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      Ligation of water to magnesium chelates of biological importance

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          Abstract

          Water binding to several Mg 2+ chelates, ethylenediamine, ethylenediamine-N,N’-diacetate, porphyrin, chlorophyll a and bacteriochlorophyll a, to form five- and six-coordinate complexes is studied by means of density functional theory. The results obtained for magnesium chelates are compared with the properties of the respective aqua complexes and the influence of the permittivity of environment on the ligand binding energies is discussed. Although the most common coordination number of Mg 2+ is six, in the tetrapyrrolic chelates it is reduced to five because the accommodation of the sixth water ligand results in no gain in energy. This is in line with the experimental observations made for coordination of chlorophylls in vivo. The binding between Mg 2+ and water is mostly of electrostatic nature, which is supported by the finding that its energy is correlated both with the electron density of the chelator and with electrostatic potential determined at the ligand binding site.

          Electronic supplementary material

          The online version of this article (doi:10.1007/s00894-012-1459-3) contains supplementary material, which is available to authorized users.

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          Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials

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            Auxiliary basis sets to approximate Coulomb potentials

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              The thermodynamics of DNA structural motifs.

              DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
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                Author and article information

                Contributors
                +48-12-6395155 , +48-12-4251923 , nczbik@cyf-kr.edu.pl
                Journal
                J Mol Model
                J Mol Model
                Journal of Molecular Modeling
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                1610-2940
                0948-5023
                29 May 2012
                29 May 2012
                2013
                : 19
                : 4661-4667
                Affiliations
                [ ]Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Krakow, Poland
                [ ]Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
                Article
                1459
                10.1007/s00894-012-1459-3
                3825143
                22643978
                c3718c5d-762f-4ee9-aeaf-0a640e92ffaa
                © The Author(s) 2012
                History
                : 15 December 2011
                : 3 May 2012
                Categories
                Original Paper
                Custom metadata
                © Springer-Verlag 2013

                Molecular biology
                chlorophylls,dft,magnesium chelates,porphyrins,water
                Molecular biology
                chlorophylls, dft, magnesium chelates, porphyrins, water

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