of absorption bands in the infrared FTIR region was performed, thus determining that antimony ions are the only glass-forming ions, setting up the lattice of fabricated glasses. Luminescence band at the wavelength of 1.8 μm corresponding to (3)F₄→(3)H₆ transition in thulium ions was obtained under 795 nm laser pumping. It was observed that combination of relatively low phonon energy and greater separation of optically active centers in the fabricated glasses influenced in decreasing the luminescence intensity at 1800 nm. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

PubMed Central

Wöhlert, David; Kühlbrandt, Werner; Yildiz, Özkan

2014-01-01

Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters. DOI: http://dx.doi.org/10.7554/eLife.03579.001 PMID:25426802

Na0.44MnO2 nanorods as a cathode material for Na-ion batteries

NASA Astrophysics Data System (ADS)

Avci, Sevda; Oz, Erdinc; Demirel, Serkan; Altin, Emine; Altin, Serdar; Bayri, Ali; Yakinci, Eyyuphan

2014-03-01

Lithium-ion batteries have dominated the rechargeable battery market because of their high energy and power capability. On the other hand, sodium is one of the more abundant elements on Earth unlike Li. Moreover, Na has similar chemical properties to Li, indicating that Na-ion batteries can be an alternative to Li counterparts. With that respect, we have synthesized Na0.44MnO2 nanorods as cathode materials for Na-ion batteries. We have investigated the effects of structural, electrical, and magnetic properties on battery performance. We report the synthesis conditions and growth mechanism of the nanorods. The structure and the morphology of the materials were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), and atomic force microscopy (AFM) techniques. Temperature dependent structural changes were determined via in situ X-ray diffraction and TG-DTA measurements showing structural changes above room temperature. This work is funded by The Scientific and Technological Research Council of Turkey with Grant No:112M487.

Fine structure of heliumlike ions and determination of the fine structure constant.

PubMed

Pachucki, Krzysztof; Yerokhin, Vladimir A

2010-02-19

We report a calculation of the fine-structure splitting in light heliumlike atoms, which accounts for all quantum electrodynamical effects up to order alpha{5} Ry. For the helium atom, we resolve the previously reported disagreement between theory and experiment and determine the fine-structure constant with an accuracy of 31 ppb. The calculational results are extensively checked by comparison with the experimental data for different nuclear charges and by evaluation of the hydrogenic limit of individual corrections.

Low-energy ion-backscattering spectroscopies applied to the determination of surface structure

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

Yarmoff, J.A.

1985-01-01

Low-Energy Ion Scattering (LEIS) was investigated as a means for determining the geometric structure at a single-crystal surface. A three-dimensional Monte-Carlo computer simulation was developed and applied to existing LEIS data. The binary collision approximation was found to yield satisfactory results in simulating Buck's time-of-flight energy spectra for 2.4 keV Ne/sup +/ scattering from Ni(001). A two-atom-layer model was used in calculations of the azimuthal anisotropy of the ion yield measured by Bernheim and Slodzian for 9.5 keV Ne/sup +/ scattering from Cu(001). The calculations were successful in reproducing most of the features that had been observed in the experiments,more » which shows that this model contained most of the physics required to interpret the data. An apparatus for performing LEIS studies was built, and Low-Energy Ion-Backscattering Angular Distributions (LEIBAD) were collected with 3-20 keV /sup 6/Li/sup +/ incident on Cu(001). For incidence along a low-index Miller axis of the crystal, shadowing effects limited the penetration depth of the elastically scattered ions. However, neutralized Li atoms, which were not filtered out of the scattered yield by the high-pass filter, provided a background characteristic of the bulk. A high-resolution electrostatic analyzer was used to collect impact Collision Ion Scattering Spectroscopy (ICISS) data for 5-keV /sup 6/Li/sup +/ ions to study the Cu(110) and Cu(110) (2 x 1)-0 surfaces.« less

Magnetic and neutron diffraction study on quaternary oxides MTeMoO6 (M = Mn and Zn)

NASA Astrophysics Data System (ADS)

Doi, Yoshihiro; Suzuki, Ryo; Hinatsu, Yukio; Ohoyama, Kenji

2009-01-01

Crystal structures and magnetic properties of quaternary oxides MTeMoO6 (M = Mn and Zn) were investigated. From the Rietveld analyses for the powder x-ray and neutron diffraction measurements, their detailed structures have been determined. Both compounds have orthorhombic structure with space group P 21212 and a charge configuration of M2+Te4+Mo6+O6. ZnTeMoO6 shows diamagnetic behavior. In this structure, M ions are arranged in a square-planar manner. The temperature dependence of the magnetic susceptibility for MnTeMoO6 shows a broad peak at ~33 K, which is due to a two-dimensional characteristic of the magnetic interaction. In addition, this compound shows an antiferromagnetic transition at 20 K. The magnetic structure was determined by the powder neutron diffraction measurement at 3.3 K. The magnetic moments of Mn2+ ions (4.45 μB) order in a collinear antiferromagnetic arrangement along the b axis.

A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution

PubMed Central

2011-01-01

The hydration of the alkali metal ions in aqueous solution has been studied by large angle X-ray scattering (LAXS) and double difference infrared spectroscopy (DDIR). The structures of the dimethyl sulfoxide solvated alkali metal ions in solution have been determined to support the studies in aqueous solution. The results of the LAXS and DDIR measurements show that the sodium, potassium, rubidium and cesium ions all are weakly hydrated with only a single shell of water molecules. The smaller lithium ion is more strongly hydrated, most probably with a second hydration shell present. The influence of the rubidium and cesium ions on the water structure was found to be very weak, and it was not possible to quantify this effect in a reliable way due to insufficient separation of the O–D stretching bands of partially deuterated water bound to these metal ions and the O–D stretching bands of the bulk water. Aqueous solutions of sodium, potassium and cesium iodide and cesium and lithium hydroxide have been studied by LAXS and M–O bond distances have been determined fairly accurately except for lithium. However, the number of water molecules binding to the alkali metal ions is very difficult to determine from the LAXS measurements as the number of distances and the temperature factor are strongly correlated. A thorough analysis of M–O bond distances in solid alkali metal compounds with ligands binding through oxygen has been made from available structure databases. There is relatively strong correlation between M–O bond distances and coordination numbers also for the alkali metal ions even though the M–O interactions are weak and the number of complexes of potassium, rubidium and cesium with well-defined coordination geometry is very small. The mean M–O bond distance in the hydrated sodium, potassium, rubidium and cesium ions in aqueous solution have been determined to be 2.43(2), 2.81(1), 2.98(1) and 3.07(1) Å, which corresponds to six-, seven-, eight- and eight-coordination. These coordination numbers are supported by the linear relationship of the hydration enthalpies and the M–O bond distances. This correlation indicates that the hydrated lithium ion is four-coordinate in aqueous solution. New ionic radii are proposed for four- and six-coordinate lithium(I), 0.60 and 0.79 Å, respectively, as well as for five- and six-coordinate sodium(I), 1.02 and 1.07 Å, respectively. The ionic radii for six- and seven-coordinate K+, 1.38 and 1.46 Å, respectively, and eight-coordinate Rb+ and Cs+, 1.64 and 1.73 Å, respectively, are confirmed from previous studies. The M–O bond distances in dimethyl sulfoxide solvated sodium, potassium, rubidium and cesium ions in solution are very similar to those observed in aqueous solution. PMID:22168370

Size-dependent structural evolution of the biomineralized iron-core nanoparticles in ferritins

NASA Astrophysics Data System (ADS)

Lee, Eunsook; Kim, D. H.; Hwang, Jihoon; Lee, Kiho; Yoon, Sungwon; Suh, B. J.; Hyun Kim, Kyung; Kim, J.-Y.; Jang, Z. H.; Kim, Bongjae; Min, B. I.; Kang, J.-S.

2013-04-01

The structural identity of the biomineralized iron core nanoparticles in Helicobacter pylori ferritins (Hpf's) has been determined by employing soft x-ray absorption spectroscopy and soft x-ray magnetic circular dichroism. Valence states of Fe ions are nearly trivalent in all Hpf's, indicating that the amount of magnetite (Fe3O4) is negligible. With increasing filling of Fe ions, the local configurations of Fe3+ ions change from the mixture of the tetrahedral and octahedral symmetries to the octahedral symmetry. These results demonstrate that the biomineralization of the ferritin core changes from maghemite-like (γ-Fe2O3) formation to hematite-like (α-Fe2O3) formation with increasing Fe content.

The interaction of human serum albumin with selected lanthanide and actinide ions: Binding affinities, protein unfolding and conformational changes.

PubMed

Ali, Manjoor; Kumar, Amit; Kumar, Mukesh; Pandey, Badri N

2016-04-01

Human serum albumin (HSA), the most abundant soluble protein in blood plays critical roles in transportation of biomolecules and maintenance of osmotic pressure. In view of increasing applications of lanthanides- and actinides-based materials in nuclear energy, space, industries and medical applications, the risk of exposure with these metal ions is a growing concern for human health. In present study, binding interaction of actinides/lanthanides [thorium: Th(IV), uranium: U(VI), lanthanum: La(III), cerium: Ce(III) and (IV)] with HSA and its structural consequences have been investigated. Ultraviolet-visible, Fourier transform-infrared, Raman, Fluorescence and Circular dichroism spectroscopic techniques were applied to study the site of metal ions interaction, binding affinity determination and the effect of metal ions on protein unfolding and HSA conformation. Results showed that these metal ions interacted with carbonyl (CO..:)/amide(N..-H) groups and induced exposure of aromatic residues of HSA. The fluorescence analysis indicated that the actinide binding altered the microenvironment around Trp214 in the subdomain IIA. Binding affinity of U(VI) to HSA was slightly higher than that of Th(IV). Actinides and Ce(IV) altered the secondary conformation of HSA with a significant decrease of α-helix and an increase of β-sheet, turn and random coil structures, indicating a partial unfolding of HSA. A correlation was observed between metal ion's ability to alter HSA conformation and protein unfolding. Both cationic effects and coordination ability of metal ions seemed to determine the consequences of their interaction with HSA. Present study improves our understanding about the protein interaction of these heavy ions and their impact on its secondary structure. In addition, binding characteristics may have important implications for the development of rational antidote for the medical management of health effects of actinides and lanthanides. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

Rapid on-site/in-situ detection of heavy metal ions in environmental water using a structure-switching DNA optical biosensor.

PubMed

Long, Feng; Zhu, Anna; Shi, Hanchang; Wang, Hongchen; Liu, Jingquan

2013-01-01

A structure-switching DNA optical biosensor for rapid on-site/in situ detection of heavy metal ions is reported. Mercury ions (Hg²⁺), highly toxic and ubiquitous pollutants, were selected as model target. In this system, fluorescence-labeled DNA containing T-T mismatch structure was introduced to bind with DNA probes immobilized onto the sensor surface. In the presence of Hg²⁺, some of the fluorescence-labeled DNAs bind with Hg²⁺ to form T-Hg²⁺-T complexes through the folding of themselves into a hairpin structure and dehybridization from the sensor surface, which leads to decrease in fluorescence signal. The total analysis time for a single sample was less than 10 min with detection limit of 1.2 nM. The rapid on-site/in situ determination of Hg²⁺ was readily performed in natural water. This sensing strategy can be extended in principle to other metal ions by substituting the T-Hg²⁺-T complexes with other specificity structures that selectively bind to other analytes.

Crystal structure of metagenomic β-xylosidase/ α-l-arabinofuranosidase activated by calcium.

PubMed

Matsuzawa, Tomohiko; Kaneko, Satoshi; Kishine, Naomi; Fujimoto, Zui; Yaoi, Katsuro

2017-09-01

The crystal structure of metagenomic β-xylosidase/α-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl β-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl α-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed β-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 Å. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

On the structure and dynamics of the hydrated sulfite ion in aqueous solution--an ab initio QMCF MD simulation and large angle X-ray scattering study.

PubMed

Eklund, Lars; Hofer, Thomas S; Pribil, Andreas B; Rode, Bernd M; Persson, Ingmar

2012-05-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism has been applied in conjunction to experimental large angle X-ray scattering to study the structure and dynamics of the hydrated sulfite ion in aqueous solution. The results show that there is a considerable effect of the lone electron-pair on sulfur concerning structure and dynamics in comparison with the sulfate ion with higher oxidation number and symmetry of the hydration shell. The S-O bond distance in the hydrated sulfite ion has been determined to 1.53(1) Å by both methods. The hydrogen bonds between the three water molecules bound to each sulfite oxygen are only slightly stronger than those in bulk water. The sulfite ion can therefore be regarded as a weak structure maker. The water exchange rate is somewhat slower for the sulfite ion than for the sulfate ion, τ(0.5) = 3.2 and 2.6 ps, respectively. An even more striking observation in the angular radial distribution (ARD) functions is that the for sulfite ion the water exchange takes place in close vicinity of the lone electron-pair directed at its sides, while in principle no water exchange did take place of the water molecules hydrogen bound to sulfite oxygens during the simulation time. This is also confirmed when detailed pathway analysis is conducted. The simulation showed that the water molecules hydrogen bound to the sulfite oxygens can move inside the hydration shell to the area outside the lone electron-pair and there be exchanged. On the other hand, for the hydrated sulfate ion in aqueous solution one can clearly see from the ARD that the distribution of exchange events is symmetrical around the entire hydration sphere.

Evaluation of the effect of roasting process on the energy transition and the crystalline structures of Arabica, Robusta, and Liberica coffee from Jambi Indonesia

NASA Astrophysics Data System (ADS)

Perdana, B. M.; Manihuruk, R.; Ashyar, R.; Heriyanti; Sutrisno

2018-04-01

The effect of the roasting process has been evaluated to determine of the energy transition and the crystalline structure of three types of coffee, Arabica, Robusta, and Liberica coffee both green and roasted coffee with the roasted temperature at 200°C and 230°C. The crystalline structure of the coffee was evaluated with X-ray powder diffraction (XRD). The result exposes that the three types of green coffee showed that an amorphous structure whereas the roasted coffee denotes a crystal structure of sucrose. The varied temperature in the roasting process leads to changes in the crystal structure shown by the peak shift of 2θ for all types of coffee. The added cations, such as Fe2+, Ca2+, and Mg2+ ions on Liberica coffee induced of changes in the crystal structures, which are assigned by the peak shift, that imply of metal ions of the sucrose complexes happened in the solution, except for the addition of Mg2+ ion.

Antioxidant study of quercetin and their metal complex and determination of stability constant by spectrophotometry method.

PubMed

Ravichandran, R; Rajendran, M; Devapiriam, D

2014-03-01

Quercetin found chelate cadmium ions, scavenge free radicals produced by cadmium. Hence new complex, quercetin with cadmium was synthesised, and the synthesised complex structures were determined by UV-vis spectrophotometry, infrared spectroscopy, thermogravimetry and differential thermal analysis techniques (UV-vis, IR, TGA and DTA). The equilibrium stability constants of quercetin-cadmium complex were determined by Job's method. The determined stability constant value of quercetin-cadminum complex at pH 4.4 is 2.27×10(6) and at pH 7.4 is 7.80×10(6). It was found that the quercetin and cadmium ion form 1:1 complex in both pH 4.4 and pH 7.4. The structure of the compounds was elucidated on the basis of obtained results. Furthermore, the antioxidant activity of the free quercetin and quercetin-cadmium complexes were determined by DPPH and ABTS assays. Copyright © 2013 Elsevier Ltd. All rights reserved.

Determination of theoretical capacity of metal ion-doped LiMn 2O 4 as the positive electrode in Li-ion batteries

NASA Astrophysics Data System (ADS)

Todorov, Yanko M.; Hideshima, Yasufumi; Noguchi, Hideyuki; Yoshio, Masaki

The theoretical capacity and cation vacancy of metal ion (M)-doped LiMn 2- xM xO 4 spinel compounds serving as positive electrodes in a 4-V lithium ion batteries are calculated. The capacity depends strongly on the mole fraction of doped metal ion and vacancies. The theoretical capacity increases with increasing oxidation number of the doped metal ion in the 16d site of LiMn 2O 4 at the same doping fraction. The validity of the proposed equation for calculation of the capacity has been initially confirmed using a metal ion with well-known valence, such as the Al ion. The oxidation state of Co, Ni and Cr ions in the spinel structure is found to be trivalent, divalent and trivalent, respectively. Analysis shows that metal ion-doped spinel compounds with low vacancy content promote high capacity.

Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.

PubMed

Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L

2014-01-23

Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. © 2013. Published by Elsevier Ltd. All rights reserved.

Effects of 200 keV Ar-ions irradiation on the structural and optical properties of reactively sputtered CrN films

NASA Astrophysics Data System (ADS)

Novaković, M.; Popović, M.; Zhang, K.; Rakočević, Z.; Bibić, N.

2016-12-01

Modification in structural and optical properties of chromium-nitride (CrN) films induced by argon ion irradiation and thermal annealings were investigated using various experimental techniques. CrN films deposited by d. c. reactive sputtering on Si substrate were implanted with 200 keV argon ions, at fluences of 5-20 × 1015 ions/cm2. As-implanted samples were then annealed in vacuum, for 2 h at 700 °C. Rutherford backscattering spectrometry, X-ray diffraction, cross-sectional (high-resolution) transmission electron microscopy and spectroscopic ellipsometry (SE) measurements were carried out in order to study structural and optical properties of the layers. After irradiation with 200 keV Ar ions a damaged surface layer of nanocrystalline structure was generated, which extended beyond the implantation profile, but left an undamaged bottom zone. Partial loss of columnar structure observed in implanted samples was recovered after annealing at 700 °C and CrN started to decompose to Cr2N. This layer geometry determined from transmission electron microscopy was inferred in the analysis of SE data using the combined Drude and Tauc-Lorentz model, and the variation of the optical bandgap was deduced. The results are discussed on the basis of the changes induced in the microstructure. It was found that the optical properties of the layers are strongly dependent on the defects' concentration of CrN.

Potentiometric and spectroscopic study of the interaction of 3d transition metal ions with inositol hexakisphosphate

NASA Astrophysics Data System (ADS)

Veiga, Nicolás; Macho, Israel; Gómez, Kerman; González, Gabriel; Kremer, Carlos; Torres, Julia

2015-10-01

Among myo-inositol phosphates, the most abundant in nature is the myo-inositol hexakisphosphate, InsP6. Although it is known to be vital to cell functioning, the biochemical research into its metabolism needs chemical and structural analysis of all the protonation, complexation and precipitation processes that it undergoes in the biological media. In view of its high negative charge at physiological level, our group has been leading a thorough research into the InsP6 chemical and structural behavior in the presence of the alkali and alkaline earth metal ions essential for life. The aim of this article is to extend these studies, dealing with the chemical and structural features of the InsP6 interaction with biologically relevant 3d transition metal ions (Fe(II), Fe(III), Mn(II), Co(II), Ni(II), Cu(II) and Zn(II)), in a non-interacting medium and under simulated physiological conditions. The metal-complex stability constants were determined by potentiometry, showing under ligand-excess conditions the formation of mononuclear species in different protonation states. Under metal ion excess, polymetallic species were detected for Fe(II), Fe(III), Zn(II) and Cu(II). Additionally, the 31P NMR and UV-vis spectroscopic studies provided interesting structural aspects of the strong metal ion-InsP6 interaction.

Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution.

PubMed

Harper, Brett; Neumann, Elizabeth K; Stow, Sarah M; May, Jody C; McLean, John A; Solouki, Touradj

2016-10-05

Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values. Copyright © 2016 Elsevier B.V. All rights reserved.

Precise Measurements of the Masses of Cs, Rb and Na A New Route to the Fine Structure Constant

NASA Astrophysics Data System (ADS)

Rainville, Simon; Bradley, Michael P.; Porto, James V.; Thompson, James K.; Pritchard, David E.

2001-01-01

We report new values for the atomic masses of the alkali 133Cs, 87Rb, 85Rb, and 23Na with uncertainties ≤ 0.2 ppb. These results, obtained using Penning trap single ion mass spectrometry, are typically two orders of magnitude more accurate than previously measured values. Combined with values of h/m atom from atom interferometry measurements and accurate wavelength measurements for different atoms, these values will lead to new ppb-level determinations of the molar Planck constant N A h and the fine structure constant α. This route to α is based on simple physics. It can potentially achieve the several ppb level of accuracy needed to test the QED determination of α extracted from measurements of the electron g factor. We also demonstrate an electronic cooling technique that cools our detector and ion below the 4 K ambient temperature. This technique improves by about a factor of three our ability to measure the ion's axial motion.

Ion Acceleration by Multiple Reflections at Martian Bow Shock

NASA Astrophysics Data System (ADS)

Yamauchi, M.; Futaana, Y.; Fedorov, A.; Frahm, R. A.; Dubinin, E.; Lundin, R.; Sauvaud, J.-A.; Winningham, J. D.; Barabash, S.; Holmström, H.

2012-04-01

The ion mass analyzer (IMA) on board Mars Express revealed bundled structures of ions in the energy domain within a distance of a proton gyroradius from the Martian bow shock. Seven prominent traversals during 2005 were examined when the energy-bunched structure was observed together with pick-up ions of exospheric origin, the latter of which is used to determine the local magnetic field orientation from its circular trajectory in velocity space. These seven traversals include different bow shock configurations: (a) quasi-perpendicular shock with its specular direction of the solar wind more perpendicular to the magnetic field (QT), (b) quasi-perpendicular shock with its specular reflection direction of the solar wind more along the magnetic field (FS), and (c) quasi-parallel (QL) shock. In all seven cases, the velocity components of the energy-bunched structure are consistent with multiple specular reflections of the solar wind at the bow shock up to at least two reflections. The accelerated solar wind ions after two specular reflections have large parallel components with respect to the magnetic field for the QL shock whereas the field-aligned speed is much smaller than the perpendicular speed for the QT shock. The reflected ions escape into the solar wind when and only when the reflection is in the field-aligned direction.

Structural characterisation by both positive- and negative-ion electrospray mass spectrometry of partially methyl-esterified oligogalacturonides purified by semi-preparative high-performance anion-exchange chromatography.

PubMed

Quéméner, Bernard; Désiré, Cédric; Lahaye, Marc; Debrauwer, Laurent; Negroni, Luc

2003-01-01

The off-line coupling of high-performance anion-exchange chromatography (HPAEC) to electrospray ionisation/ion trap mass spectrometry (ESI-ITMS) is described. The Dionex carbohydrate membrane desalter (CMD) has been assessed as an on-line chromatographic desalting system to remove the high sodium concentration necessary for the HPAEC separation of partially methyl-esterified oligogalacturonides. The developed HPAEC configuration proved to be suitable for indirect coupling with ESI-ITMS. This paper provides some interesting features of positive- and negative-ion multistage tandem mass spectrometry (MS(n)) analysis of these acidic oligosaccharides. The spectra acquired in both negative- and positive-ion modes show characteristic fragment ions resulting from glycosidic bond and cross-ring cleavages. Some new mass spectrometric fragmentation routes are also described. The positive-ion mode gave more complex spectra but was as informative as the negative-ion mode. ESI-ITMS was revealed to be, as previously reported from direct use on an unseparated enzymatic digest, a powerful sequencing technique for the determination of linkage type and the methyl ester distribution of partially methyl-esterified oligogalacturonides. Moreover, unlike matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF MS), it gives valuable information on the elution behaviour of these oligomers in relation to their structure, namely the HPAEC co-elution of isomeric structures.

g Factor of Light Ions for an Improved Determination of the Fine-Structure Constant.

PubMed

Yerokhin, V A; Berseneva, E; Harman, Z; Tupitsyn, I I; Keitel, C H

2016-03-11

A weighted difference of the g factors of the H- and Li-like ions of the same element is theoretically studied and optimized in order to maximize the cancellation of nuclear effects between the two charge states. We show that this weighted difference and its combination for two different elements can be used to extract a value for the fine-structure constant from near-future bound-electron g factor experiments with an accuracy competitive with or better than the present literature value.

Ion chemistry of 1H-1,2,3-triazole.

PubMed

Ichino, Takatoshi; Andrews, Django H; Rathbone, G Jeffery; Misaizu, Fuminori; Calvi, Ryan M D; Wren, Scott W; Kato, Shuji; Bierbaum, Veronica M; Lineberger, W Carl

2008-01-17

A combination of experimental methods, photoelectron-imaging spectroscopy, flowing afterglow-photoelectron spectroscopy and the flowing afterglow-selected ion flow tube technique, and electronic structure calculations at the B3LYP/6-311++G(d,p) level of density functional theory (DFT) have been employed to study the mechanism of the reaction of the hydroxide ion (HO-) with 1H-1,2,3-triazole. Four different product ion species have been identified experimentally, and the DFT calculations suggest that deprotonation by HO- at all sites of the triazole takes place to yield these products. Deprotonation of 1H-1,2,3-triazole at the N1-H site gives the major product ion, the 1,2,3-triazolide ion. The 335 nm photoelectron-imaging spectrum of the ion has been measured. The electron affinity (EA) of the 1,2,3-triazolyl radical has been determined to be 3.447 +/- 0.004 eV. This EA and the gas-phase acidity of 2H-1,2,3-triazole are combined in a negative ion thermochemical cycle to determine the N-H bond dissociation energy of 2H-1,2,3-triazole to be 112.2 +/- 0.6 kcal mol-1. The 363.8 nm photoelectron spectroscopic measurements have identified the other three product ions. Deprotonation of 1H-1,2,3-triazole at the C5 position initiates fragmentation of the ring structure to yield a minor product, the ketenimine anion. Another minor product, the iminodiazomethyl anion, is generated by deprotonation of 1H-1,2,3-triazole at the C4 position, followed by N1-N2 bond fission. Formation of the other minor product, the 2H-1,2,3-triazol-4-ide ion, can be rationalized by initial deprotonation of 1H-1,2,3-triazole at the N1-H site and subsequent proton exchanges within the ion-molecule complex. The EA of the 2H-1,2,3-triazol-4-yl radical is 1.865 +/- 0.004 eV.

Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming

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

Garimella, Venkata BS; Hamid, Ahmed M.; Deng, Liulin

In this work, we report an approach for spatial and temporal gas phase ion population manipulation, and demonstrate its application for the collapse of the ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventionally traveling wave (TW)-driven region to a region where the TW is intermittently halted or ‘stuttered’. This approach causes the ion packets spanning a number of TW-created traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllablemore » and determined by the ratio of stationary time of the TW in the second region to its moving time. This compression ratio ion mobility programming (CRIMP) approach has been implemented using Structures for Lossless Ion Manipulations (SLIM) in conjunction with MS. CRIMP with the SLIM-MS platform is shown to provide increased peak intensities, reduced peak widths, and improved S/N ratios with MS detection. CRIMP also provides a foundation for extremely long path length and multi-pass IM separations in SLIM providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening due to increasing peak widths.« less

Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula

PubMed Central

Artz, Jacob H.; White, Spencer N.; Zadvornyy, Oleg A.; Fugate, Corey J.; Hicks, Danny; Gauss, George H.; Posewitz, Matthew C.; Boyd, Eric S.; Peters, John W.

2015-01-01

Mercuric ion reductase (MerA), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (Hg2+) and to catalyze their reduction to a more volatile, less toxic elemental form. Here, we present a biochemical and structural characterization of MerA from the thermophilic crenarchaeon Metallosphaera sedula. MerA from M. sedula is a thermostable enzyme, and remains active after extended incubation at 97°C. At 37°C, the NADPH oxidation-linked Hg2+ reduction specific activity was found to be 1.9 μmol/min⋅mg, increasing to 3.1 μmol/min⋅mg at 70°C. M. sedula MerA crystals were obtained and the structure was solved to 1.6 Å, representing the first solved crystal structure of a thermophilic MerA. Comparison of both the crystal structure and amino acid sequence of MerA from M. sedula to mesophillic counterparts provides new insights into the structural determinants that underpin the thermal stability of the enzyme. PMID:26217660

An X-ray absorption spectroscopy study of the inversion degree in zinc ferrite nanocrystals dispersed on a highly porous silica aerogel matrix.

PubMed

Carta, D; Marras, C; Loche, D; Mountjoy, G; Ahmed, S I; Corrias, A

2013-02-07

The structural properties of zinc ferrite nanoparticles with spinel structure dispersed in a highly porous SiO(2) aerogel matrix were compared with a bulk zinc ferrite sample. In particular, the details of the cation distribution between the octahedral (B) and tetrahedral (A) sites of the spinel structure were determined using X-ray absorption spectroscopy. The analysis of both the X-ray absorption near edge structure and the extended X-ray absorption fine structure indicates that the degree of inversion of the zinc ferrite spinel structures varies with particle size. In particular, in the bulk microcrystalline sample, Zn(2+) ions are at the tetrahedral sites and trivalent Fe(3+) ions occupy octahedral sites (normal spinel). When particle size decreases, Zn(2+) ions are transferred to octahedral sites and the degree of inversion is found to increase as the nanoparticle size decreases. This is the first time that a variation of the degree of inversion with particle size is observed in ferrite nanoparticles grown within an aerogel matrix.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Differentiation of the Stereochemistry and Anomeric Configuration for 1-3 Linked Disaccharides Via Tandem Mass Spectrometry and 18O-labeling

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Bendiak, Brad; Xia, Yu

2012-02-01

Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides ( m/z 341) with 1-2, 1-4, and 1-6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1-3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1-3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. 18O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the "sidedness" of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing 18O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1-3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without 18O-labeling of the reducing sugar carbonyl group.

Dynamic hybrid materials for constitutional self-instructed membranes.

PubMed

Cazacu, Adinela; Legrand, Yves-Marie; Pasc, Andreea; Nasr, Gihane; Van der Lee, Arie; Mahon, Eugene; Barboiu, Mihail

2009-05-19

Constitutional self-instructed membranes were developed and used for mimicking the adaptive structural functionality of natural ion-channel systems. These membranes are based on dynamic hybrid materials in which the functional self-organized macrocycles are reversibly connected with the inorganic silica through hydrophobic noncovalent interactions. Supramolecular columnar ion-channel architectures can be generated by reversible confinement within scaffolding hydrophobic silica mesopores. They can be structurally determined by using X-ray diffraction and morphologically tuned by alkali-salts templating. From the conceptual point of view, these membranes express a synergistic adaptive behavior: the simultaneous binding of the fittest cation and its anion would be a case of "homotropic allosteric interactions," because in time it increases the transport efficiency of the pore-contained superstructures by a selective evolving process toward the fittest ion channel. The hybrid membranes presented here represent dynamic constitutional systems evolving over time to form the fittest ion channels from a library of molecular and supramolecular components, or selecting the fittest ion pairs from a mixture of salts demonstrating flexible adaptation.

High Mobility SiGe/Si Transistor Structures on Sapphire Substrates Using Ion Implantation

NASA Technical Reports Server (NTRS)

Alterovitz, S. A.; Mueller, C. H.; Croke, E. T.

2003-01-01

High mobility n-type SiGe/Si transistor structures have been fabricated on sapphire substrates by ion implanting phosphorus ions into strained 100 Angstrom thick silicon channels for the first time. The strained Si channels were sandwiched between Si(sub 0.7)Ge(sub 0.3) layers, which, in turn, were deposited on Si(sub 0.7)Ge(sub 0.3) virtual substrates and graded SiGe buffer layers. After the molecular beam epitaxy (MBE) film growth process was completed, ion thick silicon channels implantation and post-annealing were used to introduce donors. The phosphorous ions were preferentially located in the Si channel at a peak concentration of approximately 1x10(exp 18)/cu cm. Room temperature electron mobilities exceeding 750 sq cm/V-sec at carrier densities of 1x10(exp 12)/sq cm were measured. Electron concentration appears to be the key factor that determines mobility, with the highest mobility observed for electron densities in the 1 - 2x10(exp 12)/sq cm range.

Dynamic filtration and static adsorption of lead ions in aqueous solution by use of blended polysulfone membranes with nano size MCM-41 particles coated by polyaniline.

PubMed

Toosi, Mohammad Reza; Emami, Mohammad Reza Sarmasti; Hajian, Sudeh

2018-05-11

MCM-41 mesopore was prepared by hydrothermal method and used for synthesis of polyaniline/MCM-41 nanocomposite via in situ polymerization. The nanocomposite was blended with polysulfone to prepare mixed matrix membrane in different content of nanocomposite by phase inversion method. Structural and surface properties of the samples were characterized by SEM, XRD, FTIR, AFM, TGA, BET, and zeta potential measurements. Effect of the nanocomposite content on the hydrophilicity, porosity, and permeability of the membrane was determined. Membrane performance was evaluated for removal of lead ions in dynamic filtration and static adsorption. The membranes were found as effective adsorptive filters for removal of lead ions via interactions between active sites of nanocomposite in membrane structure and lead ions during filtration. Results of batch experiments proved adsorptive mechanism of membranes for removal of lead ions with the maximum adsorption capacity of 19.6 mg/g.

The use of Co2+ for crystallization and structure determination, using a conventional mono­chromatic X-ray source, of flax rust avirulence protein

PubMed Central

Gunčar, Gregor; Wang, Ching-I A.; Forwood, Jade K.; Teh, Trazel; Catanzariti, Ann-Maree; Ellis, Jeffrey G.; Dodds, Peter N.; Kobe, Boštjan

2007-01-01

Metal-binding sites are ubiquitous in proteins and can be readily utilized for phasing. It is shown that a protein crystal structure can be solved using single-wavelength anomalous diffraction based on the anomalous signal of a cobalt ion measured on a conventional monochromatic X-ray source. The unique absorption edge of cobalt (1.61 Å) is compatible with the Cu Kα wavelength (1.54 Å) commonly available in macromolecular crystallography laboratories. This approach was applied to the determination of the structure of Melampsora lini avirulence protein AvrL567-A, a protein with a novel fold from the fungal pathogen flax rust that induces plant disease resistance in flax plants. This approach using cobalt ions may be applicable to all cobalt-binding proteins and may be advantageous when synchrotron radiation is not readily available. PMID:17329816

Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

Determining the Effect of Environmental Conditions on Iron Corrosion by Atomic Absorption

ERIC Educational Resources Information Center

Malel, Esteban; Shalev, Deborah E.

2013-01-01

Iron corrosion is a complex process that occurs when iron is exposed to oxygen and humidity and is exacerbated by the presence of chloride ions. The deterioration of iron structures or other components can be costly to society and is usually evaluated by following the properties of the corroding material. Here, the iron ions released into solution…

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD.

PubMed

Thomas, Leonard M; Harper, Angelica R; Miner, Whitney A; Ajufo, Helen O; Branscum, Katie M; Kao, Lydia; Sims, Paul A

2013-07-01

The crystal structure of AdhP, a recombinantly expressed alcohol dehydrogenase from Escherichia coli K-12 (substrain MG1655), was determined to 2.01 Å resolution. The structure, which was solved using molecular replacement, also included the structural and catalytic zinc ions and the cofactor nicotinamide adenine dinucleotide (NAD). The crystals belonged to space group P21, with unit-cell parameters a = 68.18, b = 118.92, c = 97.87 Å, β = 106.41°. The final R factor and Rfree were 0.138 and 0.184, respectively. The structure of the active site of AdhP suggested a number of residues that may participate in a proton relay, and the overall structure of AdhP, including the coordination to structural and active-site zinc ions, is similar to those of other tetrameric alcohol dehydrogenase enzymes.

Effects of Dopant Ionic Radius on Cerium Reduction in Epitaxial Cerium Oxide Thin Films

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

Yang, Nan; Orgiani, Pasquale; Di Bartolomeo, Elisabetta

The role of trivalent rare-earth dopants in ceria epitaxial films on surface ion exchange reactivity and ion conductivity has been systematically studied. Single-crystal epitaxial films with unique crystal orientation and micro-structure nature have allowed us to rule out the influence of structural defects on both transport and surface ion exchange properties. The films conductivities were larger than those reported in literature for both polycrystalline ceramic pellets and crystalline films. An increase in oxygen vacancies and Ce 3+ concentration while decreasing the dopant ionic radius from La 3+ to Yb 3+ was observed, thus explaining the measured increased activation energy andmore » enhanced surface reactivity. The more significant ability of smaller dopant ionic radius in releasing the stress strength induced by the larger Ce 3+ ionic radius allows promoting the formation of oxygen vacancies and Ce 3+, which are two precious species in determining the efficiency of ion transport and surface ion exchange processes. This can open new perspectives in designing ceria-based materials in tailoring functional properties, either ion migration or surface reactivity, by rational cation substitutions.« less

Effects of Dopant Ionic Radius on Cerium Reduction in Epitaxial Cerium Oxide Thin Films

DOE PAGES

Yang, Nan; Orgiani, Pasquale; Di Bartolomeo, Elisabetta; ...

2017-04-17

The role of trivalent rare-earth dopants in ceria epitaxial films on surface ion exchange reactivity and ion conductivity has been systematically studied. Single-crystal epitaxial films with unique crystal orientation and micro-structure nature have allowed us to rule out the influence of structural defects on both transport and surface ion exchange properties. The films conductivities were larger than those reported in literature for both polycrystalline ceramic pellets and crystalline films. An increase in oxygen vacancies and Ce 3+ concentration while decreasing the dopant ionic radius from La 3+ to Yb 3+ was observed, thus explaining the measured increased activation energy andmore » enhanced surface reactivity. The more significant ability of smaller dopant ionic radius in releasing the stress strength induced by the larger Ce 3+ ionic radius allows promoting the formation of oxygen vacancies and Ce 3+, which are two precious species in determining the efficiency of ion transport and surface ion exchange processes. This can open new perspectives in designing ceria-based materials in tailoring functional properties, either ion migration or surface reactivity, by rational cation substitutions.« less

Ion and electron temperatures in the SUMMA mirror device by emission spectroscopy

NASA Technical Reports Server (NTRS)

Patch, R. W.; Voss, D. E.; Reinmann, J. J.; Snyder, A.

1974-01-01

Ion and electron temperatures, and ion drift were measured in a superconducting magnetic mirror apparatus by observing the Doppler-broadened charge-exchange component of the 667.8 and 587.6 nanometer He lines in He plasma, and the H sub alpha and H sub beta lines in H2 plasma. The second moment of the line profiles was used as the parameter for determining ion temperature. Corrections for magnetic splitting, fine structure, monochromator slit function, and variation in charge-exchange cross section with energy are included. Electron temperatures were measured by the line ratio method for the corona model, and correlations of ion and electron temperatures with plasma parameters are presented.

2D polymeric cadmium(II) complexes containing 1,3-imidazolidine-2-thione (Imt) ligand, [Cd(Imt)(H2O)2(SO4)]n and [Cd(Imt)2(N3)2]n

NASA Astrophysics Data System (ADS)

Mahmood, Rashid; Ahmad, Saeed; Fettouhi, Mohammed; Roisnel, Thierry; Gilani, Mazhar Amjad; Mehmood, Kashif; Murtaza, Ghulam; Isab, Anvarhusein A.

2018-03-01

The present study aims at preparing and carrying out the structural investigation of two polymeric cadmium(II) complexes of imidazolidine-2-thione (Imt) based on sulfate or azide ions, [Cd(Imt)(H2O)2(SO4)]n (1) and [Cd(Imt)2(N3)2]n (2). The structures of the complexes were determined by single crystal X-ray analysis. Both compounds, 1 and 2 crystallize in the form of 2D coordination polymers and the cadmium(II) ion is six-coordinate having a distorted octahedral geometry in each compound. In 1, the metal ion is bonded to one sulfur atom of Imt and five oxygen atoms with two from water and three of bridging sulfate ions. In 2, the cadmium coordination sphere is completed by two Imt molecules binding through the sulfur atoms and four nitrogen atoms of bridging azide ions. The crystal structures are stabilized by intra and intermolecular hydrogen bonding interactions. The complexes were also characterized by IR and NMR spectroscopy and the spectroscopic data is consistent with the binding of the ligands.

Ion acceleration by multiple reflections at Martian bow shock

NASA Astrophysics Data System (ADS)

Yamauchi, M.; Futaana, Y.; Fedorov, A.; Frahm, R. A.; Dubinin, E.; Lundin, R.; Sauvaud, J.-A.; Winningham, J. D.; Barabash, S.; Holmström, M.

2012-02-01

The ion mass analyzer (IMA) on board Mars Express revealed bundled structures of ions in the energy domain within a distance of a proton gyroradius from the Martian bow shock. Seven prominent traversals during 2005 were examined when the energy-bunched structure was observed together with pick-up ions of exospheric origin, the latter of which is used to determine the local magnetic field orientation from its circular trajectory in velocity space. These seven traversals include different bow shock configurations: (a) quasi-perpendicular shock with its specular direction of the solar wind more perpendicular to the magnetic field (QT), (b) quasi-perpendicular shock with its specular reflection direction of the solar wind more along the magnetic field (FS), and (c) quasi-parallel (QL) shock. In all seven cases, the velocity components of the energy-bunched structure are consistent with multiple specular reflections of the solar wind at the bow shock up to at least two reflections. The accelerated solar wind ions after two specular reflections have large parallel components with respect to the magnetic field for both QL cases whereas the field-aligned speed is much smaller than the perpendicular speed for all QT cases.

Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c.

PubMed

Kumar, Rajesh; Sharma, Deepak; Jain, Rishu; Kumar, Sandeep; Kumar, Rajesh

2015-12-01

Carbonmonoxycytochrome c refolds to a native-like compact state (NCO-state), where the non-native Fe(2+)-CO interaction persists. Structural and molecular properties extracted from CD, fluorescence and NMR experiments reveal that the NCO-state shows the generic properties of molten globules. Slow thermal-dissociation of CO transforms the NCO-state to native-state (N-state), where the native Fe(2+)-M80 bond recovers. To determine the role of crowding agents and salt ions on the structural-fluctuation of NCO, the kinetic and thermodynamic parameters for CO-dissociation from NCO (NCO→N+CO) were measured at varying concentrations of crowding agents (dextran 70, dextran 40, ficoll 70) and salt ions (anion: ClO4(-), I(-), Br(-), NO3(-), Cl(-); cation: NH4(+), K(+), Na(+)). As [crowding agent] or [ion] is increased, the rate coefficient of CO-dissociation (kdiss) decreases exponentially. Furthermore, the extent of decrease in kdiss is found to be dependent on (i) size, charge density and charge dispersion of the ion, and (ii) size, shape, and viscosity of the crowding agent. Copyright © 2015 Elsevier B.V. All rights reserved.

The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

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

Gopal, B.; Madan, Lalima L.; Betz, Stephen F.

2010-11-10

Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s),more » whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.« less

Isolation and Structural Characterization of Two Very Large, and Largely Empty, Endohedral Fullerenes: Tm@C3v-C94 and Ca@C3v-C94

PubMed Central

Che, Yuliang; Yang, Hua; Wang, Zhimin; Jin, Hongxiao; Lu, Chunxin; Zuo, Tianming; Beavers, Christine M.

2009-01-01

The structures of two newly synthesized endohedral fullerenes - Tm@C3v-C94 and Ca@C3v-C94 - have been determined by single crystal X-ray diffraction on samples co-crystallized with NiII(octaethylporphyrin). Both compounds exhibit the same cage geometry and conform to the isolated pentagon rule (IPR). The metal ions within these rather large cages are localized near one end and along the C3 axis. While the calcium ion is situated over a C-C bond at a 6:6 ring junction, the thulium ion is positioned above a six-membered ring of the fullerene. PMID:19507844

Understanding of the mechanical and structural changes induced by alpha particles and heavy ions in the French simulated nuclear waste glass

NASA Astrophysics Data System (ADS)

Karakurt, G.; Abdelouas, A.; Guin, J.-P.; Nivard, M.; Sauvage, T.; Paris, M.; Bardeau, J.-F.

2016-07-01

Borosilicate glasses are considered for the long-term confinement of high-level nuclear wastes. External irradiations with 1 MeV He+ ions and 7 MeV Au5+ ions were performed to simulate effects produced by alpha particles and by recoil nuclei in the simulated SON68 nuclear waste glass. To better understand the structural modifications, irradiations were also carried out on a 6-oxides borosilicate glass, a simplified version of the SON68 glass (ISG glass). The mechanical and macroscopic properties of the glasses were studied as function of the deposited electronic and nuclear energies. Alpha particles and gold ions induced a volume change up to -0.7% and -2.7%, respectively, depending on the glass composition. Nano-indentations tests were used to determine the mechanical properties of the irradiated glasses. A decrease of about -22% to -38% of the hardness and a decrease of the reduced Young's modulus by -8% were measured after irradiations. The evolution of the glass structure was studied by Raman spectroscopy, and also 11B and 27Al Nuclear Magnetic Resonance (MAS-NMR) on a 20 MeV Kr irradiated ISG glass powder. A decrease of the silica network connectivity after irradiation with alpha particles and gold ions is deduced from the structural changes observations. NMR spectra revealed a partial conversion of BO4 to BO3 units but also a formation of AlO5 and AlO6 species after irradiation with Kr ions. The relationships between the mechanical and structural changes are also discussed.

Di-μ-iodido-bis­{[(R)-(+)-2,2′-bis­(di­phenyl­phosphan­yl)-1,1′-binaphthyl-κ2 P,P′]copper(I)} 0.67-hydrate

PubMed Central

Volz, Daniel; Nieger, Martin; Bräse, Stefan

2012-01-01

The structure of the title compound, [Cu2I2(C44H32P2)2]·0.67H2O, has been determined because of its inter­esting catalytic and optical features. The mol­ecule, which has non-crystallographic C2-symmetry, consists of a core structure of two CuI ions, bridged by two iodide ions. Each CuI ion is also coordinated by one equivalent of the chiral bidentate (R)-BINAP ligand [BINAP = 2,2′-bis­(diphenyl­phosphan­yl)-1,1′-binaphth­yl]. Thus, both cations show a distorted tetra­hedral geometry being surrounded by two I atoms and two P atoms from the (R)-BINAP ligands. The complex consists of isolated butterfly-shaped mol­ecules featuring an angle of 146.11 (2)° between adjacent CuI2 planes. The structure displays intra­molecular C—H⋯I hydrogen bonding and contains disordered water. The absolute configuration of this chiral complex was determined by anomalous dispersion effects. PMID:22589832

Mass spectrometric identification of an azobenzene derivative produced by smectite-catalyzed conversion of 3-amino-4-hydroxyphenylarsonic acid

USGS Publications Warehouse

Wershaw, R. L.; Rutherford, D.W.; Rostad, C.E.; Garbarino, J.R.; Ferrer, I.; Kennedy, K.R.; Momplaisir, G.-M.; Grange, A.

2003-01-01

The compound 3-amino-4-hydroxyphenylarsonic acid (3-amino-HPAA) reacts with smectite to form a soluble azobenzene arsonic acid compound. This reaction is of particular interest because it provides a possible mechanism for the formation of a new type of arsenic compound in natural water systems. 3-Amino-HPAA is a degradation product excreted by chickens that are fed rations amended with roxarsone. Roxarsone is used to control coccidial intestinal parasites in most of the broiler chickens grown in the United States. The structure of the azobenzene arsonic acid compound was first inferred from negative-ion and positive-ion low-resolution mass-spectrometric analyses of the supernatant of the smectite suspension. Elemental composition of the parent ion determined by high-resolution positive-ion mass spectrometric measurements was consistent with the proposed structure of the azobenzene arsonic acid compound. Published by Elsevier Science B.V.

Frictional and structural characterization of ion-nitrided low and high chromium steels

NASA Technical Reports Server (NTRS)

Spalvins, T.

1985-01-01

Low Cr steels AISI 41410, AISI 4340, and high Cr austenitic stainless steels AISI 304, AISI 316 were ion nitrided in a dc glow discharge plasma consisting of a 75 percent H2 - 25 percent N2 mixture. Surface compound layer phases were identified, and compound layer microhardness and diffusion zone microhardness profiles were established. Distinct differences in surface compound layer hardness and diffusion zone profiles were determined between the low and high Cr alloy steels. The high Cr stainless steels after ion nitriding displayed a hard compound layer and an abrupt diffusion zone. The compound layers of the high Cr stainless steels had a columnar structure which accounts for brittleness when layers are exposed to contact stresses. The ion nitrided surfaces of high and low Cr steels displayed a low coefficient of friction with respect to the untreated surfaces when examined in a pin and disk tribotester.

Transmembrane helical interactions in the CFTR channel pore.

PubMed

Das, Jhuma; Aleksandrov, Andrei A; Cui, Liying; He, Lihua; Riordan, John R; Dokholyan, Nikolay V

2017-06-01

Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants. Several CFTR homology models have been developed using bacterial ABC transporters as templates but these have low sequence similarity to CFTR and are not ion channels. Here, we refine an earlier model in an outward (OWF) and develop an inward (IWF) facing model employing an integrated experimental-molecular dynamics simulation (200 ns) approach. Our IWF structure agrees well with a recently solved cryo-EM structure of a CFTR IWF state. We utilize cysteine cross-linking to verify positions and orientations of residues within trans-membrane helices (TMHs) of the OWF conformation and to reconstruct a physiologically relevant pore structure. Comparison of pore profiles of the two conformations reveal a radius sufficient to permit passage of hydrated Cl- ions in the OWF but not the IWF model. To identify structural determinants that distinguish the two conformations and possible rearrangements of TMHs within them responsible for channel gating, we perform cross-linking by bifunctional reagents of multiple predicted pairs of cysteines in TMH 6 and 12 and 6 and 9. To determine whether the effects of cross-linking on gating observed are the result of switching of the channel from open to close state, we also treat the same residue pairs with monofunctional reagents in separate experiments. Both types of reagents prevent ion currents indicating that pore blockage is primarily responsible.

Structural reconstruction of the catalytic center of LiPDF through multiple scattering calculation with MXAN

NASA Astrophysics Data System (ADS)

Guo, Xiaoyun; Chu, Wangsheng; Ma, Sixuan; Gong, Weimin; Benfatto, Maurizio; Hu, Tiandou; Xie, Yaning; Wu, ZiYu

2006-11-01

Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira Interrogans in dry powder, because it is very difficult to obtain the crystallized sample of LiPDF. We performed X-ray absorption near edge structure (XANES) calculation and reconstructed successfully the local geometry of the active center, and the results from calculations show that a water molecule (Wat1) has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly. In addition, the sensitivity of theoretical spectra to the different ligand bodies was evaluated in terms of goodness-of-fit.

Characterising the structural properties of polymer separators for lithium-ion batteries in 3D using phase contrast X-ray microscopy

NASA Astrophysics Data System (ADS)

Finegan, Donal P.; Cooper, Samuel J.; Tjaden, Bernhard; Taiwo, Oluwadamilola O.; Gelb, Jeff; Hinds, Gareth; Brett, Dan J. L.; Shearing, Paul R.

2016-11-01

Separators are an integral component for optimising performance and safety of lithium-ion batteries; therefore, a clear understanding of how their microstructure affects cell performance and safety is crucial. Phase contrast X-ray microscopy is used here to capture the microstructures of commercial monolayer, tri-layer, and ceramic-coated lithium-ion battery polymer separators. Spatial variations in key structural parameters, including porosity, tortuosity factor and pore size distribution, are determined through the application of 3D quantification techniques and stereology. The architectures of individual layers in multi-layer membranes are characterised, revealing anisotropy in porosity, tortuosity factor and mean pore size of the three types of separator. Detailed structural properties of the individual layers of multi-layered membranes are then related with their expected effect on safety and rate capability of cells.

Kinetic theory for the ion humps at the foot of the Earth's bow shock

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

Jovanovic, D.; Krasnoselskikh, V. V.

2009-10-15

The nonlinear kinetic theory is presented for the ion acoustic perturbations at the foot of the Earth's quasiperpendicular bow shock, that is characterized by weakly magnetized electrons and unmagnetized ions. The streaming ions, due to the reflection of the solar wind ions from the shock, provide the free energy source for the linear instability of the acoustic wave. In the fully nonlinear regime, a coherent localized solution is found in the form of a stationary ion hump, which is traveling with the velocity close to the phase velocity of the linear mode. The structure is supported by the nonlinearities comingmore » from the increased population of the resonant beam ions, trapped in the self-consistent potential. As their size in the direction perpendicular to the local magnetic field is somewhat smaller that the electron Larmor radius and much larger that the Debye length, their spatial properties are determined by the effects of the magnetic field on weakly magnetized electrons. These coherent structures provide a theoretical explanation for the bipolar electric pulses, observed upstream of the shock by Polar and Cluster satellite missions.« less

Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel

PubMed Central

Sauguet, Ludovic; Howard, Rebecca J.; Malherbe, Laurie; Lee, Ui S.; Corringer, Pierre-Jean; Harris, R. Adron; Delarue, Marc

2014-01-01

Ethanol alters nerve signalling by interacting with proteins in the central nervous system, particularly pentameric ligand-gated ion channels. A recent series of mutagenesis experiments on Gloeobacter violaceus ligand-gated ion channel, a prokaryotic member of this family, identified a single-site variant that is potentiated by pharmacologically relevant concentrations of ethanol. Here we determine crystal structures of the ethanol-sensitized variant in the absence and presence of ethanol and related modulators, which bind in a transmembrane cavity between channel subunits and may stabilize the open form of the channel. Structural and mutagenesis studies defined overlapping mechanisms of potentiation by alcohols and anaesthetics via the inter-subunit cavity. Furthermore, homology modelling show this cavity to be conserved in human ethanol-sensitive glycine and GABA(A) receptors, and to involve residues previously shown to influence alcohol and anaesthetic action on these proteins. These results suggest a common structural basis for ethanol potentiation of an important class of targets for neurological actions of ethanol. PMID:23591864

Xenon-ion irradiation of Co/Si bilayers: Magnetic and structural properties

NASA Astrophysics Data System (ADS)

Novaković, M.; Popović, M.; Zhang, K.; Čubrović, V.; Bibić, N.; Rakočević, Z.

2018-07-01

Evolution of the structure of cobalt-silicon films during Xe ions irradiation has been studied and the same is correlated with magnetic properties. The polycrystalline cobalt films were deposited by electron beam evaporation method to a thickness of 50 nm on crystalline silicon (c-Si) and silicon with pre-amorphized surface (a-Si). After deposition the layers were irradiated with 400 keV Xe ions to the fluences in the range of 2-30 × 1015 ions/cm2. Structural analysis was done by means of transmission electron microscopy, atomic force microscopy (AFM) and X-ray diffraction (XRD), while the magnetic properties were analyzed by using magneto-optical Kerr effect (MOKE) technique. For the both types of substrate the AFM and XRD results show that after Xe ions irradiation the layers become more rough and the grain size of the crystallites increases; the effects being more evidenced for all fluences for the layers deposited on pre-amorphized Si. The MOKE measurements provided the in-plane azimuthal angular dependence of the hysteresis loops and the change of magnetization with the structural parameters. Although the coercive field is influenced by the surface roughness, in the case of c-Si substrate we found it is much more determined by the size of the crystallites. Additionally, independently on the substrate used the magnetic anisotropy in the Co films disappeared as the Xe ion fluence increased, indicating that the changes of magnetization in both systems occur for similar reasons.

Molecular resolution and fragmentation of fulvic acid by electrospray ionization/multistage tandem mass spectrometry

USGS Publications Warehouse

Leenheer, J.A.; Rostad, C.E.; Gates, Paul M.; Furlong, E.T.; Ferrer, I.

2001-01-01

Molecular weight distributions of fulvic acid from the Suwannee River, Georgia, were investigated by electrospray ionization/quadrupole mass spectrometry (ESI/QMS), and fragmentation pathways of specific fulvic acid masses were investigated by electrospray ionization/ion trap multistage tandem mass spectrometry (ESI/MST/MS). ESI/QMS studies of the free acid form of low molecular weight poly(carboxylic acid) standards in 75% methanol/25% water mobile phase found that negative ion detection gave the optimum generation of parent ions that can be used for molecular weight determinations. However, experiments with poly(acrylic acid) mixtures and specific high molecular weight standards found multiply charged negative ions that gave a low bias to molecular mass distributions. The number of negative charges on a molecule is dependent on the distance between charges. ESI/MST/MS of model compounds found characteristic water loss from alcohol dehydration and anhydride formation, as well as CO2 loss from decarboxylation, and CO loss from ester structures. Application of these fragmentation pathways to specific masses of fulvic acid isolated and fragmented by ESI/MST/MS is indicative of specific structures that can serve as a basis for future structural confirmation after these hypothesized structures are synthesized.

Swift heavy ion irradiation of Pt nanocrystals: II. Structural changes and H desorption

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

Giulian, R.; Araujo, L.L.; Kluth, P.

2014-09-24

The structural properties and H desorption from embedded Pt nanocrystals (NCs) following irradiation with swift heavy ions were investigated as a function of energy and fluence. From x-ray absorption near-edge spectroscopy analysis, Pt-H bonding was identified in NCs annealed in a forming gas (95% N{sub 2} + 5% H{sub 2}) ambient. The H content decreased upon irradiation and the desorption process was NC-size dependent such that larger NCs required a higher fluence to achieve a H-free state. Pt-H bonding and NC dissolution both perturbed the NC structural parameters (coordination number, bond-length and mean-square relative displacement) as determined with extended x-raymore » absorption fine structure measurements.« less

Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

PubMed Central

Copp, William; Denisov, Alexey Y.; Xie, Jingwei; Noronha, Anne M.; Liczner, Christopher; Safaee, Nozhat

2017-01-01

Abstract Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. PMID:28973475

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

PubMed

Copp, William; Denisov, Alexey Y; Xie, Jingwei; Noronha, Anne M; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher J; Gehring, Kalle

2017-09-29

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels

PubMed Central

Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L.

2013-01-01

Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail ‘neck’, are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the ‘outer ion’ site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies shows that this site forms a previously unknown determinant of CaV high affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. PMID:24120938

Zn/Cd/Cu- frameworks constructed by 3,3‧-diphenyldicarboxylate and 1,4-bis(1,2,4-triazol-1-yl)butane: Syntheses, structure, luminescence and luminescence sensing for metal ion in aqueous medium

NASA Astrophysics Data System (ADS)

Zhang, Mei-Na; Fan, Ting-Ting; Wang, Qiu-Shuang; Han, Hong-Liang; Li, Xia

2018-02-01

Three metal-organic frameworks (MOFs), [M(dpdc)(btb)0.5]n (M = Zn 1, Cd 2; dpdc = 3,3‧-diphenyldicarboxylate and btb = 1,4-bis(1,2,4-triazol-1-yl)butane) and [Cu3(dpdc)3(btb)2]n (3) were prepared and structurally determined. 1 is a 2D structure with the topology of {33·47·54·6}, while 2 possesses a 3D framework with the {312·429·514} topology. Complex 3 displays a 3D framework with the topology of {315.435.55}2{36.48.512.6.7}. 1-2 exhibit intense blue luminescence and high stability in water, which make them highly promising candidates as sensors using in aqueous medium. Complex 1 is a potential bi-functional chemosensor for Fe3+ and Al3+ ions while 2 displays a selective sensing ability to Fe3+ ion. Quenching mechanism of Fe3+ on the luminescence of 1-2 is attributed to the charge transfer process LMCT. 1 and 2 have same compositions but have different structures, thermally stabilities and different luminescence sensing functions. The relationship between MOF structures and luminescence sensing toward metal ions are further discussed.

Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

NASA Astrophysics Data System (ADS)

Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

2016-10-01

In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

Versatile, high-sensitivity faraday cup array for ion implanters

DOEpatents

Musket, Ronald G.; Patterson, Robert G.

2003-01-01

An improved Faraday cup array for determining the dose of ions delivered to a substrate during ion implantation and for monitoring the uniformity of the dose delivered to the substrate. The improved Faraday cup array incorporates a variable size ion beam aperture by changing only an insertable plate that defines the aperture without changing the position of the Faraday cups which are positioned for the operation of the largest ion beam aperture. The design enables the dose sensitivity range, typically 10.sup.11 -10.sup.18 ions/cm.sup.2 to be extended to below 10.sup.6 ions/cm.sup.2. The insertable plate/aperture arrangement is structurally simple and enables scaling to aperture areas between <1 cm.sup.2 and >750 cm.sup.2, and enables ultra-high vacuum (UHV) applications by incorporation of UHV-compatible materials.

Photometric study of single-shot energy-dispersive x-ray diffraction at a laser plasma facility

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

Hoidn, O. R.; Seidler, G. T., E-mail: seidler@uw.edu

The low repetition rates and possible shot-to-shot variations in laser-plasma studies place a high value on single-shot diagnostics. For example, white-beam scattering methods based on broadband backlighter x-ray sources are used to determine changes in the structure of laser-shocked crystalline materials by the evolution of coincidences of reciprocal lattice vectors and kinematically allowed momentum transfers. Here, we demonstrate that white-beam techniques can be extended to strongly disordered dense plasma and warm dense matter systems where reciprocal space is only weakly structured and spectroscopic detection is consequently needed to determine the static structure factor and thus, the ion-ion radial distribution function.more » Specifically, we report a photometric study of energy-dispersive x-ray diffraction (ED-XRD) for structural measurement of high energy density systems at large-scale laser facilities such as OMEGA and the National Ignition Facility. We find that structural information can be obtained in single-shot ED-XRD experiments using established backlighter and spectrometer technologies.« less

Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.

PubMed

Ranaivoson, Fanomezana M; Liu, Qun; Martini, Francesca; Bergami, Francesco; von Daake, Sventja; Li, Sheng; Lee, David; Demeler, Borries; Hendrickson, Wayne A; Comoletti, Davide

2015-09-01

Latrophilins (LPHNs) are adhesion-like G-protein-coupled receptors implicated in attention-deficit/hyperactivity disorder. Recently, LPHN3 was found to regulate excitatory synapse number through trans interactions with fibronectin leucine-rich repeat transmembrane 3 (FLRT3). By isothermal titration calorimetry, we determined that only the olfactomedin (OLF) domain of LPHN3 is necessary for FLRT3 association. By multi-crystal native single-wavelength anomalous diffraction phasing, we determined the crystal structure of the OLF domain. This structure is a five-bladed β propeller with a Ca(2+) ion bound in the central pore, which is capped by a mobile loop that allows the ion to exchange with the solvent. The crystal structure of the OLF/FLRT3 complex shows that LPHN3-OLF in the closed state binds with high affinity to the concave face of FLRT3-LRR with a combination of hydrophobic and charged residues. Our study provides structural and functional insights into the molecular mechanism underlying the contribution of LPHN3/FLRT3 to the development of glutamatergic synapses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Differential subcellular distribution of ion channels and the diversity of neuronal function.

PubMed

Nusser, Zoltan

2012-06-01

Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

Communication: Ion mobility of the radical cation dimers: (Naphthalene)2+• and naphthalene+•-benzene: Evidence for stacked sandwich and T-shape structures

NASA Astrophysics Data System (ADS)

Platt, Sean P.; Attah, Isaac K.; Aziz, Saadullah; El-Shall, M. Samy

2015-05-01

Dimer radical cations of aromatic and polycyclic aromatic molecules are good model systems for a fundamental understanding of photoconductivity and ferromagnetism in organic materials which depend on the degree of charge delocalization. The structures of the dimer radical cations are difficult to determine theoretically since the potential energy surface is often very flat with multiple shallow minima representing two major classes of isomers adopting the stacked parallel or the T-shape structure. We present experimental results, based on mass-selected ion mobility measurements, on the gas phase structures of the naphthalene+ṡ ṡ naphthalene homodimer and the naphthalene+ṡ ṡ benzene heterodimer radical cations at different temperatures. Ion mobility studies reveal a persistence of the stacked parallel structure of the naphthalene+ṡ ṡ naphthalene homodimer in the temperature range 230-300 K. On the other hand, the results reveal that the naphthalene+ṡ ṡ benzene heterodimer is able to exhibit both the stacked parallel and T-shape structural isomers depending on the experimental conditions. Exploitation of the unique structural motifs among charged homo- and heteroaromatic-aromatic interactions may lead to new opportunities for molecular design and recognition involving charged aromatic systems.

Structure of the plasmapause from ISEE 1 low-energy ion and plasma wave observations

NASA Technical Reports Server (NTRS)

Nagai, T.; Horwitz, J. L.; Anderson, R. R.; Chappell, C. R.

1985-01-01

Low-energy ion pitch angle distributions are compared with plasma density profiles in the near-earth magnetosphere using ISEE 1 observations. The classical plasmapause determined by the sharp density gradient is not always observed in the dayside region, whereas there almost always exists the ion pitch angle distribution transition from cold, isotropic to warm, bidirectional, field-aligned distributions. In the nightside region the plasmapause density gradient is typically found, and it normally coincides with the ion pitch angle distribution transition. The sunward motion of the plasma is found in the outer part of the 'plasmaspheric' plasma in the dusk bulge region.

Synthesis and application of a nanoporous ion-imprinted polymer for the separation and preconcentration of trace amounts of vanadium from food samples before determination by electrothermal atomic absorption spectrometry.

PubMed

Dadfarnia, Shayessteh; Haji Shabani, Ali Mohammad; Dehghanpoor Frashah, Shahab

2016-04-01

A vanadium ion-imprinted polymer was synthesized in the presence of V(V) and N-benzoyl-N-phenyl hydroxyl amine using 4-vinyl pyridine as the monomer, ethylene glycol dimethacrylate as the cross linker and 2,2'-azobis(isobutyronitrile) as the initiator. The imprinted V(V) ions were completely removed by leaching the polymer with 5 mol/L nitric acid, and the polymer structure was characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. The ion-imprinted polymer was used as the sorbent in the development of the solid-phase extraction method for V(V) prior to its determination by electrothermal atomic absorption spectrometry. The maximum sorption capacity for V(V) ions was 26.7 mg/g at pH 4.0. Under the optimum conditions, for a sample volume of 150.0 mL, an enrichment factor of 289.0 and a detection limit of 6.4 ng/L were obtained. The developed method was successfully applied to the determination of vanadium in parsley, zucchini, black tea, rice, and water samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Split Personality of Glutamate Transporters: A Chloride Channel and a Transporter.

PubMed

Cater, Rosemary J; Ryan, Renae M; Vandenberg, Robert J

2016-03-01

Transporters and ion channels are conventionally categorised into distinct classes of membrane proteins. However, some membrane proteins have a split personality and can function as both transporters and ion channels. The excitatory amino acid transporters (EAATs) in particular, function as both glutamate transporters and chloride (Cl(-)) channels. The EAATs couple the transport of glutamate to the co-transport of three Na(+) ions and one H(+) ion into the cell, and the counter-transport of one K(+) ion out of the cell. The EAAT Cl(-) channel is activated by the binding of glutamate and Na(+), but is thermodynamically uncoupled from glutamate transport and involves molecular determinants distinct from those responsible for glutamate transport. Several crystal structures of an EAAT archaeal homologue, GltPh, at different stages of the transport cycle, alongside numerous functional studies and molecular dynamics simulations, have provided extensive insights into the mechanism of substrate transport via these transporters. However, the molecular determinants involved in Cl(-) permeation, and the mechanism by which this channel is activated are not entirely understood. Here we will discuss what is currently known about the molecular determinants involved in EAAT-mediated Cl(-) permeation and the mechanisms that underlie their split personality.

Structures and physical properties of gaseous metal cationized biological ions.

PubMed

Burt, Michael B; Fridgen, Travis D

2012-01-01

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

The molecular structure of the isopoly complex ion, decavanadate (V10O286-)

USGS Publications Warehouse

Evans, H.T.

1966-01-01

The structure of the decavanadate ion V10O286- has been found by a determination of the crystal structure of K2Zn2V10O28?? 16H2O. The soluble, orange crystals are triclinic with space group P1 and have a unit cell with a = 10.778 A, b = 11.146 A, c = 8.774 A, ?? = 104?? 57???, ?? = 109?? 3???', and ?? = 65?? 0??? (Z = 1). The structure was solved from a three-dimensional Patterson map based on 5143 Weissenberg-film data. The full-matrix, least-squares refinement gave R = 0.094 and ?? for V-O bond lengths of 0.008 A. The unit cell contains one V10O286- unit, two Zn(H2O)62+ groups, two K+ ions, and four additional water molecules. The decavanadate ion is an isolated group of ten condensed VO6 octahedra, six in a rectangular 2 x 3 array sharing edges, and four more, two fitted in above and two below by sharing sloping edges. The structure, which is based on a sodium-chloride-like arrangement of V and O atoms, has a close relationship to other isopoly complex molybdates, niobates, and tantalates. Strong distortions in the VO6 octahedra are analogous to square-pyramid and other special coordination features known in other vanadate structures.

Effects of low and high energy ion bombardment on ETFE polymer

NASA Astrophysics Data System (ADS)

Minamisawa, R. A.; De Almeida, A.; Abidzina, V.; Parada, M. A.; Muntele, I.; Ila, D.

2007-04-01

The polymer ethylenetetrafluoroethylene (ETFE) is used as anti-adherent coatings for food packages and radiation dosimeters. In this work, we compare the damage induced in ETFE bombarded with 100 keV Si ions with that induced by 1 MeV proton bombardment. The damage depends on the type, energy and intensity of the irradiation. Irradiated films were analyzed with optical absorption photospectrometry, Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy to determine the chemical nature of the structural changes caused by ion irradiation. Computer simulations were performed to evaluate the radiation damage.

Electron-ion relaxation in a dense plasma. [supernovae core physics

NASA Technical Reports Server (NTRS)

Littleton, J. E.; Buchler, J.-R.

1974-01-01

The microscopic physics of the thermonuclear runaway in highly degenerate carbon-oxygen cores is investigated to determine if and how a detonation wave is generated. An expression for the electron-ion relaxation time is derived under the assumption of large degeneracy and extreme relativity of the electrons in a two-temperature plasma. Since the nuclear burning time proves to be several orders of magnitude shorter than the relaxation time, it is concluded that in studying the structure of the detonation wave the electrons and ions must be treated as separate fluids.

Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules.

PubMed

Jašíková, Lucie; Roithová, Jana

2018-03-07

Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Redetermination of Na(3)TaF(8).

PubMed

Langer, Vratislav; Smrcok, Lubomír; Boca, Miroslav

2010-09-01

The crystal structure of trisodium octafluoridotantalate, Na(3)TaF(8), has been redetermined using diffractometer data collected at 153 K, resulting in more accurate bond distances and angles than obtained from a previous structure determination based on film data. The structure is built from layers running along [101], which are formed by distorted [TaF(8)] antiprisms and [NaF(6)] rectangular bipyramids sharing edges and corners. The individual layers are separated by eight-coordinated Na ions. Two atoms in the asymmetric unit are in special positions: the Ta atom is on a twofold axis in Wyckoff position 4e and one of the Na ions lies on an inversion centre in Wyckoff site 4d.

The influence of self-assembling supramolecular structures on the passive membrane transport of ion-paired molecules.

PubMed

Benaouda, F; Brown, M B; Shah, B; Martin, G P; Jones, S A

2012-12-15

Weak ion-ion interactions, such as those associated with ion-pair formation, are difficult to isolate and characterise in the liquid state, but they have the potential to alter significantly the physicochemical behaviour of molecules in solution. The aim of this work was to gain a better understanding of how ion-ion interactions influenced passive membrane transport. The test system was composed of propylene (PG) glycol, water and diclofenac diethylamine (DDEA). Infrared spectroscopy was employed to determine the nature of the DDEA ion-pair interactions and the drug-vehicle association. Passive transport was assessed using homogeneous synthetic membranes. Solution-state analysis demonstrated that the ion-pair was unperturbed by vehicle composition changes, but the solvent-DDEA interactions were modified. DDEA-PG/water hydrogen bonding influenced the ion-pair solubility (X(dev)) and the solvent interactions slowed transport rate in PG-rich vehicles (0.84±0.05 μg cm(-2) h(-1), at ln(X(dev))=0.57). In water-rich co-solvents, the presence of strong water structuring facilitated a significant increase (p<0.05) in transmembrane penetration rate (e.g. 4.33±0.92 μg cm(-2) h(-1), at ln(X(dev))=-0.13). The data demonstrates that weak ion-ion interactions can result in the embedding of polar entities within a stable solvent complex and spontaneous supramolecular assembly should be considered when interpreting transmembrane transport processes of ionic molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

Rotational dynamics of polyatomic ions in aqueous solutions: From continuum model to mode-coupling theory, aided by computer simulations.

PubMed

Banerjee, Puja; Bagchi, Biman

2018-06-14

Due to the presence of the rotational mode and the distributed surface charges, the dynamical behavior of polyatomic ions in water differs considerably from those of the monatomic ions. However, their fascinating dynamical properties have drawn scant attention. We carry out theoretical and computational studies of a series of well-known polyatomic ions, namely, sulfate, nitrate, and acetate ions. All three ions exhibit different rotational diffusivity, with that of the nitrate ion being considerably larger than the other two. They all defy the hydrodynamic laws of size dependence. Study of the local structure around the ions provides valuable insight into the origin of these differences. We carry out a detailed study of the rotational diffusion of these ions by extensive computer simulation and by using the theoretical approaches of the dielectric friction developed by Fatuzzo-Mason (FM) and Nee-Zwanzig (NZ), and subsequently generalized by Alavi and Waldeck. A critical element of the FM-NZ theory is the decomposition of the total rotational friction, ζ Rot , into Stokes and dielectric parts. The study shows a dominant role of dielectric friction in the sense that if the ions are made neutral, the nature of diffusion changes and the values become much larger. Our analyses further reveal that the decomposition of total friction into the Stokes and dielectric friction breaks down for sulfate ions but remains semi-quantitatively valid for nitrate and acetate ions. We discuss the relationship between translational and rotational dielectric friction on rigid spherical ions. We develop a self-consistent mode-coupling theory (SC-MCT) formalism that could provide a unified view of rotational friction of polyatomic ions in polar medium. Our SC-MCT shows that the breakdown can be attributed to the change in the microscopic structural features. The mode-coupling theory helps in elucidating the role of coupling between translational and rotational motion of these ions. In fact, these two motions self-consistently determine the value of each other. The reference interaction site model-based MCT suggests an interesting relation between the torque-torque and the force-force time correlation function with the proportionality constant being determined by the geometry and the charge distribution of the polyatomic molecule. We point out several parallelisms between the theories of translational and rotation friction calculations of ions in polar liquids.

Metal Ion-Loaded Nanofibre Matrices for Calcification Inhibition in Polyurethane Implants

PubMed Central

Singh, Charanpreet; Wang, Xungai

2017-01-01

Pathologic calcification leads to structural deterioration of implant materials via stiffening, stress cracking, and other structural disintegration mechanisms, and the effect can be critical for implants intended for long-term or permanent implantation. This study demonstrates the potential of using specific metal ions (MI)s for inhibiting pathological calcification in polyurethane (PU) implants. The hypothesis of using MIs as anti-calcification agents was based on the natural calcium-antagonist role of Mg2+ ions in human body, and the anti-calcification effect of Fe3+ ions in bio-prosthetic heart valves has previously been confirmed. In vitro calcification results indicated that a protective covering mesh of MI-doped PU can prevent calcification by preventing hydroxyapatite crystal growth. However, microstructure and mechanical characterisation revealed oxidative degradation effects from Fe3+ ions on the mechanical properties of the PU matrix. Therefore, from both a mechanical and anti-calcification effects point of view, Mg2+ ions are more promising candidates than Fe3+ ions. The in vitro MI release experiments demonstrated that PU microphase separation and the structural design of PU-MI matrices were important determinants of release kinetics. Increased phase separation in doped PU assisted in consistent long-term release of dissolved MIs from both hard and soft segments of the PU. The use of a composite-sandwich mesh design prevented an initial burst release which improved the late (>20 days) release rate of MIs from the matrix. PMID:28644382

ETD in a traveling wave ion guide at tuned Z-spray ion source conditions allows for site-specific hydrogen/deuterium exchange measurements.

PubMed

Rand, Kasper D; Pringle, Steven D; Morris, Michael; Engen, John R; Brown, Jeffery M

2011-10-01

The recent application of electron transfer dissociation (ETD) to measure the hydrogen exchange of proteins in solution at single-residue resolution (HX-ETD) paves the way for mass spectrometry-based analyses of biomolecular structure at an unprecedented level of detail. The approach requires that activation of polypeptide ions prior to ETD is minimal so as to prevent undesirable gas-phase randomization of the deuterium label from solution (i.e., hydrogen scrambling). Here we explore the use of ETD in a traveling wave ion guide of a quadrupole-time-of-flight (Q-TOF) mass spectrometer with a "Z-spray" type ion source, to measure the deuterium content of individual residues in peptides. We systematically identify key parameters of the Z-spray ion source that contribute to collisional activation and define conditions that allow ETD experiments to be performed in the traveling wave ion guide without gas-phase hydrogen scrambling. We show that ETD and supplemental collisional activation in a subsequent traveling wave ion guide allows for improved extraction of residue-specific deuterium contents in peptides with low charge. Our results demonstrate the feasibility, and illustrate the advantages of performing HX-ETD experiments on a high-resolution Q-TOF instrument equipped with traveling wave ion guides. Determination of parameters of the Z-spray ion source that contribute to ion heating are similarly pertinent to a growing number of MS applications that also rely on an energetically gentle transfer of ions into the gas-phase, such as the analysis of biomolecular structure by native mass spectrometry in combination with gas-phase ion-ion/ion-neutral reactions or ion mobility spectrometry. © American Society for Mass Spectrometry, 2011

Ion mobility and transport properties of bismuth fluoride-containing solid solutions with tysonite-type structure

NASA Astrophysics Data System (ADS)

Kavun, V. Ya.; Uvarov, N. F.; Slobodyuk, A. B.; Merkulov, E. B.; Polyantsev, M. M.

2018-07-01

The ion mobility and conductivity of solid solutions with tysonite-type structure obtained by doping bismuth trifluoride with lead (II) fluoride, and zirconium and bismuth oxides have been studied using 19F NMR, X-ray diffraction analysis, and impedance spectroscopy. The types of ionic motions in the fluoride sublattice of the synthesized solid solutions in the temperature range 150-450 K have been determined and the energy of their activation has been estimated. Due to high ionic conductivity, above 10-2 S/cm at 570 K, these solid solutions can be considered as superionic conductors.

Application of ion mobility-mass spectrometry to microRNA analysis.

PubMed

Takebayashi, Kosuke; Hirose, Kenji; Izumi, Yoshihiro; Bamba, Takeshi; Fukusaki, Eiichiro

2013-03-01

Liquid chromatography/mass spectrometry is widely used for studying sequence determination and modification analysis of small RNAs. However, the efficiency of liquid chromatography-based separation of intact small RNA species is insufficient, since the physiochemical properties among small RNAs are very similar. In this study, we focused on ion mobility-mass spectrometry (IM-MS), which is a gas-phase separation technique coupled with mass spectrometry; we have evaluated the utility of IM-MS for microRNA (miRNA) analysis. A multiply charged deprotonated ion derived from an 18-24-nt-long miRNA was formed by electrospray ionization, and then the time, called the "drift time", taken by each ion to migrate through a buffer gas was measured. Each multivalent ion was temporally separated on the basis of the charge state and structural formation; 3 types of unique mass-mobility correlation patterns (i.e., chainlike-form, hairpin-form, and dimer-form) were present on the two-dimensional mobility-mass spectrum. Moreover, we found that the ion size (sequence length) and the secondary structures of the small RNAs strongly contributed to the IM-MS-based separation, although solvent conditions such as pH had no effect. Therefore, sequence isomers could also be discerned by the selection of each specific charged ion, i.e., the 6(-) charged ion reflected a majority among chainlike-, hairpin-, and other structures. We concluded that the IM-MS provides additional capability for separation; thus, this analytical method will be a powerful tool for comprehensive small RNA analysis. Copyright © 2012. Published by Elsevier B.V.

Structural characterization of agonist and antagonist-bound acetylcholine-binding protein from Aplysia californica.

PubMed

Hansen, Scott B; Sulzenbacher, Gerlind; Huxford, Tom; Marchot, Pascale; Bourne, Yves; Taylor, Palmer

2006-01-01

Nicotinic acetylcholine receptors (nAChRs) are well-characterized allosteric transmembrane proteins involved in the rapid gating of ions elicited by ACh. These receptors belong to the Cys-loop superfamily of ligand-gated ion channels, which also includes GABAA and GABAC, 5-HT3, and glycine receptors. The nAChRs are homo- or heteromeric pentamers of structurally related subunits that encompass an extracellular N-terminal ligand-binding domain, four transmembrane-spanning regions that form the ion channel, and an extended intracellular region between spans 3 and 4. Ligand binding triggers conformational changes that are transmitted to the transmembrane-spanning region, leading to gating and changes in membrane potential. The four transmembrane spans on each of the five subunits create a substantial region of hydrophobicity that precludes facile crystallization of this protein. However the freshwater snail, Lymnaea stagnalis, produces a soluble homopentameric protein, termed the ACh-binding protein (AChBP), which binds ACh (Smit et al., 2001). Its structure was determined recently (Brejc et al., 2001) at high resolution, revealing the structural scaffold for nAChR, and has become a functional and structural surrogate of the nAChR ligand-binding domain. We have characterized an AChBP from Aplysia californica and determined distinct ligand-binding properties when compared to those of L. stagnalis, including ligand specificity for the nAChR alpha7 subtype-specific alpha-conotoxin ImI (Hansen et al., 2004).

Erbium ion implantation into different crystallographic cuts of lithium niobate

NASA Astrophysics Data System (ADS)

Nekvindova, P.; Svecova, B.; Cajzl, J.; Mackova, A.; Malinsky, P.; Oswald, J.; Kolistsch, A.; Spirkova, J.

2012-02-01

Single crystals like lithium niobate are frequently doped with optically active rare-earth or transition-metal ions for a variety of applications in optical devices such as solid-state lasers, amplifiers or sensors. To exploit the potential of the Er:LiNbO 3, one must ensure high intensity of the 1.5 μm luminescence as an inevitable prerequisite. One of the important factors influencing the luminescence properties of a lasing ion is the crystal field of the surrounding, which is inevitably determined by the crystal structure of the pertinent material. From that point it is clear that it cannot be easy to affect the resulting luminescence properties - intensity or position of the luminescence band - without changing the structure of the substrate. However, there is a possibility to utilise a potential of the ion implantation of the lasing ions, optionally accompanied with a sensitising one, that can, besides the doping, also modify the structure of the treated area od the crystal. This effect can be eventually enhanced by a post-implantation annealing that may help to recover the damaged structure and hence to improve the desired luminescence. In this paper we are going to report on our experiments with ion-implantation technique followed with subsequent annealing could be a useful way to influence the crystal field of LN. Optically active Er:LiNbO 3 layers were fabricated by medium energy implantation under various experimental conditions. The Er + ions were implanted at energies of 330 and 500 keV with fluences ranging from 1.0 × 10 15 to 1.0 × 10 16 ion cm -2 into LiNbO 3 single-crystal cuts of both common and special orientations. The as-implanted samples were annealed in air and oxygen at two different temperatures (350 and 600 °C) for 5 h. The depth concentration profiles of the implanted erbium were measured by Rutherford Backscattering Spectroscopy (RBS) using 2 MeV He + ions. The photoluminescence spectra of the samples were measured to determine the emission of 1.5 μm. It has been shown that the projected range Rp of the implanted erbium depends on the beam energies of implantation. The concentration of the implanted erbium corresponds well with the fluence and is similar in all of the cuts of lithium niobate used. What was different were the intensities of the 1.5 μm luminescence bands not only before and after the annealing but also in various types of the crystal cuts. The cut perpendicular to the cleavage plane <10-14> exhibited the best luminescence properties for all of the experimental conditions used. In order to study the damage introduced by the implantation process, the influence of the annealing procedure on the recovery of the host lattice was examined by RBS/channelling. The RBS/channelling method serves to determine the disorder density in the as-implanted surface layer.

Branches of electrostatic turbulence inside solitary plasma structures in the auroral ionosphere

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

Golovchanskaya, Irina V.; Kozelov, Boris V.; Chernyshov, Alexander A.

2014-08-15

The excitation of electrostatic turbulence inside space-observed solitary structures is a central topic of this exposition. Three representative solitary structures observed in the topside auroral ionosphere as large-amplitude nonlinear signatures in the electric field and magnetic-field-aligned current on the transverse scales of ∼10{sup 2}–10{sup 3} m are evaluated by the theories of electrostatic wave generation in inhomogeneous background configurations. A quantitative analysis shows that the structures are, in general, effective in destabilizing the inhomogeneous energy-density-driven (IEDD) waves, as well as of the ion acoustic waves modified by a shear in the parallel drift of ions. It is demonstrated that the dominatingmore » branch of the electrostatic turbulence is determined by the interplay of various driving sources inside a particular solitary structure. The sources do not generally act in unison, so that their common effect may be inhibiting for excitation of electrostatic waves of a certain type. In the presence of large magnetic-field-aligned current, which is not correlated to the inhomogeneous electric field inside the structure, the ion-acoustic branch becomes dominating. In other cases, the IEDD instability is more central.« less

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

2015-12-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

The role of monovalent cations in the ATPase reaction of DNA gyrase.

PubMed

Hearnshaw, Stephen James; Chung, Terence Tsz-Hong; Stevenson, Clare Elizabeth Mary; Maxwell, Anthony; Lawson, David Mark

2015-04-01

Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.

Product control by halide ions of ionic liquids in the ionothermal syntheses of Ni-(H)BTC metal-organic frameworks.

PubMed

Xu, Ling; Yan, Shihai; Choi, Eun-Young; Lee, Jin Yong; Kwon, Young-Uk

2009-06-21

Ni(OAc)(2)-H(3)BTC system in various ionic liquids, [RMI]X (R = ethyl, n-propyl, n-butyl; X = Cl, Br, I), produced five MOFs in two structure types; their relative thermodynamic stability varies with the size of RMI(+), and the X(-) ions govern the kinetic factors so that their combination effects determine the final product.

Ion Binding Energies Determining Functional Transport of ClC Proteins

NASA Astrophysics Data System (ADS)

Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

2014-06-01

The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

Mechanism of Metal Ion Activation of the Diphtheria Toxin Repressor DtxR

NASA Astrophysics Data System (ADS)

D'Aquino, J. Alejandro; Ringe, Dagmar

2006-08-01

The diphtheria toxin repressor, DtxR, is a metal ion-activated transcriptional regulator that has been linked to the virulence of Corynebacterium diphtheriae. Structure determination has shown that there are two metal ion binding sites per repressor monomer, and site-directed mutagenesis has demonstrated that binding site 2 (primary) is essential for recognition of the target DNA repressor, leaving the role of binding site 1 (ancillary) unclear (1 - 3). Calorimetric techniques have demonstrated that while binding site 1 (ancillary) has high affinity for metal ion with a binding constant of 2 × 10-7, binding site 2 (primary) is a low affinity binding site with a binding constant of 6.3 × 10-4. These two binding sites act independently and their contribution can be easily dissected by traditional mutational analysis. Our results clearly demonstrate that binding site 1 (ancillary) is the first one to be occupied during metal ion activation, playing a critical role in stabilization of the repressor. In addition, structural data obtained for the mutants Ni-DtxR(H79A,C102D), reported here and the previously reported DtxR(H79A) (4) has allowed us to propose a mechanism of metal ion activation for DtxR.

Ag implantation-induced modification of Ni-Ti shape memory alloy thin films

NASA Astrophysics Data System (ADS)

Kumar, V.; Singhal, R.; Vishnoi, R.; Banerjee, M. K.; Sharma, M. C.; Asokan, K.; Kumar, M.

2017-08-01

Nanocrystalline thin films of Ni-Ti shape memory alloy are deposited on an Si substrate by the DC-magnetron co-sputtering technique and 120 keV Ag ions are implanted at different fluences. The thickness and composition of the pristine films are determined by Rutherford Backscattering Spectrometry (RBS). X-Ray diffraction (XRD), atomic force microscopy (AFM) and four-point probe resistivity methods have been used to study the structural, morphological and electrical transport properties. XRD analysis has revealed the existence of martensitic and austenite phases in the pristine film and also evidenced the structural changes in Ag-implanted Ni-Ti films at different fluences. AFM studies have revealed that surface roughness and grain size of Ni-Ti films have decreased with an increase in ion fluence. The modifications in the mechanical behaviour of implanted Ni-Ti films w.r.t pristine film is determined by using a Nano-indentation tester at room temperature. Higher hardness and the ratio of higher hardness (H) to elastic modulus (Er) are observed for the film implanted at an optimized fluence of 9 × 1015 ions/cm2. This improvement in mechanical behaviour could be understood in terms of grain refinement and dislocation induced by the Ag ion implantation in the Ni-Ti thin films.

The Influence of High-Power Ion Beams and High-Intensity Short-Pulse Implantation of Ions on the Properties of Ceramic Silicon Carbide

NASA Astrophysics Data System (ADS)

Kabyshev, A. V.; Konusov, F. V.; Pavlov, S. K.; Remnev, G. E.

2016-02-01

The paper is focused on the study of the structural, electrical and optical characteristics of the ceramic silicon carbide before and after irradiation in the regimes of the high-power ion beams (HPIB) and high-intensity short-pulse implantation (HISPI) of carbon ions. The dominant mechanism of transport of charge carriers, their type and the energy spectrum of localized states (LS) of defects determining the properties of SiC were established. Electrical and optical characteristics of ceramic before and after irradiation are determined by the biographical and radiation defects whose band gap (BG) energy levels have a continuous energetic distribution. A dominant p-type activation component of conduction with participation of shallow acceptor levels 0.05-0.16 eV is complemented by hopping mechanism of conduction involving the defects LS with a density of 1.2T017-2.4T018 eV-Am-3 distributed near the Fermi level.The effect of radiation defects with deep levels in the BG on properties change dominates after HISPI. A new material with the changed electronic structure and properties is formed in the near surface layer of SiC after the impact of the HPIB.

Relativistic coupled-cluster-theory analysis of energies, hyperfine-structure constants, and dipole polarizabilities of Cd+

NASA Astrophysics Data System (ADS)

Li, Cheng-Bin; Yu, Yan-Mei; Sahoo, B. K.

2018-02-01

Roles of electron correlation effects in the determination of attachment energies, magnetic-dipole hyperfine-structure constants, and electric-dipole (E 1 ) matrix elements of the low-lying states in the singly charged cadmium ion (Cd+) have been analyzed. We employ the singles and doubles approximated relativistic coupled-cluster (RCC) method to calculate these properties. Intermediate results from the Dirac-Hartree-Fock approximation,the second-order many-body perturbation theory, and considering only the linear terms of the RCC method are given to demonstrate propagation of electron correlation effects in this ion. Contributions from important RCC terms are also given to highlight the importance of various correlation effects in the evaluation of these properties. At the end, we also determine E 1 polarizabilities (αE 1) of the ground and 5 p 2P1 /2 ;3 /2 states of Cd+ in the ab initio approach. We estimate them again by replacing some of the E 1 matrix elements and energies from the measurements to reduce their uncertainties so that they can be used in the high-precision experiments of this ion.

β-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations . Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

NASA Astrophysics Data System (ADS)

Kupka, Teobald

1997-12-01

IR studies were preformed to determine possible transition metal ion binding sites of penicillin. the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M-L complexes with engagement of -COO - and/or -CONH- functional groups. The small shift of νCO towards higher frequencies rules out direct M-L interaction via β-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic β-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and CO stretching frequencies were discussed to determine the β-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.

Physicochemical characterization, and relaxometry studies of micro-graphite oxide, graphene nanoplatelets, and nanoribbons.

PubMed

Paratala, Bhavna S; Jacobson, Barry D; Kanakia, Shruti; Francis, Leonard Deepak; Sitharaman, Balaji

2012-01-01

The chemistry of high-performance magnetic resonance imaging contrast agents remains an active area of research. In this work, we demonstrate that the potassium permanganate-based oxidative chemical procedures used to synthesize graphite oxide or graphene nanoparticles leads to the confinement (intercalation) of trace amounts of Mn(2+) ions between the graphene sheets, and that these manganese intercalated graphitic and graphene structures show disparate structural, chemical and magnetic properties, and high relaxivity (up to 2 order) and distinctly different nuclear magnetic resonance dispersion profiles compared to paramagnetic chelate compounds. The results taken together with other published reports on confinement of paramagnetic metal ions within single-walled carbon nanotubes (a rolled up graphene sheet) show that confinement (encapsulation or intercalation) of paramagnetic metal ions within graphene sheets, and not the size, shape or architecture of the graphitic carbon particles is the key determinant for increasing relaxivity, and thus, identifies nano confinement of paramagnetic ions as novel general strategy to develop paramagnetic metal-ion graphitic-carbon complexes as high relaxivity MRI contrast agents.

Physicochemical Characterization, and Relaxometry Studies of Micro-Graphite Oxide, Graphene Nanoplatelets, and Nanoribbons

PubMed Central

Paratala, Bhavna S.; Jacobson, Barry D.; Kanakia, Shruti; Francis, Leonard Deepak; Sitharaman, Balaji

2012-01-01

The chemistry of high-performance magnetic resonance imaging contrast agents remains an active area of research. In this work, we demonstrate that the potassium permanganate-based oxidative chemical procedures used to synthesize graphite oxide or graphene nanoparticles leads to the confinement (intercalation) of trace amounts of Mn2+ ions between the graphene sheets, and that these manganese intercalated graphitic and graphene structures show disparate structural, chemical and magnetic properties, and high relaxivity (up to 2 order) and distinctly different nuclear magnetic resonance dispersion profiles compared to paramagnetic chelate compounds. The results taken together with other published reports on confinement of paramagnetic metal ions within single-walled carbon nanotubes (a rolled up graphene sheet) show that confinement (encapsulation or intercalation) of paramagnetic metal ions within graphene sheets, and not the size, shape or architecture of the graphitic carbon particles is the key determinant for increasing relaxivity, and thus, identifies nano confinement of paramagnetic ions as novel general strategy to develop paramagnetic metal-ion graphitic-carbon complexes as high relaxivity MRI contrast agents. PMID:22685555

Valence, exchange interaction, and location of Mn ions in polycrystalline M nxG a1 -xN (x ≤0.04 )

NASA Astrophysics Data System (ADS)

Furrer, A.; Krämer, K. W.; Podlesnyak, A.; Pomjakushin, V.; Sheptyakov, D.; Safonova, O. V.

2018-04-01

We present an experimental study for polycrystalline samples of the diluted magnetic semiconductor M nxG a1 -xN (x ≤0.04 ) in order to address some of the existing controversial issues. X-ray and neutron diffraction, x-ray absorption near-edge structure, and electron paramagnetic resonance experiments were used to characterize the structural, electronic, and magnetic properties of the samples, and inelastic neutron scattering was employed to determine the magnetic excitations associated with Mn monomers and dimers. Our main conclusions are as follows: (i) The valence of the Mn ions is 2 + . (ii) The M n2 + ions experience a substantial single-ion axial anisotropy with parameter D =0.027 (3 )meV . (iii) Nearest-neighbor M n2 + ions are coupled antiferromagnetically. The exchange parameter J =-0.140 (7 )meV is independent of the Mn content x ; i.e., there is no evidence for hole-induced modifications of J towards a potentially high Curie temperature postulated in the literature.

Photoluminescence varied by selective excitation in BiGdWO6:Eu3+ phosphor

NASA Astrophysics Data System (ADS)

Pavani, K.; Graça, M. P. F.; Kumar, J. Suresh; Neves, A. J.

2017-12-01

Eu3+ doped bismuth gadolinium tungstate (BGW), a simplest member of Aurivillius family of layered perovskites, was synthesized by solid-state reaction method. Structural characterisation has been performed by X-Ray diffraction (XRD), Raman spectroscopy, Fourier Transform Infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). Band gap of the host matrix has been calculated using reflectance and absorption spectra. Three different mechanisms were found to explain the excitation of Eu3+ ions and are described in detail. Photoluminescence (PL) spectra of the BGW phosphor doped with Eu3+ ions consist of major emission lines associated with 5D0 → 7FJ (J = 0, 1, 2, 3 and 4) of Eu3+ ion. Site selective PL excitation and emission indicates that Eu3+ ions doped in BiGdWO6 are sensitive to the excitation wavelength without change in the structure. Change in emission spectra were observed when the excitation wavelength was changed. Judd-Ofelt (J-O) parameters were determined from the indirect method to interpret the interactions between the host and dopant ions along with detailed analysis of lifetime measurements.

Dynamic hybrid materials for constitutional self-instructed membranes

PubMed Central

Cazacu, Adinela; Legrand, Yves-Marie; Pasc, Andreea; Nasr, Gihane; Van der Lee, Arie; Mahon, Eugene; Barboiu, Mihail

2009-01-01

Constitutional self-instructed membranes were developed and used for mimicking the adaptive structural functionality of natural ion-channel systems. These membranes are based on dynamic hybrid materials in which the functional self-organized macrocycles are reversibly connected with the inorganic silica through hydrophobic noncovalent interactions. Supramolecular columnar ion-channel architectures can be generated by reversible confinement within scaffolding hydrophobic silica mesopores. They can be structurally determined by using X-ray diffraction and morphologically tuned by alkali-salts templating. From the conceptual point of view, these membranes express a synergistic adaptive behavior: the simultaneous binding of the fittest cation and its anion would be a case of “homotropic allosteric interactions,” because in time it increases the transport efficiency of the pore-contained superstructures by a selective evolving process toward the fittest ion channel. The hybrid membranes presented here represent dynamic constitutional systems evolving over time to form the fittest ion channels from a library of molecular and supramolecular components, or selecting the fittest ion pairs from a mixture of salts demonstrating flexible adaptation. PMID:19416909

Ion release and in vitro enamel fluoride uptake associated with pit and fissure sealants containing microencapsulated remineralizing agents.

PubMed

Burbank, Brant D; Cooper, Ryan L; Kava, Alyssa; Hartjes, Jennifer M; McHale, William A; Latta, Mark A; Gross, Stephen M

2017-04-01

To determine if pit-and-fissure sealants with microencapsulated remineralizing agents with sustained release of fluoride, calcium and phosphate ions could promote enamel fluoride uptake by demineralized tooth structure. Sealants that contained 5 w/w% microcapsules with aqueous solutions of 5M Ca(NO3)2 or 0.8M NaF or 6.0M K2HPO4 or a mixture of all three were prepared. Ion release profiles were measured as a function of time. Enamel fluoride uptake by demineralized tooth structure was determined. Sustained release of fluoride, calcium and phosphate ions from a sealant was demonstrated. Fluoride uptake by demineralized enamel was significantly increased compared to a control sealant manufactured without microcapsules (P< 0.01). Bovine enamel that contained 2.2±2.1 µg F/g of enamel prior to exposure to a sealant without microcapsules had 2.3±0.5 after 90 days. Enamel exposed to sealant with 5w/% NaF microcapsules went from 3.5±3.5 µg F/g of enamel prior to exposure to 148±76 after 90 days. Enamel exposed to sealant with 2 w/w% NaF, 2 w/w% Ca(NO3)2 and 1 w/w% K2HPO4 microcapsules went from 1.7±0.7 µg F/g of enamel prior to exposure to 190±137 after 90 days. Sealants with encapsulated remineralizing agents were capable of releasing biologically available fluoride, calcium, and phosphate ions. Incorporation of these microcapsules in pit and fissure sealants is a promising method for remineralization determined by enamel fluoride uptake measurements.

Computer study the oxygen release from Al melts

NASA Astrophysics Data System (ADS)

Y Galashev, Alexander; Rakhmanova, Oksana R.

2018-02-01

The behavior of oxygen ions in the Al melts under action of a constant electric field was studied by molecular dynamics. The rate of O2- ions moving up from the cathode to the melt surface increases. The time of the first ion reaching the surface decreases with increase in O2- concentration. The Al and O2- self-diffusion coefficients increase with increasing concentration of ions in the system. The structure of the neighborhood of oxygen ions was studied in detail by statistical geometry. The distributions of truncated Voronoi polyhedra according to the number of faces and of faces according to the number of sides were determined. Simplified polyhedra were obtained after elimination of small-scale thermal fluctuations from the model. The picture of the oxygen ions final location can vary greatly depending on the boundary conditions and their application sequence.

Metalloprotein Crystallography: More than a Structure.

PubMed

Bowman, Sarah E J; Bridwell-Rabb, Jennifer; Drennan, Catherine L

2016-04-19

Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25-50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of advanced detectors, and the incorporation of spectroscopic equipment at a number of synchrotron beamlines, have yielded exciting developments in metalloprotein structure determination. Here we will present results on the advantageous uses of metals in metalloprotein crystallography, including using metallocofactors to obtain phasing information, using K-edge X-ray absorption spectroscopy to identify metals coordinated in metalloprotein crystals, and using UV-vis spectroscopy on crystals to probe the enzymatic activity of the crystallized protein.

Applicability of LET to single events in microelectronic structures

NASA Astrophysics Data System (ADS)

Xapsos, Michael A.

1992-12-01

LET is often used as a single parameter to determine the energy deposited in a microelectronic structure by a single event. The accuracy of this assumption is examined for ranges of ion energies and volumes of silicon appropriate for modern microelectronics. It is shown to be accurate only under very restricted conditions. Significant differences arise because (1) LET is related to energy lost by the ion, not energy deposited in the volume; and (2) LET is an average value and does not account for statistical variations in energy deposition. Criteria are suggested for determining when factors other than LET should be considered, and new analytical approaches are presented to account for them. One implication of these results is that improvements can be made in space upset rate predictions by incorporating the new methods into currently used codes such as CREME and CRUP.

Propagation and head-on collisions of ion-acoustic solitons in a Thomas-Fermi magnetoplasma: Relativistic degeneracy effects

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

Akbari-Moghanjoughi, M.

Small amplitude propagation and quasielastic head-on collision of ion-acoustic solitary waves (IASWs) are investigated in a degenerate Thomas-Fermi electron-positron-ion magnetized plasma using extended Poincare-Lighthill-Kuo reductive perturbation method for both ultrarelativistic and nonrelativistic electron/positron degeneracy cases. It is observed that both bright- and dark-type solitary shapes can exist in such plasma, depending on two critical values. The shape of ion-acoustic solitary structures as well as sign of their collision phase shifts are both determined by the same critical values. It is further revealed that relativistic degeneracy of electrons/positrons has significant effect on the propagation as well as interaction of IASWs.

Determining the structure of tetragonal Y 2WO 6 and the site occupation of Eu 3+ dopant

NASA Astrophysics Data System (ADS)

Huang, Jinping; Xu, Jun; Li, Hexing; Luo, Hongshan; Yu, Xibin; Li, Yikang

2011-04-01

The compound Y 2WO 6 is prepared by solid state reaction at 750 °C using sodium chloride as mineralizer. Its structure is solved by ab-initio methods from X-ray powder diffraction data. This low temperature phase of yttrium tungstate crystallizes in tetragonal space group P4/ nmm (No. 129), Z=2, a=5.2596(2) Å, c=8.4158(4) Å. The tungsten atoms in the structure adopt an unusual [WO 6] distorted cubes coordination, connecting [YO 6] distorted cubes with oxygen vacancies at the O 2 layers while other yttrium ions Y 2 form [YO 8] cube coordination. Y 3+ ions occupy two crystallographic sites of 2 c ( C4v symmetry) and 2 a ( D2d symmetry) in the Y 2WO 6 host lattice. With Eu 3+ ions doped, the high resolution emission spectrum of Y 2WO 6:Eu 3+ suggests that Eu 3+ partly substituted for Y 3+ in these two sites. The result of the Rietveld structure refinement shows that the Eu 3+ dopants preferentially enter the 2 a site. The uniform cube coordination environment of Eu 3+ ions with the identical eight Eu-O bond lengths is proposed to be responsible for the intense excitation of long wavelength ultraviolet at 466-535 nm.

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex

NASA Astrophysics Data System (ADS)

Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

2016-05-01

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Lutetium(III) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex

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

Sessa, Francesco; D’Angelo, Paola, E-mail: p.dangelo@uniroma1.it; Spezia, Riccardo

2016-05-28

The structure and dynamics of the lutetium(III) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(III) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shellmore » at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(III) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.« less

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex.

PubMed

Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

2016-05-28

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Structure of the TRPV1 ion channel determined by electron cryo-microscopy.

PubMed

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2013-12-05

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.

Insights into the Phosphoryl Transfer Catalyzed by cAMP-Dependent Protein Kinase: An X-ray Crystallographic Study of Complexes with Various Metals and Peptide Substrate SP20

PubMed Central

2013-01-01

X-ray structures of several ternary substrate and product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with different bound metal ions. In the PKAc complexes, Mg2+, Ca2+, Sr2+, and Ba2+ metal ions could bind to the active site and facilitate the phosphoryl transfer reaction. ATP and a substrate peptide (SP20) were modified, and the reaction products ADP and the phosphorylated peptide were found trapped in the enzyme active site. Finally, we determined the structure of a pseudo-Michaelis complex containing Mg2+, nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5′-triphosphate) and SP20. The product structures together with the pseudo-Michaelis complex provide snapshots of different stages of the phosphorylation reaction. Comparison of these structures reveals conformational, coordination, and hydrogen bonding changes that might occur during the reaction and shed new light on its mechanism, roles of metals, and active site residues. PMID:23672593

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

PubMed Central

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2014-01-01

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here, we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane helices S5–S6 and the intervening pore loop, which is flanked by S1–S4 voltage sensor-like domains. TRPV1 has a wide extracellular ‘mouth’ with short selectivity filter. The conserved ‘TRP domain’ interacts with the S4–S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including N-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function. PMID:24305160

Cryogenically cooled octupole ion trap for spectroscopy of biomolecular ions.

PubMed

Boyarkin, Oleg V; Kopysov, Vladimir

2014-03-01

We present here the design of a linear octupole ion trap, suitable for collisional cryogenic cooling and spectroscopy of large ions. The performance of this trap has been assessed using ultraviolet (UV) photofragmentation spectroscopy of protonated dipeptides. At the trap temperature of 6.1 K, the vibrational temperature of the ions reaches 9.1 K, although their estimated translational temperature is ~150 K. This observation suggests that, despite the significant translational heating by radio-frequency electrical field, vibrational cooling of heavy ions in the octupole is at least as efficient as in the 22-pole ion traps previously used in our laboratory. In contrast to the 22-pole traps, excellent radial confinement of ions in the octupole makes it convenient for laser spectroscopy and boosts the dissociation yield of the stored ions to 30%. Overlap of the entire ion cloud by the laser beam in the octupole also allows for efficient UV depletion spectroscopy of ion-He clusters. The measured electronic spectra of the dipeptides and the clusters differ drastically, complicating a use of UV tagging spectroscopy for structural determination of large species.

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

PubMed

Forconi, Marcello; Piccirilli, Joseph A; Herschlag, Daniel

2007-10-01

Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing body of evidence about the importance of peripheral interactions in the precise structural organization of the active site. Here, we use functional studies, in conjunction with published structural information, to determine the effect of perturbation of a peripheral metal ion binding site on catalysis in a well-characterized catalytic RNA, the Tetrahymena thermophila group I ribozyme. We perturbed the metal ion binding site by site-specifically introducing a phosphorothioate substitution in the ribozyme's backbone, replacing the native ligands (the pro-R (P) oxygen atoms at positions 307 and 308) with sulfur atoms. Our data reveal that these perturbations affect several reaction steps, including the chemical step, despite the absence of direct contacts of this metal ion with the atoms involved in the chemical transformation. As structural probing with hydroxyl radicals did not reveal significant change in the three-dimensional structure upon phosphorothioate substitution, the effects are likely transmitted through local, rather subtle conformational rearrangements. Addition of Cd(2+), a thiophilic metal ion, rescues some reaction steps but has deleterious effects on other steps. These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle.

Mechanism of unassisted ion transport across membrane bilayers

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.

1996-01-01

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

A turn-on fluorescent chemosensor for Zn2+ ion: X-ray structure and application in cell imaging study

NASA Astrophysics Data System (ADS)

Ghosh, Koushik; Dey, Sudipto; Halder, Shibashis; Bhattacharjee, Aradhita; Rizzoli, Corrado; Roy, Partha

2016-08-01

The selective fluorescence zinc(II) sensing properties of a Schiff-base compound, 2-methoxy-6-(2-morpholinoethyliminomethyl)phenol (HL) have been explored. The emission intensity of HL in the presence of one equivalent of Zn2+ ion increases by about 25 times. Several other metal ions, except Cd2+ and Ni2+, have not been able to increase the emission intensity of HL significantly. The quantum yield and life-time of HL have also been increased in the presence of Zn2+ ions. The enhancement in fluorescence intensity of HL is mainly due to the restriction of ESIPT, CHEF and PET on complex formation. HL forms a complex with Zn2+ in 1:1 ratio as evidenced by Job's plot analysis and X-ray single crystal structure determination. Some theoretical calculations have been performed to get a better view on the nature of the observed electronic transitions. The probe has been applied for imaging of DLD-1, human colorectal adenocarcinoma cell.

Assessment of metal ion concentration in water with structured feature selection.

PubMed

Naula, Pekka; Airola, Antti; Pihlasalo, Sari; Montoya Perez, Ileana; Salakoski, Tapio; Pahikkala, Tapio

2017-10-01

We propose a cost-effective system for the determination of metal ion concentration in water, addressing a central issue in water resources management. The system combines novel luminometric label array technology with a machine learning algorithm that selects a minimal number of array reagents (modulators) and liquid sample dilutions, such that enable accurate quantification. The algorithm is able to identify the optimal modulators and sample dilutions leading to cost reductions since less manual labour and resources are needed. Inferring the ion detector involves a unique type of a structured feature selection problem, which we formalize in this paper. We propose a novel Cartesian greedy forward feature selection algorithm for solving the problem. The novel algorithm was evaluated in the concentration assessment of five metal ions and the performance was compared to two known feature selection approaches. The results demonstrate that the proposed system can assist in lowering the costs with minimal loss in accuracy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Focused-ion-beam induced interfacial intermixing of magnetic bilayers for nanoscale control of magnetic properties.

PubMed

Burn, D M; Hase, T P A; Atkinson, D

2014-06-11

Modification of the magnetic properties in a thin-film ferromagnetic/non-magnetic bilayer system by low-dose focused ion-beam (FIB) induced intermixing is demonstrated. The highly localized capability of FIB may be used to locally control magnetic behaviour at the nanoscale. The magnetic, electronic and structural properties of NiFe/Au bilayers were investigated as a function of the interfacial structure that was actively modified using focused Ga(+) ion irradiation. Experimental work used MOKE, SQUID, XMCD as well as magnetoresistance measurements to determine the magnetic behavior and grazing incidence x-ray reflectivity to elucidate the interfacial structure. Interfacial intermixing, induced by low-dose irradiation, is shown to lead to complex changes in the magnetic behavior that are associated with monotonic structural evolution of the interface. This behavior may be explained by changes in the local atomic environment within the interface region resulting in a combination of processes including the loss of moment on Ni and Fe, an induced moment on Au and modifications to the spin-orbit coupling between Au and NiFe.

Development of ion implanted gallium arsenide transistors

NASA Technical Reports Server (NTRS)

Hunsperger, R.; Baron, R.

1972-01-01

Techniques were developed for creating bipolar microwave transistors in GaAs by ion implantation doping. The electrical properties of doped layers produced by the implantation of the light ions Be, Mg, and S were studied. Be, Mg, and S are suitable for forming the relatively deep base-collector junction at low ion energies. The electrical characteristics of ion-implanted diodes of both the mesa and planar types were determined. Some n-p-n planar transistor structures were fabricated by implantation of Mg to form the base regions and Si to form the emitters. These devices were found to have reasonably good base-collector and emitter-base junctions, but the current gain beta was small. The low was attributable to radiative recombination in the base region, which was extremely wide.

CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1.

PubMed

Huynh, Kevin W; Jiang, Jiansen; Abuladze, Natalia; Tsirulnikov, Kirill; Kao, Liyo; Shao, Xuesi; Newman, Debra; Azimov, Rustam; Pushkin, Alexander; Zhou, Z Hong; Kurtz, Ira

2018-03-02

Na + -coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na + -coupled acid-base transporters are not available. The sodium-bicarbonate cotransporter NBCe1 functions in multiple organs and its mutations cause blindness, abnormal growth and blood chemistry, migraines, and impaired cognitive function. Here, we have determined the structure of the membrane domain dimer of human NBCe1 at 3.9 Å resolution by cryo electron microscopy. Our atomic model and functional mutagenesis revealed the ion accessibility pathway and the ion coordination site, the latter containing residues involved in human disease-causing mutations. We identified a small number of residues within the ion coordination site whose modification transformed NBCe1 into an anion exchanger. Our data suggest that symporters and exchangers utilize comparable transport machinery and that subtle differences in their substrate-binding regions have very significant effects on their transport mode.

Axisymmetric plasma equilibria in a Kerr metric

NASA Astrophysics Data System (ADS)

Elsässer, Klaus

2001-10-01

Plasma equilibria near a rotating black hole are considered within the multifluid description. An isothermal two-component plasma with electrons and positrons or ions is determined by four structure functions and the boundary conditions. These structure functions are the Bernoulli function and the toroidal canonical momentum per mass for each species. The quasi-neutrality assumption (no charge density, no toroidal current) allows to solve Maxwell's equations analytically for any axisymmetric stationary metric, and to reduce the fluid equations to one single scalar equation for the stream function \\chi of the positrons or ions, respectively. The basic smallness parameter is the ratio of the skin depth of electrons to the scale length of the metric and fluid quantities, and, in the case of an electron-ion plasma, the mass ratio m_e/m_i. The \\chi-equation can be solved by standard methods, and simple solutions for a Kerr geometry are available; they show characteristic flow patterns, depending on the structure functions and the boundary conditions.

Matrix-Assisted Laser Desorption/Ionisation - High-Energy Collision-Induced Dissociation of Steroids: Analysis of Oxysterols in Rat Brain

PubMed Central

Wang, Yuqin; Hornshaw, Martin; Alvelius, Gunvor; Bodin, Karl; Liu, Suya; Sjövall, Jan; Griffiths, William J.

2008-01-01

Neutral steroids have traditionally been analysed by gas chromatography – mass spectrometry (GC-MS) after necessary derivatisation reactions. However, GC-MS is unsuitable for the analysis of many conjugated steroids and those with unsuspected functional groups. Here we describe an alternative analytical method specifically designed for the analysis of oxosteroids and those with a 3β-hydroxy-Δ5 or 5α-hydrogen-3β-hydroxy structure. Steroids were derivatised with Girard P (GP) hydrazine to give GP hydrazones which are charged species and readily analysed by matrix-assisted laser desorption/ionization mass spectrometry. The resulting [M]+ ions were then subjected to high-energy collision-induced dissociation on a tandem time-of-flight instrument. The product-ion spectra give structurally informative fragment-ion patterns. The sensitivity of the analytical method is such that steroids structures can be determined from low pg (low fmole) amounts of sample. The utility of the method has been demonstrated by the analysis of oxysterols extracted from rat brain. PMID:16383324

Proceedings of the Cooling, Condensation, and Storage of Hydrogen Cluster Ions Workshop Held in Menlo Park, California on 8-9 January 1987.

DTIC Science & Technology

1987-12-01

a kind of race track .13 ".is " . oo 0,.& :,- .., V~e v C4 si Fig. 4. Sketch of cylinder rf-type trap for k - 2. Experimental examples of higher order...1983. 31 S 52. Hiraoka, K. and P. Kebarle, "A Determination of the Stabilities of H5*, H7 + , Hg. and H11 + from Measurement of the Gas Phase Ion...73 H. Michels and J. Montgomery -- Electronic Structure and Stability of Small Cation and Anion Hydrogen Cluster Ions

Modeling X-Ray Photoionized Plasmas: Ion Storage Ring Measurements of Low Temperature Dielectronic Recombination Rate Coefficients for L-Shell Iron

NASA Technical Reports Server (NTRS)

Savin, D. W.; Badnell, N. R.; Bartsch, T.; Brandau, C.; Chen, M. H.; Grieser, M.; Gwinner, G.; Hoffknecht, A.; Kahn, S. M.; Linkemann, J.

2000-01-01

Iron L-shell ions (Fe XVII to Fe XXIV) play an important role in determining the line emission and thermal and ionization structures of photoionized gases. Existing uncertainties in the theoretical low temperature dielectronic recombination (DR) rate coefficients for these ions significantly affects our ability to model and interpret observations of photoionized plasmas. To help address this issue, we have initiated a laboratory program to produce reliable low temperature DR rates. Here, we present some of our recent results and discuss some of their astrophysical implications.

Ion current in a magnetic neutral region - Generation of an incipient magnetopause

NASA Technical Reports Server (NTRS)

Whipple, E. C.; Silevitch, M. B.

1982-01-01

The current contributed by ions trapped in the vicinity of a magnetic X line is calculated. The three dimensional configuration of the neutral region is found to be critical in determining the current in that the escape mechanism and trapping times depend on the three-dimensional aspects. A trapping criterion is defined. In the neutral region the ions can gain substantial kinetic energy, and the current will change the X line configuration in such a way that there will be a positive feedback effect, rapidly forming an extended magnetopauselike structure for even very small incident plasma densities.

Background of the completed research; relevances to solar physics

NASA Technical Reports Server (NTRS)

Sellin, I. A.

1973-01-01

Research activities reported consider the atomic structures of highly stripped heavy ions and their modes of formation and destruction in collisions. The lifetime of the metastable 2 3p1 state of the two electron ion F-7(+) was determined by measuring the radiative decay of an excited helium-like fluorine beam, Metastable state quenching measurements were performed on a helium-like ion to obtain the 1 1S0 to 2 3p2 transition probability. Exponential exchange state dependence of X-ray production cross sections was studied in heavy target atoms during collisions with light charged particles.

A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer in Structures for Lossless Ion Manipulations

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

Prabhakaran Nair Syamala Amma, Aneesh; Hamid, Ahme

2018-02-28

Ion mobility (IM) spectrometry is becoming an important approach for analyzing molecular ions in the gas phase with applications that span a multitude of scientific areas. There are a variety of IM-based approaches that utilize either constant or oscillatory electric fields. Here, we explore the combination of constant and oscillatory fields applied in a single device to affect the separation and filtering of ions based on their mobilities. The mobility analyzer allows confining and manipulating ions utilizing a combination of radio frequency (RF), direct current (DC) fields, and traveling waves (TW) in a structures for lossless ion manipulations (SLIM) module.more » In this work, we have investigated theoretically and experimentally the concept for continuous filtering of ions based on their mobilities where ions are mobility separated and selected by a combination of TW and constant fields providing opposing forces on the ions. The SLIM module was composed of two surfaces with mirror-image arrays of electrodes and had two regions where the different TW and opposing DC fields could be applied. By appropriately choosing the DC gradient and TW parameters for the two sections, it is possible to transmit ions of a selected mobility while filtering out others. The filtering capabilities are determined by the applied DC gradient and the TW parameters, such as frequency, amplitude and the TW sequence (i.e., the duty cycle of the traveling wave). The effect of different parameters on the sensitivity and the IM resolution of the device have been investigated.« less

A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations

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

Prabhakaran, Aneesh; Hamid, Ahmed M.; Garimella, Sandilya V. B.

Ion mobility (IM) spectrometry is becoming an important approach for analyzing molecular ions in the gas phase with applications that span a multitude of scientific areas. There are a variety of IM-based approaches that utilize either constant or oscillatory electric fields. Here, we explore the combination of constant and oscillatory fields applied in a single device to affect the separation and filtering of ions based on their mobilities. The mobility analyzer allows confining and manipulating ions utilizing a combination of radio frequency (RF), direct current (DC) fields, and traveling waves (TW) in a structures for lossless ion manipulations (SLIM) module.more » In this work, we have investigated theoretically and experimentally the concept for continuous filtering of ions based on their mobilities where ions are mobility separated and selected by a combination of TW and constant fields providing opposing forces on the ions. The SLIM module was composed of two surfaces with mirror-image arrays of electrodes and had two regions where the different TW and opposing DC fields could be applied. By appropriately choosing the DC gradient and TW parameters for the two sections, it is possible to transmit ions of a selected mobility while filtering out others. The filtering capabilities are determined by the applied DC gradient and the TW parameters, such as frequency, amplitude and the TW sequence (i.e., the duty cycle of the traveling wave). The effect of different parameters on the sensitivity and the IM resolution of the device have been investigated.« less

Structure and properties of solid polymer electrolyte based on chitosan and ZrO{sub 2} nanoparticle for lithium ion battery

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

Sudaryanto,, E-mail: dryanto@batan.go.id; Yulianti, Evi, E-mail: yulianti@batan.go.id; Patimatuzzohrah, E-mail: pzohrah@yahoo.com

In order to develop all solid lithium ion battery, study on the structure and properties of solid polymer electrolytes (SPE) based on chitosan has been done. The SPE were prepared by adding Zirconia (ZrO{sub 2}) nanoparticle and LiClO{sub 4} as lithium salt into the chitosan solution followed by casting method. Effect of the ZrO{sub 2} and salt concentration to the structure and properties of SPE were elaborated using several methods. The structure of the SPE cast film, were characterized mainly by using X-ray diffractometer (XRD). While the electrical properties of SPE were studied by electrochemical impedance spectrometer (EIS) and ionmore » transference number measurement. XRD profiles show that the addition of ZrO{sub 2} and LiClO{sub 4} disrupts the crystality of chitosan. The decrease in sample crytalinity with the nanoparticle and salt addition may increase the molecular mobility result in the increasing sample conductivity and cathionic transference number as determined by EIS and ion transference number measurement, respectively. The highest ionic conductivity (3.58×10{sup −4} S cm{sup −1}) was obtained when 4 wt% of ZrO{sub 2} nanoparticle and 40 wt% of LiClO{sub 4} salt were added to the chitosan. The ion transference number with that composition was 0.55. It is high enough to be used as SPE for lithium ion battery.« less

Synthesis and structural characterization of Co2+ ions doped ZnO nanopowders by solid state reaction through sonication

NASA Astrophysics Data System (ADS)

Babu, B.; Rama Krishna, Ch.; Venkata Reddy, Ch.; Pushpa Manjari, V.; Ravikumar, R. V. S. S. N.

2013-05-01

Cobalt ions doped zinc oxide nanopowder was prepared at room temperature by a novel and simple one step solid-state reaction method through sonication in the presence of a suitable surfactant Sodium Lauryl Sulphate (SLS). The prepared powder was characterized by various spectroscopic techniques. Powder XRD data revealed that the crystal structure belongs to hexagonal and its average crystallite size was evaluated. From optical absorption data, crystal fields (Dq), inter-electronic repulsion parameters (B, C) were evaluated. By correlating optical and EPR spectral data, the site symmetry of Co2+ ion in the host lattice was determined as octahedral. Photoluminescence spectra exhibited the emission bands in ultraviolet and blue regions. The CIE chromaticity coordinates are also evaluated from the emission spectrum. FT-IR spectra showed the characteristic vibrational bands of Znsbnd O.

[2D correlation spectral study of a coordination polymer [Eu(PCPOA)3 (H2O)]n].

PubMed

Sun, Rui-qing; Zhang, Han-hui; Cao, Yan-ning; Chen, Yi-ping; Yang, Qi-yu; Wang, Zhi-yang

2007-05-01

A novel two dimensional coordination polymer [Eu(PCPOA)3 (H2O)], was synthesized under hydrothermal condition. Based on the determination of the structure, the 2D correlation FTIR spectra with the perturbation of magnetism and the 2D correlation fluorescence spectra with the perturbation of temperature were investigated. The energy bonds were calculated using CASTEP Program of Material studio. The Europium ions are nine-coordinated and the ligands adopted two different modes to connect the Eu3+ ions to 2D layer structure. The study of the 2D-FTIR reveals that the carboxylates coordinate with the center ions not only as monodentate, but also as bidentate chelate. The 2D fluorescence spectra indicates that the transition of (5)D0-->(7)F2 is influenced intensively by the perturbation of temperature.

One-Step Fast-Synthesized Foamlike Amorphous Co(OH)2 Flexible Film on Ti Foil by Plasma-Assisted Electrolytic Deposition as a Binder-Free Anode of a High-Capacity Lithium-Ion Battery.

PubMed

Li, Tao; Nie, Xueyuan

2018-05-23

This research prepared an amorphous Co(OH) 2 flexible film on Ti foil using plasma-assisted electrolytic deposition within 3.5 min. Amorphous Co(OH) 2 structure was determined by X-ray diffraction and X-ray photoelectron spectroscopy. Its areal capacity testing as the binder and adhesive-free anode of a lithium-ion battery shows that the cycling capacity can reach 2000 μAh/cm 2 and remain at 930 μAh/cm 2 after 50 charge-discharge cycles, which benefits from the emerging Co(OH) 2 active material and amorphous foamlike structure. The research introduced a new method to synthesize amorphous Co(OH) 2 as the anode in a fast-manufactured low-cost lithium-ion battery.

Hydration energies and structures of alkaline earth metal ions, M2+(H2O)n, n = 5-7, M = Mg, Ca, Sr, and Ba.

PubMed

Rodriguez-Cruz, S E; Jockusch, R A; Williams, E R

1999-09-29

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M(2+)(H(2)O)(n) (M = Mg, Ca, and Sr for n = 5-7, and M = Ba for n = 4-7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (E(o)) are determined. These reactions should have a negligible reverse activation barrier; therefore, E(o) values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca(2+), Sr(2+), and Ba(2+) are consistent with structures in which all the water molecules are located in the first solvation shell.

The study on the electrical resistivity of Cu/V multilayer films subjected to helium (He) ion irradiation

NASA Astrophysics Data System (ADS)

Wang, P. P.; Xu, C.; Fu, E. G.; Du, J. L.; Gao, Y.; Wang, X. J.; Qiu, Y. H.

2018-05-01

Sputtering-deposited Cu/V multilayer films with the individual layer thickness varying from 2.5 nm to 100 nm were irradiated by 1 MeV helium (He) ion at the fluence of 6 ×1016 ions ·cm-2 at room temperature. The resistivity of Cu/V multilayer films after ion irradiation was evaluated as a function of individual layer thickness at 300 K and compared with their resistivity before ion irradiation. The results show that the resistivity change before and after ion irradiation is largely determined by the interface structure, grain boundary and radiation induced defects. A model amended based on the model used in describing the resistivity of as-deposited Cu/V multilayer films was proposed to describe the resistivity of ion irradiated Cu/V multilayer films by considering the point defects induced by ion irradiation, the effect of interface absorption on defects and the effect of interface microstructure in the multilayer films.

Diffusion vs. concentration of chloride ions in concrete.

DOT National Transportation Integrated Search

2014-06-01

This investigation was performed to gain insight and assist in determining the long-term durability of : reinforced concrete structures where the external chloride concentrations are different than those typically : observed at the permanently immers...

Fast atom bombardment tandem mass spectrometry of carotenoids

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

van Breeman, R.B.; Schmitz, H.H.; Schwartz, S.J.

Positive ion fast atom bombardment (FAB) tandem mass spectrometry (MS-MS) using a double-focusing mass spectrometer with linked scanning at constant B/E and high-energy collisionally activated dissociation (CAD) was used to differentiate 17 different cartenoids, including {beta}-apo-8{prime}- carotenal, astaxanthin, {alpha}-carotene, {beta}-carotene, {gamma}-carotene, {zeta}-carotene, canthaxanthin, {beta}-cryptoxanthin, isozeaxanthin bis (pelargonate), neoxanthin, neurosporene, nonaprene, lutein, lycopene, phytoene, phytofluene, and zeaxanthin. The carotenoids were either synthetic or isolated from plant tissues. The use of FAB ionization minimized degradation or rearrangement of the carotenoid structures due to the inherent thermal instability generally ascribed to these compounds. Instead of protonated molecules, both polar xanthophylls and nonpolar carotenesmore » formed molecular ions, M{sup {center_dot}+}, during FAB ionization. Following collisionally activated dissociation, fragment ions of selected molecular ion precursors showed structural features indicative of the presence of hydroxyl groups, ring systems, ester groups, and aldehyde groups and the extent of aliphatic polyene conjugation. The fragmentation patterns observed in the mass spectra herein may be used as a reference for the structural determination of carotenoids isolated from plant and animal tissues. 18 refs., 4 figs.« less

Theory of the n = 2 levels in muonic helium-3 ions

NASA Astrophysics Data System (ADS)

Franke, Beatrice; Krauth, Julian J.; Antognini, Aldo; Diepold, Marc; Kottmann, Franz; Pohl, Randolf

2017-12-01

The present knowledge of Lamb shift, fine-, and hyperfine structure of the 2S and 2P states in muonic helium-3 ions is reviewed in anticipation of the results of a first measurement of several 2S → 2P transition frequencies in the muonic helium-3 ion, μ3He+. This ion is the bound state of a single negative muon μ- and a bare helium-3 nucleus (helion), 3He++. A term-by-term comparison of all available sources, including new, updated, and so far unpublished calculations, reveals reliable values and uncertainties of the QED and nuclear structure-dependent contributions to the Lamb shift and the hyperfine splitting. These values are essential for the determination of the helion rms charge radius and the nuclear structure effects to the hyperfine splitting in μ3He+. With this review we continue our series of theory summaries in light muonic atoms [see A. Antognini et al., Ann. Phys. 331, 127 (2013); J.J. Krauth et al., Ann. Phys. 366, 168 (2016); and M. Diepold et al. arXiv:1606.05231 (2016)].

Theoretical prediction of silicene as a new candidate for the anode of lithium-ion batteries.

PubMed

Seyed-Talebi, Seyedeh Mozhgan; Kazeminezhad, Iraj; Beheshtian, Javad

2015-11-28

Using density functional theory calculations, we determine the band structure and DOS of graphene and silicene supercell models. We also study the adsorption mechanism of Li metal atoms and Li-ions onto free-standing silicene (buckled, θ = 101.7°) and compare the results with those of graphene. In contrast to graphene, interactions between Li metal atoms and Li-ions with the silicene surface are quite strong due to its highly reactive buckled hexagonal structure. As a consequence of structural properties the adsorption height, the most stable adsorption site and energy barrier against Li diffusion are also discussed here to outline the prospects of using silicene in electronic devices such as Li ion batteries (LiBs), hydrogen storage and molecular machines. However, in most LiBs, graphene layers are used as anode electrodes. Here, it is shown that graphene has very limited Li storage capacity and low surface area than silicene. As our models are in good agreement with previous predictions, this finding presents a possible avenue for creating better anode materials that can replace graphene for higher capacity and better cycling performance of LiBs.

Lunar Neutral Exposphere Properties from Pickup Ion Analysis

NASA Technical Reports Server (NTRS)

Hartle, R. E.; Sarantos, M.; Killen, R.; Sittler, E. C. Jr.; Halekas, J.; Yokota, S.; Saito, Y.

2009-01-01

Composition and structure of neutral constituents in the lunar exosphere can be determined through measurements of phase space distributions of pickup ions borne from the exosphere [1]. An essential point made in an early study [ 1 ] and inferred by recent pickup ion measurements [2, 3] is that much lower neutral exosphere densities can be derived from ion mass spectrometer measurements of pickup ions than can be determined by conventional neutral mass spectrometers or remote sensing instruments. One approach for deriving properties of neutral exospheric source gasses is to first compare observed ion spectra with pickup ion model phase space distributions. Neutral exosphere properties are then inferred by adjusting exosphere model parameters to obtain the best fit between the resulting model pickup ion distributions and the observed ion spectra. Adopting this path, we obtain ion distributions from a new general pickup ion model, an extension of a simpler analytic description obtained from the Vlasov equation with an ion source [4]. In turn, the ion source is formed from a three-dimensional exospheric density distribution, which can range from the classical Chamberlain type distribution to one with variable exobase temperatures and nonthermal constituents as well as those empirically derived. The initial stage of this approach uses the Moon's known neutral He and Na exospheres to deriv e He+ and Na+ pickup ion exospheres, including their phase space distributions, densities and fluxes. The neutral exospheres used are those based on existing models and remote sensing studies. As mentioned, future ion measurements can be used to constrain the pickup ion model and subsequently improve the neutral exosphere descriptions. The pickup ion model is also used to estimate the exosphere sources of recently observed pickup ions on KAGUYA [3]. Future missions carrying ion spectrometers (e.g., ARTEMIS) will be able to study the lunar neutral exosphere with great sensitivity, yielding the necessary ion velocity spectra needed to further analysis of parent neutral exosphere properties.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

NASA Astrophysics Data System (ADS)

Di Giovanni, James P.; Barkley, Robert M.; Jones, David N. M.; Hankin, Joseph A.; Murphy, Robert C.

2018-04-01

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. [Figure not available: see fulltext.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

PubMed

Di Giovanni, James P; Barkley, Robert M; Jones, David N M; Hankin, Joseph A; Murphy, Robert C

2018-04-23

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H] - ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H] - and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H 2 O-CO 2 ] - and [M-H-H 2 O] - displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H 2 O] - ion from LTB 4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H 2 O] - product ions from LTB 4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

Accurate high-throughput structure mapping and prediction with transition metal ion FRET

PubMed Central

Yu, Xiaozhen; Wu, Xiongwu; Bermejo, Guillermo A.; Brooks, Bernard R.; Taraska, Justin W.

2013-01-01

Mapping the landscape of a protein’s conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein Maltose Binding Protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells. PMID:23273426

Relationships between structure, ionization profile and sensitivity of exogenous anabolic steroids under electrospray ionization and analysis in human urine using liquid chromatography-tandem mass spectrometry.

PubMed

Cha, Eunju; Kim, Sohee; Kim, Hee Won; Lee, Kang Mi; Kim, Ho Jun; Kwon, Oh-Seung; Lee, Jaeick

2016-04-01

The relationships between the ionization profile, sensitivity, and structures of 64 exogenous anabolic steroids (groups I-IV) was investigated under electrospray ionization (ESI) conditions. The target analytes were ionized as [M + H](+) or [M + H-nH2 O](+) in the positive mode, and these ions were used as precursor ions for selected reaction monitoring analysis. The collision energy and Q3 ions were optimized based on the sensitivity and selectivity. The limits of detection (LODs) were 0.05-20 ng/mL for the 64 steroids. The LODs for 38 compounds, 14 compounds and 12 compounds were in the range of 0.05-1, 2-5 and 10-20 ng/mL, respectively. Steroids including the conjugated keto-functional group at C3 showed good proton affinity and stability, and generated the [M + H](+) ion as the most abundant precursor ion. In addition, the LODs of steroids using the [M + H](+) ion as the precursor ion were mostly distributed at low concentrations. In contrast, steroids containing conjugated/unconjugated hydroxyl functional groups at C3 generated [M + H - H2 O](+) or [M + H - 2H2 O](+) ions, and these steroids showed relatively high LODs owing to poor stability and multiple ion formation. An LC-MS/MS method based on the present ionization profile was developed and validated for the determination of 78 steroids (groups I-V) in human urine. Copyright © 2015 John Wiley & Sons, Ltd.

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

NASA Astrophysics Data System (ADS)

Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Donohoe, Gregory C.; Valentine, Stephen J.

2016-03-01

Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H]2- ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H]3- ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H]2- ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H]3- ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

Multi-instrumental Analysis of Tissues of Sunflower Plants Treated with Silver(I) Ions – Plants as Bioindicators of Environmental Pollution

PubMed Central

Krizkova, Sona; Ryant, Pavel; Krystofova, Olga; Adam, Vojtech; Galiova, Michaela; Beklova, Miroslava; Babula, Petr; Kaiser, Jozef; Novotny, Karel; Novotny, Jan; Liska, Miroslav; Malina, Radomir; Zehnalek, Josef; Hubalek, Jaromir; Havel, Ladislav; Kizek, Rene

2008-01-01

The aim of this work is to investigate sunflower plants response on stress induced by silver(I) ions. The sunflower plants were exposed to silver(I) ions (0, 0.1, 0.5, and 1 mM) for 96 h. Primarily we aimed our attention to observation of basic physiological parameters. We found that the treated plants embodied growth depression, coloured changes and lack root hairs. Using of autofluorescence of anatomical structures, such as lignified cell walls, it was possible to determine the changes of important shoot and root structures, mainly vascular bungles and development of secondary thickening. The differences in vascular bundles organisation, parenchymatic pith development in the root centre and the reduction of phloem part of vascular bundles were well observable. Moreover with increasing silver(I) ions concentration the vitality of rhizodermal cells declined; rhizodermal cells early necrosed and were replaced by the cells of exodermis. Further we employed laser induced breakdown spectroscopy for determination of spatial distribution of silver(I) ions in tissues of the treated plants. The Ag is accumulated mainly in near-root part of the sample. Moreover basic biochemical indicators of environmental stress were investigated. The total content of proteins expressively decreased with increasing silver(I) ions dose and the time of the treatment. As we compare the results obtained by protein analysis – the total protein contents in shoot as well as root parts – we can assume on the transport of the proteins from the roots to shoots. This phenomenon can be related with the cascade of processes connecting with photosynthesis. The second biochemical parameter, which we investigated, was urease activity. If we compared the activity in treated plants with control, we found out that presence of silver(I) ions markedly enhanced the activity of urease at all applied doses of this toxic metal. Finally we studied the effect of silver(I) ions on activity of urease in in vitro conditions. PMID:27879716

Alignment and Imaging of the CS2 Dimer Inside Helium Nanodroplets

NASA Astrophysics Data System (ADS)

Pickering, James D.; Shepperson, Benjamin; Hübschmann, Bjarke A. K.; Thorning, Frederik; Stapelfeldt, Henrik

2018-03-01

The carbon disulphide (CS2) dimer is formed inside He nanodroplets and identified using fs laser-induced Coulomb explosion, by observing the CS2+ ion recoil velocity. It is then shown that a 160 ps moderately intense laser pulse can align the dimer in advantageous spatial orientations which allow us to determine the cross-shaped structure of the dimer by analysis of the correlations between the emission angles of the nascent CS2+ and S+ ions, following the explosion process. Our method will enable fs time-resolved structural imaging of weakly bound molecular complexes during conformational isomerization, including formation of exciplexes.

The Minimum M3-M4 Loop Length of Neurotransmitter-activated Pentameric Receptors Is Critical for the Structural Integrity of Cytoplasmic Portals*

PubMed Central

Baptista-Hon, Daniel T.; Deeb, Tarek Z.; Lambert, Jeremy J.; Peters, John A.; Hales, Tim G.

2013-01-01

The 5-HT3A receptor homology model, based on the partial structure of the nicotinic acetylcholine receptor from Torpedo marmorata, reveals an asymmetric ion channel with five portals framed by adjacent helical amphipathic (HA) stretches within the 114-residue loop between the M3 and M4 membrane-spanning domains. The positive charge of Arg-436, located within the HA stretch, is a rate-limiting determinant of single channel conductance (γ). Further analysis reveals that positive charge and volume of residue 436 are determinants of 5-HT3A receptor inward rectification, exposing an additional role for portals. A structurally unresolved stretch of 85 residues constitutes the bulk of the M3-M4 loop, leaving a >45-Å gap in the model between M3 and the HA stretch. There are no additional structural data for this loop, which is vestigial in bacterial pentameric ligand-gated ion channels and was largely removed for crystallization of the Caenorhabditis elegans glutamate-activated pentameric ligand-gated ion channels. We created 5-HT3A subunit loop truncation mutants, in which sequences framing the putative portals were retained, to determine the minimum number of residues required to maintain their functional integrity. Truncation to between 90 and 75 amino acids produced 5-HT3A receptors with unaltered rectification. Truncation to 70 residues abolished rectification and increased γ. These findings reveal a critical M3-M4 loop length required for functions attributable to cytoplasmic portals. Examination of all 44 subunits of the human neurotransmitter-activated Cys-loop receptors reveals that, despite considerable variability in their sequences and lengths, all M3-M4 loops exceed 70 residues, suggesting a fundamental requirement for portal integrity. PMID:23740249

Cryogenically cooled octupole ion trap for spectroscopy of biomolecular ions

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

Boyarkin, Oleg V., E-mail: oleg.boiarkin@epfl.ch; Kopysov, Vladimir

2014-03-15

We present here the design of a linear octupole ion trap, suitable for collisional cryogenic cooling and spectroscopy of large ions. The performance of this trap has been assessed using ultraviolet (UV) photofragmentation spectroscopy of protonated dipeptides. At the trap temperature of 6.1 K, the vibrational temperature of the ions reaches 9.1 K, although their estimated translational temperature is ∼150 K. This observation suggests that, despite the significant translational heating by radio-frequency electrical field, vibrational cooling of heavy ions in the octupole is at least as efficient as in the 22-pole ion traps previously used in our laboratory. In contrastmore » to the 22-pole traps, excellent radial confinement of ions in the octupole makes it convenient for laser spectroscopy and boosts the dissociation yield of the stored ions to 30%. Overlap of the entire ion cloud by the laser beam in the octupole also allows for efficient UV depletion spectroscopy of ion–He clusters. The measured electronic spectra of the dipeptides and the clusters differ drastically, complicating a use of UV tagging spectroscopy for structural determination of large species.« less

Single-ion conducting diblock terpolymers for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Morris, Melody; Epps, Thomas H., III

Block polymer (BP) electrolytes provide an attractive route to overcome the competing constraints of high conductivity and mechanical/thermal stability in lithium-ion batteries through nanoscale self-assembly. For example, macromolecules can be engineered such that one domain conducts lithium ions and the other prevents lithium dendrite formation. Herein, we report on the behavior of a single-ion conducting BP electrolyte that was designed to facilitate the transport of lithium ions. These polymers differ from traditional salt-doped BP electrolytes, which require the addition of a lithium salt to bestow conductivity and typically suffer from substantial counterion motion that reduces efficiency. New single-ion BPs were synthesized, and the nanoscale morphologies were determined using small angle X-ray scattering and transmission electron microscopy. Electrolyte performance was measured using AC impedance spectroscopy and DC polarization, and the results were correlated to nanoscale morphology and ion content. Enhanced physical understanding of single-ion BPs was gained by connecting the ion mobility to the chemistry, chain structure, and ion content of the single-ion BP. These studies can be applied to other charged-neutral block polymers to elucidate the effects of ion content on self-assembly and macroscopic properties.

Structural, electrical properties and dielectric relaxations in Na+-ion-conducting solid polymer electrolyte.

PubMed

Arya, Anil; Sharma, A L

2018-04-25

In this paper, we have studied the structural, microstructural, electrical, dielectric properties and ion dynamics of a sodium-ion-conducting solid polymer electrolyte film comprising PEO 8 -NaPF 6 +  x wt. % succinonitrile. The structural and surface morphology properties have been investigated, respectively using x-ray diffraction and field emission scanning electron microscopy. The complex formation was examined using Fourier transform infrared spectroscopy, and the fraction of free anions/ion pairs obtained via deconvolution. The complex dielectric permittivity and loss tangent has been analyzed across the whole frequency window, and enables us to estimate the DC conductivity, dielectric strength, double layer capacitance and relaxation time. The presence of relaxing dipoles was determined by the addition of succinonitrile (wt./wt.) and the peak shift towards high frequency indicates the decrease of relaxation time. Further, relations among various relaxation times ([Formula: see text]) have been elucidated. The complex conductivity has been examined across the whole frequency window; it obeys the Universal Power Law, and displays strong dependency on succinonitrile content. The sigma representation ([Formula: see text]) was introduced in order to explore the ion dynamics by highlighting the dispersion region in the Cole-Cole plot ([Formula: see text]) in the lower frequency window; increase in the semicircle radius indicates a decrease of relaxation time. This observation is accompanied by enhancement in ionic conductivity and faster ion transport. A convincing, logical scheme to justify the experimental data has been proposed.

Photoionization and ionic dissociation of the C3 H3 NS molecule induced by soft X-ray near the C1s edge.

PubMed

Lago, A F; Januário, R D; Cavasso Filho, R L; Simon, M; Dávalos, J Z

2017-10-01

Time of flight mass spectrometry, electron-ion coincidence, and ion yield spectroscopy were employed to investigate for the first time the thiazole (C 3 H 3 NS) molecule in the gas phase excited by synchrotron radiation in the soft X-ray domain. Total ion yield (TIY) and photoelectron-photoion coincidence (PEPICO) spectra were recorded as a function of the photon energy in the vicinity of the carbon K edge (C1s). The C1s resonant transitions as well as the core ionization thresholds have been determined from the profile of TIY spectrum, and the features were discussed. The corresponding partial ion yields were determined from the PEPICO spectra for the cation species produced upon the molecular photodissociation. Additional ab initio calculations have also been performed from where relevant structural and electronic configuration parameters were obtained for this molecule. Copyright © 2017 John Wiley & Sons, Ltd.

Using ion flows parallel and perpendicular to gravity to modify dust acoustic waves

NASA Astrophysics Data System (ADS)

Thomas, E.; Fisher, R.

2008-11-01

Recent studies of dust acoustic waves have shown that the dust kinetic temperature can play an important role in determining the resulting dispersion relation [M. Rosenberg, et al., Phys. Plasmas, 15, 073701 (2008)]. In these studies, it is believed that ion flows play a dominant role in determining both the kinetic temperature of the charged microparticles as well as providing the source of energy for triggering the waves. In this presentation, results will be presented on the effects of ion flow on spatial structure and velocity distribution of dust acoustic waves. Here, the waves will be formed in dusty plasmas consisting of 3 ± 1 micron diameter silica microspheres. Two separate electrodes will be used to modify the ion flow in the plasma -- one parallel to the direction of gravity and one perpendicular to the direction of gravity. Particle image velocimetry (PIV) techniques will be used to observe the particles and to measure their velocity distributions.

Structural Characterization of Laboratory Made Tholins by IRMPD Action Spectroscopy and Ultrahigh Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Thissen, R.; Somogyi, A.; Vuitton, V.; Bégué, D.; Lemaire, J.; Steinmetz, V.

2011-10-01

The complex organic material that is found on the surface and within the haze layer of Titan is attributed to chemistry occurring in its thick N2/CH4 atmosphere. Although several groups are producing in various laboratory setting the socalled tholins which have been investigated by using analytical methods including UV/Vis, fluorescence, IR, and MS1-5, these very complex organic mixtures still hold many unanswered questions, especially related to the potentiality for their prebiotic chemistry. In addition to tholins characterization and analysis, we recently investigated quantitatively the hydrolysis kinetics of tholins in pure and NH3 containing water at different temperatures.7-8 Our groups at UJF (Grenoble) and at U of Arizona (Tucson) have been collaborating on mass spectral analyses of tholins samples for several years.9 Here, we report our most recent results on the structural characterization of tholins by infrared multiphoton dissociation (IRMPD) action spectroscopy10 and ultrahigh resolution MS. IRMPD action spectroscopy is a recently developed technique that uses IR photons of variable wavelengths to activate ions trapped inside an ion trap. When photons are absorbed at a given wavelength, the selected ion fragments and this fragmentation is monitored as a function of wavelength, analog to an absorption spectrum (impossible to record otherwise because of the much reduced density). This technique can, therefore, be used to determine IR spectra of ions in the gas phase, and provides with very acute structural information. IRMPD action spectroscopy is often used to distinguish between structural isomers of isobaric ions. The drawback is that it requests for high power lasers. Only two Free Electron Lasers (FEL) are available in the world and allow to record spectra with reasonable resolution (20-25 cm-1). IRMPD action spectra of selected ions from tholins will be presented and discussed together with observed fragmentation processes that reveal structural features of the ions. We have studied ions in the mass range from 60 to 160 u, corresponding to particularly interesting species already characterized by other (e.g. tandem MS/MS) methods.

The role of monovalent cations in the ATPase reaction of DNA gyrase

PubMed Central

Hearnshaw, Stephen James; Chung, Terence Tsz-Hong; Stevenson, Clare Elizabeth Mary; Maxwell, Anthony; Lawson, David Mark

2015-01-01

Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K+, is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K+ ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na+ ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites. PMID:25849408

Impact of Ion Bombardment on the Structure and Magnetic Properties of Fe78Si13B9 Amorphous Alloy

NASA Astrophysics Data System (ADS)

Wu, Yingwei; Peng, Kun

2018-06-01

Amorphous Fe78Si13B9 alloy ribbons were bombarded by ion beams with different incident angles ( θ ). The evolution of the microstructure and magnetic properties of ribbons caused by ion beam bombardment was investigated by x-ray diffraction, transmission electron microscope and vibrating sample magnetometer analysis. Low-incident-angle bombardment led to atomic migration in the short range, and high-incident-angle bombardment resulted in the crystallization of amorphous alloys. Ion bombardment induces magnetic anisotropy and affects magnetic properties. The effective magnetic anisotropy was determined by applying the law of approach to saturation, and it increased with the increase of the ion bombardment angle. The introduction of effective magnetic anisotropy will reduce the permeability and increase the relaxation frequency. Excellent high-frequency magnetic properties can be obtained by selecting suitable ion bombardment parameters.

The network formers role of gadolinium(III) ions in some zinc-borate glass ceramics

NASA Astrophysics Data System (ADS)

Bosca, Maria; Pop, Lidia; Pascuta, Petru

2017-12-01

EPR and magnetic susceptibility measurements were performed on glass ceramics from the (Gd2O3)x.(B2O3)(60-x).(ZnO)40 system, with 0 ≤ x ≤ 15 mol%, in order to determine the role of gadolinium ions on structural and magnetic properties. At low Gd2O3 contents (x ≤ 1 mol%) the EPR spectra show four resonance lines with effective g-values of ˜ 6, 4.8, 2.8 and 2, typical for Gd3+ ions uniformly distributed in the glass and glass ceramic samples. For higher contents of gadolinium ions (x ≥ 3 mol%) the EPR spectra are dominated by a single broad line centered at g ˜ 2, which can be due to the magnetic clusters containing Gd3+ ions. The magnetic susceptibility data show that the gadolinium ions are involved in superexchange interactions in all the investigated glass ceramics, being antiferromagnetically coupled.

Combined analysis of 1,3-benzodioxoles by crystalline sponge X-ray crystallography and laser desorption ionization mass spectrometry.

PubMed

Hayashi, Yukako; Ohara, Kazuaki; Taki, Rika; Saeki, Tomomi; Yamaguchi, Kentaro

2018-03-12

The crystalline sponge (CS) method, which employs single-crystal X-ray diffraction to determine the structure of an analyte present as a liquid or an oil and having a low melting point, was used in combination with laser desorption ionization mass spectrometry (LDI-MS). 1,3-Benzodioxole derivatives were encapsulated in CS and their structures were determined by combining X-ray crystallography and MS. After the X-ray analysis, the CS was subjected to imaging mass spectrometry (IMS) with an LDI spiral-time-of-flight mass spectrometer (TOF-MS). The ion detection area matched the microscopic image of the encapsulated CS. In addition, the accumulated 1D mass spectra showed that fragmentation of the guest molecule (hereafter, guest) can be easily visualized without any interference from the fragment ions of CS except for two strong ion peaks derived from the tridentate ligand TPT (2,4,6-tris(4-pyridyl)-1,3,5-triazine) of the CS and its fragment. X-ray analysis clearly showed the presence of the guest as well as the π-π, CH-halogen, and CH-O interactions between the guest and the CS framework. However, some guests remained randomly diffused in the nanopores of CS. In addition, the detection limit was less than sub-pmol order based on the weight and density of CS determined by X-ray analysis. Spectroscopic data, such as UV-vis and NMR, also supported the encapsulation of the guest through the interaction between the guest and CS components. The results denote that the CS-LDI-MS method, which combines CS, X-ray analysis and LDI-MS, is effective for structure determination.

Temperature dependence of local structural changes around transition metal centers Cr3+ and Mn2+ in RAl3(BO3)4 crystals studied by EMR

NASA Astrophysics Data System (ADS)

Açıkgöz, Muhammed; Rudowicz, Czesław; Gnutek, Paweł

2017-11-01

Theoretical investigations are carried out to determine the temperature dependence of the local structural parameters of Cr3+ and Mn2+ ions doped into RAl3(BO3)4 (RAB, R = Y, Eu, Tm) crystals. The zero-field splitting (ZFS) parameters (ZFSPs) obtained from the spin Hamiltonian (SH) analysis of EMR (EPR) spectra serve for fine-tuning the theoretically predicted ZFSPs obtained using the semi-empirical superposition model (SPM). The SPM analysis enables to determine the local structure changes around Cr3+ and Mn2+ centers in RAB crystals and explain the observed temperature dependence of the ZFSPs. The local monoclinic C2 site symmetry of all Al sites in YAB necessitates consideration of one non-zero monoclinic ZFSP (in the Stevens notation, b21) for Cr3+ ions. However, the experimental second-rank ZFSPs (D =b20 , E = 1 / 3b22) were expressed in a nominal principal axis system. To provide additional insight into low symmetry aspects, the distortions (ligand's distances ΔRi and angular distortions Δθi) have been varied while preserving monoclinic site symmetry, in such way as to obtain the calculated values (D, E) close to the experimental ones, while keeping b21 close to zero. This procedure yields good matching of the calculated ZFSPs and the experimental ones, and enables determination of the corresponding local distortions. The present results may be useful in future studies aimed at technological applications of the Huntite-type borates with the formula RM3(BO3)4. The model parameters determined here may be utilized for ZFSP calculations for Cr3+ and Mn2+ ions at octahedral sites in single-molecule magnets and single-chain magnets.

Optical biosensing of nitrite ions using cytochrome cd1 nitrite reductase encapsulated in a sol-gel matrix.

PubMed

Ferretti, S; Lee, S K; MacCraith, B D; Oliva, A G; Richardson, D J; Russell, D A; Sapsford, K E; Vidal, M

2000-11-01

Nitrite is an important human health and environmental analyte. As such, the European Union (EU) has imposed a limit for nitrite in potable water of 0.1 mg l-1 (2.18 microM). In order to develop an optical biosensing system for the determination of nitrite ions in environmental waters, cytochrome cd1 nitrite reductase has been extracted and purified from the bacterium Paracoccus pantotrophus. The protein has been spectroscopically characterised in solution and important kinetic parameters of nitrite reduction of the cytochrome cd1 enzyme, i.e., Km, Vmax and kcat have been determined. The influence of pH on the activity of the cytochrome cd1 has been investigated and the results suggest that this enzyme can be used for the determination of nitrite in the pH range 6-9. Biosensing experiments with the cytochrome cd1 in solution suggested that the decrease in intensity of the absorption band associated with the d1 haem (which is the nitrite binding site), at 460 nm, with increasing nitrite concentrations would enable the measurement of this analyte with the optimum limit of detection. The cytochrome cd1 has been encapsulated in a bulk sol-gel monolith with no structural changes observed and retention of enzymatic activity. The detection of nitrite ions in the range 0.075-1.250 microM was achieved, with a limit of detection of 0.075 microM. In order to increase the speed of response, a sol-gel sandwich thin film structure was formulated with the cytochrome cd1. This structure enabled the determination of nitrite concentrations within ca. 5 min. The sol-gel sandwich entrapped cytochrome cd1 enzyme was found to be stable for several months when the films were stored at 4 degrees C.

Charge-induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility.

PubMed

Ickert, Stefanie; Hofmann, Johanna; Riedel, Jens; Beck, Sebastian; Pagel, Kevin; Linscheid, Michael W

2018-04-01

Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n = 15-40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence.

Lifetime Assessment of the NEXT Ion Thruster

NASA Technical Reports Server (NTRS)

VanNoord, Jonathan L.

2010-01-01

Ion thrusters are low thrust, high specific impulse devices with required operational lifetimes on the order of 10,000 to 100,000 hr. The NEXT ion thruster is the latest generation of ion thrusters under development. The NEXT ion thruster currently has a qualification level propellant throughput requirement of 450 kg of xenon, which corresponds to roughly 22,000 hr of operation at the highest throttling point. Currently, a NEXT engineering model ion thruster with prototype model ion optics is undergoing a long duration test to determine wear characteristics and establish propellant throughput capability. The NEXT thruster includes many improvements over previous generations of ion thrusters, but two of its component improvements have a larger effect on thruster lifetime. These include the ion optics with tighter tolerances, a masked region and better gap control, and the discharge cathode keeper material change to graphite. Data from the NEXT 2000 hr wear test, the NEXT long duration test, and further analysis is used to determine the expected lifetime of the NEXT ion thruster. This paper will review the predictions for all of the anticipated failure mechanisms. The mechanisms will include wear of the ion optics and cathode s orifice plate and keeper from the plasma, depletion of low work function material in each cathode s insert, and spalling of material in the discharge chamber leading to arcing. Based on the analysis of the NEXT ion thruster, the first failure mode for operation above a specific impulse of 2000 sec is expected to be the structural failure of the ion optics at 750 kg of propellant throughput, 1.7 times the qualification requirement. An assessment based on mission analyses for operation below a specific impulse of 2000 sec indicates that the NEXT thruster is capable of double the propellant throughput required by these missions.

Investigating the influence of Na+ and Sr2+ on the structure and solubility of SiO2-TiO2-CaO-Na2O/SrO bioactive glass.

PubMed

Li, Y; Placek, L M; Coughlan, A; Laffir, F R; Pradhan, D; Mellott, N P; Wren, A W

2015-02-01

This study was conducted to determine the influence that network modifiers, sodium (Na+) and strontium (Sr2+), have on the solubility of a SiO2-TiO2-CaO-Na2O/SrO bioactive glass. Glass characterization determined each composition had a similar structure, i.e. bridging to non-bridging oxygen ratio determined by X-ray photoelectron spectroscopy. Magic angle spinning nuclear magnetic resonance (MAS-NMR) confirmed structural similarities as each glass presented spectral shifts between -84 and -85 ppm. Differential thermal analysis and hardness testing revealed higher glass transition temperatures (Tg 591-760 °C) and hardness values (2.4-6.1 GPa) for the Sr2+ containing glasses. Additionally the Sr2+ (~250 mg/L) containing glasses displayed much lower ion release rates than the Na+ (~1,200 mg/L) containing glass analogues. With the reduction in ion release there was an associated reduction in solution pH. Cytotoxicity and cell adhesion studies were conducted using MC3T3 Osteoblasts. Each glass did not significantly reduce cell numbers and osteoblasts were found to adhere to each glass surface.

Structure Determination of Natural Products by Mass Spectrometry.

PubMed

Biemann, Klaus

2015-01-01

I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

Charge exchange cross sections in slow collisions of Si3+ with Hydrogen atom

NASA Astrophysics Data System (ADS)

Joseph, Dwayne; Quashie, Edwin; Saha, Bidhan

2011-05-01

In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. Work supported by NSF CREST project (grant #0630370).

Entropic effects in the electric double layer of model colloids with size-asymmetric monovalent ions

NASA Astrophysics Data System (ADS)

Guerrero-García, Guillermo Iván; González-Tovar, Enrique; Olvera de la Cruz, Mónica

2011-08-01

The structure of the electric double layer of charged nanoparticles and colloids in monovalent salts is crucial to determine their thermodynamics, solubility, and polyion adsorption. In this work, we explore the double layer structure and the possibility of charge reversal in relation to the size of both counterions and coions. We examine systems with various size-ratios between counterions and coions (ion size asymmetries) as well as different total ion volume fractions. Using Monte Carlo simulations and integral equations of a primitive-model electric double layer, we determine the highest charge neutralization and electrostatic screening near the electrified surface. Specifically, for two binary monovalent electrolytes with the same counterion properties but differing only in the coion's size surrounding a charged nanoparticle, the one with largest coion size is found to have the largest charge neutralization and screening. That is, in size-asymmetric double layers with a given counterion's size the excluded volume of the coions dictates the adsorption of the ionic charge close to the colloidal surface for monovalent salts. Furthermore, we demonstrate that charge reversal can occur at low surface charge densities, given a large enough total ion concentration, for systems of monovalent salts in a wide range of ion size asymmetries. In addition, we find a non-monotonic behavior for the corresponding maximum charge reversal, as a function of the colloidal bare charge. We also find that the reversal effect disappears for binary salts with large-size counterions and small-size coions at high surface charge densities. Lastly, we observe a good agreement between results from both Monte Carlo simulations and the integral equation theory across different colloidal charge densities and 1:1-elec-trolytes with different ion sizes.

Informatics-Aided Density Functional Theory Study on the Li Ion Transport of Tavorite-Type LiMTO4F (M(3+)-T(5+), M(2+)-T(6+)).

PubMed

Jalem, Randy; Kimura, Mayumi; Nakayama, Masanobu; Kasuga, Toshihiro

2015-06-22

The ongoing search for fast Li-ion conducting solid electrolytes has driven the deployment surge on density functional theory (DFT) computation and materials informatics for exploring novel chemistries before actual experimental testing. Existing structure prototypes can now be readily evaluated beforehand not only to map out trends on target properties or for candidate composition selection but also for gaining insights on structure-property relationships. Recently, the tavorite structure has been determined to be capable of a fast Li ion insertion rate for battery cathode applications. Taking this inspiration, we surveyed the LiMTO4F tavorite system (M(3+)-T(5+) and M(2+)-T(6+) pairs; M is nontransition metals) for solid electrolyte use, identifying promising compositions with enormously low Li migration energy (ME) and understanding how structure parameters affect or modulate ME. We employed a combination of DFT computation, variable interaction analysis, graph theory, and a neural network for building a crystal structure-based ME prediction model. Candidate compositions that were predicted include LiGaPO4F (0.25 eV), LiGdPO4F (0.30 eV), LiDyPO4F (0.30 eV), LiMgSO4F (0.21 eV), and LiMgSeO4F (0.11 eV). With chemical substitutions at M and T sites, competing effects among Li pathway bottleneck size, polyanion covalency, and local lattice distortion were determined to be crucial for controlling ME. A way to predict ME for multiple structure types within the neural network framework was also explored.

Ultrahigh-performance liquid chromatography-ion trap mass spectrometry characterization of the steroidal saponins of Dioscorea panthaica Prain et Burkill and its application for accelerating the isolation and structural elucidation of steroidal saponins.

PubMed

Wang, Weihao; Zhao, Ye; Jing, Wenguang; Zhang, Jun; Xiao, Hui; Zha, Qin; Liu, An

2015-03-01

Dioscorea panthaica is a traditional Chinese medicinal herb used in the treatment of various physiological conditions, including cardiovascular disease, gastropathy and hypertension. Steroidal saponins (SS) are the main active ingredients of this herb and have effects on myocardial ischemia and cancer. The phytochemical evaluation of SS is both time-consuming and laborious, and the isolation and structural determination steps can be especially demanding. For this reason, the development of new methods to accelerate the processes involved in the identification, isolation and structural elucidation of SS is highly desirable. In this study, a new ultrahigh performance liquid chromatography-ion trap mass spectrometry (UHPLC-IT/MS(n)) method has been developed for the identification of the SS in D. panthaica Prain et Burkill. Notably, the current method can distinguish between spirostanol and furostanol-type compounds based on the fragmentation patterns observed by electrospray ionization-ion trap mass spectrometry (ESI-IT/MS(n)) analysis. UHPLC-IT/MS(n) was used to conduct a detailed investigation of the number, structural class and order of the sugar moieties in the sugar chains of the SS present in D. panthaica. The established fragmentation features were used to analyze the compounds found in the 65% ethanol fraction of the water extracts of D. panthaica. Twenty-three SS were identified, including 11 potential new compounds and six groups of isomers. Two of these newly identified SS were selected as representative examples, and their chemical structures were confirmed by (1)H and (13)C NMR analyses. This newly developed UHPLC-IT/MS(n) method therefore allowed for the efficient identification, isolation and structural determination of the SS in D. panthaica. Copyright © 2015 Elsevier Inc. All rights reserved.

Effect of calcination temperature of a copper ferrite synthesized by a sol-gel method on its structural characteristics and performance as Fenton catalyst to remove gallic acid from water.

PubMed

López-Ramón, María V; Álvarez, Miguel A; Moreno-Castilla, Carlos; Fontecha-Cámara, María A; Yebra-Rodríguez, África; Bailón-García, Esther

2018-02-01

A copper ferrite synthesized by a sol-gel combustion method was calcined at different temperatures up to 800°C, determining changes in its structural characteristics and magnetic measurements and studying its catalytic performance in gallic acid removal by Fenton reaction. The main objective was to study the effect of the calcination temperature of copper ferrite on its crystalline phase formation and transformation, activity and metal ion leaching. The cubic-to-tetragonal transformation of the spinel occurred via its reaction with the CuO phase, displacing Fe 3+ ions in B (octahedral) sites out of the spinel structure by the following reaction: 2Fe 3+ B +3CuO→Fe 2 O 3 +3Cu 2+ B . The catalysts showed superparamagnetic or substantial superparamagnetic behaviour. At higher calcination temperatures, catalyst activity was lower, and Cu ion leaching was markedly decreased. There was no Fe ion leaching with any catalyst. The as-prepared catalyst showed better catalytic performance than a commercial copper ferrite. Leached Cu ions acted as homogeneous catalysts, and their contribution to the overall removal mechanism was examined. Cu 2 O present in the as-prepared catalysts made only a small contribution to their activity. Finally, the reutilization of various catalysts was studied by performing different catalytic cycles. Copyright © 2017 Elsevier Inc. All rights reserved.

Method of Forming Textured Silicon Substrate by Maskless Cryogenic Etching

NASA Technical Reports Server (NTRS)

Yee, Karl Y. (Inventor); Homyk, Andrew P. (Inventor)

2014-01-01

Disclosed herein is a textured substrate comprising a base comprising silicon, the base having a plurality of needle like structures depending away from the base, wherein at least one of the needle like structures has a depth of greater than or equal to about 50 micrometers determined perpendicular to the base, and wherein at least one of the needle like structures has a width of less than or equal to about 50 micrometers determined parallel to the base. An anode and a lithium ion battery comprising the textured substrate, and a method of producing the textured substrate are also disclosed.

Composites Based on Conducting Polymers and Carbon Nanomaterials for Heavy Metal Ion Sensing (Review).

PubMed

Deshmukh, Megha A; Shirsat, Mahendra D; Ramanaviciene, Almira; Ramanavicius, Arunas

2018-07-04

Current review signifies recent trends and challenges in the development of electrochemical sensors based on organic conducting polymers (OCPs), carbon nanotubes (CNTs) and their composites for the determination of trace heavy metal ions in water are reviewed. OCPs and CNTs have some suitable properties, such as good electrical, mechanical, chemical and structural properties as well as environmental stability, etc. However, some of these materials still have significant limitations toward selective and sensitive detection of trace heavy metal ions. To overcome the limitations of these individual materials, OCPs/CNTs composites were developed. Application of OCPs/CNTs composite and their novel properties for the adsorption and detection of heavy metal ions outlined and discussed in this review.

Morphology and annealing kinetics of ion tracks in minerals

NASA Astrophysics Data System (ADS)

Kluth, P.; Afra, B.; Rodriguez, M. D.; Lang, M.; Trautmann, C.; Ewing, R. C.

2012-10-01

We have studied the morphology and annealing kinetics of ion tracks in Durango apatite using synchrotron small angle X-ray scattering. The non-destructive, artefact-free technique enables us to determine the track radii with a resolution of fractions of a nanometre. The tracks were generated using different heavy ions with energies between 185 MeV and 2.6 GeV. The track morphology is consistent with the formation of long cylindrical amorphous tracks. The annealing kinetics, measured by SAXS in combination with ex situ and in situ annealing experiments, suggests structural relaxation followed by recrystallisation of the damaged material. The measurement methodology shown here provides a new means for in-depth studies of ion-track formation in minerals under a wide variety of geological conditions.

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

Leenheer, J.A.; Brown, G.K.; Cabaniss, S.E.

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca{sup 2+}, Cd{sup 2+}, Cu{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca{sup 2+} ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The metal binding fraction was characterized by quantitative {sup 13}C NMR, {sup 1}H NMR, and FT-IR spectrometry andmore » elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca{sup 2+} binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.« less

Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance

NASA Astrophysics Data System (ADS)

Wilson, Michael A.; Nguyen, Thuy Hien; Pohorille, Andrew

2014-12-01

Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.

An embedding structure of the cross-tail CSs and its relation to the ion composition according to MAVEN observations in the Martian magnetotai

NASA Astrophysics Data System (ADS)

Grigorenko, E. E.; Shuvalov, S. D.; Malova, H. V.; Zelenyi, L. M.

2017-12-01

The multilayered (embedded) Current Sheets (CS) are often observed in the Earth's magnetotail. Simulations based on quasi-adiabatic dynamics of different ion components showed that the observed embedding structures can be reconstructed by taking into account the net electric currents carried by ions with different masses and, thus, with different gyroradii. The last determines the spatial scales of the corresponding current layers. The embedding can be quantitatively described by the ratio of the magnetic field value at the edges of a thin embedded layer Bext to the value of the magnetic field outside a thick CS, B0. For the Earth's magnetotail it was shown that there is a relation between the Bext/B0 and the relative densities of heavy and light ion components. In the Martian magnetotail the embedding feature is also often observed in the cross-tail CS formed by the draping of the IMF field lines. The analysis of 100 CS crossings by MAVEN spacecraft showed that in the Martian magnetotail the relation between the embedding characteristics and ion composition is similar to the one observed in the Earth's magnetotail and the spatial scales of the embedded layers are defined by the gyroradii of the current carrying ion component.

Porous Proton- and Chloride-Ion Conducting Layers Based on Ethanolamine Derivatives of PVC on the Surfaces of Fabrics

NASA Astrophysics Data System (ADS)

Tsivadze, A. Yu.; Fridman, A. Ya.; Morozova, E. M.; Sokolova, N. P.; Voloshchuk, A. M.; Bardyshev, I. I.; Gorbunov, A. M.; Novikov, A. K.; Polyakova, I. Ya.; Titova, B. N.; Yavich, A. A.

2018-02-01

Materials are produced with porous layers based on ethanolamine derivatives of PVC or compounds of active carbon with hydroxyethylcyclam derivatives of PVC with aqua complexes of chloride hydrogen cross-linked with the surface of cellulose or asbestos fabric. Their capacity for sorption with respect to hexane and benzene in the saturated vapor and liquid phases is determined. The dependences of current on voltage in a circuit are determined for bridges composed of these materials in air, and in the vapor and liquid phases of benzene and hexane between 3 M HCl solutions and 3 M HCl solutions containing 3 M CaCl2. It is established that only H+ ions migrate along the bridges between the HCl solutions, and H+ and Cl- ions were the only species that moved along the bridges between the HCl solutions containing CaCl2. The voltages at which the movement of ions starts are determined, and constants characterizing the conductivity of the layers are found. It is shown that these parameters depend on the structure of a layer, the nature of the fabric, and the medium surrounding a bridge.

Local Structure of the Amorphous Precursor to Ba-Hexaferrite Thin Films: An Anisotropic Octahedral Fe-O Glass Network

NASA Astrophysics Data System (ADS)

Snyder, J. E.; Harris, V. G.; Koon, N. C.; Sui, X.; Kryder, M. H.

1996-10-01

Anisotropic local structure has been observed around both the Fe and Ba ions in the amorphous precursor to Ba-hexaferrite thin films, using polarization-dependent extended x-ray-absorption fine structure. This anisotropic local structure, consisting mainly of a network of Fe-O octahedra, determines the orientation of the fast-growing basal planes during crystallization, and thus the directions of the c axes and the resulting magnetic anisotropy.

High-spin europium and gadolinium centers in yttrium-aluminum garnet

NASA Astrophysics Data System (ADS)

Vazhenin, V. A.; Potapov, A. P.; Asatryan, G. R.; Uspenskaya, Yu. A.; Petrosyan, A. G.; Fokin, A. V.

2016-08-01

Electron-spin resonance spectra of Eu2+ and Gd3+ centers substituting Y3+ ions in single-crystal yttrium-aluminum garnet have been studied and the parameters of their rhombic spin Hamiltonian have been determined. The fine-structure parameters of the above ions have been calculated in the superposition model disregarding changes in the angular coordinates of the ligand environment of the impurity defect thus demonstrating the necessity of taking these changes into account.

Heavy ion action on single cells: Cellular inactivation capability of single accelerated heavy ions

NASA Technical Reports Server (NTRS)

Kost, M.; Pross, H.-D.; Russmann, C.; Schneider, E.; Kiefer, J.; Kraft, G.; Lenz, G.; Becher, W.

1994-01-01

Heavy ions (HZE-particles) constitute an important part of radiation in space. Although their number is small the high amount of energy transferred by individual particles may cause severe biological effects. Their investigation requires special techniques which were tested by experiments performed at the UNILAC at the GSI (Darmstadt). Diploid yeast was used which is a suitable eucaryotic test system because of its resistance to extreme conditions like dryness and vacuum. Cells were placed on nuclear track detector foils and exposed to ions of different atomic number and energy. To assess the action of one single ion on an individual cell, track parameters and the respective colony forming abilities (CFA) were determined with the help of computer aided image analysis. There is mounting evidence that not only the amount of energy deposited along the particle path, commonly given by the LET, is of importance but also the spatial problem of energy deposition at a submicroscopical scale. It is virtually impossible to investigate track structure effects in detail with whole cell populations and (globally applied) high particle fluences. It is, therefore, necessary to detect the action of simple ions in individual cells. The results show that the biological action depends on atomic number and specific energy of the impinging ions, which can be compared with model calculations of recent track structure models.

A mini-photofragment translational spectrometer with ion velocity map imaging using low voltage acceleration

NASA Astrophysics Data System (ADS)

Qi, Wenke; Jiang, Pan; Lin, Dan; Chi, Xiaoping; Cheng, Min; Du, Yikui; Zhu, Qihe

2018-01-01

A mini time-sliced ion velocity map imaging photofragment translational spectrometer using low voltage acceleration has been constructed. The innovation of this apparatus adopts a relative low voltage (30-150 V) to substitute the traditional high voltage (650-4000 V) to accelerate and focus the fragment ions. The overall length of the flight path is merely 12 cm. There are many advantages for this instrument, such as compact structure, less interference, and easy to operate and control. Low voltage acceleration gives a longer turn-around time to the photofragment ions forming a thicker Newton sphere, which provides sufficient time for slicing. Ion trajectory simulation has been performed for determining the structure dimensions and the operating voltages. The photodissociation and multiphoton ionization of O2 at 224.999 nm is used to calibrate the ion images and examine the overall performance of the new spectrometer. The velocity resolution (Δν/ν) of this spectrometer from O2 photodissociation is about 0.8%, which is better than most previous results using high acceleration voltage. For the case of CF3I dissociation at 277.38 nm, many CF3 vibrational states have been resolved, and the anisotropy parameter has been measured. The application of low voltage acceleration has shown its advantages on the ion velocity map imaging (VMI) apparatus. The miniaturization of the VMI instruments can be realized on the premise of high resolution.

Cation distribution in NiZn-ferrite films determined using x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Koon, N. C.; Williams, C. M.; Zhang, Q.; Abe, M.

1996-04-01

We have applied extended x-ray absorption fine structure (EXAFS) spectroscopy to study the cation distribution in a series of spin-sprayed NiZn-ferrite films, Ni0.15ZnyFe2.85-yO4 (y=0.16, 0.23, 0.40, 0.60). The Ni, Zn, and Fe EXAFS were collected from each sample and analyzed to Fourier transforms. Samples of Ni-ferrite, Zn-ferrite, and magnetite were similarly studied as empirical standards. These standards, together with EXAFS data generated from the theoretical EXAFS FEFF codes, allowed the correlation of features in the Fourier transforms with specific lattice sites in the spinel unit cell. We find that the Ni ions reside mostly on the octahedral (B) sites whereas the Zn ions are predominantly on the tetrahedral (A) sites. The Fe ions reside on both A and B sites in a ratio determined by the ratio of Zn/Fe. The addition of Zn displaces a larger fraction of Fe cations onto the B sites serving to increase the net magnetization. The fraction of A site Ni ions is measured to increase peaking at ≊25% for y=0.6. At higher Zn concentrations (y≥0.5) the lattice experiences local distortions around the Zn sites causing a decrease in the superexchange resulting in a decrease in the net magnetization.

High Affinity Binding of Indium and Ruthenium Ions by Gastrins

PubMed Central

Baldwin, Graham S.; George, Graham N.; Pushie, M. Jake

2015-01-01

The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS) spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd) of 3.3 x 10−7 and 1.1 x 10−6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10−15 and 1.7 x 10−7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10−13 and 1.2 x 10−5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0–3.3 Å, the Ru complex clearly demonstrated a short range Ru—Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy. PMID:26457677

Understanding ion association states and molecular dynamics using infrared spectroscopy

NASA Astrophysics Data System (ADS)

Masser, Hanqing

A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO microphase separates from the PEO-rich microphase, and ionic groups are preferentially solvated by PEO chains and reside in the PEO-rich microphase. As the ratio of PTMO increases, the fraction of aggregates increases, resulting in more highly coordinated aggregation states. Results on ion association states are in good agreement with previous results on ion conductivity, polymer dynamics and morphology. The effects of ion content, cation type and ionic side chain structure on ion association states are systemically studied in a series of ionomers with short ethylene oxide and ionic sulfonated styrene side chains, and then correlated to the ion and polymer dynamic characterization. It is found that ionomers with modest ion content, large cation and styrene ionic side chain have the most "free ions" and ion pairs, and highest ion conductivity. Ion conduction in ionomers is optimized by systematically changing their chemical structures. In addition to knowledge of ion association states, a IR band shape also contains information on molecular dynamics. In companion investigation, the vibrational relaxation and dynamic transitions of conformationally insensitive normal modes in two different polymer systems (atactic polystyrene and deuterated poly(methyl methacrylate)) are studied. The information on vibrational relaxations is resolved by conducting precisely controlled FTIR experiments, applying specialized curve resolving data analysis, and calculating time correlation functions through numerical Fourier transformation. The vibrational relaxations of these modes can be described by a two process model: a fast process on the time scale of 0.01 ps, which is inhomogeneously broadened by a slow process on the time scale of picoseconds.

Piezoelectric sensor for sensitive determination of metal ions based on the phosphate-modified dendrimer

NASA Astrophysics Data System (ADS)

Wang, S. H.; Shen, C. Y.; Lin, Y. M.; Du, J. C.

2016-08-01

Heavy metal ions arising from human activities are retained strongly in water; therefore public water supplies must be monitored regularly to ensure the timely detection of potential problems. A phosphate-modified dendrimer film was investigated on a quartz crystal microbalance (QCM) for sensing metal ions in water at room temperature in this study. The chemical structures and sensing properties were characterized by Fourier transform infrared spectroscopy and QCM measurement, respectively. This phosphate-modified dendrimer sensor can directly detect metal ions in aqueous solutions. This novel sensor was evaluated for its capacity to sense various metal ions. The sensor exhibited a higher sensitivity level and shorter response time to copper(II) ions than other sensors. The linear detection range of the prepared QCM based on the phosphate-modified dendrimer was 0.0001 ∼ 1 μM Cu(II) ions (R2 = 0.98). The detection properties, including sensitivity, response time, selectivity, reusability, maximum adsorption capacity, and adsorption equilibrium constants, were also investigated.

Dynamics of the EAG1 K+ channel selectivity filter assessed by molecular dynamics simulations.

PubMed

Bernsteiner, Harald; Bründl, Michael; Stary-Weinzinger, Anna

2017-02-26

EAG1 channels belong to the KCNH family of voltage gated potassium channels. They are expressed in several brain regions and increased expression is linked to certain cancer types. Recent cryo-EM structure determination finally revealed the structure of these channels in atomic detail, allowing computational investigations. In this study, we performed molecular dynamics simulations to investigate the ion binding sites and the dynamical behavior of the selectivity filter. Our simulations suggest that sites S2 and S4 form stable ion binding sites, while ions placed at sites S1 and S3 rapidly switched to sites S2 and S4. Further, ions tended to dissociate away from S0 within less than 20 ns, due to increased filter flexibility. This was followed by water influx from the extracellular side, leading to a widening of the filter in this region, and likely non-conductive filter configurations. Simulations with the inactivation-enhancing mutant Y464A or Na + ions lead to trapped water molecules behind the SF, suggesting that these simulations captured early conformational changes linked to C-type inactivation. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Valence, exchange interaction, and location of Mn ions in polycrystalline M n x G a 1 - x N ( x ≤ 0.04 )

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

Furrer, A.; Kramer, K. W.; Podlesnyak, A.

In this paper, we present an experimental study for polycrystalline samples of the diluted magnetic semiconductormore » $$\\mathrm{M}{\\mathrm{n}}_{x}\\mathrm{G}{\\mathrm{a}}_{1{-}x}\\mathrm{N}(x{\\le}0.04)$$ in order to address some of the existing controversial issues. X-ray and neutron diffraction, x-ray absorption near-edge structure, and electron paramagnetic resonance experiments were used to characterize the structural, electronic, and magnetic properties of the samples, and inelastic neutron scattering was employed to determine the magnetic excitations associated with Mn monomers and dimers. Our main conclusions are as follows: (i) The valence of the Mn ions is $2+$. (ii) The $$\\mathrm{M}{\\mathrm{n}}^{2+}$$ ions experience a substantial single-ion axial anisotropy with parameter D = 0.027(3) meV. (iii) Nearest-neighbor $$\\mathrm{M}{\\mathrm{n}}^{2+}$$ ions are coupled antiferromagnetically. Finally, the exchange parameter $$J={-}0.140(7)\\mathrm{meV}$$ is independent of the Mn content $x$; i.e., there is no evidence for hole-induced modifications of $J$ towards a potentially high Curie temperature postulated in the literature.« less

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

Haskey, S. R.; Grierson, B. A.; Stagner, L.

Recent completion of the thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on DIII-D enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the edge, providing high resolution measurements of the pedestal and steep gradient edge region of H-mode plasmas. The complexities of the D α spectrum require fitting with a comprehensive model, as well as using iterative collisional radiative modeling to determine the underlying thermal deuterium ion properties. Large differences in the structure and magnitude of impurity (Cmore » 6+) and main-ion (D +) toroidal rotation profiles are seen in the H-mode pedestal. Additionally the D + temperature can be half the value of the C 6+ temperature at the separatrix and shows more of a pedestal structure. Typically only the impurity properties are measured and the main-ion properties are either assumed to be the same, or inferred using neoclassical models, which require validation in the steep gradient region. Furthermore, these measured differences have implications for transport model validation, intrinsic rotation studies, pedestal stability, and the boundary conditions for scrape off layer and plasma material interactions studies.« less

Valence, exchange interaction, and location of Mn ions in polycrystalline M n x G a 1 - x N ( x ≤ 0.04 )

DOE PAGES

Furrer, A.; Kramer, K. W.; Podlesnyak, A.; ...

2018-04-10

In this paper, we present an experimental study for polycrystalline samples of the diluted magnetic semiconductormore » $$\\mathrm{M}{\\mathrm{n}}_{x}\\mathrm{G}{\\mathrm{a}}_{1{-}x}\\mathrm{N}(x{\\le}0.04)$$ in order to address some of the existing controversial issues. X-ray and neutron diffraction, x-ray absorption near-edge structure, and electron paramagnetic resonance experiments were used to characterize the structural, electronic, and magnetic properties of the samples, and inelastic neutron scattering was employed to determine the magnetic excitations associated with Mn monomers and dimers. Our main conclusions are as follows: (i) The valence of the Mn ions is $2+$. (ii) The $$\\mathrm{M}{\\mathrm{n}}^{2+}$$ ions experience a substantial single-ion axial anisotropy with parameter D = 0.027(3) meV. (iii) Nearest-neighbor $$\\mathrm{M}{\\mathrm{n}}^{2+}$$ ions are coupled antiferromagnetically. Finally, the exchange parameter $$J={-}0.140(7)\\mathrm{meV}$$ is independent of the Mn content $x$; i.e., there is no evidence for hole-induced modifications of $J$ towards a potentially high Curie temperature postulated in the literature.« less

SAD phasing with in-house cu Ka radiation using barium as anomalous scatterer.

PubMed

Dhanasekaran, V; Velmurugan, D

2011-12-01

Phasing of lysozyme crystals using co-crystallized barium ions was performed using single-wavelength anomalous diffraction (SAD) method using Cu Ka radiation with in-house source of data collection. As the ion binding sites vary with respect to the pH of the buffer during crystallization, the highly isomorphic forms of lysozyme crystals grown at acidic and alkaline pH were used for the study. Intrinsic sulphur anomalous signal was also utilized with anomalous signal from lower occupancy ions for phasing. The study showed that to solve the structure by SAD technique, 2.8-fold data redundancy was sufficient when barium was used as an anomalous marker in the in-house copper X-ray radiation source for data collection. Therefore, co-crystallization of proteins with barium containing salt can be a powerful tool for structure determination using lab source.

High-performance liquid chromatography–tandem mass spectrometry in the identification and determination of phase I and phase II drug metabolites

PubMed Central

Kolářová, L.; Nobilis, M.

2008-01-01

Applications of tandem mass spectrometry (MS/MS) techniques coupled with high-performance liquid chromatography (HPLC) in the identification and determination of phase I and phase II drug metabolites are reviewed with an emphasis on recent papers published predominantly within the last 6 years (2002–2007) reporting the employment of atmospheric pressure ionization techniques as the most promising approach for a sensitive detection, positive identification and quantitation of metabolites in complex biological matrices. This review is devoted to in vitro and in vivo drug biotransformation in humans and animals. The first step preceding an HPLC-MS bioanalysis consists in the choice of suitable sample preparation procedures (biomatrix sampling, homogenization, internal standard addition, deproteination, centrifugation, extraction). The subsequent step is the right optimization of chromatographic conditions providing the required separation selectivity, analysis time and also good compatibility with the MS detection. This is usually not accessible without the employment of the parent drug and synthesized or isolated chemical standards of expected phase I and sometimes also phase II metabolites. The incorporation of additional detectors (photodiode-array UV, fluorescence, polarimetric and others) between the HPLC and MS instruments can result in valuable analytical information supplementing MS results. The relation among the structural changes caused by metabolic reactions and corresponding shifts in the retention behavior in reversed-phase systems is discussed as supporting information for identification of the metabolite. The first and basic step in the interpretation of mass spectra is always the molecular weight (MW) determination based on the presence of protonated molecules [M+H]+ and sometimes adducts with ammonium or alkali-metal ions, observed in the positive-ion full-scan mass spectra. The MW determination can be confirmed by the [M-H]- ion for metabolites providing a signal in negative-ion mass spectra. MS/MS is a worthy tool for further structural characterization because of the occurrence of characteristic fragment ions, either MSn analysis for studying the fragmentation patterns using trap-based analyzers or high mass accuracy measurements for elemental composition determination using time of flight based or Fourier transform mass analyzers. The correlation between typical functional groups found in phase I and phase II drug metabolites and corresponding neutral losses is generalized and illustrated for selected examples. The choice of a suitable ionization technique and polarity mode in relation to the metabolite structure is discussed as well. PMID:18345532

[Application of precursor ion scanning method in rapid screening of illegally added phosphodiesterase-5 inhibitors and their unknown derivatives in Chinese traditional patent medicines and health foods].

PubMed

Sun, Jing; Cao, Ling; Feng, Youlong; Tan, Li

2014-11-01

The compounds with similar structure often have similar pharmacological activities. So it is a trend for illegal addition that new derivatives of effective drugs are synthesized to avoid the statutory test. This bring challenges to crack down on illegal addition behavior, however, modified derivatives usually have similar product ions, which allow for precursor ion scanning. In this work, precursor ion scanning mode of a triple quadrupole mass spectrometer was first applied to screen illegally added drugs in complex matrix such as Chinese traditional patent medicines and healthy foods. Phosphodiesterase-5 inhibitors were used as experimental examples. Through the analysis of the structure and mass spectrum characteristics of the compounds, phosphodiesterase-5 inhibitors were classified, and their common product ions were screened by full scan of product ions of typical compounds. Then high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method with precursor ion scanning mode was established based on the optimization of MS parameters. The effect of mass parameters and the choice of fragment ions were also studied. The method was applied to determine actual samples and further refined. The results demonstrated that this method can meet the need of rapid screening of unknown derivatives of phosphodiesterase-5 inhibitors in complex matrix, and prevent unknown derivatives undetected. This method shows advantages in sensitivity, specificity and efficiency, and is worth to be further investigated.

Determining Double Bond Position in Lipids Using Online Ozonolysis Coupled to Liquid Chromatography and Ion Mobility-Mass Spectrometry.

PubMed

Harris, Rachel A; May, Jody C; Stinson, Craig A; Xia, Yu; McLean, John A

2018-02-06

The increasing focus on lipid metabolism has revealed a need for analytical techniques capable of structurally characterizing lipids with a high degree of specificity. Lipids can exist as any one of a large number of double bond positional isomers, which are indistinguishable by single-stage mass spectrometry alone. Ozonolysis reactions coupled to mass spectrometry have previously been demonstrated as a means for localizing double bonds in unsaturated lipids. Here we describe an online, solution-phase reactor using ozone produced via a low-pressure mercury lamp, which generates aldehyde products diagnostic of cleavage at a particular double bond position. This flow-cell device is utilized in conjunction with structurally selective ion mobility-mass spectrometry. The lamp-mediated reaction was found to be effective for multiple lipid species in both positive and negative ionization modes, and the conversion efficiency from precursor to product ions was tunable across a wide range (20-95%) by varying the flow rate through the ozonolysis device. Ion mobility separation of the ozonolysis products generated additional structural information and revealed the presence of saturated species in a complex mixture. The method presented here is simple, robust, and readily coupled to existing instrument platforms with minimal modifications necessary. For these reasons, application to standard lipidomic workflows is possible and aids in more comprehensive structural characterization of a myriad of lipid species.

Ion Beam Analysis of Iridium-Based TES for Microcalorimeter Detectors

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

Gomes, M. Ribeiro; Galeazzi, M.; Bogorin, D.

2009-12-16

The physical properties of thin multilayer structures are deeply related to the crystalline quality and stoichiometry of the films. The interface roughness/mixing require a detailed study to determine its influence on the growth processes and surface topography. This is an important aspect when we have lattice mismatch between the superconducting thin-films and the substrates, and a high reliability/reproducibility is required as for large array microcalorimeter applications, as in the case of the MARE experiment, designed to measure the mass of the neutrino with sub-eV sensitivity by measuring the beta decay of {sup 187}Re with cryogenic microcalorimeters. Ion beam analysis techniquesmore » are ideal to determine the thickness and concentration profiles of the chemical species in ultra-thin films. Here we present the results on the Ir-based superconducting films deposited on Si-substrates based on systematic investigations of the concentration depth profiles of the multilayer structure using 2.0 MeV {sup 4}He{sup +} ions for high resolution Rutherford Backscattering Spectrometry combined with X-Ray Reflectrometry to evaluate the interface/roughness mixing and the crystalline quality in the TES prototypes.« less

Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.

PubMed

Fischer, Nina M; Polêto, Marcelo D; Steuer, Jakob; van der Spoel, David

2018-06-01

The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (ΔG‡ for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.

Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

NASA Astrophysics Data System (ADS)

Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

2018-03-01

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

NASA Astrophysics Data System (ADS)

Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

2017-12-01

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

Existence regimes for the formation of nonlinear dissipative structures in inhomogeneous magnetoplasmas with non-Maxwellian electrons

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

Masood, W.; National Centre for Physics, Shahdara Valley Road, Islamabad; Zahoor, Sara

2016-09-15

Nonlinear dissipative structures are studied in one and two dimensions in nonuniform magnetized plasmas with non-Maxwellian electrons. The dissipation is incorporated in the system through ion-neutral collisions. Employing the drift approximation, nonlinear drift waves are derived in 1D, whereas coupled drift-ion acoustic waves are derived in 2D in the weak nonlinearity limit. It is found that the ratio of the diamagnetic drift velocity to the velocity of nonlinear structure determines the nature (compressive or rarefactive) of the shock structure. The upper and lower bounds for velocity of the nonlinear shock structures are also found. It is noticed that the existencemore » regimes for the drift shock waves in one and two dimensions for Cairns distributed electrons are very distinct from those with kappa distributed electrons. Interestingly, it is found that both compressive and rarefactive shock structures could be obtained for the one dimensional drift waves with kappa distributed electrons.« less

Existence regimes for the formation of nonlinear dissipative structures in inhomogeneous magnetoplasmas with non-Maxwellian electrons

NASA Astrophysics Data System (ADS)

Masood, W.; Zahoor, Sara; Gul-e-Ali, Ahmad, Ali

2016-09-01

Nonlinear dissipative structures are studied in one and two dimensions in nonuniform magnetized plasmas with non-Maxwellian electrons. The dissipation is incorporated in the system through ion-neutral collisions. Employing the drift approximation, nonlinear drift waves are derived in 1D, whereas coupled drift-ion acoustic waves are derived in 2D in the weak nonlinearity limit. It is found that the ratio of the diamagnetic drift velocity to the velocity of nonlinear structure determines the nature (compressive or rarefactive) of the shock structure. The upper and lower bounds for velocity of the nonlinear shock structures are also found. It is noticed that the existence regimes for the drift shock waves in one and two dimensions for Cairns distributed electrons are very distinct from those with kappa distributed electrons. Interestingly, it is found that both compressive and rarefactive shock structures could be obtained for the one dimensional drift waves with kappa distributed electrons.

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

PubMed Central

2016-01-01

Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

Development of an accurate and high-throughput methodology for structural comprehension of chlorophylls derivatives. (II) Dephytylated derivatives.

PubMed

Chen, Kewei; Ríos, José Julián; Roca, María; Pérez-Gálvez, Antonio

2015-09-18

Dephytylated chlorophylls (chlorophyllides and pheophorbides) are the starting point of the chlorophyll catabolism in green tissues, components of the chlorophyll pattern in storage/processed food vegetables, as well as the favoured structural arrangement for chlorophyll absorption. In addition, dephytylated native chlorophylls are prone to several modifications of their structure yielding pyro-, 13(2)-hydroxy- and 15(1)-hydroxy-lactone derivatives. Despite of these outstanding remarks only few of them have been analysed by MS(n). Besides new protocols for obtaining standards, we have developed a new high throughput methodology able to determine the fragmentation pathway of 16 dephytylated chlorophyll derivatives, elucidating the structures of the new product ions and new mechanisms of fragmentation. The new methodology combines, by first time, high resolution time-of-flight mass spectrometry and powerful post-processing software. Native chlorophyllides and pheophorbides mainly exhibit product ions that involve the fragmentation of D ring, as well as additional exclusive product ions. The introduction of an oxygenated function at E ring enhances the progress of fragmentation reactions through the β-keto ester group, developing also exclusive product ions for 13(2)-hydroxy derivatives and for 15(1)-hydroxy-lactone ones. Consequently, while MS(2)-based reactions of phytylated chlorophyll derivatives point to fragmentations at the phytyl and propionic chains, dephytylated chlorophyll derivatives behave different as the absence of phytyl makes β-keto ester group and E ring more prone to fragmentation. Proposals of the key reaction mechanisms underlying the origin of new product ions have been made. Copyright © 2015 Elsevier B.V. All rights reserved.

Nanoscale structure and morphology of sulfonated polyphenylenes via atomistic simulations

DOE PAGES

Abbott, Lauren J.; Frischknecht, Amalie L.

2017-01-23

We performed atomistic simulations on a series of sulfonated polyphenylenes systematically varying the degree of sulfonation and water content to determine their effect on the nanoscale structure, particularly for the hydrophilic domains formed by the ionic groups and water molecules. We found that the local structure around the ionic groups depended on the sulfonation and hydration levels, with the sulfonate groups and hydronium ions less strongly coupled at higher water contents. In addition, we characterized the morphology of the ionic domains employing two complementary clustering algorithms. At low sulfonation and hydration levels, clusters were more elongated in shape and poorlymore » connected throughout the system. As the degree of sulfonation and water content were increased, the clusters became more spherical, and a fully percolated ionic domain was formed. As a result, these structural details have important implications for ion transport.« less

Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion

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

Lashkov, A. A.; Zhukhlistova, N. E.; Gabdulkhakov, A. G.

2009-03-15

The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 A resolution to R{sub work} = 16.1% and R{sub free} = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 A, 1.042{sup o}, and 0.071{sup o}, respectively. The coordinate error estimated by the Luzzati plot is 0.166 A. The coordinate error based on the maximum likelihood is 0.199 A. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure ofmore » the homodimer St UPh in the complex with a K{sup +} ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).« less

MCTBI: a web server for predicting metal ion effects in RNA structures.

PubMed

Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

2017-08-01

Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Coordination Environment of a Site-Bound Metal Ion in the Hammerhead Ribozyme Determined by 15N and 2H ESEEM Spectroscopy

PubMed Central

Vogt, Matthew; Lahiri, Simanti; Hoogstraten, Charles G.; Britt, R. David; DeRose, Victoria J.

2010-01-01

Although site-bound Mg2+ ions have been proposed to influence RNA structure and function, establishing the molecular properties of such sites has been challenging due largely to the unique electrostatic properties of the RNA biopolymer. We have previously determined that, in solution, the hammerhead ribozyme (a self-cleaving RNA) has a high-affinity metal ion binding site characterized by a Kd,app < 10 µM for Mn2+ in 1 M NaCl and speculated that this site has functional importance in the ribozyme cleavage reaction. Here we determine both the precise location and the hydration level of Mn2+ in this site using ESEEM (electron spin–echo envelope modulation) spectroscopy. Definitive assignment of the high-affinity site to the activity-sensitive A9/G10.1 region is achieved by site-specific labeling of G10.1 with 15N guanine. The coordinated metal ion retains four water ligands as measured by 2H ESEEM spectroscopy. The results presented here show that a functionally important, specific metal binding site is uniquely populated in the hammerhead ribozyme even in a background of high ionic strength. Although it has a relatively high thermodynamic affinity, this ion remains partially hydrated and is chelated to the RNA by just two ligands. PMID:17177426

Metal Cations in G-Quadruplex Folding and Stability

NASA Astrophysics Data System (ADS)

Bhattacharyya, Debmalya; Mirihana Arachchilage, Gayan; Basu, Soumitra

2016-09-01

This review is focused on the structural and physico-chemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-Quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.

Properties of ammonium ion-water clusters: analyses of structure evolution, noncovalent interactions, and temperature and humidity effects.

PubMed

Pei, Shi-Tu; Jiang, Shuai; Liu, Yi-Rong; Huang, Teng; Xu, Kang-Ming; Wen, Hui; Zhu, Yu-Peng; Huang, Wei

2015-03-26

Although ammonium ion-water clusters are abundant in the biosphere, some information regarding these clusters, such as their growth route, the influence of temperature and humidity, and the concentrations of various hydrated clusters, is lacking. In this study, theoretical calculations are performed on ammonium ion-water clusters. These theoretical calculations are focused on determining the following characteristics: (1) the pattern of cluster growth; (2) the percentages of clusters of the same size at different temperatures and humidities; (3) the distributions of different isomers for the same size clusters at different temperatures; (4) the relative strengths of the noncovalent interactions for clusters of different sizes. The results suggest that the dipole moment may be very significant for the ammonium ion-water system, and some new stable isomers were found. The nucleation of ammonium ions and water molecules is favorable at low temperatures; thus, the clusters observed at high altitudes might not be present at low altitudes. High humidity can contribute to the formation of large ammonium ion-water clusters, whereas the formation of small clusters may be favorable under low-humidity conditions. The potential energy surfaces (PES) of these different sized clusters are complicated and differ according to the distribution of isomers at different temperatures. Some similar structures are observed between NH4(+)(H2O)n and M(H2O)n (where M represents an alkali metal ion or water molecule); when n = 8, the clusters begin to form the closed-cage geometry. As the cluster size increases, these interactions become progressively weaker. The successive binding energy at the DF-MP2-F12/VDZ-F12 level is better than that at the PW91PW91/6-311++G(3df, 3pd) level and is consistent with the experimentally determined values.

Biosorption of Fe(II) and Mn(II) Ions from Aqueous Solution by Rice Husk Ash

PubMed Central

Zhao, Jiaying; Jiang, Zhao; Shan, Dexin; Lu, Yan

2014-01-01

Rice husk ash (RHA), an agricultural waste, was used as biosorbent for the removal of Iron(II) and Manganese(II) ions from aqueous solutions. The structural and morphological characteristics of RHA and its elemental compositions before and after adsorption of Fe(II) and Mn(II) were determined by scanning electron microscopic (SEM) and X-ray fluorescence (XRF) analyses. Batch experiments were carried out to determine the influence of initial pH, contact time, adsorbent dosage, and initial concentration on the removal of Fe(II) and Mn(II) ions. Langmuir, Freundlich, and Dubinin-Radushkevich (D-R) models were applied to describe the biosorption isotherm of the metal ions by RHA. The correlation coefficient (R 2) of Langmuir and Freundlich isotherm models equals 0.995 and 0.901 for Fe(II), 0.9862 and 0.8924 for Mn(II), respectively, so the Langmuir model fitted the equilibrium data better than the Freundlich isotherm model. The mean free energy values evaluated from the D-R model indicated that the biosorption of Fe(II) and Mn(II) onto RHA was physical in nature. Experimental data also showed that the biosorption processes of both metal ions complied with the pseudo-second-order kinetics. PMID:24982918

Ion Spectral Structures Observed by the Van Allen Probes and Cluster

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

2014-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

Effect of structure and thermodynamic stability on the response of lanthanide stannate pyrochlores to ion beam irradiation.

PubMed

Lian, J; Helean, K B; Kennedy, B J; Wang, L M; Navrotsky, A; Ewing, R C

2006-02-09

The lanthanide stannates, Ln2Sn2O7, Ln=La-Lu and Y, have the isometric pyrochlore structure, A2B2O7, and their structural properties have been refined by Rietveld analysis of powder neutron and synchrotron X-ray diffraction data. In this study, the enthalpies of formation of selected stannate pyrochlores, Ln=La, Nd, Sm, Eu, Dy, and Yb, were measured by high-temperature oxide melt solution calorimetry. Their radiation response was determined by 1 MeV Kr2+ ion irradiation combined with in situ TEM observation over the temperature range of 25 to 1000 K. The enthalpy of formation from binary oxides of stannate pyrochlores became more endothermic (from -145 to -40 kJ/mol) as the size of the lanthanide in the A-site decreases. A more exothermic trend of the enthalpy of formation was observed in stannate pyrochlores with larger lanthanide ions, particularly La, possibly as a result of increased covalency in the Sn-O bond. In contrast to lanthanide titanate pyrochlores, Ln2Ti2O7, that are generally susceptible to radiation-induced amorphization and zirconate pyrochlores, Ln2Zr2O7, that are generally resistant to radiation-induced amorphization, the lanthanide stannate pyrochlores show a much greater variation in their response to ion irradiation. La, Nd, and Gd stannates experience the radiation-induced transformation to the aperiodic state, and the critical amorphization temperatures are approximately 960, 700, and 350 K, respectively. Y and Er stannate pyrochlores cannot be amorphized by ion beam irradiation, even at 25 K, and instead disorder to a defect fluorite structure. Comparison of the calorimetric and ion irradiation data for titanate, zirconate, and stannate pyrochlores reveals a strong correlation among subtle changes in crystal structure with changing composition, the energetics of the disordering process, and the temperature above which the material can no longer be amorphized. In summary, as the structure approaches the ideal, ordered pyrochlore structure, radiation-induced amorphization is more easily attained. This is consistent with an increasingly exothermic trend in the enthalpies of formation of pyrochlores from the oxides, that is, the greater the thermochemical stability of the pyrochlore structure, the more likely it will be amorphized upon radiation damage rather than recover to a disordered fluorite structure.

Structural evolution of trimesic acid (TMA)/Zn2 + ion network on Au(111) to final structure of (10√3 × 10√3)

NASA Astrophysics Data System (ADS)

Kim, Jandee; Lee, Jaesung; Rhee, Choong Kyun

2016-02-01

Presented is a scanning tunneling microscopy (STM) study of structural evolution of TMA/Zn2 + ion network on Au(111) to the final structure of (10√3 × 10√3) during solution phase post-modification of pristine trimesic acid (TMA) network of a (5√3 × 5√3) structure with Zn2 + ions. Coordination of Zn2 + ions into adsorbed TMA molecules transforms crown-like TMA hexamers in pristine TMA network to chevron pairs in TMA/Zn2 + ion network. Two ordered transient structures of TMA/Zn2 + ion network were observed. One is a (5√7 × 5√7) structure consisting of Zn2 + ion-containing chevron pairs and Zn2 + ion-free TMA dimers. The other is a (5√39 × 5√21) structure made of chevron pairs and chevron-pair-missing sites. An STM image showing domains of different stages of crystallization of chevron pairs demonstrates that the TMA/Zn2 + network before reaching to the final one is quite dynamic. The observed structural evolution of the TMA/Zn2 + ion network is discussed in terms of modification of configurations of adsorbed TMA as accommodating Zn2 + ions and re-ordering of Zn2 + ion-containing chevron pairs.

Structural, electrical properties and dielectric relaxations in Na+-ion-conducting solid polymer electrolyte

NASA Astrophysics Data System (ADS)

Arya, Anil; Sharma, A. L.

2018-04-01

In this paper, we have studied the structural, microstructural, electrical, dielectric properties and ion dynamics of a sodium-ion-conducting solid polymer electrolyte film comprising PEO8-NaPF6+  x wt. % succinonitrile. The structural and surface morphology properties have been investigated, respectively using x-ray diffraction and field emission scanning electron microscopy. The complex formation was examined using Fourier transform infrared spectroscopy, and the fraction of free anions/ion pairs obtained via deconvolution. The complex dielectric permittivity and loss tangent has been analyzed across the whole frequency window, and enables us to estimate the DC conductivity, dielectric strength, double layer capacitance and relaxation time. The presence of relaxing dipoles was determined by the addition of succinonitrile (wt./wt.) and the peak shift towards high frequency indicates the decrease of relaxation time. Further, relations among various relaxation times ({{τ }{{\\varepsilon \\prime}}}>~{{τ }tanδ }>{{τ }z}>{{τ }m} ) have been elucidated. The complex conductivity has been examined across the whole frequency window; it obeys the Universal Power Law, and displays strong dependency on succinonitrile content. The sigma representation ({{σ }\\prime\\prime}~versus~{{σ }\\prime} ) was introduced in order to explore the ion dynamics by highlighting the dispersion region in the Cole–Cole plot ({{\\varepsilon }\\prime\\prime}~versus~{{\\varepsilon }\\prime} ) in the lower frequency window; increase in the semicircle radius indicates a decrease of relaxation time. This observation is accompanied by enhancement in ionic conductivity and faster ion transport. A convincing, logical scheme to justify the experimental data has been proposed.

Amorphization of Ta2O5 under swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Cusick, Alex B.; Lang, Maik; Zhang, Fuxiang; Sun, Kai; Li, Weixing; Kluth, Patrick; Trautmann, Christina; Ewing, Rodney C.

2017-09-01

Crystalline Ta2O5 powder is shown to amorphize under 2.2 GeV 197Au ion irradiation. Synchrotron X-ray diffraction (XRD), Raman spectroscopy, small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM) were used to characterize the structural transition from crystalline to fully-amorphous. Based on Rietveld refinement of XRD data, the initial structure is orthorhombic (P2mm) with a very large unit cell (a = 6.20, b = 40.29, c = 3.89 Å; V = 971.7 Å3), ideally containing 22 Ta and 55 O atoms. At a fluence of approximately 3 × 1011 ions/cm2, a diffuse amorphous background becomes evident, increasing in intensity relative to diffraction maxima until full amorphization is achieved at approximately 3 × 1012 ions/cm2. An anisotropic distortion of the orthorhombic structure occurred during the amorphization process, with an approximately constant unit cell volume. The amorphous phase fraction as a function of fluence was determined, yielding a trend that is consistent with a direct-impact model for amorphization. SAXS and TEM data indicate that ion tracks exhibit a core-shell morphology. Raman data show that the amorphous phase is comprised of TaO6 and TaO5 coordination-polyhedra in contrast to the TaO6 and TaO7 units that exist in crystalline Ta2O5. Analysis of Raman data shows that oxygen-deficiency increases with fluence, indicating a loss of oxygen that leads to an estimated final stoichiometry of Ta2O4.2 at a fluence of 1 × 1013 ions/cm2.

ESI-MS of Cucurbituril Complexes Under Negative Polarity.

PubMed

Rodrigues, Maria A A; Mendes, Débora C; Ramamurthy, Vaidhyanathan; Da Silva, José P

2017-11-01

Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool to study host-guest supramolecular interactions. ESI-MS can be used for detailed gas-phase reactivity studies, to clarify the structure, or simply to verify the formation of complexes. Depending on the structure of the host and of the guest, negative and/or positive ESI are used. Here we report the unexpected formation of host-guest complexes between cucurbit[n]urils (n = 7, 8, CB[n]) and amine, styryl pyridine, and styryl pyridine dimer cations, under negative ESI. Non-complexed CB[n] form double charged halide (Br - , Cl - , F - ) adducts. Under negative ESI, halide ions interact with CB[n] outer surface hydrogen atoms. One to one host-guest complexes (1:1) of CB[n] with positive charged guests were also observed as single and double charged ions under negative ESI. The positive charge of guests is neutralized by ion-pairing with halide anions. Depending on the number of positive charges guests retain in the gas phase, one or two additional halide ions are required for neutralization. Complexes 1:2 of CB[8] with styryl pyridines retain two halide ions in the gas phase, one per guest. Styryl pyridine dimers form 1:1 complexes possessing a single extra halide ion and therefore a single positive charge. Negative ESI is sensitive to small structural differences between complexes, distinguishing between 1:2 complexes of styryl pyridine-CB[8] and corresponding 1:1 complexes with the dimer. Negative ESI gives simpler spectra than positive ESI and allows the determination of guest charge state of CB[n] complexes in the gas phase. Graphical Abstract ᅟ.

Separation and characterization of unknown impurities and isomers in flomoxef sodium by LC-IT-TOF MS and study of their negative-ion fragmentation regularities.

PubMed

Yu, Xu; Wang, Fan; Li, Jiani; Shan, Weiguang; Zhu, Bingqi; Wang, Jian

2017-06-05

Thirteen unknown impurities in flomoxef sodium were separated and characterized by liquid chromatography coupled with high resolution ion trap/time-of-flight mass spectrometry (LC-IT-TOF MS)with positive and negative modes of electrospray ionization method for further improvement of official monographs in pharmacopoeias. The fragmentation patterns of impurities in flomoxef in the negative ion mode were studied in detail, and new negative-ion fragmentation regularities were discovered. Chromatographic separation was performed on a Kromasil C18 column (250mm×4.6mm, 5μm). The mobile phase consisted of (A) ammonium formate aqueous solution (10mM)-methanol (84:16, v/v) and (B) ammonium formate aqueous solution (10mM)-methanol (47:53, v/v). In order to determine the m/z values of the molecular ions and formulas of all detected impurities, full scan LC-MS in both positive and negative ion modes was firstly executed to obtain the m/z value of the molecules. Then LC-MS 2 and LC-MS 3 were carried out on target compounds to obtain as much structural information as possible. Complete fragmentation patterns of impurities were studied and used to obtain information about the structures of these impurities. Structures of thirteen unknown degradation products in flomoxef sodium were deduced based on the high resolution MS n data with both positive and negative modes. The forming mechanisms of degradation products in flomoxef sodium were also studied. Copyright © 2017. Published by Elsevier B.V.

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

PubMed Central

Serra, Martin J; Baird, John D; Dale, Taraka; Fey, Bridget L; Retatagos, Kimberly; Westhof, Eric

2002-01-01

Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated. PMID:12003491

Communication: Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

NASA Astrophysics Data System (ADS)

Burt, Michael; Amini, Kasra; Lee, Jason W. L.; Christiansen, Lars; Johansen, Rasmus R.; Kobayashi, Yuki; Pickering, James D.; Vallance, Claire; Brouard, Mark; Stapelfeldt, Henrik

2018-03-01

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created, following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

Negative electrospray ionization mass spectrometry: a method for sequencing and determining linkage position in oligosaccharides from branched hemicelluloses.

PubMed

Quéméner, Bernard; Vigouroux, Jacqueline; Rathahao, Estelle; Tabet, Jean Claude; Dimitrijevic, Aleksandra; Lahaye, Marc

2015-01-01

Xyloglucans of apple, tomato, bilberry and tamarind were hydrolyzed by commercial endo β-1-4-D-endoglucanase. The xylo-gluco-oligosaccharides (XylGos) released were separated on CarboPac PA 200 column in less than 15 min, and, after purification, they were structurally characterized by negative electrospray ionization mass spectrometry using a quadrupole time-of-flight (ESI-Q-TOF), a hybrid linear ion trap (LTQ)/Orbitrap and a hybrid quadrupole Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. In order to corroborate the fragmentation routes observed on XylGos, some commercial galacto-manno-oligosaccharides (GalMOs) and glucurono-xylo-oligosaccharides were also studied. The fragmentation pathways of the ionized GalMos were similar to those of XylGos ones. The product ion spectra were mainly characterized by prominent double cleavage (D) ions corresponding to the entire inner side chains. The directed fragmentation from the reducing end to the other end was observed for the main glycosylated backbone but also for the side-chains, allowing their complete sequencing. Relevant cross-ring cleavage ions from (0,2)X(j)-type revealed to be diagnostic of the 1-2-linked- glycosyl units from XylGos together with the 1-2-linked glucuronic acid unit from glucuronoxylans. Resonant activation in the LTQ Orbitrap allowed not only determining the type of all linkages but also the O-acetyl group location on fucosylated side-chains. Moreover, the fragmentation of the different side chains using the MS(n) capabilities of the LTQ/Orbitrap analyzer also allowed differentiating terminal arabinosyl and xylosyl substituents inside S and U side-chains of XylGos, respectively. The CID spectra obtained were very informative for distinction of isomeric structures differing only in their substitution pattern. These features together makes the fragmentation in negative ionization mode a relevant and powerful technique useful to highlight the subtle structural changes generally observed during the development of plant organs such as during fruit ripening and for the screening of cell wall mutants with altered hemicellulose structure. Copyright © 2015 John Wiley & Sons, Ltd.

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

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

Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng

Emergent lithium-ion (Li +) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li +, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporousmore » NiCo 2O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge–discharge cycles.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

DOE PAGES

Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng; ...

2017-02-07

Emergent lithium-ion (Li +) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li +, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporousmore » NiCo 2O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge–discharge cycles.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes.

PubMed

Bhaway, Sarang M; Qiang, Zhe; Xia, Yanfeng; Xia, Xuhui; Lee, Byeongdu; Yager, Kevin G; Zhang, Lihua; Kisslinger, Kim; Chen, Yu-Ming; Liu, Kewei; Zhu, Yu; Vogt, Bryan D

2017-02-28

Emergent lithium-ion (Li + ) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li + , but in many cases these nanostructures evolve during electrochemical charging-discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporous NiCo 2 O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge-discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Conversely, anodes with larger ordered mesopores (17-28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. This preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; however, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge-discharge cycles leads to capacity decay in battery performance. These multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) are translated to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge-discharge cycles.

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

Laskowski, Lukasz, E-mail: lukasz.laskowski@kik.pcz.pl; Laskowska, Magdalena, E-mail: magdalena.laskowska@onet.pl; Jelonkiewicz, Jerzy, E-mail: jerzy.jelonkiewicz@kik.pcz.pl

The SBA-15 silica thin films containing copper ions anchored inside channels via propyl phosphonate groups are investigated. Such materials were prepared in the form of thin films, with hexagonally arranged pores, laying rectilinear to the substrate surface. However, in the case of our thin films, their free standing form allowed for additional research possibilities, that are not obtainable for typical thin films on a substrate. The structural properties of the samples were investigated by X-ray reflectometry, atomic force microscopy (AFM) and transmission electron microscopy (TEM). The molecular structure was examined by Raman spectroscopy supported by numerical simulations. Magnetic measurements (SQUIDmore » magnetometry and EPR spectroscopy) showed weak antiferromagnetic interactions between active units inside silica channels. Consequently, the pores arrangement was determined and the process of copper ions anchoring by propyl phosphonate groups was verified in unambiguous way. Moreover, the type of interactions between magnetic atoms was determined. - Highlights: • Functionalized free-standing SBA-15 thin films were synthesized for a first time. • Thin films synthesis procedure was described in details. • Structural properties of the films were thoroughly investigated and presented. • Magnetic properties of the novel material was investigated and presented.« less

Trapping of muscle relaxant methocarbamol degradation product by complexation with copper(II) ion: Spectroscopic and quantum chemical studies

NASA Astrophysics Data System (ADS)

Mansour, Ahmed M.; Shehab, Ola R.

2014-07-01

Structural properties of methocarbamol (Mcm) were extensively studied both experimentally and theoretically using FT IR, 1H NMR, UV-Vis., geometry optimization, Mulliken charge, and molecular electrostatic potential. Stability arises from hyper-conjugative interactions, charge delocalization and H-bonding was analyzed using natural bond orbital (NBO) analysis. Mcm was decomposed in ethanol/water mixture at 80 °C to guaifenesin [(RS)-3-(2-methoxyphenoxy)propane-1,2-diol] and carbamate ion [NH2COO-], where the degradation mechanism was explained by trapping the carbamate ion via the complexation with copper(II) ion. The structure of the isolated complex ([Cu(NH2COO)2(H2O)]ṡ4H2O) was elucidated by spectral, thermal, and magnetic tools. Electronic spectra were discussed by TD-DFT and the descriptions of frontier molecular orbitals and the relocations of the electron density were determined. Calculated g-tensor values showed best agreement with experimental values from EPR when carried out using both the B3LYP and B3PW91 functional.

Hydrothermal growth of CuO nanoleaf structures, and their mercuric ion detection application.

PubMed

Ibupoto, Z H; Khun, K; Willander, M

2014-09-01

Mercury is the hazardous heavy metal ion for the environment and the human being therefore its determination is very important and herein we describe the development of mercury ion sensor on the CuO nanoleaf like nanostructures using cetyltrimethylammonium bromide (CTAB) surfactant as template for the growth by hydrothermal growth method. Scanning electron microscopy and X-ray diffraction study has shown high density and good crystal quality of the fabricated CuO nanostructures respectively. The presented mercury ion sensor has detected the wide range of 1.0 x 10(-7) to 1.0 x 10(-1) M mercury ion concentrations with an acceptable Nernstian behaviour and a sensitivity of 30.1 ± 0.6 mV/decade. The proposed mercury ion sensor exhibited low detection limit of 1.0 x 10(-8) M and also a fast response time of less than 5 s. In addition, the presented mercury ion sensor has shown an excellent repeatability, reproducibility, stability and selectivity. Moreover, the mercury ion selective electrode based on CuO nanoleaves was tested as an indicator electrode in the potentiometric titration.

Ion spectral structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

2015-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

N(+)-N and O(+)-O interaction energies, dipole transition moments, and transport cross sections

NASA Technical Reports Server (NTRS)

Partridge, H.; Stallcop, J. R.

1986-01-01

Complete sets of ion-atom interaction energies have been computed for nitrogen and oxygen with accurate large scale structure calculations. The computed energies agree well with the accurate potential curves available from spectroscopic measurement. The state functions from the nitrogen calculations have been applied to determine the transition moment for all allowed dipole transitions. These results can be combined to compute a detailed radiation spectrum such as that required to define the highly nonequilibrium environment of aeroassisted orbital transfer vehicle (AOTV). The long-range interaction energies have been used to determine the ion-atom resonance charge exchange cross sections that are important for transport processes such as diffusion. A calculation to determine reliable transport properties for energies that include the AOTV temperature range from these computed properties is described.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes

NASA Astrophysics Data System (ADS)

Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

2017-03-01

Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g-1, which is 6 times higher than disordered CNTs in HClO4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g-1), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g-1) and high energy density (98.1 Wh kg-1) in EMIBF4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation.

Impact of Lipid Oxidization on Vertical Structures and Electrostatics of Phospholipid Monolayers Revealed by Combination of Specular X-ray Reflectivity and Grazing-Incidence X-ray Fluorescence.

PubMed

Korytowski, Agatha; Abuillan, Wasim; Makky, Ali; Konovalov, Oleg; Tanaka, Motomu

2015-07-30

The influence of phospholipid oxidization of floating monolayers on the structure perpendicular to the global plane and on the density profiles of ions near the lipid monolayer has been investigated by a combination of grazing incidence X-ray fluorescence (GIXF) and specular X-ray reflectivity (XRR). Systematic variation of the composition of the floating monolayers unravels changes in the thickness, roughness and electron density of the lipid monolayers as a function of molar fraction of oxidized phospholipids. Simultaneous GIXF measurements enable one to qualitatively determine the element-specific density profiles of monovalent (K(+) or Cs(+)) and divalent ions (Ca(2+)) in the vicinity of the interface in the presence and absence of two types of oxidized phospholipids (PazePC and PoxnoPC) with high spatial accuracy (±5 Å). We found the condensation of Ca(2+) near carboxylated PazePC was more pronounced compared to PoxnoPC with an aldehyde group. In contrast, the condensation of monovalent ions could hardly be detected even for pure oxidized phospholipid monolayers. Moreover, pure phospholipid monolayers exhibited almost no ion specific condensation near the interface. The quantitative studies with well-defined floating monolayers revealed how the elevation of lipid oxidization level alters the structures and functions of cell membranes.

High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes.

PubMed

Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

2017-03-08

Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g -1 , which is 6 times higher than disordered CNTs in HClO 4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g -1 ), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g -1 ) and high energy density (98.1 Wh kg -1 ) in EMIBF 4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation.

Electron Detachment Dissociation of Underivatized Chloride-Adducted Oligosaccharides

NASA Astrophysics Data System (ADS)

Kornacki, James R.; Adamson, Julie T.; Håkansson, Kristina

2012-11-01

Chloride anion attachment has previously been shown to aid determination of saccharide anomeric configuration and generation of linkage information in negative ion post-source decay MALDI tandem mass spectrometry. Here, we employ electron detachment dissociation (EDD) and collision activated dissociation (CAD) for the structural characterization of underivatized oligosaccharides bearing a chloride ion adduct. Both neutral and sialylated oligosaccharides are examined, including maltoheptaose, an asialo biantennary glycan (NA2), disialylacto- N-tetraose (DSLNT), and two LS tetrasaccharides (LSTa and LSTb). Gas-phase chloride-adducted species are generated by negative ion mode electrospray ionization. EDD and CAD spectra of chloride-adducted oligosaccharides are compared to the corresponding spectra for doubly deprotonated species not containing a chloride anion to assess the role of chloride adduction in the stimulation of alternative fragmentation pathways and altered charge locations allowing detection of additional product ions. In all cases, EDD of singly chloridated and singly deprotonated species resulted in an increase in observed cross-ring cleavages, which are essential to providing saccharide linkage information. Glycosidic cleavages also increased in EDD of chloride-adducted oligosaccharides to reveal complementary structural information compared to traditional (non-chloride-assisted) EDD and CAD. Results indicate that chloride adduction is of interest in alternative anion activation methods such as EDD for oligosaccharide structural characterization.

High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes

PubMed Central

Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

2017-01-01

Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g−1, which is 6 times higher than disordered CNTs in HClO4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g−1), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g−1) and high energy density (98.1 Wh kg−1) in EMIBF4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation. PMID:28272474

A preliminary study of extended magnetic field structures in the ionosphere

NASA Technical Reports Server (NTRS)

Sullivan, James D.; Lane, Barton G.; Post, Richard S.

1987-01-01

Several plasma phenomena which are to be expected around a magnet in LEO were identified and analyzed qualitatively. The ASTROMAG cusp magnet will create an extended field whose strength drops to the ambient level over a scale length of approx. 15 m; the combined field has a complex topology with ring nulls and open and closed field lines. The entire configuration is moving through the partially ionized F-layer of the ionosphere at a speed slow compared to the local Alfven speed but fast compared to the ion sound speed. The ambient plasma crosses the extended field structure in a time short compared to the ion Larmor period yet long relative to the electron Larmor period. Thus, electrons behave as a magnetized fluid while ions move ballistically until reflected from higher fields near the cusp. Since the Debye length is short compared to the field scale length, an electrostatic shock-like structure forms to equilibrate the flows and achieve quasi-neutrality. The ambient plasma will be excluded from a cavity near the magnet. The size and nature of the strong interaction region in which the magnet significantly perturbs the ambient flow were determined by studying ion orbits numerically. Lecture viewgraphs summarizing these results are presented.

Secondary ionisations in a wall-less ion-counting nanodosimeter: quantitative analysis and the effect on the comparison of measured and simulated track structure parameters in nanometric volumes

NASA Astrophysics Data System (ADS)

Hilgers, Gerhard; Bug, Marion U.; Gargioni, Elisabetta; Rabus, Hans

2015-10-01

The object of investigation in nanodosimetry is the physical characteristics of the microscopic structure of ionising particle tracks, i.e. the sequence of the interaction types and interaction sites of a primary particle and all its secondaries, which reflects the stochastic nature of the radiation interaction. In view of the upcoming radiation therapy with protons and carbon ions, the ionisation structure of the ion track is of particular interest. Owing to limitations in current detector technology, the only way to determine the ionisation cluster size distribution in a DNA segment is to simulate the particle track structure in condensed matter. This is done using dedicated computer programs based on Monte Carlo procedures simulating the interaction of the primary ions with the target. Hence, there is a need to benchmark these computer codes using suitable experimental data. Ionisation cluster size distributions produced in the nanodosimeter's sensitive volume by monoenergetic protons and alpha particles (with energies between 0.1 MeV and 20 MeV) were measured at the PTB ion accelerator facilities. C3H8 and N2 were alternately used as the working gas. The measured data were compared with the simulation results obtained with the PTB Monte-Carlo code PTra [B. Grosswendt, Radiat. Environ. Biophys. 41, 103 (2002); M.U. Bug, E. Gargioni, H. Nettelbeck, W.Y. Baek, G. Hilgers, A.B. Rosenfeld, H. Rabus, Phys. Rev. E 88, 043308 (2013)]. Measured and simulated characteristics of the particle track structure are generally in good agreement for protons over the entire energy range investigated. For alpha particles with energies higher than the Bragg peak energy, a good agreement can also be seen, whereas for energies lower than the Bragg peak energy differences of as much as 25% occur. Significant deviations are only observed for large ionisation cluster sizes. These deviations can be explained by a background consisting of secondary ions. These ions are produced in the region downstream of the extraction aperture by electrons with a kinetic energy of about 2.5 keV, which are themselves released by ions of the "primary" ionisation cluster hitting an electrode in the ion transport system. Including this background of secondary ions in the simulated cluster size distributions leads to a significantly better agreement between measured and simulated data, especially for large ionisation clusters.

Structure-activity relationship of the ionic cocrystal: 5-amino-2-naphthalene sulfonate·ammonium ions for pharmaceutical applications

NASA Astrophysics Data System (ADS)

Sangeetha, M.; Mathammal, R.

2018-02-01

The ionic cocrystals of 5-amino-2-naphthalene sulfonate · ammonium ions (ANSA-ṡNH4+) were grown under slow evaporation method and examined in detail for pharmaceutical applications. The crystal structure and intermolecular interactions were studied from the single X-ray diffraction analysis and the Hirshfeld surfaces. The 2D fingerprint plots displayed the inter-contacts possible in the ionic crystal. Computational DFT method was established to determine the structural, physical and chemical properties. The molecular geometries obtained from the X-ray studies were compared with the optimized geometrical parameters calculated using DFT/6-31 + G(d,p) method. The band gap energy calculated from the UV-Visible spectral analysis and the HOMO-LUMO energy gap are compared. The theoretical UV-Visible calculations helped in determining the type of electronic transition taking place in the title molecule. The maximum absorption bands and transitions involved in the molecule represented the drug reaction possible. Non-linear optical properties were characterized from SHG efficiency measurements experimentally and the NLO parameters are also calculated from the optimized structure. The reactive sites within the molecule are detailed from the MEP surface maps. The molecular docking studies evident the structure-activity of the ionic cocrystal for anti-cancer drug property.

Structure and transport mechanism of the sodium/proton antiporter MjNhaP1

PubMed Central

Paulino, Cristina; Wöhlert, David; Kapotova, Ekaterina; Yildiz, Özkan; Kühlbrandt, Werner

2014-01-01

Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. 22Na+ uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na+ ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm. DOI: http://dx.doi.org/10.7554/eLife.03583.001 PMID:25426803

Synthesis and structure of novel lithium-ion conductor Li7Ge3PS12

NASA Astrophysics Data System (ADS)

Inoue, Yuki; Suzuki, Kota; Matsui, Naoki; Hirayama, Masaaki; Kanno, Ryoji

2017-02-01

The novel lithium-ion conductor Li7Ge3PS12 was synthesized by slow cooling from the ternary Li2S-GeS2-P2S5 system, and was shown to exhibit a cubic argyrodite-type structure. The phase composition was determined by varying the ratio of starting materials; the observed monophasic properties were close to those for the Li7Ge3PS12 composition. The lattice parameter (a =9.80192(3) Å) of Li7Ge3PS12 was slightly smaller than that of Li7PS6 (a =9.993 Å), indicating that substitution of a Li cation by the smaller Ge cation contracted the cubic lattice. In addition, the novel structure consisted of a framework composed of four isolated (Ge/P)S4 tetrahedra. Li+ ions occupied tetrahedral sites within the framework, forming a three-dimensional conduction pathway. Finally, Li7Ge3PS12 exhibited a high ionic conductivity of 1.1×10-4 S cm-1 at 25 °C and an activation energy of 25 kJ mol-1.

Initiation of viral RNA-dependent RNA polymerization.

PubMed

van Dijk, Alberdina A; Makeyev, Eugene V; Bamford, Dennis H

2004-05-01

This review summarizes the combined insights from recent structural and functional studies of viral RNA-dependent RNA polymerases (RdRPs) with the primary focus on the mechanisms of initiation of RNA synthesis. Replication of RNA viruses has traditionally been approached using a combination of biochemical and genetic methods. Recently, high-resolution structures of six viral RdRPs have been determined. For three RdRPs, enzyme complexes with metal ions, single-stranded RNA and/or nucleoside triphosphates have also been solved. These advances have expanded our understanding of the molecular mechanisms of viral RNA synthesis and facilitated further RdRP studies by informed site-directed mutagenesis. What transpires is that the basic polymerase right hand shape provides the correct geometrical arrangement of substrate molecules and metal ions at the active site for the nucleotidyl transfer catalysis, while distinct structural elements have evolved in the different systems to ensure efficient initiation of RNA synthesis. These elements feed the template, NTPs and ions into the catalytic cavity, correctly position the template 3' terminus, transfer the products out of the catalytic site and orchestrate the transition from initiation to elongation.

Velocity modulation spectroscopy of molecular ions II: The millimeter/submillimeter-wave spectrum of TiF + ( X3Φr)

NASA Astrophysics Data System (ADS)

Halfen, D. T.; Ziurys, L. M.

2006-11-01

The pure rotational spectrum of the molecular ion TiF + in its 3Φr ground state has been measured in the range 327-542 GHz using millimeter-wave direct absorption techniques combined with velocity modulation spectroscopy. TiF + was made in an AC discharge from a mixture of TiCl 4, F 2 in He, and argon. Ten transitions of this ion were recorded. In every transition, fluorine hyperfine interactions, as well as the fine structure splittings, were resolved. The fine structure pattern was found to be regular with almost equal spacing in frequency between the three spin components, in contrast to TiCl +, which is perturbed in the ground state. The data were fit with a case ( a) Hamiltonian and rotational, fine structure, and hyperfine constants were determined. The bond length established for TiF +, r0 = 1.7775 Å, was found to be shorter than that of TiF, r0 = 1.8342 Å—also established from mm-wave data. The hyperfine parameters determined are consistent with a δ1π1 electron configuration with the electrons primarily located on the titanium nucleus. The nuclear spin-orbit constant a indicates that the unpaired electrons are closer to the fluorine nucleus in TiF + relative to TiF, as expected with the decrease in bond length for the ion. The shorter bond distance is thought to arise from increased charge on the titanium nucleus as a result of a Ti 2+F - configuration. A similar decrease in bond length was found for TiCl + relative to TiCl.

Complementary study of the internal porous silicon layers formed under high-dose implantation of helium ions

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

Lomov, A. A., E-mail: lomov@ftian.ru; Myakon’kikh, A. V.; Chesnokov, Yu. M.

The surface layers of Si(001) substrates subjected to plasma-immersion implantation of helium ions with an energy of 2–5 keV and a dose of 5 × 10{sup 17} cm{sup –2} have been investigated using high-resolution X-ray reflectivity, Rutherford backscattering, and transmission electron microscopy. The electron density depth profile in the surface layer formed by helium ions is obtained, and its elemental and phase compositions are determined. This layer is found to have a complex structure and consist of an upper amorphous sublayer and a layer with a porosity of 30–35% beneath. It is shown that the porous layer has the sharpestmore » boundaries at a lower energy of implantable ions.« less

Iron-Based Nanomaterials/Graphene Composites for Advanced Electrochemical Sensors

PubMed Central

Movlaee, Kaveh; Ganjali, Mohmmad Reza; Norouzi, Parviz

2017-01-01

Iron oxide nanostructures (IONs) in combination with graphene or its derivatives—e.g., graphene oxide and reduced graphene oxide—hold great promise toward engineering of efficient nanocomposites for enhancing the performance of advanced devices in many applicative fields. Due to the peculiar electrical and electrocatalytic properties displayed by composite structures in nanoscale dimensions, increasing efforts have been directed in recent years toward tailoring the properties of IONs-graphene based nanocomposites for developing more efficient electrochemical sensors. In the present feature paper, we first reviewed the various routes for synthesizing IONs-graphene nanostructures, highlighting advantages, disadvantages and the key synthesis parameters for each method. Then, a comprehensive discussion is presented in the case of application of IONs-graphene based composites in electrochemical sensors for the determination of various kinds of (bio)chemical substances. PMID:29168771

Integrating a DNA Strand Displacement Reaction with a Whispering Gallery Mode Sensor for Label-Free Mercury (II) Ion Detection.

PubMed

Wu, Fengchi; Wu, Yuqiang; Niu, Zhongwei; Vollmer, Frank

2016-07-29

Mercury is an extremely toxic chemical pollutant of our environment. It has attracted the world's attention due to its high mobility and the ease with which it accumulates in organisms. Sensitive devices and methods specific for detecting mercury ions are, hence, in great need. Here, we have integrated a DNA strand displacement reaction with a whispering gallery mode (WGM) sensor for demonstrating the detection of Hg(2+) ions. Our approach relies on the displacement of a DNA hairpin structure, which forms after the binding of mercury ions to an aptamer DNA sequence. The strand displacement reaction of the DNA aptamer provides highly specific and quantitative means for determining the mercury ion concentration on a label-free WGM sensor platform. Our approach also shows the possibility for manipulating the kinetics of a strand displacement reaction with specific ionic species.

Integrating a DNA Strand Displacement Reaction with a Whispering Gallery Mode Sensor for Label-Free Mercury (II) Ion Detection

PubMed Central

Wu, Fengchi; Wu, Yuqiang; Niu, Zhongwei; Vollmer, Frank

2016-01-01

Mercury is an extremely toxic chemical pollutant of our environment. It has attracted the world’s attention due to its high mobility and the ease with which it accumulates in organisms. Sensitive devices and methods specific for detecting mercury ions are, hence, in great need. Here, we have integrated a DNA strand displacement reaction with a whispering gallery mode (WGM) sensor for demonstrating the detection of Hg2+ ions. Our approach relies on the displacement of a DNA hairpin structure, which forms after the binding of mercury ions to an aptamer DNA sequence. The strand displacement reaction of the DNA aptamer provides highly specific and quantitative means for determining the mercury ion concentration on a label-free WGM sensor platform. Our approach also shows the possibility for manipulating the kinetics of a strand displacement reaction with specific ionic species. PMID:27483277

Counting individual sulfur atoms in a protein by ultrahighresolution Fourier transform ion cyclotron resonance mass spectrometry: Experimental resolution of isotopic fine structure in proteins

PubMed Central

Shi, Stone D.-H.; Hendrickson, Christopher L.; Marshall, Alan G.

1998-01-01

A typical molecular ion mass spectrum consists of a sum of signals from species of various possible isotopic compositions. Only the monoisotopic peak (e.g., all carbons are 12C; all nitrogens are 14N, etc.) has a unique elemental composition. Every other isotope peak at approximately integer multiples of ∼1 Da higher in nominal mass represents a sum of contributions from isotope combinations differing by a few mDa (e.g., two 13C vs. two 15N vs. one 13C and one 15N vs. 34S, vs. 18O, etc., at ∼2 Da higher in mass than the monoisotopic mass). At sufficiently high mass resolving power, each of these nominal-mass peaks resolves into its isotopic fine structure. Here, we report resolution of the isotopic fine structure of proteins up to 15.8 kDa (isotopic 13C,15N doubly depleted tumor suppressor protein, p16), made possible by electrospray ionization followed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass analysis at 9.4 tesla. Further, a resolving power of m/Δm50% ≈8,000,000 has been achieved on bovine ubiquitin (8.6 kDa). These results represent a 10-fold increase in the highest mass at which isotopic fine structure previously had been observed. Finally, because isotopic fine structure reveals elemental composition directly, it can be used to confirm or determine molecular formula. For p16, for example, we were able to determine (5.1 ± 0.3) the correct number (five) of sulfur atoms solely from the abundance ratio of the resolved 34S peak to the monoisotopic peak. PMID:9751700

Synthesis and Structural Characterization of the Aluminosilicate LZ-135, a Zeolite Related to ZSM-10

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

McCusker, Lynne B.; Baerlocher, Christian; Wilson, Stephen T.

2009-09-02

The aluminosilicate LZ-135 was one of the first zeolites to be prepared in the presence of two or more organic structure-directing agents (in this case, Me{sub 4}N{sup +} (TMA) and Et{sub 4}N{sup +} (TEA)) and was patented 20 years ago. However, the material was polycrystalline, and at the time, its aluminosilicate framework structure could not be determined. In view of the fact that methods of structure determination from powder diffraction data have developed considerably in the meantime, a fresh analysis of the problem was undertaken. High-resolution synchrotron powder diffraction data were collected on a calcined sample of LZ-135 (as synthesizedmore » composition ca. |Na{sub 26}TMA{sub 6}|[Si{sub 76}Al{sub 32}O{sub 216}]), and the new powder charge-flipping structure-solution algorithm was applied. The framework structure (P6{sub 3}/mmc; a = 31.3830(2) {angstrom}, c = 7.6513(1) {angstrom}) was revealed immediately, and then the positions of the Na{sup +} ions and a few water molecules were located in a series of difference electron density maps. The [001] projection of the framework structure is identical to that of ZSM-10 (P6{sub 3}/mmm), but the (up-down) orientations of the (Si,Al) tetrahedra, and therefore their connectivities, are different, and this leads to a distinctly different topology with two 1-dimensional, 12-ring channel systems with effective pore widths of 7.2 and 6.5 {angstrom}. The new framework has been assigned the framework type code LTF by the International Zeolite Association. The framework structures of LZ-135 and ZSM-10 are related to one another in the same way as are those of mazzite and zeolite L. Approximately 27.5 Na{sup +} ions were located in six different sites, and all are coordinated to oxygen atoms of the framework. Twelve H{sub 2}O molecules per unit cell are associated with one of the Na{sup +} ion positions, where they serve to complete an octahedral coordination geometry around the ion, and 5.2 are located in the larger of the two 12-ring channels, where they make hydrogen-bonding contacts to framework oxygen atoms and are probably associated with protons.« less

Hydration Energies and Structures of Alkaline Earth Metal Ions, M2+ (H2O)n, n = 5–7, M = Mg, Ca, Sr, and Ba

PubMed Central

Rodriguez-Cruz, Sandra E.; Jockusch, Rebecca A.

2005-01-01

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M2+(H2O)n (M = Mg, Ca, and Sr for n = 5–7, and M = Ba for n = 4–7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (Eo) are determined. These reactions should have a negligible reverse activation barrier; therefore, Eo values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca2+, Sr2+, and Ba2+ are consistent with structures in which all the water molecules are located in the first solvation shell. PMID:16429612

Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4;#8201;Å

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

Johnson, Zachary Lee; Cheong, Cheom-Gil; Lee, Seok-Yong

2012-07-11

Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is also responsible for the termination of adenosine signalling. As a result of their hydrophilic nature, nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. In addition to nucleosides, NTs are important determinants for the transport of nucleoside-derived drugs across cell membranes. A wide range of nucleoside-derived drugs, including anticancer drugsmore » (such as Ara-C and gemcitabine) and antiviral drugs (such as zidovudine and ribavirin), have been shown to depend, at least in part, on NTs for transport across cell membranes. Concentrative nucleoside transporters, members of the solute carrier transporter superfamily SLC28, use an ion gradient in the active transport of both nucleosides and nucleoside-derived drugs against their chemical gradients. The structural basis for selective ion-coupled nucleoside transport by concentrative nucleoside transporters is unknown. Here we present the crystal structure of a concentrative nucleoside transporter from Vibrio cholerae in complex with uridine at 2.4 {angstrom}. Our functional data show that, like its human orthologues, the transporter uses a sodium-ion gradient for nucleoside transport. The structure reveals the overall architecture of this class of transporter, unravels the molecular determinants for nucleoside and sodium binding, and provides a framework for understanding the mechanism of nucleoside and nucleoside drug transport across cell membranes.« less

Influence of Carbon Nanotubes on the Structure Formation of Cement Matrix

NASA Astrophysics Data System (ADS)

Petrunin, S.; Vaganov, V.; Reshetniak, V.; Zakrevskaya, L.

2015-11-01

The potential of application of CNTs as a reinforcing agent in cement composites is governed by their unique mechanical and electronic properties. The analysis of concrete strength changes under CNTs introduction shows non-uniformity and sometimes inconsistency of results. Due to the fact that CNTs influence the hydration kinetics, structure and phase composition of concrete, an idea concerning the importance of interaction between the surface of CNTs and hydrate ions formed by the dissolution of the clinker phases has been suggested. In this paper, the theoretical and experimental study of interaction between hydrate ions and CNTs surface is discussed. Reference nanotubes and nanotubes functionalized by carboxylic groups are used in this research. Phase composition was determined by X-Ray analysis according to the Rietveld method. It was found that the presence of oxygen-containing functional groups on CNTs surface leads to intensification of the hydration process and increase in concentration of C-S-H gel from 65.9% to 74.4%. Special attention is usually paid to interactions between Ca2+ ions and CNTs, because the hardening rate and structure of cement stone are determined by principle of Ca2+ localization in the solution. In this paper the possible binding mechanisms are discussed. Based on the experimental results, the hypothesis regarding the formation of cement composite structure for different CNTs surface functionalizations is considered. According to this hypothesis, the CNTs act as the centers of crystallization for hydration products contributing to the acceleration of hydration, increase of the concentration of C-S-H gel and strength improvement of CNTs based composites.

Influence of the K+ ions and the superstoichiometric manganese on structure defects, magneto-transport and dielectric properties of magnetoresistive La0.7Ca0.3-xKxMn1+xO3-δ ceramic

NASA Astrophysics Data System (ADS)

Liedienov, N. A.; Pashchenko, A. V.; Pashchenko, V. P.; Prokopenko, V. K.; Tatarchuk, D. D.; Revenko, Yu. F.; Turchenko, V. A.; Burchovetskii, V. V.; Sycheva, V. Ya.; Sil'cheva, A. G.; Didenko, Yu. V.; Levchenko, G. G.

2017-09-01

The structure, its defects, nanostructural clustering and functional properties of the La0.7Ca0.3-xKxMn1+xO3-δ ceramic with x = 0-0.3 have been investigated by x-ray diffraction, thermogravimetric, SEM, resistance, magnetic, magnetoresistance and dielectric spectroscopy methods. We establish that the lattice parameter of the cubic structure increases when the Ca2+ ions are substituted with ions of K+. We show that the real perovskite structure contains different valence states of manganese MnA2 +,MnB3 + and MnB4 + in A- and B-positions, as well as vacancy type point defects, in the form of anionic V(a) and cationic V(c) vacancies. The increase in the content of the superstoichiometric manganese is connected to the nanostructured clustering process. We find that K+ and superstoichiometric manganese cause the increase in relative permittivity ɛ' and dielectric loss tangent angle tg δ. The experimental phase diagram of the magnetic state has been constructed and allows determining the composition of the magnetoresistant La0.7Ca0.3-xKxMn1+xO3-δ ceramics with set magnetotransport properties. The optimal La0.7Ca0.3-xKxMn1+xO3-δ composition showing the highest magnetoresistance effect at room temperature has been determined by comparing the functional properties of lanthanum-calcium, lanthanum-strontium and lanthanum-calcium-potassium manganites.

Global structure of forked DNA in solution revealed by high-resolution single-molecule FRET.

PubMed

Sabir, Tara; Schröder, Gunnar F; Toulmin, Anita; McGlynn, Peter; Magennis, Steven W

2011-02-09

Branched DNA structures play critical roles in DNA replication, repair, and recombination in addition to being key building blocks for DNA nanotechnology. Here we combine single-molecule multiparameter fluorescence detection and molecular dynamics simulations to give a general approach to global structure determination of branched DNA in solution. We reveal an open, planar structure of a forked DNA molecule with three duplex arms and demonstrate an ion-induced conformational change. This structure will serve as a benchmark for DNA-protein interaction studies.

Role of adrenal hormones in regulating distal nephron structure and ion transport.

PubMed

Stanton, B A

1985-08-01

Mineralocorticoid levels are an important determinant of membrane area and ion transport in the renal initial (ICT) and cortical (CCT) collecting tubules. Adrenalectomy leads to a dramatic and specific decrease in basolateral membrane area of principal (P) cells and depresses sodium reabsorption and potassium secretion. Although aldosterone replacement for 10 days restores basolateral membrane area and ATPase activity to control levels and dramatically elevates ion transport, glucocorticoids have no effect on basolateral membrane area, ion transport, or ATPase. It is suggested that the aldosterone-induced amplification of membrane area occurs as a mechanism whereby cells increase the number of ATPase pumps in the basolateral membrane. An acute (of 2-3 h) increase in aldosterone, but not dexamethasone, also stimulates potassium transport by the ICT. Future studies will have to establish whether the acute stimulation of transport by aldosterone involves a change in basolateral membrane area. It is concluded that mineralocorticoids, but not glucocorticoids, regulate sodium and potassium transport by P cells of the ICT and CCT, in part, by determining the number of ATPase pumps available for transport.

Location and magnetic relaxation properties of the stable tyrosine radical in photosystem II.

PubMed

Innes, J B; Brudvig, G W

1989-02-07

Dipolar interactions with neighboring metal ions can cause enhanced spin-lattice relaxation of free radicals. We have applied the theory of dipolar relaxation enhancement and shown that the dependence of the enhanced relaxation on the protein structure surrounding the free radical can be used to obtain distances from the free radical to the protein surface. To test the theoretical predictions, we have examined the effect of added Dy3+ complexes on the microwave power saturation of free radicals in two protein complexes of known structure: myoglobin nitroxide and the reaction center from Rhodobacter sphaeroides. Three cases have been considered: (1) metal ions bound to a specific site, (2) metal ions bound randomly over the protein surface, and (3) metal ions distributed randomly in solution. Only case 3, which assumes no specific binding, gave good agreement between the distances obtained by using the two model systems. The effect of added Dy3+ complexes on the microwave power saturation of signal IIslow from photosystem II (PSII) was used to determine the location of the stable tyrosine radical giving rise to signal IIslow. Assuming that the surface of a membrane-bound protein can be approximated as planar, we have obtained distances from the tyrosine radical to the membrane surface in thylakoids, in PSII membranes, and in Tris-washed PSII membranes. The distances we have determined are in good agreement with those predicted on the basis of a structural homology between the D1 and D2 subunits of PSII and the structurally characterized L and M subunits of the reaction center from purple non-sulfur bacteria. We have also examined the temperature dependence of the microwave power at half-saturation (P1/2) of signal IIslow from 4 to 200 K in dark-adapted PSII membranes. Above 70 K, the P1/2 increases as T2.5, which is consistent with a Raman relaxation mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)

From Supercomputer Modeling to Highest Mass Resolution in FT-ICR.

PubMed

N Nikolaev, Evgene; N Vladimirov, Gleb; Jertz, Roland; Baykut, Gökhan

2013-01-01

Understanding of behavior of ion ensembles inside FT-ICR cell based on the computer simulation of ion motion gives rise to the new ideas of cell designs. The recently introduced novel FT-ICR cell based on a Penning ion trap with specially shaped excitation and detection electrodes prevents distortion of ion cyclotron motion phases (normally caused by non-ideal electric trapping fields) by averaging the trapping DC electric field during the ion motion in the ICR cell. Detection times of 5 min resulting in resolving power close to 40,000,000 have been reached for reserpine at m/z 609 at a magnetic field of only 7 Tesla. Fine structures of resolved 13Cn isotopic cluster groups could be measured for molecular masses up to 5.7 kDa (insulin) with resolving power of 4,000,000 at 7 Tesla. Based on resolved fine structure patterns atomic compositions can be directly determined using a new developed algorithm for fine structure processing. Mass spectra of proteins and multimers of proteins reaching masses up to 186 kDa (enolase tetramer) could be measured with isotopic resolution. For instance, at 7 Tesla resolving power of 800,000 was achieved for enolase dimer (96 kDa) and 500,000 for molecular masses above 100 kDa. Experimental data indicate that there is practically no limit for the resolving power of this ICR cell except by collisional damping in the ultrahigh vacuum chamber.

Homogeneous alignment of nematic liquid crystals by ion beam etched surfaces

NASA Technical Reports Server (NTRS)

Wintucky, E. G.; Mahmood, R.; Johnson, D. L.

1979-01-01

A wide range of ion beam etch parameters capable of producing uniform homogeneous alignment of nematic liquid crystals on SiO2 films are discussed. The alignment surfaces were generated by obliquely incident (angles of 5 to 25 deg) argon ions with energies in the range of 0.5 to 2.0 KeV, ion current densities of 0.1 to 0.6 mA sq cm and etch times of 1 to 9 min. A smaller range of ion beam parameters (2.0 KeV, 0.2 mA sq cm, 5 to 10 deg and 1 to 5 min.) were also investigated with ZrO2 films and found suitable for homogeneous alignment. Extinction ratios were very high (1000), twist angles were small ( or = 3 deg) and tilt-bias angles very small ( or = 1 deg). Preliminary scanning electron microscopy results indicate a parallel oriented surface structure on the ion beam etched surfaces which may determine alignment.

Modeling Magnetotail Ion Distributions with Global Magnetohydrodynamic and Ion Trajectory Calculations

NASA Technical Reports Server (NTRS)

El-Alaoui, M.; Ashour-Abdalla, M.; Raeder, J.; Peroomian, V.; Frank, L. A.; Paterson, W. R.; Bosqued, J. M.

1998-01-01

On February 9, 1995, the Comprehensive Plasma Instrumentation (CPI) on the Geotail spacecraft observed a complex, structured ion distribution function near the magnetotail midplane at x approximately -30 R(sub E). On this same day the Wind spacecraft observed a quiet solar wind and an interplanetary magnetic field (IMF) that was northward for more than five hours, and an IMF B(sub y) component with a magnitude comparable to that of the RAF B(sub z) component. In this study, we determined the sources of the ions in this distribution function by following approximately 90,000 ion trajectories backward in time, using the time-dependent electric and magnetic fields obtained from a global MHD simulation. The Wind observations were used as input for the MHD model. The ion distribution function observed by Geotail at 1347 UT was found to consist primarily of particles from the dawn side low latitude boundary layer (LLBL) and from the dusk side LLBL; fewer than 2% of the particles originated in the ionosphere.

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

PubMed

Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

2012-05-01

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Ultrasensitive colorimetric detection of Cu2+ ion based on catalytic oxidation of L-cysteine.

PubMed

Yin, Kun; Li, Bowei; Wang, Xiaochun; Zhang, Weiwei; Chen, Lingxin

2015-02-15

As an essential element, copper ion (Cu(2+)) plays important roles in human beings for its participation in diverse metabolic processes as a cofactor and/or a structural component of enzymes. However, excessive uptake of Cu(2+) ion gives rise to the risk of certain diseases. So, it is important to develop simple ways to monitor and detect Cu(2+) ion. In this study, a simple, facile colorimetric sensor for the ultrasensitive determination of Cu(2+) ion was developed based on the following principle: L-cysteine and 1-chloro-2,4-dinitrobenzene (CDNB) could be conjugated to form the yellow product 2,4-dinitrophenylcysteine (DNPC), which was measurable at 355nm; however, upon addition of Cu(2+) ion, the absorbance of DNPC would be decreased owing to the Cu(2+) ion catalytic oxidation of L-cysteine to L-cystine in the presence of O2. Thus, the colorimetric detection of Cu(2+) ion could be achieved. The optimal pH, buffer, temperature and incubation time for the colorimetric sensor were obtained of pH 6.8 in 0.1M HEPES solution, 90 °C and 50 min, respectively. A good linearity within the range of 0.8-10 nM (r = 0.996) was attained, with a high detectability up to 0.5nM. Analyses of Cu(2+) ion in drinking water, lake water, seawater and biological samples were carried out and the method performances were found to agree well with that obtained by ICP-MS. The developed simple colorimetric sensor proved applicable for Cu(2+) ion determination in real samples with high sensitivity and selectivity. Copyright © 2014 Elsevier B.V. All rights reserved.

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Ionic structure in liquids confined by dielectric interfaces

NASA Astrophysics Data System (ADS)

Jing, Yufei; Jadhao, Vikram; Zwanikken, Jos W.; Olvera de la Cruz, Monica

2015-11-01

The behavior of ions in liquids confined between macromolecules determines the outcome of many nanoscale assembly processes in synthetic and biological materials such as colloidal dispersions, emulsions, hydrogels, DNA, cell membranes, and proteins. Theoretically, the macromolecule-liquid boundary is often modeled as a dielectric interface and an important quantity of interest is the ionic structure in a liquid confined between two such interfaces. The knowledge gleaned from the study of ionic structure in such models can be useful in several industrial applications, such as in the design of double-layer supercapacitors for energy storage and in the extraction of metal ions from wastewater. In this article, we compute the ionic structure in a model system of electrolyte confined by two planar dielectric interfaces using molecular dynamics simulations and liquid state theory. We explore the effects of high electrolyte concentrations, multivalent ions, dielectric contrasts, and external electric field on the ionic distributions. We observe the presence of non-monotonic ionic density profiles leading to a layered structure in the fluid which is attributed to the competition between electrostatic and steric (entropic) interactions. We find that thermal forces that arise from symmetry breaking at the interfaces can have a profound effect on the ionic structure and can oftentimes overwhelm the influence of the dielectric discontinuity. The combined effect of ionic correlations and inhomogeneous dielectric permittivity significantly changes the character of the effective interaction between the two interfaces.

STRUCTURAL DETERMINATION AND QUANTITATIVE ANALYSIS OF BACTERIAL PHOSPHOLIPIDS USING LIQUID CHROMATOGRAPHY/ELECTROSPRAY IONIZATION/MASS SPECTROMETRY

EPA Science Inventory

This report presents a comprehensive spectral analysis of common bacterial phospholipids using electrospray/mass spectrometry (ESI/MS) under both negative and positive ionization conditions. Phospholipids under positive ionization yield sodium-adduct molecular ions which are mos...

Importance of Diffuse Metal Ion Binding to RNA

PubMed Central

Tan, Zhi-Jie; Chen, Shi-Jie

2016-01-01

RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding. PMID:22010269

Importance of diffuse metal ion binding to RNA.

PubMed

Tan, Zhi-Jie; Chen, Shi-Jie

2011-01-01

RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

Persistent homology analysis of ion aggregations and hydrogen-bonding networks.

PubMed

Xia, Kelin

2018-05-16

Despite the great advancement of experimental tools and theoretical models, a quantitative characterization of the microscopic structures of ion aggregates and their associated water hydrogen-bonding networks still remains a challenging problem. In this paper, a newly-invented mathematical method called persistent homology is introduced, for the first time, to quantitatively analyze the intrinsic topological properties of ion aggregation systems and hydrogen-bonding networks. The two most distinguishable properties of persistent homology analysis of assembly systems are as follows. First, it does not require a predefined bond length to construct the ion or hydrogen-bonding network. Persistent homology results are determined by the morphological structure of the data only. Second, it can directly measure the size of circles or holes in ion aggregates and hydrogen-bonding networks. To validate our model, we consider two well-studied systems, i.e., NaCl and KSCN solutions, generated from molecular dynamics simulations. They are believed to represent two morphological types of aggregation, i.e., local clusters and extended ion networks. It has been found that the two aggregation types have distinguishable topological features and can be characterized by our topological model very well. Further, we construct two types of networks, i.e., O-networks and H2O-networks, for analyzing the topological properties of hydrogen-bonding networks. It is found that for both models, KSCN systems demonstrate much more dramatic variations in their local circle structures with a concentration increase. A consistent increase of large-sized local circle structures is observed and the sizes of these circles become more and more diverse. In contrast, NaCl systems show no obvious increase of large-sized circles. Instead a consistent decline of the average size of the circle structures is observed and the sizes of these circles become more and more uniform with a concentration increase. As far as we know, these unique intrinsic topological features in ion aggregation systems have never been pointed out before. More importantly, our models can be directly used to quantitatively analyze the intrinsic topological invariants, including circles, loops, holes, and cavities, of any network-like structures, such as nanomaterials, colloidal systems, biomolecular assemblies, among others. These topological invariants cannot be described by traditional graph and network models.

Electrochemical and density functional theory investigation on the differential behaviors of core-ring structured NiCo2O4 nanoplatelets toward heavy metal ions.

PubMed

Liao, Jianjun; Zhang, Junping; Wang, Cai-Zhuang; Lin, Shiwei

2018-08-31

In order to further improve the electroanalytical performance toward heavy metal ions, core-ring structured NiCo 2 O 4 nanoplatelets were used to modify glass carbon electrode (GCE) for the determination of heavy metal ions in water. Owing to the high surface area of NiCo 2 O 4 nanoplatelets, the Pb(II) sensitivity increased by a factor of 1.70, and the detection limit decreased by a factor of 2.64 as compared to solid NiCo 2 O 4 nanoparticles modified GCE. Interestingly, NiCo 2 O 4 nanoplatelets showed different sensitivities toward heavy metal ions with the same valence states, following the order Pb(II) > Cd(II) > Hg(II) > Cu(II). To better and scientifically understand the difference in sensitivity, adsorption and desorption abilities were integrated into account. Density functional theory calculations verified that the adsorption capability of NiCo 2 O 4 toward Pb(II) was strongest among all heavy metal ions, thereby resulting in the largest sensitivity. Further desorption current measurements indicated the large desorption barrier of Cu(II) was another important factor leading to its lowest sensitivity. Finally, the applicability of the proposed method was demonstrated by the detection of heavy metal ions in real seawater. Copyright © 2018 Elsevier B.V. All rights reserved.

Thomson scattering from a three-component plasma.

PubMed

Johnson, W R; Nilsen, J

2014-02-01

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

Analysis of a series of chlorogenic acid isomers using differential ion mobility and tandem mass spectrometry.

PubMed

Willems, Jamie L; Khamis, Mona M; Mohammed Saeid, Waleed; Purves, Randy W; Katselis, George; Low, Nicholas H; El-Aneed, Anas

2016-08-24

Chlorogenic acids are among the most abundant phenolics found in the human diet. Of these, the mono-caffeoylquinic acids are the predominant phenolics found in fruits, such as apples and pears, and products derived from them. In this research, a comprehensive study of the electrospray ionization (ESI) tandem mass spectrometric (MS/MS) dissociation behavior of the three most common mono-caffeoylquinic acids, namely 5-O-caffeoylquinic acid (5-CQA), 3-O-caffeoylquinic acid (3-CQA) and 4-O-caffeoylquinic acid (4-CQA), were determined using both positive and negative ionization. All proposed structures of the observed product ions were confirmed with second-generation MS(3) experiments. Similarities and differences between the dissociation pathways in the positive and negative ion modes are discussed, confirming the proposed structures and the established MS/MS fingerprints. MS/MS dissociation was primarily driven via the cleavage of the ester bond linking the quinic acid moiety to the caffeic acid moiety within tested molecules. Despite being structural isomers with the same m/z values and dissociation behaviors, the MS/MS data in the negative ion mode was able to differentiate the three isomers based on ion intensity for the major product ions, observed at m/z 191, 179 and 173. This differentiation was consistent among various MS instruments. In addition, ESI coupled with high-field asymmetric waveform ion mobility spectrometry-mass spectrometry (ESI-FAIMS-MS) was employed for the separation of these compounds for the first time. By combining MS/MS data and differential ion mobility, a method for the separation and identification of mono-caffeoylquinic in apple/pear juice samples was developed with a run time of less than 1 min. It is envisaged that this methodology could be used to identify pure juices based on their chlorogenic acid profile (i.e., metabolomics), and could also be used to detect juice-to-juice adulteration (e.g., apple juice addition to pear juice). Copyright © 2016 Elsevier B.V. All rights reserved.

Specificity enhancement by electrospray ionization multistage mass spectrometry--a valuable tool for differentiation and identification of 'V'-type chemical warfare agents.

PubMed

Weissberg, Avi; Tzanani, Nitzan; Dagan, Shai

2013-12-01

The use of chemical warfare agents has become an issue of emerging concern. One of the challenges in analytical monitoring of the extremely toxic 'V'-type chemical weapons [O-alkyl S-(2-dialkylamino)ethyl alkylphosphonothiolates] is to distinguish and identify compounds of similar structure. MS analysis of these compounds reveals mostly fragment/product ions representing the amine-containing residue. Hence, isomers or derivatives with the same amine residue exhibit similar mass spectral patterns in both classical EI/MS and electrospray ionization-MS, leading to unavoidable ambiguity in the identification of the phosphonate moiety. A set of five 'V'-type agents, including O-ethyl S-(2-diisopropylamino)ethyl methylphosphonothiolate (VX), O-isobutyl S-(2-diethylamino)ethyl methylphosphonothiolate (RVX) and O-ethyl S-(2-diethylamino)ethyl methylphosphonothiolate (VM) were studied by liquid chromatography/electrospray ionization/MS, utilizing a QTRAP mass detector. MS/MS enhanced product ion scans and multistage MS(3) experiments were carried out. Based on the results, possible fragmentation pathways were proposed, and a method for the differentiation and identification of structural isomers and derivatives of 'V'-type chemical warfare agents was obtained. MS/MS enhanced product ion scans at various collision energies provided information-rich spectra, although many of the product ions obtained were at low abundance. Employing MS(3) experiments enhanced the selectivity for those low abundance product ions and provided spectra indicative of the different phosphonate groups. Study of the fragmentation pathways, revealing some less expected structures, was carried out and allowed the formulation of mechanistic rules and the determination of sets of ions typical of specific groups, for example, methylphosphonothiolates versus ethylphosphonothiolates. The new group-specific ions elucidated in this work are also useful for screening unknown 'V'-type agents and related compounds, utilizing precursor ion scan experiments. Copyright © 2013 John Wiley & Sons, Ltd.

Effect of the L499M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties

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

Osipov, Evgeny; Polyakov, Konstantin; Engelhardt Institute of Molecular Biology, Vavilova Str. 32, Moscow 119991

2014-11-01

The structures of the ascomycetous B. aclada laccase and its L499M T1-site mutant have been solved at 1.7 Å resolution. The mutant enzyme shows a 140 mV lower redox potential of the type 1 copper and altered kinetic behaviour. The wild type and the mutant have very similar structures, which makes it possible to relate the changes in the redox potential to the L499M mutation Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain fourmore » Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. The redox potential of the T1 copper ion influences the enzymatic reaction and is determined by the nature of the axial ligands and the structure of the second coordination sphere. In this work, the laccase from the ascomycete Botrytis aclada was studied, which contains conserved Ile491 and nonconserved Leu499 residues in the axial positions. The three-dimensional structures of the wild-type enzyme and the L499M mutant were determined by X-ray crystallography at 1.7 Å resolution. Crystals suitable for X-ray analysis could only be grown after deglycosylation. Both structures did not contain the T2 copper ion. The catalytic properties of the enzyme were characterized and the redox potentials of both enzyme forms were determined: E{sub 0} = 720 and 580 mV for the wild-type enzyme and the mutant, respectively. Since the structures of the wild-type and mutant forms are very similar, the change in the redox potential can be related to the L499M mutation in the T1 site of the enzyme.« less

Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

2012-03-01

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

Retrograde degeneration of neurite membrane structural integrity of nerve growth cones following in vitro exposure to mercury.

PubMed

Leong, C C; Syed, N I; Lorscheider, F L

2001-03-26

Inhalation of mercury vapor (Hg0) inhibits binding of GTP to rat brain tubulin, thereby inhibiting tubulin polymerization into microtubules. A similar molecular lesion has also been observed in 80% of brains from patients with Alzheimer disease (AD) compared to age-matched controls. However the precise site and mode of action of Hg ions remain illusive. Therefore, the present study examined whether Hg ions could affect membrane dynamics of neurite growth cone morphology and behavior. Since tubulin is a highly conserved cytoskeletal protein in both vertebrates and invertebrates, we hypothesized that growth cones from animal species could be highly susceptible to Hg ions. To test this possibility, the identified, large Pedal A (PeA) neurons from the central ring ganglia of the snail Lymnoea stagnalis were cultured for 48 h in 2 ml brain conditioned medium (CM). Following neurite outgrowth, metal chloride solution (2 microl) of Hg, Al, Pb, Cd, or Mn (10(-7) M) was pressure applied directly onto individual growth cones. Time-lapse images with inverted microscopy were acquired prior to, during, and after the metal ion exposure. We demonstrate that Hg ions markedly disrupted membrane structure and linear growth rates of imaged neurites in 77% of all nerve growth cones. When growth cones were stained with antibodies specific for both tubulin and actin, it was the tubulin/microtubule structure that disintegrated following Hg exposure. Moreover, some denuded neurites were also observed to form neurofibrillary aggregates. In contrast, growth cone exposure to other metal ions did not effect growth cone morphology, nor was their motility rate compromised. To determine the growth suppressive effects of Hg ions on neuronal sprouting, cells were cultured either in the presence or absence of Hg ions. We found that in the presence of Hg ions, neuronal somata failed to sprout, whereas other metalic ions did not effect growth patterns of cultured PeA cells. We conclude that this visual evidence and previous biochemical data strongly implicate Hg as a potential etiological factor in neurodegeneration.

The structure of epitaxial V2O3 films and their surfaces: A medium energy ion scattering study

NASA Astrophysics Data System (ADS)

Window, A. J.; Hentz, A.; Sheppard, D. C.; Parkinson, G. S.; Woodruff, D. P.; Unterberger, W.; Noakes, T. C. Q.; Bailey, P.; Ganduglia-Pirovano, M. V.; Sauer, J.

2012-11-01

Medium energy ion scattering, using 100 keV H+ incident ions, has been used to investigate the growth of epitaxial films, up to thicknesses of ~ 200 Å, of V2O3 on both Pd(111) and Au(111). Scattered-ion energy spectra provide a measure of the average film thickness and the variations in this thickness, and show that, with suitable annealing, the crystalline quality is good. Plots of the scattering yield as a function of scattering angle, so-called blocking curves, have been measured for two different incidence directions and have been used to determine the surface structure. Specifically, scattering simulations for a range of different model structures show poor agreement with experiment for half-metal (….V'O3V) and vanadyl (….V'O3V=O) terminations, with and without surface interlayer relaxations. However, good agreement with experiment is found for the modified oxygen-termination structure, first proposed by Kresse et al., in which a subsurface V half-metal layer is moved up into the outermost V buckled metal layer to produce a VO2 overlayer on the underlying V2O3, with an associated layer structure of ….O3VV''V 'O3. This result is consistent with the predictions of thermodynamic equilibrium at the surface under the surface preparation conditions, but is at variance with the conclusions of earlier studies of this system that have favoured the vanadyl termination. The results of these previous studies are re-evaluated in the light of the new result.

Structural and emission characteristics of ion-irradiated Reticulated Vitreous Carbon

NASA Astrophysics Data System (ADS)

Chacon, Judith Rebecca

Cathodes formed from Reticulated Vitreous Carbon (RVC) were treated under varying conditions of Argon-ion beam current, beam voltage and irradiation duration. Surface structures, such as balls, cones, nanowires, and nanowhiskers were formed in the RVC network through a series of ion-impact sputtering and self-diffusion reactions. Raman shifts to the D and E2g' peak suggest C=C bonding within the original RVC structure was converted to the lesser-bound C-C bonding structure. Cathodes demonstrating the most stable electronic configuration exhibited significant vertical growth to graphitic domains as determined by calculations based on XRD measurements. Carbon nanotubes at the surface were observed at the surface through micro-Raman techniques. The surface structures formed by argon-bombardment, are responsible for cathodes exhibiting lower field-emission extraction fields. The electric field required for the onset of electron emission was measured to change from 6.03 V/micron in non-irradiated RVC to 1.62V/micron for RVC irradiated for 15 minutes at a beam voltage of 1200V and beam current of 200mA (ion-beam current density 2.24mA/cm2). Treated surfaces were also responsible for increased stability in emission over time. For untreated RVC, the field required for emission dropped 25% over a 48 hour training period, whilst modestly treated RVC (15min, 1200V, 100mA, or 1.52mA/cm2) rose as little as 3%. Field-emissive RVC, is an inexpensively produced, mechanically robust cathode with potential applications in lighting, displays and microwave sources.

Fingerprinting Desmosine-Containing Elastin Peptides

NASA Astrophysics Data System (ADS)

Schräder, Christoph U.; Heinz, Andrea; Majovsky, Petra; Schmelzer, Christian E. H.

2015-05-01

Elastin is a vital protein of the extracellular matrix of jawed vertebrates and provides elasticity to numerous tissues. It is secreted in the form of its soluble precursor tropoelastin, which is subsequently cross-linked in the course of the elastic fiber assembly. The process involves the formation of the two tetrafunctional amino acids desmosine (DES) and isodesmosine (IDES), which are unique to elastin. The resulting high degree of cross-linking confers remarkable properties, including mechanical integrity, insolubility, and long-term stability to the protein. These characteristics hinder the structural elucidation of mature elastin. However, MS2 data of linear and cross-linked peptides released by proteolysis can provide indirect insights into the structure of elastin. In this study, we performed energy-resolved collision-induced dissociation experiments of DES, IDES, their derivatives, and DES-/IDES-containing peptides to determine characteristic product ions. It was found that all investigated compounds yielded the same product ion clusters at elevated collision energies. Elemental composition determination using the exact masses of these ions revealed molecular formulas of the type CxHyN, suggesting that the pyridinium core of DES/IDES remains intact even at relatively high collision energies. The finding of these specific product ions enabled the development of a similarity-based scoring algorithm that was successfully applied on LC-MS/MS data of bovine elastin digests for the identification of DES-/IDES-cross-linked peptides. This approach facilitates the straightforward investigation of native cross-links in elastin.

Fingerprinting desmosine-containing elastin peptides.

PubMed

Schräder, Christoph U; Heinz, Andrea; Majovsky, Petra; Schmelzer, Christian E H

2015-05-01

Elastin is a vital protein of the extracellular matrix of jawed vertebrates and provides elasticity to numerous tissues. It is secreted in the form of its soluble precursor tropoelastin, which is subsequently cross-linked in the course of the elastic fiber assembly. The process involves the formation of the two tetrafunctional amino acids desmosine (DES) and isodesmosine (IDES), which are unique to elastin. The resulting high degree of cross-linking confers remarkable properties, including mechanical integrity, insolubility, and long-term stability to the protein. These characteristics hinder the structural elucidation of mature elastin. However, MS(2) data of linear and cross-linked peptides released by proteolysis can provide indirect insights into the structure of elastin. In this study, we performed energy-resolved collision-induced dissociation experiments of DES, IDES, their derivatives, and DES-/IDES-containing peptides to determine characteristic product ions. It was found that all investigated compounds yielded the same product ion clusters at elevated collision energies. Elemental composition determination using the exact masses of these ions revealed molecular formulas of the type CxHyN, suggesting that the pyridinium core of DES/IDES remains intact even at relatively high collision energies. The finding of these specific product ions enabled the development of a similarity-based scoring algorithm that was successfully applied on LC-MS/MS data of bovine elastin digests for the identification of DES-/IDES-cross-linked peptides. This approach facilitates the straightforward investigation of native cross-links in elastin.

Cobalt spin states and hyperfine interactions in LaCoO3 investigated by LDA+U calculations

NASA Astrophysics Data System (ADS)

Hsu, Han; Blaha, Peter; Wentzcovitch, Renata M.; Leighton, C.

2010-09-01

With a series of local-density approximation plus Hubbard U calculations, we have demonstrated that for lanthanum cobaltite (LaCoO3) , the electric field gradient at the cobalt nucleus can be used as a fingerprint to identify the spin state of the cobalt ion. Therefore, in principle, the spin state of the cobalt ion can be unambiguously determined from nuclear magnetic resonance spectra. Our calculations also suggest that a crossover from the low-spin to intermediate-spin state in the temperature range of 0-90 K is unlikely, based on the half-metallic band structure associated with isolated IS Co ions, which is incompatible with the measured conductivity.

Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

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

Suzuki, Nobuhiro; Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602; Yamazaki, Yasuo

2008-10-01

The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinitiesmore » on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn{sup 2+}-bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn{sup 2+} ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn{sup 2+} binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels.« less

Entropy-Driven Folding of an RNA Helical Junction: An Isothermal Titration Calorimetric Analysis of the Hammerhead Ribozyme†

PubMed Central

Mikulecky, Peter J.; Takach, Jennifer C.; Feig, Andrew L.

2008-01-01

Helical junctions are extremely common motifs in naturally occurring RNAs, but little is known about the thermodynamics that drive their folding. Studies of junction folding face several challenges: non-two-state folding behavior, superposition of secondary and tertiary structural energetics, and drastically opposing enthalpic and entropic contributions to folding. Here we describe a thermodynamic dissection of the folding of the hammerhead ribozyme, a three-way RNA helical junction, by using isothermal titration calorimetry of bimolecular RNA constructs. By using this method, we show that tertiary folding of the hammerhead core occurs with a highly unfavorable enthalpy change, and is therefore entropically driven. Furthermore, the enthalpies and heat capacities of core folding are the same whether supported by monovalent or divalent ions. These properties appear to be general to the core sequence of bimolecular hammerhead constructs. We present a model for the ion-induced folding of the hammerhead core that is similar to those advanced for the folding of much larger RNAs, involving ion-induced collapse to a structured, non-native state accompanied by rearrangement of core residues to produce the native fold. In agreement with previous enzymological and structural studies, our thermodynamic data suggest that the hammerhead structure is stabilized in vitro predominantly by diffusely bound ions. Our approach addresses several significant challenges that accompany the study of junction folding, and should prove useful in defining the thermodynamic determinants of stability in these important RNA motifs. PMID:15134461

Mean bond-length variations in crystals for ions bonded to oxygen

PubMed Central

2017-01-01

Variations in mean bond length are examined in oxide and oxysalt crystals for 55 cation configurations bonded to O2−. Stepwise multiple regression analysis shows that mean bond length is correlated to bond-length distortion in 42 ion configurations at the 95% confidence level, with a mean coefficient of determination (〈R 2〉) of 0.35. Previously published correlations between mean bond length and mean coordination number of the bonded anions are found not to be of general applicability to inorganic oxide and oxysalt structures. For two of 11 ions tested for the 95% confidence level, mean bond lengths predicted using a fixed radius for O2− are significantly more accurate as those predicted using an O2− radius dependent on coordination number, and are statistically identical otherwise. As a result, the currently accepted ionic radii for O2− in different coordinations are not justified by experimental data. Previously reported correlation between mean bond length and the mean electronegativity of the cations bonded to the oxygen atoms of the coordination polyhedron is shown to be statistically insignificant; similar results are obtained with regard to ionization energy. It is shown that a priori bond lengths calculated for many ion configurations in a single structure-type leads to a high correlation between a priori and observed mean bond lengths, but a priori bond lengths calculated for a single ion configuration in many different structure-types leads to negligible correlation between a priori and observed mean bond lengths. This indicates that structure type has a major effect on mean bond length, the magnitude of which goes beyond that of the other variables analyzed here.

Structure of the Magnetotail Current Sheet

NASA Technical Reports Server (NTRS)

Larson, Douglas J.; Kaufmann, Richard L.

1996-01-01

An orbit tracing technique was used to generate current sheets for three magnetotail models. Groups of ions were followed to calculate the resulting cross-tail current. Several groups then were combined to produce a current sheet. The goal is a model in which the ions and associated electrons carry the electric current distribution needed to generate the magnetic field B in which ion orbits were traced. The region -20 R(sub E) less than x less than - 14 R(sub E) in geocentric solar magnetospheric coordinates was studied. Emphasis was placed on identifying the categories of ion orbits which contribute most to the cross-tail current and on gaining physical insight into the manner by which the ions carry the observed current distribution. Ions that were trapped near z = 0, ions that magnetically mirrored throughout the current sheet, and ions that mirrored near the Earth all were needed. The current sheet structure was determined primarily by ion magnetization currents. Electrons of the observed energies carried relatively little cross-tail current in these quiet time current sheets. Distribution functions were generated and integrated to evaluate fluid parameters. An earlier model in which B depended only on z produced a consistent current sheet, but it did not provide a realistic representation of the Earth's middle magnetotail. In the present study, B changed substantially in the x and z directions but only weakly in the y direction within our region of interest. Plasmas with three characteristic particle energies were used with each of the magnetic field models. A plasma was found for each model in which the density, average energy, cross-tail current, and bulk flow velocity agreed well with satellite observations.

Structure of the Magnetotail Current Sheet

NASA Technical Reports Server (NTRS)

Larson, Douglas J.; Kaufmann, Richard L.

1996-01-01

An orbit tracing technique was used to generate current sheets for three magnetotail models. Groups of ions were followed to calculate the resulting cross-tail current. Several groups then were combined to produce a current sheet. The goal is a model in which the ions and associated electrons carry the electric current distribution needed to generate the magnetic field B in which ion orbits were traced. The region -20 R(E) less than x less than -14 R(E) in geocentric solar magnetospheric coordinates was studied. Emphasis was placed on identifying the categories of ion orbits which contribute most to the cross-tail current and on gaining physical insight into the manner by which the ions carry the observed current distribution. Ions that were trapped near z = 0, ions that magnetically mirrored throughout the current sheet, and ions that mirrored near the Earth all were needed. The current sheet structure was determined primarily by ion magnetization currents. Electrons of the observed energies carried relatively little cross-tail current in these quiet time current sheets. Distribution functions were generated and integrated to evaluate fluid parameters. An earlier model in which B depended only on z produced a consistent current sheet, but it did not provide a realistic representation of the Earth's middle magnetotail. In the present study, B changed substantially in the x and z directions but only weakly in the y direction within our region of interest. Plasmas with three characteristic particle energies were used with each of the magnetic field models. A plasma was found for each model in which the density, average energy, cross-tail current, and bulk flow velocity agreed well with satellite observations.

Collision-induced dissociation of aminophospholipids (PE, MMPE, DMPE, PS): an apparently known fragmentation process revisited.

PubMed

Pittenauer, Ernst; Rehulka, Pavel; Winkler, Wolfgang; Allmaier, Günter

2015-07-01

A new type of low-mass substituted 4-oxazolin product ions of [M + H](+) precursor ions of aminophospholipids (glycerophosphatidylethanolamine, glycerophosphatidyl-N-methylethanolamine, glycerophosphatidyl-N,N-dimethylethanolamine, glycerophosphatidylserine) resulting from high-energy collision-induced dissociation (matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry) and low-energy collision-induced dissociation (e.g., electrospray ionization quadrupole reflectron time-of-flight mass spectrometry) with accurate mass determination is described; these were previously misidentified as CHO-containing radical cationic product ions. The mechanism for the formation of these ions is proposed to be via rapid loss of water followed by cyclization to an 11-membered-ring transition state for the sn-1 fatty acid substituent and to a ten-membered-ring transition state for the sn-2 fatty acid substituent, and via final loss of monoacylglycerol phosphate, leading to substituted 4-oxazolin product ions. The minimum structural requirement for this interesting skeletal rearrangement fragmentation is an amino group linked to at least one hydrogen atom (i.e., ethanolamine, N-methylethanolamine, serine). Therefore, N,N-dimethylethanolamine derivates do not exhibit this type of fragmentation. The analytical value of these product ions is given by the fact that by post source decay and particularly high-energy collision-induced dissociation achieved via matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry, the sn-2-related substituted 4-oxazolin product ion is always significantly more abundant than the sn-1-related one, which is quite helpful for detailed structural analysis of complex lipids. All other important product ions found are described in detail (following our previously published glycerophospholipid product ion nomenclature; Pittenauer and Allmaier, Int. J. Mass. Spectrom. 301:90-1012, 2011).

Characterization of ion-irradiation-induced nanodot structures on InP surfaces by atom probe tomography.

PubMed

Gnaser, Hubert; Radny, Tobias

2015-12-01

Surfaces of InP were bombarded by 1.9 keV Ar(+) ions under normal incidence. The total accumulated ion fluence the samples were exposed to was varied from 1 × 10(17) cm(-2) to 3 × 10(18)cm(-2) and ion flux densities f of (0.4-2) × 10(14) cm(-2) s(-1) were used. Nanodot structures were found to evolve on the surface from these ion irradiations, their dimensions however, depend on the specific bombardment conditions. The resulting surface morphology was examined by atomic force microscopy (AFM). As a function of ion fluence, the mean radius, height, and spacing of the dots can be fitted by power-law dependences. In order to determine possible local compositional changes in these nanostructures induced by ion impact, selected samples were prepared for atom probe tomography (APT). The results indicate that by APT the composition of individual InP nanodots evolving under ion bombardment could be examined with atomic spatial resolution. At the InP surface, the values of the In/P concentration ratio are distinctly higher over a distance of ~1 nm and amount to 1.3-1.8. However, several aspects critical for the analyses were identified: (i) because of the small dimensions of these nanostructures a successful tip preparation proved very challenging. (ii) The elemental compositions obtained from APT were found to be influenced pronouncedly by the laser pulse energy; typically, low energies result in the correct stoichiometry whereas high ones lead to an inhomogeneous evaporation from the tips and deviations from the nominal composition. (iii) Depending again on the laser energy, a prolific emission of Pn cluster ions was observed, with n ≤ 11. Copyright © 2015. Published by Elsevier B.V.

Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides

NASA Astrophysics Data System (ADS)

Moss, Christopher L.; Chung, Thomas W.; Wyer, Jean A.; Nielsen, Steen Brøndsted; Hvelplund, Preben; Tureček, František

2011-04-01

Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H2PO4 radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.

Radiation Resistance of the U(Al, Si)3 Alloy: Ion-Induced Disordering

PubMed Central

Yaniv, Gili; Horak, Pavel; Vacik, Jiri; Mykytenko, Natalia; Rafailov, Gennady; Dahan, Itzchak; Fuks, David; Kiv, Arik

2018-01-01

During the exploitation of nuclear reactors, various U-Al based ternary intermetallides are formed in the fuel-cladding interaction layer. Structure and physical properties of these intermetallides determine the radiation resistance of cladding and, ultimately, the reliability and lifetime of the nuclear reactor. In current research, U(Al, Si)3 composition was studied as a potential constituent of an interaction layer. Phase content of the alloy of an interest was ordered U(Al, Si)3, structure of which was reported earlier, and pure Al (constituting less than 20 vol % of the alloy). This alloy was investigated prior and after the irradiation performed by Ar ions at 30 keV. The irradiation was performed on the transmission electron microscopy (TEM, JEOL, Japan) samples, characterized before and after the irradiation process. Irradiation induced disorder accompanied by stress relief. Furthermore, it was found that there is a dose threshold for disordering of the crystalline matter in the irradiated region. Irradiation at doses equal or higher than this threshold resulted in almost solely disordered phase. Using the program “Stopping and Range of Ions in Matter” (SRIM), the parameters of penetration of Ar ions into the irradiated samples were estimated. Based on these estimations, the dose threshold for ion-induced disordering of the studied material was assessed. PMID:29393870

Mechanism of Metal Ion Activation of the Diphtheria Toxin Repressor DtxR

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

D'Aquino,J.; Tetenbaum-Novatt, J.; White, A.

2005-01-01

The diphtheria toxin repressor (DtxR) is a metal ion-activated transcriptional regulator that has been linked to the virulence of Corynebacterium diphtheriae. Structure determination has shown that there are two metal ion binding sites per repressor monomer, and site-directed mutagenesis has demonstrated that binding site 2 (primary) is essential for recognition of the target DNA repressor, leaving the role of binding site 1 (ancillary) unclear. Calorimetric techniques have demonstrated that although binding site 1 (ancillary) has high affinity for metal ion with a binding constant of 2 x 10{sup -7}, binding site 2 (primary) is a low-affinity binding site with amore » binding constant of 6.3 x 10{sup -4}. These two binding sites act in an independent fashion, and their contribution can be easily dissected by traditional mutational analysis. Our results clearly demonstrate that binding site 1 (ancillary) is the first one to be occupied during metal ion activation, playing a critical role in stabilization of the repressor. In addition, structural data obtained for the mutants Ni-DtxR(H79A, C102D), reported here, and the previously reported DtxR(H79A) have allowed us to propose a mechanism of metal activation for DtxR.« less

Solvation of actinide salts in water using a polarizable continuum model.

PubMed

Kumar, Narendra; Seminario, Jorge M

2015-01-29

In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

3D lattice distortions and defect structures in ion-implanted nano-crystals

PubMed Central

Hofmann, Felix; Tarleton, Edmund; Harder, Ross J.; Phillips, Nicholas W.; Ma, Pui-Wai; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian; Liu, Wenjun; Beck, Christian E.

2017-01-01

Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga+), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology. PMID:28383028

Radiation Resistance of the U(Al, Si)₃ Alloy: Ion-Induced Disordering.

PubMed

Meshi, Louisa; Yaniv, Gili; Horak, Pavel; Vacik, Jiri; Mykytenko, Natalia; Rafailov, Gennady; Dahan, Itzchak; Fuks, David; Kiv, Arik

2018-02-02

During the exploitation of nuclear reactors, various U-Al based ternary intermetallides are formed in the fuel-cladding interaction layer. Structure and physical properties of these intermetallides determine the radiation resistance of cladding and, ultimately, the reliability and lifetime of the nuclear reactor. In current research, U(Al, Si)₃ composition was studied as a potential constituent of an interaction layer. Phase content of the alloy of an interest was ordered U(Al, Si)₃, structure of which was reported earlier, and pure Al (constituting less than 20 vol % of the alloy). This alloy was investigated prior and after the irradiation performed by Ar ions at 30 keV. The irradiation was performed on the transmission electron microscopy (TEM, JEOL, Japan) samples, characterized before and after the irradiation process. Irradiation induced disorder accompanied by stress relief. Furthermore, it was found that there is a dose threshold for disordering of the crystalline matter in the irradiated region. Irradiation at doses equal or higher than this threshold resulted in almost solely disordered phase. Using the program "Stopping and Range of Ions in Matter" (SRIM), the parameters of penetration of Ar ions into the irradiated samples were estimated. Based on these estimations, the dose threshold for ion-induced disordering of the studied material was assessed.

ESR, spectroscopic, and quantum-chemical studies on the electronic structures of complexes formed by Cu(I) with radicals (in Russian)

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

Gritsan, N.P.; Usov, O.M.; Shokhirev, N.V.

1986-07-01

The optical and ESR spectra have been examined for complexes of Cu(I) with various radicals, which contain various numbers of Cl/sup -/ ions in the central-atom coordination sphere. The spin-Hamiltonian parameters have been determined for all these radical complexes, and the observed ESR spectra have been compared with those calculated with allowance for second-order effects. The observed values for the isotropic and anisotropic components of the HFI constant from the central ion have been used to estimate the contributions from the 4s and 3d/sup 2//sub z/ orbitals of the copper ion to the unpaired-electron MO. Quantum-chemical calculations have been performedmore » by the INDO method on the electronic structures and geometries of complexes formed by CH/sub 2/OH with Cu(I) for various Cl/sup -/ contents in the coordination sphere. The radical is coordinated by the ..pi.. orbital on the carbon atom, and the stabilities of the radical complexes decrease as the number of Cl/sup -/ ions in the coordination sphere increases. A geometry close to planar for the CuCl/sub 4//sup 3 -/ fragment in a complex containing four Cl/sup -/ ions.« less

Deuterium charge exchange recombination spectroscopy from the top of the pedestal to the scrape off layer in H-mode plasmas

NASA Astrophysics Data System (ADS)

Haskey, S. R.; Grierson, B. A.; Stagner, L.; Burrell, K. H.; Chrystal, C.; Groebner, R. J.; Ashourvan, A.; Pablant, N. A.

2017-10-01

Recent completion of the thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on DIII-D [J.L. Luxon, Nucl. Fusion 42 (2002) 614] enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the edge, providing high resolution measurements of the pedestal and steep gradient edge region of H-mode plasmas. The complexities of the Dα spectrum require fitting with a comprehensive model, as well as using iterative collisional radiative modeling to determine the underlying thermal deuterium ion properties. Large differences in the structure and magnitude of impurity (C6+) and main-ion (D+) toroidal rotation profiles are seen in the H-mode pedestal. Additionally the D+ temperature can be half the value of the C6+ temperature at the separatrix and shows more of a pedestal structure. Typically only the impurity properties are measured and the main-ion properties are either assumed to be the same, or inferred using neoclassical models, which require validation in the steep gradient region. These measured differences have implications for transport model validation, intrinsic rotation studies, pedestal stability, and the boundary conditions for scrape off layer and plasma material interactions studies.

Analytic model of a laser-accelerated composite plasma target and its stability

NASA Astrophysics Data System (ADS)

Khudik, Vladimir; Shvets, Gennady

2013-10-01

A self-consistent analytical model of monoenergetic acceleration of a one and two-species ultrathin target irradiated by a circularly polarized laser pulse is developed. In the accelerated reference frame, the bulk plasma in the target is neutral and its parameters are assumed to be stationary. It is found that the structure of the target depends strongly on the temperatures of electrons and ions, which are both strongly influenced by the laser pulse pedestal. When the electron temperature is large, the hot electrons bounce back and forth inside the potential well formed by ponderomotive and electrostatic potentials while the heavy and light ions are forced-balanced by the electrostatic and non-inertial fields forming two separated layers. In the opposite limiting case when the ion temperature is large, the hot ions are trapped in the potential well formed by the ion-sheath's electric and non-inertial potentials while the cold electrons are forced-balanced by the electrostatic and ponderomotive fields. Using PIC simulations we have determined which scenario is realized in practice depending on the initial target structure and laser intensity. Target stability with respect to Rayleigh-Taylor instability will also be discussed. This work is supported by the US DOE grants DE-FG02-04ER41321 and DE-FG02-07ER54945.

3D lattice distortions and defect structures in ion-implanted nano-crystals.

PubMed

Hofmann, Felix; Tarleton, Edmund; Harder, Ross J; Phillips, Nicholas W; Ma, Pui-Wai; Clark, Jesse N; Robinson, Ian K; Abbey, Brian; Liu, Wenjun; Beck, Christian E

2017-04-06

Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga + ), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology.

Deuterium charge exchange recombination spectroscopy from the top of the pedestal to the scrape off layer in H-mode plasmas

DOE PAGES

Haskey, S. R.; Grierson, B. A.; Stagner, L.; ...

2017-10-25

Recent completion of the thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on DIII-D enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the edge, providing high resolution measurements of the pedestal and steep gradient edge region of H-mode plasmas. The complexities of the D α spectrum require fitting with a comprehensive model, as well as using iterative collisional radiative modeling to determine the underlying thermal deuterium ion properties. Large differences in the structure and magnitude of impurity (Cmore » 6+) and main-ion (D +) toroidal rotation profiles are seen in the H-mode pedestal. Additionally the D + temperature can be half the value of the C 6+ temperature at the separatrix and shows more of a pedestal structure. Typically only the impurity properties are measured and the main-ion properties are either assumed to be the same, or inferred using neoclassical models, which require validation in the steep gradient region. Furthermore, these measured differences have implications for transport model validation, intrinsic rotation studies, pedestal stability, and the boundary conditions for scrape off layer and plasma material interactions studies.« less

Magnesium-dependent RNA binding to the PA endonuclease domain of the avian influenza polymerase.

PubMed

Xiao, Shiyan; Klein, Michael L; LeBard, David N; Levine, Benjamin G; Liang, Haojun; MacDermaid, Christopher M; Alfonso-Prieto, Mercedes

2014-01-30

Influenza A viruses are highly pathogenic and pose an unpredictable public health danger to humans. An attractive target for developing new antiviral drugs is the PA N-terminal domain (PAN) of influenza polymerase, which is responsible for the endonuclease activity and essential for viral replication. Recently, the crystal structures of the holo form of PAN as well as PAN bound to different inhibitors have been reported, but the potency and selectivity of these inhibitors still need to be improved. New drug design can be guided by a better understanding of the endonuclease activity of PAN. However, this requires the structure of PAN in complex with the host mRNA, which has not been determined yet. In particular, divalent metal ions are known to be essential for RNA cleavage, but it is not clear whether there is either one or two Mg ions in the PAN active site. In the present work, we have modeled the complex of the PAN endonuclease domain with the host mRNA in the presence of either one or two Mg(2+) by using all-atom molecular dynamics. These simulations identify crucial interactions between the enzyme and the nucleic acid. Moreover, they validate a previous hypothesis that a second metal ion binds in the presence of the RNA substrate and therefore support a two-metal ion mechanism, in which K134 decreases the pKa of the nucleophilic water. Nevertheless, at low Mg concentrations an alternative, one-metal ion mechanism is possible, with K137 as the catalytic lysine and H41 as the general base, rationalizing previous unexpected mutagenesis results. The RNA-enzyme interactions determined here could likely be used to design more specific endonuclease inhibitors to fight influenza viral infections.

Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.

PubMed

Frandsen, Kristian E H; Poulsen, Jens Christian Navarro; Tovborg, Morten; Johansen, Katja S; Lo Leggio, Leila

2017-01-01

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.

[Composition and source of atmosphere aerosol water soluble ions over the East China Sea in winter].

PubMed

He, Yu-Hui; Yang, Gui-Peng; Zhang, Hong-Hai

2011-08-01

With the ion chromatographic method, the water-soluble ion concentrations of Cl(-), NO3(-), SO4(2-) , CH3SO3(-) (MSA), Na+, K+, NH4+, Mg2+ and Ca2+ in the atmospheric aerosol over the East China Sea in winter 2009 was determined and the sources of these ions was investigated through correlation analysis by SPSS (statistical package for social sciences) software. The results indicated that the concentrations of secondary ions in aerosol were the highest (non-sea-salt sulfates nss-SO4(2-), NO3(-), NH4+), accounting for 78.4% of total determining ions. The calculation results of equivalent concentration of anions and cations showed that the acid ions of aerosol were neutralized inadequately. The stoichiometry of NH4+ in different compounds showed that NH4HSO4 was the main binding form of NH4+ and SO4(2-) in the aerosol. The concentration of methanesulfonic acid (MSA) was low, and the average value was (0.0088 +/- 0.0037) microg x m(-3). According to calculation, the contribution of sea-salt sulfates was 4.5% to total sulfates, and that of biogenous sulfates was 1.4% to non-sea-salt sulfate (nss-SO4(2-)), showing that human input was the main source of sulfates in aerosol over the East China Sea. In addition, nss-SO4(2-)/NO3(-) in the aerosol was 1.08, reflecting that China's energy structure adjustment played an important role in recent years.

Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*

NASA Technical Reports Server (NTRS)

Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Garcia, J.; Witthoeft, M. C.; Kallman, T. R.

2012-01-01

Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.

Structure, chemistry, and stress corrosion cracking of grain boundaries in alloys 600 and 690

NASA Astrophysics Data System (ADS)

Stiller, Krystyna; Nilsson, Jan-Olof; Norring, Kjell

1996-02-01

The microstructure in six commercial batches of alloys 600 and 690 has been investigated using scanning electron microscopy (SEM), analytical transmission electron microscopy (ATEM), atom probe field ion microscopy (APFIM), and secondary ion mass spectroscopy (SIMS). The materials were also tested with respect to their resistance to intergranular stress corrosion cracking (IGSCC) in high-purity water at 365 °. Applied microanalytical techniques allowed direct measurement of carbon concentration in the matrix together with determination of grain boundary micro structure and microchemistry in all material conditions. The distribution of oxygen near a crack in material tested with respect to IGSCC was also investigated. The role of carbon and chromium and intergranular precipitates on IGSCC is discussed.

Investigation of drift gas selectivity in high resolution ion mobility spectrometry with mass spectrometry detection.

PubMed

Matz, Laura M; Hill, Herbert H; Beegle, Luther W; Kanik, Isik

2002-04-01

Recent studies in electrospray ionization (ESI)/ion mobility spectrometry (IMS) have focussed on employing different drift gases to alter separation efficiency for some molecules. This study investigates four structurally similar classes of molecules (cocaine and metabolites, amphetamines, benzodiazepines, and small peptides) to determine the effect of structure on relative mobility changes in four drift gases (helium, nitrogen, argon, carbon dioxide). Collision cross sections were plotted against drift gas polarizability and a linear relationship was found for the nineteen compounds evaluated in the study. Based on the reduced mobility database, all nineteen compounds could be separated in one of the four drift gases, however, the drift gas that provided optimal separation was specific for the two compounds.

Conduction in fully ionized liquid metals

NASA Technical Reports Server (NTRS)

Stevenson, D. J.; Ashcroft, N. W.

1973-01-01

Electron transport is considered in high density fully ionized liquid metals. Ionic structure is described in terms of hard-sphere correlation functions and the scattering is determined from self-consistently screened point ions. Applications to the physical properties of the deep interior of Jupiter are briefly considered.

Viscosity and Solvation

ERIC Educational Resources Information Center

Robertson, C. T.

1973-01-01

Discusses theories underlying the phenomena of solution viscosities, involving the Jones and Dole equation, B-coefficient determination, and flickering cluster model. Indicates that viscosity measurements provide a basis for the study of the structural effects of ions in aqueous solutions and are applicable in teaching high school chemistry. (CC)

Construction of nanostructures for selective lithium ion conduction using self-assembled molecular arrays in supramolecular solids

NASA Astrophysics Data System (ADS)

Moriya, Makoto

2017-12-01

In the development of innovative molecule-based materials, the identification of the structural features in supramolecular solids and the understanding of the correlation between structure and function are important factors. The author investigated the development of supramolecular solid electrolytes by constructing ion conduction paths using a supramolecular hierarchical structure in molecular crystals because the ion conduction path is an attractive key structure due to its ability to generate solid-state ion diffusivity. The obtained molecular crystals exhibited selective lithium ion diffusion via conduction paths consisting of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and small molecules such as ether or amine compounds. In the present review, the correlation between the crystal structure and ion conductivity of the obtained molecular crystals is addressed based on the systematic structural control of the ionic conduction paths through the modification of the component molecules. The relationship between the crystal structure and ion conductivity of the molecular crystals provides a guideline for the development of solid electrolytes based on supramolecular solids exhibiting rapid and selective lithium ion conduction.

Theory and simulation of ion conduction in the pentameric GLIC channel.

PubMed

Zhu, Fangqiang; Hummer, Gerhard

2012-10-09

GLIC is a bacterial member of the large family of pentameric ligand-gated ion channels. To study ion conduction through GLIC and other membrane channels, we combine the one-dimensional potential of mean force for ion passage with a Smoluchowski diffusion model, making it possible to calculate single-channel conductance in the regime of low ion concentrations from all-atom molecular dynamics (MD) simulations. We then perform MD simulations to examine sodium ion conduction through the GLIC transmembrane pore in two systems with different bulk ion concentrations. The ion potentials of mean force, calculated from umbrella sampling simulations with Hamiltonian replica exchange, reveal a major barrier at the hydrophobic constriction of the pore. The relevance of this barrier for ion transport is confirmed by a committor function that rises sharply in the barrier region. From the free evolution of Na(+) ions starting at the barrier top, we estimate the effective diffusion coefficient in the barrier region, and subsequently calculate the conductance of the pore. The resulting diffusivity compares well with the position-dependent ion diffusion coefficient obtained from restrained simulations. The ion conductance obtained from the diffusion model agrees with the value determined via a reactive-flux rate calculation. Our results show that the conformation in the GLIC crystal structure, with an estimated conductance of ~1 picosiemens at 140 mM ion concentration, is consistent with a physiologically open state of the channel.

Magnetic phase investigations on fluorine (F) doped LiFePO4

NASA Astrophysics Data System (ADS)

Radhamani, A. V.

2018-03-01

LiFePO4 (LFP) is a very promising cathode material for Li-ion batteries due to its high thermal stability, less toxicity and high theoretical capacity (170 mAh g-1). Anion doping, especially fluorine (F) at the oxygen site is one way to improve the low electronic conductivity of the material. In this line, fluorine doped LFP was prepared at different fluorine concentrations (1 to 40 mol%) to study the structural, spectroscopic and magnetic properties in view of the material property optimization for battery applications. The investigation of the magnetic properties was found to be successful for the determination of small amounts of magnetic impurities which were not noticeably observed from structural characterizations. Determination of conducting magnetic impurities has its own relevance in the current scenario of Li-ion based battery applications. Systematic characterization studies along with the implications of magnetic phases on the material activity of fluorine doped LiFePO4 nanoparticles will be discussed in detail.

International Halley Watch: Discipline specialists for near-nucleus studies

NASA Technical Reports Server (NTRS)

Larson, S.; Sekanina, Z.; Rahe, J.

1986-01-01

The purpose of the Near-Nucleus Studies Net is to study the processes taking place in the near-nucleus environment as they relate to the nature of nucleus. This is accomplisghed by measuring the spatial and temporal distribution of dust, gases and ions in the coma on high resolution images taken from many observatories around the world. By modeling the motions of discrete dust features in Comet Halley, it is often possible to determine the locations of the emission sources on the surface and learn about the nucleus structure. In addition to the general goals shared by all IHW nets, the scientific goals of the net has been to determine (1)the gross surface structure of the nucleus, (2)the nucleus spin vector, (3)the distribution and evolution of jet sources and (4)the interrelationships between the gas, dust and ion components of the coma. An additional Comet Giacobini-Zinner watch was carried out by the NNSN in support of the NASA International Cometary Explorer flyby.

Fabrication and characterization of magnesium and calcium trimesate complexes via ion-exchange and one-pot self-assembly reaction

NASA Astrophysics Data System (ADS)

Ozer, Demet; Oztas, Nursen Altuntas; Köse, Dursun A.; Şahin, Onur

2018-03-01

Using two different synthesis methods, two diversified magnesium and calcium complexes were successfully prepared. When the ion exchange method was used, C9H14MgO11.H2O and C18H30Ca3O24 complexes were obtained. When the one-pot self-assembly reaction was used, C18H34Mg3O26.4H2O and C9H12CaO10 complexes were produced. The structural characterizations were performed by using X-ray diffraction, FT-IR and elemental analyses. Thermal behavior of complexes were also determined via TGA method. The both complexes of magnesium and calcium trimesate have micro and mesoporosity with low porosity because of hydrogen bonds. Then hydrogen storage capacities of complexes were also determined. The differences in synthesis method result in the differences on complexes structure, morphology (shape, particle size and specific surface area) and hydrogen storage capacities.

Fabrication of Ca-Mn-Nb-O compounds and their structural, electrical, magnetic and thermoelectric properties

NASA Astrophysics Data System (ADS)

Oz, E.; Demirel, S.; Altin, S.; Altin, E.; Baglayan, O.; Bayri, A.; Avci, S.

2018-03-01

CaMn1-xNbxO3-δ (0 ≤ x ≤ 1) were synthesized by conventional solid state reaction method. The structural properties were determined by FTIR, Raman, XRD, XAS measurements. The FTIR and Raman modes change by increasing Nb content and the lattice volume increases by increasing Nb content. The solubility limit of Nb is determined as x ≤ 0.3 and impurity phases start to appear above this limit. The temperature dependence of the magnetization data shows an antiferromagnetic transition below 120 K for low Nb content. Increasing the Nb content causes a change in the magnetic phase from antiferromagnetic to paramagnetic. The oxygen deficiency in CaMnO3-δ may cause the formation of polaron effect which is destroyed by the Nb ions. The difference graph of XAS data for x = 0 and 0.5 show that the number of Mn3+ ions increases by increasing Nb content to maintain the charge neutrality.

Interactions between Hofmeister anions and the binding pocket of a protein.

PubMed

Fox, Jerome M; Kang, Kyungtae; Sherman, Woody; Héroux, Annie; Sastry, G Madhavi; Baghbanzadeh, Mostafa; Lockett, Matthew R; Whitesides, George M

2015-03-25

This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.

OCT structure, COB location and magmatic type of the SE Brazilian & S Angolan margins from integrated quantitative analysis of deep seismic reflection and gravity anomaly data

NASA Astrophysics Data System (ADS)

Cowie, L.; Kusznir, N. J.; Horn, B.

2013-12-01

Knowledge of ocean-continent transition (OCT) structure, continent-ocean boundary (COB) location and magmatic type are of critical importance for understanding rifted continental margin formation processes and in evaluating petroleum systems in deep-water frontier oil and gas exploration. The OCT structure, COB location and magmatic type of the SE Brazilian and S Angolan rifted continental margins are much debated; exhumed and serpentinised mantle have been reported at these margins. Integrated quantitative analysis using deep seismic reflection data and gravity inversion have been used to determine OCT structure, COB location and magmatic type for the SE Brazilian and S Angolan margins. Gravity inversion has been used to determine Moho depth, crustal basement thickness and continental lithosphere thinning. Residual Depth Anomaly (RDA) analysis has been used to investigate OCT bathymetric anomalies with respect to expected oceanic bathymetries and subsidence analysis has been used to determine the distribution of continental lithosphere thinning. These techniques have been validated on the Iberian margin for profiles IAM9 and ISE-01. In addition a joint inversion technique using deep seismic reflection and gravity anomaly data has been applied to the ION-GXT BS1-575 SE Brazil and ION-GXT CS1-2400 S Angola. The joint inversion method solves for coincident seismic and gravity Moho in the time domain and calculates the lateral variations in crustal basement densities and velocities along profile. Gravity inversion, RDA and subsidence analysis along the S Angolan ION-GXT CS1-2400 profile has been used to determine OCT structure and COB location. Analysis suggests that exhumed mantle, corresponding to a magma poor margin, is absent beneath the allochthonous salt. The thickness of earliest oceanic crust, derived from gravity and deep seismic reflection data is approximately 7km. The joint inversion predicts crustal basement densities and seismic velocities which are slightly less than expected for 'normal' oceanic crust. The difference between the sediment corrected RDA and that predicted from gravity inversion crustal thickness variation implies that this margin is experiencing ~300m of anomalous uplift attributed to mantle dynamic uplift. Gravity inversion, RDA and subsidence analysis have also been used to determine OCT structure and COB location along the ION-GXT BS1-575 profile, crossing the Sao Paulo Plateau and Florianopolis Ridge of the SE Brazilian margin. Gravity inversion, RDA and subsidence analysis predict the COB to be located SE of the Florianopolis Ridge. Analysis shows no evidence for exhumed mantle on this margin profile. The joint inversion technique predicts normal oceanic basement seismic velocities and densities and beneath the Sao Paulo Plateau and Florianopolis Ridge predicts crustal basement thicknesses between 10-15km. The Sao Paulo Plateau and Florianopolis Ridge are separated by a thin region of crustal basement beneath the salt interpreted as a regional transtensional structure. Sediment corrected RDAs and gravity derived 'synthetic' RDAs are of a similar magnitude on oceanic crust, implying negligible mantle dynamic topography.

Effective pore size and radius of capture for K(+) ions in K-channels.

PubMed

Moldenhauer, Hans; Díaz-Franulic, Ignacio; González-Nilo, Fernando; Naranjo, David

2016-02-02

Reconciling protein functional data with crystal structure is arduous because rare conformations or crystallization artifacts occur. Here we present a tool to validate the dimensions of open pore structures of potassium-selective ion channels. We used freely available algorithms to calculate the molecular contour of the pore to determine the effective internal pore radius (r(E)) in several K-channel crystal structures. r(E) was operationally defined as the radius of the biggest sphere able to enter the pore from the cytosolic side. We obtained consistent r(E) estimates for MthK and Kv1.2/2.1 structures, with r(E) = 5.3-5.9 Å and r(E) = 4.5-5.2 Å, respectively. We compared these structural estimates with functional assessments of the internal mouth radii of capture (r(C)) for two electrophysiological counterparts, the large conductance calcium activated K-channel (r(C) = 2.2 Å) and the Shaker Kv-channel (r(C) = 0.8 Å), for MthK and Kv1.2/2.1 structures, respectively. Calculating the difference between r(E) and r(C), produced consistent size radii of 3.1-3.7 Å and 3.6-4.4 Å for hydrated K(+) ions. These hydrated K(+) estimates harmonize with others obtained with diverse experimental and theoretical methods. Thus, these findings validate MthK and the Kv1.2/2.1 structures as templates for open BK and Kv-channels, respectively.

The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.

PubMed

Timsit, Youri; Bombard, Sophie

2007-12-01

Metal ions play a key role in RNA folding and activity. Elucidating the rules that govern the binding of metal ions is therefore an essential step for better understanding the RNA functions. High-resolution data are a prerequisite for a detailed structural analysis of ion binding on RNA and, in particular, the observation of monovalent cations. Here, the high-resolution crystal structures of the tridecamer duplex r(GCGUUUGAAACGC) crystallized under different conditions provides new structural insights on ion binding on GAAA/UUU sequences that exhibit both unusual structural and functional properties in RNA. The present study extends the repertory of RNA ion binding sites in showing that the two first bases of UUU triplets constitute a specific site for sodium ions. A striking asymmetric pattern of metal ion binding in the two equivalent halves of the palindromic sequence demonstrates that sequence and its environment act together to bind metal ions. A highly ionophilic half that binds six metal ions allows, for the first time, the observation of a disodium cluster in RNA. The comparison of the equivalent halves of the duplex provides experimental evidences that ion binding correlates with structural alterations and groove contraction.

Determination of copper binding in Pseudomonas putida CZ1 by chemical modifications and X-ray absorption spectroscopy.

PubMed

Chen, XinCai; Shi, JiYan; Chen, YingXu; Xu, XiangHua; Chen, LiTao; Wang, Hui; Hu, TianDou

2007-03-01

Previously performed studies have shown that Pseudomonas putida CZ1 biomass can bind an appreciable amount of Cu(II) and Zn(II) ions from aqueous solutions. The mechanisms of Cu- and Zn-binding by P. putida CZ1 were ascertained by chemical modifications of the biomass followed by Fourier transform infrared and X-ray absorption spectroscopic analyses of the living or nonliving cells. A dramatic decrease in Cu(II)- and Zn(II)-binding resulted after acidic methanol esterification of the nonliving cells, indicating that carboxyl functional groups play an important role in the binding of metal to the biomaterial. X-ray absorption spectroscopy was used to determine the speciation of Cu ions bound by living and nonliving cells, as well as to elucidate which functional groups were involved in binding of the Cu ions. The X-ray absorption near-edge structure spectra analysis showed that the majority of the Cu was bound in both samples as Cu(II). The fitting results of Cu K-edge extended X-ray absorption fine structure spectra showed that N/O ligands dominated in living and nonliving cells. Therefore, by combining different techniques, our results indicate that carboxyl functional groups are the major ligands responsible for the metal binding in P. putida CZ1.

Use of the ciliated protozoan Tetrahymena pyriformis for the assessment of toxicity and quantitative structure--activity relationships of xenobiotics: comparison with the Microtox test.

PubMed

Bogaerts, P; Bohatier, J; Bonnemoy, F

2001-07-01

Cytotoxicity and quantitative structure-activity relationships of 13 inorganic and 21 organic substances were determined using three bioassays performed on the ciliated protozoan Tetrahymena pyriformis and the luminescent bacterium Vibrio fischeri. The best concordance of toxicity results was observed between the T. pyriformis FDA--esterase activity and population growth inhibition tests for the organic compounds. The sensitivity of these two assays is compared with that of the Microtox test. The T. pyriformis FDA test showed a high sensitivity is most cases. The aim of the current research was to determine whether the relative toxicity of metal ions and organic molecules, with these three bioassays, was predictable using three ion characteristics and hydrophobicity, respectively. For metal ions, the variable that best modeled the toxicity data obtained with the two T. pyriformis tests was the softness index [sigma(p), i.e., (coordinate bond energy of the metal fluoride--coordinate bond energy of the metal iodide)/(coordinate bond energy of the metal fluoride)]. No correlation was found with the Microtox test. For organic compounds, a significant correlation was observed between the hydrophobicity coefficient and the toxicity data. This correlation is closer with the two tests using Tetrahymena. Copyright 2001 Academic Press.

Determination and prediction of the magnetic anisotropy of Mn ions.

PubMed

Duboc, Carole

2016-10-24

This tutorial is dedicated to the investigation of magnetic anisotropy using both electron paramagnetic resonance (EPR) spectroscopy for its experimental determination and quantum chemistry for its theoretical prediction. Such an approach could lead to the definition of magneto-structural correlation essential for the rational design of complexes with targeted magnetic properties or for the identification of unknown reactive metallic species involved in catalysis. To illustrate this combined approach the high spin Mn II , Mn III and Mn IV ions have been taken as specific examples. The first part deals with the analysis of the EPR experiments as a function of the ions under investigation and the conditions of the measurements, specifically: (i) EPR spectra recorded under high vs. low frequency conditions with respect to magnetic anisotropy, (ii) EPR spectra of non-integer (Kramers) vs. integer (non-Kramers) spin states and (iii) mono- vs. multi-frequency EPR spectra. In the second part, two main quantum chemical approaches, which have proven their capability to predict magnetic anisotropy, are described. More importantly, these calculations give access to the different contributions of zero field splitting, key information for the full understanding of magnetic anisotropy. The last part demonstrates that such a combined experimental and theoretical approach allows for the definition of magneto-structural correlations.

Dust ion acoustic freak waves in a plasma with two temperature electrons featuring Tsallis distribution

NASA Astrophysics Data System (ADS)

Chahal, Balwinder Singh; Singh, Manpreet; Shalini; Saini, N. S.

2018-02-01

We present an investigation for the nonlinear dust ion acoustic wave modulation in a plasma composed of charged dust grains, two temperature (cold and hot) nonextensive electrons and ions. For this purpose, the multiscale reductive perturbation technique is used to obtain a nonlinear Schrödinger equation. The critical wave number, which indicates where the modulational instability sets in, has been determined precisely for various regimes. The influence of plasma background nonextensivity on the growth rate of modulational instability is discussed. The modulated wavepackets in the form of either bright or dark type envelope solitons may exist. Formation of rogue waves from bright envelope solitons is also discussed. The investigation indicates that the structural characteristics of these envelope excitations (width, amplitude) are significantly affected by nonextensivity, dust concentration, cold electron-ion density ratio and temperature ratio.

Growth of sodium chlorate crystals in the presence of potassium sulphate

NASA Astrophysics Data System (ADS)

Kim, E. L.; Tsyganova, A. A.; Vorontsov, D. A.; Ovsetsina, T. I.; Katkova, M. R.; Lykov, V. A.; Portnov, V. N.

2015-09-01

In this work, we investigated the morphology and growth rates of NaClO3 crystals in solutions with K2SO4 additives. NaClO3 crystals were grown using the temperature gradient technique under concentration convection. We found that the crystal habitus changed from cubic to tetrahedral, and the growth of the cubic {100}, tetrahedral {111} and rhomb-dodecahedral {110} faces decelerated with an increase in the concentration of SO42- ions. The {110} face was the most and the {100} face was the least inhibited by sulphate ions. The mechanism of SO42- ions action is their adsorption on the crystal surface, which impedes attachment of the crystal's building units. We conclude that different atomic structure and charge state of various crystal faces determine their sensitivity to the action of the SO42- ions.

Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.

PubMed

Matsumura, Hiroyoshi; Xie, Yong; Shirakata, Shunsuke; Inoue, Tsuyoshi; Yoshinaga, Takeo; Ueno, Yoshihisa; Izui, Katsura; Kai, Yasushi

2002-12-01

Phosphoenolpyruvate carboxylase (PEPC) catalyzes the first step in the fixation of atmospheric CO(2) during C(4) photosynthesis. The crystal structure of C(4) form maize PEPC (ZmPEPC), the first structure of the plant PEPCs, has been determined at 3.0 A resolution. The structure includes a sulfate ion at the plausible binding site of an allosteric activator, glucose 6-phosphate. The crystal structure of E. coli PEPC (EcPEPC) complexed with Mn(2+), phosphoenolpyruvate analog (3,3-dichloro-2-dihydroxyphosphinoylmethyl-2-propenoate), and an allosteric inhibitor, aspartate, has also been determined at 2.35 A resolution. Dynamic movements were found in the ZmPEPC structure, compared with the EcPEPC structure, around two loops near the active site. On the basis of these molecular structures, the mechanisms for the carboxylation reaction and for the allosteric regulation of PEPC are proposed.

Ion aggregation in high salt solutions. VII. The effect of cations on the structures of ion aggregates and water hydrogen-bonding network

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Choi, Hyung Ran; Jeon, Jonggu; Cho, Minhaeng

2017-10-01

Ions in high salt solutions have a strong propensity to form polydisperse ion aggregates with broad size and shape distributions. In a series of previous comparative investigations using femtosecond IR pump-probe spectroscopy, molecular dynamics simulation, and graph theoretical analysis, we have shown that there exists a morphological difference in the structures of ion aggregates formed in various salt solutions. As salt concentration increases, the ions in high salt solutions form either cluster-like structures excluding water molecules or network-like structures entwined with water hydrogen-bonding networks. Interestingly, such morphological characteristics of the ion aggregates have been found to be in correlation with the solubility limits of salts. An important question that still remains unexplored is why certain salts with different cations have notably different solubility limits in water. Here, carrying out a series of molecular dynamics simulations of aqueous salt solutions and analyzing the distributions and connectivity patterns of ion aggregates with a spectral graph analysis method, we establish the relationship between the salt solubility and the ion aggregate morphology with a special emphasis on the cationic effects on water structures and ion aggregation. We anticipate that the understanding of large scale ion aggregate structures revealed in this study will be critical for elucidating the specific ion effects on the solubility and conformational stability of co-solute molecules such as proteins in water.

Determination of phospholipid regiochemistry by Ag(I) adduction and tandem mass spectrometry.

PubMed

Yoo, Hyun Ju; Håkansson, Kristina

2011-02-15

Collision-activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) of Ag-adducted phospholipids were investigated as structural tools. Previously, determination of the acyl chains at the two phospholipid esterification sites has been performed based on the R(1)COO(-)/R(2)COO(-) ratio in negative ion mode CAD tandem mass spectrometry. However, the observed product ion ratio is dependent on the extent of unsaturation of the fatty acyl group at sn-2 as well as on the total chain length. Similarly, in positive ion mode CAD with/without alkaline or alkaline earth metal adduction, the ratio of product ions resulting from either R(1)COOH or R(2)COOH neutral losses is dependent on the nature of the phospholipid polar headgroup. Ag(+) ion chromatography, in which silver ions are part of the stationary phase, can provide information on double bond number/distribution as well as double bond configuration (cis/trans) because of interaction between Ag(+) ions and olefinic π electrons of fatty acids and lipids. We hypothesized that interactions between double bonds and Ag(+) may be utilized to also reveal phospholipid esterification site information in tandem mass spectrometry. CAD and IRMPD of Ag-adducted phospholipids with unsaturated fatty acids (R(x)COOH, x = 1 or 2) provided characteristic product ions, [R(x)COOH + Ag](+), and their neutral losses. The characteristic product ions and their abundances do not depend on the type of polar headgroup or the number of double bonds of unsaturated acyl chains. Tandem mass spectrometry of Cu-adducted phospholipids was also performed for comparison based on the Lewis acid and base properties of Cu(+) and phospholipid double bonds, respectively.

Direct Acceleration of Pickup Ions at The Solar Wind Termination Shock: The Production of Anomalous Cosmic Rays

NASA Technical Reports Server (NTRS)

Ellison, Donald C.; Jones, Frank C.; Baring, Matthew G.

1998-01-01

We have modeled the injection and acceleration of pickup ions at the solar wind termination shock and investigated the parameters needed to produce the observed Anomalous Cosmic Ray (ACR) fluxes. A non-linear Monte Carlo technique was employed, which in effect solves the Boltzmann equation and is not restricted to near-isotropic particle distribution functions. This technique models the injection of thermal and pickup ions, the acceleration of these ions, and the determination of the shock structure under the influence of the accelerated ions. The essential effects of injection are treated in a mostly self-consistent manner, including effects from shock obliquity, cross- field diffusion, and pitch-angle scattering. Using recent determinations of pickup ion densities, we are able to match the absolute flux of hydrogen in the ACRs by assuming that pickup ion scattering mean free paths, at the termination shock, are much less than an AU and that modestly strong cross-field diffusion occurs. Simultaneously, we match the flux ratios He(+)/H(+) or O(+)/H(+) to within a factor approx. 5. If the conditions of strong scattering apply, no pre-termination-shock injection phase is required and the injection and acceleration of pickup ions at the termination shock is totally analogous to the injection and acceleration of ions at highly oblique interplanetary shocks recently observed by the Ulysses spacecraft. The fact that ACR fluxes can be modeled with standard shock assumptions suggests that the much-discussed "injection problem" for highly oblique shocks stems from incomplete (either mathematical or computer) modeling of these shocks rather than from any actual difficulty shocks may have in injecting and accelerating thermal or quasi-thermal particles.

New LaMAsH(x) (M = Co, Ni, or Cu) arsenides with covalent M-H chains.

PubMed

Mizoguchi, Hiroshi; Park, SangWon; Hiraka, Haruhiro; Ikeda, Kazutaka; Otomo, Toshiya; Hosono, Hideo

2014-12-17

A new series of tetragonal LaPtSi-type mixed-anion arsenides, LaMAsH(x) (M = Co, Ni, or Cu), has been synthesized using high-temperature and high-pressure techniques. The crystal structure of these intermetallic compounds determined via powder neutron diffraction is composed of a 3D framework of three connected planes with the La ions filling the cavities in the structure. Each late transition-metal ion M, all of which have relatively large electronegativities, behaves like a main group element and forms a planar coordination configuration with three As ions. The trigonal-bipyramidal coordination adopted by the H in the cavity, HM2La3, is compressed along the C3 axis, and unusual M-H chains run along the x and y directions, reinforcing the covalent framework. These chains, which are unique in solids, are stabilized by covalent interactions between the M 4s and H 1s orbitals.

Characterization of carbonyl by-products during Uniblu-A ozonation by liquid chromatography/hybrid quadrupole time-of-flight/mass spectrometry.

PubMed

Amorisco, A; Locaputo, V; Mascolo, G

2011-07-15

The structural elucidation of carbonyl-containing by-products arising from Uniblu-OH ozonation has been investigated by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) employing a quadrupole time-of-flight mass spectrometer. The by-products were derivatized with 2,4-dinitrophenylhydrazine, allowing the formation of [M-H](-) ions of the derivatives in the electrospray source. Exact mass measurements of both the [M-H](-) ions and their product ions allowed the elemental formulae and related structures of ten by-products to be determined confidently. The main degradation pathway were decarboxylation followed by further oxidation. It is noteworthy that the experimental procedure employed allowed the identification of both nitrogen- and sulphur-containing carbonyl by-products during Uniblu-OH ozonation. This result is of environmental relevance for monitoring the balance of organic nitrogen and sulphur during the ozonation of organic pollutants. These atoms, in fact, do not undergo complete mineralization. Copyright © 2011 John Wiley & Sons, Ltd.

Medium-energy heavy-ion single-event-burnout imaging of power MOSFETs

NASA Astrophysics Data System (ADS)

Musseau, O.; Torres, A.; Campbell, A. B.; Knudson, A. R.; Buchner, S.; Fischer, B.; Schlogl, M.; Briand, P.

1999-12-01

We present the first experimental determination of the SEB sensitive area in a power MOSFET irradiated with a high-LET heavy-ion microbeam. We used a spectroscopy technique to perform coincident measurements of the charge collected in both source and drain junctions together, with a nondestructive technique (current limitation). The resulting charge collection images are related to the physical structure of the individual cells. These experimental data reveal the complex 3-dimensional behavior of a real structure, which can not easily be simulated using available tools. As the drain voltage is increased, the onset of burnout is reached, characterized by a sudden change in the charge collection image. "Hot spots" are observed where the collected charge reaches its maximum value. Those spots, due to burnout triggering events, correspond to areas where the silicon is degraded through thermal effects along a single ion track. This direct observation of SEB sensitive areas as applications for, either device hardening, by modifying doping profiles or layout of the cells, or for code calibration and device simulation.

Helium Ion Beam Microscopy for Copper Grain Identification in BEOL Structures

NASA Astrophysics Data System (ADS)

van den Boom, Ruud J. J.; Parvaneh, Hamed; Voci, Dave; Huynh, Chuong; Stern, Lewis; Dunn, Kathleen A.; Lifshin, Eric

2009-09-01

Grain size determination in advanced metallization structures requires a technique with resolution ˜2 nm, with a high signal-to-noise ratio and high orientation-dependant contrast for unambiguous identification of grain boundaries. Ideally, such a technique would also be capable of high-throughput and rapid time-to-knowledge. The Helium Ion Microscope (HIM) offers one possibility for achieving these aims in a single platform. This article compares the performance of the HIM with Focused Ion Beam, Scanning Electron and Transmission Electron Microscopes, in terms of achievable image resolution and contrast, using plan-view and cross-sectional imaging of electroplated samples. Although the HIM is capable of sub-nanometer beam diameter, the low signal-to-noise ratio in the images necessitates signal averaging, which degrades the measured image resolution to 6-8 nm. Strategies for improving S/N are discussed in light of the trade-off between beam current and probe size, accelerating voltage, and dwell time.

Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing

NASA Astrophysics Data System (ADS)

Both, P.; Green, A. P.; Gray, C. J.; Šardzík, R.; Voglmeir, J.; Fontana, C.; Austeri, M.; Rejzek, M.; Richardson, D.; Field, R. A.; Widmalm, G.; Flitsch, S. L.; Eyers, C. E.

2014-01-01

Mass spectrometry is the primary analytical technique used to characterize the complex oligosaccharides that decorate cell surfaces. Monosaccharide building blocks are often simple epimers, which when combined produce diastereomeric glycoconjugates indistinguishable by mass spectrometry. Structure elucidation frequently relies on assumptions that biosynthetic pathways are highly conserved. Here, we show that biosynthetic enzymes can display unexpected promiscuity, with human glycosyltransferase pp-α-GanT2 able to utilize both uridine diphosphate N-acetylglucosamine and uridine diphosphate N-acetylgalactosamine, leading to the synthesis of epimeric glycopeptides in vitro. Ion-mobility mass spectrometry (IM-MS) was used to separate these structures and, significantly, enabled characterization of the attached glycan based on the drift times of the monosaccharide product ions generated following collision-induced dissociation. Finally, ion-mobility mass spectrometry following fragmentation was used to determine the nature of both the reducing and non-reducing glycans of a series of epimeric disaccharides and the branched pentasaccharide Man3 glycan, demonstrating that this technique may prove useful for the sequencing of complex oligosaccharides.

Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results

NASA Astrophysics Data System (ADS)

Smiatek, Jens

2017-06-01

Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.

Unusual Complex Formation and Chemical Reaction of Haloacetate Anion on the Exterior Surface of Cucurbit[6]uril in the Gas Phase

NASA Astrophysics Data System (ADS)

Choi, Tae Su; Ko, Jae Yoon; Heo, Sung Woo; Ko, Young Ho; Kim, Kimoon; Kim, Hugh I.

2012-10-01

Noncovalent interactions of cucurbit[6]uril (CB[6]) with haloacetate and halide anions are investigated in the gas phase using electrospray ionization ion mobility mass spectrometry. Strong noncovalent interactions of monoiodoacetate, monobromoacetate, monochloroacetate, dichloroacetate, and trichloroacetate on the exterior surface of CB[6] are observed in the negative mode electrospray ionization mass spectra. The strong binding energy of the complex allows intramolecular SN2 reaction of haloacetate, which yields externally bound CB[6]-halide complex, by collisional activation. Utilizing ion mobility technique, structures of exteriorly bound CB[6] complexes of haloacetate and halide anions are confirmed. Theoretically determined low energy structures using density functional theory (DFT) further support results from ion mobility studies. The DFT calculation reveals that the binding energy and conformation of haloacetate on the CB[6] surface affect the efficiency of the intramolecular SN2 reaction of haloacetate, which correlate well with the experimental observation.

Effect of Anions on Nanofiber Formation of β-sheet Propensity Amphiphile Peptide

NASA Astrophysics Data System (ADS)

Shamsudeen, H.; Tan, H. L.; Eshak, Z.

2018-05-01

Peptide self-assembly forms different nanostructures under simple alteration in the solution environment. Understanding the mechanism of the assembly will help us to control and tailor functional nanomaterials. This study aims to investigate the influence of anions on the self-assembly morphology and shape using a synthetic peptide of FFFFKK. Circular Dichoism (CD) and Environmental Scanning Electron Microscope (ESEM) were used to determine the secondary structure and self-assembly morphology, while Image J imaging software was used to measure diameter size. In the absence of anion, FFFFKK formed anti-parallel β-sheet that adopted sizeable fibrillar structure with a minimal increment over the first 7 hours of assembly. Irregular structure was observed in the presence of Iodide ion (I-) with a less stable secondary structure such as β-turn and β-loop. In the presence of perchlorate ion (ClO4 -), needle-like structure was observed with predominantly β-sheet structure. Our study showed that peptide morphology can be controlled by using different anions with careful selection of amino acid residues in peptide sequence.

Characterization of synthetic dyes by comprehensive two-dimensional liquid chromatography combining ion-exchange chromatography and fast ion-pair reversed-phase chromatography.

PubMed

Pirok, Bob W J; Knip, Jitske; van Bommel, Maarten R; Schoenmakers, Peter J

2016-03-04

In the late 19th century, newly invented synthetic dyes rapidly replaced the natural dyes on the market. The characterization of mixtures of these so-called early synthetic dyes is complicated through the occurrence of many impurities and degradation products. Conventional one-dimensional liquid chromatography does not suffice to obtain fingerprints with sufficient resolution and baseline integrity. Comprehensive two-dimensional liquid chromatography (LC×LC) is employed in this study, with ion-exchange chromatography in the first dimension and fast ion-pair liquid chromatography in the second. Retention in the first dimension is largely determined by the number of charges, while the selection of a small ion-pair reagent (tetramethylammonium hydroxide) in the second dimension causes retention to be largely determined by the molecular structure of the dye. As a result, there is a high degree of orthogonality of the two dimensions, similar to the values typically encountered in GC×GC. The proposed LC×LC method shows a theroretical peak capacity of about 2000 in an analysis time of about three hours. Clear, informative fingerprints are obtained that open a way to a more efficient characterization of dyes used in objects of cultural heritage. Copyright © 2016 Elsevier B.V. All rights reserved.

Energetic and dynamic analysis of transport of Na + and K + through a cyclic peptide nanotube in water and in lipid bilayers

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

Song, Yeonho; Lee, Ji Hye; Hwang, Hoon

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na + and K + are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(D-Leu-Trp) 4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and lipid bilayers, and that themore » selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. Here the PMF and diffusivity profiles for Na + and K + reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na + and K + ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.« less

Energetic and dynamic analysis of transport of Na + and K + through a cyclic peptide nanotube in water and in lipid bilayers

DOE PAGES

Song, Yeonho; Lee, Ji Hye; Hwang, Hoon; ...

2016-11-04

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na + and K + are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(D-Leu-Trp) 4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and lipid bilayers, and that themore » selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. Here the PMF and diffusivity profiles for Na + and K + reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na + and K + ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.« less

A simple and rapid method for high-resolution visualization of single-ion tracks

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

Omichi, Masaaki; Center for Collaborative Research, Anan National College of Technology, Anan, Tokushima 774-0017; Choi, Wookjin

2014-11-15

Prompt determination of spatial points of single-ion tracks plays a key role in high-energy particle induced-cancer therapy and gene/plant mutations. In this study, a simple method for the high-resolution visualization of single-ion tracks without etching was developed through the use of polyacrylic acid (PAA)-N, N’-methylene bisacrylamide (MBAAm) blend films. One of the steps of the proposed method includes exposure of the irradiated films to water vapor for several minutes. Water vapor was found to promote the cross-linking reaction of PAA and MBAAm to form a bulky cross-linked structure; the ion-track scars were detectable at a nanometer scale by atomic forcemore » microscopy. This study demonstrated that each scar is easily distinguishable, and the amount of generated radicals of the ion tracks can be estimated by measuring the height of the scars, even in highly dense ion tracks. This method is suitable for the visualization of the penumbra region in a single-ion track with a high spatial resolution of 50 nm, which is sufficiently small to confirm that a single ion hits a cell nucleus with a size ranging between 5 and 20 μm.« less

Physicochemical properties and ion-solvent interactions in aqueous sodium, ammonium, and lead acetate solution

NASA Astrophysics Data System (ADS)

Deosarkar, S. D.; Mendkudle, M. S.

2014-09-01

Densities (ρ), viscosities (η) and refractive indices ( n D) of aqueous sodium acetate (SA), ammonium acetate (AA), and lead acetate (LA) solutions have been measured for different concentrations of salts at 302.15 K. Apparent molar volumes (φv) for studied solutions were calculated from density data, and fitted to Masson's relation and partial molar volume (φ{v/o}) was determined. Viscosity data were fitted to Jones-Dole equation and viscosity A- and B-coefficients were determined. Refractive index and density data were fitted to Lorentz and Lorenz equation and specific refraction ( R D) were calculated. Behavior of various physicochemical properties indicated presence of strong ion-solvent interactions in present systems and the acetate salts structure maker in water.

Transition metal ions in ZnO: Effects of intrashell coulomb repulsion on electronic properties

NASA Astrophysics Data System (ADS)

Ciechan, A.; Bogusławski, P.

2018-05-01

Electronic structure of the transition metal (TM) dopants in ZnO is calculated by first principles approach. Analysis of the results is focused on the properties determined by the intrashell Coulomb coupling. The role of both direct and exchange interaction channel is analyzed. The coupling is manifested in the strong charge state dependence of the TM gap levels, which leads to the metastability of photoexcited Mn, and determines the accessible equilibrium charge states of TM ions. The varying magnitude of the exchange coupling is reflected in the dependence of the spin splitting energy on the chemical identity across the 3d series, as well as the charge state dependence of spin-up spin-down exchange splitting.

Direct evidence for the gas phase thermal polymerization of styrene. Determination of the initiation mechanism and structures of the early oligomers by ion mobility.

PubMed

Alsharaeh, Edreese H; Ibrahim, Yehia M; El-Shall, M Samy

2005-05-04

We present here direct evidence for the thermal self-initiated polymerization of styrene in the gas phase and establish that the initiation process proceeds via essentially the same mechanism (the Mayo mechanism) as in condensed phase polymerization. Furthermore, we provide structural identifications of the dimers and trimers formed in the gas phase.

Uniform Fe3O4 microflowers hierarchical structures assembled with porous nanoplates as superior anode materials for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Wang, Xiaoliang; Liu, Yanguo; Arandiyan, Hamidreza; Yang, Hongping; Bai, Lu; Mujtaba, Jawayria; Wang, Qingguo; Liu, Shanghe; Sun, Hongyu

2016-12-01

Uniform Fe3O4 microflowers assembled with porous nanoplates were successfully synthesized by a solvothermal method and subsequent annealing process. The structural and compositional analysis of the Fe3O4 microflowers were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). The Bruauer-Emmett-Teller (BET) specific surface area was calculated by the nitrogen isotherm curve and pore size distribution of Fe3O4 microflowers was determined by the Barret-Joyner-Halenda (BJH) method. When evaluated as anode material for lithium-ion batteries, the as-prepared Fe3O4 microflowers electrodes delivered superior capacity, better cycling stability and rate capability than that of Fe3O4 microspheres electrodes. The improved electrochemical performance was attributed to the microscale flowerlike architecture and the porous sheet structural nature.

Study of chloride ion transport of composite by using cement and starch as a binder

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

Armynah, Bidayatul; Halide, Halmar; Zahrawani,

This study presents the chemical bonding and the structural properties of composites from accelerator chloride test migration (ACTM). The volume fractions between binder (cement and starch) and charcoal in composites are 20:80 and 60:40. The effect of the binder to the chemical composition, chemical bonding, and structural properties before and after chloride ion passing through the composites was determined by X-ray fluorescence (XRF), by Fourier transform infra-red (FTIR), and x-ray diffraction (XRD), respectively. From the XRD data, XRF data, and the FTIR data shows the amount of chemical composition, the type of binding, and the structure of composites are dependingmore » on the type of binder. The amount of chloride migration using starch as binder is higher than that of cement as a binder due to the density effects.« less

Self-assembly of a double-helical complex of sodium.

PubMed

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

PubMed Central

Kornyshev, Alexei A.; Leikin, Sergey

2013-01-01

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation. PMID:23663846

Structure of a magnetic flux annihilation layer formed by the collision of supersonic, magnetized plasma flows

DOE PAGES

Suttle, L. G.; Hare, J. D.; Lebedev, S. V.; ...

2016-05-31

We present experiments characterizing the detailed structure of a current layer, generated by the collision of two counter-streaming, supersonic and magnetized aluminum plasma flows. The anti parallel magnetic fields advected by the flows are found to be mutually annihilated inside the layer, giving rise to a bifurcated current structure—two narrow current sheets running along the outside surfaces of the layer. Measurements with Thomson scattering show a fast outflow of plasma along the layer and a high ion temperature (T i~¯ZT e, with average ionization ¯Z=7). Lastly, analysis of the spatially resolved plasma parameters indicates that the advection and subsequent annihilationmore » of the in-flowing magnetic flux determines the structure of the layer, while the ion heating could be due to the development of kinetic, current-driven instabilities.« less

Ion acoustic solitons in an electronegative plasma with electron trapping and nonextensivity effects

NASA Astrophysics Data System (ADS)

Ali Shan, S.

2018-03-01

The impact of electron trapping and nonextensivity on the low frequency ion acoustic solitary waves in an electronegative plasma is investigated. The energy integral equation with the Sagdeev truncated approach is derived, which is then solved with the help of suitable parameters and necessary conditions to get the solitary structures. The minimum Mach (M) number needed to calculate the solitary structures is found to be varying under the impact of trapping efficiency determining factor β and entropic index q. The results have been illustrated with the help of physically acceptable parameters and the amplitude of nonlinear solitary structures is found to be modified significantly because of electron trapping efficiency β and entropic index q. This study has been made with reference to Laboratory observation, which can also be helpful in Space and astrophysical plasmas where electronegative plasmas have been reported.

Structure of a magnetic flux annihilation layer formed by the collision of supersonic, magnetized plasma flows

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

Suttle, L. G.; Hare, J. D.; Lebedev, S. V.

We present experiments characterizing the detailed structure of a current layer, generated by the collision of two counter-streaming, supersonic and magnetized aluminum plasma flows. The anti parallel magnetic fields advected by the flows are found to be mutually annihilated inside the layer, giving rise to a bifurcated current structure—two narrow current sheets running along the outside surfaces of the layer. Measurements with Thomson scattering show a fast outflow of plasma along the layer and a high ion temperature (T i~¯ZT e, with average ionization ¯Z=7). Lastly, analysis of the spatially resolved plasma parameters indicates that the advection and subsequent annihilationmore » of the in-flowing magnetic flux determines the structure of the layer, while the ion heating could be due to the development of kinetic, current-driven instabilities.« less

Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain.

PubMed

Sriram, M; Osipiuk, J; Freeman, B; Morimoto, R; Joachimiak, A

1997-03-15

The 70 kDa heat shock proteins (Hsp70) are a family of molecular chaperones, which promote protein folding and participate in many cellular functions. The Hsp70 chaperones are composed of two major domains. The N-terminal ATPase domain binds to and hydrolyzes ATP, whereas the C-terminal domain is required for polypeptide binding. Cooperation of both domains is needed for protein folding. The crystal structure of bovine Hsc70 ATPase domain (bATPase) has been determined and, more recently, the crystal structure of the peptide-binding domain of a related chaperone, DnaK, in complex with peptide substrate has been obtained. The molecular chaperone activity and conformational switch are functionally linked with ATP hydrolysis. A high-resolution structure of the ATPase domain is required to provide an understanding of the mechanism of ATP hydrolysis and how it affects communication between C- and N-terminal domains. The crystal structure of the human Hsp70 ATPase domain (hATPase) has been determined and refined at 1. 84 A, using synchrotron radiation at 120K. Two calcium sites were identified: the first calcium binds within the catalytic pocket, bridging ADP and inorganic phosphate, and the second calcium is tightly coordinated on the protein surface by Glu231, Asp232 and the carbonyl of His227. Overall, the structure of hATPase is similar to bATPase. Differences between them are found in the loops, the sites of amino acid substitution and the calcium-binding sites. Human Hsp70 chaperone is phosphorylated in vitro in the presence of divalent ions, calcium being the most effective. The structural similarity of hATPase and bATPase and the sequence similarity within the Hsp70 chaperone family suggest a universal mechanism of ATP hydrolysis among all Hsp70 molecular chaperones. Two calcium ions have been found in the hATPase structure. One corresponds to the magnesium site in bATPase and appears to be important for ATP hydrolysis and in vitro phosphorylation. Local changes in protein structure as a result of calcium binding may facilitate phosphorylation. A small, but significant, movement of metal ions and sidechains could position catalytically important threonine residues for phosphorylation. The second calcium site represents a new calcium-binding motif that can play a role in the stabilization of protein structure. We discuss how the information about catalytic events in the active site could be transmitted to the peptide-binding domain.

The role of correlation and solvation in ion interactions with B-DNA

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

Sushko, Maria L.; Thomas, Dennis G.; Pabit, Suzette

Ionic atmosphere around nucleic acids plays important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important insights into the structure and energetics of the ionic atmosphere but are time- and resource-intensive. In this paper, we demonstrate the use of classical density functional theory to model DNA-ion interactions and explore the balance between ion-DNA, ion-water, and ion-ion interactions. In particular, we compute the distribution of RbCl, SrCl2, and CoHexCl3 (cobalt hexammine chlo- ride) around a B-form DNA molecule. The accuracy of the DFT calculations was assessed by comparisonmore » between simulated and experimental ASAXS curves. As expected, these calculations revealed significant differences between the monovalent, divalent, and trivalent cations. About half of the DNA-bound Rb+ ions penetrate into the minor groove of the DNA and half adsorb on the DNA strands. The fraction of cations in the minor groove decreases for the larger Sr2+ ions and becomes zero for CoHex3+ ions, which all adsorb on the DNA strands. The distribution of CoHex3+ ions is mainly determined by Coulomb interactions, while ion-correlation forces play a central role in the monovalent Rb+ distribution and a combination of ion-correlation and hydration forces affect the Sr2+ distribution around DNA.« less

Crystal Structure and Characterization of Ba 2V 3O 9: A Vanadyl(IV) Vanadate Containing Rutile-like Chains of VO 6Octahedra

NASA Astrophysics Data System (ADS)

Dhaussy, Anne-Claire; Abraham, Francis; Mentre, Olivier; Steinfink, Hugo

1996-11-01

The crystal structure of Ba2V3O9has been determined and refined to finalRandRwvalues of 0.025 and 0.028 from 1562 independent single crystal reflections. It crystallizes in the space groupP21/mwitha= 9.302(1) Å,b= 5.969(1) Å,c= 8.118(1) Å, and β = 113.96 (1)°. The structure consists of one-dimensional rutile-type chains of edge-sharing VO6octahedra parallel to thebaxis. The VO4tetrahedra share corners with VO6octahedra of a single rutile-type chain to form one-dimensional [V3O9]4-∞columns which are held together by Ba2+ions. In this mixed valence compound V4+and V5+ions are distributed in an ordered way in octahedra and tetrahedra, respectively. In the almost perfect O6octahedron the vanadium atom is off-center so that it forms a short vanadyl V_dbO bond of 1.686(3) Å, typical of a V4+ion. This compound is a barium vanadyl vanadate Ba2(VO)(VO4)2. It is the first example of isolated rutile-type chains found with V4+ions. Magnetic susceptibility measurements show that this phase is an antiferromagnet withTN≅ 58 K. At about 20 K magnetic anisotropy causes a canted spin arrangement.

Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.

PubMed

Kaplan, Anne R; Brady, Megan R; Maciejewski, Mark W; Kammerer, Richard A; Alexandrescu, Andrei T

2017-03-21

To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1 H- 15 N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13 C rotating frame T 1 relaxation (T 1ρ ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.

Small Ion Channel Linking Molecular Simulations and Electrophysiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrzej

2017-01-01

Ion channels are pore-forming protein assemblies that mediate the transport of small ions across cell membranes. Otherwise, membrane bilayers would be almost impermeable to ions incapable to traverse the low dielectric constant, hydrophobic membrane core. Ion channels are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses, cardiac functions, muscle contraction and apoptosis. On the other extreme of biological complexity, viral ion channels (viroporins) influence many stages of the virus infection cycle either through regulating virus replication, such as entry, assembly and release or modulating the electrochemical balance in the subcellular compartments of host cells. Ion channels were crucial components of protocells. Their emergence facilitated adaptation of nascent life to different environmental conditions. The earliest ion channels must have been much simpler than most of their modern ancestors. Viral channels are among only a few naturally occurring models to study the structure, function and evolution of primordial channels. Experimental studies of these properties are difficult and often unreliable. In principle, computational methods, and molecular dynamics (MD) simulations in particular, can aid in providing information about both the structure and the function of ion channels. However, MD suffers from its own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. It is, therefore, essential to determine the reliability of MD simulations. We propose to do so on the basis of two criteria. One is channel stability on time scales that extend for several microseconds or longer. The other is the ability to reproduce the measured ionic conductance as a function of applied voltage. If both the stability and the calculated ionic conductance are satisfactory it will greatly increase our confidence that the structure and the function of a channel are described sufficiently accurately. To our knowledge, long time scale stability (approx.10 micro-sec) and the correct electrophysiology have been shown so far for only one channel - the synthetic LS3 hexamer). In this presentation, this approach will be discussed in application to two viral channels - Vpu, encoded by the HIV-1 genome and p7 of hepatitis C.

Feasibility of atomic and molecular laser-induced breakdown spectroscopy (LIBS) to in situ determination of chlorine in concrete : summary.

DOT National Transportation Integrated Search

2016-10-01

One of the most serious threats to Floridas extensive coastal transportation infrastructure is the invasion of steel-reinforced concrete structures by chloride ions. In this project, University of Florida researchers investigated the use of a nove...

Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64).

PubMed

Poznar, Monika; Hołubowicz, Rafał; Wojtas, Magdalena; Gapiński, Jacek; Banachowicz, Ewa; Patkowski, Adam; Ożyhar, Andrzej; Dobryszycki, Piotr

2017-11-01

Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystallographic site swapping of La3+ ion in BaA'LaTeO6 (A' = Na, K, Rb) double perovskite type compounds: diffraction and photoluminescence evidence for the site swapping.

PubMed

Phatak, R; Gupta, S K; Krishnan, K; Sali, S K; Godbole, S V; Das, A

2014-02-28

Double perovskite type compounds of the formula BaA'LaTeO6 (A' = Na, K, Rb) were synthesized by solid state route and their crystal structures were determined by Rietveld analysis using powder X-ray diffraction and neutron diffraction data. Na compound crystallizes in the monoclinic system with P2₁/n space group whereas, K and Rb compounds crystallize in Fm3m space group. All the three compounds show rock salt type ordering at B site. Crystal structure analysis shows that La ion occupies A site in Na compound whereas, it occupies B site in K and Rb compounds according to the general formula of AA'BB'O6 for a double perovskite type compound. Effect of this crystallographic site swapping of the La ion was also observed in the photoluminescence study by doping Eu(3+) in La(3+) site. The large decrease in the intensity of the electric dipole ((5)D0-(7)F2) transition in the Rb compound compared to the Na compound indicates that Eu(3+) ion resides in the centrosymmetric octahedral environment in the Rb compound.

The interaction of copper ions with Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli: an X-ray absorption near-edge structure (XANES) spectroscopy study.

PubMed

Zanzen, Ulrike; Bovenkamp-Langlois, Lisa; Klysubun, Wantana; Hormes, Josef; Prange, Alexander

2018-04-01

The antimicrobial properties of copper ions have been known for a long time. However, the exact mechanism of action of the transition metal on microorganisms has long been unclear. X-ray absorption near-edge structure (XANES) spectroscopy at the Cu K edge allows the determination of copper speciation in Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa that have been treated with Cu(II) and Cu(I) solutions. The death/inactivation of the bacteria was observed using plate counting and light microscopy. The Cu K-XANES spectra of the two Gram-negative bacteria are different than those of the Gram-positive strain. The results clearly show that the Cu + -S bond contributes to the antibacterial activity of copper, as in the case of silver. The detailed evaluation of the differentiated absorption spectra shows that Cu + (not Cu 2+ ) is the dominant ion that binds to the bacteria. Because Cu + is not the most common copper ion, copper is not as effective an antibacterial agent as silver, whose common valency is actually + 1. Any reaction of copper with phosphorus from the bacteria can be excluded after the evaluation of the absorption spectra.

Lanthanide binding and IgG affinity construct: Potential applications in solution NMR, MRI, and luminescence microscopy

PubMed Central

Barb, Adam W; Ho, Tienhuei Grace; Flanagan-Steet, Heather; Prestegard, James H

2012-01-01

Paramagnetic lanthanide ions when bound to proteins offer great potential for structural investigations that utilize solution nuclear magnetic resonance spectroscopy, magnetic resonance imaging, or optical microscopy. However, many proteins do not have native metal ion binding sites and engineering a chimeric protein to bind an ion while retaining affinity for a protein of interest represents a significant challenge. Here we report the characterization of an immunoglobulin G-binding protein redesigned to include a lanthanide binding motif in place of a loop between two helices (Z-L2LBT). It was shown to bind Tb3+ with 130 nM affinity. Ions such as Dy3+, Yb3+, and Ce3+ produce paramagnetic effects on NMR spectra and the utility of these effects is illustrated by their use in determining a structural model of the metal-complexed Z-L2LBT protein and a preliminary characterization of the dynamic distribution of IgG Fc glycan positions. Furthermore, this designed protein is demonstrated to be a novel IgG-binding reagent for magnetic resonance imaging (Z-L2LBT:Gd3+ complex) and luminescence microscopy (Z-L2LBT: Tb3+ complex). PMID:22851279

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

PubMed Central

Nautiyal, S.; Alber, T.

1999-01-01

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness. PMID:10210186

Structure of chitosan gels mineralized by sorption

NASA Astrophysics Data System (ADS)

Modrzejewska, Z.; Skwarczyńska, A.; Douglas, T. E. L.; Biniaś, D.; Maniukiewicz, W.; Sielski, J.

2015-10-01

The paper presents the structural studies of mineralized chitosan hydrogels. Hydrogels produced by using sodium beta-glycerophosphate (Na-β-GP) as a neutralizing agent. Mineralization was performed method "post loading", which consisted in sorption to the gels structure Ca ions. In order to obtain - in the structure of gels - compounds similar to the hydroxyapatites present naturally in bone tissue, gels after sorption were modified in: pH 7 buffer and sodium hydrogen phosphate. In order to determine the structural properties of the gels, the following methods were used: infrared spectroscopy with Fourier transformation, FTIR, X-ray diffractometry, XRD, scanning electron microscopy, SEM.

Conformational plasticity in the selectivity filter of the TRPV2 ion channel.

PubMed

Zubcevic, Lejla; Le, Son; Yang, Huanghe; Lee, Seok-Yong

2018-05-01

Transient receptor potential vanilloid (TRPV) channels are activated by ligands and heat and are involved in various physiological processes. In contrast to the architecturally related voltage-gated cation channels, TRPV1 and TRPV2 subtypes possess another activation gate at the selectivity filter that can open widely enough to permeate large organic cations. Despite recent structural advances, the mechanism of selectivity filter gating and permeation for both metal ions and large molecules by TRPV1 or TRPV2 is not well known. Here, we determined two crystal structures of rabbit TRPV2 in its Ca 2+ -bound and resiniferatoxin (RTx)- and Ca 2+ -bound forms, to 3.9 Å and 3.1 Å, respectively. Notably, our structures show that RTx binding leads to two-fold symmetric opening of the selectivity filter of TRPV2 that is wide enough for large organic cation permeation. Combined with functional characterizations, our studies reveal a structural basis for permeation of Ca 2+ and large organic cations in TRPV2.

Structure of the Zinc-Bound Amino-Terminal Domain of the NMDA Receptor NR2B Subunit

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

Karakas, E.; Simorowski, N; Furukawa, H

2009-01-01

N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors (iGluRs) that mediate the majority of fast excitatory synaptic transmission in the mammalian brain. One of the hallmarks for the function of NMDA receptors is that their ion channel activity is allosterically regulated by binding of modulator compounds to the extracellular amino-terminal domain (ATD) distinct from the L-glutamate-binding domain. The molecular basis for the ATD-mediated allosteric regulation has been enigmatic because of a complete lack of structural information on NMDA receptor ATDs. Here, we report the crystal structures of ATD from the NR2B NMDA receptor subunit in the zinc-freemore » and zinc-bound states. The structures reveal the overall clamshell-like architecture distinct from the non-NMDA receptor ATDs and molecular determinants for the zinc-binding site, ion-binding sites, and the architecture of the putative phenylethanolamine-binding site.« less

Structure of the TRPA1 ion channel suggests regulatory mechanisms.

PubMed

Paulsen, Candice E; Armache, Jean-Paul; Gao, Yuan; Cheng, Yifan; Julius, David

2015-04-23

The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here we use single-particle electron cryo- microscopy to determine the structure of full-length human TRPA1 to ∼4 Å resolution in the presence of pharmacophores, including a potent antagonist. Several unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted transient receptor potential (TRP)-like allosteric domain. These findings provide new insights into the mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents.

Active site structure and catalytic mechanism of phosphodiesterase for degradation of intracellular second messengers

NASA Astrophysics Data System (ADS)

Zhan, Chang-Guo

2002-03-01

Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulate intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it was uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand has been determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.

Structure of the TRPA1 ion channel suggests regulatory mechanisms

PubMed Central

Paulsen, Candice E.; Armache, Jean-Paul; Gao, Yuan; Cheng, Yifan; Julius, David

2015-01-01

The TRPA1 ion channel (a.k.a the ‘wasabi receptor’) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here, we use single-particle electron cryo-microscopy to determine the structure of full-length human TRPA1 to ~4Å resolution in the presence of pharmacophores, including a potent antagonist. A number of unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted TRP-like allosteric domain. These findings provide novel insights into mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents. PMID:25855297

Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

NASA Astrophysics Data System (ADS)

Sterling, Nicholas C.; Kerlin, Austin B.

2016-01-01

We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

A detailed mechanistic fragmentation analysis of methamphetamine and select regioisomers by GC/MS.

PubMed

Sachs, Sandra B; Woo, Francis

2007-03-01

A novel ring-substituted methamphetamine regioisomer, N,alpha,4-trimethyl phenmethylamine, was synthesized in order to study the validity of proposed structures for various mass spectrometry (MS)-derived peaks in a methamphetamine fragmentation pattern. While other research efforts have studied aspects of methamphetamine in detail, a full fragmentation study has not been reported previously. In addition to showing molecular structures represented by fragment peaks, mechanisms for selected processes are detailed. An empirically derived procedure to easily determine by simple spectral peak pattern recognition the geometry of dimethyl- or ethyl-substituted immonium ions (RRC = N+ RR) where m/z = 58 is outlined. These results are platform independent for electron ionization (EI) instruments, but have also proven to be helpful in explaining spectral peaks observed in spectra from ion trap systems. The spectrum for the synthesized methamphetamine regioisomer was accurately predicted using this methodology. While this approach is useful in some casework, the converse may be more useful: when an unexpected or unusual peak pattern arises in a spectrum, being able to analyze it to determine the structure of the molecule. This paper gives an analyst the means to begin such retro-synthetic analyses.

Self-Diffusion in Amorphous Silicon by Local Bond Rearrangements

NASA Astrophysics Data System (ADS)

Kirschbaum, J.; Teuber, T.; Donner, A.; Radek, M.; Bougeard, D.; Böttger, R.; Hansen, J. Lundsgaard; Larsen, A. Nylandsted; Posselt, M.; Bracht, H.

2018-06-01

Experiments on self-diffusion in amorphous silicon (Si) were performed at temperatures between 460 to 600 ° C . The amorphous structure was prepared by Si ion implantation of single crystalline Si isotope multilayers epitaxially grown on a silicon-on-insulator wafer. The Si isotope profiles before and after annealing were determined by means of secondary ion mass spectrometry. Isothermal diffusion experiments reveal that structural relaxation does not cause any significant intermixing of the isotope interfaces whereas self-diffusion is significant before the structure recrystallizes. The temperature dependence of self-diffusion is described by an Arrhenius law with an activation enthalpy Q =(2.70 ±0.11 ) eV and preexponential factor D0=(5.5-3.7+11.1)×10-2 cm2 s-1 . Remarkably, Q equals the activation enthalpy of hydrogen diffusion in amorphous Si, the migration of bond defects determining boron diffusion, and the activation enthalpy of solid phase epitaxial recrystallization reported in the literature. This close agreement provides strong evidence that self-diffusion is mediated by local bond rearrangements rather than by the migration of extended defects as suggested by Strauß et al. (Phys. Rev. Lett. 116, 025901 (2016), 10.1103/PhysRevLett.116.025901).

Automated LC-HRMS(/MS) Approach for the Annotation of Fragment Ions Derived from Stable Isotope Labeling-Assisted Untargeted Metabolomics

PubMed Central

2014-01-01

Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native 12C- and uniformly 13C (U-13C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-13C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research. PMID:24965664

Fragmentation pathways of 2-substituted pyrrole derivatives using electrospray ionization ion trap and electrospray ionization quadrupole time-of-flight mass spectrometry.

PubMed

Liang, Xianrui; Guo, Zili; Yu, Chuanming

2013-10-30

Pyrrole derivatives are of considerable importance and are present in a wide range of natural products and used extensively in drug discovery. Fragmentation pathway studies play an important role in the structural identification of pyrrole derivatives. As a part of our ongoing work on heterocycles, fragmentation pathways of 2-substituted pyrrole derivatives were investigated by mass spectrometry (MS). Twelve pyrrole derivatives were synthesized and analyzed. Low-resolution fragmentation ions of all the compounds were generated by ion trap mass spectrometry (ITMS(n) ) with an electrospray ionization (ESI) source in positive mode. Hybrid quadrupole time-of-flight mass spectrometry (QTOFMS) was used to determine the elemental compositions of the resultant product ions. The side-chain substituents at the 2-position influence the fragmentation pathways. Typical losses of H2 O, aldehydes and pyrrole moieties from the [M + H](+) ion are observed for the compounds with side chains bearing aromatic groups at the 2-position of the pyrrole. However, losses of H2 O, alcohols and C3 H6 are the main cleavage pathways for compounds 6 and 12 with nonphenyl-substituted side chains at the 2-position. Typical fragmentation mechanisms of 2-substituted pyrrole derivatives are proposed and elucidated based on the observations of ITMS(n) and QTOFMS spectra. The results showed that the fragmentation pathways were remarkably influenced by the side-chain substituents at the 2-position of pyrrole. This investigation should have value in the structural identification of this series of molecules or compounds with similar structures. Copyright © 2013 John Wiley & Sons, Ltd.

A novel route to recognizing quaternary ammonium cations using electrospray mass spectrometry.

PubMed

Shackman, Holly M; Ding, Wei; Bolgar, Mark S

2015-01-01

Characterizing and elucidating structures is a commonplace and necessary activity in the pharmaceutical industry with mass spectrometry and NMR being the primary tools for analysis. Although many functional groups are readily identifiable, quaternary ammonium cations have proven to be difficult to unequivocally identify using these techniques. Due to the lack of an N-H bond, quaternary ammonium groups can only be detected in the (1)H NMR spectra by weak signals generated from long-range (14)N-H coupling, which by themselves are inconclusive evidence of a quaternary ammonium functional group. Due to their low intensity, these signals are frequently not detected. Additionally, ions cannot be differentiated in a mass spectrum as an M(+) or [M + H](+) ion without prior knowledge of the compound's structure. In order to utilize mass spectrometry as a tool for determining this functionality, ion cluster formation of quaternary ammonium cations and non-quaternary amines was studied using electrospray ionization. Several mobile phase modifiers were compared; however, the addition of small amounts of trifluoroacetic acid proved superior in producing characteristic and intense [M +2TFA](-) clusters for compounds containing quaternary ammonium cations when using negative electrospray. By fragmenting this characteristic ion using CID, nearly all compounds studied could be unambiguously identified as containing a quaternary ammonium cation or a non-quaternary amine attributable to the presence (non-quaternary amine) or absence (quaternary ammonium cation) of the resulting [2TFA + H](-) ion in the product spectra. This method of analysis provides a rapid, novel, and reliable technique for indicating the presence of quaternary ammonium cations in order to aid in structural elucidation.

Zwitterionic-hydrophilic interaction capillary liquid chromatography coupled to tandem mass spectrometry for the characterization of human alpha-acid-glycoprotein N-glycan isomers.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Peracaula, Rosa; Sanz-Nebot, Victòria

2017-10-23

In this work, a μZIC-HILIC-MS/MS methodology was established in negative ion mode for the characterization of glycan isomers. The possibility to separate the glycan isomers by the μZIC-HILIC strategy coupled to a high resolution tandem mass spectrometry detection permitted us to obtain valuable information about each glycan structure. The most important diagnostic ion fragments previously described to characterize structural features of glycans, were evaluated in this study using hAGP as model glycoprotein. The assignation of hAGP glycan isomers performed in our previous work using the GRIL strategy in combination with exoglycosidase digestion [1] was used in this paper to confirm or discard some ion fragments reported in the literature and delve into the structural characterization of glycan isomers. Sialic acid as well as fucose linkage-type glycan isomers were assigned using this approach and daughter ions with higher diagnostic value were determined. The location of α2-3/α2-6 sialic acids on antennas and a deeper characterization of several highly sialylated tri- and tetraantennary glycans was also possible using the established MS/MS method. Moreover, relying on the characterization performed in Ref. [1], core and antenna fucosylation were differentiated in this work using specific ion fragments obtained in the tandem mass spectra. This methodology was also applied to hAGP purified from control and pathological serum samples, which corroborated its robustness and its potential for finding novel glycan-based biomarkers in patho-glycomic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Liquid chromatography method to determine polyamines in thermosetting polymers.

PubMed

Dopico-García, M S; López-Vilariño, J M; Fernández-Martínez, G; González-Rodríguez, M V

2010-05-14

A simple, robust and sensitive analytical method to determine three polyamines commonly used as hardeners in epoxy resin systems and in the manufacture of polyurethane is reported. The studied polyamines are: one tetramine, TETA (triethylenetetramine), and two diamines, IPDA (Isophorone diamine) and TCD-diamine (4,7-methano-1H-indene-5,?-dimethanamine, octahydro-). The latter has an incompletely defined structure, and, as far as we know, has not been previously determined by other methods. All three polyamines contain primary amines; TETA also contains secondary amines. The analytical method involves derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate, used for the first time for these compounds, followed by high performance liquid chromatography (HPLC) analysis with a fluorescence (FL) detector (lambda excitation 248nm, lambda emision 395nm). The HPLC-DAD-LTQ Orbitrap MS was used in order to provide structural information about the obtained derivatized compounds. The hybrid linear ion trap LTQ Orbitrap mass spectrometer has been introduced in recent years and provides a high mass accuracy. The structures of the derivatized analytes were identified from the protonated molecular ions [M+H](+) and corresponded to the fully labelled analytes. The following analytical parameters were determined for the method using the HPLC-FL: linearity, precision (2.5-10%), instrumental precision intraday (0.8-1.5%) and interday (2.9-6.3%), and detection limits (0.02-0.14mgL(-1)). The stability of stock solutions and derivatized compounds was also investigated. The method was applied to determine the amine free content in epoxy resin dust collected in workplaces. Copyright 2010 Elsevier B.V. All rights reserved.

Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.

PubMed

Satoh, Tadashi; Sato, Ken; Kanoh, Akira; Yamashita, Katsuko; Yamada, Yusuke; Igarashi, Noriyuki; Kato, Ryuichi; Nakano, Akihiko; Wakatsuki, Soichi

2006-04-14

Emp46p and Emp47p are type I membrane proteins, which cycle between the endoplasmic reticulum (ER) and the Golgi apparatus by vesicles coated with coat protein complexes I and II (COPI and COPII). They are considered to function as cargo receptors for exporting N-linked glycoproteins from the ER. We have determined crystal structures of the carbohydrate recognition domains (CRDs) of Emp46p and Emp47p of Saccharomyces cerevisiae, in the absence and presence of metal ions. Both proteins fold as a beta-sandwich, and resemble that of the mammalian ortholog, p58/ERGIC-53. However, the nature of metal binding is distinct from that of Ca(2+)-dependent p58/ERGIC-53. Interestingly, the CRD of Emp46p does not bind Ca(2+) ion but instead binds K(+) ion at the edge of a concave beta-sheet whose position is distinct from the corresponding site of the Ca(2+) ion in p58/ERGIC-53. Binding of K(+) ion to Emp46p appears essential for transport of a subset of glycoproteins because the Y131F mutant of Emp46p, which cannot bind K(+) ion fails to rescue the transport in disruptants of EMP46 and EMP47 genes. In contrast the CRD of Emp47p binds no metal ions at all. Furthermore, the CRD of Emp46p binds to glycoproteins carrying high mannosetype glycans and the is promoted by binding not the addition of Ca(2+) or K(+) ion in These results suggest that Emp46p can be regarded as a Ca(2+)-independent intracellular lectin at the ER exit sites.

Long-pore Electrostatics in Inward-rectifier Potassium Channels

PubMed Central

Robertson, Janice L.; Palmer, Lawrence G.; Roux, Benoît

2008-01-01

Inward-rectifier potassium (Kir) channels differ from the canonical K+ channel structure in that they possess a long extended pore (∼85 Å) for ion conduction that reaches deeply into the cytoplasm. This unique structural feature is presumably involved in regulating functional properties specific to Kir channels, such as conductance, rectification block, and ligand-dependent gating. To elucidate the underpinnings of these functional roles, we examine the electrostatics of an ion along this extended pore. Homology models are constructed based on the open-state model of KirBac1.1 for four mammalian Kir channels: Kir1.1/ROMK, Kir2.1/IRK, Kir3.1/GIRK, and Kir6.2/KATP. By solving the Poisson-Boltzmann equation, the electrostatic free energy of a K+ ion is determined along each pore, revealing that mammalian Kir channels provide a favorable environment for cations and suggesting the existence of high-density regions in the cytoplasmic domain and cavity. The contribution from the reaction field (the self-energy arising from the dielectric polarization induced by the ion's charge in the complex geometry of the pore) is unfavorable inside the long pore. However, this is well compensated by the electrostatic interaction with the static field arising from the protein charges and shielded by the dielectric surrounding. Decomposition of the static field provides a list of residues that display remarkable correspondence with existing mutagenesis data identifying amino acids that affect conduction and rectification. Many of these residues demonstrate interactions with the ion over long distances, up to 40 Å, suggesting that mutations potentially affect ion or blocker energetics over the entire pore. These results provide a foundation for understanding ion interactions in Kir channels and extend to the study of ion permeation, block, and gating in long, cation-specific pores. PMID:19001143

Identification of alkyl dimethylbenzylammonium surfactants in water samples by solid-phase extraction followed by ion trap LC/MS and LC/MS/MS

USGS Publications Warehouse

Ferrer, I.; Furlong, E.T.

2001-01-01

A novel methodology was developed for the determination of alkyl (C12, C14, and C16) dimethylbenzylammonium chloride (benzalkonium chloride or BAC, Chemical Abstract Service number: 8001-54-5) in water samples. This method is based on solid-phase extraction (SPE) using polymeric cartridges, followed by high-performance liquid chromatography/ion trap mass spectrometry (LC/MS) and tandem mass spectrometry(MS/MS) detection, equipped with an electrospray interface in positive ion mode. Chromatographic separation was achieved for three BAC homologues by using a C18 column and a gradient of acetonitrile/10 millimolar aqueous ammonium formate. Total method recoveries were higher than 71% in different water matrices. The main ions observed by LC/MS were at mass-to-charge ratios (m/z) of 304, 332, and 360, which correspond to the molecular ions of the C12, C14, and C16 alkyl BAC, respectively. The unequivocal structural identification of these compounds in water samples was performed by LC/MS/MS after isolation and subsequent fragmentation of each molecular ion. The main fragmentation observed for the three different homologues corresponded to the loss of the toluyl group in the chemical structure, which leads to the fragment ions at m/z 212, 240, and 268 and a tropylium ion, characteristic of all homologues, at m/z 91. Detection limits for the methodology developed in this work were in the low nanogram-per-liter range. Concentration levels of BAC - ranging from 1.2 to 36.6 micrograms per liter - were found in surface-water samples collected downstream from different wastewater-treatment discharges, thus indicating its input and persistence through the wastewater-treatment process.