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;
// #]
}
// ## operation generateReverseForBackwardReaction()
private TemplateReaction generateReverseForBackwardReaction(Structure fs, Structure fsSp) {
// #[ operation generateReverseForBackwardReaction()
// we need to only generate reverse reaction for backward reaction, so that we wont be stuck
// into a self loop.
if (!this.isBackward()) {
return null;
}
ReactionTemplate fRT = getReactionTemplate();
ReactionTemplate rRT = null;
if (fRT.isForward()) {
return null;
} else if (fRT.isNeutral()) {
rRT = fRT;
} else if (fRT.isBackward()) {
rRT = fRT.getReverseReactionTemplate();
} else {
throw new InvalidReactionTemplateDirectionException(); // Structure fs = getStructure();
}
LinkedList freactant = fs.getReactantList();
LinkedList fproduct = fs.getProductList();
Structure rs = new Structure(fproduct, freactant, -1 * this.getDirection());
Structure rsSp = new Structure(fsSp.products, fsSp.reactants, -1 * this.getDirection());
// If it's in the reverse ReactionTemplate.reactionDictionaryByStructure then just return that
// one.
TemplateReaction rr = rRT.getReactionFromStructure(rsSp);
if (rr != null) {
rr.setReverseReaction(this);
return rr;
}
int rNum = fproduct.size();
Kinetics[] k = rRT.findReverseRateConstant(rs);
// If that didnt work, what to do....
if (k == null && rRT.name.equals("R_Recombination")) {
ChemGraph cg = ((ChemGraph) fproduct.get(0));
Graph g = cg.getGraph();
Node n = (Node) g.getCentralNodeAt(2);
if (n == null) {
cg = ((ChemGraph) fproduct.get(1));
g = cg.getGraph();
n = (Node) g.getCentralNodeAt(2);
}
g.clearCentralNode();
g.setCentralNode(1, n);
k = rRT.findRateConstant(rs);
} else if (k == null && rRT.name.equals("H_Abstraction")) {
ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
Graph g1 = cg1.getGraph();
Node n3 = (Node) g1.getCentralNodeAt(3);
if (n3 == null) {
cg1 = ((ChemGraph) fproduct.get(1));
g1 = cg1.getGraph();
n3 = (Node) g1.getCentralNodeAt(3);
Node n2 = (Node) g1.getCentralNodeAt(2);
g1.clearCentralNode();
g1.setCentralNode(1, n3);
g1.setCentralNode(2, n2);
ChemGraph cg2 = ((ChemGraph) fproduct.get(0));
Graph g2 = cg2.getGraph();
Node n1 = (Node) g2.getCentralNodeAt(1);
g2.clearCentralNode();
g2.setCentralNode(3, n1);
} else {
Node n2 = (Node) g1.getCentralNodeAt(2);
g1.clearCentralNode();
g1.setCentralNode(1, n3);
g1.setCentralNode(2, n2);
ChemGraph cg2 = ((ChemGraph) fproduct.get(1));
Graph g2 = cg2.getGraph();
Node n1 = (Node) g2.getCentralNodeAt(1);
g2.clearCentralNode();
g2.setCentralNode(3, n1);
}
k = rRT.findRateConstant(rs);
}
/*
* Added by MRH on 27-Aug-2009 This hard-coding is necessary for rxn family templates that are labeled
* "thermo_consistence". After the chemgraphs are mutated, the central nodes for the products are not correct
* (see example below). These hard-coded portions are necessary for RMG to find Kinetics for the structure.
* Example: CH4 + H CH4 1 *1 C 0 {2,S} {3,S} {4,S} {5,S} 2 *2 H 0 {1,S} 3 H 0 {1,S} 4 H 0 {1,S} 5 H 0 {1,S} H 1
* *3 H 1 After RMG has "reactChemGraph" and "mutate" the chemgraphs of the reactants, the products would look
* as such: prod1 1 *1 C 1 {2,S} {3,S} {4,S} 2 H 0 {1,S} 3 H 0 {1,S} 4 H 0 {1,S} prod2 1 *3 H 0 {2,S} 2 *2 H 0
* {1,S} Assuming the reaction as written (CH4+H=CH3+H2) is endothermic at 298K, RMG will label this structure
* as direction=-1 (backward). When attempting to find Kinetics for the backward reaction, RMG will try to match
* the prod1 graph against the generic graphs X_H and Y_rad_birad. It cannot match Y_rad_birad (because there is
* no *3 node) and it cannot match X_H (because there is no *2 node). Thus, a "null" Kinetics will be returned
* from the findReverseRateConstant call. We then relabel the central nodes on prod1 and prod2 and attempt to
* get Kinetics for this structure. I am adding the following bit of code to work with the new reaction family
* Aaron Vandeputte is adding to RMG: "".
*/
else if (k == null && rRT.name.equals("intra_substitutionS_isomerization")) {
ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
Graph g1 = cg1.getGraph();
Node n1 = (Node) g1.getCentralNodeAt(1);
Node n2 = (Node) g1.getCentralNodeAt(2);
Node n3 = (Node) g1.getCentralNodeAt(3);
Node n4 = (Node) g1.getCentralNodeAt(4);
Node n5 = (Node) g1.getCentralNodeAt(5);
Node n6 = (Node) g1.getCentralNodeAt(6);
Node n7 = (Node) g1.getCentralNodeAt(7);
g1.clearCentralNode();
g1.setCentralNode(1, n1);
g1.setCentralNode(2, n3);
g1.setCentralNode(3, n2);
if (n7 != null) {
g1.setCentralNode(7, n4);
g1.setCentralNode(6, n5);
g1.setCentralNode(5, n6);
g1.setCentralNode(4, n7);
} else if (n6 != null) {
g1.setCentralNode(6, n4);
g1.setCentralNode(5, n5);
g1.setCentralNode(4, n6);
} else if (n5 != null) {
g1.setCentralNode(5, n4);
g1.setCentralNode(4, n5);
} else if (n4 != null) g1.setCentralNode(4, n4);
k = rRT.findRateConstant(rs);
}
// Adding another elseif statement for Aaron Vandeputte rxn family
// RMG expects to find *1 and *2 in the same ChemGraph (for this rxn family)
// but will instead find *1 and *3 in the same ChemGraph (if we've reached this far)
// Need to switch *2 and *3
else if (k == null && (rRT.name.equals("substitutionS") || rRT.name.equals("Substitution_O"))) {
ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
ChemGraph cg2 = ((ChemGraph) fproduct.get(1));
Graph g1 = cg1.getGraph();
Graph g2 = cg2.getGraph();
Node n3 = (Node) g1.getCentralNodeAt(3);
if (n3 == null) {
// Switch the identities of cg1/g1 and cg2/g2
cg1 = ((ChemGraph) fproduct.get(1));
g1 = cg1.getGraph();
cg2 = ((ChemGraph) fproduct.get(0));
g2 = cg2.getGraph();
n3 = (Node) g1.getCentralNodeAt(3);
}
Node n1 = (Node) g1.getCentralNodeAt(1);
g1.clearCentralNode();
g1.setCentralNode(2, n3);
g1.setCentralNode(1, n1);
Node n2 = (Node) g2.getCentralNodeAt(2);
g2.clearCentralNode();
g2.setCentralNode(3, n2);
k = rRT.findRateConstant(rs);
} else if (k == null && rRT.name.equals("intra_H_migration")) {
ChemGraph cg = ((ChemGraph) fproduct.get(0));
Graph g = cg.getGraph();
// Current max is 8 identified nodes
Node n1 = (Node) g.getCentralNodeAt(1);
Node n2 = (Node) g.getCentralNodeAt(2);
Node n3 = (Node) g.getCentralNodeAt(3);
Node n4 = (Node) g.getCentralNodeAt(4);
Node n5 = (Node) g.getCentralNodeAt(5);
Node n6 = (Node) g.getCentralNodeAt(6);
Node n7 = (Node) g.getCentralNodeAt(7);
Node n8 = (Node) g.getCentralNodeAt(8);
g.clearCentralNode();
// Swap the locations of the central nodes 1 and 2
g.setCentralNode(1, n2);
g.setCentralNode(2, n1);
// Retain the location of the central node at 3
g.setCentralNode(3, n3);
if (n8 != null) {
g.setCentralNode(4, n5);
g.setCentralNode(5, n4);
g.setCentralNode(6, n8);
g.setCentralNode(7, n7);
g.setCentralNode(8, n6);
} else if (n7 != null) {
g.setCentralNode(4, n5);
g.setCentralNode(5, n4);
g.setCentralNode(6, n7);
g.setCentralNode(7, n6);
} else if (n6 != null) {
g.setCentralNode(4, n5);
g.setCentralNode(5, n4);
g.setCentralNode(6, n6);
} else if (n5 != null) { // Swap the locations of the central nodes 4 and 5, if node 5 exists
g.setCentralNode(4, n5);
g.setCentralNode(5, n4);
} else if (n4 != null) { // if only central node 4 exists, retain that location
g.setCentralNode(4, n4);
}
k = rRT.findRateConstant(rs);
// rr = rRT.calculateForwardRateConstant(cg, rs);
// if (!rr.isForward()) {
// String err = "Backward:"
// + structure.toString()
// + String.valueOf(structure
// .calculateKeq(new Temperature(298, "K")))
// + '\n';
// err = err
// + "Forward:"
// + rr.structure.toString()
// + String.valueOf(rr.structure
// .calculateKeq(new Temperature(298, "K")));
// throw new InvalidReactionDirectionException(err);
// }
// rr.setReverseReaction(this);
// rRT.addReaction(rr);
// return rr;
} else if (k == null && rRT.name.equals("H_shift_cyclopentadiene")) {
ChemGraph cg = ((ChemGraph) fproduct.get(0));
Graph g = cg.getGraph();
// Current max is 6 identified nodes
Node n1 = (Node) g.getCentralNodeAt(1);
Node n2 = (Node) g.getCentralNodeAt(2);
Node n3 = (Node) g.getCentralNodeAt(3);
Node n4 = (Node) g.getCentralNodeAt(4);
Node n5 = (Node) g.getCentralNodeAt(5);
Node n6 = (Node) g.getCentralNodeAt(6);
g.clearCentralNode();
// Swap the locations of the central nodes 1 to 6
g.setCentralNode(1, n2);
g.setCentralNode(2, n1);
g.setCentralNode(3, n5);
g.setCentralNode(4, n4);
g.setCentralNode(5, n3);
g.setCentralNode(6, n6);
k = rRT.findRateConstant(rs);
}
if (k == null) {
Logger.error(
"Couldn't find the rate constant for reaction: "
+ rs.toChemkinString(true)
+ " with "
+ rRT.name);
// System.exit(0);
return null;
}
rr = new TemplateReaction(rsSp, k, rRT);
if (!rr.isForward()) {
String err =
"Backward:"
+ structure.toString()
+ String.valueOf(structure.calculateKeq(new Temperature(298, "K")))
+ '\n';
err =
err
+ "Forward:"
+ rr.structure.toString()
+ String.valueOf(rr.structure.calculateKeq(new Temperature(298, "K")));
throw new InvalidReactionDirectionException(err);
}
rr.setReverseReaction(this);
rRT.addReaction(rr);
return rr;
// #]
}
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;
// #]
}