Calcium-α-l-Guluronate Complexes: Ca²⁺ Binding Modes from DFT-MD Simulations

Abstract

The interactions of divalent calcium ions with a single α-L-guluronate anion and oligo(α-L-guluronate) chain have been studied in terms of the 'hybrid' molecular dynamics technique in which the selected parts of the system are treated with different level of theory (DFT-MD). The simulations were focused on obtaining the free energy profiles designed to clarify the possible calcium binding modes. In all considered cases, the calcium ion is coordinated by carboxyl oxygen atoms and water molecules exclusively. The results allowed for (i) determining the dentacy of calcium binding; (ii) estimating the calcium binding/unbinding-related free energy profiles; and (iii) positive verification of the previously [J. Comput. Chem. 2011, 32, 2988] proposed modification of the egg-box model describing the calcium alginate/guluronate structure. Additionally, the findings indicate that the polarization of the carboxyl group induced by the presence of Ca(2+) ion causes the increase of the free energy barrier separating the 'free' and 'bound' states of Ca(2+), in comparison to the classical biomolecular force fields (GROMOS/SPC and GLYCAM/TIP3P).

Theoretical Study of the Interaction of 1,2-Dithiolene Ligands with the Mg2+ and Ca2+ Aquacations: Electronic, Geometric and Energetic Analysis

“…Several studies report this methodology to determine the strength of binding of metal cations and ligands. [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][38][39][40][41][42][43][44][45][46][47] …”

“…21 The interaction between divalent metal cations and organic ligands was analyzed in a large number of studies. [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37] The interaction of alkaline earth metal cations with Oand N-coordinating ligands was quantified by binding energies, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and energy gap values as well as metal-ligand bond length, and ligand-to-metal electronic donation. It was seen that the O-coordinating ligands have the largest affinity for those cations.…”

DFT Study of The Interaction between the Ni2+ and Zn2+ Metal Cations and The 1,2-Dithiolene Ligands: Electronic, Geometric and Energetic Analysis

“…It was seen that the chemical bond, described as an acid-base interaction, has prominent donor-acceptor interactions between the ligand and the metal. Plazinski and Drach 16 analyzed the bonding affinity between transition divalent metal cations (Zn 2+ , Cd 2+ , Cu 2+ , Mn 2+ and Co 2+ ) with amino acids molecules. The affinity order of each metal for the amino acid compounds was quantified in terms of the complexation Gibbs free energy.…”

“…A large number of studies report this methodology for the measurement of metal-ligand affinity. 16,[22][23][24][25][26][27]…”

Carbon nanodots crosslinked photoluminescent alginate hydrogels

“…22 Several experimental and computational studies revealed that only the G-G residues form ionic bonding with the divalent cations, for example, Ca 2+ , to form a crosslinked network. [23][24][25] However, the mechanical properties of ionic crosslinked alginate hydrogels can undergo changes inside a physiological media containing salts. 26 Here, charged species can alter the ionic crosslinking of the alginate gels leading to mechanical failure of the gels.…”