Molecular dynamics investigation of clustering in aqueous glycine solutions

Abstract

This dataset provides molecular dynamics simulations input files required to reproduce the simulation results reported in the following paper: “Molecular dynamics investigation of clustering in aqueous glycine solutions”. URL: TBC ### Abstract: Recent experiments with undersaturated aqueous glycine solutions have repeatedly exhibited the presence of giant liquid-like clusters, or nanodroplets, around 100 nm in diameter. These droplets reappear even after careful efforts at their removal and purification of the glycine solution. The composition of these clusters is not clear, although it has been suggested they are mainly composed of glycine, a small and very soluble amino acid. To gain insight into this phenomenon, we study the aggregation of glycine in aqueous solutions at concentrations below the experimental solubility limit using large-scale molecular dynamics simulations at ambient conditions. Three protonation states of glycine (neutral=GLY, anion=GLA, cation=GLC) are simulated using molecular force fields based on the 1.14*CM1A partial charge scheme, which incorporates the OPLS all atom force field, and TIP3P water. When initiated from dispersed states, we find giant clusters do not form in our simulations unless salt impurities are present. Moreover, if simulations are initiated from giant cluster states, we find they tend to dissolve in the absence of salt impurities. Therefore, the simulation results provide little support for the possibility that the giant clusters seen in experiments are composed purely of glycine (and water). Considering that strenuous efforts are made in experiments to remove impurities such as salt, we propose that the giant clusters observed might instead result from the aggregation of reaction products of aqueous glycine, such as diketopiperazine or other oligoglycines which may be difficult to separate from glycine using conventional methods, or their co-aggregation with glycine. Detailed work is needed to explore this possibility. ### In this paper we reported molecular dynamics simulation results for 6 samples. Simulations were performed using the LAMMPS software package (See https://www.lammps.org/). Each directory in the dataset correspond to one simulated sample. The directory name has information on the concentration of each simulated molecular species, and whether the simulation was initiated from dispersed or pre-clustered state. Each directory contains the following three essential files: lammps.input (LAMMPS input script), forcefield.dat (input forcefield file), and data.dat (initial atom positions, bonds, and angles). To run these simulations on Linux, it is sufficient to use the command "/PATH-TO-LAMMPS/lammps < lammps.input".