Urea parametrization for molecular dynamics simulations

A consensus view of protein dynamics

“…Four force fields were used in production runs: AMBER (17) Control simulations were performed to determine whether force fields were able to recognize unfolding conditions and lead to the destabilization of the folded form. For this purpose, 30-ns simulations of 1CQY, 1OPC, and 1KTE were performed using 8 M urea and a temperature of 368 K. OPLS (47) parameters for urea were used for O and A simulations, whereas specific CHARMM parameters (48) were used in C simulations. Due to the lack of specific parameters, these control simulations were not performed using GROMOS force field.…”

Intermolecular hydrogen bonds in urea–water complexes: DFT, NBO, and AIM analysis

“…It's important here to notice the higher values of ρ(r) and Ñ 2 ρ in the case of urea-(H 2 O) 4 . Furthermore, the most strong intermolecular hydrogen bond within the considered molecular models (E H•••O = 13.074 kcal/mol) is observed for the urea-(H 2 O)4 . These indications were used in some earlier studies[45] as a selection tool to extract the predominant cluster in triformylmethane.…”

“…The geometries of all the considered models, urea-(H 2 O) n (n = [1][2][3][4][5], are optimized at the B3LYP/6-31+G(d, p) level and the more stable structures are given in Fig. 1 with atom numbering.…”

“…4 . The water-water hydrogen bonds are very comparable to those in bulk water and it seems that the tetrahedral structure is not broken in the mixture.…”

“…The number of hydrogen bonds between water molecules was observed to decrease with the addition of urea [3], however, the whole structure of water was kept unchanged. Recent molecular simulation studies show that urea doesn't break the local tetrahedral structure of water even at high concentrations [4][5]. The water-water H-bonds are considerably stronger than those between water and urea or urea and urea [6][7][8][9][10][11][12][13][14][15].…”