Use of Molecular Dynamics for the Refinement of an Electrostatic Model for the In Silico Design of a Polymer Antidote for the Anticoagulant Fondaparinux

Figure 1

Structures of the various amines used as binding groups: (a) R1-1; (b) R3-1; (c) R4-1; (d) R4-2; and, (e) R6-1. The nitrogen atoms are connected by –CH₂–CH₂– linkages in (b), (c), and (e) and by –CH₂–CH₂–CH₂ linkage in (d). The protonation state is for physiological pH of 7.4 and was calculated with ChemAxon pKa Calculator Plugin (Marvin 5.5.5, 2011) [15].