title: Free energy of binding of a small molecule to an amorphous polymer in a solvent.
abstract: Crystallization is a commonly used purification process in industrial practice. It usually begins with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood, but we hypothesize that a possible correlation between binding affinity to a surface and nucleation enhancement might exist. Amorphous polymers have been used in controlling crystallization. However, to our knowledge, no attempt has been made to calculate the free energy of binding of a small molecule to an amorphous polymer in a solvent, and to characterize the binding sites/conformations of this system at a molecular level. We developed a two-step approach, first using Adsorption Locator to identify probable binding sites and molecular dynamics to screen for the best binding sites and then using the Blue-Moon Ensemble method to compute the free energy of binding. A system of ethylene glycol, polyvinyl alcohol (PVA), and heavy water (D(2)O) was used for validation, since experimental data exists on a related system. Looking at four independently constructed surfaces, we found that ethylene glycol binds to an indentation on the surface or in a hole beneath the surface. We focused on the indentation binding sites because they are easily accessible and do not have large free energy barriers. The closest system for which experimental data on binding energetics exists is ethylene glycol on PVA in aqueous solutions/gels, and the magnitudes of the free energy of binding to the three best indentation binding sites are close to the experimental value, 0.4-3.7 kcal/mol higher. Our approach offers a way to compute the free energy of binding and characterize the binding sites/conformations, and is general enough to apply to other small molecule/amorphous polymer/solvent systems.
authors.affiliation: Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.
authors.forename: Surasak
authors.initials: S
authors.lastname: Chunsrivirot
authors.forename: Bernhardt L
authors.initials: BL
authors.lastname: Trout
mesh_terms: D000327:Adsorption; D001665:Binding Sites; D008958:Models, Molecular; D008968:Molecular Conformation; D011108:Polymers / Q000737:chemistry*; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011108:Polymers; D012997:Solvents