A computational study on magnesium complexation with formate and hydrogen malonate anions

Symmetry-adapted perturbation theory study for some magnesium complexes

A systematic theoretical study on Mg–ligand interactions has been carried out employing both ab initio correlated wave function and density functional methods. The interactions of the Mg(CH3N2)2moiety with BF, CO, N2, NH3, and H2O ligands have been investigated by performing calculations at the B3LYP, MP2, MP4, and CCSD(T)/6–311++G(3df,3pd) levels of theory. Results indicate that the interaction energies of the Mg(CH3N2)2–L complexes increase in the order NH3 > H2O > BF > CO > N2. Symmetry-adapted perturbation theory (SAPT) analysis has been carried out to understand the nature of the forces involved in the bonding. The SAPT results indicate that the stabilities of the Mg–L interactions are attributed mainly to electrostatic effects, while induction and dispersion forces also play a significant role. The evaluated SAPT interaction energies for the Mg(CH3N2)2–L complexes are generally in good agreement with those obtained using the supermolecule CCSD(T) methods, suggesting that SAPT is a proper method to study the intermolecular interactions in these complexes. The results also suggest an explanation for the unique role of Mg2+as a carrier of water molecules that mediate enzymatic hydrolysis reactions.

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.