THERMOSET Calculation

MOLSET Calculation

JTHERMODYNAMICS offers three methods to compute the temperature dependent thermodynamics for a molecule. The general command is:

THERMOSET MolNameList

where:

THERMO: Keyword for computing thermodynamics
MolNameList: The molecule in the form specified by Form (it might have to be put into quotes).

The form of the MolNameList is single lines where each line has two parameters (delimited by spaces):

MoleculeDescriptor MoleculeName

For example:

ch3/ch2/ch2/ch2(.) 1-butylch3/ch2/ch2/ch2/ch2(.) 1-pentylch3/ch2/ch2/ch2/ch2/ch2(.) 1-hexylch3/ch2/ch2/ch2/ch2/ch2/ch2(.) 1-heptyl

The other parameters are as for the other line commands. The ones that are particularly important are reviewed here.

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 MolNameList file:

Nancy: The Nancy linear form
IUPAC: The IUPAC standard
SMILES: The SMILES notation

Another parameter of use is the form of the output (OutputForm) and the name of the file where the output can go (OutputFile). The OutputForm determines the format of the output, Standard, csv, html, and wiki (and readable for files that can be read in as input - not always implemented). The OutputFile parameter would place the information in a file.

Example: CSV file with THERGAS

With a mollist.lst file having the following content:

ch3/ch2/ch2/ch2(.) 1-butylch3/ch2/ch2/ch2/ch2(.) 1-pentylch3/ch2/ch2/ch2/ch2/ch2(.) 1-hexylch3/ch2/ch2/ch2/ch2/ch2/ch2(.) 1-heptyl

the command:

ThermoSet molset.lst method=THERGAS OutputFormat=csv OutputFile=Radicals.csv

produces a file, Radicals.csv (in the directory where the command was run) with the following content:

Name,"Reference" ,"Hf298" ,"S298" ,"Cp300" ,"Cp400" ,"Cp500" ,"Cp600" ,"Cp800" ,"Cp1000" ,"Cp1500" "ch3/ch2/ch2/ch2(.)",""1-butyl"" ," 18.78" ," 77.57" ," 26.48" ," 32.04" ," 36.98" ," 43.10" ," 49.09" ," 51.24" ," 59.28" "ch3/ch2/ch2/ch2/ch2(.)",""1-pentyl"" ," 13.78" ," 87.24" ," 32.07" ," 39.12" ," 45.41" ," 52.63" ," 60.32" ," 63.72" ," 73.53" "ch3/ch2/ch2/ch2/ch2/ch2(.)",""1-hexyl"" ," 8.78" ," 96.90" ," 37.66" ," 46.20" ," 53.84" ," 62.16" ," 71.55" ," 76.20" ," 87.78" "ch3/ch2/ch2/ch2/ch2/ch2/ch2(.)",""1-heptyl"" ," 3.78" ,"106.56" ," 43.25" ," 53.28" ," 62.27" ," 71.69" ," 82.78" ," 88.68" ,"102.03"

Example: html file with THERM

With a mollist.lst file having the following content:

ch3/ch2/ch2/ch2(.) 1-butylch3/ch2/ch2/ch2/ch2(.) 1-pentylch3/ch2/ch2/ch2/ch2/ch2(.) 1-hexylch3/ch2/ch2/ch2/ch2/ch2/ch2(.) 1-heptyl

the command:

ThermoSet molset.lst method=THERM OutputFormat=html OutputFile=Radicals.html

produces a file, Radicals.csv (in the directory where the command was run) with the following content:

<html lang="en"><head> <meta charset="utf-8">
<title>MoleculeSet: /Users/edwardblurock/molset.lst Thermodynamics: THERM</title> <meta name="description" content="Thermodynamic Calculation"> <meta name="Edward S. Blurock" content="JThermodynamics">
</head>
<body><h1>MoleculeSet: /Users/edwardblurock/molset.lst 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>ch3/ch2/ch2/ch2(.)</td> <td>1-butyl</td> <td> 16.33</td> <td> 80.75</td> <td> 25.88</td> <td> 30.16</td> <td> 34.55</td> <td> 40.59</td> <td> 46.90</td> <td> 49.48</td> <td> 58.64</td> </tr><tr><td>ch3/ch2/ch2/ch2/ch2(.)</td> <td>1-pentyl</td> <td> 11.33</td> <td> 89.03</td> <td> 31.47</td> <td> 37.24</td> <td> 42.98</td> <td> 50.12</td> <td> 58.13</td> <td> 61.96</td> <td> 72.89</td> </tr><tr><td>ch3/ch2/ch2/ch2/ch2/ch2(.)</td> <td>1-hexyl</td> <td> 6.33</td> <td>100.05</td> <td> 37.06</td> <td> 44.32</td> <td> 51.41</td> <td> 59.65</td> <td> 69.36</td> <td> 74.44</td> <td> 87.14</td> </tr><tr><td>ch3/ch2/ch2/ch2/ch2/ch2/ch2(.)</td> <td>1-heptyl</td> <td> 1.33</td> <td>108.33</td> <td> 42.65</td> <td> 51.40</td> <td> 59.84</td> <td> 69.18</td> <td> 80.59</td> <td> 86.92</td> <td>101.39</td> </tr></table></body></html>

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