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Title: The crystal structure of Z-DNA with untypically coordinated Ca2+ ions

Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
OSTI Identifier:
Resource Type:
Journal Article
Resource Relation:
Journal Name: JBIC Journal of Biological Inorganic Chemistry; Journal Volume: 23; Journal Issue: 2
Country of Publication:
United States

Citation Formats

Luo, Zhipu, and Dauter, Zbigniew. The crystal structure of Z-DNA with untypically coordinated Ca2+ ions. United States: N. p., 2017. Web. doi:10.1007/s00775-017-1526-4.
Luo, Zhipu, & Dauter, Zbigniew. The crystal structure of Z-DNA with untypically coordinated Ca2+ ions. United States. doi:10.1007/s00775-017-1526-4.
Luo, Zhipu, and Dauter, Zbigniew. 2017. "The crystal structure of Z-DNA with untypically coordinated Ca2+ ions". United States. doi:10.1007/s00775-017-1526-4.
title = {The crystal structure of Z-DNA with untypically coordinated Ca2+ ions},
author = {Luo, Zhipu and Dauter, Zbigniew},
abstractNote = {},
doi = {10.1007/s00775-017-1526-4},
journal = {JBIC Journal of Biological Inorganic Chemistry},
number = 2,
volume = 23,
place = {United States},
year = 2017,
month =
  • The complex, Pt(bph)(COD), where bph is the biphenyl dianion and COD is 1,5-cyclooctadiene, crystallizes in the orthorhombic space group Pbca with a = 12.178(4) {Angstrom}, b = 9.693(3) {Angstrom} and c = 25.344(9) {Angstrom} and Z = 8. The Pt-C distances to the olefinic carbon atoms that result from the {pi} electron donation of the COD ligand are in the range 2.20(3)-2.27(3) {Angstrom} and the Pt-C distances to the {sigma} bonded bph ligand are shorter at 2.01(3)-2.03(2) {Angstrom}. The lowest energy absorption of the complex is at 383 nm ({epsilon}=1.2 x 10{sup 3}). The emission spectrum is structured in fluidmore » solution at room temperature with the emission energy maximum at 537 nm, {phi}{sub em} = 1.68 x 10{sup {minus}3}, and {tau} = 1.93 {mu}s. Temperature dependent emission lifetime measurements result in a k{sub o} value of 2.69 x 10{sup 4}, a preexponential factor of 2.47 x 10{sup 6} and a {delta}E{sub 1} value of 324 cm{sup {minus}1}.« less
  • The pale blue rim of olenite on a black crystal of olenite-schorl tourmaline from an abyssal pegmatite at the locality Kuklik, near Kutna Hora, Czech Republic, has been chemically and structurally characterized. The optimized formula, calculated using chemical and structural data, is {sup X}(Na{sub 0.54}Ca{sub 0.14}K{sub 0.01}{D'Alembertian}{sub 0.31}){sup Y}(Al{sub 2.15}Fe{sup 2+}{sub 0.06}Ti{sup 4+}{sub 0.01}) {sup Z}(Al{sub 5.90}Mg{sub 0.10}) {sup T}(Si{sub 5.60}Al{sub 0.40})B{sub 3}O{sub 27} {sup V}[(OH){sub 2.49}O{sub 0.51}] {sup W}(O{sub 0.99}F{sub 0.01}), with {alpha} 15.8838(3), c 7.1056(2) {angstrom} and R = 0.017. The relatively short <Y-O> bond-length, 1.992 {angstrom}, confirms the high content of Al at the Y site ({approx}2.1more » atoms per formula unit, apfu). It is similar to that of olenite from the type locality, though the olenite from Kuklik contains significant amounts of Fe at the Y site, and significant amounts of {sup [4]}Al ({approx}0.4 apfu) instead of {sup [4]}B in the T site. This finding is supported by results of the structure determination, which show an enlarged <T-O> bond-length of {approx}1.626 {angstrom}. This sample of olenite shows that nonstoichiometric content of Si does not always imply {sup [4]}B in aluminous tourmaline. No H could be found at the O1 site by refinement, and the spherical distribution of electron density in the difference-Fourier map around the O1 site supports the conclusion that this site is only or mainly occupied by O and not by OH. On a bond-angle distortion ({sigma}{sub oct}{sup 2} of the ZO{sub 6} octahedron) - <Y-O> distance diagram, the olenite from Kuklik lies between compositions containing 3 (OH) at the V site, and natural buergerite, which contains 0.3 (OH) and 2.7 O at the V site (O3 site). The (OH) content with {approx}2.5 (OH) pfu, which was calculated for a charge-balanced formula, is in a good agreement with these findings and with the integrated intensity of the OH overtones in the 7000 cm{sup -1} region (690 cm{sup -2} per cm thickness), which is one of the lowest measured to date for tourmaline. The OH seems to be ordered strongly at the O3 site. The composition of this sample of olenite shows a trend toward the proposed olenite end-member formula, which contains only 1 OH group. The low content of F (0.01 apfu) is uncommon for natural Al-rich and Mg-poor tourmaline from granitic pegmatites. Synchrotron micro-XANES was used to detect the valence state of Fe in this crystal; it was found to have 93 {+-} 10% of the total Fe as Fe{sup 2+}. Optical absorption spectra show that the blue color is derived primarily from a combination of {sup [6]}Fe{sup 2+}, together with {sup [6]}Fe{sup 2+} interaction with a minor amount of {sup [6]}Fe{sup 3+}.« less
  • A series of (diphosphonato)bis(ethylenediamine)cobalt(III) complexes, where the diphosphonate ligand has the formula HO/sub 3/P-CR(R')-PO/sub 3/H/sup 2 -/, has been prepared. Members of the series include the following R/R' combinations:H/H, H/CH/sub 3/, CH/sub 3//CH/sub 3/, H/OH, CH/sub 3//OH, phenyl/OH, tert-butyl/OH, H/NH/sub 2/, CH/sub 3//NH/sub 2/, H/N(CH/sub 3/)/sub 2/, H/Cl, and Cl/Cl. The complexes have been characterized in all cases by visible-UV, IR, /sup 1/H NMR, and /sup 31/P NMR spectra, in several cases by elemental analyses, and for the prototype title complex (R/R' = H/H) by single-crystal X-ray structural analysis refined to a conventional R factor of 0.034. Equilibrium constants governingmore » the one-to-one association with calcium(II) in dilute aqueous solution (pH 10, NH/sub 4/OH/NH/sub 4/Cl buffer, = 0.1 M (KCl), 25/sup 0/C) have been determined potentiometrically for all diphosphonate complexes as well as for the analogous pyrophosphato and oxalato complexes. Values of the equilibrium constants for the H/OH, H/H, and CH/sub 3//OH complexes are 2.4 x 10/sup 6/, 1.8 x 10/sup 4/, and 1.1 x 10/sup 4/ M/sup -1/, respectively, showing (a) that coordinated diphosphonate ligands have considerable affinity for calcium(II) and (b) that when R' = OH the calcium affinity is enhanced, presumably via coordination of this OH group to calcium and formation of a bidentate-tridentate bridge from cobalt to calcium. This ordering of affinities exactly parallels the ordering of skeletal uptake of these three diphosphonate ligands when labeled with /sup 99//sup m/Tc, implying that binding of Tc-diphosphonate complexes to calcium at the surface of bone is an important step in the mechanism of in vivo action of /sup 99//sup m/Tc-diphosphonate skeletal imaging agents.« less
  • Detailed structural analyses based on electron microprobe and X-ray diffraction data did not provide evidence for zero-coordinated potassium, but showed that all cations lie adjacent to framework oxygen atoms, with 2 to 6 oxygen neighbors within 3 A.
  • The new higher oxides of carbon 1 (C{sub 24}O{sub 6}), 2 (C{sub 32}O{sub 8}), and 3 (C{sub 40}O{sub 10}) have been prepared from the macrocyclic ketals 5-7 and characterized as stable colored solids. The electronic absorption spectra of the carbon oxides 1-3 differ from those of the ketals 5-7. The absorption bands of 1-3 are broader and shifted to longer wavelength. The X-ray crystal structure of oxide 1 has been determined, showing that 1 is planar, with bend diyne units. The laser desorption Fourier transform mass spectra of 1 and 2 show a remarkable ease of successive losses of twomore » CO molecules to give C{sub 18} and C{sub 24} ions, respectively, in both positive and negative modes. The C{sub 30} ion formed by fragmentation of oxide 3 is considerably less stable than the smaller homologues and is only observed in the negative ion mode. In the positive ion spectra recorded at low desorption laser power, ions corresponding to the dimers of the cyclocarbons are observed.« less