Recalibrating the calcium trap in amino acid carboxyl groups via classical molecular dynamics simulations

Abstract

In order to use classical molecular dynamics to complement experiments accurately, it is important to use robust descriptions of the system. The interactions between biomolecules, like aspartic and glutamic acid,...

New model for aspartic acid species in aqueous calcium carbonate growth environments: challenges and perspectives

“…Recently, Koskamp et al 32 calibrated a model for the fully deprotonated aspartate species (pH = 10) through combining parameters from the ff99SB version of AMBER 33 (aspartic acid, originally developed in combination with TIP3P 23 water) and from Raiteri et al 29 (calcium carbonate and SPC/Fw water 24 ) using combination rules. While the parameters between calcium and the carboxylate oxygen in aspartate were successfully calibrated to fit the numerical value of the experimental calcium aspartate association free energy at that pH, the model was not reparametrised to predict other properties that affect ion pairing, including the hydration free energy, conformational free energy profile, and pair distribution function.…”