Data Formats for Elementary Gas-Phase Kinetics: Part 2. Unique Representations of Reactions

Abstract

A method of extending the IUPAC International Chemical Identifier (InChI) to describe and identify elementary reactions in a standard computer-readable notation is developed. Denoted InChI-ER, the method is based on the existing InChI formalism, with certain refinements for the better identification of molecular entities as proposed in Part 1 published previously in this journal. Using this base notation, an identifier for elementary reactions on a molecular level is created by adding additional layers in a conceptually similar and extensible manner. Two of the layers describe the atoms involved in the transition state and the connectivity changes that occur during the reaction. Additional layers classify the reactions on the basis of the connectivity changes, providing chemical information useful in organizing and searching kinetic data sets found in databases or used in detailed kinetic modeling. Important aspects of the method are that the proposed layers are optional, that they do not interfere with existing InChI specifications, and that they retain extensibility should further refinements be desired in the future. C 2015 Wiley Periodicals, Inc. Int J Chem Kinet 47: [334][335][336][337][338][339][340][341][342][343][344][345][346][347][348][349][350] 2015

Data Formats for Elementary Gas Phase Kinetics, Part 3: Reaction Classification

“…We provide in Tables III and IV a list of six types (reaction classes) of unimolecular reactions involving molecular eliminations, the generic form of the reaction, an example reaction for each type, and the corresponding Reaction Connectivity and Reaction Class layer notations for each. Table IV [3,4]. The reaction can be written generically as C(O)C(H) → C=C + OH and the Reaction Class notation [CC-OH] reflects this.…”

“…Table IV illustrates the 1,1-elimination of H 2 from ethane. Analogous to the 1,2-elimination notation, [2][3]4] indicates that atoms 3 and 4 are breaking their bonds with atom 2resulting in the formation of just one new bond: a H-H single bond [3,4] plus the formation of a carbene (lone pair) on the carbon atom (#2)-the electrons are paired on the carbon atom rather than in a bond. The reaction can be written generically as C(H)H) → :C + H2, and…”

“…For the cycloelimination reaction for cyclohexene (#5 in Table IV), the C-C bonds [3][4][5] and [4][5][6] are broken resulting in a new C=C double bond [5][6] (and elimination of ethylene) and also a new double bond in the substrate (creating 1,3-butadiene). In a sense, it is a "1,4-elimination" of ethylene (CH 2 =CH 2 ) having a form R(X)-S(Y) → R*S + XY similar to a 1,2elimination R(X)S(Y) → R=S + XY.…”

“…In this case, a new double bond is formed in the substrate (RS) with the electrons relocalized, and a new (double) bond is formed between X and Y in addition to the existing single bond. The Reaction Class notation reflects the "1,4-elimination" nature of this reaction: CC-CC (4). Although this is a single-step reaction, the Reaction Connectivity layer is written as two concerted steps separated by a colon (:).…”

“…Although this is a single-step reaction, the Reaction Connectivity layer is written as two concerted steps separated by a colon (:). For this reaction, as one C-C bond [3][4][5] breaks, this weakens an adjacent (beta) C-C bond [4][5][6] that also breaks, or [/r3-5:4-6].…”