Molecular Dynamics Simulation of Methylene Blue−Guanine Complex in Water:  The Role of Solvent in Stacking

The conformation of the methylene blue (MB)−guanine (GUA) complex in water was investigated by molecular dynamics simulation. It was found that the T-shaped vacuo stable conformation becomes unstable in water and turns into a well-defined stacked conformation. The free energy of the complex formation was determined by the thermodynamic integration method and found equal to −7.2 ± 0.2 kcal/mol. The variation of the hydration energy upon complexation was found to be positive (about 14 kcal/mol), being compensated by the solute−solute interaction energy (about −21 kcal/mol). The main contribution to this solute−solute interaction energy arises from the van der Waals forces (about −14 kcal/mol).