Path-integral molecular dynamics simulations of glycine·(H2O) (n= 1–7) clusters on semi-empirical PM6 potential energy surfaces

Positron Binding Properties of Glycine and Its Aqueous Complexes

“…Clearly GlyZI is more hydrophilic than Gly, which explains why the energy of GlyZI· n H 2 O given with respect to the lowest energy Gly· n H 2 O structure systematically decreases as n increases. This is well in agreement with earlier works, which suggest that for n ≥ 5···7, GlyZI· n H 2 O and Gly· n H 2 O become isoenergetic. − The bonding of Gly and GlyZI with H 2 O is quite strong, as evidenced by Figure c. However, neither covalent nor ionic bonds are formed.…”

Unveiling Zwitterionization of Glycine in the Microhydration Limit

“…The well-known fact that amino acids exist in their neutral form in the gas phase, i.e., carrying charge-neutral −COOH and −NH 2 groups, but readily convert into their zwitterionic form in bulk water supports the key role of solvation water in the charge-separation process leading to zwitterionization and thus to charged −COO – and −NH 3 + groups. So far, extensive efforts have been made to understand zwitterion formation of both microhydrated and bulk solvated glycine as the role model for amino acids. − Whereas zwitterionization of glycine is well studied in the bulk phase limit including its hydration properties therein , (e.g., the first hydration shell of glycine in water is shown to be constituted by about 7–8 water molecules around its charged groups , ), not much is known in the microhydration limit on how zwitterionization can occur in terms of the underlying proton transfers and, second, which factors are contributing to zwitterion stabilization. To answer these questions requires not only the full mechanistic understanding of zwitterion formation in the microhydrated environment as such but also knowledge of the thermodynamics and kinetics by contrasting the generic scenario when the zwitterion is only metastable compared to its global stability.…”

Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution

“…We applied the QM/MM-FEG-ER method to the isomerization reaction from a neutral form (NF) to a zwitterion (ZW) form of glycine molecule in aqueous solution, which is a typical example to test a number of new computational methods. ,,,,− According to the previous theoretical investigations, − there are various conformers for both NF and ZW glycine molecules. Among them, we employed the cis-structure, ,− which is often considered to correspond to RS and PS for the isomerization reaction of glycine molecule in aqueous solution. ,,,,− The QM/MM-MD simulations were performed for a system consisting of a single glycine molecule and 5306 water molecules in a cubic simulation cell with a side of 54.5 Å, which was adjusted initially by executing the classical MD simulation with NPT ensemble at 1 atm. In the classical MD simulation, we used the effective atomic charges of the solute glycine molecule obtained by the Merz–Kollman scheme , at the B3LYP/6-31G­(d) level of theory.…”

“…We applied a QM/MM-FEG-ER method to an isomerization reaction of glycine in aqueous solution, which is a typical system to validate the calculation accuracy and efficiency of new computational methods. ,,,,− According to a previous quantum chemical study with the discrete continuum model, it was found that the addition of water molecules in the first solvation shell around the glycine molecule is required to reproduce the experimental reaction free energies of the tautomerization, showing that it is essential to include the explicit hydrogen-bonds (HBs) between glycine and water molecules. By using the present method, the reaction free energies can be accurately obtained by taking not only the HBs but also the thermodynamic fluctuation of water molecules under the finite temperature into consideration.…”