Clustering of Glycine Molecules in Aqueous Solution Studied by Molecular Dynamics Simulation

Abstract

The nature of glycine--glycine interactions in aqueous solution has been studied using molecular dynamics simulations at four different concentrations and, in each case, four different temperatures. Although evidence is found for formation of small, transient hydrogen-bonded clusters of glycine molecules, the main type of interaction between glycine molecules is found to be single NH...OC hydrogen bonds. Double-hydrogen-bonded "dimers", which have often been cited as a significant species present in aqueous solutions of glycine, are only observed infrequently. When double-hydrogen-bonded dimers are formed, they dissociate quickly (typically within less than ca. 4 ps), although the broken hydrogen bonds have a higher than average probability of reforming. Several aspects of the clustering of glycine molecules are investigated as a function of both temperature and concentration, including the size distribution of glycine clusters, the radii of gyration of the clusters, and aspects of the lifetimes of glycine-glycine hydrogen bonding by means of hydrogen-bond correlation functions. Diffusion coefficients for the glycine clusters and water molecules are also investigated and provide results in realistic agreement with experimental results.

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

“…It has previously been shown that the salt bridge interactions can be affected by the choice of different water models with force field [97]. In previous studies, the results from small-angle X-ray studies and simulations have been used to explain the RDF peaks in terms of the polydispersity of amino acids [34,98,99]. The different RDF peaks provide information about hydrogen bonded oligomers.…”

“…Amino acids, being simpler than proteins, are a logical stepping stone toward understanding crowded biological systems. The clustering of amino acids such as glycine has been studied using NMR diffusion experiments and molecular dynamics (MD) simulations as a function of concentration, pH and temperature [22][23][24][34][35][36][37][38]. Hughes et al [23] used a multidisciplinary approach (i.e., NMR diffusion, MD simulations and small-angle neutron scattering) to investigate the crystallization of glycine in aqueous solutions.…”

“…Hughes et al [23] used a multidisciplinary approach (i.e., NMR diffusion, MD simulations and small-angle neutron scattering) to investigate the crystallization of glycine in aqueous solutions. Hamad et al [34] have attempted to explain the size of glycine clusters using radial distribution functions (RDFs) and hydrogen bonding. Campo et al [35] used MD simulations to study the modifications of the glycine structure with changes in solution pH, and observed changes in the diffusion coefficient of glycine solutions.…”

Effect of mixing, concentration and temperature on the formation of mesostructured solutions and their role in the nucleation of dl-valine crystals

“…In the last twenty years significant effort has been made to better understand the mechanism of the nucleation process and a wide variety of 30 techniques has been used to probe the relationship between molecular self-organization in solutions and melts, formation of nuclei and the resultant crystal polymorphs. Molecular selforganization due to solute-solute and solute-solvent interactions have been examined in undersaturated, saturated and 35 supersaturated crystallizing solutions using X-ray Small-Angle Scattering (SAXS) [1][2][3] , Wide-Angle X-ray Diffraction (WAXD) 1 , Fourier Transform Infrared Spectroscopy (FTIR) 4 , Nuclear Magnetic Resonance (NMR) 5 , Small Angle Neutron Scattering (SANS) 6 , Empirical Potential Structure Refinement (EPSR) 7 and 40 molecular modelling 8,9 . A common finding from these studies has been that solutes associate to form clusters in supersaturated solutions [10][11][12][13][14] .…”

“…A common finding from these studies has been that solutes associate to form clusters in supersaturated solutions [10][11][12][13][14] . However, identification of a direct relationship between the solute molecular clusters and subsequent formed crystal has been found to be challenging [15][16][17][18] . Two recently 45 published reviews by Davey et al and Gebauer at al.…”