The temperature dependent calculation of a molecular species is done by adding up the contributions of different types of fundamental data. For example, the basis of the method are the additivity rules of the Benson. The entire set of Benson rules represent one type of fundamental data and are stored in JThermodynamicsCloud's database. The other types of fundamental data are, for example, are several types of symmetry contributions, steric contributions and ring strain contributions.
Each contribution to the temperature dependent thermodyanmic calculation is represented by an object in the fundamental data. The data structures making up the fundamental data is what makes JThermodynamics unique. The data is represented in such a way that new fundamental data contributions can be added to the thermodynamic calculation by additions of objects to the database. The fundamental data, for the most part, consists of a 2D-graphical substructure and its contribution to the thermodynamics. To identify a contribution, the substructure is matched within the radical or species being analysed. If there is a match then the corresponding contribution is added to the total thermodynamics of the species.
The flexibility and adaptability of the calculation to include new structural groups is owing to the fact that the structures are represented as 2D-graphical structures which can be stored in the database along with how they contribute to the thermodynamics.
Within Jthermodynamics, there are 6 collections of fundamental data. The type of data determines how the correspondig information contributes to the total thermodynamics:
ThermodynamicBensonRuleDefinition The structure is the classic Benson Rule with a center atom and its connection with its immediate neighboring atoms. These neighboring atoms can be single atoms or functional groups.
JThermodynamics2DSubstructureThermodynamics:The steric hindrance, nearest neighbor effects and ring strain contributions are represented as 2D-graphical substructures which represent the effect. In addition, the Hydrogen Bond Increment (HBI) structures are also included. For example, the ring strain of a 3-membered ring is represented by a general, meaning any substitution is allowed on the ring atoms, three membered ring. If this structure matches, then the thermodynamic contribution is added in.
JThermodynamicsSymmetryStructureDefinition These are the structures and contributions describing the internal, external and optical. Each symmetry contribution is represented by a substructure with conditions. For example, the external symmetry around a carbon is represented by a general carbon substructures. The four connecting structures are then analyzed. If, for example, all four connecting structures are the same and linear, the total external symmetry contribution would be 12 and this is translated into a thermodynamic contribution to enthalpy.
JThermodynamicsVibrationalStructure: In the THERGAS method, the loss of vibrational modes is analyzed. A vibrational mode is represented by a substructure representing that mode and a frequency. The database contains, for example, all the vibrational modes listed by Benson.
JThermodynamicsDisassociationEnergyOfStructure:. The disassociation energy is represented by a substructure with a single radical. The disassociation energy is calculated by finding the largest radical substructure that can be matched in the molecular species.
JThermodynamicsMetaAtomDefinition These are definitions of functional groups which are treated as a single entity or atom. Meta atoms can be benson rule structures, function groups, such as co and co2, used in definition. Another type of meta-atom is the linear structure definition. In the recognition of linear structures, the linear atom structure is substituted by a single meta-atom. This process is repeated. If, after all iterations are completed, there is one linear meta-atom left, then the whole substructure is linear. This operation is used in connection with symmetry calculations.
The fundamental data type, ThermodynamicBensonRuleDefinition , holds the information about the benson rules. The first order approximation to thermodynamics based on a structure defined as a central atom and its immediate environment, usually the atom directly connected to the central atom. This is the Benson additivity principle and was developed by Benson as early as 1969. This principle says that the thermodynamics of a molecule can be estimated by the contributions of each individual (non-hydrogen) atoms in a molecule. The atoms are distinguished first by the atomic number and then by which atoms it is bonded to (here hydrogens are included). With each of these atom descriptions, there is a temperature dependent (through the heat capacity) contribution to the thermodynamics. Each of these contributions are added up to form the total thermodynamic description.
The structure is defined as a 'center atom' and a list of connecting structures. The connecting structures can be a single atom, defined as its atomic number, or a 'meta-atom', where the structure can be made up of a multi-atom functional group and has one connection to the central atom. The meta-atoms represent the molecular environment beyond the central atom. Some examples are the central atom bonded to a double bonded carbon, a triple bonded carbon, an aldehyde or ketone group, peroxy group, etc. The meta-atom definition has just enough elements to describe the functional group. For example, if the central atom is connected to an a ketone, then the meta atom would consist of a double bonded CO where one bond is to the central atom. Associated with this structure is the standard set of temperature dependent thermodynamic information.
The fundamental data type, JThermodynamics2DSubstructureThermodynamics, represents on of the fundamental corrections to the first order Benson rules based on structures that influence the thermodynamics. Each correction has a 2D-graphical substructure and the associated correction, in the form of the standard set of temperature dependent thermodynamic information. In the calculation, the molecule is tested, through graph isomorphism, to see whether the substructure can be matched. If there is a match, then the assocated thermodynamic correction is added. Currently there are two types of corrections:
Ring strain: Each of the corrections is represented by a ring substructure. The thermodynamic data represents how that structure effects the thermodynamics.
Steric Corrections: These are structures that represent, as well as can be with a 2D-graphical representation, the steric corrections. The whole structure involved in the steric interaction is included in the correction.
The fundamental type, JThermodynamicsSymmetryStructureDefinition, represents the symmetry correction. The symmetry connection is represented by a substructure with generalized connections. For example, the structure associated with the symmetry around a carbon atom is a central carbon bonded with four substructure elements. Associated with this structure is a table specifying the which of these substructure elements have to be equivalent to match the symmetry being modeled. For example, if the carbon substructure is matched with the middle carbon of propane, then the substructure elements would consist of two sets of equivalent substructures. One set would be the two connected hydrogen atoms and the other set would be the two methyl groups. Associated with this substructure and table is the actual symmetry element. In the propane example, this matches a specification with symmetry 2 and the type of symmetry represented is an external symmetry. This symmetry number is then used as an standard entropy correction.
The fundamental type, JThermodynamicsVibrationalStructure, represents the contributions of vibrational modes. In the THERGAS calculation the difference of vibrational modes between a radical and its parent (with the hydrogen bonded where the radical was) denotes a contribution to the final radical thermodynamics. The vibrational mode data object is represented by a substructure to be matched in the molecule, a symmetry mode (some mode structures are symmetrical and this symmetry must be accounted for) and a frequency. A given vibrational mode is detected by matching, graph isomorphism, the structure in the molecule. The number of matches is divided by the symmetry mode. This result combined with the frequency gives the correction to the thermodynamics.
The fundamental type, JThermodynamicsDisassociationEnergyOfStructure, represents the contribution of the hydrogen disassocation energy in the THERGAS calculation. The data object consists of radical substructure and a parameter, with value, error bounds and unit specification, representing the disassociation energy. In the calculation, the radical substructure is matched within the target radical molecule. The value of the disassociation energy of the largest radical substructure matched is used as the correction.
The fundamental type, JThermodynamicsMetaAtomDefinition, is used to define substructures that, from the 2d-graphical representation, condensed into a single atom, called a meta-atom. One example of a meta atom is the CO group, meaning a carbon double-bonded with an oxygen atom. This CO meta-atom can be singly bonded to two substructures. For example, and aldehyde can be represented by this meta atom bonded to two substructures, one being if the bonding atom in one substructure is a carbon atom and the other substructure is a hydrogen. Meta-atom are used in the following contexts:
Benson rules: A Benson rule consists of a central atom bonded with a set of other atoms. The atoms defined within a Benson rule can either be a single atom or meta-atom representing a substructure.
Nancy Linear Form: The Nancy Linear Form (NLF) is a 'line formation' representation of a molecule, similar to SMILES. In the NLF a meta-atom can be used to within the notation to denote the corresponding substructure.
Linear Molecule Substructures: These meta-atoms are used in the recognition of linear molecule structures. Each meta-atom substructure is linear, for example, two carbons bonded with a triple bond. In the linear molecule recognition algorithm is based on the principle if two linear structures are bonded together, then the entire structure is linear. For example, the molecule CHCCCH, is two triple bonded carbons bonded together. In the recognition algorithm, the triple-bonded carbons would be substituted. And since the entire molecule is made up of linear substructures (linear meta-atoms), the entire molecule is linear.