Magnesium ion inner sphere complex in the anticodon loop of tRNAPhe

Biochemistry ◽  
1982 ◽  
Vol 21 (1) ◽  
pp. 49-53 ◽  
Author(s):  
Damian Labuda ◽  
Dietmar Poerschke
Keyword(s):  
Magnesium Ion ◽  
Anticodon Loop ◽  
Inner Sphere ◽  
Sphere Complex

Quantum chemical study of inner-sphere complexes of trivalent lanthanide and actinide ions on the corundum (110) surface

2013 ◽  
Vol 101 (9) ◽  
pp. 561-570
Author(s):  
R. Polly ◽  
B. Schimmelpfennig ◽  
M. Flörsheimer ◽  
Th. Rabung ◽  
T. Kupcik ◽  
...  
Keyword(s):  
Metal Ions ◽  
Density Functional ◽  
Single Point ◽  
Quantum Chemical Study ◽  
Basis Sets ◽  
Water Molecules ◽  
Point Energy ◽  
Inner Sphere ◽  
Sphere Complex ◽  
Inner Sphere Complexes

Summary Sorption plays a major role in the safety assessment of nuclear waste disposal. In the present theoretical study we focused on understanding the interaction of trivalent lanthanides and actinides (La3+, Eu3+ and Cm3+) with the corundum (110) surface. Optimization of the structures were carried out using density functional theory with different basis sets. Additionally, Møller-Plesset perturbation theory of second order was used for single point energy calculations. We studied the structure of different inner-sphere complexes depending on the surface deprotonation and the number of water molecules in the first coordination shell. The most likely structure of the inner-sphere complex (tri- or tetradentate) was predicted. For the calculations we used a cluster model for the surface. By deprotonating the cluster a chemical environment at elevated pH values was mimicked. Our calculations predict the highest stability for a tetradentate inner-sphere surface complexes with five water molecules remaining in the first coordination sphere of the metal ions. The formation of the inner-sphere complexes is favored when a coordination takes place with at most one deprotonated surface aluminol group located beneath the inner-sphere complex. The mutual interaction between sorbing metal ions at the surface is studied as well. The minimal possible distance between two inner-sphere sorbed metal ions at the surface was determined to be 530 pm.

Resolving the kinetics of individual aqueous reaction steps of actinyl (AnO2+ and AnO22+; An=U, Np, and Pu) tricarbonate complexes with ferrous iron and hydrogen sulfide from first principles

2020 ◽  
Vol 108 (3) ◽  
pp. 165-184
Author(s):  
Will M. Bender ◽  
Udo Becker
Keyword(s):  
Electron Transfer ◽  
Proton Transfer ◽  
Outer Sphere ◽  
Future Research ◽  
Inner Sphere ◽  
Proton Transfer Reactions ◽  
Effective Shield ◽  
Sphere Complex ◽  
Solvent Molecules ◽  
Kinetics Of

AbstractThe solubility and mobility of actinides (An), like uranium, neptunium, and plutonium, in the environment largely depends on their oxidation states. Actinyls (AnV,VIO2+/2+(aq)) form strong complexes with available ligands, like carbonate (CO32−), which may inhibit reduction to relatively insoluble AnIVO2(s). Here we use quantum-mechanical calculations to explore the kinetics of aqueous homogeneous reaction paths of actinyl tricarbonate complexes ([AnO2(CO3)3]5−/4−) with two different reductants, [Fe(OH)2(H2O)4]0 and [H2S(H2O)6]0. Energetically-favorable outer-sphere complexes (OSC) are found to form rapidly, on the order of milliseconds to seconds over a wide actinyl concentration range (pM to mM). The systems then encounter energy barriers (Ea), some of which are prohibitively high (>100 kJ/mol for some neptunyl and plutonyl reactions with Fe2+ and H2S), that define the transition from outer- to inner-sphere complex (ISC; for example, calculated Ea of ISC formation between UO2+ and UO22+ with Fe2+ are 35 and 74 kJ/mol, respectively). In some reactions, multiple OSCs are observed that represent different hydrogen bonding networks between solvent molecules and carbonate. Even when forming ISCs, electron transfer to reduce An6+ and An5+ is not observed (no change in atomic spin values or lengthening of An–Oax bond distances). Proton transfer from bicarbonate and water to actinyl O was tested as a mechanism for electron transfer from Fe2+ to U6+ and Pu6+. Not all proton transfer reactions yielded reduction of An6+ to An5+ and only a few pathways were energetically-favorable (e. g. H+ transfer from H2O to drive Pu6+ reduction to Pu5+ with ΔE = −5 kJ/mol). The results suggest that the tricarbonate complex serves as an effective shield against actinide reduction in the tested reactions and will maintain actinyl solubility at elevated pH conditions. The results highlight reaction steps, such as inner-sphere complex formation and electron transfer, which may be rate-limiting. Thus, this study may serve as the basis for future research on how they can be catalyzed by a mineral surface in a heterogeneous process.

Complex formation of beryllium sulfate in mixtures of water and dimethylformamide

1983 ◽  
Vol 36 (10) ◽  
pp. 1941 ◽  
Author(s):  
BI Gislason ◽  
H Strehlow
Keyword(s):  
Complex Formation ◽  
Sulfate Ion ◽  
Kinetic Measurements ◽  
Inner Sphere ◽  
Sphere Complex ◽  
Beryllium Sulfate ◽  
Rate Of Substitution

The complex formation of BeSO4 in mixtures of water and dimethylformamide (dmf) has been studied by using conductivity and kinetic measurements. In these solutions the complex Be(SO4)22- is shown to exist together with the outer- and inner-sphere complex of BeSO4. The rate of substitution depends on the composition of the solvatomer Be(H20)I(dmf)4-I2+ which reacts with the sulfate ion and on the kind of solvating molecule which is substituted by the ligand SO42-.

scholarly journals Silica Pillared Montmorillonites as Possible Adsorbents of Antibiotics from Water Media

2018 ◽  
Vol 8 (8) ◽  
pp. 1403 ◽  
Author(s):  
Maria Roca Jalil ◽  
Florencia Toschi ◽  
Miria Baschini ◽  
Karim Sapag
Keyword(s):  
Complex Formation ◽  
Aqueous Media ◽  
Pillared Clays ◽  
Raw Material ◽  
Van Der Waals Interactions ◽  
Adsorption Mechanisms ◽  
Adsorption Sites ◽  
Adsorption Capacities ◽  
Inner Sphere ◽  
Sphere Complex

In this work, three silica pillared clays (Si-PILC) were synthetized, characterized, and evaluated as possible adsorbents of ciprofloxacin (CPX) and tetracycline (TC) form alkaline aqueous media. The pillared clays obtained showed significant increases in their specific surface areas (SBET) and micropore volumes (Vμp) regarding the raw material, resulting in microporosity percentages higher than 57% in all materials. The studies of CPX and TC removal using pillared clays were compared with the natural clay and showed that the Si-PILC adsorption capacities have a strong relationship with their porous structures. The highest adsorption capacities were obtained for CPX on Si-PILC due to the lower molecular size of CPX respect to the TC molecule, favoring the interaction between the CPX− and the pillars adsorption sites. Tetracycline adsorption on silica pillared clays evidenced that for this molecule the porous structure limits the interaction between the TCH− and the pillars, decreasing their adsorption capacities. However, the results obtained for both antibiotics suggested that their negative species interact with adsorption sites on the pillared structure by adsorption mechanisms that involve inner-sphere complex formation as well as van der Waals interactions. The adsorption mechanism proposed for the anionic species on Si-PILC could be considered mainly as negative cooperative phenomena where firstly there is a hydrophobic effect followed by other interactions, such as der Waals or inner-sphere complex formation.

Undecagold labeling of tRNA

1991 ◽  
Vol 49 ◽  
pp. 44-45
Author(s):  
James F. Hainfeld ◽  
Kyra M. Alford ◽  
Mathias Sprinzl ◽  
Valsan Mandiyan ◽  
Santa J. Tumminia ◽  
...  
Keyword(s):  
High Resolution ◽  
Transmission Electron Micrograph ◽  
Anticodon Loop ◽  
Electron Micrograph ◽  
Reaction Conditions ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission

The undecagold (Au11) cluster was used to covalently label tRNA molecules at two specific ribonucleotides, one at position 75, and one at position 32 near the anticodon loop. Two different Au11 derivatives were used, one with a monomaleimide and one with a monoiodacetamide to effect efficient reactions.The first tRNA labeled was yeast tRNAphe which had a 2-thiocytidine (s2C) enzymatically introduced at position 75. This was found to react with the iodoacetamide-Aun derivative (Fig. 1) but not the maleimide-Aun (Fig. 2). Reaction conditions were 37° for 16 hours. Addition of dimethylformamide (DMF) up to 70% made no improvement in the labeling yield. A high resolution scanning transmission electron micrograph (STEM) taken using the darkfield elastically scattered electrons is shown in Fig. 3.

Protonation effects on dynamic flux properties of aqueous metal complexes

2009 ◽  
Vol 74 (10) ◽  
pp. 1543-1557 ◽  
Author(s):  
Herman P. Van Leeuwen ◽  
Raewyn M. Town
Keyword(s):  
Complex Formation ◽  
Metal Ion ◽  
Good Description ◽  
Minor Component ◽  
Outer Sphere ◽  
Metal Species ◽  
Central Metal ◽  
Inner Sphere ◽  
A Minor ◽  
Protonated Ligand

The degree of (de)protonation of aqueous metal species has significant consequences for the kinetics of complex formation/dissociation. All protonated forms of both the ligand and the hydrated central metal ion contribute to the rate of complex formation to an extent weighted by the pertaining outer-sphere stabilities. Likewise, the lifetime of the uncomplexed metal is determined by all the various protonated ligand species. Therefore, the interfacial reaction layer thickness, μ, and the ensuing kinetic flux, Jkin, are more involved than in the conventional case. All inner-sphere complexes contribute to the overall rate of dissociation, as weighted by their respective rate constants for dissociation, kd. The presence of inner-sphere deprotonated H2O, or of outer-sphere protonated ligand, generally has a great impact on kd of the inner-sphere complex. Consequently, the overall flux can be dominated by a species that is a minor component of the bulk speciation. The concepts are shown to provide a good description of experimental stripping chronopotentiometric data for several protonated metal–ligand systems.

scholarly journals Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding

2019 ◽  
Vol 294 (14) ◽  
pp. 5281-5291 ◽  
Author(s):  
Ha An Nguyen ◽  
Eric D. Hoffer ◽  
Christine M. Dunham
Keyword(s):  
Anticodon Loop

Stability of B12 (CN)12 2− : Implications for Lithium and Magnesium Ion Batteries

2016 ◽  
Vol 128 (11) ◽  
pp. 3768-3772 ◽  
Author(s):  
Hongmin Zhao ◽  
Jian Zhou ◽  
Puru Jena
Keyword(s):  
Magnesium Ion ◽  
Magnesium Ion Batteries
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