public ThermoData generateSolvThermoData(ChemGraph p_chemGraph) {
double r_solute = p_chemGraph.getRadius();
double r_solvent;
r_solvent =
3.498
* Math.pow(
10,
-10); // 3.311; // Manually assigned solvent radius [=] meter
// Calculated using Connolly solvent excluded volume from Chem3dPro
double r_cavity = r_solute + r_solvent; // Cavity radius [=] Angstrom
double rho;
rho =
0.00309
* Math.pow(
10,
30); // 0.00381; // number density of solvent [=]
// molecules/Angstrom^3 Value here is for decane using density =0.73 g/cm3
double parameter_y =
(88 / 21)
* rho
* Math.pow(r_solvent, 3); // Parameter y from Ashcraft Thesis Refer pg no. 60
double parameter_ymod =
parameter_y / (1 - parameter_y); // parameter_ymod= y/(1-y) Defined for convenience
double R = 8.314; // Gas constant units J/mol K
double T = 298; // Standard state temperature
// Definitions of K0, K1 and K2 correspond to those for K0', K1' and K2' respectively from
// Ashcraft's Thesis
double K0 = -R * (-Math.log(1 - parameter_y) + (4.5 * Math.pow(parameter_ymod, 2)));
double K1 = (R * 0.5 / r_solvent) * ((6 * parameter_ymod) + (18 * Math.pow(parameter_ymod, 2)));
double K2 =
-(R * 0.25 / Math.pow(r_solvent, 2))
* ((12 * parameter_ymod) + (18 * Math.pow(parameter_ymod, 2)));
// Basic definition of entropy change of solvation from Ashcfrat's Thesis
double deltaS0;
deltaS0 = K0 + (K1 * r_cavity) + (K2 * Math.pow(r_cavity, 2));
// Generation of Abraham Solute Parameters
AbramData result_Abraham = new AbramData();
result_Abraham = p_chemGraph.getAbramData();
// Solute descriptors from the Abraham Model
double S = result_Abraham.S;
double B = result_Abraham.B;
double E = result_Abraham.E;
double L = result_Abraham.L;
double A = result_Abraham.A;
// Manually specified solvent descriptors (constants here are for decane)
double c = 0.156; // -0.12;
double s = 0; // 0.56;
double b = 0; // 0.7;
double e = -0.143; // -0.2;
double l = 0.989; // 0.94;
double a = 0; // 3.56;
double logK = c + s * S + b * B + e * E + l * L + a * A; // Implementation of Abraham Model
double deltaG0_octanol = -8.314 * 298 * logK;
// System.out.println("The free energy of solvation in octanol at 298K w/o reference state
// corrections = " + deltaG0_octanol +" J/mol for " );
// Calculation of enthalpy change of solvation using the data obtained above
double deltaH0 = deltaG0_octanol + (T * deltaS0);
deltaS0 = deltaS0 / 4.18; // unit conversion from J/mol to cal/mol
deltaH0 = deltaH0 / 4180; // unit conversion from J/mol to kcal/mol
// Generation of Gas Phase data to add to the solution phase quantities
ThermoData solvationCorrection =
new ThermoData(
deltaH0,
deltaS0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
"Solvation correction");
// Now, solvationCorrection contains solution phase estimates of CORRECTION TO H298, S298 and
// all the gas phase heat capacities.
// Assuming the solution phase heat capcities to be the same as that in the gas phase we wouls
// now want to pass on this
// modified version of result to the kinetics codes. This might require reading in a keyword
// from the condition.txt file.
// Exactly how this will be done is yet to be figured out.
return solvationCorrection;
// #]
}
