Crystal structures of the ligand-binding region of uPARAP

DEFF Research Database (Denmark)

Yuan, Cai; Jürgensen, Henrik J; Engelholm, Lars H

2016-01-01

The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix...... remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH 7.4 in Ca(2+)-bound and Ca(2+)-free forms. The first domain....... These LLRs undergo a Ca(2+)-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformation of uPARAP. Our results provide a molecular mechanism to support the structural flexibility of uPARAP, and shed light on the structural flexibility of other...

A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

International Nuclear Information System (INIS)

Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

2009-01-01

The crystal structure of tear lipocalin determined in space group P2 1 revealed large structural deviations from the previously solved X-ray structure in space group C2, especially in the loop region and adjoining parts of the β-barrel which give rise to the ligand-binding site. These findings illustrate a novel mechanism for promiscuity in ligand recognition by the lipocalin protein family. Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2 1 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P2 1 crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-barrel and (iii) in the extended C-terminal segment, which is attached to the β-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family

Hydrothermal syntheses, crystal structures, and photophysical properties of two coordination polymers with mixed ligands

Science.gov (United States)

Yan, Li; Liu, Chun-Ling

2017-10-01

Two novel metal-organic coordination polymers [Cd(ipdt)(m-BDC)·3H2O]n (1) and [Pb(mip)2(NTC) ·2H2O]n (2) [ipdt = 2,6-Dimethoxy-4-(1H-1,3,7,8-tetraaza-cyclopenta[l]phenanthren-2-yl)-phenol, mip = 2-(3-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline, m-BDC = isophthalic acid, NTC = nicotinic acid] have been synthesized by hydrothermal reactions and characterized by elemental analysis, thermogravimetric (TG) analysis, infrared spectrum (IR) and single-crystal X-ray diffraction. Single-crystal X-ray diffraction reveals that 1 exhibits two-dimensional (2D) layer architecture, and 2 shows 1D chain architecture. TG analysis shows clear courses of weight loss, which corresponds to the decomposition of different ligands. The luminescent properties for the ligand ipdt, mip and complexes 1-2 are also discussed in detail, which should be acted as potential luminescent material.

Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme

International Nuclear Information System (INIS)

Lee, Jun Hyuck; Park, Soo Jeong; Rho, Seong-Hwan; Im, Young Jun; Kim, Mun-Kyoung; Kang, Gil Bu; Eom, Soo Hyun

2005-01-01

The GluR0 ligand-binding core from N. punctiforme was expressed, purified and crystallized in the presence of l-glutamate. A diffraction data set was collected to a resolution of 2.1 Å. GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The l-glutamate-complexed crystal belongs to space group C222 1 , with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 Å. The crystals contain three subunits in the asymmetric unit, with a V M value of 2.49 Å 3 Da −1 . The diffraction limit of the l-glutamate complex data set was 2.1 Å using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea)

Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme

Energy Technology Data Exchange (ETDEWEB)

Lee, Jun Hyuck; Park, Soo Jeong; Rho, Seong-Hwan; Im, Young Jun; Kim, Mun-Kyoung; Kang, Gil Bu; Eom, Soo Hyun, E-mail: eom@gist.ac.kr [Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of)

2005-11-01

The GluR0 ligand-binding core from N. punctiforme was expressed, purified and crystallized in the presence of l-glutamate. A diffraction data set was collected to a resolution of 2.1 Å. GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The l-glutamate-complexed crystal belongs to space group C222{sub 1}, with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 Å. The crystals contain three subunits in the asymmetric unit, with a V{sub M} value of 2.49 Å{sup 3} Da{sup −1}. The diffraction limit of the l-glutamate complex data set was 2.1 Å using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea)

Reversible Single-Crystal-to-Single-Crystal Structural Transformation in a Mixed-Ligand 2D Layered Metal-Organic Framework: Structural Characterization and Sorption Study

Directory of Open Access Journals (Sweden)

Chih-Chieh Wang

2017-12-01

Full Text Available A 3D supramolecular network, [Cd(bipy(C4O4(H2O2]·3H2O (1 (bipy = 4,4′-bipyridine and C4O42− = dianion of H2C4O4, constructed by mixed-ligand two-dimensional (2D metal-organic frameworks (MOFs has been reported and structurally determined by the single-crystal X-ray diffraction method and characterized by other physicochemical methods. In 1, the C4O42− and bipy both act as bridging ligands connecting the Cd(II ions to form a 2D layered MOF, which are then extended to a 3D supramolecular network via the mutually parallel and interpenetrating arrangements among the 2D-layered MOFs. Compound 1 shows a two-step dehydration process with weight losses of 11.0% and 7.3%, corresponding to the weight-loss of three guest and two coordinated water molecules, respectively, and exhibits an interesting reversible single-crystal-to-single-crystal (SCSC structural transformation upon de-hydration and re-hydration for guest water molecules. The SCSC structural transformation have been demonstrated and monitored by single-crystal and X-ray powder diffraction, and thermogravimetic analysis studies.

Crystallization and preliminary crystal structure analysis of the ligand-binding domain of PqsR (MvfR), the Pseudomonas quinolone signal (PQS) responsive quorum-sensing transcription factor of Pseudomonas aeruginosa

International Nuclear Information System (INIS)

Xu, Ningna; Yu, Shen; Moniot, Sébastien; Weyand, Michael; Blankenfeldt, Wulf

2012-01-01

The ligand-binding domain of the transcription factor PqsR from P. aeruginosa has been crystallized and initial phases have been obtained using SAD data from seleno-l-methionine-labelled crystals. The opportunistic bacterial pathogen Pseudomonas aeruginosa employs three transcriptional regulators, LasR, RhlR and PqsR, to control the transcription of a large subset of its genes in a cell-density-dependent process known as quorum sensing. Here, the recombinant production, crystallization and structure solution of the ligand-binding domain of PqsR (MvfR), the LysR-type transcription factor that responds to the Pseudomonas quinolone signal (PQS), a quinolone-based quorum-sensing signal that is unique to P. aeruginosa and possibly a small number of other bacteria, is reported. PqsR regulates the expression of many virulence genes and may therefore be an interesting drug target. The ligand-binding domain (residues 91–319) was produced as a fusion with SUMO, and hexagonal-shaped crystals of purified PqsR-91–319 were obtained using the vapour-diffusion method. Crystallization in the presence of a PQS precursor allowed data collection to 3.25 Å resolution on a synchrotron beamline, and initial phases have been obtained using single-wavelength anomalous diffraction data from seleno-l-methionine-labelled crystals, revealing the space group to be P6 5 22, with unit-cell parameters a = b = 116–120, c = 115–117 Å

Magnetic ions in crystals

CERN Document Server

Stevens, K W

2014-01-01

There have been many demonstrations, particularly for magnetic impurity ions in crystals, that spin-Hamiltonians are able to account for a wide range of experimental results in terms of much smaller numbers of parameters. Yet they were originally derived from crystal field theory, which contains a logical flaw; electrons on the magnetic ions are distinguished from those on the ligands. Thus there is a challenge: to replace crystal field theory with one of equal or greater predictive power that is based on a surer footing. The theory developed in this book begins with a generic Hamiltonian, on

Synthesis, thermogravimetric study and crystal structure of an N-rich copper(II) compound with tren ligands and nitrate counter-anions

Energy Technology Data Exchange (ETDEWEB)

Pérez-Toro, Inmaculada; Domínguez-Martín, Alicia [Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada (Spain); Choquesillo-Lazarte, Duane [Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Av. de las Palmeras 4, E-18100 Armilla, Granada (Spain); Vílchez-Rodríguez, Esther [Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada (Spain); Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Castiñeiras, Alfonso [Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Niclós-Gutiérrez, Juan, E-mail: jniclos@ugr.es [Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada (Spain)

2014-10-10

The N-rich salt [{Cu(tren)}{sub 3}(μ{sub 3}-tren)]{sub 2}(NO{sub 3}){sub 12}·3H{sub 2}O has been studied by XRD and by coupled TG and FT-IR spectroscopy of the evolved gases. After water loss, thermal decomposition of the nitrate ions and some tren ligands in the salt are overlapped. - Highlights: • A novel N-rich copper(II)-tren complex has been crystallized as a 3-hydrated nitrate salt. • Tren acts both as tripodal tetradentate and as μ{sub 3}-tren bridging ligand. • Copper(II) centers exhibit distorted trigonal bipyramidal coordination. • Coupled thermogravimetry and FT-IR spectra of evolved gases have been used. • Decomposition of nitrate anions and tren ligands occurs in an overlapped step. - Abstract: The compound [{Cu(tren)}{sub 3}(μ3-tren)]{sub 2}(NO{sub 3}){sub 12}·3H{sub 2}O has been synthesized, crystallized and characterized by single crystal X-ray diffraction, thermogravimetry (TG) coupled to FT-IR spectroscopy of the evolved gases, TG–differential scanning calorimetry (DSC) and electronic (diffuse reflectance) and FT-IR spectroscopies. The sample loses the crystallization water between room temperature and 200 °C. The decomposition of the salt begins with an overlapped decomposition of nitrate anions and some tren ligands where CO{sub 2}, H{sub 2}O, CO, NH{sub 3}, N{sub 2}O, NO and NO{sub 2} are evolved (205–235 °C). Then decomposition of additional tren ligands takes place (235–725 °C). Finally a non-pure CuO residue is obtained at 725 °C.

Crystal field parameters in UCl/sub 4/: Experiment versus theory

Energy Technology Data Exchange (ETDEWEB)

Zolnierek, Z.; Gajek, Z. (Polska Akademia Nauk, Wroclaw. Inst. Niskich Temperatur i Badan Strukturalnych); Khan Malek, C. (Paris-11 Univ., 91 - Orsay (France). Inst. de Physique Nucleaire)

1984-08-01

Crystal field effect on U/sup 4 +/ ion with the /sup 3/H/sub 4/ ground term in tetragonal ligand field of UCl/sub 4/ has been studied in detail. Crystal field parameters determined experimentally from optical spectroscopy and magnetic susceptibility are in good agreement with CEP sets derived from the modified point charge model and the ab initio method. Theoretical calculations lead to overestimating the A/sub 4//sup 4/ and lowering the A/sub 2//sup 0/ values in comparison to those found in the experiments. The discrepancies are, however, within an accuracy of calculations. A large similar reduction of expectation values of the magnetic moment operator for the eigenvectors of lowest CF levels (17.8%), determined from magnetic susceptibility, cannot be attributed to the overlap and covalency effects only. The detailed calculations have shown that the latter effects provide about 4.6% reduction of respective matrix elements, and the applied J-J mixing procedure increases this factor up to 6.5%. Since similar reduction factor has already been observed in a number of different uranium compounds, as in UCl/sub 4/ it seems to be likely that this feature is involved in the intrinsic properties of the U/sup 4 +/ ion. The authors endeavor to explain this effect in terms of configuration interaction mechanisms.

Infrared transmission study of Pr.sub.2./sub.CuO.sub.4./sub. crystal-field excitations

Czech Academy of Sciences Publication Activity Database

Riou, G.; Jandl, S.; Poirier, M.; Nekvasil, Vladimír; Diviš, M.; Fournier, P.; Greene, R. L.; Zhigunov, D. I.; Barilo, S. N.

2001-01-01

Roč. 23, - (2001), s. 179-182 ISSN 1434-6028 R&D Projects: GA ČR GA202/00/1602; GA ČR GA202/99/0184 Grant - others:GA UK(XC) 145/2000/B-FYZ; DMR(XX) 9732796 Institutional research plan: CEZ:AV0Z1010914 Keywords : optical properties * crystal and ligand fields * other cuprates Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.811, year: 2001

Synthesis and crystal structure of two lead (II) complexes with 1,10-phenanthroline ligand

International Nuclear Information System (INIS)

Olivera, Fiorella L.; Santillan, Guillermo A.

2012-01-01

Two coordination complexes have been synthesized by the reaction of lead nitrate (II) with 1,10-phenanthroline in methanol/water. The crystals of these complexes were obtained by using the diffusion method and structurally characterized by X-ray single crystal diffraction. Both complexes crystallized in the monoclinic space group P2 1 /c. The analysis by crystal X-ray diffraction reveals that in both complexes the coordination around the lead (II) ion is a distorted octahedral structure where the ion is bonded to the heterocyclic nitrogen atoms of chelating ligand 1,10-phenanthroline, three oxygen atoms of three nitrate groups and one oxygen from the water molecule. The difference between the complexes lies in the way of nitrate ion in presence of carboxylic acid aromatics. In addition, the crystal structure of complexes can be regarded as a 3D coordination polymer through Pb-O weak interactions, hydrogen bonds and π-π stacking interactions. (author).

Application of X-ray single crystal diffractometry to investigation of Np(5) complexes with n-donor ligands

International Nuclear Information System (INIS)

Andreev, G.

2007-01-01

Full text of publication follows. We present here some results of application of conventional X-ray single crystal diffractometry to the research on the interaction of Np(V) with N-donor ligands. Compounds that can coordinate to actinides through one or several nitrogen atoms are of a great variety and occur widely in the biosphere. For example, imidazole, pyridine and their derivatives are the building blocks of many biologically important molecules; triazines are known to occur in some aquatic plants. The presence of anthropogenic organic agents like amine-N-carboxylic acids in surface waters has the potential to re-mobilize metals from sediments and aquifers and to influence their bioavailability. The interaction of radionuclides with such ligands needs to be studied in detail to give fundamental understanding the conditions of the incorporation of long lived a-emitters (Np and Pu primarily) into the food chain. Another aspect of the same problem is the design of new chelating ligands for selective co-ordination of actinide ions as an alternative to the traditional sequestering agents. The problem of the separation of long-lived minor actinides and their transmutation also calls for design of new highly selective ligands for solvent extraction. Polydentate N-donor ligands are now considered to be very promising. A detailed study of structural chemistry is crucial for understanding the relationship between the architecture of the ligands and their binding affinity for actinides. The X-ray single crystal diffractometry became conventional technique as applied to the investigation of actinides in spite of difficulties regarding safe handling of radionuclides. This technique provides unambiguous information about modes of the ligand co-ordination to the metal ion and geometrical parameters of complexes. Moreover, the employment of a synchrotron radiation shows considerable promise for determination of solid state structures as well as obtaining structural

Modeling local structure using crystal field and spin Hamiltonian parameters: the tetragonal FeK3+-OI2- defect center in KTaO3 crystal

International Nuclear Information System (INIS)

Gnutek, P; Rudowicz, C; Yang, Z Y

2009-01-01

The local structure and the spin Hamiltonian (SH) parameters, including the zero-field-splitting (ZFS) parameters D and (a+2F/3), and the Zeeman g factors g || and g perpendicular , are theoretically investigated for the Fe K 3+ -O I 2- center in KTaO 3 crystal. The microscopic SH (MSH) parameters are modeled within the framework of the crystal field (CF) theory employing the CF analysis (CFA) package, which also incorporates the MSH modules. Our approach takes into account the spin-orbit interaction as well as the spin-spin and spin-other-orbit interactions omitted in previous studies. The superposition model (SPM) calculations are carried out to provide input CF parameters for the CFA/MSH package. The combined SPM-CFA/MSH approach is used to consider various structural models for the Fe K 3+ -O I 2- defect center in KTaO 3 . This modeling reveals that the off-center displacement of the Fe 3+ ions, Δ 1 (Fe 3+ ), combined with an inward relaxation of the nearest oxygen ligands, Δ 2 (O 2- ), and the existence of the interstitial oxygen O I 2- give rise to a strong tetragonal crystal field. This finding may explain the large ZFS experimentally observed for the Fe K 3+ -O I 2- center in KTaO 3 . Matching the theoretical MSH predictions with the available structural data as well as electron magnetic resonance (EMR) and optical spectroscopy data enables predicting reasonable ranges of values of Δ 1 (Fe 3+ ) and Δ 2 (O 2- ) as well as the possible location of O I 2- ligands around Fe 3+ ions in KTaO 3 . The defect structure model obtained using the SPM-CFA/MSH approach reproduces very well the ranges of the experimental SH parameters D, g || and g perpendicular and importantly yields not only the correct magnitude of D but also the sign, unlike previous studies. More reliable predictions may be achieved when experimental data on (a+2F/3) and/or crystal field energy levels become available. Comparison of our results with those arising from alternative models existing

Conformational change of adenosine deaminase during ligand-exchange in a crystal.

Science.gov (United States)

Kinoshita, Takayoshi; Tada, Toshiji; Nakanishi, Isao

2008-08-15

Adenosine deaminase (ADA) perpetuates chronic inflammation by degrading extracellular adenosine which is toxic for lymphocytes. ADA has two distinct conformations: open form and closed form. From the crystal structures with various ligands, the non-nucleoside type inhibitors bind to the active site occupying the critical water-binding-position and sustain the open form of apo-ADA. In contrast, substrate mimics do not occupy the critical position, and induce the large conformational change to the closed form. However, it is difficult to predict the binding of (+)-erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA), as it possesses characteristic parts of both the substrate and the non-nucleoside inhibitors. The crystal structure shows that EHNA binds to the open form through a novel recognition of the adenine base accompanying conformational change from the closed form of the PR-ADA complex in crystalline state.

Syntheses, crystal structures and spectroscopic properties of copper(II)-tetracyanometallate(II) complexes with nicotinamide and isonicotinamide ligands

Science.gov (United States)

Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

2015-09-01

Four new one dimensional (1D) cyanide complexes, namely {[Cu(NH3)4(μ-na)][M‧(CN)4]}n and {[Cu(NH3)2(ina)2M‧(μ-CN)2(CN)2]}n (M‧(II) = Pd (1 and 3) or Pt (2 and 4), na:nicotinamide and ina:isonicotinamide) have been synthesized and characterized by elemental, spectral (FT-IR and Raman), and thermal (TG, DTG and DTA) analyses. The crystal structures of complexes 1-3 have been determined by single crystal X-ray diffraction technique. In complexes 1 and 2, na ligand is coordinated to the adjacent Cu(II) ions as a bridging ligand, giving rise to 1D linear cationic chain and the [M‧(CN)4]2- anionic complex acts as a counter ion. Complexes 3 and 4 are also 1D linear chain in which two cyanide ligands bridged neighboring M‧(II) and Cu(II) ions, while ina ligand is coordinated Cu(II) ion through nitrogen atom of pyridine ring. In the complexes, the Cu(II) ions adopt distorted octahedral geometries, while M‧(II) ions are four coordinated with four carbon atoms from cyanide ligands in square-planar geometries. The adjacent chains are further stacked through intermolecular hydrogen bond, Nsbnd Hṡṡṡπ, Csbnd H⋯M‧ and M‧⋯π interactions to form 3D supramolecular networks. Vibration assignments are given for all the observed bands. In addition, thermal stabilities of the compounds are also discussed.

Synthesis, crystal structure, fluorescence and electrochemical studies of a new tridentate Schiff base ligand and its nickel(II) and palladium(II) complexes

Science.gov (United States)

Shafaatian, Bita; Soleymanpour, Ahmad; Kholghi Oskouei, Nasim; Notash, Behrouz; Rezvani, Seyyed Ahmad

2014-07-01

A new unsymmetrical tridentate Schiff base ligand was derived from the 1:1 M condensation of ortho-vanillin with 2-mercaptoethylamine. Nickel and palladium complexes were obtained by the reaction of the tridentate Schiff base ligand with nickel(II) acetate tetrahydrate and palladium(II) acetate in 2:1 M ratio. In nickel and palladium complexes the ligand was coordinated to metals via the imine N and enolic O atoms. The S groups of Schiff bases were not coordinated to the metals and S-S coupling was occured. The complexes have been found to possess 1:2 Metal:Ligand stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The complexes exhibited octahedral coordination geometry. The emission spectra of the ligand and its complexes were studied in methanol. Electrochemical properties of the ligand and its metal complexes were investigated in the CH3CN solvent at the 100 mV s-1 scan rate. The ligand and metal complexes showed both reversible and quasi-reversible processes at this scan rate. The Schiff base and its complexes have been characterized by IR, 1H NMR, UV/Vis, elemental analyses and conductometry. The crystal structure of nickel complex has been determined by single crystal X-ray diffraction.

Zinc(II) halide complexes with 2-methoxyaniline ligand: Synthesis, characterization, thermal analyses, crystal structure determination and luminescent properties

Science.gov (United States)

Amani, Vahid

2018-03-01

Three new mononuclear zinc(II) complexes, [Zn(2-MeO-C6H4NH2)2X2] (X is Cl in 1, Br in 2 and I in 3), were prepared from the reactions of ZnX2 with 2-methoxyaniline (2-MeO-C6H4NH2) ligand in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurements by slow evaporation of methanol solution at room temperature. The three complexes were thoroughly characterized by thermogravimetric analysis, elemental analysis (CHNO), spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the zinc(II) cation is four-coordinated in a distorted tetrahedral configuration by two N atoms from two 2-methoxyanyline ligands and two halide anions. Also, in these complexes intermolecular interactions, for example Nsbnd H⋯X hydrogen bonds (in 1-3), Csbnd H⋯X hydrogen bonds (in 3), Csbnd H⋯π interactions (in 1 and 2) and π⋯π interactions (in 3), are effective in the stabilization of the crystal structures. In addition, the luminescence spectra of all complexes in methanolic solution show that the intensity of their emission bands is stronger than that for free 2-methoxyaniline ligand.

Crystal-field effect in UO2

International Nuclear Information System (INIS)

Gajek, Z.; Lahalle, M.P.; Krupa, J.C.; Mulak, J.

1988-01-01

Simple ab initio model perturbation calculations of the crystal-field parameters for the U 4+ ion in UO 2 crystals are reported. The crystal-field parameters obtained, B 0 4 = -7130 cm -1 and B 0 6 = 2890 cm -1 , turn out to be much lower in value, particularly the first one, than those usually assumed for this compound. They are found, however, to agree with new spectroscopic data and recent inelastic neutron scattering measurements. (orig.)

Ligand binding and crystal structures of the substrate-binding domain of the ABC transporter OpuA.

Directory of Open Access Journals (Sweden)

Justina C Wolters

2010-04-01

Full Text Available The ABC transporter OpuA from Lactococcus lactis transports glycine betaine upon activation by threshold values of ionic strength. In this study, the ligand binding characteristics of purified OpuA in a detergent-solubilized state and of its substrate-binding domain produced as soluble protein (OpuAC was characterized.The binding of glycine betaine to purified OpuA and OpuAC (K(D = 4-6 microM did not show any salt dependence or cooperative effects, in contrast to the transport activity. OpuAC is highly specific for glycine betaine and the related proline betaine. Other compatible solutes like proline and carnitine bound with affinities that were 3 to 4 orders of magnitude lower. The low affinity substrates were not noticeably transported by membrane-reconstituted OpuA. OpuAC was crystallized in an open (1.9 A and closed-liganded (2.3 A conformation. The binding pocket is formed by three tryptophans (Trp-prism coordinating the quaternary ammonium group of glycine betaine in the closed-liganded structure. Even though the binding site of OpuAC is identical to that of its B. subtilis homolog, the affinity for glycine betaine is 4-fold higher.Ionic strength did not affect substrate binding to OpuA, indicating that regulation of transport is not at the level of substrate binding, but rather at the level of translocation. The overlap between the crystal structures of OpuAC from L.lactis and B.subtilis, comprising the classical Trp-prism, show that the differences observed in the binding affinities originate from outside of the ligand binding site.

Crystal growth under external electric fields

International Nuclear Information System (INIS)

Uda, Satoshi; Koizumi, Haruhiko; Nozawa, Jun; Fujiwara, Kozo

2014-01-01

This is a review article concerning the crystal growth under external electric fields that has been studied in our lab for the past 10 years. An external field is applied electrostatically either through an electrically insulating phase or a direct injection of an electric current to the solid-interface-liquid. The former changes the chemical potential of both solid and liquid and controls the phase relationship while the latter modifies the transport and partitioning of ionic solutes in the oxide melt during crystallization and changes the solute distribution in the crystal

Crystal growth under external electric fields

Energy Technology Data Exchange (ETDEWEB)

Uda, Satoshi; Koizumi, Haruhiko; Nozawa, Jun; Fujiwara, Kozo [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan)

2014-10-06

This is a review article concerning the crystal growth under external electric fields that has been studied in our lab for the past 10 years. An external field is applied electrostatically either through an electrically insulating phase or a direct injection of an electric current to the solid-interface-liquid. The former changes the chemical potential of both solid and liquid and controls the phase relationship while the latter modifies the transport and partitioning of ionic solutes in the oxide melt during crystallization and changes the solute distribution in the crystal.

Significant Enhancement of the Chiral Correlation Length in Nematic Liquid Crystals by Gold Nanoparticle Surfaces Featuring Axially Chiral Binaphthyl Ligands.

Science.gov (United States)

Mori, Taizo; Sharma, Anshul; Hegmann, Torsten

2016-01-26

Chirality is a fundamental scientific concept best described by the absence of mirror symmetry and the inability to superimpose an object onto its mirror image by translation and rotation. Chirality is expressed at almost all molecular levels, from single molecules to supramolecular systems, and present virtually everywhere in nature. Here, to explore how chirality propagates from a chiral nanoscale surface, we study gold nanoparticles functionalized with axially chiral binaphthyl molecules. In particular, we synthesized three enantiomeric pairs of chiral ligand-capped gold nanoparticles differing in size, curvature, and ligand density to tune the chirality transfer from nanoscale solid surfaces to a bulk anisotropic liquid crystal medium. Ultimately, we are examining how far the chirality from a nanoparticle surface reaches into a bulk material. Circular dichroism spectra of the gold nanoparticles decorated with binaphthyl thiols confirmed that the binaphthyl moieties form a cisoid conformation in isotropic organic solvents. In the chiral nematic liquid crystal phase, induced by dispersing the gold nanoparticles into an achiral anisotropic nematic liquid crystal solvent, the binaphthyl moieties on the nanoparticle surface form a transoid conformation as determined by imaging the helical twist direction of the induced cholesteric phase. This suggests that the ligand density on the nanoscale metal surfaces provides a dynamic space to alter and adjust the helicity of binaphthyl derivatives in response to the ordering of the surrounding medium. The helical pitch values of the induced chiral nematic phase were determined, and the helical twisting power (HTP) of the chiral gold nanoparticles calculated to elucidate the chirality transfer efficiency of the binaphthyl ligand capped gold nanoparticles. Remarkably, the HTP increases with increasing diameter of the particles, that is, the efficiency of the chirality transfer of the binaphthyl units bound to the nanoparticle

EMR-related problems at the interface between the crystal field Hamiltonians and the zero-field splitting Hamiltonians

Directory of Open Access Journals (Sweden)

Rudowicz Czesław

2015-07-01

Full Text Available The interface between optical spectroscopy, electron magnetic resonance (EMR, and magnetism of transition ions forms the intricate web of interrelated notions. Major notions are the physical Hamiltonians, which include the crystal field (CF (or equivalently ligand field (LF Hamiltonians, and the effective spin Hamiltonians (SH, which include the zero-field splitting (ZFS Hamiltonians as well as to a certain extent also the notion of magnetic anisotropy (MA. Survey of recent literature has revealed that this interface, denoted CF (LF ↔ SH (ZFS, has become dangerously entangled over the years. The same notion is referred to by three names that are not synonymous: CF (LF, SH (ZFS, and MA. In view of the strong need for systematization of nomenclature aimed at bringing order to the multitude of different Hamiltonians and the associated quantities, we have embarked on this systematization. In this article, we do an overview of our efforts aimed at providing a deeper understanding of the major intricacies occurring at the CF (LF ↔ SH (ZFS interface with the focus on the EMR-related problems for transition ions.

Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms

International Nuclear Information System (INIS)

Park, Joon Kyu; Moon, Jin Ho; Kim, Jae-Hong; Kim, Eunice EunKyeong

2004-01-01

Peptide deformylase (PDF) from B. cereus has been overexpressed, purified and crystallized in ligand-free and actinonin-bound forms. Diffraction data have been collected from these crystals to 1.7 and 2.0 Å resolution, respectively. In bacteria, protein expression initiates with an N-formyl group and this needs to be removed in order to ensure proper bacterial growth. These formylation and deformylation processes are unique to eubacteria; therefore, inhibition of these would provide a novel antibacterial therapy. Deformylation is carried out by peptide deformylase (PDF). PDF from Bacillus cereus, one of the major pathogenic bacteria, was cloned into expression plasmid pET-28a (Novagen), overexpressed in Escherichia coli BL21 (DE3) and purified to high quality. Crystals have been obtained of both ligand-free PDF and PDF to which actinonin, a highly potent naturally occurring inhibitor, is bound. Both crystals belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 42.72, b = 44.04, c = 85.19 Å and a = 41.31, b = 44.56, c = 84.47 Å, respectively. Diffraction data were collected to 1.7 Å resolution for the inhibitor-free crystals and to 2.0 Å resolution for the actinonin-bound crystals

Synthesis and crystal structure of novel fluorescent 1,3,4-oxadiazole-containing carboxylate ligands

Science.gov (United States)

Mikhailov, Igor E.; Popov, Leonid D.; Tkachev, Valery V.; Aldoshin, Sergey M.; Dushenko, Galina A.; Revinskii, Yurii V.; Minkin, Vladimir I.

2018-04-01

Novel chelating ligands, 3-(5-aryl-1,3,4-oxadiazol-2-yl)acrylic acids and their zinc complexes were synthesized and their spectral and luminescent properties studied. The compounds intensively (quantum efficiencies φ = 0.18-0.76) luminesce in nonpolar solvents in the blue-green region (λmaxPL = 458-504 nm) of the spectrum. Molecular and crystal structures of 3-[5-(4-dimethylaminophenyl)-1,3,4-oxadiazol-2-yl]acrylic acid were established using X-ray crystallography. In crystal, the infinite chains of the molecules lie in the parallel planes and are arranged by the "head to tail" type to provide for strong π-π stacking interactions between the layers facilitating appearance of high electron transport properties and formation of excimers.

Synthesis, crystal structure and luminescence properties of lanthanide coordination polymers with a new semirigid bridging thenylsalicylamide ligand

International Nuclear Information System (INIS)

Song, Xue-Qin; Wang, Li; Zhao, Meng-Meng; Wang, Xiao-Run; Peng, Yun-Qiao; Cheng, Guo-Quan

2013-01-01

Two new lanthanide coordination polymers based on a semirigid bridging thenylsalicylamide ligand ([Ln 2 L 3 (NO 3 ) 6 ]·(C 4 H 8 O 2 ) 2 ) ∞ were obtained and characterized by elemental analysis, X-ray diffraction, IR and TGA measurements. The two compounds are isostructure and possess one dimensional trapezoid ladder-like chain built up from the connection of isolated LnO 3 (NO 3 ) 3 polyhedra (distorted monocapped antisquare prism) through the ligand. The photoluminescence analysis suggest that there is an efficient ligand-to-Ln(III) energy transfer in Tb(III) complex and the ligand is an efficient “antenna” for Tb(III). From a more general perspective, the results demonstrated herein provide the possibility of controlling the formation of the desired lanthanide coordination structure to enrich the crystal engineering strategy and enlarge the arsenal for developing excellent luminescent lanthanide coordination polymers. - Graphical abstract: We present herein one dimensional lanthanide coordination polymers of a new semirigid exo-bidentate ligand which not only display interesting structures but also possess strong luminescence properties. Display Omitted - Highlights: • We present lanthanide coordination polymers of a new semirigid exo-bidentate ligand. • The lanthanide coordination polymers exhibit interesting structures. • The luminescent properties of Tb(III) complexes are discussed in detail

Link between optical spectra, crystal-field parameters, and local environments of Eu3+ ions in Eu2O3-doped sodium disilicate glass

International Nuclear Information System (INIS)

Qin, T.; Mountjoy, G.; Afify, N. D.; Reid, M. F.; Yeung, Y. Y.; Speghini, A.; Bettinelli, M.

2011-01-01

Rare-earth-doped glasses are key materials for optical technology due to the luminescent properties of 4f n ions. The crystal-field model describes the effect of local environment on transitions between 4f electrons. We present a detailed modeling study of the optical spectra of sodium disilicate glass, 33Na 2 O·67SiO 2 , doped with 0.2% and 1.0 mol%Eu 2 O 3 . This study uses very large molecular dynamics models with up to 100 Eu 3+ ions, the superposition model for covalent and overlap effects on crystal-field parameters, and realistic values for homogeneous linewidth broadening. The simulated spectra are in reasonable agreement with experiment. The trends in 7 F J energy levels across different Eu 3+ ion sites have been examined and a very detailed analysis is presented that looks at how features of the spectra are related to features of the local environment of Eu 3+ ions. Increasing the crystal-field strength S total causes the 7 F 0 energy level to decrease and causes the splitting of 7 F J manifolds to increase, and this is due to increasing mixing of 4f wave functions. To a reasonable approximation the crystal-field strength components S k depend on angular positions of ligands independently of distances to ligands. The former are seen to be more significant in determining S k , which are closely related to the rotationally invariant bond-orientational order parameters Q k . The values of S 2 are approximately linear in Q 2 , and the values of Q 2 are higher for fivefold than sixfold coordinated rare-earth ions. These results can be of importance for efforts to enhance the local environment of rare-earth ions in oxide glasses for optical applications.

Mononuclear mercury(II) complexes containing bipyridine derivatives and thiocyanate ligands: Synthesis, characterization, crystal structure determination, and luminescent properties

Science.gov (United States)

Amani, Vahid; Alizadeh, Robabeh; Alavije, Hanieh Soleimani; Heydari, Samira Fadaei; Abafat, Marzieh

2017-08-01

A series of mercury(II) complexes, [Hg(Nsbnd N)(SCN)2] (Nsbnd N is 4,4‧-dimethyl-2,2‧-bipyridine in 1, 5,5‧-dimethyl-2,2‧-bipyridine in 2, 6,6‧-dimethyl-2,2‧-bipyridine in 3 and 6-methyl-2,2‧-bipyridine in 4), were prepared from the reactions of Hg(SCN)2 with mentioned ligands in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurement by methanol diffusion into a DMSO solution. The four complexes were thoroughly characterized by spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), elemental analysis (CHNS) and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the mercury(II) cation is four-coordinated in a distorted tetrahedral configuration by two S atoms from two thiocyanate anions and two N atoms from one chelating 2,2‧-bipyridine derivative ligand. Also, in these complexes intermolecular interactions, for example Csbnd H⋯N hydrogen bonds (in 1-4), Csbnd H⋯S hydrogen bonds (in 1, 2 and 4), π … π interactions (in 2-4), Hg⋯N interactions (in 2) and S⋯S interactions (in 4), are effective in the stabilization of the crystal structures and the formation of the 3D supramolecular complexes. Furthermore, the luminescence spectra of the title complexes show that the intensity of their emission bands are stronger than the emission bands for the free bipyridine derivative ligands.

Crystal structures of a manganese(I and a rhenium(I complex of a bipyridine ligand with a non-coordinating benzoic acid moiety

Directory of Open Access Journals (Sweden)

Sheri Lense

2018-05-01

Full Text Available The structures of two facially coordinated Group VII metal complexes are reported, namely: fac-bromido[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylmanganese(I tetrahydrofuran monosolvate, [MnBr(C17H12N2O2(CO3]·C4H8O, I, and fac-[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylchloridorhenium(I tetrahydrofuran monosolvate, [ReCl(C17H12N2O2(CO3]·C4H8O, II. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ion, and a 2-(2,2′-bipyridin-6-ylbenzoic acid ligand, in a distorted octahedral geometry. In manganese complex I, the tetrahydrofuran (THF solvent molecule could not be refined due to disorder. The benzoic acid fragment is also disordered over two positions, such that the carboxylic acid group is either positioned near to the bromide ligand or to the axial carbonyl ligand. In the crystal of I, the complex molecules are linked by a pair of C—H...Br hydrogen bonds, forming inversion dimers that stack up the a-axis direction. In the rhenium complex II, there is hydrogen bonding between the benzoic acid moiety and a disordered co-crystallized THF molecule. In the crystal, the molecules are linked by C—H...Cl hydrogen bonds, forming layers parallel to (100 separated by layers of THF solvent molecules.

Synthesis, characterization, single crystal X-ray determination, fluorescence and electrochemical studies of new dinuclear nickel(II) and oxovanadium(IV) complexes containing double Schiff base ligands

Science.gov (United States)

Shafaatian, Bita; Ozbakzaei, Zahra; Notash, Behrouz; Rezvani, S. Ahmad

2015-04-01

A series of new bimetallic complexes of nickel(II) and vanadium(IV) have been synthesized by the reaction of the new double bidentate Schiff base ligands with nickel acetate and vanadyl acetylacetonate in 1:1 M ratio. In nickel and also vanadyl complexes the ligands were coordinated to the metals via the imine N and enolic O atoms. The complexes have been found to possess 1:1 metals to ligands stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The nickel and vanadyl complexes exhibited distorted square planar and square pyramidal coordination geometries, respectively. The emission spectra of the ligands and their complexes were studied in methanol. Electrochemical properties of the ligands and their metal complexes were also investigated in DMSO solvent at 150 mV s-1 scan rate. The ligands and metal complexes showed both quasi-reversible and irreversible processes at this scan rate. The Schiff bases and their complexes have been characterized by FT-IR, 1H NMR, UV/Vis spectroscopies, elemental analysis and conductometry. The crystal structure of the nickel complex has been determined by single crystal X-ray diffraction.

Experimental investigation and crystal-field modeling of Er{sup 3+} energy levels in GSGG crystal

Energy Technology Data Exchange (ETDEWEB)

Gao, J.Y., E-mail: jygao1985@sina.com [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China); Sun, D.L.; Zhang, Q.L. [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China); Wang, X.F. [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Liu, W.P.; Luo, J.Q.; Sun, G.H.; Yin, S.T. [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China)

2016-06-25

The Er{sup 3+}-doped Gd{sub 3}Sc{sub 2}Ga{sub 3}O{sub 12} (Er{sup 3+}:GSGG) single crystal, a excellent medium of the mid-infrared and anti-radiation solid state laser pumped by laser diode, was grown by Czochralski method successfully. The absorption spectra were measured and analyzed in a wider spectral wavelength range of 350–1700 nm at different temperatures of 7.6, 77, 200 and 300 K. The free-ions and crystal-field parameters were fitted to the experimental energy levels with the root mean square deviation of 9.86 cm{sup −1}. According to the crystal-field calculations, 124 degenerate energy levels of Er{sup 3+} in GSGG host crystals were assigned. The fitting results of free-ions and crystal-field parameters were compared with those already reported of Er{sup 3+}:YSGG. The results indicated that the free-ions parameters for Er{sup 3+} in GSGG host are similar to those in YSGG host crystals, and the crystal-field interaction of GSGG is weaker than that of YSGG, which may result in the better laser characterization of Er{sup 3+}:GSGG crystal. - Highlights: • The efficient diode-end-pumped laser crystal Er:GSGG has been grown successfully. • The absorption spectra of Er:GSGG have been measured in range of 350–1700 nm. • The fitting result is very well for the root mean square deviation is 9.86 cm{sup −1}. • The 124 levels of Er:GSGG have been assigned from the crystal-field calculations.

Colorimetric detection of hydrogen peroxide by dioxido-vanadium(V) complex containing hydrazone ligand: synthesis and crystal structure

Science.gov (United States)

Kurbah, Sunshine D.; Syiemlieh, Ibanphylla; Lal, Ram A.

2018-03-01

Dioxido-vanadium(V) complex has been synthesized in good yield, the complex was characterized by IR, UV-visible and 1H NMR spectroscopy. Single crystal X-ray crystallography techniques were used to assign the structure of the complex. Complex crystallized with monoclinic P21/c space group with cell parameters a (Å) = 39.516(5), b (Å) = 6.2571(11), c (Å) = 17.424(2), α (°) = 90, β (°) = 102.668(12) and γ (°) = 90. The hydrazone ligand is coordinate to metal ion in tridentate fashion through -ONO- donor atoms forming a distorted square pyramidal geometry around the metal ion.

Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

Science.gov (United States)

Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

2016-07-28

The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

A Guided Inquiry Activity for Teaching Ligand Field Theory

Science.gov (United States)

Johnson, Brian J.; Graham, Kate J.

2015-01-01

This paper will describe a guided inquiry activity for teaching ligand field theory. Previous research suggests the guided inquiry approach is highly effective for student learning. This activity familiarizes students with the key concepts of molecular orbital theory applied to coordination complexes. Students will learn to identify factors that…

Synthesis and Crystal Structures of Ni(II)/(III) and Zn(II) Complexes with Schiff Base Ligands

International Nuclear Information System (INIS)

Koo, Bon Kweon

2013-01-01

Coordination polymers are of great interest due to their intriguing structural motifs and potential applications in optical, electronic, magnetic, and porous materials. The most commonly used strategy for designing such materials relies on the utilization of multidentate N- or Odonor ligands which have the capacity to bridge between metal centers to form polymeric structures. The Schiff bases with N,O,S donor atoms are an useful source as they are readily available and easily form stable complexes with most transition metal ions. Schiff bases are also important intermediates in synthesis of some bioactive compounds and are potent anti-bacterial, anti-fungal, anticancer and antiviral compounds. In this work, the Schiff bases, Hapb and Hbpb, derived from 2-acetylpyridene or 2-benzoylpyridine and benzhydrazide were taken as trifunctional (N,N,O) monobasic ligand (Scheme 1). This ligand is of important because the π-delocalization of charge and the configurational flexibility of their molecular chain can give rise to a great variety of coordination modes. Although many metal.Schiff base complexes have been reported, the 1D, 2D, and 3D networks of coordination polymers linked through the bridging of ligands such as dicyanamide, N(CN) 2 - as coligand have been little published. In the process of working to extend the dimensionality of the metal-Schiff base complexes using benzilic acid as a bridging ligand, we obtained three simple metal (II)/(III) complexes of acetylpyridine/2-benzoyl pyridine based benzhydrazide ligand. Therefore, we report here the synthesis and crystal structures of the complexes

Synthesis, crystal structures, and thermal and spectroscopic properties of two Cd(II) metal-organic frameworks with a versatile ligand

Energy Technology Data Exchange (ETDEWEB)

Li, Jia-Ming; He, Kun-Huan; Shi, Zhong-Feng [Qinzhou Univ. (China). Guangxi Colleges and Univs. Key Lab. of Beibu Gulf Oil and Natural Gas Resource Effective Utilization; Gao, Hui-Yuan; Jiang, Yi-Min [Guangxi Normal Univ., Guilin (China). Key Lab. for the Chemistry and Molecular Engineering of Medicinal Resources

2016-11-01

Two new metal-organic frameworks, namely, [Cd(L)(H{sub 2}O)]{sub n} (1) and {[Cd_0_._5(L)(4,4"'-bipy)_0_._5][Cd_0_._5(H_2O)(4,4"'-bipy)_0_._5].H_2O}{sub n} (2), where H{sub 2}L = N-pyrazinesulfonyl-glycine and 4,4{sup '}-bipy = 4,4{sup '}-bipyridine, have been synthesized and characterized by single-crystal X-ray diffraction, IR spectroscopy, elemental, thermogravimetric, and photoluminescent analysis. X-ray diffraction crystallographic analyses indicate that 1 displays a distorted octahedral metal coordination in a 3-connected (4, 8{sup 2}) topology, while the molecular structure of 2 has a 4-connected (4, 4) topology with two perfectly octahedrally coordinated Cd centers. The L{sup 2-} ligand serves as a N,N,O-tridentate, μ{sub 2}-pyrazine-bridging, and μ{sub 2}-carboxylate-bridging ligand in 1, and as a N,O-bidentate and μ{sub 2}-carboxylate-bridging ligand in 2. In the crystal, a 3D supramolecular architecture is formed by O-H..O hydrogen bond interactions in 1, but through O-H..O as well as π..π stacking in 2. The two compounds show intense fluorescence in the solid state at room temperature.

Ligands in PSI structures

International Nuclear Information System (INIS)

Kumar, Abhinav; Chiu, Hsiu-Ju; Axelrod, Herbert L.; Morse, Andrew; Elsliger, Marc-André; Wilson, Ian A.; Deacon, Ashley

2010-01-01

A survey of the types and frequency of ligands that are bound to PSI structures is analyzed as well as their utility in functional annotation of previously uncharacterized proteins. Approximately 65% of PSI structures report some type of ligand(s) that is bound in the crystal structure. Here, a description is given of how such ligands are handled and analyzed at the JCSG and a survey of the types, variety and frequency of ligands that are observed in the PSI structures is also compiled and analyzed, including illustrations of how these bound ligands have provided functional clues for annotation of proteins with little or no previous experimental characterization. Furthermore, a web server was developed as a tool to mine and analyze the PSI structures for bound ligands and other identifying features

Chiral ligand-protected gold nanoclusters: Considering the optical activity from a viewpoint of ligand dissymmetric field

Directory of Open Access Journals (Sweden)

Hiroshi Yao

2016-10-01

Full Text Available Chirality is a geometric property of a physical, chemical, or biological object, which is not superimposable on its mirror image. Its significant presence has led to a strong demand in the development of chiral drugs, sensors, catalysts, and photofunctional materials. In recent years, chirality of nanoscale organic/inorganic hybrids has received tremendous attention owing to potential applications in chiral nanotechnology. In particular, with the recent progress in the syntheses and characterizations of atomically precise gold nanoclusters protected by achiral thiolates, atomic level origins of their chirality have been unveiled. On the other hand, chirality or optical activity in metal nanoclusters can also be introduced via the surface chiral ligands, which should be universal for the nanosystems. This tutorial review presents some optically-active metal (gold nanoclusters protected by chiral thiolates or phosphines, and their chiroptical (or circular dichroism; CD properties are discussed mostly from a viewpoint of the ligand dissymmetric field scheme. The examples are the gold nanoclusters protected by (R-/(S-2-phenylpropane-1-thiol, (R-/(S-mercaptosuccinic acid, phenylboronate-D/L-fructose complexes, phosphine sulfonate-ephedrinium ion pairs, or glutathione. Some methodologies for versatile asymmetric transformation and chiroptical controls of the nanocluster compounds are also described. In the dissymmetric field model as the origin of optical activity, the chiroptical responses of the gold nanoclusters are strongly associated with coupled oscillator and/or CD stealing mechanisms based on the concept of induced CD (ICD derived from a perturbation theory, so on this basis, some characteristic features of the observed CD responses of chiral ligand-protected gold nanoclusters are presented in detail. We believe that various kinds of origins of chirality found in ligand-protected gold nanoclusters may provide models for understanding those of

Unifying the crystallization behavior of hexagonal and square crystals with the phase-field-crystal model

International Nuclear Information System (INIS)

Yang Tao; Chen Zheng; Zhang Jing; Wang Yongxin; Lu Yanli

2016-01-01

By employing the phase-field-crystal models, the atomic crystallization process of hexagonal and square crystals is investigated with the emphasis on the growth mechanism and morphological change. A unified regime describing the crystallization behavior of both crystals is obtained with the thermodynamic driving force varying. By increasing the driving force, both crystals (in the steady-state) transform from a faceted polygon to an apex-bulged polygon, and then into a symmetric dendrite. For the faceted polygon, the interface advances by a layer-by-layer (LL) mode while for the apex-bulged polygonal and the dendritic crystals, it first adopts the LL mode and then transits into the multi-layer (ML) mode in the later stage. In particular, a shift of the nucleation sites from the face center to the area around the crystal tips is detected in the early growth stage of both crystals and is rationalized in terms of the relation between the crystal size and the driving force distribution. Finally, a parameter characterizing the complex shape change of square crystal is introduced. (paper)

Preparations and crystal structures of 8 coordinate uranyl(VI) complexes having macrocyclic ligands derived from pyrroledicarboxialdehydes and diamines

International Nuclear Information System (INIS)

Komagine, J.; Takeda, M.; Takahashi, M.

2006-01-01

Six 8-coordinate uranyl(VI) complexes with macrocyclic Schiff base ligands derived from 2,6-pyrroledicarboxialdehyde and diamines are prepared and the crystal structures for two of them are determined focusing on the relation between the size of the ligands and U-N bond distances. No difference in average uranyl bond distances and bond angles are observed between [UO 2 (bipytn)](a) and [UO 2 (bipydmtn)](b). U-N bonds of these complexes are, however, not equal; the U-N(pyrrole) bonds [2.45(a), 2.44(b) A] are much shorter than the U-N(imine) bonds [2.67(a), 2.67(b) A]. (author)

Organic field-effect transistors using single crystals

International Nuclear Information System (INIS)

Hasegawa, Tatsuo; Takeya, Jun

2009-01-01

Organic field-effect transistors using small-molecule organic single crystals are developed to investigate fundamental aspects of organic thin-film transistors that have been widely studied for possible future markets for 'plastic electronics'. In reviewing the physics and chemistry of single-crystal organic field-effect transistors (SC-OFETs), the nature of intrinsic charge dynamics is elucidated for the carriers induced at the single crystal surfaces of molecular semiconductors. Materials for SC-OFETs are first reviewed with descriptions of the fabrication methods and the field-effect characteristics. In particular, a benchmark carrier mobility of 20-40 cm 2 Vs -1 , achieved with thin platelets of rubrene single crystals, demonstrates the significance of the SC-OFETs and clarifies material limitations for organic devices. In the latter part of this review, we discuss the physics of microscopic charge transport by using SC-OFETs at metal/semiconductor contacts and along semiconductor/insulator interfaces. Most importantly, Hall effect and electron spin resonance (ESR) measurements reveal that interface charge transport in molecular semiconductors is properly described in terms of band transport and localization by charge traps. (topical review)

Simultaneous near field imaging of electric and magnetic field in photonic crystal nanocavities

NARCIS (Netherlands)

Vignolini, S.; Intonti, F.; Riboli, F.; Wiersma, D.S.; Balet, L.P.; Li, L.H.; Francardi, M.; Gerardino, A.; Fiore, A.; Gurioli, M.

2012-01-01

The insertion of a metal-coated tip on the surface of a photonic crystal microcavity is used for simultaneous near field imaging of electric and magnetic fields in photonic crystal nanocavities, via the radiative emission of embedded semiconductor quantum dots (QD). The photoluminescence intensity

Rotation of dust plasma crystals in an axial magnetic field

International Nuclear Information System (INIS)

Cheung, F.; Prior, N.; Mitchell, L.

2000-01-01

Full text: Micron-sized melamine formaldehyde particles were introduced into argon plasma. As a result, the particles were negatively charged due to collision with the electrons within the plasma. With the right conditions, these particles formed a stable macroscopic crystal lattice, known as dust plasma crystal. In our experiment we conduct at Flinders University, we apply an external axial magnetic field to various configurations of dust plasma crystal. These configurations include small crystal lattices consisting of one to several particles, and large crystal lattices with many hundreds of particles. The magnetic field strength ranged from 0-32G and was uniform over the extent of the crystal. The crystals were observed to be rotating collectively in the left-handed direction under the influence of the axial magnetic field. In the case of the large crystals, the angular velocity was about 2 complete rotations per minute and was proportional to the applied magnetic field. The angular velocity changes only slightly depending on the plasma conditions. Neither radial variance in the angular velocity nor shear velocity in the vertical direction was observed in the crystal's rotational motion. In the case of the small crystals, we managed to rotate 2-6 particles (whether they are planar, 2 layers or tetrahedral). We discovered that the ease and the uniformity of the rotation of the different crystals increase as its rotational symmetry increases. Also an increase in the magnetic field strength will correspond to an increase in the angular velocity. Crystals in the shape of an annulus were also tested for theoretical reasons. The poster presentation will contain the experimental procedures, a detailed analysis and an explanation for such dust plasma crystal rotational motion

Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein-Ligand Docking Method.

Science.gov (United States)

Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Virtual screening is a computational technique for predicting a potent binding compound for a receptor protein from a ligand library. It has been a widely used in the drug discovery field to reduce the efforts of medicinal chemists to find hit compounds by experiments.Here, we introduce our novel structure-based virtual screening program, PL-PatchSurfer, which uses molecular surface representation with the three-dimensional Zernike descriptors, which is an effective mathematical representation for identifying physicochemical complementarities between local surfaces of a target protein and a ligand. The advantage of the surface-patch description is its tolerance on a receptor and compound structure variation. PL-PatchSurfer2 achieves higher accuracy on apo form and computationally modeled receptor structures than conventional structure-based virtual screening programs. Thus, PL-PatchSurfer2 opens up an opportunity for targets that do not have their crystal structures. The program is provided as a stand-alone program at http://kiharalab.org/plps2 . We also provide files for two ligand libraries, ChEMBL and ZINC Drug-like.

Synthesis, characterization, crystal structure and HSA binding of two new N,O,O-donor Schiff-base ligands derived from dihydroxybenzaldehyde and tert-butylamine

Science.gov (United States)

Khosravi, Iman; Hosseini, Farnaz; Khorshidifard, Mahsa; Sahihi, Mehdi; Rudbari, Hadi Amiri

2016-09-01

Two new o-hydroxy Schiff-bases compounds, L1 and L2, were derived from the 1:1 M condensation of 2,3-dihydroxybenzaldehyde and 2,4-dihydroxybenzaldehyde with tert-butylamine and were characterized by elemental analysis, FT-IR, 1H and 13C NMR spectroscopies. The crystal structure of L2 was also determined by single crystal X-ray analysis. The crystal structure of L2 showed that the compound exists as a zwitterionic form in the solid state, with the H atom of the phenol group being transferred to the imine N atom. It adopts an E configuration about the central Cdbnd N double bond. Furthermore, binding of these Schiff base ligands to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation methods. The fluorescence emission of HSA was quenched by ligands. Also, suitable models were used to analyze the UV-vis absorption spectroscopy data for titration of HSA solution by various amounts of Schiff bases. The spectroscopic studies revealed that these Schiff bases formed 1:1 complex with HSA. Energy transfer mechanism of quenching was discussed and the values of 3.35 and 1.57 nm as the mean distances between the bound ligands and the HSA were calculated for L1 and L2, respectively. Molecular docking results indicated that the main active binding site for these Schiff bases ligands is in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, with a slight modification of its tertiary structure.

Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain.

Science.gov (United States)

Runge, Steffen; Thøgersen, Henning; Madsen, Kjeld; Lau, Jesper; Rudolph, Rainer

2008-04-25

The glucagon-like peptide-1 receptor (GLP-1R) belongs to Family B1 of the seven-transmembrane G protein-coupled receptors, and its natural agonist ligand is the peptide hormone glucagon-like peptide-1 (GLP-1). GLP-1 is involved in glucose homeostasis, and activation of GLP-1R in the plasma membrane of pancreatic beta-cells potentiates glucose-dependent insulin secretion. The N-terminal extracellular domain (nGLP-1R) is an important ligand binding domain that binds GLP-1 and the homologous peptide Exendin-4 with differential affinity. Exendin-4 has a C-terminal extension of nine amino acid residues known as the "Trp cage", which is absent in GLP-1. The Trp cage was believed to interact with nGLP-1R and thereby explain the superior affinity of Exendin-4. However, the molecular details that govern ligand binding and specificity of nGLP-1R remain undefined. Here we report the crystal structure of human nGLP-1R in complex with the antagonist Exendin-4(9-39) solved by the multiwavelength anomalous dispersion method to 2.2A resolution. The structure reveals that Exendin-4(9-39) is an amphipathic alpha-helix forming both hydrophobic and hydrophilic interactions with nGLP-1R. The Trp cage of Exendin-4 is not involved in binding to nGLP-1R. The hydrophobic binding site of nGLP-1R is defined by discontinuous segments including primarily a well defined alpha-helix in the N terminus of nGLP-1R and a loop between two antiparallel beta-strands. The structure provides for the first time detailed molecular insight into ligand binding of the human GLP-1 receptor, an established target for treatment of type 2 diabetes.

Crystal field and magnetocrystalline anisotropy in various crystalline systems

International Nuclear Information System (INIS)

Adam, S.A.

1983-01-01

Systematic derivation of the one-perticle crystal field Hamiltonians is given for all possible site symmetries in crystals. Distinct parametrizations are found to occur for the eleven Laue-symmetry groups. The functional dependence of the Hamiltonian on the choice of the coordinate axes is also investigated. A general method is developed for the derivation of the one-particle crYstal field potential characteristic of a given crystallographic symmetry, for arbitrary effective interatomic forces. Calculations performed for cubic and hexagonal structures lead to the standard representations in spherical harmonics with the coefficients given, however, by power series of rsup(n) rather than by simgle rsup(n) terms as obtained within the usual hypothesis of Coulombian interatomic forces. This result has implications on the interpretation of some theoretical and experimental data. Theoretical results are obtained for the crystal field coefficients which enable us to develop an approach to the use of the crystal field data for the derivation of information on the effective interatomic forces in crystals. The method is applied to the magnetic Sm 3+ ion in SmCo 5 , and it is shown to provide valuable results both for the effective interatomic potential and for the consistency of various sets of crystal field parameters previously proposed in the literature. Maqnetocrystalline anisotropy of the rare-earth intermetallic compounds are discussed. Single-ion anisotropy model is used for SmCo 5 and the theoreticalpr predictions are compared with the experimental data. (author)

Temperature fields in a growing solar silicon crystal

Directory of Open Access Journals (Sweden)

Kondrik A. I.

2012-06-01

Full Text Available The optimal thermal terms for growing by Czochralski method Si single-crystals, suitable for making photoelectric energy converters, has been defined by the computer simulation method. Dependences of temperature fields character and crystallization front form on the diameter of the crystal, stage and speed of growing, and also on correlation between diameter and height of the crystal has been studied.

Crystal field effect in light actinide dioxides and oxychalcogenides - a unified phenomenological description

Energy Technology Data Exchange (ETDEWEB)

Gajek, Z. E-mail: gajek@int.pan.wroc.pl

2004-05-01

The electronic properties of the actinide ions in the series of semi-conducting, antiferromagnetic compounds: dioxides, AnO{sub 2} and oxychalcogenides, AnOY, where An=U, Np and Y=S, Se, are re-examined from the point of view of the consistency of the crystal field (CF) model. The discussion is based on the supposition that the effective metal-ligand interaction solely determines the net CF effect in non-metallic compounds. The main question we address here is, whether a reliable, consistent description of the CF effect in terms of the intrinsic parameters can be achieved for this particular family of compounds. Encouraging calculations reported previously for the AnO{sub 2} and UOY series serve as a reference data in the present estimation of electronic structure parameters for neptunium oxychalcogenides.

Crystal field effect in light actinide dioxides and oxychalcogenides-a unified phenomenological description

Science.gov (United States)

Gajek, Z.

2004-05-01

The electronic properties of the actinide ions in the series of semi-conducting, antiferromagnetic compounds: dioxides, AnO2 and oxychalcogenides, AnOY, where An=U, Np and Y=S, Se, are re-examined from the point of view of the consistency of the crystal field (CF) model. The discussion is based on the supposition that the effective metal-ligand interaction solely determines the net CF effect in non-metallic compounds. The main question we address here is, whether a reliable, consistent description of the CF effect in terms of the intrinsic parameters can be achieved for this particular family of compounds. Encouraging calculations reported previously for the AnO2 and UOY series serve as a reference data in the present estimation of electronic structure parameters for neptunium oxychalcogenides.

Crystal field effect in light actinide dioxides and oxychalcogenides - a unified phenomenological description

International Nuclear Information System (INIS)

Gajek, Z.

2004-01-01

The electronic properties of the actinide ions in the series of semi-conducting, antiferromagnetic compounds: dioxides, AnO 2 and oxychalcogenides, AnOY, where An=U, Np and Y=S, Se, are re-examined from the point of view of the consistency of the crystal field (CF) model. The discussion is based on the supposition that the effective metal-ligand interaction solely determines the net CF effect in non-metallic compounds. The main question we address here is, whether a reliable, consistent description of the CF effect in terms of the intrinsic parameters can be achieved for this particular family of compounds. Encouraging calculations reported previously for the AnO 2 and UOY series serve as a reference data in the present estimation of electronic structure parameters for neptunium oxychalcogenides

Organic field-effect transistors using single crystals

Directory of Open Access Journals (Sweden)

Tatsuo Hasegawa and Jun Takeya

2009-01-01

Full Text Available Organic field-effect transistors using small-molecule organic single crystals are developed to investigate fundamental aspects of organic thin-film transistors that have been widely studied for possible future markets for 'plastic electronics'. In reviewing the physics and chemistry of single-crystal organic field-effect transistors (SC-OFETs, the nature of intrinsic charge dynamics is elucidated for the carriers induced at the single crystal surfaces of molecular semiconductors. Materials for SC-OFETs are first reviewed with descriptions of the fabrication methods and the field-effect characteristics. In particular, a benchmark carrier mobility of 20–40 cm2 Vs−1, achieved with thin platelets of rubrene single crystals, demonstrates the significance of the SC-OFETs and clarifies material limitations for organic devices. In the latter part of this review, we discuss the physics of microscopic charge transport by using SC-OFETs at metal/semiconductor contacts and along semiconductor/insulator interfaces. Most importantly, Hall effect and electron spin resonance (ESR measurements reveal that interface charge transport in molecular semiconductors is properly described in terms of band transport and localization by charge traps.

The use of single-crystal iron frames in transient field measurements

International Nuclear Information System (INIS)

Zalm, P.C.; Laan, J. van der; Middelkoop, G. van

1979-01-01

Single-crystal Fe frames have been investigated for use as a ferromagnetic backing in transient magnetic field experiments. For this purpose the surface magnetization as a function of applied magnetic field has been determined with the magneto-optical Kerr effect. The frames, which have two sides parallel to the crystal axis, can be fully magnetized at low external fields such that fringing fields are negligibly small. These single-crystal Fe backings have been used in several transient magnetic field experiments. Comparison of the measured precession angles with previous results, obtained in polycrystalline Fe foils at high external magnetic fields, shows that the single-crystal backings are satisfactory. After extended periods of heavy-ion bombardment the crystals exhibited no radiation damage effects. The absence of fringing fields leads to a reduction of a factor of four in the measuring time for transient field experiments. (Auth.)

Phase-field crystal simulation facet and branch crystal growth

Science.gov (United States)

Chen, Zhi; Wang, Zhaoyang; Gu, Xinrui; Chen, Yufei; Hao, Limei; de Wit, Jos; Jin, Kexin

2018-05-01

Phase-field crystal model with one mode is introduced to describe morphological transition. The relationship between growth morphology and smooth density distribution was investigated. The results indicate that the pattern selection of dendrite growth is caused by the competition between interface energy anisotropy and interface kinetic anisotropy based on the 2D phase diagram. When the calculation time increases, the crystal grows to secondary dendrite at the dimensionless undercooling equal to - 0.4. Moreover, when noise is introduced in the growth progress, the symmetry is broken in the growth mode, and there becomes irregular fractal-like growth morphology. Furthermore, the single crystal shape develops into polycrystalline when the noise amplitude is large enough. When the dimensionless undercooling is less than - 0.3, the noise has a significant effect on the growth shape. In addition, the growth velocity of crystal near to liquid phase line is slow, while the shape far away from the liquid adapts to fast growth. Based on the simulation results, the method was proved to be effective, and it can easily obtain different crystal shapes by choosing the different points in 2D phase diagram.

Synthesis and Crystal Structure of Dinuclear Cadmium(II) Complex with Dipodal Ligand

International Nuclear Information System (INIS)

Kang, Young Jin; Moon, Suk Hee; Byun, Jong Chul; Park, Ki Min

2010-01-01

the preparation and structural characterization of the discrete dinuclear cadmium(II) complex with the formula [Cd(μ 2 -Cl) 2 Cl 2 ]· 2 (H 2 O)·0.5(CH 3 OH)·0.5(CH 3 CN) obtained from the reaction of CdCl 2 ·2.5H 2 O and podal ligand with quinoline end-groups has been reported. In two cadmium ions are triply bridged by two chloride and one donor atoms of ligand L and adopt distorted pentagonal bipyramidal geometries with seven coordinations. It is notable that example of discrete dinuclear complex which one podal ligand accommodates simultaneously two metal ions is very rare. During the last four decades, the chemistry of macrocyclic and non-cyclic polyethers has attracted an increasing attention because of their selective complexation, cation transport and enzyme chemistry. In the field of coordination chemistry, generally, non-cyclic, crown-type polyether affords the low complexation ability because of its conformational freedom while macrocyclic polyethers such as 18-crown-6 show the excellent complexing ability

Characteristic Ligand-Induced Crystal Forms of HIV-1 Protease Complexes: A Novel Discovery of X-Ray Crystallography

International Nuclear Information System (INIS)

Olajuyigbe, Folasade M.; Geremia, Silvano

2009-10-01

Mixtures of saquinavir (SQV) and ritonavir (RTV) were cocrystallized with HIV-1 protease (PR) in an attempt to compare their relative potencies using a crystallographic approach and factors responsible for the respective crystal forms obtained were examined. The mixture ratio of the SQV/RTV was in the range of 1:1 to 1:50 with increasing concentration of dimethyl sulphoxide (DMSO) used. Two crystal forms of PR complexes were obtained. At concentrations of 0.8 and 1.2 % DMSO using 1:1 and 1:15 ratios of SQV/RTV, the crystal form was monoclinic while increasing the concentration of DMSO to 3.2 and 5.0% using 1:15 and 1:50 ratios of SQV/RTV, the orthorhombic crystal form was obtained. The high resolution X-ray crystal structures of the PR/ inhibitor complexes reveal that crystal forms with respective space groups are dependent on the occupancy of either SQV or RTV in the active site of the PR. The occupancy of either of the PR inhibitors in the active site of PR has interestingly demonstrated unique cooperativity effects in crystallization of protein-ligand complexes. The crystal forms obtained were also related to the concentration of DMSO and ammonium sulphate in crystallization, and storage conditions of purified PR. Surprisingly, the relative occupancies of these inhibitors in the active site suggested a competition between the two inhibitors which were not inhibition constants related. Analysis of the structures in both crystal forms show no difference in DMSO content but at higher concentration of DMSO (3.2 - 5.0%) in the orthorhombic crystal forms, there were protein-sulphate interactions which were absent in the monoclinic forms with lower concentration (0.8 - 1.2%) of DMSO. This work has clearly demonstrated that there is cooperativity in crystallization and the conditions of crystallization influence specific intermolecular contacts in crystal packing (crystal form). (author)

An Overview of Hardware for Protein Crystallization in a Magnetic Field

Directory of Open Access Journals (Sweden)

Er-Kai Yan

2016-11-01

Full Text Available Protein crystallization under a magnetic field is an interesting research topic because a magnetic field may provide a special environment to acquire improved quality protein crystals. Because high-quality protein crystals are very useful in high-resolution structure determination using diffraction techniques (X-ray, neutron, and electron diffraction, research using magnetic fields in protein crystallization has attracted substantial interest; some studies have been performed in the past two decades. In this research field, the hardware is especially essential for successful studies because the environment is special and the design and utilization of the research apparatus in such an environment requires special considerations related to the magnetic field. This paper reviews the hardware for protein crystallization (including the magnet systems and the apparatus designed for use in a magnetic field and progress in this area. Future prospects in this field will also be discussed.

Rosetta Ligand docking with flexible XML protocols.

Science.gov (United States)

Lemmon, Gordon; Meiler, Jens

2012-01-01

RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

Non-empirical Prediction of the Photophysical and Magnetic Properties of Systems with Open d- and f-Shells Based on Combined Ligand Field and Density Functional Theory (LFDFT).

Science.gov (United States)

Daul, Claude

2014-09-01

Despite the important growth of ab initio and computational techniques, ligand field theory in molecular science or crystal field theory in condensed matter offers the most intuitive way to calculate multiplet energy levels arising from systems with open shells d and/or f electrons. Over the past decade we have developed a ligand field treatment of inorganic molecular modelling taking advantage of the dominant localization of the frontier orbitals within the metal-sphere. This feature, which is observed in any inorganic coordination compound, especially if treated by Density Functional Theory calculation, allows the determination of the electronic structure and properties with a surprising good accuracy. In ligand field theory, the theoretical concepts consider only a single atom center; and treat its interaction with the chemical environment essentially as a perturbation. Therefore success in the simple ligand field theory is no longer questionable, while the more accurate molecular orbital theory does in general over-estimate the metal-ligand covalence, thus yields wave functions that are too delocalized. Although LF theory has always been popular as a semi-empirical method when dealing with molecules of high symmetry e.g. cubic symmetry where the number of parameters needed is reasonably small (3 or 5), this is no more the case for molecules without symmetry and involving both an open d- and f-shell (# parameters ∼90). However, the combination of LF theory and Density Functional (DF) theory that we introduced twenty years ago can easily deal with complex molecules of any symmetry with two and more open shells. The accuracy of these predictions from 1(st) principles achieves quite a high accuracy (<5%) in terms of states energies. Hence, this approach is well suited to predict the magnetic and photo-physical properties arbitrary molecules and materials prior to their synthesis, which is the ultimate goal of each computational chemist. We will illustrate the

Multi-structure docking analysis of BACE1 crystal structures and non-peptidic ligands.

Science.gov (United States)

Haghighijoo, Zahra; Hemmateenejad, Bahram; Edraki, Najmeh; Miri, Ramin; Emami, Saeed

2017-09-01

In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis. It was found that using one crystal structure for docking did not result in high accuracy for predicting activity of the BACE1 inhibitors. Instead, using of the multi-structural docking scores, post-processed by chemometrics methods arrived to highly accurate predictive models. In this regards, the PDB accession codes of 4B70, 4DVF and 2WEZ could discriminate between active and inactive compounds, with higher accuracy. Clustering of the BACE1 structures based on principal component analysis of the crystallographic structures the revealed that the discriminant structures are in the center of the clusters. Thus, these structures can be selected as predominant crystal structures for docking studies of non-peptidic BACE1 inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Optical and dielectric studies of KH2PO4 crystal influenced by organic ligand of citric acid and l-valine: A single crystal growth and comparative study

Directory of Open Access Journals (Sweden)

Mohd Anis

Full Text Available In the present study pure, citric acid (CA and l-valine (LV doped potassium dihydrogen phosphate (KDP crystals have been grown with the aim to investigate the nonlinear optical applications facilitated by UV–visible, third order nonlinear optical (TONLO and dielectric properties. The structural parameters of grown crystals have been confirmed by single crystal X-ray diffraction analysis. The enhancement in optical transparency of KDP crystal due to addition of CA and LV has been examined within 200–900 nm by means of UV–visible spectral analysis. In addition, the transmittance data have been used to evaluate the effect of dopants on reflectance, refractive index and extinction coefficient of grown crystals in the visible region. The Z-scan analysis has been performed at 632.8 nm to identify the nature of photoinduced nonlinear refraction and nonlinear absorption in doped KDP crystals. The influence of π-bonded ligand of dopant CA and LV on TONLO susceptibility (χ3, refractive index (n2 and absorption coefficient (β of KDP crystals has been evaluated to discuss laser assisted device applications. The decrease in dielectric constant and dielectric loss of KDP crystal due to addition of CA and LV has been explored using the temperature dependent dielectric studies. Keywords: Crystal growth, Nonlinear optical materials, UV–visible studies, Z-scan analysis, Dielectric studies

Local fields in ionic crystals

International Nuclear Information System (INIS)

Claro, F.

1981-08-01

Local fields arising from the electronic distortion in perfect ionic crystals are described in terms of multipolar excitations. Field factors for the alkali halides and chalcogenide ions are found to differ significantly from the Lorentz value of 4π/3, the correction size following an exponential dependence on the difference in ionic radii. Local fields are only slightly modified by these corrections however, and together with the Clausius-Mossotti relation may be regarded as accurate to within 2% if the Lorentz value is adopted. (author)

Mapping the absolute electromagnetic field strength of individual field components inside a photonic crystal

NARCIS (Netherlands)

Denis, T.; Reijnders, B.; Lee, J.H.H.; Vos, Willem L.; Boller, Klaus J.; van der Slot, Petrus J.M.

2013-01-01

We present a method to map the absolute electromagnetic field strength inside photonic crystals. We demonstrate our method by applying it to map the electric field component Ez of a two-dimensional photonic crystal slab at microwave frequencies. The slab is placed between two mirrors to create a

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.

Science.gov (United States)

Sulimov, Alexey V; Zheltkov, Dmitry A; Oferkin, Igor V; Kutov, Danil C; Katkova, Ekaterina V; Tyrtyshnikov, Eugene E; Sulimov, Vladimir B

2017-01-01

We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.

Role of ligand-ligand vs. core-core interactions in gold nanoclusters.

Science.gov (United States)

Milowska, Karolina Z; Stolarczyk, Jacek K

2016-05-14

The controlled assembly of ligand-coated gold nanoclusters (NCs) into larger structures paves the way for new applications ranging from electronics to nanomedicine. Here, we demonstrate through rigorous density functional theory (DFT) calculations employing novel functionals accounting for van der Waals forces that the ligand-ligand interactions determine whether stable assemblies can be formed. The study of NCs with different core sizes, symmetry forms, ligand lengths, mutual crystal orientations, and in the presence of a solvent suggests that core-to-core van der Waals interactions play a lesser role in the assembly. The dominant interactions originate from combination of steric effects, augmented by ligand bundling on NC facets, and related to them changes in electronic properties induced by neighbouring NCs. We also show that, in contrast to standard colloidal theory approach, DFT correctly reproduces the surprising experimental trends in the strength of the inter-particle interaction observed when varying the length of the ligands. The results underpin the importance of understanding NC interactions in designing gold NCs for a specific function.

Determining the magnitude and direction of photoinduced ligand field switching in photochromic metal-organic complexes: molybdenum-tetracarbonyl spirooxazine complexes.

Science.gov (United States)

Paquette, Michelle M; Patrick, Brian O; Frank, Natia L

2011-07-06

The ability to optically switch or tune the intrinsic properties of transition metals (e.g., redox potentials, emission/absorption energies, and spin states) with photochromic metal-ligand complexes is an important strategy for developing "smart" materials. We have described a methodology for using metal-carbonyl complexes as spectroscopic probes of ligand field changes associated with light-induced isomerization of photochromic ligands. Changes in ligand field between the ring-closed spirooxazine (SO) and ring-opened photomerocyanine (PMC) forms of photochromic azahomoadamantyl and indolyl phenanthroline-spirooxazine ligands are demonstrated through FT-IR, (13)C NMR, and computational studies of their molybdenum-tetracarbonyl complexes. The frontier molecular orbitals (MOs) of the SO and PMC forms differ considerably in both electron density distributions and energies. Of the multiple π* MOs in the SO and PMC forms of the ligands, the LUMO+1, a pseudo-b(1)-symmetry phenanthroline-based MO, mixes primarily with the Mo(CO)(4) fragment and provides the major pathway for Mo(d)→phen(π*) backbonding. The LUMO+1 is found to be 0.2-0.3 eV lower in energy in the SO form relative to the PMC form, suggesting that the SO form is a better π-acceptor. Light-induced isomerization of the photochromic ligands was therefore found to lead to changes in the energies of their frontier MOs, which in turn leads to changes in π-acceptor ability and ligand field strength. Ligand field changes associated with photoisomerizable ligands allow tuning of excited-state and ground-state energies that dictate energy/electron transfer, optical/electrical properties, and spin states of a metal center upon photoisomerization, positioning photochromic ligand-metal complexes as promising targets for smart materials.

Method for fitting crystal field parameters and the energy level fitting for Yb3+ in crystal SC2O3

International Nuclear Information System (INIS)

Qing-Li, Zhang; Kai-Jie, Ning; Jin, Xiao; Li-Hua, Ding; Wen-Long, Zhou; Wen-Peng, Liu; Shao-Tang, Yin; Hai-He, Jiang

2010-01-01

A method to compute the numerical derivative of eigenvalues of parameterized crystal field Hamiltonian matrix is given, based on the numerical derivatives the general iteration methods such as Levenberg–Marquardt, Newton method, and so on, can be used to solve crystal field parameters by fitting to experimental energy levels. With the numerical eigenvalue derivative, a detailed iteration algorithm to compute crystal field parameters by fitting experimental energy levels has also been described. This method is used to compute the crystal parameters of Yb 3+ in Sc 2 O 3 crystal, which is prepared by a co-precipitation method and whose structure was refined by Rietveld method. By fitting on the parameters of a simple overlap model of crystal field, the results show that the new method can fit the crystal field energy splitting with fast convergence and good stability. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Internal bias field in glycine phosphite crystal

International Nuclear Information System (INIS)

Nayeem, Jannatul; Wakabayashi, Hiroshi; Kikuta, Toshio; Yamazaki, Toshinari; Nakatani, Noriyuki

2003-01-01

The distributions of internal bias field E b have been investigated under the carbon-powder pattern and mercury electrode techniques in GPI ferroelectric crystals. Polarity and intensity of E b are distributed depending on crystal growth sectors. Crystal symmetry 2/m is observed obviously in the distribution of E b . The polarities of E b are head-to-head manner in those growth sectors where a surface is growing parallel to the crystallographic a-axis and tail-to-tail manner in the other growth sectors in the crystal. The maximum intensity of E b is found in the sectors (010) where the growing surfaces are perpendicular to the ferroelectric b-axis

Enhancement of crystal homogeneity of protein crystals under application of an external alternating current electric field

Energy Technology Data Exchange (ETDEWEB)

Koizumi, H.; Uda, S.; Fujiwara, K.; Nozawa, J. [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577 (Japan); Tachibana, M. [Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 (Japan); Kojima, K. [Department of Education, Yokohama Soei University, 1 Miho-tyou, Midori-ku, Yokohama, 226-0015 (Japan)

2014-10-06

X-ray diffraction rocking-curve measurements were performed on tetragonal hen egg white (HEW) lysozyme crystals grown with and without the application of an external alternating current (AC) electric field. The crystal quality was assessed by the full width at half maximum (FWHM) value for each rocking curve. For two-dimensional maps of the FWHMs measured on the 440 and the 12 12 0 reflection, the crystal homogeneity was improved under application of an external electric field at 1 MHz, compared with that without. In particular, the significant improvement of the crystal homogeneity was observed for the 12 12 0 reflection.

Crystal field in ErGa3 - a neutron spectroscopy study

International Nuclear Information System (INIS)

Murasik, A.; Czopnik, A.; Clementyev, E.; Schefer, J.

2000-01-01

The splitting of the J = 15/2 multiplet of Er in a cubic crystal field has been determined by inelastic scattering from a polycrystalline sample of ErGa 3 . On the base of observed intensities and their temperature variation we have been able to determine two crystal electric fields (CEF) parameters required for cubic symmetry. Least-squares fits of calculated crystal field transitions of the observed neutron inelastic scattering spectra taken at 12, 24, 32, 40, 50 and 80 K, gave the crystal field parameters: B 4 (7.15±0.05) x 10 -5 and B 6 = (1.28±0.05) x 1- -6 MeV yielding the Γ 7 doublet as a ground level with the overall splitting of 10.92 MeV. The results are used to calculate the temperature-depended zero field magnetization and the Schottky anomaly of the heat capacity of the ErGa 3 which yield reasonable agreement with experimental data obtained earlier. (author)

Self-Aligned Growth of Organic Semiconductor Single Crystals by Electric Field.

Science.gov (United States)

Kotsuki, Kenji; Obata, Seiji; Saiki, Koichiro

2016-01-19

We proposed a novel but facile method for growing organic semiconductor single-crystals via solvent vapor annealing (SVA) under electric field. In the conventional SVA growth process, nuclei of crystals appeared anywhere on the substrate and their crystallographic axes were randomly distributed. We applied electric field during the SVA growth of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) on the SiO2/Si substrate on which a pair of electrodes had been deposited beforehand. Real-time observation of the SVA process revealed that rodlike single crystals grew with their long axes parallel to the electric field and bridged the prepatterned electrodes. As a result, C8-BTBT crystals automatically formed a field effect transistor (FET) structure and the mobility reached 1.9 cm(2)/(V s). Electric-field-assisted SVA proved a promising method for constructing high-mobility single-crystal FETs at the desired position by a low-cost solution process.

Far-field coupling in nanobeam photonic crystal cavities

Energy Technology Data Exchange (ETDEWEB)

Rousseau, Ian, E-mail: ian.rousseau@epfl.ch; Sánchez-Arribas, Irene; Carlin, Jean-François; Butté, Raphaël; Grandjean, Nicolas [Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)

2016-05-16

We optimized the far-field emission pattern of one-dimensional photonic crystal nanobeams by modulating the nanobeam width, forming a sidewall Bragg cross-grating far-field coupler. By setting the period of the cross-grating to twice the photonic crystal period, we showed using three-dimensional finite-difference time-domain simulations that the intensity extracted to the far-field could be improved by more than three orders of magnitude compared to the unmodified ideal cavity geometry. We then experimentally studied the evolution of the quality factor and far-field intensity as a function of cross-grating coupler amplitude. High quality factor (>4000) blue (λ = 455 nm) nanobeam photonic crystals were fabricated out of GaN thin films on silicon incorporating a single InGaN quantum well gain medium. Micro-photoluminescence spectroscopy of sets of twelve identical nanobeams revealed a nine-fold average increase in integrated far-field emission intensity and no change in average quality factor for the optimized structure compared to the unmodulated reference. These results are useful for research environments and future nanophotonic light-emitting applications where vertical in- and out-coupling of light to nanocavities is required.

Dependence of magnetization on crystal fields and exchange interactions in magnetite

Energy Technology Data Exchange (ETDEWEB)

Ouaissa, Mohamed, E-mail: m.ouaissa@yahoo.fr [Laboratoire de Génie Physique et Environnement, Faculté des Sciences, Université Ibn Tofail, Campus Universitaire BP 133, Kénitra 14000 (Morocco); Benyoussef, Abdelilah [Laboratory of Magnetism and Physics of High Energy, Faculty of Science, Mohammed V-Agdal University, Rabat (Morocco); Abo, Gavin S. [Department of Electrical and Computer Engineering and MINT Center, The University of Alabama, Tuscaloosa, AL 35487 (United States); Ouaissa, Samia; Hafid, Mustapha [Laboratoire de Génie Physique et Environnement, Faculté des Sciences, Université Ibn Tofail, Campus Universitaire BP 133, Kénitra 14000 (Morocco); Belaiche, Mohammed [Laboratoire de Magnétisme, Matériaux Magnétiques, Microonde et Céramique, Ecole Normale Supérieure, Université Mohammed V-Agdal, B.P. 9235, Océan, Rabat (Morocco)

2015-11-15

In this work, we study the magnetization of magnetite (Fe{sub 3}O{sub 4}) with different exchange interactions and crystal fields using variational method based on the Bogoliubov inequality for the Gibbs free energy within the mean field theory. The magnetic behavior was investigated in the absence and presence of crystal fields. The investigations also revealed that the transition temperature depends on the crystal fields of the octahedral and tetrahedral sites. Magnetite exhibits ferrimagnetic phase with second order transition to paramagnetic phase at 850 K. This result is confirmed using the mean field theory within the Heisenberg model. Important factors that can affect the magnetic behavior of the system are exchange interactions and crystal field. Indeed, a new magnetic behavior was observed depending on these parameters. A first order phase transition from ferrimagnetic to ferromagnetic was found at low temperature, and a second order transition from ferromagnetic to paramagnetic was observed at high temperature. - Highlights: • Magnetization of magnetite versus temperature was studied by mean field theory. • The critical temperature of magnetite (Fe{sub 3}O{sub 4}) was approximately obtained. • Effect of sublattice crystal fields on the magnetization of Fe{sub 3}O{sub 4} was investigated.

Optical spectroscopy and crystal-field analysis of U3+: Ba2YCl7

International Nuclear Information System (INIS)

Karbowiak, M.; Mech, A.; Drozdzyndki, J.; Gajek, Z.; Edelstein, N.M.

2002-01-01

High resolution absorption spectra of a U 3+ (0.3%): Ba 2 YCl 7 single crystal were recorded in the 4000-50 000 cm -1 range at 7 K. The observed crystal-field levels were assigned and fit to the parameters of the simplified angular overlap model (AOM) as well as a semi-empirical Hamiltonian representing the combined atomic and one-electron crystal-field interactions. The starting values of the AOM parameters were obtained from ab initio calculations. The analysis of the spectra allowed the assignment of 65 crystal-field levels with a relatively small rms deviation of 25 cm -1 and has shown that the AOM approach can predict quite well the B q k crystal-field parameters. The value determined for the crystal-field strength parameter, N v , corresponds well with those determined for U 3+ in other chloride single crystals. (authors)

The Role of Coulomb Interactions for Spin Crossover Behaviors and Crystal Structural Transformation in Novel Anionic Fe(III Complexes from a π-Extended ONO Ligand

Directory of Open Access Journals (Sweden)

Suguru Murata

2016-05-01

Full Text Available To investigate the π-extension effect on an unusual negative-charged spin crossover (SCO FeIII complex with a weak N2O4 first coordination sphere, we designed and synthesized a series of anionic FeIII complexes from a π-extended naphthalene derivative ligand. Acetonitrile-solvate tetramethylammonium (TMA salt 1 exhibited an SCO conversion, while acetone-solvate TMA salt 2 was in a high-spin state. The crystal structural analysis for 2 revealed that two-leg ladder-like cation-anion arrays derived from π-stacking interactions between π-ligands of the FeIII complex anion and Coulomb interactions were found and the solvated acetone molecules were in one-dimensional channels between the cation-anion arrays. A desolvation-induced single-crystal-to-single-crystal transformation to desolvate compound 2’ may be driven by Coulomb energy gain. Furthermore, the structural comparison between quasi-polymorphic compounds 1 and 2 revealed that the synergy between Coulomb and π-stacking interactions induces a significant distortion of coordination structure of 2.

Two novel mixed-ligand complexes containing organosulfonate ligands.

Science.gov (United States)

Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

2008-07-01

The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N'-diacetato)-chromium(III): development of vibrationally optimized force field (VOFF).

Science.gov (United States)

Choi, Jong-Ha; Niketić, Svetozar R; Djordjević, Ivana; Clegg, William; Harrington, Ross W

2012-05-01

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N'-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2(1)/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) Å, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) Å while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N-H···O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.

A terminal fluoride ligand generates axial magnetic anisotropy in dysprosium complexes

Energy Technology Data Exchange (ETDEWEB)

Norel, Lucie [Department of Chemistry, University of California, Berkeley, CA (United States); Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, Rennes (France); Darago, Lucy E.; Chakarawet, Khetpakorn; Gonzalez, Miguel I.; Olshansky, Jacob H.; Long, Jeffrey R. [Department of Chemistry, University of California, Berkeley, CA (United States); Le Guennic, Boris; Rigaut, Stephane [Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, Rennes (France)

2018-02-12

The first dysprosium complexes with a terminal fluoride ligand are obtained as air-stable compounds. The strong, highly electrostatic dysprosium-fluoride bond generates a large axial crystal-field splitting of the J=15/2 ground state, as evidenced by high-resolution luminescence spectroscopy and correlated with the single-molecule magnet behavior through experimental magnetic susceptibility data and ab initio calculations. (copyright 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Reliability of conventional crystal field models in f-electron systems

Energy Technology Data Exchange (ETDEWEB)

Gajek, Z. [Polska Akademia Nauk, Wroclaw (Poland). Inst. Niskich Temperatur i Badan Strukturalnych

1995-03-15

Crystal field models commonly applied to explain the electronic properties of solid f-electron compounds are discussed from the point of view of their inherent limitations and the false conclusions they may lead to. Both phenomenological and ab initio approximate models are considered. The discussion is based on generalized perturbation model calculations of the crystal field parameters for europium, uranium, plutonium and neptunium ions in various crystals. The results reveal the inadequacy of various electrostatic approaches and the correctness of models based on renormalization terms. ((orig.))

Two crystal structures of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveal protein–ligand interactions including a structural basis for observed antifolate resistance

Energy Technology Data Exchange (ETDEWEB)

Anderson, Amy C., E-mail: aca@dartmouth.edu [Dartmouth College, Department of Chemistry, Burke Laboratories, Hanover, NH 03755 (United States)

2005-03-01

An analysis of the protein–ligand interactions in two crystal structures of DHFR-TS from C. hominis reveals a possible structural basis for observed antifolate resistance in C. hominis DHFR. A comparison with the structure of human DHFR reveals residue substitutions that may be exploited for the design of species-selective inhibitors. Cryptosporidium hominis is a protozoan parasite that causes acute gastrointestinal illness. There are no effective therapies for cryptosporidiosis, highlighting the need for new drug-lead discovery. An analysis of the protein–ligand interactions in two crystal structures of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from C. hominis, determined at 2.8 and 2.87 Å resolution, reveals that the interactions of residues Ile29, Thr58 and Cys113 in the active site of C. hominis DHFR provide a possible structural basis for the observed antifolate resistance. A comparison with the structure of human DHFR reveals active-site differences that may be exploited for the design of species-selective inhibitors.

EPR and optical investigation of Mn2+ doped L-histidine-4-nitrophenolate 4-nitrophenol single crystal

Science.gov (United States)

Prabakaran, R.; Subramanian, P.

2018-04-01

Single crystals of L-histidine-4-nitrophenolate 4-nitrophenol[LHFNP] complex doped with Mn2+ were grown by the slow evaporation method at room temperature. The EPR spectrum reveals the entry of one Mn2+ ion in the lattice. The angular variation plot was drawn between the angles and the magnetic field position. The spin Hamiltonian parameters were obtained by EPR-NMR program. The D and E values show the rhombic field around the ion and is an interstitial one. The g value obtained here suggests that the Mn2+ ion experiences a strong field and there is a transfer of electron from the metal ion to the ligand atom. The optical absorption study shows various bands and are assigned to the transition from the ground state 6A1g(S). The Racah and crystal field parameters have also been evaluated and fitted to the experimental values. The Racah parameter shows the covalent bonding between the metal ion to the ligand.

Intermittent dislocation density fluctuations in crystal plasticity from a phase-field crystal model

DEFF Research Database (Denmark)

Tarp, Jens M.; Angheluta, Luiza; Mathiesen, Joachim

2014-01-01

Plastic deformation mediated by collective dislocation dynamics is investigated in the two-dimensional phase-field crystal model of sheared single crystals. We find that intermittent fluctuations in the dislocation population number accompany bursts in the plastic strain-rate fluctuations...... propose a simple stochastic model of dislocation reaction kinetics that is able to capture these statistical properties of the dislocation density fluctuations as a function of shear rate....

Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands

International Nuclear Information System (INIS)

Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S.; Damborsky, Jiri; Kuta Smatanova, Ivana

2011-01-01

Crystals of the wild-type haloalkane dehalogenase DhaA derived from R. rhodochrous NCIMB 13064 and of its catalytically inactive variant DhaA13 were grown in the presence of various ligands and diffraction data were collected to high and atomic resolution. Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon–halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2 1 2 1 2 1 as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively

Crystal-fields at rare-earth sites in R2Fe14B compounds

International Nuclear Information System (INIS)

Adam, S.; Adam, G.; Burzo, E.

1985-12-01

Crystal-field effects are expected to be important in R 2 Fe 14 B compounds. Within a model-independent approach, it is proved that four distinct rare-earth sites exist with respect to the crystalline electric fields, namely, R(4f; z=0), R(4f; z=0.5 c), R(4g; z=0), and R(4g; z=0.5 c), and relationships are established between the corresponding crystal-fields coefficients. Further, generalized Stevens parametrizations of the crystal field coefficients are derived at three levels of approximation for the interatomic forces inside the crystal. A crystal lattice dressing effect upon the radial electronic integrals is found to occur, the magnitude of which depends on the deviation of the interatomic forces from Coulombian. Finally, computation of crystal-field coefficients in Nd 2 Fe 14 B leads to results which raise questions about the validity of the simple Coulomb point-charge model. (author)

Global mean-field phase diagram of the spin-1 Ising ferromagnet in a random crystal field

Science.gov (United States)

Borelli, M. E. S.; Carneiro, C. E. I.

1996-02-01

We study the phase diagram of the mean-field spin-1 Ising ferromagnet in a uniform magnetic field H and a random crystal field Δi, with probability distribution P( Δi) = pδ( Δi - Δ) + (1 - p) δ( Δi). We analyse the effects of randomness on the first-order surfaces of the Δ- T- H phase diagram for different values of the concentration p and show how these surfaces are affected by the dilution of the crystal field.

Improving NASICON Sinterability through Crystallization under High Frequency Electrical Fields

Directory of Open Access Journals (Sweden)

Ilya eLisenker

2016-03-01

Full Text Available The effect of high frequency (HF electric fields on the crystallization and sintering rates of a lithium aluminum germanium phosphate (LAGP ion conducting ceramic was investigated. LAGP with the nominal composition Li1.5Al0.5Ge1.5(PO43 was crystallized and sintered, both conventionally and under effect of electrical field. Electrical field application, of 300V/cm at 1MHz, produced up to a 40% improvement in sintering rate of LAGP that was crystallized and sintered under the HF field. Heat sink effect of the electrodes appears to arrest thermal runaway and subsequent flash behavior. Sintered pellets were characterized using XRD, SEM, TEM and EIS to compare conventionally and field sintered processes. The as-sintered structure appears largely unaffected by the field as the sintering curves tend to converge beyond initial stages of sintering. Differences in densities and microstructure after 1 hour of sintering were minor with measured sintering strains of 31% vs. 26% with and without field, respectively . Ionic conductivity of the sintered pellets was evaluated and no deterioration due to the use of HF field was noted, though capacitance of grain boundaries due to secondary phases was significantly increased.

Dislocation motion in InSb crystals under a magnetic field

CERN Document Server

Darinskaya, E V; Erofeeva, S A

2002-01-01

Dislocation displacements under the action of a permanent magnetic field without mechanical loading in differently doped InSb crystals are investigated. The dependences of the mean dislocation path length and the relative number of divergence and tightening half-loops on the magnetic induction and preliminary load are obtained. Experiments on n-InSb crystals with Te impurities and on p-InSb crystals with Ge impurities have shown a sensitivity of the magnetoplasticity to the conductivity type and the dopant content. Study of the magnetoplastic effect in the initial deformed InSb crystals shows that internal stresses decrease the lengths of divergence dislocation paths and simultaneously increase the threshold magnetic field above which the magnetoplastic effect exists. Possible reasons for the observed phenomena are discussed.

Method to map individual electromagnetic field components inside a photonic crystal

NARCIS (Netherlands)

Denis, T.; Reijnders, B.; Lee, J.H.H.; van der Slot, Petrus J.M.; Vos, Willem L.; Boller, Klaus J.

2012-01-01

We present a method to map the absolute electromagnetic field strength inside photonic crystals. We apply the method to map the dominant electric field component Ez of a two-dimensional photonic crystal slab at microwave frequencies. The slab is placed between two mirrors to select Bloch standing

Crystal field in rare-earth metals and intermetallic compounds

International Nuclear Information System (INIS)

Ray, D.K.

1978-01-01

Reasons for the success of the crystal-field model for the rare-earth metals and intermetallic compounds are discussed. A review of some of the available experimental results is made with emphasis on cubic intermetallic compounds. Various sources of the origin of the crystal field in these metals are discussed in the background of the recent APW picture of the conduction electrons. The importance of the non-spherical part of the muffin-tin potential on the single-ion anisotropy is stressed. (author)

Tetrathiafulvalene-based azine ligands for anion and metal cation coordination

Directory of Open Access Journals (Sweden)

Awatef Ayadi

2015-08-01

Full Text Available The synthesis and full characterization of two tetrathiafulvalene-appended azine ligands, namely 2-([2,2’-bi(1,3-dithiolylidene]-4-yl-6-((2,4-dinitrophenylhydrazonomethylpyridine (L1 and 5-([2,2’-bi(1,3-dithiolylidene]-4-yl-2-((2,4-dinitrophenylhydrazonomethylpyridine (L2 are described. The crystal structure of ligand L1 indicates that the ligand is completely planar with the presence of a strong intramolecular N3–H3···O1 hydrogen bonding. Titration experiments with inorganic anions showed that both ligands are suitable candidates for the sensing of fluoride anions. Ligand L2 was reacted with a Re(I cation to yield the corresponding rhenium tricarbonyl complex 3. In the crystal structure of the newly prepared electroactive rhenium complex the TTF is neutral and the rhenium cation is hexacoordinated. The electrochemical behavior of the three compounds indicates that they are promising for the construction of crystalline radical cation salts.

A Navier-Stokes phase-field crystal model for colloidal suspensions.

Science.gov (United States)

Praetorius, Simon; Voigt, Axel

2015-04-21

We develop a fully continuous model for colloidal suspensions with hydrodynamic interactions. The Navier-Stokes Phase-Field Crystal model combines ideas of dynamic density functional theory with particulate flow approaches and is derived in detail and related to other dynamic density functional theory approaches with hydrodynamic interactions. The derived system is numerically solved using adaptive finite elements and is used to analyze colloidal crystallization in flowing environments demonstrating a strong coupling in both directions between the crystal shape and the flow field. We further validate the model against other computational approaches for particulate flow systems for various colloidal sedimentation problems.

Crystal-field analysis of U3+ ions in K2LaX5 (X=Cl, Br or I) single crystals

Science.gov (United States)

Karbowiak, M.; Edelstein, N.; Gajek, Z.; Drożdżyński, J.

1998-11-01

An analysis of low temperature absorption spectra of U3+ ions doped in K2LaX5 (X=Cl, Br or I) single crystals is reported. The energy levels of the U3+ ion in the single crystals were assigned and fitted to a semiempirical Hamiltonian representing the combined atomic and crystal-field interactions at the Cs symmetry site. An analysis of the nephelauxetic effect and crystal-field splittings in the series of compounds is also reported.

Coordination chemistry and bioactivity of Ni2+, Cu2+, and Zn2+ complexes containing a bidentate NS ligand, β-N-phenyldithiocarbazic acid, and the crystal structure of β-hydroxy-β-phenylmethylene α-phenylimine

International Nuclear Information System (INIS)

Tarafder, M.T.H.; Ahmed Faizal Shamsuddin; Grouse, Karen A.; Yamin, B.M.; Ali, A.M.; Fun, H.-K.

2003-07-01

A bidentate ligand (PhDTCH) with NS donor sequence was prepared from the reaction between carbon disulfide and phenylhydrazine in ethanol. Complexes of this ligand with Ni(II), Cu(II) and Zn(II) were synthesized and characterized by elemental analyses, and various physicochemical techniques. The metal complexes were all four coordinated. In an attempt to resolve the crystal structure of PhDTCH, an ethanolic solution, after leaving for a few days gave bright crystals of PhD6, β-hydroxy-β-phenylmethylene α-phenylimine, the crystal structure of which has been resolved. The crystal packing indicated that it is monoclinic with a space group of P21/n. All of the compounds were tested against different bacteria and fungi, and also against leukemic cell lines. All of the compounds showed weak biological properties compared to standard drugs. (author)

Correlation theory of crystal field and anisotropic exchange effects

DEFF Research Database (Denmark)

Lindgård, Per-Anker

1985-01-01

A general theory for including correlation effects in static and dynamic properties is presented in terms of Raccah or Stevens operators. It is explicitly developed for general crystal fields and anisotropic interactions and systems with several sublattices, like the rare earth compounds....... The theory gives explicitly a temperature dependent renormalization of both the crystal field and the interactions, and a damping of the excitations and in addition a central park component. The general theory is illustrated by a discussion of the singlet-doublet system. The correlation effects...

Crystal fields at light rare-earth ions in Y and Lu

DEFF Research Database (Denmark)

Touborg, P.; Nevald, Rolf; Johansson, Torben

1978-01-01

Crystal-field parameters have been deduced for the light rare-earth solutes Ce, Pr, and Nd in Y or Lu hosts from measurements of the paramagnetic susceptibilities. In the analysis all multiplets in the lowest LS term were included. For a given host, crystal-field parameters divided by Stevens fac...

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies

Science.gov (United States)

Gaieb, Zied; Liu, Shuai; Gathiaka, Symon; Chiu, Michael; Yang, Huanwang; Shao, Chenghua; Feher, Victoria A.; Walters, W. Patrick; Kuhn, Bernd; Rudolph, Markus G.; Burley, Stephen K.; Gilson, Michael K.; Amaro, Rommie E.

2018-01-01

The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank (http://www.pdb.org), and in affinity ranking and scoring of bound ligands.

Custom Coordination Environments for Lanthanoids: Tripodal Ligands Achieve Near-Perfect Octahedral Coordination for Two Dysprosium-Based Molecular Nanomagnets.

Science.gov (United States)

Lim, Kwang Soo; Baldoví, José J; Jiang, ShangDa; Koo, Bong Ho; Kang, Dong Won; Lee, Woo Ram; Koh, Eui Kwan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Slota, Michael; Bogani, Lapo; Hong, Chang Seop

2017-05-01

Controlling the coordination sphere of lanthanoid complexes is a challenging critical step toward controlling their relaxation properties. Here we present the synthesis of hexacoordinated dysprosium single-molecule magnets, where tripodal ligands achieve a near-perfect octahedral coordination. We perform a complete experimental and theoretical investigation of their magnetic properties, including a full single-crystal magnetic anisotropy analysis. The combination of electrostatic and crystal-field computational tools (SIMPRE and CONDON codes) allows us to explain the static behavior of these systems in detail.

Improving NASICON Sinterability through Crystallization under High-Frequency Electrical Fields

Energy Technology Data Exchange (ETDEWEB)

Lisenker, Ilya; Stoldt, Conrad R., E-mail: stoldt@colorado.edu [Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO (United States)

2016-03-31

The effect of high-frequency (HF) electric fields on the crystallization and sintering rates of a lithium aluminum germanium phosphate (LAGP) ion conducting ceramic was investigated. LAGP with the nominal composition Li{sub 1.5}Al{sub 0.5}Ge{sub 1.5}(PO{sub 4}){sub 3} was crystallized and sintered, both conventionally and under effect of electrical field. Electrical field application, of 300 V/cm at 1 MHz, produced up to a 40% improvement in sintering rate of LAGP that was crystallized and sintered under the HF field. Heat sink effect of the electrodes appears to arrest thermal runaway and subsequent flash behavior. Sintered pellets were characterized using X-ray diffraction, scanning electron microscope, TEM, and electrochemical impedance spectroscopy to compare conventionally and field-sintered processes. The as-sintered structure appears largely unaffected by the field as the sintering curves tend to converge beyond initial stages of sintering. Differences in densities and microstructure after 1 h of sintering were minor with measured sintering strains of 31 vs. 26% with and without field, respectively. Ionic conductivity of the sintered pellets was evaluated, and no deterioration due to the use of HF field was noted, though capacitance of grain boundaries due to secondary phases was significantly increased.

Integral parameters of crystal field for RE spectra

International Nuclear Information System (INIS)

Kustov, E.F.; Maketov, T.K.; Prgevudsky, A.K.; Steczko, G.

1980-01-01

The integral parameters of the crystal field are introduced for the interpretation of the spectra of RE ions in various crystals. The main formula of the method, the expression of the parameters for various states of Ce, Pr, Nd, Eu, Tb, Er, Tu, and Yb are determined. Integral parameters of A 2 , A 4 , A 6 and parameter of the spin-orbit interaction xi are calculated for 40 laser crystals with Nd, Er. An interpretation of the symmetry of the Eu 3+ centres of the NaBaZn silicate glass is given using integral parameters A 2 , A 4 . (author)

ESR studies of electron irradiated K3Ir(CN)6 in KCl single crystals

International Nuclear Information System (INIS)

Vugman, N.V.; Pinhal, N.M.

1983-01-01

ESR studies of KCl single crystals doped with small amounts of K 3 Ir(CN) 6 and submitted to a prolongued 2 MeV electron irradiation at room temperature reveal the presence of the [IR(CN) 5 Cl] 4- and [Ir(CN) 4 Cl 2 ] 4- new molecular species. Ligand spin densities and ligand field parameters are calculated from the experimental hyperfine and superhyperfine interactions and compared to previous data on the [Ir(CN) 5 ] 4- species. (Author) [pt

Unexpected self-sorting self-assembly formation of a [4:4] sulfate:ligand cage from a preorganized tripodal urea ligand.

Science.gov (United States)

Pandurangan, Komala; Kitchen, Jonathan A; Blasco, Salvador; Boyle, Elaine M; Fitzpatrick, Bella; Feeney, Martin; Kruger, Paul E; Gunnlaugsson, Thorfinnur

2015-04-07

The design and synthesis of tripodal ligands 1-3 based upon the N-methyl-1,3,5-benzenetricarboxamide platform appended with three aryl urea arms is reported. This ligand platform gives rise to highly preorganized structures and is ideally suited for binding SO4 (2-) and H2 PO4 (-) ions through multiple hydrogen-bonding interactions. The solid-state crystal structures of 1-3 with SO4 (2-) show the encapsulation of a single anion within a cage structure, whereas the crystal structure of 1 with H2 PO4 (-) showed that two anions are encapsulated. We further demonstrate that ligand 4, based on the same platform but consisting of two bis-urea moieties and a single ammonium moiety, also recognizes SO4 (2-) to form a self-assembled capsule with [4:4] SO4 (2-) :4 stoichiometry in which the anions are clustered within a cavity formed by the four ligands. This is the first example of a self-sorting self-assembled capsule where four tetrahedrally arranged SO4 (2-) ions are embedded within a hydrophobic cavity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selectivity in ligand recognition of G-quadruplex loops.

Science.gov (United States)

Campbell, Nancy H; Patel, Manisha; Tofa, Amina B; Ghosh, Ragina; Parkinson, Gary N; Neidle, Stephen

2009-03-03

A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.

Rational Ligand Design for U(VI) and Pu(IV)

International Nuclear Information System (INIS)

Szigethy, Geza

2009-01-01

ligands exhibited increased uranyl affinity compared to bis-Me-3,2-HOPO ligands. This result is due in part to their increased denticity, but is primarily the result of the presence of the TAM moiety. In an effort to explore the relatively unexplored coordination chemistry of Pu(IV) with bidentate moieties, a series of Pu(IV) complexes were also crystallized using bidentate hydroxypyridinone and hydroxypyrone ligands. The geometries of these complexes are compared to that of the analogous Ce(IV) complexes. While in some cases these showed the expected structural similarities, some ligand systems led to significant coordination changes. A series of crystal structure analyses with Ce(IV) indicated that these differences are most likely the result of crystallization condition differences and solvent inclusion effects.

Rational Ligand Design for U(VI) and Pu(IV)

Energy Technology Data Exchange (ETDEWEB)

Szigethy, Geza [Univ. of California, Berkeley, CA (United States)

2009-08-12

saturation, these ligands exhibited increased uranyl affinity compared to bis-Me-3,2-HOPO ligands. This result is due in part to their increased denticity, but is primarily the result of the presence of the TAM moiety. In an effort to explore the relatively unexplored coordination chemistry of Pu(IV) with bidentate moieties, a series of Pu(IV) complexes were also crystallized using bidentate hydroxypyridinone and hydroxypyrone ligands. The geometries of these complexes are compared to that of the analogous Ce(IV) complexes. While in some cases these showed the expected structural similarities, some ligand systems led to significant coordination changes. A series of crystal structure analyses with Ce(IV) indicated that these differences are most likely the result of crystallization condition differences and solvent inclusion effects.

Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms.

Science.gov (United States)

Park, Joon Kyu; Moon, Jin Ho; Kim, Jae-Hong; Kim, Eunice EunKyeong

2005-01-01

In bacteria, protein expression initiates with an N-formyl group and this needs to be removed in order to ensure proper bacterial growth. These formylation and deformylation processes are unique to eubacteria; therefore, inhibition of these would provide a novel antibacterial therapy. Deformylation is carried out by peptide deformylase (PDF). PDF from Bacillus cereus, one of the major pathogenic bacteria, was cloned into expression plasmid pET-28a (Novagen), overexpressed in Escherichia coli BL21 (DE3) and purified to high quality. Crystals have been obtained of both ligand-free PDF and PDF to which actinonin, a highly potent naturally occurring inhibitor, is bound. Both crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 42.72, b = 44.04, c = 85.19 A and a = 41.31, b = 44.56, c = 84.47 A, respectively. Diffraction data were collected to 1.7 A resolution for the inhibitor-free crystals and to 2.0 A resolution for the actinonin-bound crystals.

Synthesis and crystal structure of an oxovanadium(IV) complex with a pyrazolone ligand and its use as a heterogeneous catalyst for the oxidation of styrene under mild conditions.

Science.gov (United States)

Parihar, Sanjay; Pathan, Soyeb; Jadeja, R N; Patel, Anjali; Gupta, Vivek K

2012-01-16

1-Phenyl-3-methyl-4-touloyl-5-pyrazolone (ligand) was synthesized and used to prepare an oxovanadium(IV) complex. The complex was characterized by single-crystal X-ray analysis and various spectroscopic techniques. The single-crystal X-ray analysis of the complex shows that the ligands are coordinated in a syn configuration to each other and create a distorted octahedral environment around the metal ion. A heterogeneous catalyst comprising an oxovanadium(IV) complex and hydrous zirconia was synthesized, characterized by various physicochemical techniques, and successfully used for the solvent-free oxidation of styrene. The influence of the reaction parameters (percent loading, molar ratio of the substrate to H(2)O(2), amount of catalyst, and reaction time) was studied. The catalyst was reused three times without any significant loss in the catalytic activity.

On the laws of disordering of the Ln3+ -ion crystal field in insulating crystals

International Nuclear Information System (INIS)

Kaminskij, A.A.

1988-01-01

Results of the study of fundamental regularities, which cause crystal field (CF) disordering on Ln 3+ ions in dielectric crystals are summed up. Analysis and systematization of the investigation results of atomic structure of disordered laser crystals and conducted investigations on spectroscopic properties and induced radiation (IR) permitted to come to the conclusion that the nature of disordering on CF is related to two fundamental regularities. The first regularity- the structural-dynamic one- is pronounced in numerous nonstoichiometric phases; the second one - determines spectroscopic properties and IR character

Organo-gallium and indium complexes with dithiolate and oxo ligands

Indian Academy of Sciences (India)

Page 1 ... of several of these com- plexes have been established by single crystal X-ray diffraction analyses. Complexes derived from oxo ligands ... diode) applications.8. Organometallic complexes derived from chelating ligands, such as substituted. 8-hydroxyqunoline and azomethine linkages, are emerging as potential ...

Crystal structure of a mononuclear Ru(II) complex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy-tpy)](.).

Science.gov (United States)

Rein, Francisca N; Chen, Weizhong; Scott, Brian L; Rocha, Reginaldo C

2015-09-01

We report the structural characterization of [6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine](2,2'-bi-pyridine)-chlorido-ruthenium(II) hexa-fluorido-phosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2'-bi-pyridine (bpy) and the tridendate ligand 6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine (tpy-tpy). The [RuCl(bpy)(tpy-tpy)](+) monocation has a distorted octa-hedral geometry at the central Ru(II) ion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru-N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru-Cl. For tpy-tpy, the mean Ru-N distance involving the outer N atoms trans to each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru-Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy-tpy adopts a trans,trans conformation about the inter-annular C-C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π-π stacking inter-actions based on tpy-tpy. The crystal structure reported here is the first for a tpy-tpy complex of ruthenium.

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex

Energy Technology Data Exchange (ETDEWEB)

Andersen, Jacob Lauwring, E-mail: jla@mb.au.dk [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark); Schrøder, Tenna Juul; Christensen, Søren [H. Lundbeck A/S, Ottiliavej 9, 2500 Valby (Denmark); Strandbygård, Dorthe [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark); Pallesen, Lone Tjener [Aarhus University, Ole Worms Allé 3, 8000 Aarhus C (Denmark); García-Alai, Maria Marta [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark); Lindberg, Samsa; Langgård, Morten; Eskildsen, Jørgen Calí; David, Laurent; Tagmose, Lena; Simonsen, Klaus Baek; Maltas, Philip James; Rønn, Lars Christian Biilmann; Jong, Inge E. M. de; Malik, Ibrahim John; Egebjerg, Jan; Karlsson, Jens-Jacob [H. Lundbeck A/S, Ottiliavej 9, 2500 Valby (Denmark); Uppalanchi, Srinivas; Sakumudi, Durga Rao; Eradi, Pradheep [GVK BioScience, Plot No. 28 A, IDA Nacharam, Hyderabad 500 076 (India); Watson, Steven P., E-mail: jla@mb.au.dk [H. Lundbeck A/S, Ottiliavej 9, 2500 Valby (Denmark); Thirup, Søren, E-mail: jla@mb.au.dk [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark)

2014-02-01

The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex are reported. Sortilin is a type I membrane glycoprotein belonging to the vacuolar protein sorting 10 protein (Vps10p) family of sorting receptors and is most abundantly expressed in the central nervous system. Sortilin has emerged as a key player in the regulation of neuronal viability and has been implicated as a possible therapeutic target in a range of disorders. Here, the identification of AF40431, the first reported small-molecule ligand of sortilin, is reported. Crystals of the sortilin–AF40431 complex were obtained by co-crystallization and the structure of the complex was solved to 2.7 Å resolution. AF40431 is bound in the neurotensin-binding site of sortilin, with the leucine moiety of AF40431 mimicking the binding mode of the C-terminal leucine of neurotensin and the 4-methylumbelliferone moiety of AF40431 forming π-stacking with a phenylalanine.

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex

International Nuclear Information System (INIS)

Andersen, Jacob Lauwring; Schrøder, Tenna Juul; Christensen, Søren; Strandbygård, Dorthe; Pallesen, Lone Tjener; García-Alai, Maria Marta; Lindberg, Samsa; Langgård, Morten; Eskildsen, Jørgen Calí; David, Laurent; Tagmose, Lena; Simonsen, Klaus Baek; Maltas, Philip James; Rønn, Lars Christian Biilmann; Jong, Inge E. M. de; Malik, Ibrahim John; Egebjerg, Jan; Karlsson, Jens-Jacob; Uppalanchi, Srinivas; Sakumudi, Durga Rao; Eradi, Pradheep; Watson, Steven P.; Thirup, Søren

2014-01-01

The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex are reported. Sortilin is a type I membrane glycoprotein belonging to the vacuolar protein sorting 10 protein (Vps10p) family of sorting receptors and is most abundantly expressed in the central nervous system. Sortilin has emerged as a key player in the regulation of neuronal viability and has been implicated as a possible therapeutic target in a range of disorders. Here, the identification of AF40431, the first reported small-molecule ligand of sortilin, is reported. Crystals of the sortilin–AF40431 complex were obtained by co-crystallization and the structure of the complex was solved to 2.7 Å resolution. AF40431 is bound in the neurotensin-binding site of sortilin, with the leucine moiety of AF40431 mimicking the binding mode of the C-terminal leucine of neurotensin and the 4-methylumbelliferone moiety of AF40431 forming π-stacking with a phenylalanine

Mixed spin Ising model with four-spin interaction and random crystal field

International Nuclear Information System (INIS)

Benayad, N.; Ghliyem, M.

2012-01-01

The effects of fluctuations of the crystal field on the phase diagram of the mixed spin-1/2 and spin-1 Ising model with four-spin interactions are investigated within the finite cluster approximation based on a single-site cluster theory. The state equations are derived for the two-dimensional square lattice. It has been found that the system exhibits a variety of interesting features resulting from the fluctuation of the crystal field interactions. In particular, for low mean value D of the crystal field, the critical temperature is not very sensitive to fluctuations and all transitions are of second order for any value of the four-spin interactions. But for relatively high D, the transition temperature depends on the fluctuation of the crystal field, and the system undergoes tricritical behaviour for any strength of the four-spin interactions. We have also found that the model may exhibit reentrance for appropriate values of the system parameters.

Effect of Ligand Field Tuning on the SMM Behavior for Three Related Alkoxide-Bridged Dysprosium Dimers.

Science.gov (United States)

Peng, Yan; Mereacre, Valeriu; Baniodeh, Amer; Lan, Yanhua; Schlageter, Martin; Kostakis, George E; Powell, Annie K

2016-01-04

The synthesis and characterization of three Dy2 compounds, [Dy2(HL1)2(NO3)4] (1), [Dy2(L2)2(NO3)4] (2), and [Dy2(HL3)2(NO3)4] (3), formed using related tripodal ligands with a central tertiary amine bearing picolyl and alkoxy arms, 2-[(2-hydroxy-ethyl)-pyridin-2-ylmethylamino]-ethanol (H2L1), 2-(bis-pyridin-2-ylmethylamino)-ethanol (HL2), and 2-(bis-pyridin-2-ylmethylamino)-propane-1,3-diol (H2L3), are reported. The compounds are rare examples of alkoxide-bridged {Dy2} complexes and display capped square antiprism coordination geometry around each Dy(III) ion. Changes in the ligand field environment around the Dy(III) ions brought about through variations in the ligand donors can be gauged from the magnetic properties, with compounds 1 and 2 showing antiparallel coupling between the Dy(III) ions and 3 showing parallel coupling. Furthermore, slow relaxation of the magnetization typical of SMM behavior could be observed for compounds 2 and 3, suggesting that small variations in the ligand field can have a significant influence on the slow relaxation processes responsible for SMM behavior of Dy(III)-based systems.

Crystal Fields in Dilute Rare-Earth Metals Obtained from Magnetization Measurements on Dilute Rare-Earth Alloys

DEFF Research Database (Denmark)

Touborg, P.; Høg, J.

1974-01-01

Crystal field parameters of Tb, Dy, and Er in Sc, Y, and Lu are summarized. These parameters are obtained from magnetization measurements on dilute single crystals, and successfully checked by a number of different methods. The crystal field parameters vary unpredictably with the rare-earth solute....... B40, B60, and B66 are similar in Y and Lu. Crystal field parameters for the pure metals Tb, Dy, and Er are estimated from the crystal fields in Y and Lu....

Influence of magnetic field on the morphology of the andrographolide crystal from supercritical carbon dioxide extraction crystallization

Science.gov (United States)

Chen, Kexun; Zhang, Xingyuan; Pan, Jian; Zhang, Wencheng; Yong, Ji; Yin, Wenhong

2003-10-01

In this paper, a supercritical fluid extraction-crystallization of andrographolide, a kind of Chinese traditional medicine, was investigated. We have studied the extraction-crystallization process with or without magnet in the extractor, respectively. It was found that the presence of magnetic field is an important factor influencing the quality of the products. SEM images showed that the crystal was slice-like in shape, and many slices reunited together in the absence of magnet. Further research showed that pressure had a certain effect on the morphology of the crystal.

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology.

Science.gov (United States)

Shinoda, Akira; Tanaka, Yoshikazu; Yao, Min; Tanaka, Isao

2014-11-01

X-ray crystallography is an important technique for structure-based drug discovery, mainly because it is the only technique that can reveal whether a ligand binds to the target protein as well as where and how it binds. However, ligand screening by X-ray crystallography involves a crystal-soaking experiment, which is usually performed manually. Thus, the throughput is not satisfactory for screening large numbers of candidate ligands. In this study, a technique to anchor protein crystals to mounting loops by using gel and inkjet technology has been developed; the method allows soaking of the mounted crystals in ligand-containing solution. This new technique may assist in the design of a fully automated drug-screening pipeline.

Crystal-field splittings in rare-earth-based hard magnets: An ab initio approach

Science.gov (United States)

Delange, Pascal; Biermann, Silke; Miyake, Takashi; Pourovskii, Leonid

2017-10-01

We apply the first-principles density functional theory + dynamical mean-field theory framework to evaluate the crystal-field splitting on rare-earth sites in hard magnetic intermetallics. An atomic (Hubbard-I) approximation is employed for local correlations on the rare-earth 4 f shell and self-consistency in the charge density is implemented. We reduce the density functional theory self-interaction contribution to the crystal-field splitting by properly averaging the 4 f charge density before recalculating the one-electron Kohn-Sham potential. Our approach is shown to reproduce the experimental crystal-field splitting in the prototypical rare-earth hard magnet SmCo5. Applying it to R Fe12 and R Fe12X hard magnets (R =Nd , Sm and X =N , Li), we obtain in particular a large positive value of the crystal-field parameter A20〈r2〉 in NdFe12N resulting in a strong out-of-plane anisotropy observed experimentally. The sign of A20〈r2〉 is predicted to be reversed by substituting N with Li, leading to a strong out-of-plane anisotropy in SmFe12Li . We discuss the origin of this strong impact of N and Li interstitials on the crystal-field splitting on rare-earth sites.

Thermal conductivity of niobium single crystals in a magnetic field

International Nuclear Information System (INIS)

Gladun, C.; Vinzelberg, H.

1980-01-01

The thermal conductivity in longitudinal magnetic fields up to 5 T and in the temperature range 3.5 to 15 K is measured in two high purity niobium single crystals having residual resistivity ratios of 22700 and 19200 and orientations of the rod axis [110] and [100]. The investigations show that by means of the longitudinal magnetic field the thermal conductivity may decrease only to a limiting value. In the crystal directions [110] and [100] for the ratio of the thermal conductivity in zero field and the thermal conductivity in the saturation field the temperature-independent factors 1.92 and 1.27, respectively, are determined. With the aid of these factors the thermal conductivity in the normal state is evaluated from the measured values of thermal conductivity below Tsub(c) in the magnetic field. The different conduction and scattering mechanisms are discussed. (author)

Soaking suggests "alternative facts": Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition.

Directory of Open Access Journals (Sweden)

Frederik Rainer Ehrmann

Full Text Available For the efficient pathogenesis of Shigella, the causative agent of bacillary dysentery, full functionality of tRNA-guanine transglycosylase (TGT is mandatory. TGT performs post-transcriptional modifications of tRNAs in the anticodon loop taking impact on virulence development. This suggests TGT as a putative target for selective anti-shigellosis drug therapy. Since bacterial TGT is only functional as homodimer, its activity can be inhibited either by blocking its active site or by preventing dimerization. Recently, we discovered that in some crystal structures obtained by soaking the full conformational adaptation most likely induced in solution upon ligand binding is not displayed. Thus, soaked structures may be misleading and suggest irrelevant binding modes. Accordingly, we re-investigated these complexes by co-crystallization. The obtained structures revealed large conformational rearrangements not visible in the soaked complexes. They result from spatial perturbations in the ribose-34/phosphate-35 recognition pocket and, consequently, an extended loop-helix motif required to prevent access of water molecules into the dimer interface loses its geometric integrity. Thermodynamic profiles of ligand binding in solution indicate favorable entropic contributions to complex formation when large conformational adaptations in the dimer interface are involved. Native MS titration experiments reveal the extent to which the homodimer is destabilized in the presence of each inhibitor. Unexpectedly, one ligand causes a complete rearrangement of subunit packing within the homodimer, never observed in any other TGT crystal structure before. Likely, this novel twisted dimer is catalytically inactive and, therefore, suggests that stabilizing this non-productive subunit arrangement may be used as a further strategy for TGT inhibition.

Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7

Directory of Open Access Journals (Sweden)

A. V. Sulimov

2017-01-01

Full Text Available Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

Science.gov (United States)

Sulimov, A V; Kutov, D C; Katkova, E V; Sulimov, V B

2017-01-01

Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

Stroboscopic topographies on iron borate crystal in 9.6 MHz rf magnetic field

International Nuclear Information System (INIS)

Mitsui, Takaya; Imai, Yasuhiko; Kikuta, Seishi

2003-01-01

The influence of magnetoacoustic wave on the crystal deformation was studied by stroboscopic double crystal X-ray topography. The acoustic wave was excited by the rf magnetic field, which was synchronized with synchrotron radiation X-ray pulse. In measured rocking curves of FeBO 3 (4 4 4) reflection, we observed, for the first time, that the application of rf magnetic field (|H rf | max >8.4 Oe) brought about the extreme narrowing of full width at half maximum (FWHM). Recorded topographs showed that the narrowing of FWHM was due to the magnetoacoustic standing wave which is excited in FeBO 3 crystal. In our experiments, the influence of additional static magnetic field on the magnetoacoustic standing wave of FeBO 3 crystal was investigated too

Magnetic properties and electronic structure of neptunyl(VI) complexes: wavefunctions, orbitals, and crystal-field models

Energy Technology Data Exchange (ETDEWEB)

Gendron, Frederic; Pritchard, Ben; Autschbach, Jochen [Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY (United States); Paez-Hernandez, Dayan; Bolvin, Helene [Laboratoire de Physique et de Chimie Quantiques, Universite Toulouse 3 (France); Notter, Francois-Paul [Laboratoire de Chimie Quantique, Universite de Strasbourg (France)

2014-06-23

The electronic structure and magnetic properties of neptunyl(VI), NpO{sub 2}{sup 2+}, and two neptunyl complexes, [NpO{sub 2}(NO{sub 3}){sub 3}]{sup -} and [NpO{sub 2}Cl{sub 4}]{sup 2-}, were studied with a combination of theoretical methods: ab initio relativistic wavefunction methods and density functional theory (DFT), as well as crystal-field (CF) models with parameters extracted from the ab initio calculations. Natural orbitals for electron density and spin magnetization from wavefunctions including spin-orbit coupling were employed to analyze the connection between the electronic structure and magnetic properties, and to link the results from CF models to the ab initio data. Free complex ions and systems embedded in a crystal environment were studied. Of prime interest were the electron paramagnetic resonance g-factors and their relation to the complex geometry, ligand coordination, and nature of the nonbonding 5f orbitals. The g-factors were calculated for the ground and excited states. For [NpO{sub 2}Cl{sub 4}]{sup 2-}, a strong influence of the environment of the complex on its magnetic behavior was demonstrated. Kohn-Sham DFT with standard functionals can produce reasonable g-factors as long as the calculation converges to a solution resembling the electronic state of interest. However, this is not always straightforward. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Crystal orientation effects on wurtzite quantum well electromechanical fields

DEFF Research Database (Denmark)

Duggen, Lars; Willatzen, Morten

2010-01-01

in the literature for semiconductors, is inaccurate for ZnO/MgZnO heterostructures where shear-strain components play an important role. An interesting observation is that a growth direction apart from [1̅ 21̅ 0] exists for which the electric field in the quantum well region becomes zero. This is important for, e......A one-dimensional continuum model for calculating strain and electric field in wurtzite semiconductor heterostructures with arbitrary crystal orientation is presented and applied to GaN/AlGaN and ZnO/MgZnO heterostructure combinations. The model is self-consistent involving feedback couplings...... of spontaneous polarization, strain, and electric field. Significant differences between fully coupled and semicoupled models are found for the longitudinal and shear-strain components as a function of the crystal-growth direction. In particular, we find that the semicoupled model, typically used...

Crystal fields of dilute Tb, Dy, Ho, or Er in Lu obtained by magnetization measurements

International Nuclear Information System (INIS)

Touborg, P.; Hog, J.

1975-01-01

Magnetization measurements are reported on single crystals of dilute Tb, Dy, Ho, or Er in Lu. These measurements were performed in the temperature range 1.5--100 K and field range 0--6 T and include measurements of initial susceptibility, isothermal and isofield magnetization, and basal-plane anisotropy. The results show features similar to the corresponding Y-R alloys, where R is a rare earth. Crystal-field and molecular-field parameters could be unabiguously deduced from the experimental data. The effects of crystal-field level broadening were investigated and demonstrated for Ho. Comparison of the Y-R and Lu-R results makes possible an estimate of the crystal-field parameters in the pure-rare-earth metals

Optical spectroscopy and crystal-field analysis of U{sup 3+}: Ba{sub 2}YCl{sub 7}

Energy Technology Data Exchange (ETDEWEB)

Karbowiak, M.; Mech, A.; Drozdzyndki, J. [Wroclaw Univ., Faculty of Chemistry (Poland); Gajek, Z. [Polish Academy of Sciences, W. Trzebiatowski Institute of Low Temperature and Structure Research, Wroclaw (Poland); Edelstein, N.M. [Lawrence Berkeley National Lab., Chemical Sciences Div., CA (United States)

2002-11-01

High resolution absorption spectra of a U{sup 3+}(0.3%): Ba{sub 2}YCl{sub 7} single crystal were recorded in the 4000-50 000 cm{sup -1} range at 7 K. The observed crystal-field levels were assigned and fit to the parameters of the simplified angular overlap model (AOM) as well as a semi-empirical Hamiltonian representing the combined atomic and one-electron crystal-field interactions. The starting values of the AOM parameters were obtained from ab initio calculations. The analysis of the spectra allowed the assignment of 65 crystal-field levels with a relatively small rms deviation of 25 cm{sup -1} and has shown that the AOM approach can predict quite well the B{sub q}{sup k} crystal-field parameters. The value determined for the crystal-field strength parameter, N{sub v}, corresponds well with those determined for U{sup 3+} in other chloride single crystals. (authors)

Strong ligand field effects of blue phosphorescent mono-cyclometalated iridium(III) complexes

International Nuclear Information System (INIS)

Ham, Ho Wan; Jung, Kyung Yoon; Kim, Young Sik

2010-01-01

A series of mono-cyclometalated blue phosphorescent iridium(III) complexes with two phosphines trans to each other and two cis-ancillary ligands, such as Ir(F 2 Meppy)(PPhMe 2 ) 2 (H)(Cl), [Ir(F 2 Meppy)(PPhMe 2 ) 2 (H)(NCMe)] + and Ir(F 2 Meppy)(PPhMe 2 ) 2 -(H)(CN), [F 2 Meppy = 2-(2',4'-difluorophenyl)-4-methyl-pyridine] were synthesized and studied to tune the phosphorescence wavelength to the deep blue region and to enhance the luminescence efficiencies. We investigate the electron-withdrawing capabilities of ancillary ligands using the DFT and TD-DFT calculations on the ground and excited states of the three complexes to gain insight into the factors responsible for the emission color change and the different luminescence efficiency. Reducing the molecular weight of phosphine ligand with PPhMe 2 leads to a strategy of the efficient deep blue organic light-emitting devices (OLED) by thermal processing instead of the solution processing. The electron-withdrawing difluoro group substituted on the phenyl ring and the cyano strong field ancillary ligand in the trans position to the carbon atom of phenyl ring increased HOMO-LUMO gap and achieved the hypsochromic shift in emission color. As a result, the maximum emission spectra of Ir(F 2 Meppy)(PPhMe 2 ) 2 (H)(Cl), [Ir(F 2 Meppy)(PPhMe 2 ) 2 (H)-(NCMe)] + and Ir(F 2 Meppy)(PPh-Me 2 ) 2 (H)(CN) were in the ranges of 446, 440, 439 nm, respectively.

Far-Field Focus and Dispersionless Anticrossing Bands in Two-Dimensional Photonic Crystals

Directory of Open Access Journals (Sweden)

Xiaoshuang Chen

2007-01-01

Full Text Available We review the simulation work for the far-field focus and dispersionless anticrossing bands in two-dimensional (2D photonic crystals. In a two-dimensional photonic-crystal-based concave lens, the far-field focus of a plane wave is given by the distance between the focusing point and the lens. Strong and good-quality far-field focusing of a transmitted wave, explicitly following the well-known wave-beam negative refraction law, can be achieved. The spatial frequency information of the Bloch mode in multiple Brillouin zones (BZs is investigated in order to indicate the wave propagation in two different regions. When considering the photonic transmission in a 2D photonic crystal composed of a negative phase-velocity medium (NPVM, it is shown that the dispersionless anticrossing bands are generated by the couplings among the localized surface polaritons of the NPVM rods. The photonic band structures of the NPVM photonic crystals are characterized by a topographical continuous dispersion relationship accompanied by many anticrossing bands.

Terminological confusions and problems at the interface between the crystal field Hamiltonians and the zero-field splitting Hamiltonians—Survey of the CF=ZFS confusion in recent literature

Energy Technology Data Exchange (ETDEWEB)

Rudowicz, Czesław, E-mail: crudowicz@zut.edu.pl [Institute of Physics, West Pomeranian University of Technology, Al. Piastów 17, 70-310 Szczecin (Poland); Karbowiak, Mirosław [Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław (Poland)

2014-10-15

The single transition ions in various crystals or molecules as well as the exchange coupled systems (ECS) of transition ions, especially the single molecule magnets (SMM) or molecular nanomagnets (MNM), have been extensively studied in recent decades using electron magnetic resonance (EMR), optical spectroscopy, and magnetic measurements. Interpretation of magnetic and spectroscopic properties of transition ions is based on two physically distinct types of Hamiltonians: the physical crystal field (CF), or equivalently ligand field (LF), Hamiltonians and the effective spin Hamiltonians (SH), which include the zero-field splitting (ZFS) Hamiltonians. Survey of recent literature has revealed a number of terminological confusions and specific problems occurring at the interface between these Hamiltonians (denoted CF (LF)↔SH (ZFS)). Elucidation of sloppy or incorrect usage of crucial notions, especially those describing or parameterizing crystal fields and zero field splittings, is a very challenging task that requires several reviews. Here we focus on the prevailing confusion between the CF (LF) and SH (ZFS) quantities, denoted as the CF=ZFS confusion, which consists in referring to the parameters (or Hamiltonians), which are the true ZFS (or SH) quantities, as purportedly the CF (LF) quantities. The inverse ZFS=CF confusion, which pertains to the cases of labeling the true CF (LF) quantities as purportedly the ZFS quantities, is considered in a follow-up paper. The two reviews prepare grounds for a systematization of nomenclature aimed at bringing order to the zoo of different Hamiltonians. Specific cases of the CF=ZFS confusion identified in the recent textbooks, review articles, and SMM (MNM)- and EMR-related papers are surveyed and the pertinent misconceptions are outlined. The consequences of the terminological confusions go far beyond simple semantic issues or misleading keyword classifications of papers in journals and scientific databases. Serious

Synthesis, crystal structure, and spectroscopic characterization of two new binuclear complexes of manganese(II) and vanadium(V) with dipicolinate ligands containing 2-aminopyrimidinium as a counter cation

Czech Academy of Sciences Publication Activity Database

Tabatabaee, M.; Mahmoodikhah, H.; Ahadiat, G.; Dušek, Michal; Pojarová, Michaela

2013-01-01

Roč. 144, č. 5 (2013), s. 621-626 ISSN 0026-9247 R&D Projects: GA ČR(CZ) GAP204/11/0809 Institutional support: RVO:68378271 Keywords : manganese complex * vanadium complex * dipicolinic ligand * crystal structure Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.347, year: 2013

Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.

Science.gov (United States)

Lawson, D M; Williams, C E; Mitchenall, L A; Pau, R N

1998-12-15

. Periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. Nevertheless, almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. The ligand is bound at the bottom of a deep cleft, which lies at the interface between these two domains. The oxyanion-binding proteins are notable in that they can discriminate between very similar ligands. . Azotobacter vinelandii is unusual in that it possesses two periplasmic molybdate-binding proteins. The crystal structure of one of these with bound ligand has been determined at 1.2 A resolution. It superficially resembles the structure of sulphate-binding protein (SBP) from Salmonella typhimurium and uses a similar constellation of hydrogen-bonding interactions to bind its ligand. However, the detailed interactions are distinct from those of SBP and the more closely related molybdate-binding protein of Escherichia coli. . Despite differences in the residues involved in binding, the volumes of the binding pockets in the A. vinelandii and E. coli molybdate-binding proteins are similar and are significantly larger than that of SBP. We conclude that the discrimination between molybdate and sulphate shown by these binding proteins is largely dependent upon small differences in the sizes of these two oxyanions.

Crystal-field energy level analysis for Nd3+ ions at the low symmetry C1 site in [Nd(hfa)4(H2O)](N(C2H5)4) single crystals

International Nuclear Information System (INIS)

Mech, Agnieszka; Gajek, Zbigniew; Karbowiak, Miroslaw; Rudowicz, Czeslaw

2008-01-01

Optical absorption measurements of Nd 3+ ions in single crystals of [Nd(hfa) 4 (H 2 O)](N(C 2 H 5 ) 4 ) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 2 1 /n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd 3+ (4f 3 ) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C 1 symmetry at the Nd 3+ ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation B kq , admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm -1 . Our approach also allows prediction of the energy levels of Nd 3+ ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low (triclinic) symmetry sites

Crystal-field energy level analysis for Nd(3+) ions at the low symmetry C(1) site in [Nd(hfa)(4)(H(2)O)](N(C(2)H(5))(4)) single crystals.

Science.gov (United States)

Mech, Agnieszka; Gajek, Zbigniew; Karbowiak, Mirosław; Rudowicz, Czesław

2008-09-24

Optical absorption measurements of Nd(3+) ions in single crystals of [Nd(hfa)(4)(H(2)O)](N(C(2)H(5))(4)) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 2(1)/n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd(3+) (4f(3)) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C(1) symmetry at the Nd(3+) ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation B(kq), admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm(-1). Our approach also allows prediction of the energy levels of Nd(3+) ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low (triclinic) symmetry sites.

Crystal-field energy level analysis for Nd3+ ions at the low symmetry C1 site in [Nd(hfa)4(H2O)](N(C2H5)4) single crystals

Science.gov (United States)

Mech, Agnieszka; Gajek, Zbigniew; Karbowiak, Mirosław; Rudowicz, Czesław

2008-09-01

Optical absorption measurements of Nd3+ ions in single crystals of [Nd(hfa)4(H2O)](N(C2H5)4) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 21/n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd3+ (4f3) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C1 symmetry at the Nd3+ ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation Bkq, admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm-1. Our approach also allows prediction of the energy levels of Nd3+ ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low (triclinic) symmetry sites.

A simple model for localized-itinerant magnetic systems: crystal field effects

International Nuclear Information System (INIS)

Iannarella, L.; Silva, X.A. da; Guimarares, A.P.

1989-01-01

The magnetic behavior of a system consisting of localized electrons coupled to conduction electrons and submitted to an axial crystral field at T=0 K is ivestigated within the framework of the molecular field approximation. An analytical ionic magnetic state equation is deduced; it shows how the magnetization depends on the model parameters (exchange, crystal field, band occupation) and external magnetic field. A condition for the onset of spontaneous magnetic order is obtained and the ferro - and paramagnetic phases are studied. This study displays several features of real magnetic systems, including quenching or total suppression of the magnetic moments (depending on the relative value of the crystal field parameter) and exchange enhacement. The relevance of such model for the description of rare-earth intermetallic compounds is discussed. (author) [pt

Moessbauer radiation dynamical diffraction in crystals being subjected to the action of external variable fields

International Nuclear Information System (INIS)

Baryshevskii, V.G.; Skadorov, V.V.

1986-01-01

A dynamical theory is developed of the Moessbauer radiation diffraction by crystals being subjected to an variable external field action. Equations describing the dynamical diffraction by nonstationary crystals are obtained. It is shown that the resonant interaction between Moessbauer radiation and shift field induced in the crystal by a variable external field giving rise to an effective conversion of the incident wave into a wave with changed frequency. (author)

Static magnetic susceptibility, crystal field and exchange interactions in rare earth titanate pyrochlores.

Science.gov (United States)

Malkin, B Z; Lummen, T T A; van Loosdrecht, P H M; Dhalenne, G; Zakirov, A R

2010-07-14

The experimental temperature dependence (T = 2-300 K) of single crystal bulk and site susceptibilities of rare earth titanate pyrochlores R(2)Ti(2)O(7) (R = Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb) is analyzed in the framework of crystal field theory and a mean field approximation. Analytical expressions for the site and bulk susceptibilities of the pyrochlore lattice are derived taking into account long range dipole-dipole interactions and anisotropic exchange interactions between the nearest neighbor rare earth ions. The sets of crystal field parameters and anisotropic exchange coupling constants have been determined and their variations along the lanthanide series are discussed.

On standardization of low symmetry crystal fields

Science.gov (United States)

Gajek, Zbigniew

2015-07-01

Standardization methods of low symmetry - orthorhombic, monoclinic and triclinic - crystal fields are formulated and discussed. Two alternative approaches are presented, the conventional one, based on the second-rank parameters and the standardization based on the fourth-rank parameters. Mainly f-electron systems are considered but some guidelines for d-electron systems and the spin Hamiltonian describing the zero-field splitting are given. The discussion focuses on premises for choosing the most suitable method, in particular on inadequacy of the conventional one. Few examples from the literature illustrate this situation.

Electromagnetic-field amplification in finite one-dimensional photonic crystals

International Nuclear Information System (INIS)

Gorelik, V. S.; Kapaev, V. V.

2016-01-01

The electromagnetic-field distribution in a finite one-dimensional photonic crystal is studied using the numerical solution of Maxwell’s equations by the transfer-matrix method. The dependence of the transmission coefficient T on the period d (or the wavelength λ) has the characteristic form with M–1 (M is the number of periods in the structure) maxima with T = 1 in the allowed band of an infinite crystal and zero values in the forbidden band. The field-modulus distribution E(x) in the structure for parameters that correspond to the transmission maxima closest to the boundaries of forbidden bands has maxima at the center of the structure; the value at the maximum considerably exceeds the incident-field strength. For the number of periods M ~ 50, more than an order of magnitude increase in the field amplification is observed. The numerical results are interpreted with an analytic theory constructed by representing the solution in the form of a linear combination of counterpropagating Floquet modes in a periodic structure.

Ligand identification using electron-density map correlations

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.; Cohn, Judith D.

2007-01-01

An automated ligand-fitting procedure is applied to (F o − F c )exp(iϕ c ) difference density for 200 commonly found ligands from macromolecular structures in the Protein Data Bank to identify ligands from density maps. A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F o − F c )exp(iϕ c ) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule

Near-field probing of photonic crystal directional couplers

DEFF Research Database (Denmark)

Volkov, V. S.; Bozhevolnyi, S. I.; Borel, Peter Ingo

2006-01-01

We report the design, fabrication and characterization of a photonic crystal directional with a size of ~20 x 20 mm2 fabricated in silicon-on-insulator material. Using a scanning near-field optical microscope we demonstrate a high coupling efficiency for TM polarized light at telecom wavelengths....... By comparing the near-field optical images recorded in and after the directional coupler area, the features of light distribution are analyzed. Finally, the scanning near-field optical microscope observations are found to be in agreement with the transmission measurements conducted with the same sample....

The effect of magnetic field on the shape of etch pits of paracetamol crystals

Energy Technology Data Exchange (ETDEWEB)

Ivashchenko, V.E. [Kemerovo State University, Novosibirsk (Russian Federation); Research and Educational Center, Novosibirsk State University (Russian Federation); Boldyrev, V.V.; Shakhtshneider, T.P. [Institute of Solid State Chemistry and Mechanochemistry, RAS, Novosibirsk (Russian Federation); Zakharov, Yu.A.; Krasheninin, V.I. [Kemerovo State University, Novosibirsk (Russian Federation); Ermakov, A.E. [Institute of Physics of Metals, Ural Branch of RAS, Ekaterinburg (Russian Federation)

2002-04-01

In the present study we investigate the effect of magnetic field on the shape of etch pits of the crystals of p-hydroxyacetanilide (paracetamol), which is widely used in pharmacy as antipyretic, antiphlogistic medicine. It was discovered that the magnetic field (H=0.5 T, {tau}=15 min) changes the morphology of etch pits and shifts dislocations in paracetamol crystal. Activation energy of the changes induced by the action of the magnetic field was determined to be 63 kJ/mol, which is comparable with the energy of hydrogen bonds in crystal lattice. (orig.)

Assembly of new polyoxometalate–templated metal–organic frameworks based on flexible ligands

Energy Technology Data Exchange (ETDEWEB)

Li, Na; Mu, Bao; Lv, Lei; Huang, Rudan, E-mail: huangrd@bit.edu.cn

2015-03-15

Four new polyoxometalate(POM)–templated metal–organic frameworks based on flexible ligands, namely, [Cu{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}Mo{sup VI}{sub 11}O{sub 40}O{sub 2})]·8H{sub 2}O(1), [Cu{sup I}{sub 3}Cu{sup II}{sub 3}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}{sub 12}O{sub 34})]·8H{sub 2}O(2), [Ni{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40})(PMo{sup VI}{sub 11}Mo{sup V}O{sub 40}){sub 2}]Cl·6H{sub 2}O(3), [Co{sup II}{sub 3}Co{sup III}{sub 2}(H{sub 2}bib){sub 2}(Hbib){sub 2}(PW{sub 9}O{sub 34}){sub 2}(H{sub 2}O){sub 6}]·6H{sub 2}O(4) (bip=1,3-bis(imidazolyl)propane, bib=1,4-bis(imidazolyl)butane) have been obtained under hydrothermal condition and characterized by single-crystal X-ray diffraction analyses, elemental analyses, and thermogravimetric (TG) analyses. The studies of single crystal X-ray indicate that compounds 1–3 crystallize in the trigonal space group P-3, and compound 4 crystallizes in the triclinic space group P-1. Compounds 1 and 3 represent 3D frameworks, and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals, while compounds 2 and 4 show 3D frameworks by hydrogen bonds. This compounds provide new examples of host–guest compounds based on flexible bis(imidazole) ligands. In addition, the electrochemical property and the catalytic property of compound 1 have also been investigated. - Graphical abstract: Four inorganic–organic hybrid compounds based polyoxometalates (POMs) and flexible ligands, namely, have been obtained under hydrothermal conditions and characterized by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, and thermogravimetric (TG) analyses. Compounds 1–3 are new examples of host–guest compounds based on flexible bis(imidazole) ligands and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals. - Highlights: • Polyoxometalate�

Static magnetic susceptibility, crystal field and exchange interactions in rare earth titanate pyrochlores

NARCIS (Netherlands)

Malkin, B. Z.; Lummen, T. T. A.; van Loosdrecht, P. H. M.; Dhalenne, G.; Zakirov, A. R.

2010-01-01

The experimental temperature dependence (T = 2-300 K) of single crystal bulk and site susceptibilities of rare earth titanate pyrochlores R2Ti2O7 (R = Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb) is analyzed in the framework of crystal field theory and a mean field approximation. Analytical expressions for the

Strong ligand field effects of blue phosphorescent mono-cyclometalated iridium(III) complexes

Energy Technology Data Exchange (ETDEWEB)

Ham, Ho Wan [Department of Information Display, Hongik University, Seoul, 121-791 (Korea, Republic of); Jung, Kyung Yoon [International Design School for Advanced Studies, Hongik University, Seoul 121-791 (Korea, Republic of); Kim, Young Sik, E-mail: youngkim@hongik.ac.k [Department of Information Display, Hongik University, Seoul, 121-791 (Korea, Republic of)

2010-09-01

A series of mono-cyclometalated blue phosphorescent iridium(III) complexes with two phosphines trans to each other and two cis-ancillary ligands, such as Ir(F{sub 2}Meppy)(PPhMe{sub 2}){sub 2}(H)(Cl), [Ir(F{sub 2}Meppy)(PPhMe{sub 2}){sub 2}(H)(NCMe)]{sup +} and Ir(F{sub 2}Meppy)(PPhMe{sub 2}){sub 2}-(H)(CN), [F{sub 2}Meppy = 2-(2',4'-difluorophenyl)-4-methyl-pyridine] were synthesized and studied to tune the phosphorescence wavelength to the deep blue region and to enhance the luminescence efficiencies. We investigate the electron-withdrawing capabilities of ancillary ligands using the DFT and TD-DFT calculations on the ground and excited states of the three complexes to gain insight into the factors responsible for the emission color change and the different luminescence efficiency. Reducing the molecular weight of phosphine ligand with PPhMe{sub 2} leads to a strategy of the efficient deep blue organic light-emitting devices (OLED) by thermal processing instead of the solution processing. The electron-withdrawing difluoro group substituted on the phenyl ring and the cyano strong field ancillary ligand in the trans position to the carbon atom of phenyl ring increased HOMO-LUMO gap and achieved the hypsochromic shift in emission color. As a result, the maximum emission spectra of Ir(F{sub 2}Meppy)(PPhMe{sub 2}){sub 2}(H)(Cl), [Ir(F{sub 2}Meppy)(PPhMe{sub 2}){sub 2}(H)-(NCMe)]{sup +} and Ir(F{sub 2}Meppy)(PPh-Me{sub 2}){sub 2} (H)(CN) were in the ranges of 446, 440, 439 nm, respectively.

Magnetic Field Applications in Semiconductor Crystal Growth and Metallurgy

Science.gov (United States)

Mazuruk, Konstantin; Ramachandran, Narayanan; Grugel, Richard; Curreri, Peter A. (Technical Monitor)

2002-01-01

The Traveling Magnetic Field (TMF) technique, recently proposed to control meridional flow in electrically conducting melts, is reviewed. In particular, the natural convection damping capability of this technique has been numerically demonstrated with the implication of significantly improving crystal quality. Advantages of the traveling magnetic field, in comparison to the more mature rotating magnetic field method, are discussed. Finally, results of experiments with mixing metallic alloys in long ampoules using TMF is presented

The diluted tri-dimensional spin-one Ising model with crystal field interactions

International Nuclear Information System (INIS)

Saber, M.

1988-09-01

3D spin-one Ising models with nearest-neighbour ferromagnetic interactions with crystal-field exhibit tricritical behaviour. A new method that applies to a wide class of random systems is used to study the influence of site and bond dilution on this behaviour. We have calculated temperature-crystal-field-concentration phase diagrams and determined, in particular, the influence of dilution on the zero temperature tricritical temperature. (author). 10 refs, 8 figs

Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

International Nuclear Information System (INIS)

Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei

2015-01-01

Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H_2ndc) or 4,4′-(hydroxymethylene)dibenzoic acid (H_2hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd_2(2,6-ndc)_2(bpp)(DMF)]·2DMF (1) and [Cd_3(hmdb)_3(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional ‘Lucky Clover’ shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process. - Graphical abstract: Compound 1 exhibits a 3D self-penetrating 6-connected framework based on dinuclear cluster, and 2 displays an infinite 3D ‘Lucky Clover’ shape (2,10)-connected network based on the trinuclear cluster. The flexible 1,3-bis(4-pyridyl)propane ligand displays different conformations in 1 and 2, which successfully controlled by size-matching mixed ligands during the self-assembly process.

Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

Energy Technology Data Exchange (ETDEWEB)

Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei, E-mail: hanlei@nbu.edu.cn

2015-12-15

Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H{sub 2}ndc) or 4,4′-(hydroxymethylene)dibenzoic acid (H{sub 2}hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd{sub 2}(2,6-ndc){sub 2}(bpp)(DMF)]·2DMF (1) and [Cd{sub 3}(hmdb){sub 3}(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional ‘Lucky Clover’ shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process. - Graphical abstract: Compound 1 exhibits a 3D self-penetrating 6-connected framework based on dinuclear cluster, and 2 displays an infinite 3D ‘Lucky Clover’ shape (2,10)-connected network based on the trinuclear cluster. The flexible 1,3-bis(4-pyridyl)propane ligand displays different conformations in 1 and 2, which successfully controlled by size-matching mixed ligands during the self-assembly process.

A thermal model for czochralski silicon crystal growth with an axial magnetic field

Science.gov (United States)

Hjellming, L. N.

1990-07-01

This paper presents a thermal model for molten silicon in a Czochralski crystal puller system with an applied uniform axial magnetic field. The melt depth is treated as continually decreasing, which affects the thermal environment of the melt and crystal. The radiative heat loss and the input heat flux are treated as functions of time, with a constraint placed on the heat lost to the crystal from the melt. As the melt motion reaches a steady state rapidly, the temperature and flow fields are treated as instantaneously steady at each melt depth. The heat transport is a mixture of conduction and convection, and by considering the crystal and crucible to be rotating with the same angular velocity, the flows driven by buoyancy and thermocapillarity are isolated and provide the convective heat transport in the melt for the range of magnetic field strengths 0.2 ≤ B ≤ 1.0T.

Synthesis of the hexaamine ligand 1,4,7-tris(3-aminopropyl)-1,4,7-triazacyclononane: Reactivity and x-ray crystal structures of the nickel(II) and cobalt(III) complexes

International Nuclear Information System (INIS)

Bushnell, G.W.; Fortier, D.G.; McAuley, A.

1988-01-01

The synthesis of the ligand 1,4,7-tris(3-aminopropyl)-1,4,7-triazacyclononane(tapacn) can be achieved by the reaction of 1,4,7-triazacyclononane with an excess of acetonitrile, followed by reduction of the nitrile with sodium metal in toluene. Halide salts of the cobalt(III)(complex A) and nickel(II)(complex B) ions have been prepared and examined by using x-ray crystallography. The crystal structures are reported. The 13 C NMR spectrum of the dismagnetic d 6 Co(III) complex ion is reported. A discussion of the two ligand structures deals with the ligand opening and with trigonal twist angle as related to metal ion size and mechanism for redox processes of the complex. 45 refs., 6 figs., 9 tabs

Crystal Growth of High-Quality Protein Crystals under the Presence of an Alternant Electric Field in Pulse-Wave Mode, and a Strong Magnetic Field with Radio Frequency Pulses Characterized by X-ray Diffraction

Directory of Open Access Journals (Sweden)

Adela Rodríguez-Romero

2017-06-01

Full Text Available The first part of this research was devoted to investigating the effect of alternate current (AC using four different types of wave modes (pulse-wave at 2 Hz on the crystal growth of lysozyme in solution. The best results, in terms of size and crystal quality, were obtained when protein crystals were grown under the influence of electric fields in a very specific wave mode (“breathing” wave, giving the highest resolution up to 1.34 Å in X-ray diffraction analysis compared with controls and with those crystals grown in gel. In the second part, we evaluated the effect of a strong magnetic field of 16.5 Tesla combined with radiofrequency pulses of 0.43 μs on the crystal growth in gels of tetragonal hen egg white (HEW lysozyme. The lysozyme crystals grown, both in solution applying breathing-wave and in gel under the influence of this strong magnetic field with pulses of radio frequencies, produced the larger-in-size crystals and the highest resolution structures. Data processing and refinement statistics are very good in terms of the resolution, mosaicity and Wilson B factor obtained for each crystal. Besides, electron density maps show well-defined and distinctly separated atoms at several selected tryptophan residues for the crystal grown using the “breathing wave pulses”.

An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

International Nuclear Information System (INIS)

Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

2016-01-01

An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

GPCR crystal structures: Medicinal chemistry in the pocket.

Science.gov (United States)

Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Löber, Stefan

2015-07-15

Recent breakthroughs in GPCR structural biology have significantly increased our understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystallized in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand binding pockets in GPCRs. In this review, we summarise the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity or efficacy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels.

Science.gov (United States)

Lomash, Suvendu; Chittori, Sagar; Brown, Patrick; Mayer, Mark L

2013-03-05

AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine, and phenylalanine, which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate, and serine. AvGluR1 LBD crystal structures reveal an unusual scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, whereas in the alanine, methionine, and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl(-) lowers affinity for these ligands but not for glutamate or aspartate nor for phenylalanine, which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure-based studies on iGluR-ligand interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Near-field characterization of photonic crystal Y-splitters

DEFF Research Database (Denmark)

Volkov, V. S.; Bozhevolnyi, S. I.; Borel, Peter Ingo

2005-01-01

A scanning near-field optical microscope (SNOM) is used to directly map the propagation of light in a specially designed 50/50 photonic crystal (PC) Y-splitter fabricated on silicon-on-insulator (SOI) wafers. SNOM images are obtained for TE- and TM-polarized light in the wavelength range 1425...

Crystal-field-modulated magnon squeezing states in a ferromagnet

International Nuclear Information System (INIS)

Peng Feng

2003-01-01

The magnon squeezing states in some magnetic crystals allow a reduction in the quantum fluctuations of the spin component to below the zero-point quantum noise level of the coherent magnon states. It is known that there are the magnon squeezing states in an antiferromagnet. However, their generating mechanism is not suitable for the ferromagnet. In this paper, we discuss the possibility of generating the magnon squeezing states in a ferromagnet, and discuss the effect of the crystal field on the magnon squeezing states

The Hirshfeld surface of three new isonicotinylhydrazine co-crystals: Comparison of hydrogen bonds and crystal structures

Science.gov (United States)

Cunha, Mariana S.; Ribeiro, Carlos Eduardo P.; Corrêa, Charlane C.; Diniz, Renata

2017-12-01

The influence of the change of aromatic acids ligand in the interactions with isonicotinylhydrazine (ISO) molecule in three new co-crystals has been investigated as well as a study of the hydrogen bonds formed between the ligands through Hirshfeld surface analysis and fingerprint plots. These analyses are extremely sensitive to the chemical environment of the molecule and are unique to a particular molecule so they can identify the differences between the crystal packing in the solid state. Although the conformation of ISO molecule being practically identical in all three compounds and the interactions mainly involve the Nsbnd H⋯O and Osbnd H⋯N type, the fingerprint plots only for ISO molecule in the three compounds are different and exhibit the influence in this molecule due to the modification of the functional groups of ligands.

Analyses of crystal field and exchange interaction of Dy3Ga5O12 under extreme conditions

International Nuclear Information System (INIS)

Wang Wei; Qi Xin; Yue Yuan

2011-01-01

This paper theoretically investigates the effects of crystal field and exchange interaction field on magnetic properties in dysprosium gallium garnet under extreme conditions (low temperatures and high magnetic fields) based on quantum theory. Here, five sets of crystal field parameters are discussed and compared. It demonstrates that, only considering the crystal field effect, the experiments can not be successfully explained. Thus, referring to the molecular field theory, an effective exchange field associated with the Dy—Dy exchange interaction is further taken into account. Under special consideration of crystal field and the exchange interaction field, it obtains an excellent agreement between the theoretical results and experiments, and further confirms that the exchange interaction field between rare-earth ions has great importance to magnetic properties in paramagnetic rare-earth gallium garnets. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Crystal and molecular structure of mixed-ligand calcium, strontium and barium complexes with dipivaloylmethane and 1,10-phenanthroline of composition MDpm2Phen2

International Nuclear Information System (INIS)

Soboleva, I.E.; Troyanov, S.I.; Kuz'mina, N.P.; Ivanov, V.K.; Martynenko, L.I.; Struchkov, Yu.T.; AN SSSR, Moscow

1995-01-01

Mixed-ligand complexes (MLC) of MDpm P hen 2 composition were prepared for the first time in result of interaction of calcium and strontium dipivaloylmethane (MDpm 2 ) with 1,10-phenanthroline (Phen · H 2 O) in benzene-acetonitrile mixture. Method of x-ray diffraction analysis was used to establish, that they were crystallized in monoclinic syngony with C2/c space group for CaDpm 2 Phen 2 and P2 1 /n space group for SrDpm 2 Phen 2 and were composed of monomeric molecules. The central atom (Ca,Sr) coordinates 4 oxygen atoms of two dipivaloylmethane ligands and 4 nitrogen atoms of two 1,10-phenanthroline molecules. Correlation with x-ray diffraction data for similar MZC of barium (BaDpm 2 Phen 2 ) was conducted. 4 refs.; 4 tabs

Absorption measurement s in InSe single crystal under an applied electric field

International Nuclear Information System (INIS)

Ates, A.; Guerbulak, B.; Guer, E.; Yildirim, T.; Yildirim, M.

2002-01-01

InSe single crystal was grown by Bridgman-Stockberger method. Electric field effect on the absorption measurements have been investigated as a function of temperature in InSe single crystal. The absorption edge shifted towards longer wavelengths and decreased of intensity in absorption spectra under an electric field. Using absorption measurements, Urbach energy was calculated under an electric field. Applied electric field caused a increasing in the Urbach energy. At 10 K and 320 K, the first exciton energies were calculated as 1.350 and 1.311 eV for zero voltage and 1.334 and 1.301 eV for electric field respectively

Field-induced optically isotropic state in bent core nematic liquid crystals: unambiguous proof of field-induced optical biaxiality

International Nuclear Information System (INIS)

Elamain, Omaima; Komitov, Lachezar; Hegde, Gurumurthy; Fodor-Csorba, Katalin

2013-01-01

The behaviour of bent core (BC) nematic liquid crystals was investigated under dc applied electric field. The optically isotropic state of a sample containing BC nematic was observed under application of low dc electric fields. The quality of the dark state when the sample was inserted between two crossed polarizers was found to be superb and it did not change when rotating the sample between the polarizers. The coupling between the net molecular dipole moment and the applied dc electric field was considered as the origin of the out-of-plane switching of the BC molecules resulting in switching from the field-off bright state to the field-on dark state. The field-induced optically isotropic state is an unambiguous proof of the field-induced biaxiality in the BC nematic liquid crystal. A simple model explaining the appearance of the isotropic optical state in BC nematics and the switching of the sample slow axis between three mutually orthogonal directions under dc applied electric field is proposed. (paper)

Ligand field theory and the origin of life as an emergent feature of the periodic table of elements.

Science.gov (United States)

Morowitz, Harold J; Srinivasan, Vijayasarathy; Smith, Eric

2010-08-01

The assumption that all biological catalysts are either proteins or ribozymes leads to an outstanding enigma of biogenesis-how to determine the synthetic pathways to the monomers for the efficient formation of catalytic macromolecules in the absence of any such macromolecules. The last 60 years have witnessed chemists developing an understanding of organocatalysis and ligand field theory, both of which give demonstrable low-molecular-weight catalysts. We assume that transition-metal-ligand complexes are likely to have occurred in the deep ocean trenches by the combination of naturally occurring oceanic metals and ligands synthesized from the emergent CO(2), H(2), NH(3), H(2)S, and H(3)PO(4). We are now in a position to investigate experimentally the metal-ligand complexes, their catalytic function, and the reaction networks that could have played a role in the development of metabolism and life itself.

Crystal-field magnetic anisotropy of dilute dysprosium or erbium in yttrium single crystals

DEFF Research Database (Denmark)

Høg, J.; Touborg, P.

1974-01-01

Magnetization measurements have been performed between 1.3 and 300 K in fields up to 50 × 105 A/m in the a, b, and c directions of hcp crystals of pure Y and Y doped with 0.14-at.% Dy or 0.14-at.% Er, using the Faraday method and a vibrating-sample method. The characteristic behavior of both...

Crystallization of inorganic salts from aqueous solutions in a microwave field

International Nuclear Information System (INIS)

Kochetkov, S. E.; Kuznetsov, V. A.; Lyashenko, A. V.; Bakshutov, V. S.

2006-01-01

The crystallization of some inorganic salts (KH 2 PO 4 , NaCl, Sr(NO 3 ) 2 , KNO 2 , Ca(OH) 2 ) by the thermal-gradient (with decreasing temperature) and solvent-evaporation methods using microwave heating of solutions is investigated. It is established that the growth rates of single crystals in a microwave field are an order of magnitude higher than obtained in other known techniques at comparable crystallization temperatures and supersaturations. For example, the growth rate of prismatic faces {100} of KH 2 PO 4 crystals is as high as 11 mm/day at supersaturations of ∼1.2%. The results obtained are discussed in the context of the effect of microwave radiation on the adsorption surface layers of crystals. Fine-grained phases of the salts under study are obtained by evaporation of the solvent

Strong ligand field effects of blue phosphorescent Ir(III) complexes with phenylpyrazole and phosphines.

Science.gov (United States)

Park, Se Won; Ham, Ho Wan; Kim, Young Sik

2012-04-01

In the paper, we describe new Ir complexes for achieving efficient blue phosphorescence. New blue-emitting mixed-ligand Ir complexes comprising one cyclometalating, two phosphines trans to each other such as Ir(dppz)(PPh3)2(H)(L) (Ll= Cl, NCMe+, CN), [dppz = 3,5-Diphenylpyrazole] were synthesized and studied to tune the phosphorescence wavelength to the deep blue region and to enhance the luminescence efficiencies. To gain insight into the factors responsible for the emission color change and the variation of luminescence efficiency, we investigate the electron-withdrawing capabilities of ancillary ligands using DFT and TD-DFT calculations on the ground and excited states of the complexes. To achieve deep blue emission and increase the emission efficiency, (1) we substitute the phenyl group on the 3-position of the pyrazole ring that lowers the triplet energy enough that the quenching channel is not thermally accessible and (2) change the ancillary ligands coordinated to iridium atom to phosphine and cyano groups known as very strong field ligands. Their inclusion in the coordination sphere can increase the HOMO-LUMO gap to achieve the hypsochromic shift in emission color and lower the HOMO and LUMO energy level, which causes a large d-orbital energy splitting and avoids the quenching effect to improve the luminescence efficiency. The maximum emission spectra of Ir(dppz)(PPh3)2(H)(CI) and Ir(dppz)(PPh3)2(H)(CN) were in the ranges of 439, 432 nm, respectively.

A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

KAUST Repository

Li, Huaifeng

2014-12-01

Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands\\' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

KAUST Repository

Li, Huaifeng; Zheng, Bin; Huang, Kuo-Wei

2014-01-01

Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

Effect of grain boundary on the field-effect mobility of microrod single crystal organic transistors.

Science.gov (United States)

Kim, Jaekyun; Kang, Jingu; Cho, Sangho; Yoo, Byungwook; Kim, Yong-Hoon; Park, Sung Kyu

2014-11-01

High-performance microrod single crystal organic transistors based on a p-type 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) semiconductor are fabricated and the effects of grain boundaries on the carrier transport have been investigated. The spin-coating of C8-BTBT and subsequent solvent vapor annealing process enabled the formation of organic single crystals with high aspect ratio in the range of 10 - 20. It was found that the organic field-effect transistors (OFETs) based on these single crystals yield a field-effect mobility and an on/off current ratio of 8.04 cm2/Vs and > 10(5), respectively. However, single crystal OFETs with a kink, in which two single crystals are fused together, exhibited a noticeable drop of field-effect mobility, and we claim that this phenomenon results from the carrier scattering at the grain boundary.

Variable valence ion spectra in a crystal field

International Nuclear Information System (INIS)

Ghiordanescu, V.

1979-01-01

Using the Cadmium chloride as a host lattice, the optical spectra and RES of Mnsup(2+) were studied and the following results were obtained: a) By controlled dopings, the absorbtion and excitation spectra of ion Mnsup(2+) in CdCl 2 within the concentration range between 0.01 M and 25 M were plotted. Thus, the band structure for small concentrations was pointed out to differ from the structure observed for high concentrations. In the literature, this effect has not been observed on similar compounds, due to the small intensity values of the absorbtion spectra. b) Considering that for CdCl 2 :Mnsup(2+) 0.1 M, the optical spectra correspond to the isolated ion in the lattice, the energy levels were evaluated using electrostatic and spin-orbit terms in a perturbation calculation of the crystal field approximation. c) The calculation of parameter a which represents the effect of the cubic field in the spjn Hamiltonian of Mnsup(2+), is closer to the experjmental value -0.5.10 -4 cm -1 of the crystal field Dq and zeta parameters are used, respectively, parameters of the spin-orbit interaction obtained under b). d) The coupling effects of spins into more concentrated crystals with Mn 2+ are a function of temperature. The emjssion yield was given a quasi-cantitative evaluation in thjs paper as a function of temperature and concentratjon on the basis of which the isolated centers of Mn 2+ were found to display ectra whose intensity vary with temperature according to the Laporte forbidden transitions and spin rule theory, and the clusters including Mn 2+ - Mn 2+ pairs provide spectra whose intensity vary with the strength of the spin-spin coupling. (author)

Spin-Orbit Qubits of Rare-Earth-Metal Ions in Axially Symmetric Crystal Fields

Science.gov (United States)

Bertaina, S.; Shim, J. H.; Gambarelli, S.; Malkin, B. Z.; Barbara, B.

2009-11-01

Contrary to the well-known spin qubits, rare-earth-metal qubits are characterized by a strong influence of crystal field due to large spin-orbit coupling. At low temperature and in the presence of resonance microwaves, it is the magnetic moment of the crystal-field ground state which nutates (for several μs) and the Rabi frequency ΩR is anisotropic. Here, we present a study of the variations of ΩR(H→0) with the magnitude and direction of the static magnetic field H→0 for the odd Er167 isotope in a single crystal CaWO4:Er3+. The hyperfine interactions split the ΩR(H→0) curve into eight different curves which are fitted numerically and described analytically. These “spin-orbit qubits” should allow detailed studies of decoherence mechanisms which become relevant at high temperature and open new ways for qubit addressing using properly oriented magnetic fields.

Photodegradation of luminescence in organic-ligand-capped Eu3+:LaF3 nano-particles

International Nuclear Information System (INIS)

King, Gavin G. G.; Taylor, Luke R.; Longdell, Jevon J.; Clarke, David J.; Quilty, J. W.

2014-01-01

The luminescence from europium doped lanthanum trifluoride (Eu 3+ :LaF 3 ) nano-crystals can be greatly enhanced by capping with β-diketonate organic ligands. Here, we report on photo-stability measurements for the case of nano-crystals capped with thenoyltrifluroacetone (TTA) and compared with those capped with an inactive ligand, oleic acid. With exposure to UV pump light, we observed significant decrease in fluorescence and change in emission spectrum of the TTA-capped nano-particles whilst the fluorescence lifetime remained approximately constant. After a dose of order 70 kJ cm −2 , the luminescence level was similar to that of oleic acid capped nano-crystals. We discuss possible mechanisms

Crystal structures of bis[2-(pyridin-2-ylphenyl-κ2N,C1]rhodium(III complexes containing an acetonitrile or monodentate thyminate(1− ligand

Directory of Open Access Journals (Sweden)

Mika Sakate

2016-04-01

Full Text Available The crystal structures of bis[2-(pyridin-2-ylphenyl]rhodium(III complexes with the metal in an octahedral coordination containing chloride and acetonitrile ligands, namely (OC-6-42-acetonitrilechloridobis[2-(pyridin-2-ylphenyl-κ2N,C1]rhodium(III, [RhCl(C11H8N2(CH3CN] (1, thyminate(1− and methanol, namely (OC-6-42-methanol(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ido-κN1bis[2-(pyridin-2-ylphenyl-κ2N,C1]rhodium(III, [Rh(C11H8N2(C5H5N2O2(CH3OH]·CH3OH·0.5H2O (2, and thyminate(1− and ethanol, namely (OC-6-42-ethanol(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ido-κN1bis[2-(pyridin-2-ylphenyl-κ2N,C1]rhodium(III, [Rh(C11H8N2(C5H5N2O2(C2H5OH]·C2H5OH (3, are reported. The acetonitrile complex, 1, is isostructural with the IrIII analog. In complexes 2 and 3, the monodeprotonated thyminate (Hthym− ligand coordinates to the RhIII atom through the N atom, and the resulting Rh—N(Hthym bond lengths are relatively long [2.261 (2 and 2.252 (2 Å for 2 and 3, respectively] as compared to the Rh—N bonds in the related thyminate complexes. In each of the crystals of 2 and 3, the complexes are linked via a pair of intermolecular N—H...O hydrogen bonds between neighbouring Hthym− ligands, forming an inversion dimer. A strong intramolecular O—H...O hydrogen bond between the thyminate(1− and alcohol ligands in mutually cis positions to each other is also observed.

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

Science.gov (United States)

Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

2009-10-01

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

Origin of gigantic magnetostriction and crystal field effects in terbium dititanate

International Nuclear Information System (INIS)

Aleksandrov, I.V.; Lidskij, B.V.; Mamsurova, L.G.

1985-01-01

The temperature and magnetic field dependences of the magnetostriction and magnetization and the temperature dependences of the magnetic susceptibility, specific heat and lattice parameter are investigated experimentally in a broad range of temperature and field strength for polycrystalline and single crystal Tb 2 Ti 2 O 7 . A conclusion is drawn regarding the structure of the energy levels of Tb 3+ in Tb 2 Ti 2 O 7 . A qualitative and quantitative explanation of all observed magnetic effects, and in particular of gigantic magnetostriction in Tb 2 Ti 2 O 7 , is presented which is based on the crystal field theory. It is shown that the huge magnitude of the magnetostriction in terbium dititanate is due to the specificity of the energy spectrum of Tb 3+ in Tb 2 Ti 2 O 7

Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration.

Directory of Open Access Journals (Sweden)

Vibha Gupta

Full Text Available Mycobacterium tuberculosis (Mtb, a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC, an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA. The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In

Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol.

Science.gov (United States)

Fili, S; Valmas, A; Norrman, M; Schluckebier, G; Beckers, D; Degen, T; Wright, J; Fitch, A; Gozzo, F; Giannopoulou, A E; Karavassili, F; Margiolaki, I

2015-09-01

This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50-8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.

Dual gauge field theory of quantum liquid crystals in three dimensions

International Nuclear Information System (INIS)

Beekman, Aron J.; Nissinen, Jaakko; Wu, Kai; Zaanen, Jan

2017-01-01

The dislocation-mediated quantum melting of solids into quantum liquid crystals is extended from two to three spatial dimensions, using a generalization of boson-vortex or Abelian-Higgs duality. Dislocations are now Burgers-vector-valued strings that trace out worldsheets in space-time while the phonons of the solid dualize into two-form (Kalb-Ramond) gauge fields. We propose an effective dual Higgs potential that allows for restoring translational symmetry in either one, two, or three directions, leading to the quantum analogues of columnar, smectic, or nematic liquid crystals. In these phases, transverse phonons turn into gapped, propagating modes, while compressional stress remains massless. Rotational Goldstone modes emerge whenever translational symmetry is restored. Lastly, we also consider the effective electromagnetic response of electrically charged quantum liquid crystals, and find among other things that as a hard principle only two out of the possible three rotational Goldstone modes are observable using propagating electromagnetic fields.

Dual gauge field theory of quantum liquid crystals in three dimensions

Science.gov (United States)

Beekman, Aron J.; Nissinen, Jaakko; Wu, Kai; Zaanen, Jan

2017-10-01

The dislocation-mediated quantum melting of solids into quantum liquid crystals is extended from two to three spatial dimensions, using a generalization of boson-vortex or Abelian-Higgs duality. Dislocations are now Burgers-vector-valued strings that trace out worldsheets in space-time while the phonons of the solid dualize into two-form (Kalb-Ramond) gauge fields. We propose an effective dual Higgs potential that allows for restoring translational symmetry in either one, two, or three directions, leading to the quantum analogues of columnar, smectic, or nematic liquid crystals. In these phases, transverse phonons turn into gapped, propagating modes, while compressional stress remains massless. Rotational Goldstone modes emerge whenever translational symmetry is restored. We also consider the effective electromagnetic response of electrically charged quantum liquid crystals, and find among other things that as a hard principle only two out of the possible three rotational Goldstone modes are observable using propagating electromagnetic fields.

Metal–organic coordination architectures of tetrazole heterocycle ligands bearing acetate groups: Synthesis, characterization and magnetic properties

International Nuclear Information System (INIS)

Hu, Bo-Wen; Zheng, Xiang-Yu; Ding, Cheng

2015-01-01

Two new coordination complexes with tetrazole heterocycle ligands bearing acetate groups, [Co(L) 2 ] n (1) and [Co 3 (L) 4 (N 3 ) 2 ·2MeOH] n (2) (L=tetrazole-1-acetate) have been synthesized and structurally characterized. Single crystal structure analysis shows that the cobalt-complex 1 has the 3D 3,6-connected (4 2 .6) 2 (4 4 .6 2 .8 8 .10)-ant topology. By introducing azide in this system, complex 2 forms the 2D network containing the [Co 3 ] units. And the magnetic properties of 1 and 2 have been studied. - Graphical abstract: The synthesis, crystal structure, and magnetic properties of the new coordination complexes with tetrazole heterocycle ligands bearing acetate groups are reported. - Highlights: • Two novel Cobalt(II) complexes with tetrazole acetate ligands were synthesized. • The magnetic properties of two complexes were studied. • Azide as co-ligand resulted in different structures and magnetic properties. • The new coordination mode of tetrazole acetate ligand was obtained.

Magnetic response of localized spins coupled to itinerant electrons in an inhomogeneous crystal field

International Nuclear Information System (INIS)

Iannarella, L.; Guimaraes, A.P.; Silva, X.A. da.

1990-01-01

The magnetic behavior at T = O K of a system consisting of conduction electrons coupled to localized electrons, the latter submitted to an inhomogeneous crystal field distribution, is studied. The study implies that the inhomogeneity of the crystal field attenuates the quenching effects. The model is interesting to the study of disordered rare-earth intermetallic compounds. (A.C.A.S.) [pt

Effect of pressure on the crystal field splitting in rare earth pnictides and chalcogenides

International Nuclear Information System (INIS)

Schirber, J.E.; Weaver, H.T.

1978-01-01

The experimental situation for the pressure dependence of the crystal field of praseodymium pnictides and chalcogenides is reviewed and compared with the predictions of the point charge model. The problem of separating exchange and crystal field contributions from the measured NMR frequency shift or susceptibility measurements is discussed as well as problems explaining these effects with conduction electron related models

Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

Directory of Open Access Journals (Sweden)

Tino Wolter

Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

Neutron Crystal-Field Spectroscopy and Susceptibility in ErcY1-cA1

DEFF Research Database (Denmark)

Heer, H.; Furrer, A.; Walker, E.

1974-01-01

Inelastic neutron scattering experiments and susceptibility measurements have been carried out on polycrystalline ErcY1-cAl2. A least-squares fitting procedure has been applied to the neutron data which favours four sets of crystal-field parameters. The results are compared with the measured...... susceptibility and other bulk magnetic properties. From this it is concluded that the crystal-field parameters x=-0.54 and W=-0.018 meV are the most probable ones....

Field-controllable Spin-Hall Effect of Light in Optical Crystals: A Conoscopic Mueller Matrix Analysis.

Science.gov (United States)

Samlan, C T; Viswanathan, Nirmal K

2018-01-31

Electric-field applied perpendicular to the direction of propagation of paraxial beam through an optical crystal dynamically modifies the spin-orbit interaction (SOI), leading to the demonstration of controllable spin-Hall effect of light (SHEL). The electro- and piezo-optic effects of the crystal modifies the radially symmetric spatial variation in the fast-axis orientation of the crystal, resulting in a complex pattern with different topologies due to the symmetry-breaking effect of the applied field. This introduces spatially-varying Pancharatnam-Berry type geometric phase on to the paraxial beam of light, leading to the observation of SHEL in addition to the spin-to-vortex conversion. A wave-vector resolved conoscopic Mueller matrix measurement and analysis provides a first glimpse of the SHEL in the biaxial crystal, identified via the appearance of weak circular birefringence. The emergence of field-controllable fast-axis orientation of the crystal and the resulting SHEL provides a new degree of freedom for affecting and controlling the spin and orbital angular momentum of photons to unravel the rich underlying physics of optical crystals and aid in the development of active photonic spin-Hall devices.

Scanning near-field optical microscopy of quantum dots in photonic crystal cavities

Energy Technology Data Exchange (ETDEWEB)

Skacel, Matthias; Fiore, Andrea [COBRA Research Institute, Technical University Eindhoven, Den Dolech 2, 5600 MB Eindhoven (Netherlands); Prancardi, Marco; Gerardino, Annamaria [Institute of Photonics and Nanotechnology, CNR, via del Cineto Romano 42, 00156 Roma (Italy); Alloing, Blandine; Li Lianhe, E-mail: m.s.skacel@tue.n [Institute of Photonics and Quantum Electronics, EPFL, CH-1015 Lausanne (Switzerland)

2010-09-01

Nanophotonic devices are of major interest for research and future quantum communication applications. Due to their nanometer feature size the resolution limit of far-field microscopy poses a limitation on the characterization of their optical properties. A method to overcome the resolution limit is the Scanning Near-Field Optical Microscope (SNOM). By approaching a fiber tip into the close vicinity of the sample the optical emission in the near-field regime is collected. This way of collecting the light is not affected by the diffraction limit. We employ a low temperature SNOM to investigate the photoluminescence of InAs QDs emitting at 1300nm wavelength embedded in photonic crystal cavities. At each location of an image scan the tip is stopped and a spectrum is acquired. We then plot maps of the photoluminescence for each wavelength. With this instrument it is now possible to directly observe the coupling of QDs to photonic crystal cavities both spectrally and spatially. We show first results of photoluminescence mapping of InAs QDs in photonic crystal cavities.

Tricritical behavior in the diluted transverse spin-1 Ising model with a longitudinal crystal field

International Nuclear Information System (INIS)

Htoutou, K.; Oubelkacem, A.; Ainane, A.; Saber, M.

2005-01-01

The transverse spin-1 Ising model with a longitudinal crystal field exhibits a tricritical behavior. Within the effective field theory with a probability distribution technique that accounts for the self-spin correlations, we have studied the influence of site dilution on this behavior and have calculated the temperature-transverse field-longitudinal crystal field-concentration phase diagrams and determined, in particular, the influence of the concentration of magnetic atoms c on the tricritical behavior. We have found that the tricritical point appears for large values of the concentration c of magnetic atoms and disappears with the increase in dilution (small values of c). Results for square lattice are calculated numerically and some interesting results are obtained. In certain ranges of values of the strength of the longitudinal crystal field D/J when it becomes sufficiently negative, we found re-entrant phenomenon, which disappears with increase in the value of the strength of the transverse field

Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatecobalt(II

Directory of Open Access Journals (Sweden)

Mouhamadou Birame Diop

2016-01-01

Full Text Available The structure of the mononuclear title complex, [{(H3CS2C=NC[triple-bond] N}2CoCl2], consists of a CoII atom coordinated in a distorted tetrahedral manner by two Cl− ligands and the terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515 (su? Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.

Organic-inorganic hybrid perovskite quantum dots with high PLQY and enhanced carrier mobility through crystallinity control by solvent engineering and solid-state ligand exchange.

Science.gov (United States)

Woo Choi, Jin; Woo, Hee Chul; Huang, Xiaoguang; Jung, Wan-Gil; Kim, Bong-Joong; Jeon, Sie-Wook; Yim, Sang-Youp; Lee, Jae-Suk; Lee, Chang-Lyoul

2018-05-22

The photoluminescence quantum yield (PLQY) and charge carrier mobility of organic-inorganic perovskite QDs were enhanced by the optimization of crystallinity and surface passivation as well as solid-state ligand exchange. The crystallinity of perovskite QDs was determined by the Effective solvent field (Esol) of various solvents for precipitation. The solvent with high Esol could more quickly countervail the localized field generated by the polar solvent, and it causes fast crystallization of the dissolved precursor, which results in poor crystallinity. The post-ligand adding process (PLAP) and post-ligand exchange process (PLEP) increase the PLQY of perovskite QDs by reducing non-radiative recombination and the density of surface defect states through surface passivation. Particularly, the post ligand exchange process (PLEP) in the solid-state improved the charge carrier mobility of perovskite QDs in addition to the PLQY enhancement. The ligand exchange with short alkyl chain length ligands could improve the packing density of perovskite QDs in films by reducing the inter-particle distance between perovskite QDs. The maximum hole mobility of 6.2 × 10-3 cm2 V-1 s-1, one order higher than that of pristine QDs without the PLEP, is obtained at perovskite QDs with hexyl ligands. By using PLEP treatment, compared to the pristine device, a 2.5 times higher current efficiency in perovskite QD-LEDs was achieved due to the improved charge carrier mobility and PLQY.

Crystal structure of mixed ligand compound [HgPhen{(C2H5)2NCS2}2] and character of intermolecular interaction in the structures of [MPhen{(C2H5)2NCS2}2] (M = Zn, Cd, Hg) complexes

International Nuclear Information System (INIS)

Klevtsova, R.F.; Glinskaya, L.A.; Zemskova, S.M.; Larionov, S.V.

2002-01-01

Monocrystals of mixed ligand complex [HgPhen(Et 2 NCS 2 ) 2 ] (Phen = 1, 10-phenanthroline) have been prepared and by the method of X-ray diffraction its crystal structure has been determined. The structure of mercury complex has been compared with structures of previously studied cadmium and zinc complexes similar in composition. The character of interaction between molecules of cadmium, zinc, mercury mixed ligand complexes and ways of their packing have been considered. It is shown that the structure of the complexes presents a molecular group assembled from two monomeric compounds at the expense of interaction between heterocyclic ligands contained in the mixed ligand complexes [ru

Synthesis and crystal structure of the rhodium(I) cyclooctadiene complex with bis(3-tert-butylimidazol-2-ylidene)borate ligand

Energy Technology Data Exchange (ETDEWEB)

Chen, F.; Shao, K.-J.; Xiao, Y.-C.; Pu, X.-J.; Zhu, B., E-mail: zhubao-999@126.com [Affiliated Wuxi Peoples Hospital, Department of Nuclear Medicine, Nanjing Medical University (China); Jiang, M.-J., E-mail: jmj16888@126.com [Affiliated Wuxi Peoples Hospital, Department of Clinical Laboratory Science, Nanjing Medical University (China)

2015-12-15

The rhodium(I) cyclooctadiene complex with the bis(3-tert-butylimidazol-2-ylidene)borate ligand [H{sub 2}B(Im{sup t}Bu){sup 2}]Rh(COD) C{sup 22}H{sup 36}BN{sup 4}Rh, has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal center, which is coordinated by the bidentate H{sup 2}B(Im{sup t}Bu){sub 2} and one cyclooctadiene group. The Rh–C{sub carbene} bond lengths are 2.043(4) and 2.074(4) Å, and the bond angle C–Rh1–C is 82.59°. The dihedral angle between two imidazol-2-ylidene rings is 67.30°.

Theory of electrolyte crystallization in magnetic field

DEFF Research Database (Denmark)

Madsen, Hans Erik Lundager

2007-01-01

phenomena. The basis of the theory is a crystal model of a sparingly soluble salt with NaCl structure, where the ions are divalent, and the anion is a base. It is assumed that almost all the anions in the surface layer are protonized, and that an approaching metal ion pushes the proton away...... enter an excited state due to its momentum. Spin relaxation in magnetic field may remove hindrances to proton transfer. The theory is supported by numerical results from model calculations....

Crystal field excitations of YbMn{sub 2}Si{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Mole, R.A. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234 (Australia); School of Physical, Environmental and Mathematical Sciences, The University of New South Wales at the Australian Defence Force Academy, Canberra, ACT 2600 (Australia); Hofmann, M. [School of Physical, Environmental and Mathematical Sciences, The University of New South Wales at the Australian Defence Force Academy, Canberra, ACT 2600 (Australia); Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM II), Technische Universität München, 85747 Garching (Germany); Adroja, D.T. [ISIS Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 OQX (United Kingdom); Moze, O. [Dipartimento di Fisica, Università degli Studi di Modena e Reggio Emilia, Modena (Italy); Campbell, S.J., E-mail: stewart.campbell@adfa.edu.au [School of Physical, Environmental and Mathematical Sciences, The University of New South Wales at the Australian Defence Force Academy, Canberra, ACT 2600 (Australia)

2013-12-15

The crystal field excitations of the rare earth intermetallic compound YbMn{sub 2}Si{sub 2} have been measured by inelastic neutron scattering over the temperature range 2.5–50 K. The YbMn{sub 2}Si{sub 2} spectra exhibit three low energy excitations (∼3–7 meV) in the antiferromagnetic AFil region above the magnetic phase transition at T{sub N2} = 30(5) K. The crystal field parameters have been determined for YbMn{sub 2}Si{sub 2} in the antiferromagnetic AFil region. A further two inelastic excitations (∼9 meV, 17 meV) are observed below T{sub N2}=30(5) K, the temperature at which the high temperature antiferromagnetic structure is reported to exhibit doubling of the magnetic cell. Energy level diagrams have been determined for Yb{sup 3+} ions in the different sites above (single site) and below the magnetic transition temperature (two sites). The excitation energies for both sites are shown to be temperature independent with the temperature dependences of the transition intensities for the two sites described well by a simple Boltzmann model. The spectra below T{sub N2} cannot be described fully in terms of molecular field models based on either a single Yb{sup 3+} site or two Yb{sup 3+} sites. This indicates that the magnetic behaviour of YbMn{sub 2}Si{sub 2} is more complicated than previously considered. The inability to account fully for excitations below the magnetic phase transition may be due to an, as yet, unresolved structural transition associated with the magnetic transition. - Highlights: • The inelastic neutron scattering from YbMn{sub 2}Si{sub 2} has been investigated over the temperature range 2.5–50 K. • The crystal field splitting has been monitored through the magnetic transition at 30(5) K. • We have determined the crystal field parameters for the antiferromagnetic AFil region. • The transition intensities are described well by Boltzmann occupancy models. • The spectra below the magnetic transition have been analysed by

Low-frequency electromagnetic field in a Wigner crystal

OpenAIRE

Stupka, Anton

2016-01-01

Long-wave low-frequency oscillations are described in a Wigner crystal by generalization of the reverse continuum model for the case of electronic lattice. The internal self-consistent long-wave electromagnetic field is used to describe the collective motions in the system. The eigenvectors and eigenvalues of the obtained system of equations are derived. The velocities of longitudinal and transversal sound waves are found.

Strong crystal field effect in ? - optical absorption study

Science.gov (United States)

Gajek, Z.; Krupa, J. C.

1998-12-01

=-1 Results of optical absorption measurements in polarized light on tetravalent neptunium diluted in a 0953-8984/10/50/021/img6 single crystal are reported. The recorded spectra are complex, pointing to the presence of an 0953-8984/10/50/021/img7 impurity. The electronic transitions assigned to the 0953-8984/10/50/021/img8 ion are interpreted in terms of the usual model, following the actual understanding of the neptunium electronic structure and independent theoretical predictions. R.m.s. deviations of the order of 0953-8984/10/50/021/img9 have been obtained for 42 levels fitted with 11 free parameters. The crystal field effect resulting from the fitting is considerably larger than that observed for the uranium ion in the same host.

Influence of axial and peripheral ligands on the electronic structure of titanium phthalocyanines

DEFF Research Database (Denmark)

Pickup, David F.; García Lastra, Juan Maria; Rogero, Celia

2013-01-01

core-level binding energy was observed in the bidentate complex and compared to a calculated core-level stabilization. DFT predicts a change of the LUMO from the inner phthalocyanine ring to the Ti dxy orbital and a reversal of the high-lying dx2-y2 and d z2 orbitals. The N 1s edge was calculated using......-ray absorption spectroscopy and photoelectron spectroscopy were combined with density functional theory (DFT) and crystal-field multiplet calculations to characterize the Ti 3d and N 2p valence electrons that form the frontier orbitals. When a monodentate oxo axial ligand was replaced by a bidentate catechol...... ligand, the multiplet structure of the Ti 2p-to-3d transitions was found to change systematically. The most noticeable change was an additional transition into the low-lying 3dxy level, which is attributed to a reduction in local symmetry from 4-fold to 2-fold at the Ti center. An increase of the Ti 2p...

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURES ...

African Journals Online (AJOL)

B. S. Chandravanshi

ABSTRACT. Reaction of [VO(acac)2] (acac = acetylacetonate) with ... Single crystal X-ray structural studies indicate that the hydrazone ligands coordinate to ..... Molecular structure of complex (1) at 30% probability displacement. Figure 4.

AOM reconciling of crystal field parameters for UCl 3, UBr 3, UI 3 series

Science.gov (United States)

Gajek, Z.; Mulak, J.

1990-07-01

Available inelastic neutron scattering interpretations of crystal field effect in the uranium trihalides have been verified in terms of Angular Overlap Model. For UCl 3 a good reconciling of both INS and optical interpretations of crystal field effect has been obtained. On the contrary, the parameterizations for UBr 3 and UI 3 were found to be highly artificial and suggestion is given to experimentalists to reinterpret their INS spectra.

AOM reconciling of crystal field parameters for UCl3, UBr3, Ul3 series

International Nuclear Information System (INIS)

Gajek, Z.; Mulak, J.

1990-01-01

Available inelastic neutron scattering interpretations of crystal field effect in the uranium trihalides have been verified in terms of Angular Overlap Model. For UCl 3 a good reconciling of both INS and optical interpretations of crystal field effect has been obtained. On the contrary, the parameterizations for UBr 3 and UI 3 were found to be highly artificial and suggestion is given to experimentalists to reinterpret their INS spectra

Fine structure of fields in 2D photonic crystal waveguides

DEFF Research Database (Denmark)

Lavrinenko, Andrei; Volkov, V. S.; Bozhevolnyi, S. I.

2006-01-01

We resolve fine structure of fields in a single-row missing photonic crystal waveguide by finite-difference time-domain modelling and SNOM measurements. Both linear dispersion and slow-light regimes in proximity of the cutoff are addressed in the analysis....

The use of single-crystal iron frames in transient field measurements, ch. 3

International Nuclear Information System (INIS)

Zalm, P.C.

1977-01-01

An experimental technique for measuring g-factors of short-lived states (tausub(m)=0.1-10 ps) is discussed. In this method, one uses the strong hyperfine interaction caused by the transient magnetic field. The transient field method dates from 1967. A gain in measuring time of at least a factor of four is shown to be obtained by the use of a single crystal iron frame as a ferromagnetic target backing in which the excited nuclei, formed in a nuclear reaction, recoil. Such frames can be fully magnetized with low external fields as shown by magneto-optical Kerr-effect measurements. The important improvement is that the associated magnetic fringing field near the target is negligible. This is in contrast to the conventional set-up in which strong external fields, with corresponding large disturbing fringing fields, were necessary. The single-crystal set-up is compared to the conventional set-up in several transient field experiments and proves to be successful

radiation and electric field induced effects on the order-disorder phase in lithium sodium sulphate crystals

Science.gov (United States)

Hamed, A. E.; Kassem, M. E.; El-Wahidy, E. F.; El-Abshehy, M. A.

1995-03-01

The temperature dependence of specific heat at constant pressure, Cp(T), has been measured for lithium sodium sulphate, LiNaSo4 crystals, at different ?-radiation doses and external bias electric field (Eb), in the temperature range 300-900 K. A nonlinear dependence of transition temperature, T1 and a remarkable change in the thermodynamic parameters, were obtained as the effect of both electric field and ?-radiation. The effect of ?-radiation doses on the phase transition in LiNaSO4 crystals was explained as due to an internal bias field, Eb, originating from the interaction of polar defects with the order parameter of the host lattice. The internal bias field effect on the behaviour of Cp(T) in LiNaSO4 crystals was similar to that of the external electric field (E).

Triosmium cluster compounds containing isocyanide and hydride ligands. Crystal and molecular structure of (μ-H)(μ-eta1-C==N(H)(t-C4H9))Os3(CO)10

International Nuclear Information System (INIS)

Adams, R.D.; Golembeski, N.M.

1979-01-01

The crystal and molecular structure of the compound (μ-H)(μ-eta 1 -C==N(H)(t-C 4 H 9 ))Os 3 (CO) 10 has been determined by X-ray crystallographic methods. The compound crystallizes in the centrosymmetric monoclinic space group P2 1 /n[C/sub 2h/ 5 ]:a = 13.651 (4) A, b = 9.156 (4) A, c = 18.275 (5) A, β = 111.42 (2) 0 , V = 2126.3 (25) A 3 , Z = 4, rho/sub calcd/ = 2.92 g cm -3 . A uniform triangular cluster of three osmium atoms contains ten linear carbonyl groups and a μ-eta 1 -C==N(H)(t-C 4 H 9 ) iminyl ligand. The carbon atom of the iminyl ligand symmetrically bridges one osmium-osmium bond, as is shown by the internuclear separations Os(2)-C(11) = 2.066 (8) A and Os(3)-C(11) = 2.043 (8) A. The iminyl bond, C(11)-N, is double with the C-N distance being 1.298 (10) A

Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands.

Science.gov (United States)

Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S; Damborsky, Jiri; Smatanova, Ivana Kuta

2011-02-01

Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon-halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2(1)2(1)2(1) as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively.

A Cosserat crystal plasticity and phase field theory for grain boundary migration

Science.gov (United States)

Ask, Anna; Forest, Samuel; Appolaire, Benoit; Ammar, Kais; Salman, Oguz Umut

2018-06-01

The microstructure evolution due to thermomechanical treatment of metals can largely be described by viscoplastic deformation, nucleation and grain growth. These processes take place over different length and time scales which present significant challenges when formulating simulation models. In particular, no overall unified field framework exists to model concurrent viscoplastic deformation and recrystallization and grain growth in metal polycrystals. In this work a thermodynamically consistent diffuse interface framework incorporating crystal viscoplasticity and grain boundary migration is elaborated. The Kobayashi-Warren-Carter (KWC) phase field model is extended to incorporate the full mechanical coupling with material and lattice rotations and evolution of dislocation densities. The Cosserat crystal plasticity theory is shown to be the appropriate framework to formulate the coupling between phase field and mechanics with proper distinction between bulk and grain boundary behaviour.

Simulation of diffusion time of small molecules in protein crystals.

Science.gov (United States)

Geremia, Silvano; Campagnolo, Mara; Demitri, Nicola; Johnson, Louise N

2006-03-01

A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.

Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.

Directory of Open Access Journals (Sweden)

Stéphanie Pérot

Full Text Available Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely

Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.

Science.gov (United States)

Pérot, Stéphanie; Regad, Leslie; Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A; Villoutreix, Bruno O; Camproux, Anne-Claude

2013-01-01

Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket

The operator technique in the theory of the rare earth ion interaction with ligand nuclei

International Nuclear Information System (INIS)

Anikeenok, O.A.; Eremin, M.V.; Khutsishvili, O.G.

1986-01-01

The tensor structure of the operator of rare earth ion interaction with nuclei of close ligands conditioned by virtual processes of charge transport is established. It is taken into account that virtual processes of electron transport from the ligand can take place to the non-filled 4f-, void 5d- and 6s- and preliminarily excited 5p-shells of the rare earth ion. Effects of 4f- and 5d-state mixing by the odd crystal field are considered for the first time. In contrast to the usual multipole-dipole interaction the given one is characterized by anomalously greater significance of highest multipole momenta of the rare earth ion and in the common case it does not have axial symmetry. The theory is compared with data on double electron-nuclear resonance and radiofrequency discrete saturation, taking CaF 2 :Ce 3+ impurity centers as an example

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

African Journals Online (AJOL)

Preferred Customer

Reaction of [MoO2(acac)2] (where acac = acetylacetonate) with N'-(2-hydroxy-4- ... Single crystal X-ray structural studies indicate that the hydrazone ligand coordinates .... Molecular structure of the complex at 30% probability displacement.

Syntheses, crystal structures and properties of novel copper(II) complexes obtained by reactions of copper(II) sulfate pentahydrate with tripodal ligands.

Science.gov (United States)

Zhao, Wei; Fan, Jian; Song, You; Kawaguchi, Hiroyuki; Okamura, Taka-aki; Sun, Wei-Yin; Ueyama, Norikazu

2005-04-21

Three novel metal-organic frameworks (MOFs), [Cu(1)SO4].H2O (4), [Cu2(2)2(SO4)2].4H2O (5) and [Cu(3)(H2O)]SO4.5.5H2O (6), were obtained by hydrothermal reactions of CuSO4.5H2O with the corresponding ligands, which have different flexibility. The structures of the synthesized complexes were determined by single-crystal X-ray diffraction analyses. Complex 4 has a 2D network structure with two types of metallacycles. Complex 5 also has a 2D network structure in which each independent 2D sheet contains two sub-layers bridged by oxygen atoms of the sulfate anions. Complex 6 has a 2D puckered structure in which the sulfate anions serve as counter anions, which are different from those in complexes 4 (terminators) and 5 (bridges). The different structures of complexes 4, 5 and 6 indicate that the nature of organic ligands affected the structures of the assemblies greatly. The magnetic behavior of complex 5 and anion-exchange properties of complex 6 were investigated.

A simple localized-itinerant model for PrAl3: crystal field and exchange effects

International Nuclear Information System (INIS)

Ranke, P.J. von; Palermo, L.

1990-01-01

We present a simple magnetic model for PrAl sub(3). The effects of crystal field are treated using a reduced set of levels and the corresponding wave functions are extracted from the actual crystal field levels of Pr sup(+3) in a hexagonal symmetry. The exchange between 4f- and conduction electrons are dealt within a molecular field approximation. An analytical magnetic state equation is derived and the magnetic behaviour discussed. The parameters of the model are estimated from a fitting of the inverse susceptibility of PrAl sub(3) given in the literature. (author)

Waveguide modes of 1D photonic crystals in a transverse magnetic field

Energy Technology Data Exchange (ETDEWEB)

Sylgacheva, D. A., E-mail: sylgacheva.darjja@physics.msu.ru; Khokhlov, N. E.; Kalish, A. N.; Belotelov, V. I. [Moscow State University, Physics Department (Russian Federation)

2016-11-15

We analyze waveguide modes in 1D photonic crystals containing layers magnetized in the plane. It is shown that the magnetooptical nonreciprocity effect emerges in such structures during the propagation of waveguide modes along the layers and perpendicularly to the magnetization. This effect involves a change in the phase velocity of the mode upon reversal of the direction of magnetization. Comparison of the effects in a nonmagnetic photonic crystal with an additional magnetic layer and in a photonic crystal with magnetic layers shows that the magnitude of this effect is several times larger in the former case in spite of the fact that the electromagnetic field of the modes in the latter case is localized in magnetic regions more strongly. This is associated with asymmetry of the dielectric layers contacting with the magnetic layer in the former case. This effect is important for controlling waveguide structure modes with the help of an external magnetic field.

Crystal-field energy level analysis for Nd{sup 3+} ions at the low symmetry C{sub 1} site in [Nd(hfa){sub 4}(H{sub 2}O)](N(C{sub 2}H{sub 5}){sub 4}) single crystals

Energy Technology Data Exchange (ETDEWEB)

Mech, Agnieszka; Gajek, Zbigniew [Institute of Low Temperature and Structure Research, Polish Academy Of Sciences, ulica Okolna 2, 54-422 Wroclaw (Poland); Karbowiak, Miroslaw [Faculty of Chemistry, University of Wroclaw, ulica F Joliot-Curie 14, 50-383 Wroclaw (Poland); Rudowicz, Czeslaw [Institute of Physics, Szczecin University of Technology, Aleja Piastow 17, 70-310 Szczecin (Poland)], E-mail: karb@wchuwr.pl

2008-09-24

Optical absorption measurements of Nd{sup 3+} ions in single crystals of [Nd(hfa){sub 4}(H{sub 2}O)](N(C{sub 2}H{sub 5}){sub 4}) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 2{sub 1}/n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd{sup 3+} (4f{sup 3}) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C{sub 1} symmetry at the Nd{sup 3+} ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation B{sub kq}, admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm{sup -1}. Our approach also allows prediction of the energy levels of Nd{sup 3+} ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low

Crystal Structures and Physical Properties of Ag(I) Coordination Polymers with Unsymmetrical Dipyridyl Ligand

International Nuclear Information System (INIS)

Lee, Eunji; Ryu, Hyunsoo; Park, Kimin

2013-01-01

Three Ag(I) coordination polymers with the formula [Ag(L)]·(X)·(DMSO) n (X = ClO 4 (1), BF 4 (2), and PF 6 (3), and L = dipyridyl ligand) were prepared and characterized fully their structures. All three compounds are isostructures and stable 2-D honeycomb type coordination polymers, in which 1-D zigzag chains with -(Ag-L)- motif are linked by the argentophilic interactions and the π···π stacking interactions between pyridine rings. The investigation on photophysical properties of all compounds shows that the nature of emission can be attributed to the metal-to-ligand charge transfer as well as the formation of the polymeric structures with restriction of the flexibility of the free ligand. Based on the present solid state results, further investigation on the development and characterization of new coordination polymers using flexible unsymmetrical ligand is in progress. During last two decades, silver coordination polymers based on dipyridyl type ligands have attracted particular interest because of the various intriguing architectures caused by a variety of coordination geometry of Ag(I) ion as well as their potential applications as functional materials

Drift of nonequilibrium charge carriers in GaAs-crystals with traps in ultrasonic fields

International Nuclear Information System (INIS)

Zaveryukhina, N.N.; Zaveryukhin, B.N.; Zaveryukhina, E.B.

2007-01-01

Full text: The drift of nonequilibrium charge carriers in a semiconductor is one of the basic processes determining the efficiency of semiconductor photodetectors. Gallium arsenide possesses certain advantages to other semiconductors in this respect, which allow GaAs-photodetectors to be obtained which possess the maximum efficiency in comparison with all other systems. The purpose of this study was to deepen and expand our knowledge about the acoustic-drift processes in GaAs- crystals. As is known, the drift of nonequilibrium charge carriers in a semiconductor is determined either by external electric fields and/or by internal (built-in) electrostatic fields related to an impurity concentration gradient in the semiconductor. Gallium arsenide is a piezoelectric semiconductor with a structure possessing no center of symmetry. An electric field applied to such a crystal produces deformation of the crystal, and vice versa, any deformation of the crystal leads to the appearance of an induced electric field. Therefore, investigation of the effect of deformation on the drift of nonequilibrium charge carriers is a very important task. One of the possible straining factors is ultrasonic wave. Interaction of the charge carriers with ultrasonic waves in piezo-semiconductors is mediated by piezo exertion. Straining a semiconductor by an ultrasonic wave field gives rise to a force acting upon the charge carriers, which is proportional to the wave vector and the piezoelectric constant of the crystal. The physics of interaction between an ultrasonic wave and nonequilibrium charge carriers in GaAs, as well as in non-polar semiconductors (Si, Ge), consists in the energy and momentum exchange between the wave and the carriers. Besides the ultrasonic waves interact with the traps of carriers and devastate them. These both acoustic effects lead to rise of amplitude of signal of GaAs-photodetectors. (authors)

Dynamic ligand-based pharmacophore modeling and virtual ...

Indian Academy of Sciences (India)

Five ligand-based pharmacophore models were generated from 40 different .... the Phase module of the Schrodinger program.35 Each model consisted of six types of ... ligand preparation included the OPLS_2005 force field and to retain the ...

Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study

International Nuclear Information System (INIS)

Alnemrat, Sufian; Hooper, Joseph P.

2014-01-01

We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O 2 molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O 2 diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material

New Mn(II, Ni(II, Cd(II, Pb(II complexes with 2-methylbenzimidazole and other ligands. Synthesis, spectroscopic characterization, crystal structure, magnetic susceptibility and biological activity studies

Directory of Open Access Journals (Sweden)

Shayma A. Shaker

2016-11-01

Full Text Available Synthesis and characterization of Mn(II, Ni(II, Cd(II and Pb(II mixed ligand complexes of 2-methylbenzimidazole with other ligands have been reported. The structure of the ligands and their complexes was investigated using elemental analysis, IR, UV–Vis, (1H, 13C NMR spectroscopy, molar conductivity and magnetic susceptibility measurements. In all the studies of complexes, the 2-methylbenzimidazole behaves as a neutral monodentate ligand which is coordinated with the metal ions through the N atom. While benzotriazole behaves as a neutral bidentate ligand which is coordinated with the Ni(II ion through the two N atoms. Moreover, the N-acetylglycine behaves as a bidentate ligand which is coordinated with the Mn(II, Ni(II and Pb(II ions through the N atom and the terminal carboxyl oxygen atom. The magnetic and spectral data indicate the tetrahedral geometry for Mn(II complex, irregular tetrahedral geometry for Pb(II complex and octahedral geometry for Ni(II complex. The X-ray single crystal diffraction method was used to confirm a centrosymmetric dinuclear Cd(II complex as each two metal ions are linked by a pair of thiocyanate N = S bridge. Two 2-methylbenzimidazole N-atom donors and one terminal thiocyanate N atom complete a highly distorted square pyramid geometry around the Cd atom. Besides, different cell types were used to determine the inhibitory effect of Mn(II, Ni(II, Cd(II and Pb(II complexes on cell growth using MTT assay. Cd(II complex showed cytotoxic effect on various types of cancer cell lines with different EC50 values.

Ab Initio Ligand Field Molecular Mechanics and the Nature of Metal-Ligand π-Bonding in Fe(II) 2,6-di(pyrazol-1-yl)pyridine Spin Crossover Complexes.

Science.gov (United States)

Deeth, Robert J; Halcrow, Malcolm A; Kershaw Cook, Laurence J; Raithby, Paul R

2018-04-06

A ligand field molecular mechanics (LFMM) force field has been constructed for the spin states of [Fe(bpp) 2 ] 2+ (bpp=2,6-di(pyrazol-1-yl)pyridine) and related complexes. A new charge scheme is employed which interpolates between partial charges for neutral bpp and protonated [H 3 bpp] 3+ to achieve a target metal charge. The LFMM angular overlap model (AOM) parameters are fitted to fully ab initio d orbital energies. However, several AOM parameter sets are possible. The ambiguity is resolved by calculating the Jahn-Teller distortion mode for high spin, which indicates that in [Fe(bpp) 2 ] 2+ pyridine is a π-acceptor and pyrazole a weak π-donor. The alternative fit, assumed previously, where both ligands act as π-donors leads to an inconsistent distortion. LFMM optimisations in the presence of [BF 4 ] - or [PF 6 ] - anions are in good agreement with experiment and the model also correctly predicts the spin state energetics for 3-pyrazolyl substituents where the interactions are mainly steric. However, for 4-pyridyl or 4-pyrazolyl substituents, LFMM only treats the electrostatic contribution which, for the pyridyl substituents, generates a fair correlation with the spin crossover transition temperatures, T 1/2 , but in the reverse sense to the dominant electronic effect. Thus, LFMM generates its smallest spin state energy difference for the substituent with the highest T 1/2 . One parameter set for all substituted bpp ligands is insufficient and further LFMM development will be required. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dipolar local field in homogeneously magnetized quasi-two-dimensional crystals

International Nuclear Information System (INIS)

Leon, H; Estevez-Rams, E

2009-01-01

A formalism to calculate the dipolar local field in homogeneously magnetized quasi-two-dimensional (Q2D) crystals is comprehensively presented. Two fundamental tests for this formalism are accomplished: the transition from the Q2D quantities to the corresponding 3D ones; and the recovering of the macroscopic quantities of the 3D continuum theory. The additive separation between lattice and shape contributions to the local field allows an unambiguous interpretation of the respective effects. Calculated demagnetization tensors for square and circular lateral geometries of dipole layers show that for a single crystal layer an extremely thin film, but still with a finite thickness, is a better physical representation than a strictly 2D plane. Distinct close-packed structures are simulated and calculations of the local field at the nodes of the stacked 2D lattices allow one to establish the number of significantly coupled dipole layers, depending on the ratio between the interlayer distance and the 2D lattice constant. The conclusions drawn are of interest for the study of the dipolar interaction in magnetic ultrathin films and other nanostructured materials, where magnetic nanoparticles are embedded in non-magnetic matrices.

Ambipolar Cu- and Fe-phthalocyanine single-crystal field-effect transistors

NARCIS (Netherlands)

De Boer, R.W.I.; Stassen, A.F.; Craciun, M.F.; Mulder, C.L.; Molinari, A.; Rogge, S.; Morpurgo, A.F.

2005-01-01

We report the observation of ambipolar transport in field-effect transistors fabricated on single crystals of copper- and iron-phthalocyanine, using gold as a high work-function metal for the fabrication of source and drain electrodes. In these devices, the room-temperature mobility of holes reaches

Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel

Energy Technology Data Exchange (ETDEWEB)

Basak, Sandip [Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States; Schmandt, Nicolaus [Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, United States; Gicheru, Yvonne [Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States; Chakrapani, Sudha [Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States

2017-03-06

Desensitization in pentameric ligand-gated ion channels plays an important role in regulating neuronal excitability. Here, we show that docosahexaenoic acid (DHA), a key ω-3 polyunsaturated fatty acid in synaptic membranes, enhances the agonist-induced transition to the desensitized state in the prokaryotic channel GLIC. We determined a 3.25 Å crystal structure of the GLIC-DHA complex in a potentially desensitized conformation. The DHA molecule is bound at the channel-periphery near the M4 helix and exerts a long-range allosteric effect on the pore across domain-interfaces. In this previously unobserved conformation, the extracellular-half of the pore-lining M2 is splayed open, reminiscent of the open conformation, while the intracellular-half is constricted, leading to a loss of both water and permeant ions. These findings, in combination with spin-labeling/EPR spectroscopic measurements in reconstituted-membranes, provide novel mechanistic details of desensitization in pentameric channels.

Numerical investigation of magnetic field effect on pressure in cylindrical and hemispherical silicon CZ crystal growth

International Nuclear Information System (INIS)

Mokhtari, F.; Bouabdallah, A.; Merah, A.; Oualli, H.

2012-01-01

The effect of axial magnetic field of different intensities on pressure in silicon Czochralski crystal growth is investigated in cylindrical and hemispherical geometries with rotating crystal and crucible and thermocapillary convection. As one important thermodynamic variable, the pressure is found to be more sensitive than temperature to magnetic field with strong dependence upon the vorticity field. The pressure at the triple point is proposed as a convenient parameter to control the homogeneity of the grown crystal. With a gradual increase of the magnetic field intensity the convection effect can be reduced without thermal fluctuations in the silicon melt. An evaluation of the magnetic interaction parameter critical value corresponding to flow, pressure and temperature homogenization leads to the important result that a relatively low axial magnetic field is required for the spherical system comparatively to the cylindrical one. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Numerical investigation of magnetic field effect on pressure in cylindrical and hemispherical silicon CZ crystal growth

Energy Technology Data Exchange (ETDEWEB)

Mokhtari, F. [Universite Mouloud Mammeri de Tizi Ouzou (Algeria); LTSE Laboratory, University of Science and Technology. BP 32 Elalia, Babezzouar, Algiers (Algeria); Bouabdallah, A. [LTSE Laboratory, University of Science and Technology. BP 32 Elalia, Babezzouar, Algiers (Algeria); Merah, A. [LTSE Laboratory, University of Science and Technology. BP 32 Elalia, Babezzouar, Algiers (Algeria); M' hamed Bougara University, Boumerdes (Algeria); Oualli, H. [EMP, Bordj ElBahri, Algiers (Algeria)

2012-12-15

The effect of axial magnetic field of different intensities on pressure in silicon Czochralski crystal growth is investigated in cylindrical and hemispherical geometries with rotating crystal and crucible and thermocapillary convection. As one important thermodynamic variable, the pressure is found to be more sensitive than temperature to magnetic field with strong dependence upon the vorticity field. The pressure at the triple point is proposed as a convenient parameter to control the homogeneity of the grown crystal. With a gradual increase of the magnetic field intensity the convection effect can be reduced without thermal fluctuations in the silicon melt. An evaluation of the magnetic interaction parameter critical value corresponding to flow, pressure and temperature homogenization leads to the important result that a relatively low axial magnetic field is required for the spherical system comparatively to the cylindrical one. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Random crystal field effect on the magnetic and hysteresis behaviors of a spin-1 cylindrical nanowire

Energy Technology Data Exchange (ETDEWEB)

Zaim, N.; Zaim, A., E-mail: ah_zaim@yahoo.fr; Kerouad, M., E-mail: kerouad@fs-umi.ac.ma

2017-02-15

In this work, the magnetic behavior of the cylindrical nanowire, consisting of a ferromagnetic core of spin-1 atoms surrounded by a ferromagnetic shell of spin-1 atoms is studied in the presence of a random crystal field interaction. Based on Metropolis algorithm, the Monte Carlo simulation has been used to investigate the effects of the concentration of the random crystal field p, the crystal field D and the shell exchange interaction J{sub s} on the phase diagrams and the hysteresis behavior of the system. Some characteristic behaviors have been found, such as the first and second-order phase transitions joined by tricritical point for appropriate values of the system parameters, triple and isolated critical points can be also found. Depending on the Hamiltonian parameters, single, double and para hysteresis regions are explicitly determined. - Highlights: • Phase diagrams of a ferromagnetic nanowire are examined by the Monte Carlo simulation. • Different types of the phase diagrams are obtained. • The effect of the random crystal field on the hysteresis loops is studied. • Single, double and para hysteresis regions are explicitly determined.

Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches.

Science.gov (United States)

Jain, Niyati; Zhao, Liang; Liu, John D; Xia, Tianbing

2010-05-04

High-resolution crystal structures and biophysical analyses of purine-sensing riboswitches have revealed that a network of hydrogen bonding interactions appear to be largey responsible for discrimination of cognate ligands against structurally related compounds. Here we report that by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand, we have detected the presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches. All three riboswitches have similar conformational distributions of the ligand-bound state. The known crystal structures represent the global minimum that accounts for 50-60% of the population, where there is no significant stacking interaction between the ligand and bases of the binding pocket, but the hydrogen-bonding cage collectively provides an electronic environment that promotes an ultrafast ( approximately 1 ps) charge transfer pathway. The ligand also samples multiple conformations in which it significantly stacks with either the adenine or the uracil bases of the A21-U75 and A52-U22 base pairs that form the ceiling and floor of the binding pocket, respectively, but favors the larger adenine bases. These alternative conformations with well-defined base stacking interactions are approximately 1-1.5 kcal/mol higher in DeltaG degrees than the global minimum and have distinct charge transfer dynamics within the picosecond to nanosecond time regime. Inside the pocket, the purine ligand undergoes dynamic motion on the low nanosecond time scale, sampling the multiple conformations based on time-resolved anisotropy decay dynamics. These results allowed a description of the energy landscape of the bound ligand with intricate details and demonstrated the elastic nature of the ligand recognition mode by the purine-sensing riboswitches, where there is a dynamic balance between hydrogen bonding

Superconducting transition and low-field magnetoresistance of a niobium single crystal at 4.2 deg. K

International Nuclear Information System (INIS)

Perriot, G.

1967-01-01

We report the study of the electrical resistance of a niobium single crystal, at 4.2 deg. K, from the beginning of the superconductive transition to 80 kilo oersteds. Critical fieldsH c2 and H c3 have been determined. Influences on superconductive transition of current density, field-current angle, crystal orientation and magnetoresistance have been studied. Variation laws of low-field transverse and longitudinal magneto-resistances have been determined. (author) [fr

Identification of VDR Antagonists among Nuclear Receptor Ligands Using Virtual Screening

Directory of Open Access Journals (Sweden)

Kelly Teske

2014-04-01

Full Text Available Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR antagonists among nuclear receptor (NR ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available “Binding Database.” Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2D3 and 25(OH2D3. The first virtual screen identified 32 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 μM. The second screen identified 162 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/β ligands (26%, TRα/β ligands (7%, and LxRα/β ligands (7%. The binding between VDR and ERα ligand H6036 as well as TRα/β ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.

Ruthenium(II) bipyridine complexes bearing quinoline-azoimine (NN'N″) tridentate ligands: synthesis, spectral characterization, electrochemical properties and single-crystal X-ray structure analysis.

Science.gov (United States)

Al-Noaimi, Mousa; Abdel-Rahman, Obadah S; Fasfous, Ismail I; El-khateeb, Mohammad; Awwadi, Firas F; Warad, Ismail

2014-05-05

Four octahedral ruthenium(II) azoimine-quinoline complexes having the general molecular formula [Ru(II)(L-Y)(bpy)Cl](PF6) {L-Y=YC6H4N=NC(COCH3)=NC9H6N, Y=H (1), CH3 (2), Br (3), NO2 (4) and bpy=2,2'-bipyrdine} were synthesized. The azoimine-quinoline based ligands behave as NN'N″ tridentate donors and coordinated to ruthenium via azo-N', imine-N' and quinolone-N″ nitrogen atoms. The composition of the complexes has been established by elemental analysis, spectral methods (FT-IR, electronic, (1)H NMR, UV/Vis and electrochemical (cyclic voltammetry) techniques. The crystal structure of complex 1 is reported. The Ru(II) oxidation state is greatly stabilized by the novel tridentate ligands, showing Ru(III/II) couples ranging from 0.93-1.27 V vs. Cp2Fe/Cp2Fe(+). The absorption spectrum of 1 in dichloromethane was modeled by time-dependent density functional theory (TD-DFT). Copyright © 2014 Elsevier B.V. All rights reserved.

Phase field modeling of rapid crystallization in the phase-change material AIST

Science.gov (United States)

Tabatabaei, Fatemeh; Boussinot, Guillaume; Spatschek, Robert; Brener, Efim A.; Apel, Markus

2017-07-01

We carry out phase field modeling as a continuum simulation technique in order to study rapid crystallization processes in the phase-change material AIST (Ag4In3Sb67Te26). In particular, we simulate the spatio-temporal evolution of the crystallization of a molten area of the phase-change material embedded in a layer stack. The simulation model is adapted to the experimental conditions used for recent measurements of crystallization rates by a laser pulse technique. Simulations are performed for substrate temperatures close to the melting temperature of AIST down to low temperatures when an amorphous state is involved. The design of the phase field model using the thin interface limit allows us to retrieve the two limiting regimes of interface controlled (low temperatures) and thermal transport controlled (high temperatures) dynamics. Our simulations show that, generically, the crystallization velocity presents a maximum in the intermediate regime where both the interface mobility and the thermal transport, through the molten area as well as through the layer stack, are important. Simulations reveal the complex interplay of all different contributions. This suggests that the maximum switching velocity depends not only on material properties but also on the precise design of the thin film structure into which the phase-change material is embedded.

Crystal structures and luminescence of two cadmium-carboxylate cluster-based compounds with mixed ligands

Energy Technology Data Exchange (ETDEWEB)

Ma, Hui-Fang; Lei, Qian; Wang, Yu-Ling; Yin, Shun-Gao; Liu, Qing-Yan [College of Chemistry and Chemical Engineering and Key Lab. of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal Univ., Nanchang (China)

2017-04-04

Reactions of Cd(NO{sub 3}){sub 2}.4H{sub 2}O with 2-quinolinecarboxylic acid (H-QLC) in the presence of 1,4-benzenedicarboxylic acid (H{sub 2}-BDC) or 1,3,5-benzenetricarboxylic acid (H-BTC) in DMF/H{sub 2}O solvent afforded two compounds, namely, [Cd(QLC)(BDC){sub 1/2}(H{sub 2}O)]{sub n} (1) and [Cd(QLC)(BTC){sub 1/3}]{sub n} (2). Both compounds are two-dimensional (2D) frameworks but feature different cadmium-carboxylate clusters as a result of the presence of the polycarboxylate ligands with different geometries and coordination preference. The dinuclear Cd{sub 2}(QLC){sub 2} units in 1 are bridged by the pairs of bridging water ligands to give a one-dimensional (1D) chain, which is further linked by the second ligand of BDC{sup 2-} to form a 2D structure. Compound 2 is constructed from unique hexanuclear macrometallacyclic Cd{sub 6}(QLC){sub 6} clusters, which are linked by the surrounding BTC{sup 3-} ligands to generate a 2D structure. Photoluminescence studies showed both compounds exhibit ligand-centered luminescent emissions with emission maxima at 405 and 401 nm, respectively. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

High-field Transport in Low Symmetry β-Ga2O3 Crystal

Science.gov (United States)

Ghosh, Krishnendu; Singisetti, Uttam

High-field carrier transport plays an important role in many disciplines of electronics. Conventional transport theories work well on high-symmetry materials but lacks insight as the crystal symmetry goes down. Newly emerging materials, many of which possess low symmetry, demand more rigorous treatment of charge transport. We will present a comprehensive study of high-field transport using ab initio electron-phonon interaction (EPI) elements in a full-band Monte Carlo (FBMC) algorithm. We use monoclinic β-Ga2O3 as a benchmark low-symmetry material which is also an emerging wide-bandgap semiconductor. β-Ga2O3 has a C2m space group and a 10 atom primitive cell. In this work the EPIs are calculated under density-functional perturbation theory framework. We will focus on the computational challenges arising from many phonon modes and low crystal symmetry. Significant insights will be presented on the details of energy relaxation by the hot electrons mediated by different phonon modes. We will also show the velocity-field curves of electrons in different crystal directions. The authors acknowledge the support from the National Science Foundation Grant (ECCS 1607833). The authors also acknowledge the computing support provided by the Center for Computational Research at the University at Buffalo.

Crystal field effect in YbMnO.sub.3./sub..

Czech Academy of Sciences Publication Activity Database

Diviš, M.; Hölsä, J.; Lastusaari, M.; Litvinchuk, A. P.; Nekvasil, Vladimír

2008-01-01

Roč. 451, 1-2 (2008), s. 662-665 ISSN 0925-8388 R&D Projects: GA AV ČR IAA100100627 Institutional research plan: CEZ:AV0Z10100521 Keywords : ytterbium * manganites * IR spectroscopy * crystal field Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.510, year: 2008

Phase field simulations of ice crystal growth in sugar solutions

NARCIS (Netherlands)

Sman, Van Der R.G.M.

2016-01-01

We present the first model ever, that describes explicitly ice crystal growth in a sugar solution during freezing. This 2-D model uses the phase field method, supplemented with realistic, and predictive theories on the thermodynamics and (diffusion) kinetics of this food system. We have to make

The influence of magnetic fields on protein crystal growth and quality; Zum Einfluss magnetischer Felder auf das Wachstum und die Qualitaet von Proteinkristallen

Energy Technology Data Exchange (ETDEWEB)

Meents, Alke

2005-08-01

Magnetic fields can affect protein crystal growth in several ways. In homogeneous magnetic fields molecules and crystallites line up themselves along the magnetic field direction due to their magnetic anisotropy. Inhomogeneous magnetic fields exert a force on diamagnetic and paramagnetic compounds towards regions of lower or higher field strength. This effect can be used to create a microgravity-like environment for diamagnetic proteins and an environment comparable to hypergravity for paramagnetic proteins. Crystallization in homogeneous magnetic fields and a microgravity-like environment are reported to have a positive effect on crystal quality. The aim of this work was to systematically investigate the effect of protein crystallization in magnetic fields on the crystal quality by comparing a large number of crystals grown under identical conditions with- and without magnetic fields. Crystal quality was determined by means of high resolution rocking-curve measurements. Furthermore in certain cases complete diffraction datasets were collected. Any possible influence of magnetic fields on the mosaicity and the quality of the diffraction data was evaluated statistically by applying Wilcoxon-Ranksum tests. To investigate the effect of protein crystallization in homogeneous magnetic fields the diamagnetic proteins Thaumatin, Trypsin, and Lysozyme and paramagnetic Myoglobin were crystallized in magnetic fields of 5 T, 8.8 T, and 15.8 T. The analysis of crystal mosaicity and quality of the diffraction data of the diamagnetic proteins did not reveal a significant influence on the crystal quality. In contrast the crystals of paramagnetic Myoglobin grew up to 14 times larger than the ones in the control experiment. In addition they had a significant lower mosaicity, and diffracted to a higher resolution than ever reported before. Special pole pieces for an existing magnet were designed and build to grow protein crystals in an inhomogeneous magnetic field The experimental

Wide-field imaging of birefringent synovial fluid crystals using lens-free polarized microscopy for gout diagnosis

Science.gov (United States)

Zhang, Yibo; Lee, Seung Yoon Celine; Zhang, Yun; Furst, Daniel; Fitzgerald, John; Ozcan, Aydogan

2016-06-01

Gout is a form of crystal arthropathy where monosodium urate (MSU) crystals deposit and elicit inflammation in a joint. Diagnosis of gout relies on identification of MSU crystals under a compensated polarized light microscope (CPLM) in synovial fluid aspirated from the patient’s joint. The detection of MSU crystals by optical microscopy is enhanced by their birefringent properties. However, CPLM partially suffers from the high-cost and bulkiness of conventional lens-based microscopy, and its relatively small field-of-view (FOV) limits the efficiency and accuracy of gout diagnosis. Here we present a lens-free polarized microscope which adopts a novel differential and angle-mismatched polarizing optical design achieving wide-field and high-resolution holographic imaging of birefringent objects with a color contrast similar to that of a standard CPLM. The performance of this computational polarization microscope is validated by imaging MSU crystals made from a gout patient’s tophus and steroid crystals used as negative control. This lens-free polarized microscope, with its wide FOV (>20 mm2), cost-effectiveness and field-portability, can significantly improve the efficiency and accuracy of gout diagnosis, reduce costs, and can be deployed even at the point-of-care and in resource-limited clinical settings.

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

Science.gov (United States)

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

Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

DEFF Research Database (Denmark)

Nguyen, E.D.; Meiler, J.; Norn, C.

2013-01-01

screening and to design and optimize drug candidates. However, low sequence identity between receptors, conformational flexibility, and chemical diversity of ligands present an enormous challenge to molecular modeling approaches. It is our hypothesis that rapid Monte-Carlo sampling of protein backbone...... extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves...

Effect of an external magnetic field on polytypism of CdI2 crystals grown from solutions

International Nuclear Information System (INIS)

Palosz, B.; Przedmojski, J.

1982-01-01

The effect of growth conditions on the polytypic structure of crystals of CdI 2 was analyzed for crystallization from solutions. Three solvents were used: H 2 O, 3 H 2 O + 1 C 2 H 5 OH and 1 H 2 O + 1 C 2 H 5 OH. Crystals were grown at two temperatures: 5 and 25 0 C with low and high growth rates; an external magnetic field of about 0.25 tesla was used. The effect of the above three parameters on the formation of the basic polytypes 2H and 4H and on the ordering of faults in disordered structures and in polytype cells was studied by X-ray analysis of crystal surfaces. Some distinct relations between the polytypic structure of crystals of CdI 2 and the magnetic field were found. (author)

Synthesis, Crystal Structure and Luminescent Property of A Novel Cd(II) Coordination Polymer with Bis-imidazole Ligand

International Nuclear Information System (INIS)

Zhou, Yong Hong

2013-01-01

The key to the successful design of metal-organic coordination polymers is the judicious selection of organic ligand. Recently, polydentate aromatic nitrogen heterocyclic ligands with five-membered rings have been well-studied in the construction of supramolecular structure for their N-coordinated sites apt to coordinating to transition metals. Similar to six-membered N-heterocyclic ligands, the azole-based five-membered N-heterocyclic ligands, such as imidazoles, triazoles and tetrazoles have been extensively employed in the construction of various coordination polymers with diverse topologies and interesting properties. The bis(azole) ligands in which N-donor azole rings (imidazole, triazole, or tetrazole) are separated by alkyl, (CH 2 ) n , spacers are good choices for flexible bridging ligands. The conformational flexibility of the spacers makes the ligands adaptable to various coordination networks with one-, two-, and three dimensional structures

Implication of Crystal Water Molecules in Inhibitor Binding at ALR2 Active Site

Directory of Open Access Journals (Sweden)

Hymavati

2012-01-01

Full Text Available Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecule. The solvent environment around such biomolecule controls their structure and plays important role in protein-ligand interactions. An understanding of the nature and role of these water molecules in the active site of a protein could greatly increase the efficiency of rational drug design approaches. We have performed the comparative crystal structure analysis of aldose reductase to understand the role of crystal water in protein-ligand interaction. Molecular dynamics simulation has shown the versatile nature of water molecules in bridge H bonding during interaction. Occupancy and life time of water molecules depend on the type of cocrystallized ligand present in the structure. The information may be useful in rational approach to customize the ligand, and thereby longer occupancy and life time for bridge H-bonding.

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE OF BIS-(2-HYDROXYBENZALDEHYDEDIAMINOGUANIZONE

Directory of Open Access Journals (Sweden)

Diana Dragancea, Vladimir B. Arion, Sergiu Shova

2008-12-01

Full Text Available The new ligand, bis(2-hydroxybenzaldehydediaminoguanizone (1 has been synthesized and characterized by elemental analysis, IR and 1H NMR spectroscopies. The crystal structure of the compound was determined by X-ray diffraction. The ligand C15H15N5O2·C2H5OH crystallizes in the monoclinic space group P21/c with unit cell parameters a = 8.9102(3, b = 10.0357(3, c = 19.7618(6 Å, β = 98.385(2°, Z = 4, V = 1748.21(9 Å3, R1 = 0.040. The amino form of the ligand adopts a planar conformation stabilized by two intramolecular hydrogen bonds of the type O–H···N, in which the H atoms of the central amino group are directed to the lone-pair regions of the azomethine nitrogen atoms.

Evaluation of a focused virtual library of heterobifunctional ligands for Clostridium difficile toxins.

Science.gov (United States)

Sanhueza, Carlos A; Cartmell, Jonathan; El-Hawiet, Amr; Szpacenko, Adam; Kitova, Elena N; Daneshfar, Rambod; Klassen, John S; Lang, Dean E; Eugenio, Luiz; Ng, Kenneth K-S; Kitov, Pavel I; Bundle, David R

2015-01-07

A focused library of virtual heterobifunctional ligands was generated in silico and a set of ligands with recombined fragments was synthesized and evaluated for binding to Clostridium difficile toxins. The position of the trisaccharide fragment was used as a reference for filtering docked poses during virtual screening to match the trisaccharide ligand in a crystal structure. The peptoid, a diversity fragment probing the protein surface area adjacent to a known binding site, was generated by a multi-component Ugi reaction. Our approach combines modular fragment-based design with in silico screening of synthetically feasible compounds and lays the groundwork for future efforts in development of composite bifunctional ligands for large clostridial toxins.

Crystal structure and solid-state properties of discrete hexa cationic ...

Indian Academy of Sciences (India)

Subsequently, weight loss of 33% in two stages from 242 to 691◦C can be assigned to the decomposition of triazole ligands. 3.3 Description of the crystal structure. The solid-state structure of ZnT was unambiguously determined by the single crystal X-ray diffraction tech- nique (figures 2 and 3). Compound ZnT crystallizes in.

On the neutron diffraction in a crystal in the field of a standing laser wave

International Nuclear Information System (INIS)

Grigoryan, K.K.; Hayrapetyan, A.G.; Petrosyan, R.G.

2010-01-01

The possibility of high-energy neutron diffraction in a crystal is shown by applying the solution of time-dependent Schroedinger equation for a neutron in the field of a standing laser wave. The scattering picture is examined within the framework of non-stationary S-matrix theory, where the neutron-laser field interaction is considered exactly and the neutron-crystal interaction is considered as a perturbation described by Fermi pseudopotential (Farri representation). The neutron-crystal interaction is elastic, and the neutron-laser field interaction has both inelastic and elastic behaviors which results in the observation of an analogous to the Kapitza-Dirac effect for neutrons. The neutron scattering probability is calculated and the analysis of the results are adduced. Both inelastic and elastic diffraction conditions are obtained and the formation of a 'sublattice' is illustrated in the process of neutron-photon-phonon elastic interaction.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

Energy Technology Data Exchange (ETDEWEB)

Beer, Tjaart A. P. de; Laskowski, Roman A. [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Duban, Mark-Eugene [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Chan, A. W. Edith [University College London, London WC1E 6BT (United Kingdom); Anderson, Wayne F. [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Thornton, Janet M., E-mail: thornton@ebi.ac.uk [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom)

2013-12-01

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Coordination polymers with the chiral ligand N-p-tolylsulfonyl-L-glutamic acid: Influence of metal ions and different bipyridine ligands on structural chirality

International Nuclear Information System (INIS)

He Rong; Song Huihua; Wei Zhen; Zhang Jianjun; Gao Yuanzhe

2010-01-01

Four new polymers, namely [Ni(-tsgluO)(2,4'-bipy) 2 (H 2 O) 2 ] n .5nH 2 O (1), [Co(-tsgluO)(2,4'-bipy) 2 (H 2 O) 2 ] n .5nH 2 O (2), [Ni(-tsgluO)(4,4'-bipy)] n .0.5nH 2 O (3), and [Co(-tsgluO)(4,4'-bipy)] n .0.5nH 2 O (4), where tsgluO 2- =(+)-N-p-tolylsulfonyl-L-glutamate dianion, 2,4'-bipy=2,4'-bipyridine, and 4,4'-bipy=4,4'-bipyridine, have been prepared and structurally characterized. Compounds 1 and 2 are isostructural and mononuclear, and crystallize in the acentric monoclinic space group Cc, forming 1D chain structures. Compound 3 is also mononuclear, but crystallizes in the chiral space group P2 1 , forming a homochiral 2D architecture. In contrast to the other complexes, compound 4 crystallizes in the space group P-1 and is composed of binuclear [Co 2 O 6 N 2 ] n 4- units, which give rise to a 2D bilayer framework. Moreover, compounds 1, 2, and 4 self-assemble to form 3D supramolecular structures through π-π stacking and hydrogen-bonding interactions, while compound 3 is further hydrogen-bonded to form 3D frameworks. We have demonstrated the influence of the central metal and bipyridine ligands on the framework chirality of the coordination complexes. - Graphical abstract: Four novel polymers based on a chiral ligand were prepared and structurally characterized; it represents the first series of investigations about the effect of central metals and bipyridine ligands on framework chirality.

Field-effect measurements of mobility and carrier concentration of Cu2S colloidal quantum dot thin films after ligand exchange

International Nuclear Information System (INIS)

Brewer, Adam S.; Arnold, Michael S.

2014-01-01

Colloidal quantum dots (CQDs) of copper sulfide (Cu 2 S), an earth-abundant semiconductor, have a number of intriguing applications that require knowledge of their electrical properties. Depending on stoichiometry, mobility, and surface treatment, applications include photoabsorbers for solar cells, tunable plasmonics, and counter-electrodes for polysulfate electrolytes. However, there have not been any direct measurements of electrical properties in Cu 2 S CQD thin films. Here, we exchange as synthesized dodecanethiol ligands with short ethanedithiol or ethylenediamine ligands to form thin films of coupled Cu 2 S CQDs. The mobility and carrier concentration were found to vary by ligand treatment from 10 −5 cm 2 /Vs and 10 19 holes/cm 3 for ethanedithiol ligands to 10 −3 cm 2 /Vs and 10 20 holes/cm 3 for ethylenediamine. These results are consistent with the carrier concentrations inferred from sub-bandgap surface-plasmon-resonances measured by infrared spectroscopy. These results will be useful when designing Cu 2 S materials for future applications. - Highlights: • Colloidal Cu2S quantum dots were synthesized and characterized. • Ligand exchange was performed to alter the Cu2S nanocrystal properties. • Ligand exchange was studied using photoluminescence and infrared spectroscopy. • Field effect mobility and carrier concentration were directly measured. • Carrier concentration was compared to estimates from surface plasmon resonances

Crystal structure of LGR4-Rspo1 complex: insights into the divergent mechanisms of ligand recognition by leucine-rich repeat G-protein-coupled receptors (LGRs).

Science.gov (United States)

Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

2015-01-23

Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4-6) recognize R-spondin family proteins (Rspo1-4) to stimulate Wnt signaling. In this study, we successfully utilized the "hybrid leucine-rich repeat technique," which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4-6, suggesting that LGR4-6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4-6 in ligand recognition. The molecular mechanism of LGR4-6 is distinct from the two-step mechanism of group A receptors LGR1-3 and the multiple-interface binding model of group C receptors LGR7-8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Construction and characterization on composite electrospinning fibers doped with iridium complex owing fluorine atoms in its auxiliary ligand.

Science.gov (United States)

Gao, Yu-Qian; Zhang, Shimin; Wang, Pengju; Xu, Shuxia; Wu, Kun; Mou, Wanzhi

2014-10-15

The authors synthesized a fluorine-containing Ir(III) complex Ir(PTZ)2(HFD) and the corresponding composite electrospinning fibers PVP@Ir(PTZ)2(HFD), where PTZ, HFD and PVP stood for 2-phenylbenzo[d]thiazole, 1,1,1,5,5,5-hexafluoropentane-2,4-dione and poly(vinylpyrrolidone), respectively. The molecular structure of the Ir(III) complex was confirmed by its single crystal analysis, which suggested that Ir(PTZ)2(HFD) molecules crystallized as monoclinic system with two molecules in each unit cell. Density functional theory calculation on the crystal revealed that the onset electronic transitions possessed a mixed character of metal-to-ligand-charge-transfer (MLCT) and ligand-to-ligand-charge-transfer (LLCT). Ir(PTZ)2(HFD) was then doped into electrospinning fibers so that the photophysical comparison between bulk Ir(PTZ)2(HFD) and composite samples could be performed. It was found that both face-to-face π-π attraction in crystal and the immobilization in PVP host could improve photoluminescence performance by restraining the geometric relaxation of MLCT excited state, showing emission blue shift, longer excited state lifetime and improved photostability. Copyright © 2014 Elsevier B.V. All rights reserved.

Creating physically-based three-dimensional microstructures: Bridging phase-field and crystal plasticity models.

Energy Technology Data Exchange (ETDEWEB)

Lim, Hojun [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Owen, Steven J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Abdeljawad, Fadi F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hanks, Byron [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Battaile, Corbett Chandler [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2015-09-01

In order to better incorporate microstructures in continuum scale models, we use a novel finite element (FE) meshing technique to generate three-dimensional polycrystalline aggregates from a phase field grain growth model of grain microstructures. The proposed meshing technique creates hexahedral FE meshes that capture smooth interfaces between adjacent grains. Three dimensional realizations of grain microstructures from the phase field model are used in crystal plasticity-finite element (CP-FE) simulations of polycrystalline a -iron. We show that the interface conformal meshes significantly reduce artificial stress localizations in voxelated meshes that exhibit the so-called "wedding cake" interfaces. This framework provides a direct link between two mesoscale models - phase field and crystal plasticity - and for the first time allows mechanics simulations of polycrystalline materials using three-dimensional hexahedral finite element meshes with realistic topological features.

Electrical resistance of flaky crystals in the longitudinal quantizing magnetic field

International Nuclear Information System (INIS)

Askerov, B.M.; Figarova, S.R.; Makhmudov, M.M.

2005-01-01

Specific resistance of the quasi-two-dimensional electrical gas in the longitudinal quantizing magnetic field is investigated in this work. Common expression for resistivity in the flaky crystals was received. In quantum limit was analyzed dependence of the resistivity from the size of magnetic field and parameters energetic spectra in case of strong degenerate gas. It was tagged that, the conduct of specific resistance is formed by the dependence of chemical potential from the size of magnetic field. At the defined value of the chemical potential and size of magnetic field obtains inflation of the specific resistance. (author)

Fast fringe-field switching of a liquid crystal cell by two-dimensional confinement with virtual walls

OpenAIRE

Choi, Tae-Hoon; Oh, Seung-Won; Park, Young-Jin; Choi, Yeongyu; Yoon, Tae-Hoon

2016-01-01

We report a simple method for reducing the response time of a fringe-field switching liquid crystal cell by using two-dimensional confinement of the liquid crystals. Through both numerical calculations and experiments, we show that the switching speed can be increased by several fold in a fringe-field switching cell by simply using a rubbing angle of zero, which causes virtual walls to be built when an electric field is applied between the interdigitated electrodes and the common electrode, w...

Actual and Idealized Crystal Field Parameterizations for the Uranium Ions in UF 4

Science.gov (United States)

Gajek, Z.; Mulak, J.; Krupa, J. C.

1993-12-01

The crystal field parameters for the actual coordination symmetries of the uranium ions in UF 4, C2 and C1, and for their idealizations to D2, C2 v , D4, D4 d , and the Archimedean antiprism point symmetries are given. They have been calculated by means of both the perturbative ab initio model and the angular overlap model and are referenced to the recent results fitted by Carnall's group. The equivalency of some different sets of parameters has been verified with the standardization procedure. The adequacy of several idealized approaches has been tested by comparison of the corresponding splitting patterns of the 3H 4 ground state. Our results support the parameterization given by Carnall. Furthermore, the parameterization of the crystal field potential and the splitting diagram for the symmetryless uranium ion U( C1) are given. Having at our disposal the crystal field splittings for the two kinds of uranium ions in UF 4, U( C2) and U( C1), we calculate the model plots of the paramagnetic susceptibility χ( T) and the magnetic entropy associated with the Schottky anomaly Δ S( T) for UF 4.

Crystal field and magnetism with Wannier functions: Orthorhombic rare-earth manganites

Czech Academy of Sciences Publication Activity Database

Novák, Pavel; Nekvasil, Vladimír; Knížek, Karel

358-359, MAY (2014), s. 228-232 ISSN 0304-8853 R&D Projects: GA ČR GA13-25251S Institutional support: RVO:68378271 Keywords : crystal field * rare- earth magnetism Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.970, year: 2014

Crystal-field tuning of photoluminescence in two-dimensional materials with embedded lanthanide ions

Energy Technology Data Exchange (ETDEWEB)

Xu, Ding; Chen, Weiyin; Zeng, Mengqi; Xue, Haifeng; Chen, Yunxu; Xiao, Yao; Zhang, Tao; Fu, Lei [College of Chemistry and Molecular Sciences, Institute for Advanced Studies, Wuhan University, Wuhan (China); Sang, Xiahan; Unocic, Raymond R.; Xiao, Kai [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN (United States)

2018-01-15

Lanthanide (Ln) group elements have been attracting considerable attention owing to the distinct optical properties. The crystal-field surroundings of Ln ions in the host materials can determine their energy level splitting, which is of vital importance to tailor their optical properties. 2D MoS{sub 2} single crystals were utilized as the host material to embed Eu{sup 3+} and energy-level splitting was achieved for tuning its photoluminescence (PL). The high anisotropy of the 2D host materials makes them distort the degenerate orbitals of the Ln ions more efficiently than the symmetrical bulk host materials. A significant red-shift of the PL peak for Eu{sup 3+} was observed. The strategy for tailoring the energy level splitting of Ln ions by the highly designable 2D material crystal field provides a new method to extend their optical properties. (copyright 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Crystal structures and conformers of CyMe4-BTBP

Directory of Open Access Journals (Sweden)

Lyczko Krzysztof

2015-12-01

Full Text Available The crystal structure of new conformation of the CyMe4-BTBP ligand (ttc has been presented. The ttt conformer of this compound in a form of THF solvate has been also crystallized. The geometries of six possible conformations (ttt, ttc, tct, tcc, ctc and ccc of the CyMe4-BTBP ligand have been modeled in the gas phase and in solutions (MeOH and H2O by DFT calculations using B3LYP/6-31G(d,p method. According to the calculations, in the three different media the conformers with trans orientation of the N atoms in the bipyridyl moiety are the most stable.

Photonic crystal fiber injected with Fe{sub 3}O{sub 4} nanofluid for magnetic field detection

Energy Technology Data Exchange (ETDEWEB)

Thakur, Harneet V.; Nalawade, Sandipan M.; Gupta, Swati [Photonics Group, Department of Applied Physics, Defence Institute of Advanced Technology, Girinagar, Pune 411 025 (India); Kitture, Rohini [Department of Electronic-Science, Fergusson College, Pune 411 004 (India); Kale, S. N. [Nanotechnology Group, Department of Applied Physics, Defence Institute of Advanced Technology, Girinagar, Pune 411 025 (India)

2011-10-17

We report a magnetic field sensor having advantages of both photonic crystal fiber and optofluidics, combining them on a single platform by infiltrating small amount of Fe{sub 3}O{sub 4} magnetic optofluid/nanofluid in cladding holes of polarization-maintaining photonic crystal fiber. We demonstrated that magnetic field of few mT can be easily and very well detected with higher sensitivity of 242 pm/mT. The change in the birefringence values has been correlated to the response of nanofluid to applied field.

Ruthenium(II) carbonyl compounds with the 4'-chloro-2,2':6',2''-terpyridine ligand.

Science.gov (United States)

Tatikonda, Rajendhraprasad; Haukka, Matti

2017-04-01

Two ruthenium carbonyl complexes with the 4'-chloro-2,2':6',2''-terpyridine ligand (tpy-Cl, C 15 H 10 ClN 3 ), i.e. [RuCl(tpy-Cl)(CO) 2 ][RuCl 3 (CO) 3 ] (I) [systematic name: cis -di-carbonyl-chlorido(4'-chloro-2,2':6',2''-terpyridine-κ 3 N )ruthenium(II) fac -tricarbonyltri-chlorido-ruthenate(II)], and [RuCl 2 (tpy-Cl)(CO) 2 ] (II) [ cis -dicarbonyl- trans -di-chlorido(4'-chloro-2,2':6',2''-terpyridine-κ 2 N 1 , N 1' )ruthenium(II)], were synthesized and characterized by single-crystal X-ray diffraction. The Ru II atoms in both centrosymmetric structures (I) and (II) display similar, slightly distorted octa-hedral coordination spheres. The coordination sphere in the complex cation in compound (I) is defined by three N atoms of the tridentate tpy-Cl ligand, two carbonyl carbon atoms and one chlorido ligand; the charge is balanced by an octa-hedral [Ru(CO) 3 Cl 3 ] - counter-anion. In the neutral compound (II), the tpy-Cl ligand coordinates to the metal only through two of its N atoms. The coordination sphere of the Ru II atom is completed by two carbonyl and two chlorido ligands. In the crystal structures of both (I) and (II), weak C-H⋯Cl inter-actions are observed.

Alkyl group dependence on structure and magnetic properties in layered cobalt coordination polymers containing substituted glutarate ligands and 4,4'-bipyridine

International Nuclear Information System (INIS)

Nettleman, Joseph H.; Supkowski, Ronald M.; LaDuca, Robert L.

2010-01-01

Five two-dimensional divalent cobalt coordination polymers containing 4,4'-bipyridine (bpy) and substituted or unsubstituted glutarate ligands have been prepared hydrothermally and structurally characterized by single-crystal X-ray diffraction. [Co(mg)(bpy)] n (1, mg=3-methylglutarate) forms a (4,4) rhomboid grid structure based on the connection of {Co 2 (CO 2 ) 2 } dimeric units. Using the more sterically encumbered ligands 3,3-dimethylglutarate (dmg) and 3-ethyl, 3-methylglutarate (emg) generated {[Co(dmg)(bpy)(H 2 O)].2H 2 O} n (2) and {[Co(emg)(bpy)(H 2 O)].H 2 O} n (3), respectively. These complexes manifest {Co(CO 2 )} n chains linked into 2-D by aliphatic dicarboxylate and bpy ligands. The 'tied-back' substituted glutarate ligand 1,1-cyclopentanediacetate (cda) afforded [Co(cda)(bpy)] n (4), and the unsubstituted glutarate (glu) generated [Co(glu)(bpy)] n (5), both of which exhibit a topology similar to that of 1. The magnetic properties of complexes 1-4 were analyzed successfully with a recently developed phenomenological chain model accounting for both magnetic coupling (J) and zero-field splitting effects (D), even though 1 and 4 contain isolated, discrete {Co 2 (CO 2 ) 2 } dimers. The D parameter in this series varied between 21.8(8) and 48.0(9) cm -1 . However weak antiferromagnetic coupling was observed in 1 (J=-2.43(4) cm -1 ) and 4 (J=-0.89(2) cm -1 ), while weak ferromagnetic coupling appears to be operative in both 2 (J=0.324(5) cm -1 ) and 3 (J=0.24(1) cm -1 ). - Five two-dimensional divalent cobalt coordination polymers containing 4,4'-bipyridine (bpy) and substituted or unsubstituted glutarate ligands have been prepared and structurally characterized by single-crystal X-ray diffraction. Three contain dimeric {Co 2 (CO 2 ) 2 } units, while two manifest {Co(CO 2 )} n chains, depending on the steric bulk of the substituent. The magnetic properties of the complexes were analyzed successfully with a recently developed phenomenological chain model

Evaluation of the exchange interaction and crystal fields in a prototype Dy2 SMM

Science.gov (United States)

Zhang, Qing; Sarachik, Myriam; Baker, Michael; Chen, Yizhang; Kent, Andrew; Pineda, Eufemio; McInnes, Eric

In order to gain an understanding of the INS and magnetization data obtained for Dy2, the simplest member of a newly synthesized family of dysprosium-based molecular magnets, we report on calculations of the magnetic behavior of a Dy2 cluster with the formula [hqH2][Dy2(hq)4(NO3)3].MeOH. The molecular complex contains one high symmetry Dy(III) ion and one low symmetry Dy(III) ion. Our calculations suggest that exchange coupling between the two ions controls the behavior of the magnetization at low temperature, while the crystal field of the low symmetry Dy(III) ion controls the behavior at higher temperature. A point charge electrostatic model, based on crystallographic coordinates, provides a starting point for the determination of the crystal field. Parameters in these calculations are adjusted to provide best fits to inelastic neutron scattering data (INS) and low temperature magnetometry: the INS measurements access crystal field energies and low temperature magnetization probes the Dy-Dy exchange interaction. Work supported by ARO W911NF-13-1-1025 (CCNY) and NSF-DMR-1309202 (NYU).

Crystal structure of (benzenecarbothioamide-κSchloridobis(triphenylphosphane-κPsilver(I

Directory of Open Access Journals (Sweden)

Wattana Ruangwut

2014-09-01

Full Text Available In the mononuclear mixed-ligand title complex, [AgCl(C7H7NS(C18H15P2], the AgI ion is four coordinated by one S atom of a benzenecarbothioamide ligand, two P atoms of two triphenylphosphane ligands and one chloride ion, displaying a distorted tetrahedral coordination geometry. In the crystal, pairs of N—H...Cl hydrogen bonds form inversion dimers. An intramolecular N—H...Cl hydrogen bond is also observed.

Chiral multichromic single crystals for optical devices (LDRD 99406).

Energy Technology Data Exchange (ETDEWEB)

Kemp, Richard Alan; Felix, Ana M. (University of New Mexico, Albuquerque, NM)

2006-12-01

This report summarizes our findings during the study of a novel system that yields multi-colored materials as products. This system is quite unusual as it leads to multi-chromic behavior in single crystals, where one would expect that only a single color would exist. We have speculated that these novel solids might play a role in materials applications such as non-linear optics, liquid crystal displays, piezoelectric devices, and other similar applications. The system examined consisted of a main-group alkyl compound (a p block element such as gallium or aluminum) complexed with various organic di-imines. The di-imines had substituents of two types--either alkyl or aromatic groups attached to the nitrogen atoms. We observed that single crystals, characterized by X-ray crystallography, were obtained in most cases. Our research during January-July, 2006, was geared towards understanding the factors leading to the multi-chromic nature of the complexes. The main possibilities put forth initially considered (a) the chiral nature of the main group metal, (b) possible reduction of the metal to a lower-valent, radical state, (c) the nature of the ligand(s) attached to the main group metal, and (d) possible degradation products of the ligand leading to highly-colored products. The work carried out indicates that the most likely explanation considered involves degradation of the aromatic ligands (a combination of (c) and (d)), as the experiments performed can clearly rule out (a) and (b).

Selective extraction of americium(III) over europium(III) ions with pyridylpyrazole ligands. Structure-property relationships

Energy Technology Data Exchange (ETDEWEB)

Su, Dongping; Liu, Ying; Li, Shimeng; Ding, Songdong; Jin, Yongdong; Wang, Zhipeng; Hu, Xiaoyang; Zhang, Lirong [Department of chemistry, Sichuan University, Chengdu (China)

2017-01-18

To clarify the structure-property relationships of pyridylpyrazole ligands and provide guidance for the design of new and more efficient ligands for the selective extraction of actinides over lanthanides, a series of alkyl-substituted pyridylpyrazole ligands with different branched chains at different positions of the pyrazole ring were synthesized. Extraction experiments showed that the pyridylpyrazole ligands exhibited good selective extraction abilities for Am{sup III} ions, and the steric effects of the branched chain had a significant impact on the distribution ratios of Am{sup III} and Eu{sup III} ions as well as the separation factor. Moreover, both slope analyses and UV/Vis spectrometry titrations indicated the formation of a 1:1 complex of 2-(1-octyl-1H-pyrazol-3-yl)pyridine (C8-PypzH) with Eu{sup III} ions. The stability constant (log K) for this complex obtained from the UV/Vis titration was 4.45 ± 0.04. Single crystals of the complexes of 3-(2-pyridyl)pyrazole (PypzH) with Eu(NO{sub 3}){sub 3} and Sm(NO{sub 3}){sub 3} were obtained; PypzH acts as a bidentate ligand in the crystal structures, and the N atom with a bound H atom did not participate in the coordination. In general, this study revealed some interesting findings on the effects of the alkyl-chain structure and the special complexation between pyridylpyrazole ligands and Ln{sup III} ions. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Random crystal field effects on the integer and half-integer mixed-spin system

Science.gov (United States)

Yigit, Ali; Albayrak, Erhan

2018-05-01

In this work, we have focused on the random crystal field effects on the phase diagrams of the mixed spin-1 and spin-5/2 Ising system obtained by utilizing the exact recursion relations (ERR) on the Bethe lattice (BL). The distribution function P(Di) = pδ [Di - D(1 + α) ] +(1 - p) δ [Di - D(1 - α) ] is used to randomize the crystal field.The phase diagrams are found to exhibit second- and first-order phase transitions depending on the values of α, D and p. It is also observed that the model displays tricritical point, isolated point, critical end point and three compensation temperatures for suitable values of the system parameters.

Far-field and Fresnel Liquid Crystal Geometric Phase Holograms via Direct-Write Photo-Alignment

Directory of Open Access Journals (Sweden)

Xiao Xiang

2017-12-01

Full Text Available We study computer-generated geometric-phase holograms (GPHs realized by photo-aligned liquid crystals, in both simulation and experiment. We demonstrate both far-field and Fresnel holograms capable of producing far-field and near-field images with preserved fidelity for all wavelengths. The GPHs are fabricated by patterning a photo-alignment layer (PAL using a direct-write laser scanner and coating the surface with a polymerizable liquid crystal (i.e., a reactive mesogen. We study various recording pixel sizes, down to 3 μm, that are easily recorded in the PAL. We characterize the fabricated elements and find good agreement with theory and numerical simulation. Because of the wavelength independent geometric phase, the (phase fidelity of the replay images is preserved for all wavelengths, unlike conventional dynamic phase holograms. However, governed by the diffraction equation, the size and location of a reconstructed image depends on the replay wavelength for far-field and near-field GPHs, respectively. These offer interesting opportunities for white-light holography.

A method for fast energy estimation and visualization of protein-ligand interaction

Science.gov (United States)

Tomioka, Nobuo; Itai, Akiko; Iitaka, Yoichi

1987-10-01

A new computational and graphical method for facilitating ligand-protein docking studies is developed on a three-dimensional computer graphics display. Various physical and chemical properties inside the ligand binding pocket of a receptor protein, whose structure is elucidated by X-ray crystal analysis, are calculated on three-dimensional grid points and are stored in advance. By utilizing those tabulated data, it is possible to estimate the non-bonded and electrostatic interaction energy and the number of possible hydrogen bonds between protein and ligand molecules in real time during an interactive docking operation. The method also provides a comprehensive visualization of the local environment inside the binding pocket. With this method, it becomes easier to find a roughly stable geometry of ligand molecules, and one can therefore make a rapid survey of the binding capability of many drug candidates. The method will be useful for drug design as well as for the examination of protein-ligand interactions.

Structural variability in Cu(I) and Ag(I) coordination polymers with a flexible dithione ligand: Synthesis, crystal structure, microbiological and theoretical studies

Energy Technology Data Exchange (ETDEWEB)

Beheshti, Azizolla, E-mail: a.beheshti@scu.ac.ir [Department of Chemistry, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz (Iran, Islamic Republic of); Nozarian, Kimia; Babadi, Susan Soleymani; Noorizadeh, Siamak [Department of Chemistry, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz (Iran, Islamic Republic of); Motamedi, Hossein [Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz (Iran, Islamic Republic of); Mayer, Peter [LMU München Department Chemie, Butenandtstr 5-13, D-81377 München (Germany); Bruno, Giuseppe [Dipartimento di Chimica Inorganica, Università di Messina, Vill. S. Agata, Salita Sperone 31, 98166 Messina (Italy); Rudbari, Hadi Amiri [Faculty of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of)

2017-05-15

Two new compounds namely [Cu(SCN)(µ-L)]{sub n} (1) and ([Ag (µ{sub 2}-L)](ClO{sub 4})){sub n} (2) have been synthesized at room temperature by one-pot reactions between the 1,1-(1,4-butanediyl)bis(1,3-dihydro-3-methyl-1H-imidazole- 2-thione) (L) and appropriate copper(I) and silver(I) salts. These polymers have been characterized by single crystal X-ray diffraction, XRPD, TGA, elemental analysis, infrared spectroscopy, antibacterial activity and scanning probe microscopy studies. In the crystal structure of 1, copper atoms have a distorted trigonal planar geometry with a CuS{sub 2}N coordination environment. Each of the ligands in the structure of 1 acting as a bidentate S-bridging ligand to form a 1D chain structure. Additionally, the adjacent 1D chains are interconnected by the intermolecular C-H…S interactions to create a 2D network structure. In contrast to 1, in the cationic 3D structure of 2 each of the silver atoms exhibits an AgS{sub 4} tetrahedral geometry with 4-membered Ag{sub 2}S{sub 2} rings. In the structure of 2, the flexible ligand adopts two different conformations; gauche-anti-gauche and anti-anti-anti. The antibacterial studies of these polymers showed that polymer 2 is more potent antibacterial agent than 1. Scanning probe microscopy (SPM) study of the treated bacteria was carried out to investigate the structural changes cause by the interactions between the polymers and target bacteria. Theoretical study of polymer 1 investigated by the DFT calculations indicates that observed transitions at 266 nm and 302 nm in the UV–vis spectrum could be attributed to the π→π* and MLCT transitions, respectively. - Graphical abstract: Two new Cu(I) and Ag(I) coordination polymers have been have been synthesized by one-pot reactions. Copper complex has a 2D non-covalent structure, but silver compound is a 3D coordination compound. These compounds have effective antibacterial activity. - Highlights: • Cu(I) and Ag(I) based coordination polymers

Crystal field and magnetism with Wannier functions: rare-earth dopedaluminum garnets

Czech Academy of Sciences Publication Activity Database

Mihóková, Eva; Novák, Pavel; Laguta, Valentyn

2015-01-01

Roč. 33, č. 12 (2015), 1316-1323 ISSN 1002-0721 R&D Projects: GA ČR GA13-09876S Institutional support: RVO:68378271 Keywords : crystal field * ab initio calculations * garnets * rare earths Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.188, year: 2015

3,4-Dimethyl diphenyldithiophosphate of mononuclear cobalt(II) with N-donor ligands: Synthesis, structural characterization, DFT and antibacterial studies

Science.gov (United States)

Kumar, Sandeep; Kour, Gurpreet; Schreckenbach, Georg; Andotra, Savit; Hundal, Geeta; Sharma, Vishal; Jaglan, Sundeep; Pandey, Sushil K.

2017-08-01

3,4-Dimethyl diphenyldithiophosphate of cobalt(II) with N-donor ligands [{(ArO)2PS2}2CoL2] [Ar = 3,4-(CH3)2C6H3 (1-3); L = C5H5N (1), 3,4-(CH3)2C5H3N (2) and 4-(C2H5)C5H4N (3)] have been synthesized and characterized by elemental analyses, infrared spectroscopy (IR), powder X-ray diffraction (PXRD) and single crystal X-ray analysis. Complex 1 crystallizes in the monoclinic space group P21/n whereas complexes 2 and 3 crystallize in the triclinic space group Pbar1. The crystal structures of complexes 1-3 reveal mononuclear units with the Co(II) center chelated in bidentate fashion by four S atoms of the two diphenyldithiophosphate ligands. The N atoms from two donor ligands are axially coordinated, leading to distorted octahedral geometry around Co(II). The complexes have been optimized using density functional theory (DFT), structural parameters have been calculated, and the energy gaps of the frontier orbitals (HOMO-LUMO) have been predicted. Mayer bond orders have also been calculated. Structural parameters from the crystallographic and DFT studies are in good agreement with each other. To explore the biological potential, complexes were evaluated for their antibacterial activity against three bacterial strains. The bacterial growth inhibition capacity of the ligand and complexes followed the order of 3 > 2 > 1 > L1.

Crystal-field investigations of rare-earth-doped wide band gap semiconductors

CERN Multimedia

Muller, S; Wahl, U

Crystal field investigations play a central role in the studies of rare earth doped semiconductors. Optical stark level spectroscopy and lattice location studies of radioactive rare earth isotopes implanted at ISOLDE have provided important insight into these systems during the last years. It has been shown that despite a major site preference of the probe atoms in the lattice, several defect configurations do exist. These sites are visible in the optical spectra but their origin and nature aren't deducible from these spectra alone. Hyperfine measurements on the other hand should reveal these defect configurations and yield the parameters necessary for a description of the optical properties at the atomic scale. In order to study the crystal field with this alternative approach, we propose a new concept for perturbed $\\gamma\\gamma$-angular correlation (PAC) experiments at ISOLDE based on digital signal processing in contrast to earlier analog setups. The general functionality of the spectrometer is explained ...

40-Tesla pulsed-field cryomagnet for single crystal neutron diffraction

Science.gov (United States)

Duc, F.; Tonon, X.; Billette, J.; Rollet, B.; Knafo, W.; Bourdarot, F.; Béard, J.; Mantegazza, F.; Longuet, B.; Lorenzo, J. E.; Lelièvre-Berna, E.; Frings, P.; Regnault, L.-P.

2018-05-01

We present the first long-duration and high duty cycle 40-T pulsed-field cryomagnet addressed to single crystal neutron diffraction experiments at temperatures down to 2 K. The magnet produces a horizontal field in a bi-conical geometry, ±15° and ±30° upstream and downstream of the sample, respectively. Using a 1.15 MJ mobile generator, magnetic field pulses of 100 ms length are generated in the magnet, with a rise time of 23 ms and a repetition rate of 6-7 pulses per hour at 40 T. The setup was validated for neutron diffraction on the CEA-CRG three-axis spectrometer IN22 at the Institut Laue Langevin.

Exchange and crystal field effects in the ESR spectra of Eu2+ in LaB6

Science.gov (United States)

Duque, J. G. S.; Urbano, R. R.; Venegas, P. A.; Pagliuso, P. G.; Rettori, C.; Fisk, Z.; Oseroff, S. B.

2007-09-01

Electron spin resonance of Eu2+ ( 4f7 , S=7/2 ) in a La hexaboride (LaB6) single crystal shows a single anisotropic Dysonian resonance. From the observed negative g shift of the resonance, it is inferred that the Eu2+ ions are covalent exchange coupled to the B2p -like host conduction electrons. From the anisotropy of the spectra (linewidth and field for resonance), we found that the S ground state of Eu2+ ions experience a cubic crystal field of a negative fourth order crystal field parameter (CFP), b4=-11.5(2.0)Oe , in agreement with the negative fourth order CFP, A4 , found for the non- S ground state R hexaborides. These results support covalency as the dominant contribution to the fourth order CFP for the whole R hexaboride family.

Electron paramagnetic resonance spectral study of [Mn(acs){sub 2}(2–pic){sub 2}(H{sub 2}O){sub 2}] single crystals

Energy Technology Data Exchange (ETDEWEB)

Kocakoç, Mehpeyker, E-mail: mkocakoc@cu.edu.tr [Çukurova University (Turkey); Tapramaz, Recep, E-mail: recept@omu.edu.tr [Ondokuz Mayıs University (Turkey)

2016-03-25

Acesulfame potassium salt is a synthetic and non-caloric sweetener. It is also important chemically for its capability of being ligand in coordination compounds, because it can bind over Nitrogen and Oxygen atoms of carbonyl and sulfonyl groups and ring oxygen. Some acesulfame containing transition metal ion complexes with mixed ligands exhibit solvato and thermo chromic properties and these properties make them physically important. In this work single crystals of Mn{sup +2} ion complex with mixed ligand, [Mn(acs){sub 2}(2-pic){sub 2}(H{sub 2}O){sub 2}], was studied with electron paramagnetic resonance (EPR) spectroscopy. EPR parameters were determined. Zero field splitting parameters indicated that the complex was highly symmetric. Variable temperature studies showed no detectable chance in spectra.

Unified calculations of the optical band positions and EPR g factors for NaCrS2 crystal

International Nuclear Information System (INIS)

Mei, Yang; Zheng, Wen-Chen; Zhang, Lin

2014-01-01

Six optical band positions and EPR g factors g || , g ⊥ for the trigonal Cr 3+ octahedral clusters in NaCrS 2 crystal are calculated together through the complete diagonalization (of energy matrix) method based on the two-spin–orbit-parameter model, where besides the contribution due to the spin–orbit parameter of central d n ion in the conventional crystal-field theory, the contribution due to the spin–orbit parameter of ligand ion via the covalence effect is also considered. In the calculations, the crystal-field parameters B kl are obtained from the superposition model with the structural data of Cr 3+ octahedral clusters in NaCrS 2 crystal measured exactly by the X-ray diffraction method. The calculated optical and EPR spectral data are in a reasonable agreement with the observed values. So, the reliability of the superposition model in the studies of crystal-field parameters for d n ions in crystals is confirmed, and the complete diagonalization (of energy matrix) method based on the two-spin–orbit-model is effective in the unified calculations of optical and EPR spectral data for d n ions in crystals. - Highlights: • Six optical band positions and g factors g || , g ⊥ of NaCrS 2 are calculated together. • Calculation is using the complete diagonalization (of energy matrix) method. • The diagonalization method is based on the two-spin–orbit-parameter model. • Reliability of superposition model in the studies of CF parameters is confirmed

Ag-ligand modified tungstovandates and their efficient catalysis degradation properties for methylene blue

Energy Technology Data Exchange (ETDEWEB)

Zheng, Ran; Zhang, Huixia; Liu, Yunping; Wang, Xiaoxiao; Han, Zhangang, E-mail: hanzg116@126.com

2017-02-15

Two polytungstovandates [Ag(mbpy){sub 2}][Ag{sub 2}(mbpy){sub 3}][VW{sub 5}O{sub 19}]·H{sub 2}O (1) and [Ag(mbpy)]{sub 2}[Ag(mbpy){sub 2}]{sub 4}[VW{sub 12}O{sub 40}] (2) (mbpy =4,4′-dimethyl-2,2′-bipyridyl), had been hydrothermally synthesized and characterized by IR, TG, and single-crystal X-ray diffraction techniques. Single-crystal structural analysis revealed that the polyanionic clusters in two compounds are different: Lindqvist-type in 1 and α-Keggin-type in 2, respectively, while the cationic moieties in them are Ag-mbpy units. The experiments showed that this kind of hybrid crystal materials possesses more efficiently catalytic performance for the degradation of organic dye methylene blue (MB) in water solution under the UV irradiation. The significant degradation rate of MB can reach 89.9%, 94.9% by crystals 1 and 2 (40 mg) in the course of about 5 min. - Graphical abstract: Two Ag-ligand modified polytungstovandates had been synthesized and characterized, which were active in the catalytic degradation of organic dye methylene blue under the UV irradiation. - Highlights: • Two Ag-ligand modified tungstovandates were synthesized and characterized. • Weak interactions play important roles in constructing crystal frameworks. • Compounds are active to catalyze the degradation of methylene blue.

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

Science.gov (United States)

2014-01-01

We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

Relative work function of clean molybdenum single-crystal planes determined by field emission microscopy

International Nuclear Information System (INIS)

Bergeret, G.; Abon, M.; Tardy, B.; Teichner, S.J.

1974-01-01

A probe-hole field emission microscope was used to determine the work function of clean molybdenum single crystal planes relative to the average work function of the field emitter, assumed to be 4.20 eV. Results are compared with other available data

An energy-stable convex splitting for the phase-field crystal equation

KAUST Repository

Vignal, P.; Dalcin, L.; Brown, D. L.; Collier, N.; Calo, V. M.

2015-01-01

Abstract The phase-field crystal equation, a parabolic, sixth-order and nonlinear partial differential equation, has generated considerable interest as a possible solution to problems arising in molecular dynamics. Nonetheless, solving this equation is not a trivial task, as energy dissipation and mass conservation need to be verified for the numerical solution to be valid. This work addresses these issues, and proposes a novel algorithm that guarantees mass conservation, unconditional energy stability and second-order accuracy in time. Numerical results validating our proofs are presented, and two and three dimensional simulations involving crystal growth are shown, highlighting the robustness of the method. © 2015 Elsevier Ltd.

An energy-stable convex splitting for the phase-field crystal equation

KAUST Repository

Vignal, P.

2015-10-01

Abstract The phase-field crystal equation, a parabolic, sixth-order and nonlinear partial differential equation, has generated considerable interest as a possible solution to problems arising in molecular dynamics. Nonetheless, solving this equation is not a trivial task, as energy dissipation and mass conservation need to be verified for the numerical solution to be valid. This work addresses these issues, and proposes a novel algorithm that guarantees mass conservation, unconditional energy stability and second-order accuracy in time. Numerical results validating our proofs are presented, and two and three dimensional simulations involving crystal growth are shown, highlighting the robustness of the method. © 2015 Elsevier Ltd.

Wave dispersion relation of two-dimensional plasma crystals in a magnetic field

International Nuclear Information System (INIS)

Uchida, G.; Konopka, U.; Morfill, G.

2004-01-01

The wave dispersion relation in a two-dimensional strongly coupled plasma crystal is studied by theoretical analysis and molecular dynamics simulation taking into account a constant magnetic field parallel to the crystal normal. The expression for the wave dispersion relation clearly shows that high-frequency and low-frequency branches exist as a result of the coupling of longitudinal and transverse modes due to the Lorenz force acting on the dust particles. The high-frequency and the low-frequency branches are found to belong to right-hand and left-hand polarized waves, respectively

Selective oxoanion separation using a tripodal ligand

Energy Technology Data Exchange (ETDEWEB)

Custelcean, Radu; Moyer, Bruce A.; Rajbanshi, Arbin

2016-02-16

The present invention relates to urea-functionalized crystalline capsules self-assembled by sodium or potassium cation coordination and by hydrogen-bonding water bridges to selectively encapsulate tetrahedral divalent oxoanions from highly competitive aqueous alkaline solutions and methods using this system for selective anion separations from industrial solutions. The method involves competitive crystallizations using a tripodal tris(urea) functionalized ligand and, in particular, provides a viable approach to sulfate separation from nuclear wastes.

L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain

DEFF Research Database (Denmark)

Krintel, Christian; Frydenvang, Karla; Ceravalls de Rabassa, Anna

2014-01-01

In purification of the ionotropic glutamate receptor A2 (GluA2) ligand-binding domain (LBD), L-Glu supplemented buffers have previously been used for protein stabilization during the procedure. This sometimes hampers structural studies of low affinity ligands because L-Glu is difficult to displace...... crystallized as a mixed dimer with L-Glu present in one subunit while neither L-Asp nor L-Glu were found in the other subunit. Thus, residual L-Glu is still present from the expression. On the other hand, only L-Asp was found at the binding site when using 50 mM or 250 mM L-Asp for crystallization. The binding...... mode observed for L-Asp at the GluA2 LBD is very similar to that described for L-Glu. Taken together, we have shown that L-Asp can be used instead of L-Glu for ligand-dependent stabilization of the GluA2 LBD during purification. This will enable structural studies of low affinity ligands for lead...

Residue preference mapping of ligand fragments in the Protein Data Bank.

Science.gov (United States)

Wang, Lirong; Xie, Zhaojun; Wipf, Peter; Xie, Xiang-Qun

2011-04-25

The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71 798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.

Electron paramagnetic resonance investigations of Fe3+ doped layered TiInS2 and TiGaSe2 single crystals

International Nuclear Information System (INIS)

Faik, Mikailov; Bulat, Rameev; Sinan, Kazan; Bekir, Aktash; Faik, Mikailov; Bulat, Rameev

2005-01-01

Full text : TiInS 2 and TiGaSe 2 single crystals doped by paramagnetic Fe ions have been studied at room temperature by Electron Paramagnetic Resonance (EPR) technique. A fine structure of EPR spectra of paramagnetic Fe 3 + ions was observed. The spectra were interpreted to correspond to the transitions among spin multiplet which are splitted by the local ligand crystal field (CF) of orthorhombic symmetry. Four equivalent Fe 3 + centers have been observed in the EPR spectra and the local symmetry of crystal field at the Fe 3 + site and CF parameters were determined. It was established that symmetry axis of the axial component in the CF is making an angle of about 48 and 43 degree with the plane of layers of TiInS 2 and TiGaSe 2 crystals respectively. Experimental results indicate that the Fe ions substitute In (GA) at the center of InS 4 (GaSe 4 ) tetrahedrons, and the rhombic distortion of the CF is caused by the TI ions located in the trigonal cavities between the tethedral complexes

The concept of mixed organic ligands in metal-organic frameworks: design, tuning and functions.

Science.gov (United States)

Yin, Zheng; Zhou, Yan-Ling; Zeng, Ming-Hua; Kurmoo, Mohamedally

2015-03-28

The research on metal-organic frameworks (MOFs) has been developing at an extraordinary pace in its two decades of existence, as judged by the exponential growth of novel structures and the constant expansion of its applicability and research scope. A major part of the research and its success are due to the vital role of the concept of mixed organic ligands in the design, tuning and functions. This perspective, therefore, reviews the recent advances in MOFs based on this concept, which is generally based on employing a small polydentate ligand (here labelled as "nodal ligand") to form either clusters, rods or layers, which are then connected by a second ditopic linker ligand to form the framework. The structures of the materials can be grouped into the following three categories: layer-spacer (usually known as pillared-layer), rod-spacer, and cluster-spacer based MOFs. Depending on the size and geometry of the spacer ligands, interpenetrations of frameworks are occasionally found. These MOFs show a wide range of properties such as (a) crystal-to-crystal transformations upon solvent modifications, post-synthetic metal exchange or ligand reactions, (b) gas sorption, solvent selectivity and purification, (c) specific catalysis, (d) optical properties including colour change, luminescence, non-linear optic, (e) short- and long range magnetic ordering, metamagnetism and reversible ground-state modifications and (f) drug and iodine carriers with controlled release. In the following, we will highlight the importance of the above concept in the design, tuning, and functions of a selection of existing MOFs having mixed organic ligands and their associated structures and properties. The results obtained so far using this concept look very promising for fine-tuning the pore size and shape for selective adsorption and specificity in catalytic reactions, which appears to be one way to propel the advances in the application and commercialization of MOFs.

Effect of magnetic field on the wave dispersion relation in three-dimensional dusty plasma crystals

International Nuclear Information System (INIS)

Yang Xuefeng; Wang Zhengxiong

2012-01-01

Three-dimensional plasma crystals under microgravity condition are investigated by taking into account an external magnetic field. The wave dispersion relations of dust lattice modes in the body centered cubic (bcc) and the face centered cubic (fcc) plasma crystals are obtained explicitly when the magnetic field is perpendicular to the wave motion. The wave dispersion relations of dust lattice modes in the bcc and fcc plasma crystals are calculated numerically when the magnetic field is in an arbitrary direction. The numerical results show that one longitudinal mode and two transverse modes are coupled due to the Lorentz force in the magnetic field. Moreover, three wave modes, i.e., the high frequency phonon mode, the low frequency phonon mode, and the optical mode, are obtained. The optical mode and at least one phonon mode are hybrid modes. When the magnetic field is neither parallel nor perpendicular to the primitive wave motion, all the three wave modes are hybrid modes and do not have any intersection points. It is also found that with increasing the magnetic field strength, the frequency of the optical mode increases and has a cutoff at the cyclotron frequency of the dust particles in the limit of long wavelength, and the mode mixings for both the optical mode and the high frequency phonon mode increase. The acoustic velocity of the low frequency phonon mode is zero. In addition, the acoustic velocity of the high frequency phonon mode depends on the angle of the magnetic field and the wave motion but does not depend on the magnetic field strength.

Automating crystallographic structure solution and refinement of protein–ligand complexes

International Nuclear Information System (INIS)

Echols, Nathaniel; Moriarty, Nigel W.; Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

2013-01-01

A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation

Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR.

Directory of Open Access Journals (Sweden)

Sean Ekins

2009-12-01

Full Text Available Transcriptional regulation of some genes involved in xenobiotic detoxification and apoptosis is performed via the human pregnane X receptor (PXR which in turn is activated by structurally diverse agonists including steroid hormones. Activation of PXR has the potential to initiate adverse effects, altering drug pharmacokinetics or perturbing physiological processes. Reliable computational prediction of PXR agonists would be valuable for pharmaceutical and toxicological research. There has been limited success with structure-based modeling approaches to predict human PXR activators. Slightly better success has been achieved with ligand-based modeling methods including quantitative structure-activity relationship (QSAR analysis, pharmacophore modeling and machine learning. In this study, we present a comprehensive analysis focused on prediction of 115 steroids for ligand binding activity towards human PXR. Six crystal structures were used as templates for docking and ligand-based modeling approaches (two-, three-, four- and five-dimensional analyses. The best success at external prediction was achieved with 5D-QSAR. Bayesian models with FCFP_6 descriptors were validated after leaving a large percentage of the dataset out and using an external test set. Docking of ligands to the PXR structure co-crystallized with hyperforin had the best statistics for this method. Sulfated steroids (which are activators were consistently predicted as non-activators while, poorly predicted steroids were docked in a reverse mode compared to 5alpha-androstan-3beta-ol. Modeling of human PXR represents a complex challenge by virtue of the large, flexible ligand-binding cavity. This study emphasizes this aspect, illustrating modest success using the largest quantitative data set to date and multiple modeling approaches.

Synthesis and Characterization of Divalent Manganese, Iron, and Cobalt Complexes in Tripodal Phenolate/N-Heterocyclic Carbene Ligand Environments

DEFF Research Database (Denmark)

Käß, Martina; Hohenberger, Johannes; Adelhardt, Mario

2014-01-01

. The complete ligand series offers a convenient way of tuning the electronic and steric environment around the metal center, thus, allowing for control of the complex’s reactivity. This series of divalent complexes of Mn, Fe, and Co was synthesized and characterized by 1H NMR, IR, and UV/vis spectroscopy...... as well as by single-crystal X-ray diffraction studies. Variable-temperature SQUID magnetization measurements in the range from 2 to 300 K confirmed high-spin ground states for all divalent complexes and revealed a trend of increasing zero-field splitting |D| from Mn(II), to Fe(II), to Co(II) complexes...

Preparation and crystal and molecular structure of mer-trichlorotris(dimethylphenylphosphine)technetium(III)

Energy Technology Data Exchange (ETDEWEB)

Bandoli, G; Clemente, D A; Mazzi, U [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi

1976-01-01

The crystal and molecular structure of the title compound has been determined from single-crystal X-ray diffractometer data by Fourier methods and refined by anisotropic block-diagonal least-squares to R 0.054 for 4 065 independent observed reflections. Crystals are monoclinic, space group P2/sub 1//n, with cell parameters a = 10.935(9), b = 39.191(11), c = 13.738(7) A, ..beta.. = 107.33(7)/sup 0/, and Z = 8. The two crystallographically independent molecules are stereochemically equivalent (there is only a small difference in the orientation of a benzene ring) and the metal atom has a somewhat distorted octahedral co-ordination, with two pairs of like ligands mutually trans. Technetium-ligand bond distances are: Tc-Cl(trans to P) 2.46(1), Tc-Cl(trans to Cl) both 2.33(1), Tc-P(trans to Cl) 2.42(1) and Tc-P(trans to P) both 2.47(1) A. The noticeable trans-influence of the phosphine ligands on Tc-Cl bonds is discussed.

Reorientation of single-wall carbon nanotubes in negative anisotropy liquid crystals by an electric field

Directory of Open Access Journals (Sweden)

Amanda García-García

2016-06-01

Full Text Available Single-wall carbon nanotubes (SWCNT are anisotropic nanoparticles that can cause modifications in the electrical and electro-optical properties of liquid crystals. The control of the SWCNT concentration, distribution and reorientation in such self-organized fluids allows for the possibility of tuning the liquid crystal properties. The alignment and reorientation of CNTs are studied in a system where the liquid crystal orientation effect has been isolated. Complementary studies including Raman spectroscopy, microscopic inspection and impedance studies were carried out. The results reveal an ordered reorientation of the CNTs induced by an electric field, which does not alter the orientation of the liquid crystal molecules. Moreover, impedance spectroscopy suggests a nonnegligible anchoring force between the CNTs and the liquid crystal molecules.

Flood field uniformity testing - effects of crystal hydration

International Nuclear Information System (INIS)

Dimcheva, M.; Sergieva, S.; Doldurova, M.; Jovanovska, A.

2012-01-01

The most basic and sensitive routine quality control (QC) of gamma camera is that of intrinsic flood-field uniformity. The routine QC test must be assessed daily and any nonuniformity must be eliminated before patient testing to eliminate artifacts and false positive or false-negative patient results. The purpose of this study was to compare uniformity analysis results for scintillation crystal hydration with symmetric and asymmetric energy window on the Siemens Symbia T2 SPECTCT camera. Integral and differential uniformity analysis was performed by placing a point source 99m Tc in front of the detector with removed collimator to measure the effect of correction matrix, a count rate and activity volume on intrinsic uniformity. A 15% energy window set symmetrically over the 99m Tc photo peak is equivalent to 140±10% keV or a window spanning 126-154 keV. The results, received from Detector 2 gave the following uniformity parameter values: Both asymmetric energy window images show clearly multiple focal spots due to crystal hydration: discrete hot spots in the asymmetric low window image and discrete cold spots in the asymmetric high window image. The above results are not seen yet on the symmetric window image. We had replaced Detector 2 in order to avoid spots become visible in flood images obtained with the clinical energy window. The uniformity of a gamma camera is maybe the most important parameter that expresses the quality of the camera's performance. Non uniform areas in the field of view can result in misdiagnosed patients and low quality of clinical services. (authors)

Sampling and energy evaluation challenges in ligand binding protein design.

Science.gov (United States)

Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David

2017-12-01

The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Pressure-induced effects on the spectroscopic properties of Nd{sup 3+} in MgO:LiNbO{sub 3} single crystal. A crystal field approach

Energy Technology Data Exchange (ETDEWEB)

Muñoz Santiuste, J.E., E-mail: jems@fis.uc3m.es [Departamento de Física, Escuela Politécnica Superior, Universidad Carlos III de Madrid, Avenida de la Universidad 30, E-28913 Leganés, Madrid (Spain); MALTA Consolider Team (Spain); Lavín, V.; Rodríguez-Mendoza, U.R. [MALTA Consolider Team (Spain); Departamento de Física, INM and IUdEA, Universidad de La Laguna, Apdo. 456. E-38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Tardio, M.M.; Ramírez-Jiménez, R. [Departamento de Física, Escuela Politécnica Superior, Universidad Carlos III de Madrid, Avenida de la Universidad 30, E-28913 Leganés, Madrid (Spain)

2017-04-15

The effects of pressure on the Nd{sup 3+}-doped MgO:LiNbO{sub 3} single crystal have been studied by luminescence spectroscopy at low temperature and high pressures from ambient conditions up to 33 GPa. Specifically, the pressure-induced evolution of the emission spectra, corresponding to the {sup 4}F{sub 3/2}→{sup 4}I{sub 9/2},{sup 4}I{sub 11/2} transitions, and the excitation spectra, corresponding to the {sup 4}I{sub 9/2}→{sup 4}F{sub 5/2}+{sup 2}H{sub 9/2}, and {sup 4}I{sub 9/2}→{sup 4}F{sub 7/2}+{sup 4}S{sub 3/2} transitions, show a gradual red-shift that follows a linear pressure dependence and a decrease in the intensity of the spectra with increasing pressure. The initial effect of increasing pressure on the MgO:LiNbO{sub 3} crystal is the modification of the relative amount of the several centers in the sample. At pressures around 20 GPa the characteristic multicenter Nd{sup 3+} structure eventually disappears indicating that all the centers have very similar environments near this pressure. At higher pressures, observed changes seem to have a different origin. The evolution of Nd{sup 3+} luminescence is studied in the frame of crystal-field theory in order to evaluate its capability of monitoring the pressure-induced structural changes. Crystal-field analysis, under approximated C{sub 3v} symmetry, shows a smooth increase of the overall crystal-field strength on the luminescent ion, which can be related to the volume reduction as pressure increases. Crystal-field parameters also show a general monotonic behavior with pressure that indicates a structural modification of the local structure that, maintaining the trigonal symmetry around the impurity ion, evolves towards a lower axial character. No evidences of a phase transition have been observed in the studied pressure range.

Synthesis, Crystal Structures, and Photoluminescent Properties of Two Supramolecular Architectures Based on Difunctional Ligands Containing Imidazolyl and Carboxyl Groups

Directory of Open Access Journals (Sweden)

Mei-An Zhu

2017-07-01

Full Text Available Two new supramolecular architectures, namely, [Cd(L12(H2O]n (1 and [Ni(L22(H2O]n (2, were synthesized by the reaction of corresponding metal salts of CdCl2·2.5H2O and NiCl2·6H2O with 2-(1H-imidazol-4-ylbenzoic acid (HL1 and 3-(1H-imidazol-4-ylbenzoic acid (HL2 respectively, and characterized by single-crystal X-ray diffraction, IR spectroscopy, elemental analysis and powder X-ray diffraction (PXRD. Both HL1 and HL2 ligands are deprotonated to be L1- and L2- anions that coordinate with Cd(II and Ni(II atoms to form two-dimensional (2D layer structure. Topologically, complex 1 is a 2D network with (4, 4 sql topology, while 2 is a typical 63-hcb topology net. Complex 1 exhibits intense light blue emission in the solid state at room temperature.

The Evaluation of Novel Camphor-derived Ligands as Catalysts in ...

African Journals Online (AJOL)

The evaluation of a series of camphor-derived ligands as catalysts in the asymmetric Henry reaction is reported. The synthesis of two novel derivatives is detailed and these molecules are also screened as catalysts in this reaction. The single crystal X-ray structure of one of the novel compounds is reported. The reaction is ...

Synthesis and characterization of an iron complex bearing a cyclic tetra-N-heterocyclic carbene ligand: An artifical heme analogue?

KAUST Repository

Anneser, Markus R.

2015-04-20

An iron(II) complex with a cyclic tetradentate ligand containing four N-heterocyclic carbenes was synthesized and characterized by means of NMR and IR spectroscopies, as well as by single-crystal X-ray structure analysis. The iron center exhibits an octahedral coordination geometry with two acetonitrile ligands in axial positions, showing structural analogies with porphyrine-ligated iron complexes. The acetonitrile ligands can readily be substituted by other ligands, for instance, dimethyl sulfoxide, carbon monoxide, and nitric oxide. Cyclic voltammetry was used to examine the electronic properties of the synthesized compounds. © 2015 American Chemical Society.

Lattice distortion under an electric field in BaTiO3 piezoelectric single crystal

International Nuclear Information System (INIS)

Tazaki, Ryoko; Fu Desheng; Daimon, Masahiro; Koshihara, Shin-ya; Itoh, Mitsuru

2009-01-01

Lattice distortions under an electric field in a mono-domain of BaTiO 3 ferroelectric crystal have been detected with synchrotron x-ray radiation. The variation of the lattice constant with an electric field observed with high angle diffraction shows a linear response nature of the piezoelectric effect. When an electric field is applied along the spontaneous polarization direction, the c-axis of the lattice elongates and the a-axis of the lattice shrinks at a rate of d 33 = 149 ± 54 pm V -1 and d 31 = -82 ± 61 pm V -1 ; these represent the longitudinal and transverse piezoelectric coefficients of BaTiO 3 crystal, respectively. These results give an insight into the intrinsic piezoelectric response on the lattice scale in BaTiO 3 that has been widely used to explore high performance lead-free piezoelectric alloys.

Pulsed zero field NMR of solids and liquid crystals

International Nuclear Information System (INIS)

Thayer, A.M.

1987-02-01

This work describes the development and applications to solids and liquid crystals of zero field nuclear magnetic resonance (NMR) experiments with pulsed dc magnetic fields. Zero field NMR experiments are one approach for obtaining high resolution spectra of amorphous and polycrystalline materials which normally (in high field) display broad featureless spectra. The behavior of the spin system can be coherently manipulated and probed in zero field with dc magnetic field pulses which are employed in a similar manner to radiofrequency pulses in high field NMR experiments. Nematic phases of liquid crystalline systems are studied in order to observe the effects of the removal of an applied magnetic field on sample alignment and molecular order parameters. In nematic phases with positive and negative magnetic susceptibility anisotropies, a comparison between the forms of the spin interactions in high and low fields is made. High resolution zero field NMR spectra of unaligned smectic samples are also obtained and reflect the symmetry of the liquid crystalline environment. These experiments are a sensitive measure of the motionally induced asymmetry in biaxial phases. Homonuclear and heteronuclear solute spin systems are compared in the nematic and smectic phases. Nonaxially symmetric dipolar couplings are reported for several systems. The effects of residual fields in the presence of a non-zero asymmetry parameter are discussed theoretically and presented experimentally. Computer programs for simulations of these and other experimental results are also reported. 179 refs., 75 figs

Magnetic properties and crystal field effects in TlLnX2 compounds (X=S, Se, Te)

International Nuclear Information System (INIS)

Duczmal, M.; Pawlak, L.

1997-01-01

Ternary thallium lanthanide chalcogenides TlLnX 2 (X=S, Se or Te) crystallize in the α-NaFeO 2 type of structure (R anti 3m). Each kind of the metal ions, surrounded by the distorted chalcogenide octahedra, forms separate layers. The TlX 6 octahedra are strongly elongated and the LnX 6 octahedra slightly shrunk along the threefold axis. The deformations of the coordination polyhedra and the cell volumes change regularly with the lanthanide ionic radii. The difference between the experimental and the calculated M-X distances increases on going from sulphides to tellurides, as a result of the growing covalent character of the bonds. The crystal field parameters were estimated from the high field magnetization (0-14 T) assuming trigonal distortion of the octahedral symmetry of LnX 6 polyhedra. The second-order crystal field parameters were found to correlate with the deformation of the lanthanide ions' environments. No magnetic transition was observed down to 4.2 K. (orig.)

Crystal structures of a copper(II and the isotypic nickel(II and palladium(II complexes of the ligand (E-1-[(2,4,6-tribromophenyldiazenyl]naphthalen-2-ol

Directory of Open Access Journals (Sweden)

Souheyla Chetioui

2016-08-01

Full Text Available In the copper(II complex, bis{(E-1-[(2,4,6-tribromophenyldiazenyl]naphthalen-2-olato}copper(II, [Cu(C16H8Br3N2O2], (I, the metal cation is coordinated by two N atoms and two O atoms from two bidentate (E-1-[(2,4,6-tribromophenyldiazenyl]naphthalen-2-olate ligands, forming a slightly distorted square-planar environment. In one of the ligands, the tribromobenzene ring is inclined to the naphthalene ring system by 37.4 (5°, creating a weak intramolecular Cu...Br interaction [3.134 (2 Å], while in the other ligand, the tribromobenzene ring is inclined to the naphthalene ring system by 72.1 (6°. In the isotypic nickel(II and palladium(II complexes, namely bis{(E-1-[(2,4,6-tribromophenyldiazenyl]naphthalen-2-olato}nickel(II, [Ni(C16H8Br3N2O2], (II, and bis{(E-1-[(2,4,6-tribromophenyldiazenyl]naphthalen-2-olato}palladium(II, [Pd(C16H8Br3N2O2], (III, respectively, the metal atoms are located on centres of inversion, hence the metal coordination spheres have perfect square-planar geometries. The tribromobenzene rings are inclined to the naphthalene ring systems by 80.79 (18° in (II and by 80.8 (3° in (III. In the crystal of (I, molecules are linked by C—H...Br hydrogen bonds, forming chains along [010]. The chains are linked by C—H...π interactions, forming sheets parallel to (011. In the crystals of (II and (III, molecules are linked by C—H...π interactions, forming slabs parallel to (10-1. For the copper(II complex (I, a region of disordered electron density was corrected for using the SQUEEZE routine in PLATON [Spek (2015. Acta Cryst. C71, 9–18]. The formula mass and unit-cell characteristics of the disordered solvent molecules were not taken into account during refinement.

Colloidal Quantum Dot Inks for Single-Step-Fabricated Field-Effect Transistors: The Importance of Postdeposition Ligand Removal.

Science.gov (United States)

Balazs, Daniel M; Rizkia, Nisrina; Fang, Hong-Hua; Dirin, Dmitry N; Momand, Jamo; Kooi, Bart J; Kovalenko, Maksym V; Loi, Maria Antonietta

2018-02-14

Colloidal quantum dots are a class of solution-processed semiconductors with good prospects for photovoltaic and optoelectronic applications. Removal of the surfactant, so-called ligand exchange, is a crucial step in making the solid films conductive, but performing it in solid state introduces surface defects and cracks in the films. Hence, the formation of thick, device-grade films have only been possible through layer-by-layer processing, limiting the technological interest for quantum dot solids. Solution-phase ligand exchange before the deposition allows for the direct deposition of thick, homogeneous films suitable for device applications. In this work, fabrication of field-effect transistors in a single step is reported using blade-coating, an upscalable, industrially relevant technique. Most importantly, a postdeposition washing step results in device properties comparable to the best layer-by-layer processed devices, opening the way for large-scale fabrication and further interest from the research community.

Probing Ligand Exchange in the P450 Enzyme CYP121 from Mycobacterium tuberculosis: Dynamic Equilibrium of the Distal Heme Ligand as a Function of pH and Temperature.

Science.gov (United States)

Fielding, Andrew J; Dornevil, Kednerlin; Ma, Li; Davis, Ian; Liu, Aimin

2017-12-06

CYP121 is a cytochrome P450 enzyme from Mycobacterium tuberculosis that catalyzes the formation of a C-C bond between the aromatic groups of its cyclodityrosine substrate (cYY). The crystal structure of CYP121 in complex with cYY reveals that the solvent-derived ligand remains bound to the ferric ion in the enzyme-substrate complex. Whereas in the generally accepted P450 mechanism, binding of the primary substrate in the active-site triggers the release of the solvent-derived ligand, priming the metal center for reduction and subsequent O 2 binding. Here we employed sodium cyanide to probe the metal-ligand exchange of the enzyme and the enzyme-substrate complex. The cyano adducts were characterized by UV-vis, EPR, and ENDOR spectroscopies and X-ray crystallography. A 100-fold increase in the affinity of cyanide binding to the enzyme-substrate complex over the ligand-free enzyme was observed. The crystal structure of the [CYP121(cYY)CN] ternary complex showed a rearrangement of the substrate in the active-site, when compared to the structure of the binary [CYP121(cYY)] complex. Transient kinetic studies showed that cYY binding resulted in a lower second-order rate constant (k on (CN) ) but a much more stable cyanide adduct with 3 orders of magnitude slower k off (CN) rate. A dynamic equilibrium between multiple high- and low-spin species for both the enzyme and enzyme-substrate complex was also observed, which is sensitive to changes in both pH and temperature. Our data reveal the chemical and physical properties of the solvent-derived ligand of the enzyme, which will help to understand the initial steps of the catalytic mechanism.

Ligand field and intermolecular interactions tuning the magnetic properties of spin-crossover Fe(II) polymer with 4,4′-bipyridine

Energy Technology Data Exchange (ETDEWEB)

Luo, Yang-Hui; Liu, Qing-Ling; Yang, Li-Jing; Ling, Yang; Wang, Wei; Sun, Bai-Wang, E-mail: chmsunbw@seu.edu.cn

2015-02-15

A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4′-bipyridine (4,4′-bipy) family: (Fe(4,4′-bipy){sub 2}(H{sub 2}O){sub 2})·(4,4′-bipy)· 8(H{sub 2}O)·2(ClO{sub 4}) (3), which displays half spin transitions between 100 and 300 K, has been synthesized and structurally characterized. Compound 3 featured with two-dimensional (2-D) grids connected by hydrogen bonds and π…π packing between one-dimensional (1-D) chains, the 2-D grids expand to three-dimensional (3-D) architecture supported by a “S-shaped holder” involving lattice 4-4′-bipy, water molecules and perchlorate anion. We compared 3 with the other two analogous complexes: ((Fe(4,4′-bipy) (H{sub 2}O){sub 2} (NCS){sub 2})·4,4′-bipy, 1 and (Fe(4,4′-bipy){sub 2}(NCS){sub 2})·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS{sup −}) and lone-pair…H contacts contribute to the stabilization of HS (high-spin) state of the Fe(II) ion, while the high ligand field strength (4,4′-bipy) and strong intermolecular contacts (hydrogen bonds and π…π packing interactions) make for the LS (low-spin) state. - Highlights: ●A new member of Fe(||)-4,4′-bipy family has been prepared. ●It displays half spin transitions tuned by ligand field and intermolecular interactions. ●We have made a detailed comparison of this new member with two other analogous complexes.

Symmetry-adaptation and selection rules for effective crystal field Hamiltonians

International Nuclear Information System (INIS)

Tuszynski, J.A.

1986-01-01

The intention of this paper is to systematically derive an effective Hamiltonian in the presence of crystal fields in such a way as to incorporate relativistic effects and higher order perturbation corrections including configuration mixing. This Hamiltonian will then be conveniently represented as a symmetry-adapted series of one- and two-body double tensor operators whose matrix elements will be analyzed for selection rules. 16 references, 4 tables

Ligand design for alkali-metal-templated self-assembly of unique high-nuclearity CuII aggregates with diverse coordination cage units: crystal structures and properties.

Science.gov (United States)

Du, Miao; Bu, Xian-He; Guo, Ya-Mei; Ribas, Joan

2004-03-19

The construction of two unique, high-nuclearity Cu(II) supramolecular aggregates with tetrahedral or octahedral cage units, [(mu(3)-Cl)[Li subset Cu(4)(mu-L(1))(3)](3)](ClO(4))(8)(H(2)O)(4.5) (1) and [[Na(2) subset Cu(12)(mu-L(2))(8)(mu-Cl)(4)](ClO(4))(8)(H(2)O)(10)(H(3)O(+))(2)](infinity) (2) by alkali-metal-templated (Li(+) or Na(+)) self-assembly, was achieved by the use of two newly designed carboxylic-functionalized diazamesocyclic ligands, N,N'-bis(3-propionyloxy)-1,4-diazacycloheptane (H(2)L(1)) or 1,5-diazacyclooctane-N,N'-diacetate acid (H(2)L(2)). Complex 1 crystallizes in the trigonal R3c space group (a = b = 20.866(3), c = 126.26(4) A and Z = 12), and 2 in the triclinic P1 space group (a = 13.632(4), b = 14.754(4), c = 19.517(6) A, alpha = 99.836(6), beta = 95.793(5), gamma = 116.124(5) degrees and Z = 1). By subtle variation of the ligand structures and the alkali-metal templates, different polymeric motifs were obtained: a dodecanuclear architecture 1 consisting of three Cu(4) tetrahedral cage units with a Li(+) template, and a supramolecular chain 2 consisting of two crystallographically nonequivalent octahedral Cu(6) polyhedra with a Na(+) template. The effects of ligand functionality and alkali metal template ions on the self-assembly processes of both coordination supramolecular aggregates, and their magnetic behaviors are discussed in detail.

Synthesis, crystal structure, antibacterial activity and theoretical studies on a novel mononuclear cobalt(II) complex based on 2,4,6-tris(2-pyridyl)-1,3,5-triazine ligand

Science.gov (United States)

Maghami, Mahboobeh; Farzaneh, Faezeh; Simpson, Jim; Ghiasi, Mina; Azarkish, Mohammad

2015-08-01

A cobalt complex was prepared from CoCl2·6H2O and 2,4,6-tris(2-pyridyl)-1,3,5-triazine (tptz) in methanol and designated as [Co(tptz)(CH3OH)Cl2]·CH3OH·0.5H2O (1). It was characterized by several techniques including TGA analysis and FT-IR, UV-Vis and 1H NMR spectral studies. The crystal structure of 1 was determined by single-crystal X-ray diffraction. The Co(II) metal center in 1 is six coordinated with a distorted octahedral geometry. The tptz ligand is tridentate and coordinates to the cobalt through coplanar nitrogen atoms from the triazine and two pyridyl rings. Two chloride anions and a methanol molecule complete the inner coordination sphere of the metal ion. The optimized geometrical parameters obtained by DFT calculation are in good agreement with single XRD data. The in vitro antibacterial activity of various tptz complexes of Co(II), Ni(II), Cu(II), Mn(II) and Rh(III) were evaluated against Gram-positive (Bacillus subtilis, Staphylococcus aureus and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria. Whereas all complexes exhibited good activity in comparison to standard antibacterial drugs, the inhibitory effects of complexes were found to be more than that of the parent ligand. Overall, the obtained results strongly suggest that the cobalt(II) complex is a suitable candidate for counteracting antibiotic resistant microorganisms.

The future of type 1 cannabinoid receptor allosteric ligands.

Science.gov (United States)

Alaverdashvili, Mariam; Laprairie, Robert B

2018-02-01

Allosteric modulation of the type 1 cannabinoid receptor (CB1R) holds great therapeutic potential. This is because allosteric modulators do not possess intrinsic efficacy, but instead augment (positive allosteric modulation) or diminish (negative allosteric modulation) the receptor's response to endogenous ligand. Consequently, CB1R allosteric modulators have an effect ceiling which allows for the tempering of CB1R signaling without the desensitization, tolerance, dependence, and psychoactivity associated with orthosteric compounds. Pain, movement disorders, epilepsy, obesity are all potential therapeutic targets for CB1R allosteric modulation. Several challenges exist for the development of CB1R allosteric modulators, such as receptor subtype specificity, translation to in vivo systems, and mixed allosteric/agonist/inverse agonist activity. Despite these challenges, elucidation of crystal structures of CB1R and compound design based on structure-activity relationships will advance the field. In this review, we will cover recent progress for CB1R allosteric modulators and discuss the future promise of this research.

Crystal structure of an iridium(III complex of the [C(dppm2] PCP pincer ligand system and its conjugate CH acid form

Directory of Open Access Journals (Sweden)

Christian Reitsamer

2018-05-01

Full Text Available After the successful creation of the newly designed PCP carbodiphosphorane (CDP ligand [Reitsamer et al. (2012. Dalton Trans. 41, 3503–3514; Stallinger et al. (2007. Chem. Commun. pp. 510–512], the treatment of this PCP pincer system with the transition metal iridium and further the analysis of the structures by single-crystal diffraction and by NMR spectroscopy were of major interest. Two different iridium complexes, namely (bis{[(diphenylphosphanylmethyl]diphenylphosphanylidene}methane-κ3P,C,P′carbonylchloridohydridoiridium(III chloride dichloromethane trisolvate, [IrIII(CO{C(dppm2-κ3P,C,P′}ClH]Cl·3CH2Cl2 (1 and the closely related (bis{[(diphenylphosphanylmethyl]diphenylphosphanylidene}methanide(1+-κ3P,C,P′carbonylchloridohydridoiridium(III dichloride–hydrochloric acid–water (1/2/5.5, [IrIII(CO{CH(dppm2-κ3P,C,P′ClH]Cl}2 (2, have been designed and both complexes show a slightly distorted octahedral coordinated IrIII centre. The PCP pincer ligand system is arranged in a meridional manner, the CO ligand is located trans to the central PCP carbon and a hydride and chloride are located perpendicular above and below the P2C2 plane. With an Ir—CCDP distance of 2.157 (5 Å, an Ir—CO distance of 1.891 (6 Å and a quite short C—O distance of 1.117 (7 Å, complex 1 presents a strong carbonyl bond. Complex 2, the corresponding CH acid of 1, shows an additionally attached proton at the carbodiphosphorane carbon atom located antiperiplanar to the hydride of the metal centre. In comparison with complex 1, the Ir—CCDP distance of 2.207 (3 Å is lengthened and the Ir—C—O values indicate a weaker trans influence of the central carbodiphosphorane carbon atom.

Protein crystal growth on board Shenzhou 3: a concerted effort improves crystal diffraction quality and facilitates structure determination

International Nuclear Information System (INIS)

Han, Y.; Cang, H.-X.; Zhou, J.-X.; Wang, Y.-P.; Bi, R.-C.; Colelesage, J.; Delbaere, L.T.J.; Nahoum, V.; Shi, R.; Zhou, M.; Zhu, D.-W.; Lin, S.-X.

2004-01-01

The crystallization of 16 proteins was carried out using 60 wells on board Shenzhou 3 in 2002. Although the mission was only 7 days, careful and concerted planning at all stages made it possible to obtain crystals of improved quality compared to their ground controls for some of the proteins. Significantly improved resolutions were obtained from diffracted crystals of 4 proteins. A complete data set from a space crystal of the PEP carboxykinase yielded significantly higher resolution (1.46 A vs. 1.87 A), I/sigma (22.4 vs. 15.5), and a lower average temperature factor (29.2 A 2 vs. 42.9 A 2 ) than the best ground-based control crystal. The 3-D structure of the enzyme is well improved with significant ligand density. It has been postulated that the reduced convection and absence of macromolecule sedimentation under microgravity have advantages/benefits for protein crystal growth. Improvements in experimental design for protein crystal growth in microgravity are ongoing

Neat and complete: Thiolate-ligand exchange on a silver molecular nanoparticle

KAUST Repository

AbdulHalim, Lina G.

2014-11-12

Atomically precise thiolate-protected noble metal molecular nanoparticles are a promising class of model nanomaterials for catalysis, optoelectronics, and the bottom-up assembly of true molecular crystals. However, these applications have not fully materialized due to a lack of ligand exchange strategies that add functionality, but preserve the properties of these remarkable particles. Here we present a method for the rapid (<30 s) and complete thiolate-for-thiolate exchange of the highly sought after silver molecular nanoparticle [Ag44(SR)30]-4. Only by using this method were we able to preserve the precise nature of the particles and simultaneously replace the native ligands with ligands containing a variety of functional groups. Crucially, as a result of our method we were able to process the particles into smooth thin films, paving the way for their integration into solution-processed devices.

Neat and complete: Thiolate-ligand exchange on a silver molecular nanoparticle

KAUST Repository

AbdulHalim, Lina G.; Kothalawala, Nuwan; Sinatra, Lutfan; Dass, Amala; Bakr, Osman

2014-01-01

Atomically precise thiolate-protected noble metal molecular nanoparticles are a promising class of model nanomaterials for catalysis, optoelectronics, and the bottom-up assembly of true molecular crystals. However, these applications have not fully materialized due to a lack of ligand exchange strategies that add functionality, but preserve the properties of these remarkable particles. Here we present a method for the rapid (<30 s) and complete thiolate-for-thiolate exchange of the highly sought after silver molecular nanoparticle [Ag44(SR)30]-4. Only by using this method were we able to preserve the precise nature of the particles and simultaneously replace the native ligands with ligands containing a variety of functional groups. Crucially, as a result of our method we were able to process the particles into smooth thin films, paving the way for their integration into solution-processed devices.

Structure of the ligand-binding domain (LBD) of human androgen receptor in complex with a selective modulator LGD2226

International Nuclear Information System (INIS)

Wang, Feng; Liu, Xiao-qin; Li, He; Liang, Kai-ni; Miner, Jeffrey N.; Hong, Mei; Kallel, E. Adam; Oeveren, Arjan van; Zhi, Lin; Jiang, Tao

2006-01-01

Crystal structure of the ligand-binding domain of androgen receptor in complex with LGD2226. The androgen receptor (AR) is a ligand-inducible steroid hormone receptor that mediates androgen action, determining male sexual phenotypes and promoting spermatogenesis. As the androgens play a dominant role in male sexual development and function, steroidal androgen agonists have been used clinically for some years. However, there is a risk of potential side effects and most steroidal androgens cannot be dosed orally, which limits the use of these substances. 1,2-Dihydro-6-N,N-bis(2,2,2-trifluoroethyl) amino-4-trifluoromethyl-2-quinolinone (LGD2226) is a synthetic nonsteroidal ligand and a novel selective AR modulator. The crystal structure of the complex of LGD2226 with the androgen receptor ligand-binding domain (AR LBD) at 2.1 Å was solved and compared with the structure of the AR LBD–R1881 complex. It is hoped that this will aid in further explaining the selectivity of LGD2226 observed in in vitro and in vivo assays and in developing more selective and effective therapeutic agents

Efficacy of the semiempirical sparkle model as compared to ECP ab-initio calculations for the prediction of ligand field parameters of europium (III) complexes

International Nuclear Information System (INIS)

Freire, Ricardo O.; Rocha, Gerd B.; Albuquerque, Rodrigo Q.; Simas, Alfredo M.

2005-01-01

The second version of the sparkle model for the calculation of lanthanide complexes (SMLC II) as well as ab-initio calculations (HF/STO-3G and HF/3-21G) have been used to calculate the geometries of a series of europium (III) complexes with different coordination numbers (CN=7, 8 and 9), ligating atoms (O and N) and ligands (mono, bi and polydentate). The so-called ligand field parameters, Bqk's, have been calculated from both SMLC II and ab-initio optimized structures and compared to the ones calculated from crystallographic data. The results show that the SMLC II model represents a significant improvement over the previous version (SMLC) and has given good results when compared to ab-initio methods, which demand a much higher computational effort. Indeed, ab-initio methods take around a hundred times more computing time than SMLC. As such, our results indicate that our sparkle model can be a very useful and a fast tool when applied to the prediction of both ground state geometries and ligand field parameters of europium (III) complexes

Spectroscopy of Charge Carriers and Traps in Field-Doped Single Crystal Organic Semiconductors

Energy Technology Data Exchange (ETDEWEB)

Zhu, Xiaoyang [Columbia Univ., New York, NY (United States); Frisbie, Daniel [Univ. of Minnesota, Minneapolis, MN (United States)

2017-03-31

The proposed research aims to achieve quantitative, molecular level understanding of charge carriers and traps in field-doped crystalline organic semiconductors via in situ linear and nonlinear optical spectroscopy, in conjunction with transport measurements and molecular/crystal engineering.

Preliminary Molecular Dynamic Simulations of the Estrogen Receptor Alpha Ligand Binding Domain from Antagonist to Apo

Directory of Open Access Journals (Sweden)

Adrian E. Roitberg

2008-06-01

Full Text Available Estrogen receptors (ER are known as nuclear receptors. They exist in the cytoplasm of human cells and serves as a DNA binding transcription factor that regulates gene expression. However the estrogen receptor also has additional functions independent of DNA binding. The human estrogen receptor comes in two forms, alpha and beta. This work focuses on the alpha form of the estrogen receptor. The ERα is found in breast cancer cells, ovarian stroma cells, endometrium, and the hypothalamus. It has been suggested that exposure to DDE, a metabolite of DDT, and other pesticides causes conformational changes in the estrogen receptor. Before examining these factors, this work examines the protein unfolding from the antagonist form found in the 3ERT PDB crystal structure. The 3ERT PDB crystal structure has the estrogen receptor bound to the cancer drug 4-hydroxytamoxifen. The 4-hydroxytamoxifen ligand was extracted before the simulation, resulting in new conformational freedom due to absence of van der Waals contacts between the ligand and the receptor. The conformational changes that result expose the binding clef of the co peptide beside Helix 12 of the receptor forming an apo conformation. Two key conformations in the loops at either end of the H12 are produced resulting in the antagonist to apo conformation transformation. The results were produced over a 42ns Molecular Dynamics simulation using the AMBER FF99SB force field.

Formation of temperature fields in doped anisotropic crystals under spatially inhomogeneous light beams passing through them

Energy Technology Data Exchange (ETDEWEB)

Zaitseva, E. V.; Markelov, A. S.; Trushin, V. N., E-mail: trushin@phys.unn.ru; Chuprunov, E. V. [Nizhni Novgorod State University (Russian Federation)

2013-12-15

The features of formation of thermal fields in potassium dihydrophosphate crystal doped with potassium permanganate under a 532-nm laser beam passing through it have been investigated. Data on the influence of birefringence on the temperature distribution in an anisotropic crystal whose surface is illuminated by a spatially modulated light beam are presented.

Ligand-field symmetry effects in Fe(ii) polypyridyl compounds probed by transient X-ray absorption spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Cho, Hana; Strader, Matthew L.; Hong, Kiryong; Jamula, Lindsey; Gullikson, Eric M.; Kim, Tae Kyu; de Groot, Frank M. F.; McCusker, James K.; Schoenlein, Robert W.; Huse, Nils

2012-01-01

Ultrafast excited-state evolution in polypyridyl FeII complexes are of fundamental interest for understanding the origins of the sub-ps spin-state changes that occur upon photoexcitation of this class of compounds as well as for the potential impact such ultrafast dynamics have on incorporation of these compounds in solar energy conversion schemes or switchable optical storage technologies. We have demonstrated that ground-state and, more importantly, ultrafast time-resolved x-ray absorption methods can offer unique insights into the interplay between electronic and geometric structure that underpin the photo-induced dynamics of this class of compounds. The present contribution examines in greater detail how the symmetry of the ligand field surrounding the metal ion can be probed using these x-ray techniques. In particular, we show that steady-state K-edge spectroscopy of the nearest-neighbour nitrogen atoms reveals the characteristic chemical environment of the respective ligands and suggests an interesting target for future charge-transfer femtosecond and attosecond spectroscopy in the x-ray water window.

Crystal field parameters with Wannier functions: application to rare-earth aluminates

Czech Academy of Sciences Publication Activity Database

Novák, Pavel; Knížek, Karel; Kuneš, Jan

2013-01-01

Roč. 87, č. 20 (2013), "205139-1"-"205139-7" ISSN 1098-0121 R&D Projects: GA ČR(CZ) GAP204/11/0713 Institutional support: RVO:68378271 Keywords : crystal-field * rare earths * Wannier functions Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013 http://link.aps.org/doi/10.1103/PhysRevB.87.205139

Coordination of bis(pyrazol-1-ylamine to palladium(II: influence of the co-ligands and counter-ions on the molecular and crystal structures

Directory of Open Access Journals (Sweden)

María de los Angeles Mendoza

2015-01-01

Full Text Available The structures of a series of complexes with general formula n[Pd(pzaX]Y·mH2O (n = 1, 2; X = Cl, Br, I, N3, NCS; Y = NO3, I, N3, [Pd(SCN4]; m = 0, 0.5, 1 have been determined, where pza is the tridentate ligand bis[2-(3,5-dimethylpyrazol-1-ylethyl]amine, C14H23N5. In all complexes, {bis[2-(3,5-dimethylpyrazol-1-yl-κN2ethyl]amine-κN}chloridopalladium nitrate, [Pd(pzaCl]NO3, (1, {bis[2-(3,5-dimethylpyrazol-1-yl-κN2ethyl]amine-κN}bromidopalladium nitrate, [Pd(pzaBr]NO3, (2, {bis[2-(3,5-dimethylpyrazol-1-yl-κN2ethyl]amine-κN}iodidopalladium iodide hemihydrate, [Pd(pzaI]I·0.5H2O, (3, azido{bis[2-(3,5-dimethylpyrazol-1-yl-κN2ethyl]amine-κN}palladium azide monohydrate, [Pd(pzaN3]N3·H2O, (4, and bis[{bis[2-(3,5-dimethylpyrazol-1-yl-κN2ethyl]amine-κN}(thiocyanato-κNpalladium] tetrakis(thiocyanato-κSpalladate, [Pd(pzaNCS]2[Pd(SCN4], (5, the [Pd(pzaX]+ complex cation displays a square-planar coordination geometry, and the pza ligand is twisted, approximating twofold rotation symmetry. Although the pza ligand is found with the same conformation along the series, the dihedral angle between pyrazole rings depends on the co-ligand X. This angle span the range 79.0 (3–88.6 (1° for the studied complexes. In (3, two complex cations, two I− anions and one water molecule of crystallization are present in the asymmetric unit. In (5, the central amine group of pza is disordered over two positions [occupancy ratio 0.770 (18:0.230 (18]. The complex [Pd(SCN4]2− anion of this compound exhibits inversion symmetry and shows the Pd2+ transition metal cation likewise in a square-planar coordination environment. Compound (5 is also a rare occurrence of a non-polymeric compound in which the pseudohalide ligand NCS− behaves both as thiocyanate and isothiocyanate, i.e. is coordinating either through the N atom (in the cation or the S atom (in the anion.

Crystal structure of a mixed-ligand terbium(III coordination polymer containing oxalate and formate ligands, having a three-dimensional fcu topology

Directory of Open Access Journals (Sweden)

Chainok Kittipong

2016-01-01

Full Text Available The title compound, poly[(μ3-formato(μ4-oxalatoterbium(III], [Tb(CHO2(C2O4]n, is a three-dimensional coordination polymer, and is isotypic with the LaIII, CeIII and SmIII analogues. The asymmetric unit contains one TbIII ion, one formate anion (CHO2− and half of an oxalate anion (C2O42−, the latter being completed by application of inversion symmetry. The TbIII ion is nine-coordinated in a distorted tricapped trigonal–prismatic manner by two chelating carboxylate groups from two C2O42− ligands, two carboxylate oxygen atoms from another two C2O42− ligands and three oxygen atoms from three CHO2− ligands, with the Tb—O bond lengths and the O—Tb—O bond angles ranging from 2.4165 (19 to 2.478 (3 Å and 64.53 (6 to 144.49 (4°, respectively. The CHO2− and C2O42− anions adopt μ3-bridging and μ4-chelating-bridging coordination modes, respectively, linking adjacent TbIII ions into a three-dimensional 12-connected fcu topology with point symbol (324.436.56. The title compound exhibits thermal stability up to 623 K, and also displays strong green photoluminescence in the solid state at room temperature.

Near-field-optical-microscopy studies of micro-modifications caused by femtosecond laser irradiation in lithium niobate crystals

International Nuclear Information System (INIS)

Lamela, J.; Jaque, D.; Rodenas, A.; Jaque, F.; Torchia, G.A.; Vazquez, J.R.; Mendez, C.; Roso, L.

2008-01-01

Near-field-optical-microscopy has been used to study the micro-modifications caused by femtosecond laser pulses focused at the surface and in the volume of lithium niobate crystals. We have found experimental evidence of the existence, close to femtosecond ablation craters, of periodic modifications in the surface reflectivity. In addition, the potential application of near-field-optical microscopy for the spatial location of permanent modifications caused by femtosecond pulses focused inside lithium niobate crystals has been also demonstrated. (orig.)

Macrocyclic ligands for uranium complexation: Progress report, August 15, 1987-present

International Nuclear Information System (INIS)

Potts, K.T.

1988-03-01

The synthesis of several macrocyclic ligands, designed by a computer modeling approach for the complexation of the uranyl ion, has now been completed and their structures established. Preliminary indicate that these macrocycles successfully complex the uranyl ion. Other synthetic efforts have led to a variety of intermediates suitable for final ring closure to the desired macrocycles, providing appreciable potential for variation of the macrocyclic peripheral atoms. A 1:1-uranyl ion complex of one of these precursor products has been shown to undergo a DMSO-induced rearrangement to a 2:1 uranyl ion to ligand complex, both structures having been established by single crystal x-ray data. 10 refs

Retinal Ligand Mobility Explains Internal Hydration and Reconciles Active Rhodopsin Structures

Science.gov (United States)

Leioatts, Nicholas; Mertz, Blake; Martínez-Mayorga, Karina; Romo, Tod D.; Pitman, Michael C.; Feller, Scott E.; Grossfield, Alan; Brown, Michael F.

2014-01-01

Rhodopsin, the mammalian dim-light receptor, is one of the best-characterized G-protein-coupled receptors, a pharmaceutically important class of membrane proteins that has garnered a great deal of attention because of the recent availability of structural information. Yet the mechanism of rhodopsin activation is not fully understood. Here, we use microsecond-scale all-atom molecular dynamics simulations, validated by solid-state 2H nuclear magnetic resonance spectroscopy, to understand the transition between the dark and metarhodopsin I (Meta I) states. Our analysis of these simulations reveals striking differences in ligand flexibility between the two states. Retinal is much more dynamic in Meta I, adopting an elongated conformation similar to that seen in the recent activelike crystal structures. Surprisingly, this elongation corresponds to both a dramatic influx of bulk water into the hydrophobic core of the protein and a concerted transition in the highly conserved Trp2656.48 residue. In addition, enhanced ligand flexibility upon light activation provides an explanation for the different retinal orientations observed in X-ray crystal structures of active rhodopsin. PMID:24328554

Syntheses, crystal structures, and properties of four coordination polymers based on mixed multi-N donor and polycarboxylate ligands

Science.gov (United States)

Chen, Shui-Sheng; Guo, Xing-Zhe; Zhao, Yue; Li, Wei-Dong

2018-02-01

Four new coordination polymers [Ni2(HL1)2(L1)3(BTC)2]·6H2O (1), [Ni2(L1)3(HBTC)2]·4H2O (2), [Cd2(L2)(BTC)(H2O)3]·2H2O (3) and [Cd2(HL2)(BTCA)] (4) were synthesized by reactions of nickel(II)/ cadmium(II) salts with rigid ligands of 1,4-di(1H-imidazol-4-yl)benzene (L1), 1,3-di(1-imidazolyl)-5-(4H-tetrazol-5-yl)benzene (HL2) and polycarboxylic acids of 1,3,5-benzenetricarboxylic acid (H3BTC), 1,2,4,5-benzenetetracarboxylic acid (H4BTCA), respectively. The structures of the complexes were determined by single crystal X-ray diffraction analysis. The complex 1 is one-dimensional (1D) chain while 2 is a (4, 4)-connected two-dimensional (2D) layered structure with 2D → 2D parallel interpenetration. Complex 3 is a rare tetranodal (3,4)-connected three-dimensional (3D) CrVTiSc architecture with Point (Schläfli) symbol of (4·82)(4·84·10)(42·82·102)(83), and compound 4 has the 2D network with (4,4) topology based on the [Cd2(COO)4] SBUs. The weak interactions such as hydrogen bonds and π···π stacking contribute to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. The UV-vis absorption spectra of 1 - 4 are discussed. Moreover, the photo luminescent properties of 3 and 4 and gas sorption property of 2 have been investigated.

Facile construction of terpridine-based metallo-polymers in hydrogels, crystals and solutions directed by metal ions.

Science.gov (United States)

Li, Yajuan; Guo, Jiangbo; Dai, Bo; Geng, Lijun; Shen, Fengjuan; Zhang, Yajun; Yu, Xudong

2018-07-01

Driven by tunable metal-ligand interactions, a polydentate ligand TC containing terpyridine and carboxylic acid units was developed to construct metallo-polymers that showed multiple aggregation modes with controlled macroscopic properties. In the presence of different kind of Zn 2+ ions or NaOH, TC could form metallo-polymers via π-π stacking and metal-ligand interaction that further trapped water molecules, resulting in hydrogels and crystals. Moreover, these TC/Zn 2+ hydrogels could transform to soluble and fluorescent aggregates in the presence of NaOH due to the formation of binuclear metallo-polymers with enhanced ICT emission. The metal-ligand interactions tuned by different metal salts in gels, crystals, and sols were also studied and illustrated in detail, it was also proved that water was an essential linker for constructing Na + -based metallo-polymers from the TC/NaOH crystal data. This work demonstrated the engineered coordination pathways in generating controllable hydrogels and metallo-polymers for the first time, which led to novel approach for facilely constructing a number of hydrogels with tailorable macroscopic properties. Copyright © 2018 Elsevier Inc. All rights reserved.

Spectrochemical Series and the Dependence of Racah and 10Dq Parameters on the Metal−Ligand Distance: Microscopic Origin

DEFF Research Database (Denmark)

Trueba, A.; Garcia-Fernandez, P.; García Lastra, Juan Maria

2011-01-01

The origin of the spectrochemical series and the different dependence of crystal-field splitting (10Dq) and Racah parameters on the metal−ligand distance, R, is explored through ab initio calculations on Cr3+-doped K2NaScF6, Cs2NaYCl6, Cs2NaYBr6, and Cs2NaYI6 lattices. For this purpose both...... is actually responsible for the reduction of Racah parameters. This study thus reveals the microscopic origin of the stronger dependence upon R of 10Dq when compared to that observed for Racah parameters, thus explaining why electronic transitions which are 10Dq-independent give rise to sharp optical bands...

Anisotropically Swelling Gels Attained through Axis-Dependent Crosslinking of MOF Crystals.

Science.gov (United States)

Ishiwata, Takumi; Kokado, Kenta; Sada, Kazuki

2017-03-01

Anisotropically deforming objects have attracted considerable interest for use in molecular machines and artificial muscles. Herein, we focus on a new approach based on the crystal crosslinking of organic ligands in a pillared-layer metal-organic framework (PLMOF). The approach involves the transformation from crosslinked PLMOF to polymer gels through hydrolysis of the coordination bonds between the organic ligands and metal ions, giving a network polymer that exhibits anisotropic swelling. The anisotropic monomer arrangement in the PLMOF underwent axis-dependent crosslinking to yield anisotropically swelling gels. Therefore, the crystal crosslinking of MOFs should be a useful method for creating actuators with designable deformation properties. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure and spin state of mixed-crystals of iron with zinc and cobalt for the assembled complexes bridged by 1,3-bis(4-pyridyl)propanes

Energy Technology Data Exchange (ETDEWEB)

Dote, Haruka [Hiroshima University, Graduate School of Science (Japan); Nakashima, Satoru, E-mail: snaka@hiroshima-u.ac.jp [Hiroshima University, Natural Science Center for Basic Research and Development (Japan)

2012-03-15

Mixed crystals of cobalt and zinc were synthesized using 1,3-bis(4-pyridyl)propane (bpp) as bridging ligand and NCS{sup - } as anion. Red crystals and blue crystals were obtained. Powder X-ray diffraction patterns showed that the former is in 2D interpenetrated structure, while the latter has the same structure with Zn(NCS){sub 2}(bpp). Iron ion was introduced both into the red crystals and blue crystals of the mixed crystals of cobalt with zinc. {sup 57}Fe Moessbauer spectrum of the red crystals showed a main doublet of Fe{sup II} high-spin state at 78 K, while the spectrum of blue crystals did not show Fe{sup II} high-spin state at 78 K.

Crystal structure and spin state of mixed-crystals of iron with zinc and cobalt for the assembled complexes bridged by 1,3-bis(4-pyridyl)propanes

International Nuclear Information System (INIS)

Dote, Haruka; Nakashima, Satoru

2012-01-01

Mixed crystals of cobalt and zinc were synthesized using 1,3–bis(4–pyridyl)propane (bpp) as bridging ligand and NCS  −  as anion. Red crystals and blue crystals were obtained. Powder X-ray diffraction patterns showed that the former is in 2D interpenetrated structure, while the latter has the same structure with Zn(NCS) 2 (bpp). Iron ion was introduced both into the red crystals and blue crystals of the mixed crystals of cobalt with zinc. 57 Fe Mössbauer spectrum of the red crystals showed a main doublet of Fe II high-spin state at 78 K, while the spectrum of blue crystals did not show Fe II high-spin state at 78 K.

Crystal field levels of tetravalent actinide ions in actinide dioxides UO2, NpO2 and PuO2

International Nuclear Information System (INIS)

Krupa, J.C.; Gajek, Z.

1991-01-01

Crystal-field parameters resulting from analysis of optical spectroscopy and neutron diffraction data recorded on UO 2 and NpO 2 as well as ab-initio calculated parameters were used to calculate the crystal-field eigenfunctions and eigenvalues for the J ground-state manifold of U 4+ , Np 4+ and Pu 4+ in UO 2 , NpO 2 and PuO 2

Control of spontaneous emission from a microwave-field-driven four-level atom in an anisotropic photonic crystal

Science.gov (United States)

Zhang, Duo; Li, Jiahua; Ding, Chunling; Yang, Xiaoxue

2012-05-01

The spontaneous emission properties of a microwave-field-driven four-level atom embedded in anisotropic double-band photonic crystals (PCs) are investigated. We discuss the influences of the band-edge positions, Rabi frequency and detuning of the microwave field on the emission spectrum. It is found that several interesting features such as spectral-line enhancement, spectral-line suppression, spectral-line overlap, and multi-peak structures can be observed in the spectra. The proposed scheme can be achieved by use of a microwave-coupled field into hyperfine levels in rubidium atom confined in a photonic crystal. These theoretical investigations may provide more degrees of freedom to manipulate the atomic spontaneous emission.

Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

International Nuclear Information System (INIS)

Vognsen, Tina; Kristensen, Ole

2012-01-01

Highlights: ► The crystal structure of the NTF2-like domain of Rasputin protein is presented. ► Differences to known ligand binding sites of nuclear transport factor 2 are discussed. ► A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a β-sheet and three α-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

Ligand design for riboswitches, an emerging target class for novel antibiotics.

Science.gov (United States)

Rekand, Illimar Hugo; Brenk, Ruth

2017-09-01

Riboswitches are cis-acting gene regulatory elements and constitute potential targets for new antibiotics. Recent studies in this field have started to explore these targets for drug discovery. New ligands found by fragment screening, design of analogs of the natural ligands or serendipitously by phenotypic screening have shown antibacterial effects in cell assays against a range of bacteria strains and in animal models. In this review, we highlight the most advanced drug design work of riboswitch ligands and discuss the challenges in the field with respect to the development of antibiotics with a new mechanism of action.

Unit-cell design for two-dimensional phase-field simulation of microstructure evolution in single-crystal Ni-based superalloys during solidification

Directory of Open Access Journals (Sweden)

Dongjia Cao

2017-12-01

Full Text Available Phase-field simulation serves as an effective tool for quantitative characterization of microstructure evolution in single-crystal Ni-based superalloys during solidification nowadays. The classic unit cell is either limited to γ dendrites along crystal orientation or too ideal to cover complex morphologies for γ dendrites. An attempt to design the unit cell for two-dimensional (2-D phase-field simulations of microstructure evolution in single-crystal Ni-based superalloys during solidification was thus performed by using the MICRESS (MICRostructure Evolution Simulation Software in the framework of the multi-phase-field (MPF model, and demonstrated in a commercial TMS-113 superalloy. The coupling to CALPHAD (CALculation of PHAse Diagram thermodynamic database was realized via the TQ interface and the experimental diffusion coefficients were utilized in the simulation. Firstly, the classic unit cell with a single γ dendrite along crystal orientation was employed for the phase-field simulation in order to reproduce the microstructure features. Then, such simple unit cell was extended into the cases with two other different crystal orientations, i.e., and . Thirdly, for crystal orientations, the effect of γ dendritic orientations and unit cell sizes on microstructure and microsegregation was comprehensively studied, from which a new unit cell with multiple γ dendrites was proposed. The phase-field simulation with the newly proposed unit cell was further performed in the TMS-113 superalloy, and the microstructure features including the competitive growth of γ dendrites, microsegregation of different solutes and distribution of γ′ grains, can be nicely reproduced.

Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.

Science.gov (United States)

Amero, Carlos D; Byerly, Douglas W; McElroy, Craig A; Simmons, Amber; Foster, Mark P

2009-08-18

Peptide deformylase (PDF) is an enzyme that is responsible for removing the formyl group from nascently synthesized polypeptides in bacteria, attracting much attention as a potential target for novel antibacterial agents. Efforts to develop potent inhibitors of the enzyme have progressed on the basis of classical medicinal chemistry, combinatorial chemistry, and structural approaches, yet the validity of PDF as an antibacterial target hangs, in part, on the ability of inhibitors to selectively target this enzyme in favor of structurally related metallohydrolases. We have used (15)N NMR spectroscopy and isothermal titration calorimetry to investigate the high-affinity interaction of EcPDF with actinonin, a naturally occurring potent EcPDF inhibitor. Backbone amide chemical shifts, residual dipolar couplings, hydrogen-deuterium exchange, and (15)N relaxation reveal structural and dynamic effects of ligand binding in the immediate vicinity of the ligand-binding site as well as at remote sites. A comparison of the crystal structures of free and actinonin-bound EcPDF with the solution data suggests that most of the consequences of the ligand binding to the protein are lost or obscured during crystallization. The results of these studies improve our understanding of the thermodynamic global minimum and have important implications for structure-based drug design.

Structural and Electrochemical Consequences of [Cp*] Ligand Protonation.

Science.gov (United States)

Peng, Yun; Ramos-Garcés, Mario V; Lionetti, Davide; Blakemore, James D

2017-09-05

There are few examples of the isolation of analogous metal complexes bearing [η 5 -Cp*] and [η 4 -Cp*H] (Cp* = pentamethylcyclopentadienyl) complexes within the same metal/ligand framework, despite the relevance of such structures to catalytic applications. Recently, protonation of Cp*Rh(bpy) (bpy = 2,2'-bipyridyl) has been shown to yield a complex bearing the uncommon [η 4 -Cp*H] ligand, rather than generating a [Rh III -H] complex. We now report the purification and isolation of this protonated species, as well as characterization of analogous complexes of 1,10-phenanthroline (phen). Specifically, reaction of Cp*Rh(bpy) or Cp*Rh(phen) with 1 equiv of Et 3 NH + Br - affords rhodium compounds bearing endo-η 4 -pentamethylcyclopentadiene (η 4 -Cp*H) as a ligand. NMR spectroscopy and single-crystal X-ray diffraction studies confirm protonation of the Cp* ligand, rather than formation of metal hydride complexes. Analysis of new structural data and electronic spectra suggests that phen is significantly reduced in Cp*Rh(phen), similar to the case of Cp*Rh(bpy). Backbonding interactions with olefinic motifs are activated by formation of [η 4 -Cp*H]; protonation of [Cp*] stabilizes the low-valent metal center and results in loss of reduced character on the diimine ligands. In accord with these changes in electronic structure, electrochemical studies reveal a distinct manifold of redox processes that are accessible in the [Cp*H] complexes in comparison with their [Cp*] analogues; these processes suggest new applications in catalysis for the complexes bearing endo-η 4 -Cp*H.

Ligand field and interference effects in L-edge X-ray Raman scattering of MnF{sub 2} and CoF{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Jimenez M, J.; Herrera P, G. M.; Olalde V, P. [Instituto de Ciencias Nucleares, UNAM, Ciudad Universitaria, 04510 Mexico D. F. (Mexico); Ederer, D. L.; Schuler, T. [Department of Physics, Tulane University, New Orleans, LA 70118 (United States)

2008-02-15

We present experimental results for x-ray absorption and resonant emission at the L-edge of the transition metal in MnF{sub 2} and CoF{sub 2}. The emission data are corrected for self-absorption. The data are compared with calculations in both the free-ion approximation and with the effect of the ligand field of D{sub 4h} symmetry included. The results of the calculations take into account interference terms in the Kramers-Heisenberg expression. We obtain very good agreement between experiment and theory for both x-ray absorption and resonant emission in the two compounds. The inclusion of the ligand field is important to achieve such agreement. However, the results of the calculation that does not take into account the interference terms are in better agreement with experiment, indicating that the model used probably overestimates the importance of interference effects. (Author)

PRO_LIGAND: an approach to de novo molecular design. 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores.

Science.gov (United States)

Waszkowycz, B; Clark, D E; Frenkel, D; Li, J; Murray, C W; Robson, B; Westhead, D R

1994-11-11

A computational approach for molecular design, PRO_LIGAND, has been developed within the PROMETHEUS molecular design and simulation system in order to provide a unified framework for the de novo generation of diverse molecules which are either similar or complementary to a specified target. In this instance, the target is a pharmacophore derived from a series of active structures either by a novel interpretation of molecular field analysis data or by a pharmacophore-mapping procedure based on clique detection. After a brief introduction to PRO_LIGAND, a detailed description is given of the two pharmacophore generation procedures and their abilities are demonstrated by the elucidation of pharmacophores for steroid binding and ACE inhibition, respectively. As a further indication of its efficacy in aiding the rational drug design process, PRO_LIGAND is then employed to build novel organic molecules to satisfy the physicochemical constraints implied by the pharmacophores.

Magnetic islands modelled by a phase-field-crystal approach

Science.gov (United States)

Faghihi, Niloufar; Mkhonta, Simiso; Elder, Ken R.; Grant, Martin

2018-03-01

Using a minimal model based on the phase-field-crystal formalism, we study the coupling between the density and magnetization in ferromagnetic solids. Analytical calculations for the square phase in two dimensions are presented and the small deformation properties of the system are examined. Furthermore, numerical simulations are conducted to study the influence of an external magnetic field on various phase transitions, the anisotropic properties of the free energy functional, and the scaling behaviour of the growth of the magnetic domains in a crystalline solid. It is shown that the energy of the system can depend on the direction of the magnetic moments, with respect to the crystalline direction. Furthermore, the growth of the magnetic domains in a crystalline solid is studied and is shown that the growth of domains is in agreement with expected behaviour.

One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

Science.gov (United States)

Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

2016-11-01

Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding

Science.gov (United States)

Verdonk, Marcel L.; Boks, Gertjan J.; Kooijman, Huub; Kanters, Jan A.; Kroon, Jan

1993-04-01

Recently, new evidence was found for the involvement of charged nitrogen-aromatic interactions in ligand-receptor binding. In this study we report two favourable orientations of a phenyl ring with respect to a R-N+(CH3)3 group, based on crystal structure statistics from the Cambridge Structural Database. In the first orientation, the phenyl ring is situated in between the substituents at about 4.5 Å from the nitrogen atom, and the ring is approximately oriented on the sphere around the nitrogen atom. In the second orientation, the phenyl ring is situated in the same direction as one of the N-C bonds at about 6.0 Å from the nitrogen atom, and the ring is tilted with respect to the sphere around the nitrogen atom. The same two orientations were also found in the crystal structures of three ligand-receptor complexes, which implies that these orientations probably play a major role in molecular recognition mechanisms.

X-ray diffraction from ideal mosaic crystals in external fields of certain types. I. Atomic displacements and the corresponding diffraction patterns

International Nuclear Information System (INIS)

Treushnikov, E.N.

2000-01-01

The problem of the theoretical description of X-ray diffraction from ideal mosaic crystals under the effect of various external fields has been formulated. Electric, magnetic, electromagnetic, and acoustic perturbations are considered. The atomic displacements in crystals under the effect of external fields and the types of the corresponding diffraction patterns are analyzed for various types of perturbations. The crystal classes are determined in which atomic displacements can be recorded experimentally. Diffraction patterns formed under the effect of various external factors are considered on the basis of the derived dependence of the structure factor on the characteristics of an applied force field

Self-assembly of novel manganese (II) compounds based on bifunctional-group ligands: Synthesis, structures, and magnetic properties

Science.gov (United States)

Yan, Juan-zhi; Lu, Li-ping; Zhu, Miao-li; Feng, Si-si

2018-06-01

Four manganese (II) compounds are obtained by the reaction of manganese salts, triazole-derivatives and auxiliary reagents in aqueous solution or mix-solvents by routine or hydrothermal reactions. X-ray crystal structure analyses reveal that a neutral 0D compound [Mn(Hmctrz)2(H2O)2] (1) (H2mctrz = 1H-1,2,4-triazole-3-carboxylic acid) displays a centro-symmetric mononuclear octahedral entity with two Hmctrz- anions and two water molecules; two neutral 2D clusters [Mn(Hdctrz)(H2O)2]n (2) (H3dctrz = 1H-1,2,4-triazole-3,5-dicarboxylic acid) and [Mn2(pbtrz)(btca)]n·4nH2O (3) (pbtrz = 1,3-bis(1,2,4-triazol-1-yl)-propane&H4btca = benzene-1,2,4,5-tetracarboxylic acid) possess layer structures with Hdctrz2- linkers (2) and Mn(II)-pbtrz-Mn(II) building blocks periodically extended by μ-btca4- connectors (3); [Mn(pbtrz)]n·nOAc·nOH (4) shows a 3D diamond-shaped cationic framework with the anion void volume of 49.2%. Nitrogenous bases are used as the auxiliary ligand in compound 3 and the temple ligand in compounds 1, 2, and 4. Compounds 1-4 show antiferromagnetic coupling that has been fitted by different models with the molecular field approximate with D = - 0.129(1) cm-1 for 1, J = - 0.354(4) cm-1 for 2 and J = - 0.696(6) cm-1 for 3, respectively. The magnetic differences can be related to different superexchange interactions transmitted by the crystal lattice and/or the zero field splitting (ZFS) of the 6A1g single-ion states of 1 and the syn-anti-COO- of 2 as well as the mixed magnetic bridges of μ1-O and μ-pbtrz-μ-COO- of 3.

Plutonium(IV) complexation by diglycolamide ligands - coordination chemistry insight into TODGA-based actinide separations

NARCIS (Netherlands)

Reilly, S.D.; Gaunt, A.J.; Scott, B.L.; Modolo, G.; Iqbal, M.; Verboom, Willem; Sarsfield, M.J.

2012-01-01

Complexation of Pu(IV) with TMDGA, TEDGA, and TODGA diglycolamide ligands was followed by vis-NIR spectroscopy. A crystal structure determination reveals that TMDGA forms a 1:3 homoleptic Pu(IV) complex with the nitrate anions forced into the outer coordination sphere

Crystal field influence on vibration spectra: anhydrous uranyl chloride and dihydroxodiuranyl chloride tetrahydrate

International Nuclear Information System (INIS)

Perrin, Andre; Caillet, Paul

1976-01-01

Vibrational spectra of anhydrous uranyl chloride UO 2 Cl 2 and so called basic uranyl chloride: dihydroxodiuranyl chloride tetrahydrate /UO 2 (OH) 2 UO 2 /Cl 2 (H 2 O) 4 are reported. Factor group method analysis leads for the first time to complete and comprehensive interpretation of their spectra. Two extreme examples of crystal field influence on vibrational spectra are pointed out: for UO 2 Cl 2 , one is unable to explain spectra without taking into account all the elements of primitive crystalline cell, whilst for dihydroxodiuranyl dichloride tetrahydrate the crystal packing has very little effect on vibrational spectra [fr

Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

Science.gov (United States)

Corbett, Michael S P; Mark, Alan E; Poger, David

2017-02-28

Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Near-field imaging of out-of-plane light scattering in photonic crystal slabs

DEFF Research Database (Denmark)

Volkov, Valentyn; Bozhevolnyi, Sergey; Taillaert, Dirk

2003-01-01

A collection scanning near-field optical microscope (SNOM) is used to image the propagating of light at telecommunication wavelengths (1520-1570 nm) along photonic crystal (PC) slabs, which combine slab waveguides with in-plane PCs consisting of one- and two-dimensional gratings. The efficient out...

Structural characterization and antimicrobial activities of transition metal complexes of a hydrazone ligand

Science.gov (United States)

Bakale, Raghavendra P.; Naik, Ganesh N.; Machakanur, Shrinath S.; Mangannavar, Chandrashekhar V.; Muchchandi, Iranna S.; Gudasi, Kalagouda B.

2018-02-01

A hydrazone ligand has been synthesized by the condensation of 2-nitrobenzaldehyde and hydralazine, and its Co(II), Ni(II), Cu(II) and Zn(II) complexes have been reported. Structural characterization of the ligand and its metal complexes has been performed by various spectroscopic [IR, NMR, UV-Vis, Mass], thermal and other physicochemical methods. The structure of the ligand and its Ni(II) complex has been characterized by single crystal X-ray diffraction studies. All the synthesized compounds have been screened for in vitro antimicrobial activity. The antibacterial activity is tested against Gram-positive strains Enterococcus faecalis, Streptococcus mutans and Staphylococcus aureus and Gram-negative strains Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae using ciprofloxacin as the reference standard. Antifungal activity is tested against Candida albicans, Aspergillus fumigatus and Aspergillus niger using ketoconazole as the reference standard. The minimum inhibitory concentration (MIC) was determined for test compounds as well as for reference standard. Ligand, Cu(II) and Zn(II) complexes have shown excellent activity against Candida albicans.

Crystal field effect in the uranium compounds - model calculations for CsUF6, Cs2UCl6 and UCl4

International Nuclear Information System (INIS)

Gajek, Z.; Mulak, J.

1987-01-01

A practical crystal field model allowing one to estimate the crystal field parameters from first principles is presented and applied to the actinide compounds. The model results directly from the renormalization (and reduction) procedure of the true Schroedinger equation for an effective Hamiltonian acting on the 5f spin-orbitals only. In practice this approach becomes convergent with the ab initio model of Newman. Three ionic uranium compounds: CsUF 6 , Cs 2 UCl 6 and UCl 4 have served as examples of the application. The results obtained, particularly for the first two compounds, are in good agreement with the experimental data. The contributions of different mechanisms responsible for the crystal field effect are discussed. (author)

Angular and magnetic field dependences of critical current in irradiated YBaCuO single crystals

International Nuclear Information System (INIS)

Petrusenko, Yu.

2010-01-01

The investigation of mechanisms responsible for the current-carrying capability of irradiated high-temperature superconductors (HTSC) was realized. For the purpose, experiments were made to investigate the effect of point defects generated by high-energy electron irradiation on the critical temperature and the critical current in high-Tc superconducting single crystals YBa 2 Cu 3 O 7-x . The transport current density measured in HTSC single crystals YBa 2 Cu 3 O 7-x by the dc-method was found to exceed 80000 A/cm 2 . The experiments have demonstrated a more than 30-fold increase in the critical current density in single crystals irradiated with 2.5 MeV electrons to a dose of 3·10 18 el/cm 2 . Detailed studies were made into the anisotropy of critical current and the dependence of critical current on the external magnetic field strength in irradiated single crystals. A high efficiency of point defects as centers of magnetic vortex pinning in HTSC single crystals was first demonstrated.

Thermal field emission observation of single-crystal LaB6

International Nuclear Information System (INIS)

Nagata, H.; Harada, K.; Shimizu, R.

1990-01-01

TFE (thermal field emission) properties of LaB 6 left-angle 100 right-angle and left-angle 310 right-angle single crystals were investigated by emission pattern observation. It was found that field evaporation with the tip temperature held at ∼1500 degree C is very useful to get a clean pattern of fourfold symmetry. Each of four bright spots in the clean pattern was presumed to correspond to left-angle 310 right-angle emission. It is proposed, as the most appropriate operating condition, to use the left-angle 310 right-angle LaB 6 tip at a temperature ∼1000 degree C in vacuum of 10 -9 Torr region, promising a new TF emitter of high brightness and stability for practical use

All-electron ab initio calculations of YBa2Cu3O7 with self-consistence crystal field

Institute of Scientific and Technical Information of China (English)

刘洪霖; 陈念贻

1995-01-01

The quantum chemical calculations of cluster YBa2Cu3O7 considering all electrons have been per-formed by using the ab initio HF method with self-consistence crystal field.A Hartree-Fork surface potentialis proposed to make an asymmetric duster model possess a relatively symmetric potential field and to obtaina relatively symmetric electronic structure,electronic distributions,frontier orbitals,and bond order,etc.Thesuggestions that there exists a covalent bonding complex,[CuO2-O-CuO-O-Cu2]6,8-,in the cell unit ofthe crystal,and the cell units are connected with each other by ionic bonds along the c direction of the crys-tal lattice are offered based on the chemical bonding characteristics from the calculated results.The importantcontribution of the apical oxygen to superconductivities is emphasized as well.

Synthesis and X-Ray Crystal Structures of Mononuclear Complexes of 1,3-Bis(8-quinolyloxy)propane

International Nuclear Information System (INIS)

Al-Mandhary, M.R.; Steel, P.

2002-01-01

The preparations and X-ray crystal structures of the first transition metal complexes of 1,3-bis(8-quinolyloxy)propane are described. The ligand acts as a trans-chelating N,N'-bidentate ligand in the three-coordinate silver nitrate complex and four-coordinate copper chloride complex, but as an N,O,O',N'-tetradentate ligand in the octahedral nickel chloride complex. Copyright (2002) CSIRO Australia

Mixed-ligand Pt(II) dithione-dithiolato complexes: influence of the dicyanobenzodithiolato ligand on the second-order NLO properties.

Science.gov (United States)

Espa, Davide; Pilia, Luca; Marchiò, Luciano; Artizzu, Flavia; Serpe, Angela; Mercuri, Maria Laura; Simão, Dulce; Almeida, Manuel; Pizzotti, Maddalena; Tessore, Francesca; Deplano, Paola

2012-03-28

The mixed-ligand dithiolene complex [Pt(Bz(2)pipdt)(dcbdt)] (1) bearing the two ligands Bz(2)pipdt = 1,4-dibenzyl-piperazine-3,2-dithione and dcbdt = dicyanobenzodithiolato, has been synthesized, characterized and studied to evaluate its second-order optical nonlinearity. The dithione/dithiolato character of the two ligands gives rise to an asymmetric distribution of the charge in the molecule. This is reflected by structural data showing that in the C(2)S(2)PtS(2)C(2) dithiolene core the four sulfur atoms define a square-planar coordination environment of the metal where the Pt-S bond distances involving the two ligands are similar, while the C-S bond distances in the C(2)S(2) units exhibit a significant difference in Bz(2)pipdt (dithione) and dcbdt (dithiolato). 1 shows a moderately strong absorption peak in the visible region, which can be related to a HOMO-LUMO transition, where the dcbdt ligand (dithiolato) contributes mostly to the HOMO, and the Bz(2)pipdt one (dithione) mostly to the LUMO. Thus this transition has ligand-to-ligand charge transfer (CT) character with some contribution of the metal and undergoes negative solvatochromism and molecular quadratic optical nonlinearity (μβ(0) = -1296 × 10(-48) esu), which was determined by the EFISH (electric-field-induced second-harmonic generation) technique and compared with the values of similar complexes on varying the dithiolato ligand (mnt = maleonitriledithiolato, dmit = 2-thioxo-1,3-dithiole-4,5-dithiolato). Theoretical calculations help to elucidate the role of the dithiolato ligands in affecting the molecular quadratic optical nonlinearity of these complexes.

Origin of the Anomalous Color of Egyptian and Han Blue Historical Pigments: Going beyond the Complex Approximation in Ligand Field Theory

Science.gov (United States)

García-Fernandez, Pablo; Moreno, Miguel; Aramburu, José Antonio

2016-01-01

The complex approximation is widely used in the framework of the Ligand Field Theory for explaining the optical properties of crystalline coordination compounds. Here, we show that there are essential features of these systems that cannot be understood with the usual approximation that only considers an isolated complex at the correct equilibrium…

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

Science.gov (United States)

Onuk, Emre; Badger, John; Wang, Yu Jing; Bardhan, Jaydeep; Chishti, Yasmin; Akcakaya, Murat; Brooks, Dana H; Erdogmus, Deniz; Minh, David D L; Makowski, Lee

2017-08-29

Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands. Scattering data from apo AdK are consistent with scattering predicted from the crystal structure of AdK in the open conformation. In contrast, data from AdK samples saturated with Ap5A do not agree with that calculated from AdK in the closed conformation. Using cluster analysis of available structures, we selected representative structures in five conformational states: open, partially open, intermediate, partially closed, and closed. We used these structures to estimate the relative abundances of these states for each experimental condition. X-ray solution scattering data obtained from AdK with AMP are dominated by scattering from AdK in the open conformation. For AdK in the presence of high concentrations of ATP and ADP, the conformational ensemble shifts to a mixture of partially open and closed states. Even when AdK is saturated with Ap5A, a significant proportion of AdK remains in a partially open conformation. These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding.

Electric-field-induced flow-aligning state in a nematic liquid crystal.

Science.gov (United States)

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2015-04-01

The response of shear stress to a weak ac electric field as a probe is measured in a nematic liquid crystal under shear flow and dc electric fields. Two states with different responses are clearly observed when the dc electric field is changed at a constant shear rate: the flow aligning and non-flow aligning states. The director lies in the shear plane in the flow aligning state and out of the plane in the non-flow aligning state. Through application of dc electric field, the non-flow aligning state can be changed to the flow aligning state. In the transition from the flow aligning state to the non-flow aligning state, it is found that the response increases and the relaxation time becomes longer. Here, the experimental results in the flow aligning state are discussed on the basis of the Ericksen-Leslie theory.

Effect of elastic deformation and the magnetic field on the electrical conductivity of p-Si crystals

Science.gov (United States)

Lys, R.; Pavlyk, B.; Didyk, R.; Shykorjak, J.; Karbovnyk, I.

2018-03-01

It is shown that at a deformation rate of 0.41 kg/min, the characteristic feature of the dependence of the surface resistance of the p-Si sample on the magnitude of its elastic deformation (R(σ)) is the reduction of the resistance during compression and unclamping. With the increase in the number of "compression-unclamping" cycles, the difference between the positions of the compression and unclamping curves decreases. The transformation of two types of magnetically sensitive defects occurs under the impact of a magnetic field on p-Si crystals. The defects are interrelated with two factors that cause the mutually opposite influence on the conductivity of the crystal. The first factor is that the action of the magnetic field decreases the activation energy of the dislocation holders, which leads to an increase in the electrical conductivity of the sample. The second factor is that due to the decay of molecules of oxygen-containing impurities in the magnetic field, the stable chemisorption bonds appear in the crystal that leads to a decrease in its conductivity. If the sample stays in the magnetic field for a long time, the one or the other mechanism predominates, causing a slow growth or decrease in resistance around a certain (averaged) value. Moreover, the frequency of such changes is greater in the deformed sample. The value of the surface resistance of p-Si samples does not change for a long time without the influence of the magnetic field.

Large piezoelectricity in electric-field modified single crystals of SrTiO3

Science.gov (United States)

Khanbabaee, B.; Mehner, E.; Richter, C.; Hanzig, J.; Zschornak, M.; Pietsch, U.; Stöcker, H.; Leisegang, T.; Meyer, D. C.; Gorfman, S.

2016-11-01

Defect engineering is an effective and powerful tool to control the existing material properties and produce completely new ones, which are symmetry-forbidden in a defect-free crystal. For example, the application of a static electric field to a single crystal of SrTiO3 forms a strained near-surface layer through the migration of oxygen vacancies out of the area beneath the positively charged electrode. While it was previously shown that this near-surface phase holds pyroelectric properties, which are symmetry-forbidden in centrosymmetric bulk SrTiO3, this paper reports that the same phase is strongly piezoelectric. We demonstrate the piezoelectricity of this phase through stroboscopic time-resolved X-ray diffraction under alternating electric field and show that the effective piezoelectric coefficient d33 ranges between 60 and 100 pC/N. The possible atomistic origins of the piezoelectric activity are discussed as a coupling between the electrostrictive effect and spontaneous polarization of this near-surface phase.

Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

Energy Technology Data Exchange (ETDEWEB)

Vognsen, Tina, E-mail: tv@farma.ku.dk [Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen (Denmark); Kristensen, Ole, E-mail: ok@farma.ku.dk [Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen (Denmark)

2012-03-30

Highlights: Black-Right-Pointing-Pointer The crystal structure of the NTF2-like domain of Rasputin protein is presented. Black-Right-Pointing-Pointer Differences to known ligand binding sites of nuclear transport factor 2 are discussed. Black-Right-Pointing-Pointer A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 A resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a {beta}-sheet and three {alpha}-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

Mutation of the His ligand in mitoNEET stabilizes the 2Fe–2S cluster despite conformational heterogeneity in the ligand environment

Energy Technology Data Exchange (ETDEWEB)

Conlan, Andrea R.; Paddock, Mark L.; Homer, Christina [University of California at San Diego, La Jolla, CA 92093 (United States); Axelrod, Herbert L.; Cohen, Aina E. [Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Abresch, Edward C.; Zuris, John A. [University of California at San Diego, La Jolla, CA 92093 (United States); Nechushtai, Rachel [Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904 (Israel); Jennings, Patricia A., E-mail: pajennin@ucsd.edu [University of California at San Diego, La Jolla, CA 92093 (United States)

2011-06-01

The spectroscopic and stability properties and X-ray crystal structure of the H87C mutant of the 2Fe–2S ligand mitoNEET are reported. Strikingly, the single point mutation leads to changes in its absorbance and CD spectra and an increase of around sixfold in the stability of the 2Fe–2S clusters over the pH range 5–7. However, the crystal structure of the H87C mutant displays heterogeneity in a few key residues, including the introduced cysteine ligand. Nonetheless, the cluster is highly stabilized from release. MitoNEET is the only identified Fe–S protein localized to the outer mitochondrial membrane and a 1.5 Å resolution X-ray analysis has revealed a unique structure [Paddock et al. (2007 ▶), Proc. Natl Acad. Sci. USA, 104, 14342–14347]. The 2Fe–2S cluster is bound with a 3Cys–1His coordination which defines a new class of 2Fe–2S proteins. The hallmark feature of this class is the single noncysteine ligand His87, which when replaced by Cys decreases the redox potential (E{sub m}) by ∼300 mV and increases the stability of the cluster by around sixfold. Unexpectedly, the pH dependence of the lifetime of the 2Fe–2S cluster remains the same as in the wild-type protein. Here, the crystal structure of H87C mitoNEET was determined to 1.7 Å resolution (R factor = 18%) to investigate the structural basis of the changes in the properties of the 2Fe–2S cluster. In comparison to the wild type, structural changes are localized to the immediate vicinity of the cluster-binding region. Despite the increased stability, Cys87 displays two distinct conformations, with distances of 2.3 and 3.2 Å between the S{sup γ} and the outer Fe of the 2Fe–2S cluster. In addition, Lys55 exhibits multiple conformations in the H87C mutant protein. The structure and distinct characteristics of the H87C mutant provide a framework for further studies investigating the effects of mutation on the properties of the 2Fe–2S cluster in this new class of proteins.

Parameterization of phosphine ligands demonstrates enhancement of nickel catalysis via remote steric effects

Science.gov (United States)

Wu, Kevin; Doyle, Abigail G.

2017-08-01

The field of Ni-catalysed cross-coupling has seen rapid recent growth because of the low cost of Ni, its earth abundance, and its ability to promote unique cross-coupling reactions. Whereas advances in the related field of Pd-catalysed cross-coupling have been driven by ligand design, the development of ligands specifically for Ni has received minimal attention. Here, we disclose a class of phosphines that enable the Ni-catalysed Csp3 Suzuki coupling of acetals with boronic acids to generate benzylic ethers, a reaction that failed with known ligands for Ni and designer phosphines for Pd. Using parameters to quantify phosphine steric and electronic properties together with regression statistical analysis, we identify a model for ligand success. The study suggests that effective phosphines feature remote steric hindrance, a concept that could guide future ligand design tailored to Ni. Our analysis also reveals that two classic descriptors for ligand steric environment—cone angle and % buried volume—are not equivalent, despite their treatment in the literature.

Simvastatin-nicotinamide co-crystal: design, preparation and ...

African Journals Online (AJOL)

Methods: In silico molecular modeling of Nic counter to SV were investigated using ... Results: In silico results showed that the interaction of Nic with SV took place through ... Conclusion: Co-crystallization using Nic has the potential to enhance drug ... directed to convert the ligand protein data bank ... after each sampling.

Influence of Superconductivity on Crystal Electric Field Transitions in La1-xTbxAl2

DEFF Research Database (Denmark)

Feile, R.; Loewenhaupt, M.; Kjems, Jørgen

1981-01-01

Inelastic neutron scattering from the crystal electric field transitions in La1-xTbxAl2 single crystals has revealed an abrupt increase in the lifetimes of these transitions when the system becomes superconducting. An increase in the integrated intensities is also observed. The lifetime effects...... are quantitatively reproduced by existing theories, which take into account the reduced scattering of the conduction electrons by the magnetic ions due to the creation of the superconducting energy gap 2Δ(T)....

Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima.

Science.gov (United States)

Oferkin, Igor V; Katkova, Ekaterina V; Sulimov, Alexey V; Kutov, Danil C; Sobolev, Sergey I; Voevodin, Vladimir V; Sulimov, Vladimir B

2015-01-01

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

Directory of Open Access Journals (Sweden)

Igor V. Oferkin

2015-01-01

Full Text Available The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

Orientation selection process during the early stage of cubic dendrite growth: A phase-field crystal study

International Nuclear Information System (INIS)

Tang Sai; Wang Zhijun; Guo Yaolin; Wang Jincheng; Yu Yanmei; Zhou Yaohe

2012-01-01

Using the phase-field crystal model, we investigate the orientation selection of the cubic dendrite growth at the atomic scale. Our simulation results reproduce how a face-centered cubic (fcc) octahedral nucleus and a body-centered cubic (bcc) truncated-rhombic dodecahedral nucleus choose the preferred growth direction and then evolve into the dendrite pattern. The interface energy anisotropy inherent in the fcc crystal structure leads to the fastest growth velocity in the 〈1 0 0〉 directions. New { 1 1 1} atomic layers prefer to nucleate at positions near the tips of the fcc octahedron, which leads to the directed growth of the fcc dendrite tips in the 〈1 0 0〉 directions. A similar orientation selection process is also found during the early stage of bcc dendrite growth. The orientation selection regime obtained by phase-field crystal simulation is helpful for understanding the orientation selection processes of real dendrite growth.

Phenomenological crystal-field model of the magnetic and thermal properties of the Kondo-like system UCu2Si2

Science.gov (United States)

Troć, R.; Gajek, Z.; Pikul, A.; Misiorek, H.; Colineau, E.; Wastin, F.

2013-07-01

The transport properties described previously [Troć , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.85.224434 85, 224434 (2012)] as well as the magnetic and thermal properties presented in this paper, observed for single-crystalline UCu2Si2, are discussed by assuming a dual (localized-itinerant) scenario. The electronic states of the localized 5f electrons in UCu2Si2 are constructed using the effective Hamiltonian known for ionic systems, allowing us to treat the Coulomb, spin-orbital, and crystal-field interactions on equal footing. The space of parameters has been restricted in the initial steps with the aid of the angular overlap model approximation. The final crystal-field parameters, obtained from the refined steps of calculations, are relatively large (in absolute values), which we attribute to the hybridization characteristic of the metallic systems on the verge of localization. The proposed crystal-field model reproduces correctly with satisfactory accuracy the magnetic and thermal properties of UCu2Si2 in agreement also with the transport properties reported previously. Considerable crystal-field splitting of the ground multiplet of 2760 K is responsible for a large anisotropy in the magnetic behavior, observed in the whole temperature range explored.

Electric field influence on exciton absorption of Er doped and undoped InSe single crystals

International Nuclear Information System (INIS)

Guerbulak, B; Kundakci, M; Ates, A; Yildirim, M

2007-01-01

Undoped InSe and Er doped InSe (InSe:Er) single crystals were grown by using the Stockbarger method. Ingots had no cracks and voids on the surface. The absorption measurements were carried out in InSe and InSe:Er samples for U=0 and U=30 V in the temperature range 10-320 K with a step of 10 K. Electric field effects on excitons are observed in InSe and InSe:Er single crystals. The absorption edge shifted towards longer wavelengths and decreased intensity in absorption spectra under an electric field E≅5.9 kV cm -1 . The applied electric field caused a shifting and a decreasing of intensity in the absorption spectra. The shifting of the absorption edge can be explained on the basis of the Franz-Keldysh effect (FKE) or thermal heating of the sample under the electric field. At 10 and 320 K, the first exciton energies for InSe were calculated as 1.336 and 1.291 eV for zero voltage and 1.331 and 1.280 eV for electric field and InSe:Er as 1.329 and 1.251 eV for zero voltage and 1.318 and 1.248 eV for electric field, respectively

Modelling of thermal field and point defect dynamics during silicon single crystal growth using CZ technique

Science.gov (United States)

Sabanskis, A.; Virbulis, J.

2018-05-01

Mathematical modelling is employed to numerically analyse the dynamics of the Czochralski (CZ) silicon single crystal growth. The model is axisymmetric, its thermal part describes heat transfer by conduction and thermal radiation, and allows to predict the time-dependent shape of the crystal-melt interface. Besides the thermal field, the point defect dynamics is modelled using the finite element method. The considered process consists of cone growth and cylindrical phases, including a short period of a reduced crystal pull rate, and a power jump to avoid large diameter changes. The influence of the thermal stresses on the point defects is also investigated.

Ruthenium(II carbonyl compounds with the 4′-chloro-2,2′:6′,2′′-terpyridine ligand

Directory of Open Access Journals (Sweden)

Rajendhraprasad Tatikonda

2017-04-01

Full Text Available Two ruthenium carbonyl complexes with the 4′-chloro-2,2′:6′,2′′-terpyridine ligand (tpy-Cl, C15H10ClN3, i.e. [RuCl(tpy-Cl(CO2][RuCl3(CO3] (I [systematic name: cis-dicarbonylchlorido(4′-chloro-2,2′:6′,2′′-terpyridine-κ3Nruthenium(II fac-tricarbonyltrichloridoruthenate(II], and [RuCl2(tpy-Cl(CO2] (II [cis-dicarbonyl-trans-dichlorido(4′-chloro-2,2′:6′,2′′-terpyridine-κ2N1,N1′ruthenium(II], were synthesized and characterized by single-crystal X-ray diffraction. The RuII atoms in both centrosymmetric structures (I and (II display similar, slightly distorted octahedral coordination spheres. The coordination sphere in the complex cation in compound (I is defined by three N atoms of the tridentate tpy-Cl ligand, two carbonyl carbon atoms and one chlorido ligand; the charge is balanced by an octahedral [Ru(CO3Cl3]− counter-anion. In the neutral compound (II, the tpy-Cl ligand coordinates to the metal only through two of its N atoms. The coordination sphere of the RuII atom is completed by two carbonyl and two chlorido ligands. In the crystal structures of both (I and (II, weak C—H...Cl interactions are observed.

Tellurium adsorption on single crystal faces of molybdenum and tungsten field emitters

International Nuclear Information System (INIS)

Collins, R.A.; Kiwanga, C.A.

1978-01-01

The purpose of this letter is to report the extension of previous studies of Te adsorption on Mo and W field emitters to measurements on single crystal planes. The adsorption of semiconductors on metallic emitters has been found to be characterized by simultaneous decreases in emission current and the Fowler-Nordheim work function for adsorbate coverages of less than a monolayer. (Auth.)

Zinc acetylacetonate hydrate adducted with nitrogen donor ligands: Synthesis, spectroscopic characterization, and thermal analysis

Science.gov (United States)

Brahma, Sanjaya; Shivashankar, S. A.

2015-12-01

We report synthesis, spectroscopic characterization, and thermal analysis of zinc acetylacetonate complex adducted by nitrogen donor ligands, such as pyridine, bipyridine, and phenanthroline. The pyridine adducted complex crystallizes to monoclinic crystal structure, whereas other two adducted complexes have orthorhombic structure. Addition of nitrogen donor ligands enhances the thermal property of these complexes as that with parent metal-organic complex. Zinc acetylacetonate adducted with pyridine shows much higher volatility (106 °C), decomposition temperature (202 °C) as that with zinc acetylacetonate (136 °C, 220 °C), and other adducted complexes. All the adducted complexes are thermally stable, highly volatile and are considered to be suitable precursors for metal organic chemical vapor deposition. The formation of these complexes is confirmed by powder X-ray diffraction, Fourier transform infrared spectroscopy, mass spectroscopy, and elemental analysis. The complexes are widely used as starting precursor materials for the synthesis of ZnO nanostructures by microwave irradiation assisted coating process.

Solid state structure of thorium(IV) complexes with common aminopoly-carboxylate ligands

International Nuclear Information System (INIS)

Thuery, Pierre

2011-01-01

The crystal structures of the complexes formed by reaction of thorium(IV) nitrate with iminodiacetic acid (H 2 IDA), nitrilotriacetic acid (H 3 NTA), and ethylenediaminetetraacetic acid (H 4 EDTA) under hydrothermal conditions are reported. In [Th(HIDA) 2 (C 2 O 4 )].H 2 O (1), the metal atom is chelated by two carboxylate groups from two HIDA - anions and by two oxalate ligands formed in situ; two additional oxygen atoms from two more HIDA - anions complete the ten-coordinate environment of bi-capped square anti-prismatic geometry. The uncoordinated nitrogen atom is protonated and involved in hydrogen bonding. Two different ligands are present in [Th(NTA)(H 2 NTA)(H 2 O)].H 2 O (2), one of them being a O 3 ,N-chelating tri-anion which acts also as a bridge toward two neighboring metal ions, and the other being a bis-monodentate bridging species with an uncoordinated carboxylic arm and a central ammonium group. An aqua ligand completes the nine-coordinated, capped square anti-prismatic metal environment. The EDTA 4- anion in [Th(EDTA)(H 2 O)].2H 2 O (3) is chelating through one oxygen atom from each carboxylate group and the two nitrogen atoms, as in a previously reported molecular complex. Two carboxylate groups are bridging, which, with the addition of an aqua ligand, gives a capped square anti-prismatic coordination polyhedron. Aminopoly-carboxylate ligands have been much investigated in relation with actinide decorporation and nuclear wastes management studies, and the present results add to the structural information available on their complexes with thorium(IV), which has mainly been obtained up to now by extended X-ray absorption fine structure (EXAFS) spectroscopy. In particular, the bridging (non-chelating) coordination mode of H 2 NTA - is a novel feature in this context. All three complexes crystallize as two-dimensional assemblies and are thus novel examples of thorium-organic coordination polymers. (author)

Broken symmetry phase transition in solid p-H 2, o-D 2 and HD: crystal field effects

Science.gov (United States)

Freiman, Yu. A.; Hemley, R. J.; Jezowski, A.; Tretyak, S. M.

1999-04-01

We report the effect of the crystal field (CF) on the broken symmetry phase transition (BSP) in solid parahydrogen, orthodeuterium, and hydrogen deuteride. The CF was calculated taking into account a distortion from the ideal HCP structure. We find that, in addition to the molecular field generated by the coupling terms in the intermolecular potential, the Hamiltonian of the system contains a crystal-field term, originating from single-molecular terms in the intermolecular potential. Ignoring the CF is the main cause of the systematic underestimation of the transition pressure, characteristic of published theories of the BSP transition. The distortion of the lattice that gives rise to the negative CF in response to the applied pressure is in accord with the general Le Chatelier-Braun principle.

Zinc(II) complexes of carboxamide derivatives: Crystal structures ...

Indian Academy of Sciences (India)

can form complexes with a variety of metal ions. Recently, bi- ... tural analyses of both ligands and complex 1 by single crystal X-ray ..... software over a Red Hat Linux IBM cluster using den- .... Change in the relative viscosity (η/ηo)1/3 of CT-.

Magnetic Order and Crystal Field Excitations in Er2Ru2O7: A Neutron Scattering Study

International Nuclear Information System (INIS)

Ehlers, Georg; Gardner, Jason

2009-01-01

The magnetic pyrochlore Er 2 Ru 2 O 7 has been studied with neutron scattering and susceptibility measurements down to a base temperature of 270 mK. For the low temperature phase in which the Er sublattice orders, new magnetic Bragg peaks are reported which can be indexed with integer (hkl) for a face centered cubic cell. Inelastic measurements reveal a wealth of crystal field levels of the Er ion and a copious amount of magnetic scattering below 15 meV. The three lowest groups of crystal field levels are at 6.7, 9.1 and 18.5 meV.

MyCrystals - a simple visual data management program for laboratory-scale crystallization experiments

DEFF Research Database (Denmark)

Løvgreen, Monika Nøhr; Løvgreen, Mikkel; Christensen, Hans Erik Mølager

2009-01-01

MyCrystals is designed as a user-friendly program to display crystal images and list crystallization conditions. The crystallization conditions entry fields can be customized to suit the experiments. MyCrystals is also able to sort the images by the entered crystallization conditions, which...

Crystal Structure of [Bis(DIMETHYLFORMAMIDE Bis (2,2’-PYRIDYLQUINOLINE Iron (II] Bis-(TETRAPHENYLBORATE

Directory of Open Access Journals (Sweden)

Bohari M. Yamin

2009-11-01

Full Text Available The goal of this research is to obtain single crystal and structural information of iron(II complex with 2,(2'-pyridylquinoline(pq ligands. The reaction of iron(II salt with 2,(2'-pyridylquinoline ligand and sodiumtetraphenylborate in the molar ratio of 1:3:2 in methanol-N,N-dimethylformamide(dmf solution results in an iron(IIcomplex. The formula of the [Fe(pq2(dmf2](BPh42 complex has been obtained from the iron(II and C, H, N contents.Single crystal of [Fe(pq2(dmf2](BPh42 suitable for X-ray investigation was obtained by evaporation of the complexsolution in N,N-dimethylformamide at room temperature after 24 hours. This compound crystallizes in monoclinicsystem with C2/c space group, a = 27.950(4, b = 14.169(7, c = 17.717(9 Å and b = 105.669(11°. The structureconsist of iron(II is chelated by two pq ligands through the N atoms and two dmf molecules in a six-coordinationenvironment. The charge of the [Fe(pq2(dmf2]2+ cation is balanced by two tetraphenylborate (BPh4- anions.

Structure-activity relationships of constrained phenylethylamine ligands for the serotonin 5-ht2 receptors

DEFF Research Database (Denmark)

Isberg, Vignir; Paine, James; Leth-Petersen, Sebastian

2013-01-01

Serotonergic ligands have proven effective drugs in the treatment of migraine, pain, obesity, and a wide range of psychiatric and neurological disorders. There is a clinical need for more highly 5-HT2 receptor subtype-selective ligands and the most attention has been given to the phenethylamine...... about the bioactive conformation of the amine functionality. However, combined 1,2-constriction by cyclization has only been tested with one compound. Here, we present three new 1,2-cyclized phenylethylamines, 9-11, and describe their synthetic routes. Ligand docking in the 5-HT2B crystal structure...... but shift the placement of the core scaffold. The constraints in 9-11 resulted in docking poses with the 4-bromine in closer vicinity to 5.46, which is polar only in the human 5-HT2A subtype, for which 9-11 have the lowest affinity. The new ligands, conformational analysis and docking expand the structure...

Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor

Energy Technology Data Exchange (ETDEWEB)

Bokoch, Michael P.; Zou, Yaozhong; Rasmussen, Søren G.F.; Liu, Corey W.; Nygaard, Rie; Rosenbaum, Daniel M.; Fung, Juan José; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Puglisi, Joseph D.; Weis, William I.; Pardo, Leonardo; Prosser, R. Scott; Mueller, Luciano; Kobilka, Brian K. (Stanford-MED); (Toronto); (BMS); (UAB, Spain)

2010-01-14

G-protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters. They are the largest group of therapeutic targets for a broad spectrum of diseases. Recent crystal structures of GPCRs have revealed structural conservation extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the native ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the {beta}{sub 2} adrenergic receptor: a salt bridge linking extracellular loops 2 and 3. Small-molecule drugs that bind within the transmembrane core and exhibit different efficacies towards G-protein activation (agonist, neutral antagonist and inverse agonist) also stabilize distinct conformations of the ECS. We thereby demonstrate conformational coupling between the ECS and the orthosteric binding site, showing that drugs targeting this diverse surface could function as allosteric modulators with high subtype selectivity. Moreover, these studies provide a new insight into the dynamic behaviour of GPCRs not addressable by static, inactive-state crystal structures.

Photonic time crystals.

Science.gov (United States)

Zeng, Lunwu; Xu, Jin; Wang, Chengen; Zhang, Jianhua; Zhao, Yuting; Zeng, Jing; Song, Runxia

2017-12-07

When space (time) translation symmetry is spontaneously broken, the space crystal (time crystal) forms; when permittivity and permeability periodically vary with space (time), the photonic crystal (photonic time crystal) forms. We proposed the concept of photonic time crystal and rewritten the Maxwell's equations. Utilizing Finite Difference Time Domain (FDTD) method, we simulated electromagnetic wave propagation in photonic time crystal and photonic space-time crystal, the simulation results show that more intensive scatter fields can obtained in photonic time crystal and photonic space-time crystal.

Magnetic field effect on microplastic strain rate in C690 single crystals

International Nuclear Information System (INIS)

Smirnov, B.I.; Shpejzman, V.V.; Peschanskaya, N.N.; Nikolaev, R.K.

2002-01-01

Microplastic strain in magnetic field and beyond it, as well as, subsequent to preliminary exposure of C 60 crystals to magnetic field was investigated by means of laser interferometer enabling to measure rate of strain on the basis of 0.15 μm linear shifting. It is shown that introduction and removal of specimen from 0.2 T induction field immediately during deformation of specimen result in variation of its rate, and at reduction of rate one observes discontinuous interruption of deformation. Sign of effect depends on temperature: at room temperature magnetic field promotes deformation, at 100 K - shows it down. Effect of preliminary exposure within 0.2 and 2T induction field turned to be analogous one. One analyzed possible reasons of the observed manifestation of magnetoplastic effect in C 60 and relation of its sign with phase transition under 260 K temperature [ru

Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets.

Science.gov (United States)

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Camproux, Anne-Claude; Petitjean, Michel

2017-11-01

We analyzed 78 binding pockets of the human urokinase plasminogen activator (uPA) catalytic domain extracted from a data set of crystallized uPA-ligand complexes. These binding pockets were computed with an original geometric method that does NOT involve any arbitrary parameter, such as cutoff distances, angles, and so on. We measured the deviation from convexity of each pocket shape with the pocket convexity index (PCI). We defined a new pocket descriptor called distributional sphericity coefficient (DISC), which indicates to which extent the protein atoms of a given pocket lie on the surface of a sphere. The DISC values were computed with the freeware PCI. The pocket descriptors and their high correspondences with ligand descriptors are crucial for polypharmacology prediction. We found that the protein heavy atoms lining the urokinases binding pockets are either located on the surface of their convex hull or lie close to this surface. We also found that the radii of the urokinases binding pockets and the radii of their ligands are highly correlated (r = 0.9).

Extensional flow of nematic liquid crystal with an applied electric field

KAUST Repository

CUMMINGS, L. J.; LOW, J.; MYERS, T. G.

2013-01-01

Systematic asymptotic methods are used to formulate a model for the extensional flow of a thin sheet of nematic liquid crystal. With no external body forces applied, the model is found to be equivalent to the so-called Trouton model for Newtonian sheets (and fibres), albeit with a modified 'Trouton ratio'. However, with a symmetry-breaking electric field gradient applied, behaviour deviates from the Newtonian case, and the sheet can undergo finite-time breakup if a suitable destabilizing field is applied. Some simple exact solutions are presented to illustrate the results in certain idealized limits, as well as sample numerical results to the full model equations. Copyright © Cambridge University Press 2013.

Extensional flow of nematic liquid crystal with an applied electric field

KAUST Repository

CUMMINGS, L. J.

2013-10-17

Systematic asymptotic methods are used to formulate a model for the extensional flow of a thin sheet of nematic liquid crystal. With no external body forces applied, the model is found to be equivalent to the so-called Trouton model for Newtonian sheets (and fibres), albeit with a modified \\'Trouton ratio\\'. However, with a symmetry-breaking electric field gradient applied, behaviour deviates from the Newtonian case, and the sheet can undergo finite-time breakup if a suitable destabilizing field is applied. Some simple exact solutions are presented to illustrate the results in certain idealized limits, as well as sample numerical results to the full model equations. Copyright © Cambridge University Press 2013.

Crystallization In Multicomponent Glasses

International Nuclear Information System (INIS)

Kruger, A.A.; Hrma, P.R.

2009-01-01

In glass processing situations involving glass crystallization, various crystalline forms nucleate, grow, and dissolve, typically in a nonuniform temperature field of molten glass subjected to convection. Nuclear waste glasses are remarkable examples of multicomponent vitrified mixtures involving partial crystallization. In the glass melter, crystals form and dissolve during batch-to-glass conversion, melter processing, and product cooling. Crystals often agglomerate and sink, and they may settle at the melter bottom. Within the body of cooling glass, multiple phases crystallize in a non-uniform time-dependent temperature field. Self-organizing periodic distribution (the Liesegnang effect) is common. Various crystallization phenomena that occur in glass making are reviewed.

CRYSTALLIZATION IN MULTICOMPONENT GLASSES

Energy Technology Data Exchange (ETDEWEB)

KRUGER AA; HRMA PR

2009-10-08

In glass processing situations involving glass crystallization, various crystalline forms nucleate, grow, and dissolve, typically in a nonuniform temperature field of molten glass subjected to convection. Nuclear waste glasses are remarkable examples of multicomponent vitrified mixtures involving partial crystallization. In the glass melter, crystals form and dissolve during batch-to-glass conversion, melter processing, and product cooling. Crystals often agglomerate and sink, and they may settle at the melter bottom. Within the body of cooling glass, multiple phases crystallize in a non-uniform time-dependent temperature field. Self-organizing periodic distribution (the Liesegnang effect) is common. Various crystallization phenomena that occur in glass making are reviewed.

Concurrent coordination of ligand in metal chloride complexes with 1-vinyl-2-(2-pyridyl)benzimidazole

International Nuclear Information System (INIS)

Bajkalov, L.V.; Domnina, E.S.

1996-01-01

The properties and structure of bivalent cadmium and 1-vinyl-2-(2-pyridyl)benzimidazole chloride complexes, which have been prepared for the first time, have been studied by the methods of potentiometric titration and PMR, 35 Cl NQR, UV and IR spectroscopy. For the complexes above di- and polymeric structures in crystal phase are suggested, where ligand plays the role of a bridge. N,N-bidentate ligand. In solution the complexes dissociate with formation of monomeric coordination compounds, their metal being bound by different ways, stemming from participation of N benzimidazole or pyridine fragment of the ligand. Adducts of ionic type with second sphere 1-vinyl-2-(2-pyridyl)benzimidazole cation have been obtained in the course of hydrochlorination of the complexes prepared

Sensitized charge carrier injection into organic crystals studied by isotope effects in weak magnetic fields

International Nuclear Information System (INIS)

Bube, W.; Michel-Beyerle, M.E.; Haberkorn, R.; Steffens, E.

1977-01-01

The magnetic field (H approximately 50 Oe) dependence of the rhodamine sensitized triplet exciton density in anthracene crystals is influenced by isotopic substitution. This confirms the hyperfine interaction as mechanism explaining the change of the spin multiplicity in the initially formed singlet state of the radical pair. The isotope effect occurs in the sensitizing dye ( 14 N/ 15 N) rather than at the molecular site of the injected charge within the crystal. This can be understood in terms of the high hopping frequency of the charge carriers as compared to the time constant of the hyperfine induced singlet-triplet transition. Since the dye molecules adsorb in an oriented fashion, the angular dependence of the magnetic field modulation of the triplet exciton density can be interpreted without assuming any additional interactions. (Auth.)

Particles at fluid-fluid interfaces: A new Navier-Stokes-Cahn-Hilliard surface- phase-field-crystal model.

Science.gov (United States)

Aland, Sebastian; Lowengrub, John; Voigt, Axel

2012-10-01

Colloid particles that are partially wetted by two immiscible fluids can become confined to fluid-fluid interfaces. At sufficiently high volume fractions, the colloids may jam and the interface may crystallize. The fluids together with the interfacial colloids form an emulsion with interesting material properties and offer an important route to new soft materials. A promising approach to simulate these emulsions was presented in Aland et al. [Phys. Fluids 23, 062103 (2011)], where a Navier-Stokes-Cahn-Hilliard model for the macroscopic two-phase fluid system was combined with a surface phase-field-crystal model for the microscopic colloidal particles along the interface. Unfortunately this model leads to spurious velocities which require very fine spatial and temporal resolutions to accurately and stably simulate. In this paper we develop an improved Navier-Stokes-Cahn-Hilliard-surface phase-field-crystal model based on the principles of mass conservation and thermodynamic consistency. To validate our approach, we derive a sharp interface model and show agreement with the improved diffuse interface model. Using simple flow configurations, we show that the new model has much better properties and does not lead to spurious velocities. Finally, we demonstrate the solid-like behavior of the crystallized interface by simulating the fall of a solid ball through a colloid-laden multiphase fluid.

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

Directory of Open Access Journals (Sweden)

Maike Bublitz

2015-07-01

Full Text Available Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

Energy Technology Data Exchange (ETDEWEB)

Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai-Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

2015-06-11

Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields

Energy Technology Data Exchange (ETDEWEB)

Armas-Pérez, Julio C.; Londono-Hurtado, Alejandro [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Guzmán, Orlando [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, DF 09340, México (Mexico); Hernández-Ortiz, Juan P. [Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín (Colombia); Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Pablo, Juan J. de, E-mail: depablo@uchicago.edu [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2015-07-28

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields.

Energy Technology Data Exchange (ETDEWEB)

Armas-Perez, Julio C.; Londono-Hurtado, Alejandro; Guzman, Orlando; Hernandez-Ortiz, Juan P.; de Pablo, Juan J.

2015-07-27

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Synthesis, characterization and crystal structure of a ...

African Journals Online (AJOL)

The Mo atom in the complex is in octahedral coordination. Thermal stability of the complex has also been studied. KEY WORDS: Molybdenum complex, Hydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. Bull. Chem. Soc. Ethiop. 2014, 28(3), 409-414. DOI: http://dx.doi.org/10.4314/bcse.v28i3.10 ...

Elimination of image flicker in a fringe-field switching liquid crystal display by applying a bipolar voltage wave.

Science.gov (United States)

Oh, Seung-Won; Park, Jun-Hee; Lee, Ji-Hoon; Yoon, Tae-Hoon

2015-09-07

Recently, low-frequency driving of liquid crystal display (LCD) panels to minimize power consumption has drawn much attention. In the case in which an LCD panel is driven by a fringe-field at a low frequency, the image flickering phenomenon occurs when the sign of the applied electric field is reversed. We investigated image flickering induced by the flexoelectric effect in a fringe-field switching (FFS) liquid crystal cell in terms of the transmittance difference between frames and the ripple phenomenon. Experimental results show that image flicker due to transmittance difference can be eliminated completely and that the ripple phenomena can be reduced significantly by applying a bipolar voltage wave to the FFS cell.

The plug-based nanovolume Microcapillary Protein Crystallization System (MPCS)

International Nuclear Information System (INIS)

Gerdts, Cory J.; Elliott, Mark; Lovell, Scott; Mixon, Mark B.; Napuli, Alberto J.; Staker, Bart L.; Nollert, Peter; Stewart, Lance

2008-01-01

The Microcapillary Protein Crystallization System (MPCS) is a new protein-crystallization technology used to generate nanolitre-sized crystallization experiments for crystal screening and optimization. Using the MPCS, diffraction-ready crystals were grown in the plastic MPCS CrystalCard and were used to solve the structure of methionine-R-sulfoxide reductase. The Microcapillary Protein Crystallization System (MPCS) embodies a new semi-automated plug-based crystallization technology which enables nanolitre-volume screening of crystallization conditions in a plasticware format that allows crystals to be easily removed for traditional cryoprotection and X-ray diffraction data collection. Protein crystals grown in these plastic devices can be directly subjected to in situ X-ray diffraction studies. The MPCS integrates the formulation of crystallization cocktails with the preparation of the crystallization experiments. Within microfluidic Teflon tubing or the microfluidic circuitry of a plastic CrystalCard, ∼10–20 nl volume droplets are generated, each representing a microbatch-style crystallization experiment with a different chemical composition. The entire protein sample is utilized in crystallization experiments. Sparse-matrix screening and chemical gradient screening can be combined in one comprehensive ‘hybrid’ crystallization trial. The technology lends itself well to optimization by high-granularity gradient screening using optimization reagents such as precipitation agents, ligands or cryoprotectants

Crystal structure of chlorido(dimethyl sulfoxide-κSbis[4-(pyridin-2-ylbenzaldehyde-κ3C2,N]iridium(III acetonitrile monosolvate

Directory of Open Access Journals (Sweden)

Andrew J. Peloquin

2017-09-01

Full Text Available The title compound, [IrCl(C12H8NO2{(CH32SO}]·H3CCN or [IrCl(fppy2(DMSO]·H3CCN [where fppy is 4-(pyridin-2-ylbenzaldehyde and DMSO is dimethyl sulfoxide], is a mononuclear iridium(III complex including two fppy ligands, a sulfur-coordinating DMSO ligand, and one terminal chloride ligand that define a distorted octahedral coordination sphere. The complex crystallizes from 1:1 DMSO–acetonitrile as an acetonitrile solvate. In the crystal, weak C—H...O and C—H...N hydrogen-bonding interactions between adjacent complexes and between the acetonitrile solvent and the complex consolidate the packing.

Prediction of ligand effects in platinum-amyloid-β coordination.

Science.gov (United States)

Turner, Matthew; Deeth, Robert J; Platts, James A

2017-08-01

Ligand field molecular mechanics (LFMM) and semi-empirical Parametric Model 7 (PM7) methods are applied to a series of six Pt II -Ligand systems binding to the N-terminal domain of the amyloid-β (Aβ) peptide. Molecular dynamics using a combined LFMM/Assisted Model Building with Energy Refinement (AMBER) approach is used to explore the conformational freedom of the peptide fragment, and identifies favourable platinum binding modes and peptide conformations for each ligand investigated. Platinum coordination is found to depend on the nature of the ligand, providing evidence that binding mode may be controlled by suitable ligand design. Boltzmann populations at 310K indicate that each Pt-Aβ complex has a small number of thermodynamically accessible states. Ramachandran maps are constructed for the sampled Pt-Aβ conformations and secondary structural analysis of the obtained complex structures is performed and contrasted with the free peptide; coordination of these platinum complexes disrupts existing secondary structure in the Aβ peptide and promotes formation of ligand-specific turn-type secondary structure. Copyright © 2017 Elsevier Inc. All rights reserved.

Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants

International Nuclear Information System (INIS)

Wan, Qun; Kovalevsky, Andrey; Zhang, Qiu; Hamilton-Brehm, Scott; Upton, Rosalynd; Weiss, Kevin L.; Mustyakimov, Marat; Graham, David; Coates, Leighton; Langan, Paul

2013-01-01

The wild-type protein and four active-site mutants of xylanase II from Trichoderma reesei that catalyzes the hydrolysis of glycosidic bonds in xylan have successfully been crystallized. The crystallization of several structures including ligand-free and protein ligand complexes containing the substrate (xylohexaose) or product (xylotriose) are detailed. Xylanase II from Trichoderma reesei catalyzes the hydrolysis of glycosidic bonds in xylan. Crystallographic studies of this commercially important enzyme have been initiated to investigate its reaction mechanism, substrate binding and dependence on basic pH conditions. The wild-type protein was heterologously expressed in an Escherichia coli host using the defined medium and four active-site amino acids were replaced to abolish its activity (E177Q and E86Q) or to change its pH optimum (N44D and N44H). Cation-exchange and size-exclusion chromatography were used to obtain >90% protein purity. The ligand-free proteins and variant complexes containing substrate (xylohexaose) or product (xylotriose) were crystallized in several different space groups and diffracted to high resolutions (from 1.07 to 1.55 Å)