Calculation of solvation free energy using RISM theory for peptide in salt solution

We developed a robust, highly efficient algorithm for solving the full reference interaction site model (RISM) equations for salt solutions near a solute molecule with many atomic sites. It was obtained as an extension of our previously reported algorithm for pure water near the solute molecule. The algorithm is a judicious hybrid of the Newton–Raphson and Picard methods. The most striking advantage is that the Jacobian matrix is just part of the input data and need not be recalculated at all. To illustrate the algorithm, we solved the full RISM equations for a dipeptide (NH2(SINGLE BOND)CHCH3(SINGLE BOND)CONH(SINGLE BOND)CHCH3(SINGLE BOND)COOH) in a 1 M NaCl solution. The extended simple point charge (SPC/E) model was employed for water molecules. Two different conformations of the dipeptide were considered. It was assumed for each conformation that the dipeptide was present either as an un-ionized form or as a zwitterion. The structure of the salt solution near the dipeptide and salt effects on the solvation free energy were also discussed.