The purpose of this project is to calculate thermodynamic quantities, to be used in combustion mechanisms, from 2D-graphical forms of the molecular species. This project has its roots in the THERGAS system of Frederique Battin-LeClerc where in a cooperation JTHERGAS was developed. The current project is to re-implement JTHERGAS on a cloud platform providing all the tools needed for individually or collectively enhance the basic database of information needed to perform the calculation. The cloud version is found at http://www.2dthermodynamics.info (though due to cost reasons, the database may be offline, contact Edward S. Blurock, if you are interested). Further information (also under development) is available here.
JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML.
This is the general structure of the 'original' JTHERGAS. The key elements that will stay similar in the cloud version are the Web-Services interface, an API to access data and to calculate thermodynamics, and the fundamental algorithm used to calculating thermodyanamics.
Benson rules consists of identifying all the center atoms (in the form shown in equation 1) and adding up all their contributions. The JTHERGAS system has a library consisting of 366 Benson rules, the majority of which correspond to the tables in Benson's book:
1. Table A.1: Hydrocarbons
2. Table A.2 Oxygen-containing Compounds
3. Table A.3 Nitrogen-containing Compounds
4. Table A.4 Halogen-containing Compounds
5. Table A.5 Sulfur-containing Compounds
6. Table A.6 Organometallic, Organophosphorous, Compounds
Recognition of Symmetry within the molecule
One of the second order corrections involves the automatic recognition of molecular symmetries: internal and external symmetry and optical isomers. Symmetry is inherently based on the three dimensional structure. However, the information available to JTHERGAS is a molecular graph. The three dimensional information has to be inferred and assumptions have to be made. This is a design decision that has to be made when creating the database for symmetry structures.
The generalized procedure can be said to be:
1. Match the symmetry structure within the target
2. For each match, identify the groups attached to each of the unspecified atoms (labeled R in the example).
3. Identify which ligands are the same and group them together.
4. Identify the symmetry of each group or whether the group is linear or not.
5. Condense this information into a table of groups where each group has the number of equivalent ligands and the symmetry or linearity of ligand.
Calculations of Radicals
The method of calculating radical thermodynamics in JTHERGAS is based on the difference between the radical and the parent molecule with a hydrogen added. The full Benson method is applied to the parent molecule (Benson rules with corrections). For the radical only the corrective terms are calculated:
1. Internal Symmetry
2. External Symmetry
3. Optical Isomers
4. Steric Corrections
These are calculated for the radical in the same way as for the parent molecule. The difference of these corrections are added into the final result. In addition, for the radical species the following are estimated:
1. Dissociation Energy
2. Loss of Vibrational modes
3. Loss of Rotational modes
The vibrational and rotational modes are translated to corrections to the temperature dependent heat capacities and to entropies. In this implementation, the loss of rotational modes is neglected. This analysis will appear in later implementations.