JThermodynamicsCloud is the fourth generation of the development of the calculation of temperature dependent thermodynamic properties from 2D-graphical (Lewis structures) representations ^5,6,19. The implementation calculates thermodynamics of radical species based on three fundamental techniques, THERGAS ²⁰, Benson Radical Rules ⁵ and THERM ⁶. All these methods are based on structure additivity rules, meaning that the thermodynamic contributions of local structures can be added together to the final total temperature dependent thermodynamics of the species. These methods differ primarily on how they calculate radical species. The temperature dependent thermodynamics of the parent molecule are calculated in the same way.  The symmetry of the molecule and radicals are determined by JThermodynamics based on the methods and data of THERGAS and Benson’s book.

The evolution of JThermodynamics cloud can be seen as starting with the group additivity rules outlined by Benson and the HBI method of Bozzelli, through increasing levels of software development:

Group Additivity: The basis of the calculation is the additivity method devised by Benson. The basis of the method is that the temperature dependent thermodynamics of a molecular species can be calculated by adding (additivity rules) up structural features. The library of these structural features constitutes the database from which the calculation is performed.

THERGAS: This is a software implementation of Benson’s method from 1995 for radical species. THERGAS calculates radicals based on the difference between the parent molecule (hydrogen added to radical) and the radical, including the disassociation energy. The changes in symmetry, vibrational moments and rotational energies are found and used to correct both the entropy and the heat capacity values. Energetic contributions due to disassociation energies and steric energies are taken into account relative to the parent molecule.

THERM: Ritter and Bozzelli implemented the Hydrogen Bond Increment with the THERM method (THermo Estimation for Radicals and Molecules), and is an extension of the Benson additivity rule method to radical species. It differs from THERGAS in that it has a single structure which accounts for the differences between the radical and the parent molecule (the radical with the hydrogen added): ‘Properties for radical and biradical species are calculated by applying bond dissociation increments to a stable parent molecule to reflect loss of H atom’.

JTHERGAS: JTHERGAS is a re-implementation of the THERGAS method, whose goal was to make modifications to the fundamental data more flexible and the fundamental data itself more transparent (the beginnings of FAIR data practices). This was done by translating each group correction into a 2D-graphical substructure (as defined by the Chemical Development Toolkit, CDK ²²). This substructure is then linked to an associated correction. If the substructure is recognized within the species to be calculated, then the correction is applied. New corrections could be easily added by creating new substructures and their corresponding values through input files or the web interface. The use of these substructures transfers all updates to the mySQL database and not to the implementation (platform independent programmed in JAVA). The major advance was the correction representation (2D-graphical, Lewis structures) and the use of the database (and the web interface) to clearly delineate the implementation from the data used for the calculation.

JThermodynamics: JThermodynamics is the third-generation implementation following JTHERGAS. It uses the same calculational methodology and continues to store the relevant data in a mySQL database. Group corrections using the Hydrogen Bond Increment (HBI) structures and methodology were also added. The software technical advance of this implementation was to further debug and cleanup the methodology and to create a stand-alone platform independent application based on command lines at the terminal that could be easily downloaded and installed on the user’s local computer ²³. JThermodynamics has been used to further advance the database of fundamental data.

JThermodynamicsCloud: JThermodynamicsCloud is the fourth generation of development and is built upon JThermodynamics. Its primary advancements are putting the implementation, including the database, in a SaaS Cloud service and the extensive use of ontologies to describe all data objects within the system and to drive the system. In addition, each user can create and manage their own database. Also, it promotes data management principles, for example the use of transactions, that map and link the entire journey of the data from source files to the fundamental data used for the calculation. The state-of-the-art data management techniques used emphasize data provenance, data lineage and FAIR data practices. How this is accomplished is the theme of this paper.