Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,315 records · Page 73Linked to original sources
PubMed1998

Synthesis, Characterization, and Crystal Structure of Dicalcium Glutarylbis(phosphonate) Dihydrate: A Covalently Pillared Layer Structure with the Potential for Epitaxial Growth on Hydroxyapatite.

A new bis(acylphosphonate), glutarylbis(phosphonate) (GlBP), was synthesized. Sodium and calcium salts of the GlBP, disodium dihydrogen glutarylbis(phosphonate), NaHO(3)PC(O)(CH(2))(3)C(O)PO(3)HNa, and dicalcium glutarylbis(phosphonate) dihydrate, Ca(2)[O(3)PC(O)(CH(2))(3)C(O)PO(3)].2H(2)O, were prepared and characterized by chemical analyses, thermogravimetry and Fourier transform infrared spectroscopy (FTIR). The crystal structure of the Ca salt was determined by single-crystal X-ray diffraction. The crystals are orthorhombic with a = 10.970(1) Å, b = 23.694(2) Å, c = 5.580(1) Å, space group Pnma, and Z = 4. This study provides the first example of a structure of a calcium complex involving a nongeminal bis(phosphonate). The structure can be described in terms of a covalently pillared layer-type arrangement of neutral Ca-GlBP-Ca units along the b-axis. Each oxygen atom of the phosphonate group is bonded to a different Ca ion, and each Ca in turn is linked to three phosphonate groups. The Ca octahedra and the phosphonate tetrahedra form a two-dimensional polar sheet perpendicular to the b-axis. The chelate bonds involving the keto groups appear to be important links in the stabilization of the structure and, in turn, to the biological activity of bis(acylphosphonates). A near-perfect lattice match, found between the Ca phosphonate layer and the major crystal faces of hydroxyapatite, indicates that epitaxial growth or incorporation of GlBP can occur on the apatitic surface which may be the mode of action in the inhibition of calcification.

Journal Article↗
PubMed1999

Structural Analysis of All the Nickel 14-Membered Tetraaza Macrocycles in the Cambridge Structural Database.

One hundred and thirty-nine nickel complexes containing the 1,4,8,11-tetraazacyclotetradecane backbone were found in the Cambridge Structural Database. Cluster analysis was used to separate the structures according to their macrocyclic configurations, using their conformations as a separation criteria. The most commonly found configuration was the trans III configuration. The amount of trans I macrocycles relative to trans III macrocycles was found to be higher for square-planar complexes than octahedral ones. Molecular mechanical conformational searches were done for select structures found in the Cambridge Structural Database.

Journal Article↗
PubMed1999

Y(21)I(18)C(14)B(7): Synthesis, Average Structure, and Structural Misfit.

The new compound Y(21)I(18)C(14)B(7) was prepared from YI(3), Y, C, and B at 1450 K. The average crystal structure was determined from single-crystal X-ray data. The structure consists of pseudoorthorhombic twisted metal atom double layers containing quasi-molecular CBC units. These are sandwiched by pseudohexagonal iodine layers. Owing to the symmetry and metric misfit the structure must be described with a large triclinic unit cell (space group P&onemacr;, a = 10.660(2) Å, b = 15.546(3) Å, c = 18.416(3) Å, alpha = 82.49(2) degrees, beta = 85.01(2) degrees, gamma = 82.92(2) degrees, Z = 2), which is probably only a good space-averaged approximation. Significant deviations from the averaged structure are indicated by unusual displacement parameters and the results of high-resolution electron microscopy.

Journal Article↗
PubMed2000

Polynuclear chromium(III) carboxylates. 1. Synthesis, structure, and magnetic properties of an octanuclear complex with a ring structure.

A novel cyclic octanuclear chromium(III) complex with hydroxo and acetato bridging ligands was isolated and its structure determined by X-ray crystallography. The complex [Cr8(OH)12(OAc)12] (1) (OAc- = CH3CO2-), as found in crystals of 1.34H2O, is obtained by refluxing an aqueous solution of the trinuclear "basic" chromium acetate. 1.34H2O crystallizes in the tetragonal space group I42d with the following unit cell dimensions: a = 16.592(2) A, c = 31.557(4) A, V = 8687(1) A3, and Z = 2. A total of 2000 unique data with I > 3 sigma (I) were used to solve and refine the structure to R(Fo) = 0.066 and Rw(Fo) = 0.085. The structure consists of eight Cr(III) ions that form a ring structure and are bridged by hydroxo and acetato ligands. Each of the two neighboring metal atoms in 1 is bridged either by two OH- ligands and one OAc- ligand, with a Cr...Cr distance of 2.949(2) A, or by two OAc- ligands and one OH- ligand, with a Cr...Cr distance of 3.383(2) A in an alternating fashion. The complex resides on a crystallographic 4 center, and the overall symmetry of 1 is S4. The magnetic susceptibility of 1.34H2O was measured in the temperature range of 5-240 K. Our theoretical modeling of the susceptibility data indicates alternating antiferromagnetic exchange interactions between adjacent spin 3/2 Cr3+ ions around the ring, of magnitude J/kB = 13.7 and 8.9 K, respectively.

Journal Article↗
PubMed2001

Crystal structure of ClF(4)(+)SbF(6)(-), normal coordinate analyses of ClF(4)(+), BrF(4)(+), IF(4)(+), SF(4), SeF(4), and TeF(4), and simple method for calculating the effects of fluorine bridging on the structure and vibrational spectra of ions in a strongly interacting ionic solid.

The crystal structure of the 1:1 adduct ClF(5).SbF(5) was determined and contains discrete ClF(4)(+) and SbF(6)(-) ions. The ClF(4)(+) cation has a pseudotrigonal bipyramidal structure with two longer and more ionic axial bonds and two shorter and more covalent equatorial bonds. The third equatorial position is occupied by a sterically active free valence electron pair of chlorine. The coordination about the chlorine atom is completed by two longer fluorine contacts in the equatorial plane, resulting in the formation of infinite zigzag chains of alternating ClF(4)(+) and cis-fluorine bridged SbF(6)(-) ions. Electronic structure calculations were carried out for the isoelectronic series ClF(4)(+), BrF(4)(+), IF(4)(+) and SF(4), SeF(4), TeF(4) at the B3LYP, MP2, and CCSD(T) levels of theory and used to revise the previous vibrational assignments and force fields. The discrepancies between the vibrational spectra observed for ClF(4)(+) in ClF(4)(+)SbF(6)(-) and those calculated for free ClF(4)(+) are largely due to the fluorine bridging that compresses the equatorial F-Cl-F bond angle and increases the barrier toward equatorial-axial fluorine exchange by the Berry mechanism. A computationally simple model, involving ClF(4)(+) and two fluorine-bridged HF molecules at a fixed distance as additional equatorial ligands, was used to simulate the bridging in the infinite chain structure and greatly improved the fit between observed and calculated spectra.

Journal Article↗
PubMed2002

Three-dimensional structure determination of N-(p-Tolyl)-dodecylsulfonamide from powder diffraction data and validation of structure using solid-state NMR spectroscopy.

The three-dimensional structure, conformation, and packing of molecules in the solid state are crucial components used in the optimization of many technologically useful materials properties. Single-crystal X-ray diffraction is the traditional and most effective method of determining 3-D structures in the solid state. Obtaining single crystals that are sufficiently large and free of imperfections is often laborious, time-consuming, and, occasionally, impossible. The feasibility of an integrated approach to the determination and verification of a complete three-dimensional structure for a medium-sized organic molecule without using single crystals is demonstrated for the case of an organic stabilizer compound N-(p-tolyl)-dodecylsulfonamide. The approach uses a combination of powder XRD data, several computational packages involving Monte Carlo simulations and ab initio quantum mechanical calculations, and experimental solid-state NMR chemical shifts. Structure elucidation of N-(p-tolyl)-dodecylsulfonamide revealed that the Bravais lattice is monoclinic, with cell dimensions of a = 38.773 A, b = 5.507 A, c = 9.509 A, and beta = 86.35 degrees, and a space group of P21/c.

Journal Article↗
PubMed2005

Solid state NMR method for the determination of 3D zeolite framework/sorbate structures: 1H/29Si CP MAS NMR study of the high-loaded form of p-xylene in ZSM-5 and determination of the unknown structure of the low-loaded form.

A general protocol is described for structure determinations of organic sorbate-zeolite complexes based on the selective, through-space, distance-dependent transfer of magnetization from protons in selectively deuterated organics to framework silicon nuclei. The method was developed using the known structure of the high-loaded ZSM-5/p-xylene complex containing p-xylene-d(6) or p-xylene-d(4). It was then applied to determine the unknown structure of the low-loaded ZSM-5/p-xylene complex using NMR alone. For the high-loaded complex improved data were obtained below 273 K, where slow motions and exchange processes of the p-xylene are eliminated. The general approach was validated by the exact agreement of the experimental (1)H-(29)Si CPMAS spectra obtained at a specific contact time and the complete 24-line spectra simulated using 1/T(CP) vs M(2) correlations from only the six clearly resolved resonances. For the low-loaded complex the (29)Si resonances were assigned at 267 K, and variable contact time CP experiments were carried out between 243 and 173 K using the same specifically deuterated p-xylenes. All possible locations and orientations of the p-xylene guests were sampled, and those solutions that gave acceptable linear 1/T(CP) vs M(2) correlations were selected. The optimum p-xylene location in this temperature range was determined to be in the channel intersection with the long molecular axis parallel to [0,1,0] (ring center fractional coordinates {-0.009, 0.250, 0.541}) with the ring plane oriented at an angle of 30 +/- 3 degrees about the crystallographic b axis. A subsequent single-crystal X-ray study confirmed this predicted structure.

Deuterium↗
PubMed2005

Bonding and oxidation state of a transition metal atom encapsulated in an isolated octahedral cluster cation of main group elements: synthesis, crystal structure, and electronic structure of Pt2In14Ga3(O)8F15 containing highly positive 18-electron complex [PtIn6]10+ and low-valent In+ ions.

Colorless transparent single crystals and white polycrystalline powder samples of Pt2In14Ga3(O)8F15 were obtained by heating a mixture of stoichiometric amounts of Pt, In, InF3, and Ga2(O)3, in a Pt crucible under Ar at 600 degrees C. The new oxyfluoride crystallizes in a new structure type in the trigonal space group Rm (No. 166) with a = 709.0(6) pm, c = 4556.4(3) pm, and Z = 6 with characteristic building units of PtIn6 octahedra (Pt-In = 255-257 pm), GaF6 octahedra (Ga-F = 189 pm), and GaO(4) tetrahedra (Ga-O = 186-187 pm). This oxyfluoride consists of a highly positive 18-electron complex [PtIn6]10+ as well as low-valent In+ ions. Electronic band structure calculations for Pt2In14(Ga3)O(8)F15 and molecular orbital (MO) calculations for [PtIn6]10+ were carried out to analyze the electronic structure of [PtIn6]10+ and estimate the oxidation state of Pt. Our analysis indicates that the oxidation state of the Pt atom in [PtIn6]10+ is negative rather than positive. For other octahedral cluster cations of main group elements stuffed with a transition metal atom (e.g., [RuSn6]14+ and "[IrBi6]11+") as well, we showed that the oxidation state of the transition metal atom is most probably negative by studying their electronic structures.

Journal Article↗
PubMed2006

Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex.

The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K(+) ions between the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2(1) unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T(4) loops. A total of seven independent T(3) loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.

Crystallization↗
PubMed2006

Synthesis and structure of hydroxyl acids of general structure 7,7-alkenyl/alkynyl-5-hydroxymethyl-6-oxabicyclo[3.2.1]octane-1-carboxylic acid.

The open-ended hollow tubular structure formed by inclusion of water molecules in the packing of the hydroxyl acid 1 (R1 = CH2OH, R2 = ethyl groups) led to the synthesis and structural study of their unsaturated analogues. In this article we report on a general and practical large-scale synthesis of hydroxyl acids that possess alkenyl and alkynyl appendages. Substitution of the ethyl groups in 1 with unsaturated two-carbon appendages has a different effect on the molecular structure and on the hydrogen-bonding pattern. No variation has been induced by substitution of only one ethyl group with a vinyl one, although the substitution of both ethyl groups with vinyl or acetylene appendages has the greatest effect on the molecular structure and results in different hydrogen-bonding motifs.

Journal Article↗
PubMed2005

Structural characterization of nickel oxide nanowires by X-ray absorption near-edge structure spectroscopy.

Nickel oxide nanowires modified by poly(vinylpyrrolidone) (PVP) were synthesized via a simple chemical pattern. For the first time NiO nanowires with diameters ranging from 40 to 100 nm with the expected ratio (length vs diameter) ranging from 54 to 90 were grown using a simple solution-phase approach (mild method). These nickel nanowires exhibited unique photoluminescence features and displayed a significant UV luminescence. X-ray absorption near-edge spectroscopy has been used to characterize the local Ni environment and identify the electronic structure. Comparing experimental and theoretical spectra at the Ni and O K edges, we determine the lattice distortion via the analysis of the characteristic preedge features and the multiple-scattering structures detected in the X-ray absorption near-edge structure spectra. The correlation between experimental features and the disordered or distorted local structures is also discussed.

Journal Article↗
PubMed2005

Investigation of the scanning tunneling microscopy image, the stacking pattern, and the bias-voltage-dependent structural instability of 1,10'-phenanthroline molecules adsorbed on Au(111) in terms of electronic structure calculations.

A self-assembled monolayer of 1,10'-phenanthroline (phen) molecules on Au(111) was found to undergo a structural phase transition when the bias voltage is switched in scanning tunneling microscopy (STM) experiments (Phys. Rev. Lett. 1995, 75, 2376; Surf. Sci. 1997, 389, 19). The nature of two bright spots representing each phen molecule in the high-resolution STM images of phen molecules on Au(111) was identified by calculating the partial density plots for a monolayer of phen molecules adsorbed on Au(111) with tight-binding electronic structure calculations. The stacking pattern of chains of phen molecules on Au(111) was explained by studying the intermolecular interactions between phen molecules on the basis of first-principles electronic structure calculations for a phen dimer, (phen)(2). The structural instability of phen molecule arrangement caused by the bias-voltage switch was probed by estimating the adsorbate-surface interaction energy with the point-charge approximation for Au(111).

Journal Article↗
PubMed2005

Characterization of the surface structure of gold nanoparticles and nanorods using structure sensitive reactions.

The surface structure of gold nanorods has been determined by studying the behavior of electrochemical reactions sensitive to the structure and compared to that obtained by other structure characterization techniques. Lead underpotential deposition (UPD) reveals that the surface of the nanorods is composed by (111) and (110) domains, while (100) domains are practically absent from the surface. In the case of the oxygen reduction reaction, the formation of hydrogen peroxide as a final product of the reaction in the whole potential range also indicates that (100) domains are absent on the surface of the nanoparticles, corroborating the previous result. These results are compared with other surface structure information provided by other techniques.

Letter↗
PubMed2006

Structure-directing agent location and non-centrosymmetric structure of fluoride-containing zeolite SSZ-55.

Single crystals of pure silica zeolite SSZ-55 were prepared using the fluoride route. Single-crystal X-ray diffraction at a synchrotron source revealed the framework structure of the material, but the unit cell (orthorhombic a = 12.905(2) A, b = 21.344(4) A, c = 5.1279(10)) is too small to accommodate ordered arrays of the organic structure-directing agent. Molecular modeling was used to simulate the docking of the structure-directing agent in the channels of the material, and this revealed a strong space-filling interaction with a number of possible orientations of the organic cation. The overall non-centrosymmetric structure of the solid (spacegroup C222(1)) was confirmed using second harmonic generation experiments.

Journal Article↗
PubMed2006

Structural change in Li and Na aluminophosphate glasses: evidence of a "structural mixed alkali effect".

The short- and long-range structure of a series of single and mixed aluminophosphate glasses with the general composition [xNa(2)O (46 - x)Li(2)O], [yAl(2)O(3) (54 - y)P(2)O(5)] is analyzed using (31)P and (27)Al magic-angle spinning (MAS) NMR as well as small-angle X-ray scattering. These series of glasses allow analyzing both the effect of alumina incorporation in these glasses, for small alumina content (y = 0, 4, 8), and the structural changes associated with the so-called mixed alkali effect (x = 0, 11.5, 23, 34.5, 46). Our results indicate that aluminum is mainly octahedrally coordinated in these glasses and that there is most likely some segregation of the Al(OP)(6) species. In the pure phosphate glasses, we observe a "classical" continuous variation of the structural properties with the relative alkali content, but in the aluminophosphate, both local and long-range structural results reveal for the first time some nonlinear change as a function of the relative alkali content.

Journal Article↗
PubMed2006

Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

We have investigated to what extent molecular dynamics (MD) simulations can reproduce DNA sequence-specific features, given different electrostatic descriptions and different cell environments. For this purpose, we have carried out multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2. With respect to the electrostatic descriptions, two different force fields are studied: a traditional description based on atomic point charges and a polarizable force field. With respect to the cell environment, the difference between crystal and solution environments is emphasized, as well as the structural importance of divalent ions. By imposing the correct experimental unit cell environment, an initial configuration with two ideal B-DNA duplexes in the unit cell is shown to converge to the crystallographic structure. This convergence is measured by the appearance of sequence-dependent features that very closely resemble the crystallographic ones as well as by the decay of the all-atom root-mean-squared coordinates deviations (RMSD) with respect to the crystallographic structure. Given the appropriate crystallographic constraints, this is the first example of multiple nanosecond molecular dynamics trajectory that shows an ideal B-DNA model converging to an experimental structure, with a significant decay of RMSD.

Base Sequence↗
PubMed2003

Relationships between personality structure, structure of word meaning, and cognitive ability: a study of cultural mechanisms of personality.

Native-born Estonian men (N=912), 17-68 years old, participated in a study on relationships between personality characteristics, dominant structure of word meaning ("everyday concepts" thinking or "scientific concepts" thinking), and level of cognitive ability. Individuals who primarily used everyday concepts thinking or who possessed relatively low levels of cognitive ability did not reveal a coherent Big Five personality structure, whereas individuals who primarily used scientific concepts thinking or possessed high levels of cognitive ability did. Thus, personality may be shaped by a cultural factor--word meaning structure. Earlier studies, which seem to support the idea that Big Five personality structure is a biologically determined human universal, suffer from serious sampling problems and insufficient data analyses.

Adolescent↗
PubMed1996

Structural transitions during activation and ligand binding in hexadecameric Rubisco inferred from the crystal structure of the activated unliganded spinach enzyme.

Activation of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco; EC 4.1.1.39) by CO2 involves carbamylation of Lys 201 and the subsequent binding of a magnesium ion to complete the active site. The refined crystal structure of activated Rubisco shows that the magnesium ligands are Asp 203, Glu 204, the carbamate of Lys 201, and three water molecules. Structural differences between the unactivated and activated forms are minimal. Substrate binding replaces water ligands around the metal and triggers substantial structural changes in loops covering the active site. This leads to a contraction and tightening of the structure of the large subunits with the movements transmitted to and modulated by the small subunits.

Crystallography, X-Ray↗