OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms.

An ontology for capturing both data and the semantics of chemical kinetic reaction mechanisms has been developed. Such mechanisms can be applied to simulate and understand the behavior of chemical processes, for example, the emission of pollutants from internal combustion engines. An ontology development methodology was used to produce the semantic model of the mechanisms, and a tool was developed to automate the assertion process. As part of the development methodology, the ontology is formally represented using a web ontology language (OWL), assessed by domain experts, and validated by applying a reasoning tool. The resulting ontology, termed OntoKin, has been used to represent example mechanisms from the literature. OntoKin and its instantiations are integrated to create a knowledge base (KB), which is deployed using the RDF4J triple store. The use of the OntoKin ontology and the KB is demonstrated for three use cases-querying across mechanisms, modeling atmospheric pollution dispersion, and as a mechanism browser tool. As part of the query use case, the OntoKin tools have been applied by a chemist to identify variations in the rate of a prompt NOx formation reaction in the combustion of ammonia as represented by four mechanisms in the literature.

An Ontology and Semantic Web Service for Quantum Chemistry Calculations.

The purpose of this article is to present an ontology, termed OntoCompChem, for quantum chemistry calculations as performed by the Gaussian quantum chemistry software, as well as a semantic web service named MolHub. The OntoCompChem ontology has been developed based on the semantics of concepts specified in the CompChem convention of Chemical Markup Language (CML) and by extending the Gainesville Core (GNVC) ontology. MolHub is developed in order to establish semantic interoperability between different tools used in quantum chemistry and thermochemistry calculations, and as such is integrated into the J-Park Simulator (JPS)-a multidomain interactive simulation platform and expert system. It uses the OntoCompChem ontology and implements a formal language based on propositional logic as a part of its query engine, which verifies satisfiability through reasoning. This paper also presents a NASA polynomial use-case scenario to demonstrate semantic interoperability between Gaussian and a tool for thermodynamic data calculations within MolHub.

First-Principles Thermochemistry for the Thermal Decomposition of Titanium Tetraisopropoxide.

The thermal decomposition of titanium tetraisopropoxide (TTIP) is investigated using quantum chemistry, statistical thermodynamics, and equilibrium composition analysis. A set of 981 Ti-containing candidate species are proposed systematically on the basis of the thermal breakage of bonds within a TTIP molecule. The ground state geometry, vibrational frequencies and hindrance potentials are calculated for each species at the B97-1/6-311+G(d,p) level of theory. Thermochemical data are computed by applying statistical thermodynamics and, if unknown, the standard enthalpy of formation is estimated using balanced reactions. Equilibrium composition calculations are performed under typical combustion conditions for premixed flames. The thermodynamically stable decomposition products for different fuel mixtures are identified. A strong positive correlation is found between the mole fractions of Ti species containing carbon and the TTIP precursor concentration.