The role of silica and alkaline earth metals with biomolecules in the biomineralization processes: the eggshell's formation and the crystallization in vivo for x-ray crystallography

2020 ◽  
Vol 66 (1) ◽  
pp. 100473 ◽  
Author(s):  
Nerith Rocío Elejalde-Cadena ◽  
Mayra Cuéllar-Cruz ◽  
Abel Moreno
Keyword(s):  
Alkaline Earth ◽  
Alkaline Earth Metals ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Effect of Boron in a Hierarchical Nanoporous Layer Formation on Silicate Glass

Materials ◽  
2020 ◽  
Vol 13 (8) ◽  
pp. 1817
Author(s):  
Takumi Ito ◽  
Erika Tabata ◽  
Yuki Ushioda ◽  
Takuya Fujima
Keyword(s):  
Silicate Glass ◽  
Photoelectron Spectroscopy ◽  
Alkaline Earth ◽  
Alkaline Earth Metals ◽  
Layer Formation ◽  
X Ray ◽  
Formation Behavior ◽  
Nanoporous Layer ◽  
Skeleton Structure

A hierarchical nanoporous layer (HNL) can be formed on the silicate glass surface by simple alkali etching. Though it reportedly exhibits various useful functions, such as superhydrophilicity, optical anti-reflection, and material impregnation, the principle of its formation still remains unclear. In this study, HNL formation behavior was experimentally investigated while using scanning electron microscope (SEM) and X-ray photoelectron spectroscopy (XPS) to clarify the role of boron contained in glass. As a result, it was found that HNL formation was significantly promoted by boron, which was rapidly eluted prior to alkali and alkaline earth metals. This suggests that boron, which forms the skeleton structure of glass together with Si and O, elutes to partially decompose the skeleton, and extends the elution route for HNL formation.

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>

Effects of dietary alteration of bicarbonate and magnesium on rat bone

1986 ◽  
Vol 250 (2) ◽  
pp. F302-F307 ◽  
Author(s):  
J. M. Burnell ◽  
C. Liu ◽  
A. G. Miller ◽  
E. Teubner
Keyword(s):  
Crystal Structure ◽  
Bone Formation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Growing Rats ◽  
Final Composition ◽  
Rat Bone

To study the effects of bicarbonate and magnesium on bone, mild acidosis and/or hypermagnesemia were produced in growing rats by feeding ammonium chloride and/or magnesium sulfate. Bone composition, quantitative histomorphometry, and mineral x-ray diffraction (XRD) characteristics were measured after 6 wk of treatment. The results demonstrated that both acidosis (decreased HCO3) and hypermagnesemia inhibited periosteal bone formation, and, when combined, results were summative; and the previously observed in vitro role of HCO3- and Mg2+ as inhibitors of crystal growth were confirmed in vivo. XRD measurements demonstrated that decreased plasma HCO3 resulted in larger crystals and increased Mg resulted in smaller crystals. However, the combined XRD effects of acidosis and hypermagnesemia resembled acidosis alone. It is postulated that the final composition and crystal structure of bone are strongly influenced by HCO3- and Mg2+, and the effects are mediated by the combined influence on both osteoblastic bone formation and the growth of hydroxyapatite.

Niobium-bearing arsenides and germanides from elemental mixtures not involving niobium: a new twist to an old problem in solid-state synthesis

2018 ◽  
Vol 74 (5) ◽  
pp. 623-627 ◽  
Author(s):  
Sviatoslav Baranets ◽  
Hua He ◽  
Svilen Bobev
Keyword(s):  
High Temperature ◽  
Solid State ◽  
Diffraction Data ◽  
Alkaline Earth ◽  
Alkaline Earth Metals ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Temperature Reactions ◽  
First Time ◽  
Synthetic Work

Three isostructural transition-metal arsenides and germanides, namely niobium nickel arsenide, Nb0.92(1)NiAs, niobium cobalt arsenide, NbCoAs, and niobium nickel germanide, NbNiGe, were obtained as inadvertent side products of high-temperature reactions in sealed niobium containers. In addition to reporting for the very first time the structures of the title compounds, refined from single-crystal X-ray diffraction data, this article also serves as a reminder that niobium containers may not be suitable for the synthesis of ternary arsenides and germanides by traditional high-temperature reactions. Synthetic work involving alkali or alkaline-earth metals, transition or early post-transition metals, and elements from groups 14 or 15 under such conditions may yield Nb-containing products, which at times could be the major products of such reactions.

scholarly journals Probing the Role of Divalent Metal Ions in a Bacterial Psychrophilic Metalloprotease: Binding Studies of an Enzyme in the Crystalline State by X-Ray Crystallography

2003 ◽  
Vol 185 (14) ◽  
pp. 4195-4203 ◽  
Author(s):  
Stephanie Ravaud ◽  
Patrice Gouet ◽  
Richard Haser ◽  
Nushin Aghajari
Keyword(s):  
Metal Ions ◽  
Calcium Ions ◽  
Calcium Ion ◽  
Crystalline State ◽  
Zinc Ion ◽  
Binding Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Catalytic Zinc

ABSTRACT The psychrophilic alkaline metalloprotease (PAP) produced by a Pseudomonas bacterium isolated in Antarctica belongs to the clan of metzincins, for which a zinc ion is essential for catalytic activity. Binding studies in the crystalline state have been performed by X-ray crystallography in order to improve the understanding of the role of the zinc and calcium ions bound to this protease. Cocrystallization and soaking experiments with EDTA in a concentration range from 1 to 85 mM have resulted in five three-dimensional structures with a distinct number of metal ions occupying the ion-binding sites. Evolution of the structural changes observed in the vicinity of each cation-binding site has been studied as a function of the concentration of EDTA, as well as of time, in the presence of the chelator. Among others, we have found that the catalytic zinc ion was the first ion to be chelated, ahead of a weakly bound calcium ion (Ca 700) exclusive to the psychrophilic enzyme. Upon removal of the catalytic zinc ion, the side chains of the active-site residues His-173, His-179 and Tyr-209 shifted ∼4, 1.0, and 1.6 Å, respectively. Our studies confirm and also explain the sensitivity of PAP toward moderate EDTA concentrations and propose distinct roles for the calcium ions. A new crystal form of native PAP validates our previous predictions regarding the adaptation of this enzyme to cold environments as well as the proteolytic domain calcium ion being exclusive for PAP independent of crystallization conditions.

scholarly journals The Influence of Alkali and Alkaline Earth Metals and the Role of Acid Pretreatments in Production of Sugars from Switchgrass Based on Solvent Liquefaction

2014 ◽  
Vol 28 (2) ◽  
pp. 1111-1120 ◽  
Author(s):  
Xianglan Bai ◽  
Robert C. Brown ◽  
Jie Fu ◽  
Brent H. Shanks ◽  
Matthew Kieffer
Keyword(s):  
Alkaline Earth ◽  
Alkaline Earth Metals

A comparative study of 2,4-quinazolinediones by X-ray crystallography. The role of the OMe group on the hydrogen bonding motifs formation

2012 ◽  
Vol 11 (4) ◽  
pp. 259-265
Author(s):  
Leticia Guerrero ◽  
Ruben Montalvo ◽  
Ignacio A. Rivero ◽  
Victor Barba
Keyword(s):  
Hydrogen Bonding ◽  
Comparative Study ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

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