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Effects of metal ion substitutions

The potential parameters used in the present calculations are identical to those in [18]. The ion interacts via electrostatic and Lennard-Jones terms, Vjj= - 332Qjgi/rjj + AjAj/r f - BjBj/rfj, where the subscript / denotes the ion and j is another atom with which it interacts. In order to calibrate the calculated hydration energies for different ions versus the non-bonded parameters, we first carry out FEP/MD simulations of a solvated ion in water. In these calculations, the Lennard-Jones parameters of the ion were gradually changed from (X , B ) = (2340.0,25.0) to (/4, B ) = (5.0,1.0). The calibration calculations in water covered a total simulation time of 40 ps for both the forward and backward transformation direction. [Pg.124]

The same calculation is then performed with the ion in the active site of SNase for each of the three states 2-.3- Hence, with the previously [Pg.124]

As mentioned above, we must start by calibrating the ion interaction parameters versus the free energy of hydration (see [20] for details). Without the calibration of these parameters in water, it would not be possible to make meaningful comparisons to experimental data. If one were to use, for example, ab initio potentials for the ion inter-actions without verifying that these reproduce the observed hydration energies, attempts to make quantitative comparisons to kinetic data would involve significant uncertainties. [Pg.124]

The calibration procedure is quite straightforward for the alkaline earth metals and these ions can be reasonably well modelled by simple charged Lennard-Jones spheres. That is, the non-bonded parameters can be adjusted so that the solvation energy and the first peak of the radial distribution function (REF) in water coincide with experimental values. For transition metals, however, the situation becomes more complicated and we return to this issue below. [Pg.124]

2 An empirical model for transition metals. In addition to the alkaline earth metal ions, which lack d-orbital valence electrons, it is important to try to extend the applicability of our model to also include transition metals. Unfortunately, the hydration energies of the transition metal ions cannot be well modelled by a simple Lennard-Jones sphere with a charge in the centre in order to reproduce the observed hydration energy, the ion radius must be [Pg.129]


Aqvist, J. and Warshel, A. Free energy relationship in metalloenzyme-catalyzed reactions. Calculations of the effects of metal ion substitutions in staphylococcal nuclease, J.Am.Chem.Soc., 112 (1990), 2860-2868... [Pg.348]

Aqvist, J., Warshel, A., Free Energy Relationships in Metalloenzyme-Catalyzed Reactions. Calculations of the Effects of Metal Ion Substitutions in Staphylococcal Nuclease, J. Am. Chem. Soc. 1990, 112, 2860-2868. [Pg.1204]

Figure 5.9 Calculated effect of metal ion substitutions on the overall activation barrier relative to the case with Ca bound. Each point is calculated according to eqn. (5.19) from the quantities AAGi, AAGj, AAG j and AG (Ca ). The value of AAG for Mn is plotted above that of a spherical ion with the same radius (as given by the RDF), so that the value of corresponds to that of the latter ion and not to the actual value used for Mn. The observed values for Sr and Ca are denoted by circles and experimentally estimated limits for Ba , Mg " and by f. Figure 5.9 Calculated effect of metal ion substitutions on the overall activation barrier relative to the case with Ca bound. Each point is calculated according to eqn. (5.19) from the quantities AAGi, AAGj, AAG j and AG (Ca ). The value of AAG for Mn is plotted above that of a spherical ion with the same radius (as given by the RDF), so that the value of corresponds to that of the latter ion and not to the actual value used for Mn. The observed values for Sr and Ca are denoted by circles and experimentally estimated limits for Ba , Mg " and by f.
In a number of classes of systems, the catalytic and other chemical effects of metal ions on reactions of organic and inorganic molecules are generally recognized the catalysis of nucleophilic reactions such as ester hydrolysis the reactions of alkenes and alkynes in the presence of metal carbonyls (8, 9, 69) stereospecific polymerization in the presence of Ziegler catalysts (20, 55, 56) the activation of such small molecules as H2 (37), 02 (13), H202 (13), and possibly N2 (58) and aromatic substitution reactions of metal-cyclopentadienyl compounds (59, 63). [Pg.6]

Eberhardt MK. (1977) Radiation induced homolytic aromatic substitution. 6. The effect of metal ions on the hydroxylation of benzonitrile, anisole, and fluorobenzene. /Phys Chem 81 1051-1057. [Pg.407]

Abstract Amino acids are the basic building blocks in the chemistry of life. This chapter describes the controllable assembly, structures and properties of lathanide(III)-transition metal-amino acid clusters developed recently by our group. The effects on the assembly of several factors of influence, such as presence of a secondary ligand, lanthanides, crystallization conditions, the ratio of metal ions to amino acids, and transition metal ions have been expounded. The dynamic balance of metalloligands and the substitution of weak coordination bonds account for the occurrence of diverse structures in this series of compounds. [Pg.171]

In substitutional metallic solid solutions and in liquid alloys the experimental data have been described by Epstein and Paskin (1967) in terms of a predominant frictional force which leads to the accumulation of one species towards the anode. The relative movement of metallic ion cores in an alloy phase is related to the scattering cross-section for the conduction electrons, which in turn can be correlated with the relative resistance of the pure metals. Thus iron, which has a higher specific resistance than copper, will accumulate towards the anode in a Cu-Fe alloy. Similarly in a germanium-lithium alloy, the solute lithium atoms accumulate towards the cathode. In liquid alloys the same qualitative effect is observed, thus magnesium accumulates near the cathode in solution in bismuth, while uranium, which is in a higher Group of the Periodic Table than bismuth, accumulated near the anode in the same solvent. [Pg.154]

My other question concerns the general theme of the effect of ligands in the coordination shell of a metal ion on the rate of water displacement. I refer particularly to the effect of hydroxide as a ligand,—i.e., to the effect of hydrolysis of metal ions on the substitution of water. [Pg.70]

The IR spectra of 15N-labelled complexes of A-p-tolylsalicylaldimines with zinc, copper and cobalt have yielded assignments of the metal-ligand stretching frequency and certain ligand vibrations.336 The v(M—N) values are metal-ion dependent in the order CoZn as expected from crystal field theory. Substituent-induced shifts are related to the residual polar effects of salicylaldimine substitution and to the inductive effects of N-aryl substitutents. [Pg.942]

Mg2+ is associated with a large number of enzymes involving the hydrolysis and transfer of phosphates. The MgATP complex serves as the substrate in many cases. As noted in Section 62.1.2.2.2, the interaction of Mg2+ with the ATP enhances the transfer (to a substrate or water) of the terminal phosphoryl group. The results of many studies with model compounds lead to the postulate of an SN2 mechanism for this reaction.125 Associative pathways allow greater control of the stereochemistry of the substitution, and the rates of such processes are accelerated more effectively by metal ions. [Pg.565]

An aqueous solution of sulfuric acid and a salt of periodic add, trisodium paraperiodate, or one of the potassium periodates, has been used frequently as a substitute for pure periodic add. When the product of the oxidation reaction is to be isolated, the effect of the presence of metal ions on the yield should be considered. If the product is volatile or slightly soluble, or is isolated either as a slightly soluble derivative or by extraction with organic solvents, the presence of metal ions should not reduce the yield. In the Case of certain methylhexosides34 which were oxidized by periodic acid formed from potassium metaperiodate and an equivalent of sulfuric add in aqueous solution, the presence of potassium ions was found to cause a low yield of the crystalline strontium salt prepared by the strontium hypobromite oxidation of the dialdehyde resulting from the periodic add reaction. Oxidation by pure periodic add, a solution of which is prepared either from crystalline paraperiodic add or by the previously mentioned method from potassium metaperiodate, is desirable when the presence of difficultly removed metal ions affects the yield adversely. [Pg.359]


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