Example #1
0
  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;
    // #]
  }
Example #2
0
  public AbrahamGAValue getABGroup(ChemGraph p_chemGraph) {
    // #[ operation getGAGroup(ChemGraph)

    AbramData result_abram = new AbramData();
    Graph g = p_chemGraph.getGraph();
    HashMap oldCentralNode = (HashMap) (p_chemGraph.getCentralNode()).clone();

    // satuate radical site
    int max_radNum_molecule = ChemGraph.getMAX_RADICAL_NUM();
    int max_radNum_atom = Math.min(8, max_radNum_molecule);
    int[] idArray = new int[max_radNum_molecule];
    Atom[] atomArray = new Atom[max_radNum_molecule];
    Node[][] newnode = new Node[max_radNum_molecule][max_radNum_atom];

    int radicalSite = 0;
    Iterator iter = p_chemGraph.getNodeList();
    FreeElectron satuated = FreeElectron.make("0");
    while (iter.hasNext()) {
      Node node = (Node) iter.next();
      Atom atom = (Atom) node.getElement();
      if (atom.isRadical()) {
        radicalSite++;
        // save the old radical atom
        idArray[radicalSite - 1] = node.getID().intValue();
        atomArray[radicalSite - 1] = atom;
        // new a satuated atom and replace the old one
        Atom newAtom = new Atom(atom.getChemElement(), satuated);
        node.setElement(newAtom);
        node.updateFeElement();
      }
    }

    // add H to satuate chem graph
    Atom H = Atom.make(ChemElement.make("H"), satuated);
    Bond S = Bond.make("S");
    for (int i = 0; i < radicalSite; i++) {
      Node node = p_chemGraph.getNodeAt(idArray[i]);
      Atom atom = atomArray[i];
      int HNum = atom.getRadicalNumber();
      for (int j = 0; j < HNum; j++) {
        newnode[i][j] = g.addNode(H);
        g.addArcBetween(node, S, newnode[i][j]);
      }
      node.updateFgElement();
    }

    // find all the thermo groups
    iter = p_chemGraph.getNodeList();
    while (iter.hasNext()) {
      Node node = (Node) iter.next();
      Atom atom = (Atom) node.getElement();
      if (!(atom.getType().equals("H"))) {
        if (!atom.isRadical()) {

          p_chemGraph.resetThermoSite(node);
          AbrahamGAValue thisAbrahamValue = thermoLibrary.findAbrahamGroup(p_chemGraph);

          if (thisAbrahamValue == null) {
            System.err.println("Abraham group not found: " + node.getID());
          } else {
            // System.out.println(node.getID() + " " + thisGAValue.getName()+ "
            // "+thisGAValue.toString());

            result_abram.plus(thisAbrahamValue);
          }
        } else {
          System.err.println("Error: Radical detected after satuation!");
        }
      }
    }

    //        // find the BDE for all radical groups
    //        for (int i=0; i<radicalSite; i++) {
    //          	int id = idArray[i];
    //           	Node node = g.getNodeAt(id);
    //           	Atom old = (Atom)node.getElement();
    //           	node.setElement(atomArray[i]);
    //           	node.updateFeElement();
    //
    //            // get rid of the extra H at ith site
    //          	int HNum = atomArray[i].getRadicalNumber();
    //           	for (int j=0;j<HNum;j++) {
    //           		g.removeNode(newnode[i][j]);
    //           	}
    //           	node.updateFgElement();
    //
    //           	p_chemGraph.resetThermoSite(node);
    //           	ThermoGAValue thisGAValue = thermoLibrary.findRadicalGroup(p_chemGraph);
    //           	if (thisGAValue == null) {
    //           		System.err.println("Radical group not found: " + node.getID());
    //           	}
    //           	else {
    //           		//System.out.println(node.getID() + " radical correction: " +
    // thisGAValue.getName() + "  "+thisGAValue.toString());
    //           		result.plus(thisGAValue);
    //            }
    //
    //            //recover the satuated site for next radical site calculation
    //          	node.setElement(old);
    //          	node.updateFeElement();
    //           	for (int j=0;j<HNum;j++) {
    //           		newnode[i][j] = g.addNode(H);
    //           		g.addArcBetween(node,S,newnode[i][j]);
    //           	}
    //           	node.updateFgElement();
    //
    //         }
    //
    //         // recover the chem graph structure
    //         // recover the radical
    //         for (int i=0; i<radicalSite; i++) {
    //           	int id = idArray[i];
    //           	Node node = g.getNodeAt(id);
    //           	node.setElement(atomArray[i]);
    //           	node.updateFeElement();
    //           	int HNum = atomArray[i].getRadicalNumber();
    //         	//get rid of extra H
    //           	for (int j=0;j<HNum;j++) {
    //          	g.removeNode(newnode[i][j]);
    //           	}
    //           	node.updateFgElement();
    //         }
    //
    //         // substrate the enthalphy of H from the result
    //         int rad_number = p_chemGraph.getRadicalNumber();
    //         ThermoGAValue enthalpy_H = new ThermoGAValue(ENTHALPY_HYDROGEN * rad_number,
    // 0,0,0,0,0,0,0,0,0,0,0,null);
    //         result.minus(enthalpy_H);
    //
    //         // make the symmetric number correction to entropy
    //
    //         if (p_chemGraph.isAcyclic()){
    //			 int sigma = p_chemGraph.getSymmetryNumber();
    //	         ThermoGAValue symmtryNumberCorrection = new
    // ThermoGAValue(0,GasConstant.getCalMolK()*Math.log(sigma),0,0,0,0,0,0,0,0,0,0,null);
    //			 result.minus(symmtryNumberCorrection);
    //         }

    p_chemGraph.setCentralNode(oldCentralNode);

    return result_abram;

    // #]
  }