Steric factor in ligand displacement of zirconium alkoxides dissolved in alcohols

The present study indicates EXAFS direct structural data obtained for zirconium ethoxide, iso- and n-propoxide are alike those for zirconium n-butoxide complexes. This is evident for agreement of structural units of abovementioned alkoxides complexes. Our group developed structural model of n-butoxide earlier. Six interconnected tetramers assemble a structural unit of the alkoxides under study. The tetramers build of zirconium atoms in the highly flattened pyramid corners. Four zirconium atoms are bonded in series by double bridges through oxygen atoms of alkoxide ligands. Two of the four zirconium atoms are bias bonded by single ligand bridges. The distances between pairs of zirconium atoms inside the tetramer are 3.3 and 3.5 Å. Tetramers are linked together also by a single ligand bridges. The distance between zirconium atoms of the two neighbor tetramers is 3.9 Å. Primary particles (tetramer sextet) form aggregates in a solution. Possible shapes of the anisotropically sized aggregates is a large diameter cylinder with small height (a disk), or a small diameter cylinder with large height (a rod). Primary particles composed through ligands. The distance between the neighbor zirconium atoms of different primary particles is 4.8 or 5.1 Å depending on the coordination nature and the neighboring particles number.     

The role of additional solvents in transition metal complex catalyzed asymmetric reductions in ionic liquid containing systems

When ionic liquids (ILs) are employed as solvents for transition metal complex (TMC) catalyzed reductions, a second solvent can be added to increase the efficiency of the catalytic cycle and the solubility of the reactant in the IL phase. Two industrially relevant asymmetric hydrogenations, the enantioselective reductions of methyl 2-acetamidoacrylate with Rh-EtDuPHOS and methyl acetoacetate with Ru-BINAP, were performed in different catalytic systems including 1-butyl-3-methylimidazolium hexafluorophosphate/ tetrafluoroborate as ILs. Product separation and TMC recycling was performed by extracting the product from the reaction mixture. This can be accomplished by cooling the system, by adding an excess of the second solvent or by adding a third solvent. A high solubility of the second solvent in the IL catalytic phase favors the reaction activity, but can induce leaching of the IL and TMC.     

The role of thermodynamics and kinetics in ligand binding to G-quadruplex DNA

Molecular dynamics simulations were used to investigate the binding of four different 2,4,6-triarylpyridines to G-quadruplex DNA. Both the binding free energies, and the kinetics of binding are required to explain the measured degree of ligand induced stabilisation of the compounds, with bulky substituents having the potential to prevent the ligand from reaching the lowest energy binding site.     

Controllable DNA strand displacement by independent metal–ligand complexation

Introduction of artificial metal–ligand base pairs can enrich the structural diversity and functional controllability of nucleic acids. In this work, we revealed a novel approach by placing a ligand-type nucleoside as an independent toehold to control DNA strand-displacement reactions based on metal–ligand complexation. This metal-mediated artificial base pair could initiate strand invasion similar to the natural toehold DNA, but exhibited flexible controllability to manipulate the dynamics of strand displacement that was only governed by its intrinsic coordination properties. External factors that influence the intrinsic properties of metal–ligand complexation, including metal species, metal concentrations and pH conditions, could be utilized to regulate the strand dynamics. Reversible control of DNA strand-displacement reactions was also achieved through combination of the metal-mediated artificial base pair with the conventional toehold-mediated strand exchange by cyclical treatments of the metal ion and the chelating reagent. Unlike previous studies of embedded metal-mediated base pairs within natural base pairs, this metal–ligand complexation is not integrated into the nucleic acid structure, but functions as an independent toehold to regulate strand displacement, which would open a new door for the development of versatile dynamic DNA nanotechnologies.

This metal-mediated artificial base pair can function as an independent toehold based on metal–ligand coordination and exhibit flexible and reversible controllability to manipulate the dynamics of strand displacement.     

Ligand displacement reactions of dimer and trimer pyridyl ligand/transition metal complexes

Ligand exchange reactions of pyridyl ligand/transition metal complexes are examined in a quadrupole ion trap mass spectrometer to evaluate the ability of multidentate ligands to displace other pyridyl ligands in complexes where the charge is highly delocalized and there is a great degree of ligand repulsions. Partially or fully coordinated transition metal ions in dimer or trimer species involving small mono- or bidentate pyridyl ligands undergo ligand displacement reactions with larger bi- and tridentate pyridyl ligands. Larger ligands with greater chelation abilities, such as 1,10-phenanthroline and 2,2′:6,2″-terpyridine, are often able to simultaneously displace two nonchelating ligands from a partially coordinated metal ion. However, the analogous reactions involving displacement of bidentate chelating ligands from more fully coordinated transition metal ion complexes are nearly quenched. In other cases, mixed-ligand dimer and trimer complexes are observed, indicating step-wise displacement of the initially complexed ligands.     

On the role of samarium/HMPA in the post electron-transfer steps in SmI2 reductions

The reaction of p,p'-dichlorobenzophenone with SmI2 was studied in the presence of variable amounts of HMPA. The electron-transfer step takes place instantaneously. In the presence of excess substrate, the addition of HMPA retarded the rate of coupling to pinacol by a factor of 250. In the presence of an excess of SmI2, the initial rate retardation is followed by a dramatic increase in rate.     

Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes

Noncovalent interactions are sometimes treated as additive and this enables useful average binding energies for common interactions in aqueous solution to be derived. However, the additive approach is often not applicable, since noncovalent interactions are often either mutually reinforcing (positively cooperative) or mutually weakening (negatively cooperative). Ligand binding energy is derived (positively cooperative binding) when a ligand reduces motion within a receptor. Similarly, transition-state binding energy is derived in enzyme-catalyzed reactions when the substrate transition state reduces the motions within an enzyme. Ligands and substrates can in this way improve their affinities for these proteins. The further organization occurs with a benefit in bonding (enthalpy) and a limitation in dynamics (cost in entropy), but does not demand the making of new noncovalent interactions, simply the strengthening of existing ones. Negative cooperativity induces converse effects: less efficient packing, a cost in enthalpy, and a benefit in entropy.     

The role of solvent structure in ligand substitution and solvent exchange at some divalent transition-metal cations

The role of the solvent in reactions involving ions is considered in relation to the structure of liquids. The rate constants and activation parameters for ligand substitutions at divalent transition metal cations in various solvents are compared with those for solvent exchanges. The differences are related to structural properties of the solvents, represented by their heats of evaporation and fluidities, and interpreted with the aid of a model developed from that of Frank and Wen. Water is not a typical solvent.This paper was presented at the symposium, The Physical Chemistry of Aqueous Systems, held at the University of Pittsburgh, Pittsburgh, Pennsylvania, June 12–14, 1972, in honor of the 70th birthday of Professor H. S. Frank.     

An unconventional role of ligand in continuously tuning of metal-metal interfacial strain

We show that embedding of a surface ligand can dramatically affect the metal-metal interfacial energy, making it possible to create nanostructures in defiance of traditional wisdom. Despite matching Au-Ag lattices, Au-Ag hybrid NPs can be continuously tuned from concentric core-shell, eccentric core-shell, acorn, to dimer structures. This method can be extended to tune even Au-Au and Ag-Ag interfaces.     

The stereochemistry of sodium dithionite reductions of cyclic ketones

The stereochemistry of reduction of several substituted cyclohexanones, norcamphor, and camphor by sodium dithionite (sodium hydrosulfite, Na₂S₂O₄) in aqueous DMF solution has been studied. The cyclohexanones yield mainly equatorial alcohols while the bicyclic ketones give mainly endo alcohols.     

Orientation in metal ammonia reductions

The unique orientation effects observed in the alkali metal-ammonia reactions of aromatic compounds are considered from a molecular orbital viewpoint. The Birch rule governing the reduction of substituted aromatics, the peculiar effect of substituents on the ease of hydrogenolysis of benzyl alcohols, the similar effect in the dealkylation and dearylation of alkyl aryl ethers and aryl ethers, the course of dealkoxylation of alkyl aryl ethers, are all found to be reasonably accommodated by molecular orbital theory.     

Nucleophilic displacement reactions on fluorine. II. The role of σ- and π-bond nucleophiles

S_N2 displacement reactions on fluorine by σ- and π-bond nucleophiles are discussed and shown to constitute a general class of reaction. Mechanisms are suggested for reactions mentioned in the literature which are consistent with this generalization.     

The role of monomers and dimers in the reduction of ruthenium(II) complexes of redox-active tetraazatetrapyridopentacene ligand

A combination of electrochemistry, spectroelectrochemistry, and 1H NMR has been used to study the reduction and solution speciation in acetonitrile of two mononuclear Ru complexes containing the redox-active 9,11,20,22-tetraazatetrapyrido [3,2-a:2',3'-c:3' ',2' '-l:2' ',3' '-n]pentacene (tatpp) ligand. These complexes, [(bpy)2Ru(tatpp)][PF6]2 (1[PF6]2), and [(phen)2Ru(tatpp)][PF6]2 (2[PF6]2) (where bpy is 2,2'-bipyridine and phen is 1,10-phenanthroline), form pi-pi stacked dimers (e.g., pi-{1}24+ and pi-{2}24+) in solution as determined by 1H NMR studies in an extended concentration range (90 - 5000 microM) as well as via simulation of the electrochemical data. The dimerization constant for 12+ in acetonitrile is 2 x 10(4) M(-1) as determined from the NMR data. Slightly higher dimerization constants (8 x 10(4) M(-1)) were obtained via simulation of the electrochemical data and are attributed to the presence of the supporting eletrolyte. Electrochemical and spectroelectrochemical data show that the pi-pi stacked dimers are electroreduced in two consecutive steps at -0.31 and -0.47 V vs Ag/AgCl, which is assigned to the uptake of one electron by each tatpp ligand in pi-{1}24+ to give first pi-{1}23+and then pi-{1}22+. At potentials negative of -0.6 V, the electrochemical data reveal two different reaction pathways depending on the complex concentration in solution. At low concentrations (< or =20 microM), the next electroreduction occurs on a monomeric species (e.g., [(bpy)2Ru(tatpp)]+/0) showing that the doubly reduced pi-pi dimer (pi-{1}22+ and pi-{2}22+) dissociates into monomers. At high concentrations (> or =100 microM), reduction of pi-{1}22+ or pi-{2}22+ induces another dimerization reaction, which we attribute to the formation of a sigma-bond between the radical tatpp ligands and is accompanied by the appearance of a new peak in the absorption spectrum at 535 nm. This new sigma-dimer can undergo one additional tatpp based reduction to form sigma-{1}20 or sigma-{2}20, in which the tatpp-bridged assembly is the site of all four reductions. Finally, potentials negative of -1.2 V result in the electroreduction of the bpy or phen ligands for complexes 12+ or 22+, respectively. For the latter complex 22+, this process is accompanied by the formation of an electrode adsorbed species.     

The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge

We study the ligand (tetramethylammonium) recognition by the peripheral anionic site and its penetration of the human AChE gorge by using atomistic molecular dynamics simulations and our recently developed metadynamics method. The role of both the peripheral anionic site and the formation of cation-pi interactions in the ligand entrance are clearly shown. In particular, a simulation with the W286A mutant shows the fundamental role of this residue in anchoring the ligand at the peripheral anionic site of the enzyme and in positioning it prior to the gorge entrance. Once the ligand is properly oriented, the formation of specific and synchronized cation-pi interactions with W86, F295, and Y341 enables the gorge penetration. Eventually, the ligand is stabilized in a free energy basin by means of cation-pi interactions with W86.     

The role of ligand coordination on the spectral features of Yb3+ ions in lead aluminum silicate glasses

The glasses of the composition (40 ? x)PbO–(5 + x)Al₂O₃–54SiO₂:1.0Yb₂O₃ (in mol%) with x ranging from 5 to 10 have been synthesized. The IR spectral studies of these glasses have indicated that there is a gradual transformation of Al³⁺ ions from tetrahedral to octahedral coordination with increase of Al₂O₃ content in the glass network. The optical absorption and luminescence spectra have exhibited bands originating from ²F_7/2 → ²F_5/2 and ²F_5/2 → ²F_7/2 transitions, respectively. From these spectra, the absorption and emission cross-sections and fluorescence lifetime of Yb³⁺ ions have been evaluated. Quantitative analysis of these data indicated a decreasing radiative trapping and increasing fluorescence lifetime of Yb³⁺ ions with increasing Al₂O₃ content. This may be explained by structural variations in the vicinity of Yb³⁺ ions due to variation in the concentration of Al₂O₃ in the glass network.     

New methods for the detection of cyanide based on displacement of the glutathione ligand of glutathionylcobalamin by cyanide

Glutathionylcobalamin (GSCbl) is a vitamin B₁₂ derivative that contains glutathione as the upper axial ligand to cobalt via a Co–S bond. In the present study, we discovered that cyanide reacted with GSCbl, generating cyanocobalamin (CNCbl) and reduced glutathione (GSH) via dicyanocobalamin (diCNCbl) intermediate. This reaction was induced specifically by the nucleophilic attack of cyanide anion displacing the glutathione ligand of GSCbl. Based on the reaction of GSCbl with cyanide, we developed new methods for the detection of cyanide. The reaction intermediate, violet-coloured diCNCbl, could be applied for naked eye detection of cyanide and the detection limit was estimated to be as low as 520 μg L^?1 (20 μM) at pH = 10.0. The reaction product, CNCbl, could be applied for a spectrophotometric quantitative determination of cyanide with a detection limit of 26 μg L^?1 (1.0 μM) at pH = 9.0 and a linear range of 26–520 μg L^?1 (1.0–50 μM). In addition, the other reaction product, GSH, could be applied for a fluorometric quantitative determination of cyanide with a detection limit of 31 μg L^?1 (1.2 μM) at pH = 9.0 and a linear range of 31–520 μg L^?1 (1.2–20 μM). These new GSCbl-based methods are simple, highly specific and sensitive with great applicability for the detection of cyanide in biological and non-biological samples.