Article

1998 ◽  
Vol 76 (12) ◽  
pp. 1853-1859
Author(s):  
Herbert Höpfl ◽  
Norberto Farfán
Keyword(s):  
Structural Changes ◽  
Heterocyclic Ring ◽  
Boron Chelates ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chelate Formation ◽  
Structural Differences ◽  
Boron Complex ◽  
Potential Applications ◽  
Diphenylboron Chelate

Boron chelates obtained from salicylaldehyde and 2prime-hydroxyacetophenone azines are colored compounds with potential applications in analytical chemistry. Up to now these complexes have not been studied by X-ray crystallography, although two structures with a six- or a seven-membered chelate ring are possible. This contribution presents the X-ray analysis of 2prime-hydroxyacetophenone azine and its corresponding new mono(diphenylboron) chelate with a six-membered boron heterocyclic ring. With these data structural changes of the ligand on chelate formation and structural differences in comparison to salicylaldehyde azomethine boron chelates are discussed.Key words: boron complex, borinate, azine, azomethine.

Tele-Substitution Reactions in the Synthesis of a Promising Class of Antimalarials

2020 ◽  
Author(s):  
Marat Korsik ◽  
Edwin Tse ◽  
David Smith ◽  
William Lewis ◽  
Peter J. Rutledge ◽  
...  
Keyword(s):  
Heterocyclic Ring ◽  
Ring System ◽  
Substitution Reactions ◽  
Laboratory Notebook ◽  
Polar Solvents ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Core ◽  
Nmr Data

<p></p><p>We have discovered and studied a <i>tele</i>substitution reaction in a biologically important heterocyclic ring system. Conditions that favour the <i>tele</i>-substitution pathway were identified: the use of increased equivalents of the nucleophile or decreased equivalents of base, or the use of softer nucleophiles, less polar solvents and larger halogens on the electrophile. Using results from X-ray crystallography and isotope labelling experiments a mechanism for this unusual transformation is proposed. We focused on this triazolopyrazine as it is the core structure of the <i>in vivo </i>active anti-plasmodium compounds of Series 4 of the Open Source Malaria consortium.</p> <p> </p> <p>Archive of the electronic laboratory notebook with the description of all conducted experiments and raw NMR data could be accessed via following link <a href="https://ses.library.usyd.edu.au/handle/2123/21890">https://ses.library.usyd.edu.au/handle/2123/21890</a> . For navigation between entries of laboratory notebook please use file "Strings for compounds in the article.pdf" that works as a reference between article codes and notebook codes, also this file contain SMILES for these compounds. </p><br><p></p>

Structure and nuclear magnetic resonance spectra of 6-bromo-3,3′,4′,5,7-penta-O-methylcatechin

1985 ◽  
Vol 63 (8) ◽  
pp. 2176-2180 ◽  
Author(s):  
F. W. B. Einstein ◽  
E. Kiehlmann ◽  
E. K. Wolowidnyk
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Title Compound ◽  
Bromine Atom ◽  
Heterocyclic Ring ◽  
Equatorial Orientation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Nuclear Magnetic Resonance Spectra ◽  
Ring Conformations

The title compound has been synthesized by selective debromination of 6,8-dibromocatechin and indirect methylation of the resulting 6-bromocatechin via its pentaacetate. The structure of C20H23BrO6 has been determined by X-ray crystallography. The compound crystallizes in the space group P1 with a = 9.589(3) Å, b = 11.576(3) Å, c = 11.326(3) Å, α = 118.80(3)°, β = 93.23(3)°, γ = 111.44(3)°, ρc = 1.481 g cm−3, and Z = 2. Intensities were measured for 2584 independent reflections (2θ < 45°) of which 2213 were observed (I > 3.0σ(I)) and used in subsequent refinement (final R values were R = 0.0268 and Rw = 0.0344). Crystallographic and pmr data confirm the position of the bromine atom at C-6, the trans-diaxial arrangement of H-2/H-3 and the quasi-equatorial orientation of the 3,4-dimethoxyphenyl group (ring B). The two heterocyclic ring conformations are consistent with the expected flexibility of the molecule.

Humidity Controlled Diffractometry and its Applications

1992 ◽  
Vol 36 ◽  
pp. 439-449 ◽  
Author(s):  
Radko A. Kühnel ◽  
Sjerry J. van der Gaast
Keyword(s):  
Structural Changes ◽  
Basic Research ◽  
Xrd Analysis ◽  
Reaction Rates ◽  
Hydrous Minerals ◽  
X Ray ◽  
Special Attachment ◽  
Potential Applications ◽  
Total Structure ◽  
Structure Collapse

AbstractHumidity sensitive mineral phases change their structure when humidity varies resulting in X-ray pattern changes in intensity, position, and shape of lines. These structural changes in hydrous minerals are induced by dehydration and rehydration, which can lead to phase transformations or to steady depletion which may result in a total structure collapse. By means of X-ray diffraction with a special attachment, such reactions can be followed. The controlled relative humidity is provided in situ, in a closed cell, by a flow of moistened helium gas which is flushed through the cell during the XRD analysis. Humidity diffractometry allows studies of reaction rates of dehydration-rehydration reactions and their reversibilities, as well as effects of additives and impurities on these reactions. Potential applications in basic research and in industry are demonstrated using montmorilionite, ettringites, sodium carbonates and calcium sulfates.

Influence of metal ions on the formation of new metal complexes constructed from tetrachlorophthalic acid

2015 ◽  
Vol 70 (10) ◽  
pp. 711-718
Author(s):  
An-Qi Dai ◽  
Qi Yan ◽  
Jing Zhong ◽  
Sheng-Chun Chen ◽  
Ming-Yang He ◽  
...  
Keyword(s):  
Metal Ions ◽  
Significant Contribution ◽  
Transition Metal Ions ◽  
Planar Geometry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transitional Metal ◽  
Square Planar ◽  
Structural Differences ◽  
Metal Effect

AbstractReaction of 3,4,5,6-tetrachloro-1,2-benzenedicarboxylyic acid (1,2-H2BDC-Cl4) with transitional metal salts at room temperature in mixed DMF/H2O solvent affords three complexes formulated as [Cu(1,2-HBDC-Cl4)2(DMF)2] (1), {[Cd(1,2-HBDC-Cl4)2(H2O)4]·2DMF} (2), and {[Ni(1,2-BDC-Cl4)(H2O)5]·DMF·H2O} (3) (DMF = N,N-dimethylformamide). All these complexes have been characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, and single-crystal X-ray crystallography. In 1, the CuII ion is four-coordinated with a square-planar geometry formed by two 1,2-HBDC-Cl4 anions and two DMF ligands; in 2, the CdII ion takes an octahedral geometry coordinated by two 1,2-HBDC-Cl4 anions and four aqua ligands; while in 3, the NiII ion is octahedrally coordinated by one 1,2-BDC-Cl4 dianion and five aqua ligands. Intermolecular O–H···O hydrogen bonds and Cl···Cl (or C–H···Cl) interactions provide a significant contribution to stabilizing the three mononuclear structures in the solid state. The results suggest that structural differences among them are attributed to the influence of transition metal ions. The fluorescence of the complexes and of 1,2-H2BDC-Cl4 has been investigated. No significant metal effect has been observed.

scholarly journals Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

2017 ◽  
Vol 114 (9) ◽  
pp. 2247-2252 ◽  
Author(s):  
Cornelius Gati ◽  
Dominik Oberthuer ◽  
Oleksandr Yefanov ◽  
Richard D. Bunker ◽  
Francesco Stellato ◽  
...  
Keyword(s):  
High Resolution ◽  
Single Molecule ◽  
Free Electron ◽  
Structural Changes ◽  
Protein Crystals ◽  
Experimental Conditions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Unit Cells ◽  
Resolution Structure

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

scholarly journals Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130568 ◽  
Author(s):  
Keith Moffat
Keyword(s):  
Protein Design ◽  
Structural Changes ◽  
Fast Time ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
X Ray ◽  
Biological Targets ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Exciting Possibility

Time-resolved X-ray crystallography and solution scattering have been successfully conducted on proteins on time-scales down to around 100 ps, set by the duration of the hard X-ray pulses emitted by synchrotron sources. The advent of hard X-ray free-electron lasers (FELs), which emit extremely intense, very brief, coherent X-ray pulses, opens the exciting possibility of time-resolved experiments with femtosecond time resolution on macromolecular structure, in both single crystals and solution. The X-ray pulses emitted by an FEL differ greatly in many properties from those emitted by a synchrotron, in ways that at first glance make time-resolved measurements of X-ray scattering with the required accuracy extremely challenging. This opens up several questions which I consider in this brief overview. Are there likely to be chemically and biologically interesting structural changes to be revealed on the femtosecond time-scale? How shall time-resolved experiments best be designed and conducted to exploit the properties of FELs and overcome challenges that they pose? To date, fast time-resolved reactions have been initiated by a brief laser pulse, which obviously requires that the system under study be light-sensitive. Although this is true for proteins of the visual system and for signalling photoreceptors, it is not naturally the case for most interesting biological systems. To generate more biological targets for time-resolved study, can this limitation be overcome by optogenetic, chemical or other means?

scholarly journals Comparison of the Photochemical Reaction of Photoactive Yellow Protein in Crystal with Reaction in Solution1

2003 ◽  
Vol 17 (2-3) ◽  
pp. 345-353 ◽  
Author(s):  
Eriko Mano ◽  
Hironari Kamikubo ◽  
Yasushi Imamoto ◽  
Mikio Kataoka
Keyword(s):  
Photochemical Reaction ◽  
Structural Changes ◽  
Spectroscopic Studies ◽  
Crystalline Lattice ◽  
Photoactive Yellow Protein ◽  
X Ray ◽  
X Ray Crystallography ◽  
Solution Condition ◽  
Active Intermediate ◽  
Ectothiorhodospira Halophila

Photoactive yellow protein (PYP) is a photoreceptor protein for the negative phototaxis ofEctothiorhodospira halophila. The crystal structures of several photo‒intermediates have been revealed by X-ray crystallography. In the crystal structure of the active intermediate, PYPM, no significant structural changes were observed except for the vicinity of the chromophore. On the contrary, spectroscopic studies with solution condition demonstrated that global structural changes occur during the photo‒cycle. In order to reveal the origin of the discrepancies, we measured the reaction kinetics upon illumination under crystal condition and to compare them with those observed under solution condition. The reactive portion decreases with the increase of crystallinity. The rate constant of PYPMdecay also decreases with the increase of crystallinity. These results suggest two possibilities: (1) PYP in crystal does not react by the illumination; (2) the photoreaction rate is highly accelerated in crystal. Consequently, the photoreaction in crystal is considered to be highly influenced by the force constraint from crystalline lattice.

Proton-Coupled Structural Changes upon Binding of Carbon Monoxide to Cytochromecd1:  A Combined Flash Photolysis and X-ray Crystallography Study†,‡

Biochemistry ◽  
2000 ◽  
Vol 39 (36) ◽  
pp. 10967-10974 ◽  
Author(s):  
Tove Sjögren ◽  
Margareta Svensson-Ek ◽  
Janos Hajdu ◽  
Peter Brzezinski
Keyword(s):  
Carbon Monoxide ◽  
Structural Changes ◽  
Flash Photolysis ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Structural Changes ofEscherichia coliFerric Uptake Regulator during Metal-dependent Dimerization and Activation Explored by NMR and X-ray Crystallography

2006 ◽  
Vol 281 (30) ◽  
pp. 21286-21295 ◽  
Author(s):  
Ludovic Pecqueur ◽  
Benoît D'Autréaux ◽  
Jérome Dupuy ◽  
Yvain Nicolet ◽  
Lilian Jacquamet ◽  
...  
Keyword(s):  
Structural Changes ◽  
X Ray ◽  
X Ray Crystallography

Schiff-base porphyrin and expanded porphyrin analogs

2004 ◽  
Vol 08 (01) ◽  
pp. 1-25 ◽  
Author(s):  
Wyeth B. Callaway ◽  
Jacqueline M. Veauthier ◽  
Jonathan L. Sessler
Keyword(s):  
Schiff Base ◽  
Coordination Chemistry ◽  
Nmr Spectra ◽  
X Ray ◽  
X Ray Crystallography ◽  
Potential Applications ◽  
The Rich ◽  
Schiff Base Macrocycles ◽  
Porphyrin Analogs

In recent years, the field of porphyrin chemistry has expanded to include several new analogs of the original four pyrrole, carbon-bridged systems. This review traces the development of one such class of new macrocycles, namely Schiff-base porphyrin analogs. The review's focus is on the synthesis and properties of these new Schiff-base macrocycles that for ease of division have been divided into four classes: systems with two pyrrole rings, systems with three pyrrole or heterocyclic rings, systems with four pyrrole or heterocyclic rings, and systems with five or more pyrrole or heterocyclic rings. In addition to the role of metal ions as templating agents in the synthesis of these complexes, the rich coordination chemistry of several of the macrocycles is also discussed. X-ray crystallography has played an important role in determining the structures of many of these Schiff-base porphyrin analogs and many of the available structures have been incorporated into this review. Aromaticity of the macrocycles is discussed and has been evaluated from available electronic and NMR spectra. Finally, several potential applications of these molecules are discussed, briefly.

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