scholarly journals Ensemble–function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole

2021 ◽  
Author(s):  
Filip Yabukarski ◽  
Tzanko Doukov ◽  
Margaux Pinney ◽  
Justin Biel ◽  
James Fraser ◽  
...  
Keyword(s):  
Function Analysis ◽  
X Ray Diffraction ◽  
Ketosteroid Isomerase ◽  
Oxyanion Hole ◽  
X Ray ◽  
General Base ◽  
Dynamic View ◽  
Rate Effects ◽  
Bond Network ◽  
Functional Analyses

Following decades of insights from structure–function studies, there is now a need to progress from a static to dynamic view of enzymes. Comparison of prior cryo X-ray structures suggested that deleterious effects from ketosteroid isomerase (KSI) mutants arise from misalignment of the oxyanion hole catalytic residue, Y16. However, multi-conformer models from room temperature X-ray diffraction revealed an ensemble of Y16 conformers indistinguishable from WT for Y32F/Y57F KSI and a distinct, non-native ensemble for Y16 in Y57F KSI. Functional analyses suggested rate effects arise from weakened hydrogen bonding, due to disruption of the Y16/Y57/Y32 hydrogen bond network, and repositioning of the general base. In general, catalytic changes can be deconvoluted into effects on the probability of occupying a state (P-effects) and the reactivity of each state (k-effects). Our results underscore the need for ensemble–function analysis to decipher enzyme function and ultimately manipulate their extraordinary capabilities.

scholarly journals Effect of pressure on a mixed valence FeiiFeiii2complex

2014 ◽  
Vol 70 (a1) ◽  
pp. C901-C901
Author(s):  
Solveig Madsen ◽  
Jacob Overgaard ◽  
Bo Iversen
Keyword(s):  
Phase Transition ◽  
Hydrogen Bond ◽  
Mixed Valence ◽  
Hydrogen Bond Network ◽  
X Ray Diffraction ◽  
X Ray ◽  
Effect Of Pressure ◽  
Bond Network ◽  
Fe Sites ◽  
Cyano Groups

Intramolecular electron transfer (ET) in mixed valence (MV) oxo-centered [FeiiFeiii2O(carboxylate)6(ligand)3]·solvent complexes is highly dependent on temperature, on the nature of the ligands, and on the presence of crystal solvent molecules [1]. Whereas the effects of temperature, crystal solvent, and ligand variation on the details of the ET have been explored thoroughly, the effect of pressure is less well described [2]. The effect of pressure on the ET in MV Fe3O(cyanoacetate)6(water)3has been investigated with single crystal X-ray diffraction and Mössbauer spectroscopy. Previous multi-temperature studies have shown that at room temperature the ET between the three Fe sites is fast and the observed structure of the Fe3core is a perfectly equilateral triangle [3]. Cooling the complex below 130 K induces a phase transition as the ET slows down. Below 120 K the Fe3core is distorted due to the localization of the itinerant electron on one of the three Fe sites in the triangle (the complex is then in the valence trapped state). The valence trapping is complete within a temperature interval of just 10 K. The abruptness of the transition has been attributed to the extended hydrogen bond network involving water ligands and cyano groups, promoting intermolecular cooperative effects. The high-pressure X-ray diffraction data show that there is a 900flip of half the cyano groups at 3.5 GPa, which dramatically changes the hydrogen bond network. At a slightly higher pressure, a phase transition is found to occur. The five single crystals investigated all broke into minor fragments at the transition; however triclinic unit cells, similar to the low temperature unit cell, could be indexed from selected spots. Additional evidence that the complex is valence trapped comes from high pressure Mössbauer spectra measured above the phase transition (4 GPa). The relationship between valence trapping and the structural changes will in this work be highlighted using void space and Hirshfeld surface analysis.

Cobalt(II) chloride adducts with acetonitrile, propan-2-ol and tetrahydrofuran: considerations on nuclearity, reactivity and synthetic applications

2017 ◽  
Vol 73 (2) ◽  
pp. 104-114 ◽  
Author(s):  
Danilo Stinghen ◽  
André Luis Rüdiger ◽  
Siddhartha O. K. Giese ◽  
Giovana G. Nunes ◽  
Jaísa F. Soares ◽  
...  
Keyword(s):  
Single Molecule ◽  
Building Blocks ◽  
Direct Reaction ◽  
X Ray Diffraction ◽  
Single Molecule Magnets ◽  
X Ray ◽  
Ft Ir ◽  
Bond Network ◽  
Solvent Molecules ◽  
Intramolecular Hydrogen

High-spin cobalt(II) complexes are considered useful building blocks for the synthesis of single-molecule magnets (SMM) because of their intrinsic magnetic anisotropy. In this work, three new cobalt(II) chloride adducts with labile ligands have been synthesized from anhydrous CoCl2, to be subsequently employed as starting materials for heterobimetallic compounds. The products were characterized by elemental, spectroscopic (EPR and FT–IR) and single-crystal X-ray diffraction analyses.trans-Tetrakis(acetonitrile-κN)bis(tetrahydrofuran-κO)cobalt(II) bis[(acetonitrile-κN)trichloridocobaltate(II)], [Co(C2H3N)4(C4H8O)2][CoCl3(C2H3N)]2, (1), comprises mononuclear ions and contains both acetonitrile and tetrahydrofuran (thf) ligands, The coordination polymercatena-poly[[tetrakis(propan-2-ol-κO)cobalt(II)]-μ-chlorido-[dichloridocobalt(II)]-μ-chlorido], [Co2Cl4(C3H8O)4], (2′), was prepared by direct reaction between anhydrous CoCl2and propan-2-ol in an attempt to rationalize the formation of the CoCl2–alcohol adduct (2), probably CoCl2(HOiPr)m. The binuclear complex di-μ-chlorido-1:2κ4Cl:Cl-dichlorido-2κ2Cl-tetrakis(tetrahydrofuran-1κO)dicobalt(II), [Co2Cl4(C4H8O)4], (3), was obtained from (2) after recrystallization from tetrahydrofuran. All three products present cobalt(II) centres in both octahedral and tetrahedral environments, the former usually less distorted than the latter, regardless of the nature of the neutral ligand. Product (2′) is stabilized by an intramolecular hydrogen-bond network that appears to favour atransarrangement of the chloride ligands in the octahedral moiety; this differs from thecisdisposition found in (3). The expected easy displacement of the bound solvent molecules from the metal coordination sphere makes the three compounds good candidates for suitable starting materials in a number of synthetic applications.

Thermal stability of Mg3Sb1.475Bi0.475Te0.05 high performance n-type thermoelectric investigated through powder X-ray diffraction and pair distribution function analysis

2018 ◽  
Vol 6 (35) ◽  
pp. 17171-17176 ◽  
Author(s):  
Lasse Rabøl Jørgensen ◽  
Jiawei Zhang ◽  
Christian Bonar Zeuthen ◽  
Bo Brummerstedt Iversen
Keyword(s):  
Thermal Stability ◽  
Distribution Function ◽  
Pair Distribution Function ◽  
High Performance ◽  
Function Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Thermal Stability Of

The thermal stability of the high performance n-type Te-doped Mg3Sb1.5Bi0.5 system is investigated.

Effect of Li, Fe, and B Addition on the Crystallization Behavior of Sodium Aluminosilicate Glasses as Analogues for Hanford High Level Waste Glasses

MRS Advances ◽  
2016 ◽  
Vol 2 (10) ◽  
pp. 549-555 ◽  
Author(s):  
José Marcial ◽  
Mostafa Ahmadzadeh ◽  
John S. McCloy
Keyword(s):  
Function Analysis ◽  
High Level Waste ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Sodium ◽  
Chemical Ordering ◽  
Sodium Aluminosilicate ◽  
Aluminosilicate Glasses ◽  
Heat Treated ◽  
High Level

ABSTRACTCrystallization of aluminosilicates during the conversion of Hanford high-level waste (HLW) to glass is a function of the composition of the glass-forming melt. In high-sodium, high-aluminum waste streams, the crystallization of nepheline (NaAlSiO4) removes chemically durable glass-formers from the melt, leaving behind a residual melt that is enriched in less durable components, such as sodium and boron. We seek to further understand the effect of lithium, boron, and iron addition on the crystallization of model silicate glasses as analogues for the complex waste glass. Boron and iron behave as glass intermediates which allow for crystallization when present in low additions but frustrate crystallization in high additions. In this work, we seek to compare the average structures of quenched and heat treated glasses through Raman spectroscopy, X-ray diffraction, vibrating sample magnetometry, and X-ray pair distribution function analysis. The endmembers of this study are feldspathoid-like (LiAlSiO4, NaAlSiO4, NaBSiO4, and NaFeSiO4), pyroxene-like (LiAlSi2O6, NaAlSi2O6, NaBSi2O6, and NaFeSi2O6), and feldspar-like (LiAlSi3O8, NaAlSi3O8, NaBSi3O8, and NaFeSi3O8). Such a comparison will provide further insight on the complex relationship between the average chemical ordering and topology of glass on crystallization.

Pair distribution function analysis of X-ray diffraction from amorphous spheres in an asymmetric transmission geometry: application to a Zr58.5Cu15.6Ni12.8Al10.3Nb2.8glass

2013 ◽  
Vol 46 (4) ◽  
pp. 999-1007 ◽  
Author(s):  
J. C. Bendert ◽  
N. A. Mauro ◽  
K. F. Kelton
Keyword(s):  
Distribution Function ◽  
Error Propagation ◽  
Pair Distribution Function ◽  
Function Analysis ◽  
X Ray Diffraction ◽  
Asymmetric Transmission ◽  
X Ray ◽  
Area Detector ◽  
Spherical Sample ◽  
Transmission Geometry

A method for the calculation of the pair distribution and structure functions from X-ray intensity data obtained with an area detector for an off-center incident X-ray beam on an amorphous sphere is presented. Error propagation for converting from the structure function to the pair distribution function is also described, including a summation series approach to treat the error from a high-qtruncation. A Zr58.5Cu15.6Ni12.8Al10.3Nb2.8glass (Vitreloy 106a) is used to demonstrate the techniques. In particular, the semi-analytical corrections presented to calculate the effects of secondary scatter within and asymmetric transmission through a spherical sample are verified.

Coordination Chemistry of N-(2-Hydroxybenzyl)-(S)-amino Acids. Absolute Configuration of LAMBDA-mer-R,R-[Co(ohb-(S)-Ala)2]- Anion

1997 ◽  
Vol 62 (8) ◽  
pp. 1205-1213 ◽  
Author(s):  
Svetlana Pakhomova ◽  
Jan Ondráček ◽  
František Jursík
Keyword(s):  
Absolute Configuration ◽  
Diffraction Method ◽  
Cd Spectroscopy ◽  
X Ray Diffraction ◽  
Aromatic Rings ◽  
Molecular Mechanics Calculations ◽  
X Ray ◽  
Bond Network ◽  
Twist Boat ◽  
C Nmr

The crystal and molecular structure of the Ag[Co(ohb-(S)-Ala)2] . 5 H2O have been determined by X-ray diffraction method. The crystals are hexagonal with a = b = 9.039(0.002) Å, c = 24.896(0.006) Å, space group P3221, and Z = 3. Each Ag+ counterion coordinated by one water molecule which is a part of hydrogen bond network, is bonded to aromatic rings. The anion adopts LAMBDA-mer absolute configuration. Mer geometry is in accord with the molecular mechanics calculations. Since CD spectroscopy does not reflect configurational chirality, the absolute configuration has been determined by the X-ray structure analysis and assigned using chirality descriptors. The arrangements at the chiral centers are R for both N atoms. The two five-membered rings each assume envelope conformation with C1 and C2 atoms exceptionally deviated (0.378(7) and 1.210(7) Å) from the N-Co-O plane. Both six-membered rings have delta twist boat conformations. The complex described has been also characterized by the electronic and 13C NMR spectroscopies.

scholarly journals Exploring the origins of crystallisation kinetics in hierarchical materials using in situ X-ray diffraction and pair distribution function analysis

2020 ◽  
Vol 22 (34) ◽  
pp. 18860-18867 ◽  
Author(s):  
Matthew E. Potter ◽  
Mark E. Light ◽  
Daniel J. M. Irving ◽  
Alice E. Oakley ◽  
Stephanie Chapman ◽  
...  
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Function Analysis ◽  
X Ray Diffraction ◽  
Crystallisation Kinetics ◽  
Total Scattering ◽  
Hierarchically Porous ◽  
X Ray ◽  
Scattering Measurements

Novel in situ synchrotron total scattering measurements probe the assembly of primary building units into templated hierarchically porous aluminophosphate catalysts, providing unique insights to understanding crystallisation kinetics.

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