JThermodnamicsCloud Standard Data
JThermodynamicsCloud is built to be a flexible database of thermodynamics data. But there is a standard database that can be used as basis for further database development.
This page gives an overview of the standard database of JThermodynamicsCloud.
The current version of the standard version is found in the resources of a github project ChemConnectCoreOntologyBase.
A standard version of the standard database can be found on the Open Science Framework website, where each dataset is assigned a DOI number.
Meta Atoms
An important concept within JTHERGAS is that of a meta-atom. This is where the basic
atom node information (in the graphical representation) is extended beyond the ‘normal’
molecular atom representation mentioned previously. Meta-atoms are used at many levels
within JTHERGAS. All meta-atoms within JTHERGAS are defined through the database
and is one of the keys to JTHERGAS’s flexibility.
Two examples of meta atoms are the extended atom definitions of the atoms in the definition
of a Benson rule and the Nancy linear forms. More complex meta-atoms exist within
JTHERGAS such as one more a methyl (CH3) or a phenyl (aromatic ring) group which can
be used to simplify molecular matching.
One of the flexibilities within the JTHERGAS system is that all the meta-atoms are not
hard-coded within the library, but are defined within the extendable database. With each
meta-atom there is associated a complete molecular structure. This means that any new meta
atom can be defined when needed without modifying the base code. Figure 2 shows the
meta atom structures in the database for a doubly bonded carbon and a carboxyl group. The
structure on the right is used to describe the doubly bonded carbon, which can have the meta
atom name Cd, and the structure on the left describes a multi-atom carbonyl (ketone) meta
atom, co.
More information about the structure of the input can be found in JTHERGAS: Thermodynamic estimation from 2D graphical representations of molecules, Edward S. Blurock, Valérie Warth, Xavier Grandmougin, Roda Bounaceur, Pierre-Alexandre Glaude, Frédérique Battin-Leclerc
Symmetry
The source of these rules is an extropolation of TherGas rules for symmetry contributions as outlined in the thesis:
More information about the structure of the input can be found in JTHERGAS: Thermodynamic estimation from 2D graphical representations of molecules, Edward S. Blurock, Valérie Warth, Xavier Grandmougin, Roda Bounaceur, Pierre-Alexandre Glaude, Frédérique Battin-Leclerc
External Symmetry
External Symmetry Rules for Carbon Atom.
English