PubMed HealthSearch

PubMed · 8603132

Multiple ligand-ion solutions: a guide for solution preparation and computer program understanding.

Abstract

This paper first gives an overview of the multitude of chemical reactions taking place in aqueous solutions with multiple ligands and ions. Then, recommendations to avoid pitfalls in preparing such solutions in daily laboratory work are summarized. Thereafter, the theoretical aspects for calculating multiple ligand-ion solutions are described in detail. Information necessary to perform corrections of the absolute stability constants for the influences of pH, ionic strength, and temperature are given. The calculation of apparent reaction constants for ligand-ion interactions by using the corrected absolute stability constants and considering all possible reactions between a ligand and an ion in an aqueous solution will be introduced. Thereafter, by employing the apparent reaction constants and an iterative method, the determination of multiple ligand-ion equilibria to find the desired ligand or ion concentrations are presented. Thus, this paper can be used as a guide to the principles of programs calculating multiple ligand-ion solutions, to choosing the appropriate program for one's special requirements, and to preparing multiple ligand-ion solutions properly.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

R Schubert. Multiple ligand-ion solutions: a guide for solution preparation and computer program understanding.. https://doi.org/10.1159/000159136

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

Lalpha-phase separation in phosphatidylcholine-water systems induced by alkali chlorides.

The effects of alkali chlorides on phosphatidylcholine-water bilayer systems in the Lalpha-phase were investigated by using small- and wide-angle X-ray scattering. The ternary system LiCl-POPC-H2O under isothermal conditions has shown that above Li+/POPC molar ratios of 0.1 and a lipid concentration above 5% (w/w), a splitting of the lamellar Bragg diffraction peaks into discrete components indicates a phase separation into different lamellar liquid crystalline (smectic A) phases. It is also shown that in saturated distearoyl phosphatidylcholine and in egg phosphatidylcholine, alkali chlorides induce Lalpha-phase separation. The number and repeat distance of the coexisting lamellar phases depend on the nature and concentration of the alkali chloride, the concentration of the phosphatidylcholine, and the degree of the acyl chain unsaturation.

Chemical Phenomena

Extracting contact energies from protein structures: a study using a simplified model.

In this study, we exploited an elementary 2-dimensional square lattice model of HP polymers to test the premise of extracting contact energies from protein structures. Given a set of prespecified energies for H-H, H-P, and P-P contacts, all possible sequences of various lengths were exhaustively enumerated to find sequences that have unique lowest-energy conformations. The lowest-energy structures (or native structures) of such (native) sequences were used to extract contact energies using the Miyazawa-Jernigan procedure and here-defined reference state. The relative magnitudes of the original energies were restored reasonably well, but the extracted contact energies were independent of the absolute magnitudes of the initial energies. We turned to a more detailed characterization of the energy landscapes of the native sequences in light of a new theoretical framework on protein folding. Foldability of such sequences imposes two limits on the absolute value of the prespecified energies: a lower bound entailed by the minimum requirement for thermodynamic stability and an upper bound associated with the entrapment of the chain to local minima. We found that these two limits confine the prespecified energy values to a rather narrow range which, surprisingly, also contains the extracted energies in all the cases examined. These results indicate that the quasi-chemical approximation can be used to connect quantitatively the occurrence of various residue-residue contacts in an ensemble of native structures with the energies of the contacts. More importantly, they suggest that the extracted contact energies do contain information on structural stability and can be used to estimate actual structural energetics. This study also encourages the use of structure-derived contact energies in threading. The finding that there is a rather narrow range of energies that are optimal for folding a sequence also cautions the use of arbitrary energy Hamiltonion in minimal folding models.

Chemical Phenomena

Conduction-band-edge ionization thresholds of DNA components in aqueous solution.

Numerous investigations have focused on DNA damage induced by ionizing radiation; however, photoionization threshold energies of nucleic acid components in aqueous solution are not known. Herein, data from gas-phase photoelectron experiments have been combined with results from self-consistent field and post-self-consistent field molecular orbital calculations and with theoretical Gibbs free energies of hydration to describe aqueous ionization energies of 2'-deoxythymidine 5'-phosphate (5'-dTMP-) and 2'-deoxycytidine 5'-phosphate (5'-dCMP-). For the test molecules, indole and tryptophan, this approach yields aqueous ionization energies (4.46 and 4.58 eV, respectively) in agreement with experimental values (4. 35 and 4.45 eV). When uridine and 2'-deoxythymidine ionization energies are evaluated, the results agree with recent data from 193-nm laser measurements indicating that uridine ionization occurs via a one-photon event. For 5'-dCMP- and 5'-dTMP-, a comparison of aqueous ionization energies with gas-phase ionization potentials (IPs) indicates that hydration alters the relative energies of ionization events. In the gas phase, phosphate vertical IPs are approximately 1.3 eV smaller than base IPs. In aqueous solution, the base and phosphate ionization energies are more similar, and only differ by approximately 0.5 eV. For 5'-dCMP- and 5'-dTMP-, the increased favorableness of base ionization, which accompanies hydration, is consistent with experimental data indicating that, at 77 K in aqueous perchlorate glasses, the primary photoionization pathway involves base ionization followed by deprotonation.

Chemical Phenomena