scholarly journals QM/MM calculations reveal a bridging hydroxo group in a vanadium nitrogenase crystal structure

2018 ◽  
Vol 54 (53) ◽  
pp. 7310-7313 ◽  
Author(s):  
Bardi Benediktsson ◽  
Albert Th. Thorhallsson ◽  
Ragnar Bjornsson
Keyword(s):  
Crystal Structure ◽  
Hydroxo Group ◽  
Vanadium Nitrogenase

A recent crystal structure of VFe protein is revealed via QM/MM calculations to contain an hydroxo group, likely derived from water.

scholarly journals Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

2020 ◽  
Vol 25 (6) ◽  
pp. 847-861
Author(s):  
Lili Cao ◽  
Octav Caldararu ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Bound State ◽  
Real Space ◽  
Quantum Mechanical ◽  
Storage Site ◽  
Quantum Mechanical Calculations ◽  
Reaction Intermediate ◽  
Sulphide Ions ◽  
Vanadium Nitrogenase

Abstract Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH−-bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract

The structure of the tetrachlorohydroxotellurate(IV) anion in KTeCl4(OH)•0.5H2O and KTeCl4(OH)

1991 ◽  
Vol 69 (4) ◽  
pp. 648-652 ◽  
Author(s):  
J. B. Milne ◽  
E. J. Gabe ◽  
C. Bensimon
Keyword(s):  
Crystal Structure ◽  
Key Words ◽  
Vibrational Spectroscopy ◽  
X Ray ◽  
Hydroxo Group

Three compounds containing the tetrachlorohydroxotellurate(IV) anion, [Formula: see text] K[TeCl4(OH)]•0.5H2O, and K[TeCl4(OH)], have been prepared. The crystal structure of K[TeCl4(OH)]•0.5H2O has been determined. The structure contains isolated square pyramidal TeCl4(OH)− anions with OH axial. Vibrational spectroscopy shows that [Formula: see text] and K[TeCl4(OH)]•0.5H2O both contain isolated anions but that, in K[TeCl4(OH)], the anion is polymerized with chloride bridging. The hydroxo group, like the fluoro group, acts to hinder coordination at the site trans to it on Te(IV). Key words: tellurium(IV) complexes, chlorotellurate(IV), X-ray structure, vibrational spectroscopy.

scholarly journals Synthesis, Crystal Structure and Hydrogen Bonding of μ- Hydroxo-μ-peroxo-bis[bis(ethylenediamine)cobalt(III)] squarate

2019 ◽  
Author(s):  
Roberto Köferstein
Keyword(s):  
Crystal Structure ◽  
Room Temperature ◽  
Water Molecules ◽  
Supramolecular Network ◽  
Electron Configuration ◽  
Coordination Polyhedra ◽  
Thermoanalytical Investigations ◽  
Hydroxo Group ◽  
Decomposition Processes ◽  
Subsequent Decomposition

Black-brown needle-shaped single crystals of [Co2(en)4(O2)(OH)][C4O4]1.5 4H2O(en = ethylenediamine) have been prepared in aqueous solution at room temperature. Spacegroup P-1 (no.2) with a = 800.20(8), b = 1225.48(7), c = 1403.84(9) pm, = 100.282(5), =94.515(7), = 95.596(6)°. The Co3+ cations [Co(1), Co(2)] are coordinated in an octahedralmanner by four nitrogen atoms stemming from the ethylenediamine molecules and twooxygen atoms each from a hydroxo group and a peroxo group, respectively. Both Co3+coordination polyhedra are connected by a common corner and by the peroxo group leadingto the binuclear [(en)2Co(O2)(OH)Co(en)2]3+ cation. The squarate dianions, not bonded toCo3+, and the [(en)2Co(O2)(OH)Co(en)2]3+ cations are linked by hydrogen bonds forming athree-dimensional supramolecular network containing water molecules. Magneticmeasurements reveal a diamagnetic behaviour indicating a low-spin electron configuration ofCo3+. The UV-Vis spectra shows two LMCT bands ( *(O22 ) d *(Co3+)) at 274 and 368nm and the d-d transition (1A1g 1T1g) at 542 nm. Thermoanalytical investigations in airshow that the compound is stable up to 120 °C. Subsequent decomposition processes to cobaltoxide are finished at 460 °C.

Crystal structure of VnfH, the iron protein component of vanadium nitrogenase

2018 ◽  
Vol 23 (7) ◽  
pp. 1049-1056 ◽  
Author(s):  
Michael Rohde ◽  
Christian Trncik ◽  
Daniel Sippel ◽  
Stefan Gerhardt ◽  
Oliver Einsle
Keyword(s):  
Crystal Structure ◽  
Protein Component ◽  
Iron Protein ◽  
Vanadium Nitrogenase

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

Spherulitic crystal growth in the prodissoconch larval of Crassostrea virginica

1983 ◽  
Vol 41 ◽  
pp. 518-519
Author(s):  
George G. Cocks ◽  
Louis Leibovitz ◽  
DoSuk D. Lee
Keyword(s):  
Crystal Structure ◽  
Crassostrea Virginica ◽  
Crystal Orientation ◽  
Developmental Changes ◽  
Gastrula Stage ◽  
Orthorhombic Crystal ◽  
Orthorhombic Crystal Structure ◽  
Stages Of Growth ◽  
Early Stages ◽  
Initial Deposition

Our understanding of the structure and the formation of inorganic minerals in the bivalve shells has been considerably advanced by the use of electron microscope. However, very little is known about the ultrastructure of valves in the larval stage of the oysters. The present study examines the developmental changes which occur between the time of conception to the early stages of Dissoconch in the Crassostrea virginica(Gmelin), focusing on the initial deposition of inorganic crystals by the oysters.The spawning was induced by elevating the temperature of the seawater where the adult oysters were conditioned. The eggs and sperm were collected separately, then immediately mixed for the fertilizations to occur. Fertilized animals were kept in the incubator where various stages of development were stopped and observed. The detailed analysis of the early stages of growth showed that CaCO3 crystals(aragonite), with orthorhombic crystal structure, are deposited as early as gastrula stage(Figuresla-b). The next stage in development, the prodissoconch, revealed that the crystal orientation is in the form of spherulites.

Transmission Electron Microscopy studies of the vacancy ordering in YSI2-X thin films

1991 ◽  
Vol 49 ◽  
pp. 562-563
Author(s):  
F.-R. Chen ◽  
T. L. Lee ◽  
L. J. Chen
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Thin Films ◽  
Diffraction Pattern ◽  
Annealing Temperature ◽  
Lattice Mismatch ◽  
Si Substrate ◽  
Metal Thin Films ◽  
Transmission Electron ◽  
Vacancy Ordering

YSi2-x thin films were grown by depositing the yttrium metal thin films on (111)Si substrate followed by a rapid thermal annealing (RTA) at 450 to 1100°C. The x value of the YSi2-x films ranges from 0 to 0.3. The (0001) plane of the YSi2-x films have an ideal zero lattice mismatch relative to (111)Si surface lattice. The YSi2 has the hexagonal AlB2 crystal structure. The orientation relationship with Si was determined from the diffraction pattern shown in figure 1(a) to be and . The diffraction pattern in figure 1(a) was taken from a specimen annealed at 500°C for 15 second. As the annealing temperature was increased to 600°C, superlattice diffraction spots appear at position as seen in figure 1(b) which may be due to vacancy ordering in the YSi2-x films. The ordered vacancies in YSi2-x form a mesh in Si plane suggested by a LEED experiment.

Crystal Structure Analysis of Cu-Zr Alloys by Convergent Beam Diffraction

1981 ◽  
Vol 39 ◽  
pp. 354-355
Author(s):  
A. F. Marshall ◽  
J. W. Steeds ◽  
D. Bouchet ◽  
S. L. Shinde ◽  
R. G. Walmsley
Keyword(s):  
Crystal Structure ◽  
Point Group ◽  
Intermetallic Phase ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Ion Milling ◽  
Composition And Structure ◽  
Unit Cells ◽  
Sputter Deposited ◽  
Convergent Beam

Convergent beam electron diffraction is a powerful technique for determining the crystal structure of a material in TEM. In this paper we have applied it to the study of the intermetallic phases in the Cu-rich end of the Cu-Zr system. These phases are highly ordered. Their composition and structure has been previously studied by microprobe and x-ray diffraction with sometimes conflicting results.The crystalline phases were obtained by annealing amorphous sputter-deposited Cu-Zr. Specimens were thinned for TEM by ion milling and observed in a Philips EM 400. Due to the large unit cells involved, a small convergence angle of diffraction was used; however, the three-dimensional lattice and symmetry information of convergent beam microdiffraction patterns is still present. The results are as follows:1) 21 at% Zr in Cu: annealed at 500°C for 5 hours. An intermetallic phase, Cu3.6Zr (21.7% Zr), space group P6/m has been proposed near this composition (2). The major phase of our annealed material was hexagonal with a point group determined as 6/m.

High resolution STEM imaging study on high Tc superconductor YBa2CuaO7-x

1988 ◽  
Vol 46 ◽  
pp. 882-883
Author(s):  
H.-J. Ou ◽  
J. M. Cowley
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Grain Boundary ◽  
Strong Field ◽  
Imaging Study ◽  
Structure Defects ◽  
High Tc ◽  
High Tc Superconductor ◽  
Diffraction Patterns ◽  
Lattice Planes

Using the dedicate VG-HB5 STEM microscope, the crystal structure of high Tc superconductor of YBa2Cu3O7-x has been studied via high resolution STEM (HRSTEM) imaging and nanobeam (∽3A) diffraction patterns. Figure 1(a) and 2(a) illustrate the HRSTEM image taken at 10' times magnification along [001] direction and [100] direction, respectively. In figure 1(a), a grain boundary with strong field contrast is seen between two crystal regions A and B. The grain boundary appears to be parallel to a (110) plane, although it is not possible to determine [100] and [001] axes as it is in other regions which contain twin planes [3]. Following the horizontal lattice lines, from left to right across the grain boundary, a lattice bending of ∽4° is noticed. Three extra lattice planes, indicated by arrows, were found to terminate at the grain boundary and form dislocations. It is believed that due to different chemical composition, such structure defects occur during crystal growth. No bending is observed along the vertical lattice lines.

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