Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study.

Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations. The influence of an explicit water solvent is also studied with DFTB, which was made possible by its lower computational cost compared to ADFT. Simulations lengths of 2.1 and 15 ns were achieved with ADFT and DFTB, respectively, in a reasonably short computational time. ADFT leads to a free energy difference (ΔF eq-ax) of ∼ -3 kcal mol-1 between the two low energy conformers, C7eq and C7ax, which is lower by only 1.5 kcal mol-1 than the ΔF eq-ax computed with DFTB. The two minima in ADFT FES are separated by an energy barrier of 9 kcal mol-1, which is higher than the DFTB barriers by 2-4 kcal mol-1. Despite these small quantitative differences, the DFTB method reveals FES shapes, confor-mation geometries and energies of the stationary points in good agreement with these found with ADFT. This validates the promising applicability of DFTB to FES of reactions occurring in larger-size systems placed in complex environments.

Complexation of Trivalent Metal Cations to Mannuronate Type Alginate Models from a Density Functional Study.

Complexation of alginate models, built of ß-d-mannuronic units (M) linked by a 1-4 glycosidic bridge, to Al(3+), Sc(3+), Cr(3+), Fe(3+), Ga(3+), and La(3+) cations was studied by applying the quantum chemical density functional theory (DFT) based method. The binding modes and energies were obtained for complexes with one, two, and three truncated alginate chain(s). In all the hydrated structures a monodentate binding mode is established to be the energetically most favored with shorter M(3+)···O(COO(-)) bonds than M(3+)···O(OH) bonds. Coordination bond lengths are found to be specific to each cation and to depend very little on the water in the coordination sphere and on the number of saccharide units used to model an alginate chain. The binding energy tendency Fe(3+) ≈ Cr(3+) > Al(3+) ≈ Ga(3+) ≫ Sc(3+) ≥ La(3+) is not affected by the alginate models, the coordination to water molecules, and the number of chains. A significant covalent contribution that arises predominantly from a charge donation from the carboxylate oxygen to the metal cation was established from the orbital population analysis. An exothermic chain-chain association is predicted by the computed enthalpy variations. A comparison between the structural features of alginate complexation to trivalent and divalent cations is provided and discussed.