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Single Molecule/Radical Thermodynamics
Single Molecule/Radical Thermodynamics
JTHERMODYNAMICS offers three methods to compute the temperature dependent thermodynamics for a molecule. The general command is:
THERMO MolDescription MoleculeName
where:
THERMO: Keyword for computing thermodynamics
MolDescription: The molecule in the form specified by Form (it might have to be put into quotes).
MoleculeName: The name of the molecule (a reference in the NASA polynomial).
The output to the terminal is the computation for this molecule itself. The final output is a summary of the benson rules with the corrections and the NASA polynomial.
The Method keyword determines which method should be used to calculate the thermodynamics. The distinction for the method refers mainly to the computation of radical terms. All three methods give the same answer for non-radical molecules. There are three methods that are available (Boldface is the keyword):
THERGAS: This computes the molecule using the THERGAS method.
BensonRadical: This computes the radical using Benson group additivity rules for radicals
THERM: This computes radicals using the hydrogen bond increment (HBI) corrections.
It is not said that all methods cover all classes of molecules. Benson rules may be missing (this will be reflected in the output), corrections may not be taken into account and, for example in THERM, HBI corrections may not be present.
The MolForm determines which text representation will used in the MolDescription:
Nancy: The Nancy linear form
IUPAC: The IUPAC standard
SMILES: The SMILES notation
Example: Defaults (JTHERGAS with Nancy Linear Form)
Example: Defaults (JTHERGAS with Nancy Linear Form)
Thermo 'ch3/ch2/ch2/ch2(.)' '1-butyl'
The default molecule format is the Nancy Linear Form and the default method is JTHERGAS. The output is to the terminal:
BensonThermodynamicBase(c-(h)/3-(c)): Reference: 'Benson20210129'H298: -10.01 S298: 30.29 [ 300.0, 7.74] [ 400.0, 9.24] [ 500.0, 10.62] [ 600.0, 12.84] [ 800.0, 14.59] [ 1000.0, 14.77] [ 1500.0, 17.58]BensonThermodynamicBase(c-(h)/2-(c)/2): Reference: 'Benson20210129'H298: -5.00 S298: 9.65 [ 300.0, 5.59] [ 400.0, 7.08] [ 500.0, 8.43] [ 600.0, 9.53] [ 800.0, 11.23] [ 1000.0, 12.48] [ 1500.0, 14.25]BensonThermodynamicBase(c-(h)/2-(c)/2): Reference: 'Benson20210129'H298: -5.00 S298: 9.65 [ 300.0, 5.59] [ 400.0, 7.08] [ 500.0, 8.43] [ 600.0, 9.53] [ 800.0, 11.23] [ 1000.0, 12.48] [ 1500.0, 14.25]BensonThermodynamicBase(c-(h)/3-(c)): Reference: 'Benson20210129'H298: -10.01 S298: 30.29 [ 300.0, 7.74] [ 400.0, 9.24] [ 500.0, 10.62] [ 600.0, 12.84] [ 800.0, 14.59] [ 1000.0, 14.77] [ 1500.0, 17.58]BensonThermodynamicBase(Disassociation Energy From: n-c4h9): Reference: 'Disassociation Energy'H298: 100.90 S298: 0.00BensonThermodynamicBase(Translational Energy Correction): Reference: 'Radical Correction'H298: 0.00 S298: -0.10BensonThermodynamicBase(Spin Contribution: Rln(2) = (1.98587755)*(0.6931471805599453)): Reference: 'Radical Correction'H298: 0.00 S298: 1.38BensonThermodynamicBase(Hydrogen Radical): Reference: 'Radical Correction'H298: -52.10 S298: 0.00BensonThermodynamicBase(InternalSymmetry-B(B1)(B2)(B2)(B2) (3)): Reference: 'Symmetry'H298: 0.00 S298: -2.18BensonThermodynamicBase(InternalSymmetry-B(B1)(B2)(B2) (2)): Reference: 'Symmetry'H298: 0.00 S298: -1.38BensonThermodynamicBase(Correction: CH-Stretch: 3100.0 Count=-3.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.00 [ 300.0, -0.00] [ 400.0, -0.01] [ 500.0, -0.06] [ 600.0, -0.19] [ 800.0, -0.71] [ 1000.0, -1.40] [ 1500.0, -2.99]BensonThermodynamicBase(Correction: CCHSecondary(tw)-Bend: 1150.0 Count=-2.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.10 [ 300.0, -0.49] [ 400.0, -1.12] [ 500.0, -1.71] [ 600.0, -2.18] [ 800.0, -2.81] [ 1000.0, -3.18] [ 1500.0, -3.59]BensonThermodynamicBase(Correction: CCHPrimary(tw)-Bend: 1150.0 Count=2.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.10 [ 300.0, 0.49] [ 400.0, 1.12] [ 500.0, 1.71] [ 600.0, 2.18] [ 800.0, 2.81] [ 1000.0, 3.18] [ 1500.0, 3.59]BensonThermodynamicBase(Correction: CCHPrimary(rk)-Bend: 1150.0 Count=-2.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.10 [ 300.0, -0.49] [ 400.0, -1.12] [ 500.0, -1.71] [ 600.0, -2.18] [ 800.0, -2.81] [ 1000.0, -3.18] [ 1500.0, -3.59]BensonThermodynamicBase(Correction: CCHSecondary-Bend: 1150.0 Count=1.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.05 [ 300.0, 0.24] [ 400.0, 0.56] [ 500.0, 0.86] [ 600.0, 1.09] [ 800.0, 1.41] [ 1000.0, 1.59] [ 1500.0, 1.80]BensonThermodynamicBase(Correction: CCHSecondary(rk)-Bend: 700.0 Count=-1.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.30 [ 300.0, -0.84] [ 400.0, -1.20] [ 500.0, -1.43] [ 600.0, -1.58] [ 800.0, -1.74] [ 1000.0, -1.83] [ 1500.0, -1.91]BensonThermodynamicBase(Correction: CHH-Bend: 1450.0 Count=-3.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.04 [ 300.0, -0.27] [ 400.0, -0.89] [ 500.0, -1.65] [ 600.0, -2.37] [ 800.0, -3.48] [ 1000.0, -4.19] [ 1500.0, -5.08]BensonThermodynamicBase(Correction: CCHSecondary(op)-Bend: 700.0 Count=1.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.30 [ 300.0, 0.84] [ 400.0, 1.20] [ 500.0, 1.43] [ 600.0, 1.58] [ 800.0, 1.74] [ 1000.0, 1.83] [ 1500.0, 1.91]BensonThermodynamicBase(Correction: CHH-Bend-RadicalCompC.HH: 1450.0 Count=1.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.01 [ 300.0, 0.09] [ 400.0, 0.30] [ 500.0, 0.55] [ 600.0, 0.79] [ 800.0, 1.16] [ 1000.0, 1.40] [ 1500.0, 1.69]BensonThermodynamicBase(Correction: CCHSecondary(tw)-BendRadical.CCH: 1150.0 Count=2.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.10 [ 300.0, 0.49] [ 400.0, 1.12] [ 500.0, 1.71] [ 600.0, 2.18] [ 800.0, 2.81] [ 1000.0, 3.18] [ 1500.0, 3.59]BensonThermodynamicBase(Correction: CCHSecondary(rk)-BendRadical.CCH: 700.0 Count=1.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.30 [ 300.0, 0.84] [ 400.0, 1.20] [ 500.0, 1.43] [ 600.0, 1.58] [ 800.0, 1.74] [ 1000.0, 1.83] [ 1500.0, 1.91]BensonThermodynamicBase(Correction: CH-Stretch-RadicalCompC.H: 3100.0 Count=2.0): Reference: 'Vibration Correction'H298: 0.00 S298: 0.00 [ 300.0, 0.00] [ 400.0, 0.01] [ 500.0, 0.04] [ 600.0, 0.13] [ 800.0, 0.47] [ 1000.0, 0.93] [ 1500.0, 1.99]BensonThermodynamicBase(Correction: CCHSecondary-BendRadical.CCH: 1150.0 Count=-1.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.05 [ 300.0, -0.24] [ 400.0, -0.56] [ 500.0, -0.86] [ 600.0, -1.09] [ 800.0, -1.41] [ 1000.0, -1.59] [ 1500.0, -1.80]BensonThermodynamicBase(Correction: CCHSecondary(op)-BendRadical.CCH: 700.0 Count=-1.0): Reference: 'Vibration Correction'H298: 0.00 S298: -0.30 [ 300.0, -0.84] [ 400.0, -1.20] [ 500.0, -1.43] [ 600.0, -1.58] [ 800.0, -1.74] [ 1000.0, -1.83] [ 1500.0, -1.91]BensonThermodynamicBase(Total): Reference: 'Sum Total'H298: 18.78 S298: 77.57 [ 300.0, 26.48] [ 400.0, 32.04] [ 500.0, 36.98] [ 600.0, 43.10] [ 800.0, 49.09] [ 1000.0, 51.24] [ 1500.0, 59.28]method= THERGASmolform= NANCYmoldescription= ch3/ch2/ch2/ch2(.)moleculename= 1-butyloutputform= Standardoutdetail= detailedoutfile= nullExample: THERM calculation
Example: THERM calculation
Thermo 'ch3/ch2/ch2/ch2(.)' '1-butyl' method=THERM
The parameter method=THERM selects the THERM method for calculation:
Example: Benson Radical
Example: Benson Radical
Thermo 'ch3/ch2/ch2/ch2(.)' '1-butyl' method=BensonRadical
The output is:
BensonThermodynamicBase(c-(h)/3-(c)): Reference: 'Benson20210129'H298: -10.01 S298: 30.29 [ 300.0, 7.74] [ 400.0, 9.24] [ 500.0, 10.62] [ 600.0, 12.84] [ 800.0, 14.59] [ 1000.0, 14.77] [ 1500.0, 17.58]BensonThermodynamicBase(c-(h)/2-(c)/2): Reference: 'Benson20210129'H298: -5.00 S298: 9.65 [ 300.0, 5.59] [ 400.0, 7.08] [ 500.0, 8.43] [ 600.0, 9.53] [ 800.0, 11.23] [ 1000.0, 12.48] [ 1500.0, 14.25]BensonThermodynamicBase(c/r-(c)-(h)/2): Reference: 'BensonRadicals'H298: 35.82 S298: 30.70 [ 300.0, 5.99] [ 400.0, 7.24] [ 500.0, 8.29] [ 600.0, 9.13] [ 800.0, 10.44] [ 1000.0, 11.47] [ 1500.0, 13.14]BensonThermodynamicBase(c-(c/r)-(c)-(h)/2): Reference: 'BensonRadicals'H298: -4.95 S298: 9.42 [ 300.0, 5.50] [ 400.0, 6.95] [ 500.0, 8.25] [ 600.0, 9.35] [ 800.0, 11.07] [ 1000.0, 12.34] [ 1500.0, 14.25]BensonThermodynamicBase(InternalSymmetry-B(B1)(B2)(B2)(B2) (3)): Reference: 'Symmetry'H298: 0.00 S298: -2.18BensonThermodynamicBase(InternalSymmetry-B(B1)(B2)(B2) (2)): Reference: 'Symmetry'H298: 0.00 S298: -1.38BensonThermodynamicBase(Total): Reference: 'Sum Total'H298: 15.86 S298: 76.50 [ 300.0, 24.82] [ 400.0, 30.51] [ 500.0, 35.59] [ 600.0, 40.85] [ 800.0, 47.33] [ 1000.0, 51.06] [ 1500.0, 59.22]method= BensonRadicalmolform= NANCYmoldescription= ch3/ch2/ch2/ch2(.)moleculename= 1-butyloutputform= Standardoutdetail= detailedoutfile= nullHTML output
<html lang="en"><head> <meta charset="utf-8">HTML output
<title>Molecule: ch3/ch2/ch2/ch2(.) Thermodynamics: THERM</title> <meta name="description" content="Thermodynamic Calculation"> <meta name="Edward S. Blurock" content="JThermodynamics">
</head>
<body><h1>Molecule: ch3/ch2/ch2/ch2(.) Thermodynamics: THERM</h1><table style="width:100%"><tr><th>Name</th> <th>Reference</th> <th>Hf298</th> <th>S298</th> <th>Cp300</th> <th>Cp400</th> <th>Cp500</th> <th>Cp600</th> <th>Cp800</th> <th>Cp1000</th> <th>Cp1500</th> </tr><tr><td>"c-(h)/3-(c)"</td> <td>"Benson20210129"</td> <td>-10.01</td> <td> 30.29</td> <td> 7.74</td> <td> 9.24</td> <td> 10.62</td> <td> 12.84</td> <td> 14.59</td> <td> 14.77</td> <td> 17.58</td> </tr><tr><td>"c-(h)/2-(c)/2"</td> <td>"Benson20210129"</td> <td> -5.00</td> <td> 9.65</td> <td> 5.59</td> <td> 7.08</td> <td> 8.43</td> <td> 9.53</td> <td> 11.23</td> <td> 12.48</td> <td> 14.25</td> </tr><tr><td>"c-(h)/2-(c)/2"</td> <td>"Benson20210129"</td> <td> -5.00</td> <td> 9.65</td> <td> 5.59</td> <td> 7.08</td> <td> 8.43</td> <td> 9.53</td> <td> 11.23</td> <td> 12.48</td> <td> 14.25</td> </tr><tr><td>"c-(h)/3-(c)"</td> <td>"Benson20210129"</td> <td>-10.01</td> <td> 30.29</td> <td> 7.74</td> <td> 9.24</td> <td> 10.62</td> <td> 12.84</td> <td> 14.59</td> <td> 14.77</td> <td> 17.58</td> </tr><tr><td>"InternalSymmetry-B(B1)(B2)(B2)(B2) (9)"</td> <td>"Symmetry"</td> <td> 0.00</td> <td> -4.36</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> </tr><tr><td>"RCCJ"</td> <td>"HBI-Bozzelli"</td> <td>101.10</td> <td> 1.24</td> <td> -0.77</td> <td> -1.36</td> <td> -1.91</td> <td> -2.40</td> <td> -3.16</td> <td> -3.74</td> <td> -3.74</td> </tr><tr><td>"Spin Contribution: Rln(2) = (1.98587755)*(0.6931471805599453)"</td> <td>"Radical Correction"</td> <td> 0.00</td> <td> 1.38</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> </tr><tr><td>"Hydrogen Radical"</td> <td>"Radical Correction"</td> <td>-52.10</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> <td> 0.00</td> </tr><tr><td>"Total"</td> <td>"Sum Total"</td> <td> 18.98</td> <td> 78.13</td> <td> 25.89</td> <td> 31.28</td> <td> 36.19</td> <td> 42.34</td> <td> 48.48</td> <td> 50.76</td> <td> 59.92</td> </tr></table></body></html>
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