MECHGEN: Computer aided generation and reduction of reaction mechanisms

Journal of Chemical Information and Computer Sciences

Volumn 42, Issue 2, 2002, Pages 208-214

  Németh, András ^a   Vidóczy, Tamás ^a   Héberger, Károly ^a   Kúti, Zsolt ^a   Wágner, János ^a  

^a CHEMICAL RESEARCH CENTER   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER AIDED GENERATION;

CHEMICAL BONDS; COMPUTER SOFTWARE; CONSTRAINT THEORY; MATRIX ALGEBRA; ORGANOMETALLICS; STOICHIOMETRY; THERMODYNAMIC PROPERTIES;

REACTION KINETICS;

EID: 0036522794     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci010365i     Document Type: Article

References (45)

1. Barone, R.; Chanon, M.; Green, M.L.H. Possible Mechanisms for Ethylene Dimerization Derived by Use of a New Computer Program. Organomet. Chem. 1980, 185, 85-93.
2. Theodosiou, I.; Barone, R.; Chanon M. New Computer Program Able to Propose Mechanistic Schemes and Secondary Products for Transformations Catalyzed by Transition Metal Complexes: Possible Mechanisms for Hydroformylation of Ethylene. J. Mol. Catal. 1985, 32, 27-50.
3. Theodosiou, I.; Barone, R.; Chanon, M. Computer Aids for Organometallic Chemistry and Catalysis. Adv. Organomet. Chem. 1986, 26, 165-216.
4. Clymans, P.J.; Froment, G.F. Computer-Generation of Reaction Paths and Rate Equations in the Thermal Cracking of Normal and Branched Paraffins. Comput. Chem. Eng. 1984, 8, 137-142.
5. Baltanas, M.A.; Froment, G.F. Computer Generation of Reaction Networks and Calculation of Product Distributions in the Hydroisomerization and Hydrocracking of Paraffins on Pt-containing Bifunctional Catalysts. Comput. Chem. Eng. 1985, 9, 71-81.
6. Fontain, E.; Reitsam, K. The Generation of Reaction Networks with RAIN. 1. The Reaction Generator. J. Chem. Inf. Comput. Sci. 1991, 31, 96-101.
7. Fontain, E. The Generation of Reaction Networks with RAIN. 2. Resonance Structures and Tautomerism. Tetrahedron Comput. Methodol. 1990, 3, 469-477.
8. Likholobov, V.A.; Mayer, L.I.; Bulgakov, N.N.; Fedotov, A.V.; Shteingauer, L.G. Computer-Aided Prognosis of the Catalytic Properties of Metal Atoms in the Gas-Phase Hydrogenation of Carbon Monoxide. In Homogeneous and Heterogeneous Catalysis; Yermakov, Yu., Likholobov, V.A., Eds.; Inst. of Catalysis: Novosibirsk, 1986; pp 229-244.
9. Di Maio, F.P.; Lignola, P.G. A Kinetic Network Generator. Chem. Eng. Sci. 1992, 47, 2713-2718.
10. Chinnick, S.J.; Baulch, D.L.; Ayscough, P.B. Au expert system for hydrocarbon pyrolysis reactions. Chemometrics Intelligent Laboratory Systems 1988, 5, 39-52.
11. Chevalier, C.; Warnatz, J.; Melenk, H. Automatic generation of reaction mechanisms for the description of higher hydrocarbons. Ben Bunsenges. Phys. Chem. 1990, 94, 1362-1367.
12. Gasteiger, J.; Jochum, C. EROS/A Computer Program for Generating sequences of Reactions. Topics. Curr. Chem. 1978, 74, 93-126.
13. Gasteiger, J.; Houdelmann, U.; Rose, P.; Witzenbichler, J. Computer-assisted prediction of degradation of chemicals: Hydrolysis of amides and benzoylphenylureas. J. Chem. Soc., Perkin Trans. 2 1995, 193-204.
14. Peters, N.; Williams, F.A. The Asymptotic Structure of stoichiometric methane/air Flames. Combust. Flame 1987, 68, 185-207.
15. Peters, N. Reducing Reaction Mechanisms. In Lecture Notes in Physics, Reducing Kinetic Mechanisms and Asymptotic Approximation for Methane/air Flames; Smoke, M.D., Ed.; Springer: Berlin, 1991; pp 48-67.
16. Peters, N.; Rogg, B. Reduced Kinetics Mechanisms for Applications in Combustion Systems; Springer: New York, 1993.
17. Come, G.M.; Sacchi, G.; Warth, V.; Michel, V.; Battin-Leclerc, F.; Bizot, P. Computer Aided Design of Gas-phase Free Radical Reaction Mechanism. In Oxidation Kinetics and Autoignition of Hydrocarbons; Pilling, M.J., Ed.; Elsevier: 1995; p 308.
18. Warth, V.; Stef, N.; Glaude, P.A.; Battin-Leclerc, F.; Scacchi, G.; Côme, G.M. Computer-aided Derivation of Gas-phase Oxidation Mechanisms. Combust. Flame 1998, 114, 81-102.
19. Lam, S.H.; Goussis, D.A. Conventional Asymptotics and Computational Singular Perturbation. In Lecture Notes in Physics, Reducing Kinetic Mechanisms and Asymptotic Approximation for Methane/air Flames; Smoke, M.D., Ed.; Springer: Berlin, 1991; pp 193-226.
20. Seshadri, K.; Bollig, M.; Peters, N. Numerical and Asymptotic Studies of Structure of Stoichiometric and Lean Premixed Heptane Flames. Combustion Flame 1997, 108, 518-536.
21. Maas, U.; Pope, S.B. Simplifying chemical kinetics: Intrinsic Low-dimensional Manifolds in Composition Space. Combust. Flame 1992, 88, 239-264.
22. Eggels, R.L.G.M.; de Goey, L.P.H. Mathematically Reduced Reaction Mechanisms Applied to Adiabatic Flat Hydrogen/air Flames. Combust. Flame 1995, 100, 559-569.
23. Bruk, L.G.; Gorodskii, S.N.; Zeigarnik, A.V.; Valdes-Perez, R.E.; Temkin, O.N. Mechanism of Oxidative Carbonylation of Phenylacetylene and Methylacetylene: Generation of Hypotheses and Their Experimental Discrimination. Russ. Chem. Bull. 1999, 48, 873-880.
24. Zeigarnik, A.V.; Bruk, L.G.; Temkin, O.N.; Likholobov, V.A.; Maier, L.I. Computer-Assisted Mechanistic Studies. Usp. Khim. 1996, 65, 125-139; [Russ. Chem. Rev. 1996, 6, 117-130].
25. Shalgunov, S.I.; Zeigarnik, A.V.; Bruk, L.G.; Temkin, O.N. Computer-assisted Generation of Chemical Reaction Networks: Applications in the Mechanistic Studies of Organometallic Catalysis. Russ. Chem. Bull. 1999, 48, 1876-1874.
26. Bruk, L.G.; Gorodskii, S.N.; Zeigarnik, A.V.; Valdes-Perez, R.E.; Temkin, O.N. Oxidative Carbonylation of Phenylacetylene Catalyzed by Pd(II) and Cu(I): Experimental Tests of Forty-one Computer-Generated Mechanistic Hypotheses. J. Mol. Catal., A: Chemical 1998, 130, 29-40.
27. Zeigamik, A.V.; Valdes-Perez, R.E.; Temkin, O.N.; Bruk, L.G.; Shalgunov, S.I. Computer-Aided Mechanism Elucidation of Acetylene Hydrocarboxylation to Acrylic Acid Based on a Novel Union of Empirical and Formal Methods. Organometallics 1997, 16, 3114-3127.
28. Porollo, A.A.; Lushnikov, D.E.; Pivina, T.S.; Ivshin V.P.; Computer Representation and Generation of Possible Pathways for Thermal Decomposition Reactions of Organic Compounds. J. Mol. Struct. (Theochem) 1997, 391, 117-124.
29. Porollo, A.A.; Lushnikov, D.E.; Pivina; T.S.; Ivshin, V.P.; Zefirov, N.S. Computer simulation of thermal decomposition reactions of alkyl nitrates. Russ. Chem. Bull. 1999, 48, 1845-1857.
30. Yoneda, Y.A Computer Program Package for the Analysis, Creation, and Estimation of Generalized Reactions/GRACE. I. Generation of Elementary Reaction Network in Radical Reactions. Bull. Chem. Soc. Jpn. 1979, 52, 8-14.
31. Nemes, I.; Vidóczy, T.; Botár, L.; Gál, D. A Possible Construction of a Complex Chemical Reaction Network I. Definitions and Procedure for Construction. Theor. Chim. Acta 1977, 45, 215-223.
32. Even though this definition does nut consider certain concerted reactions as elementary reactions, it agrees with common chemical considerations very well.
33. Héberger, K.; Keszler, A.; Vidóczy, T.; Gál, D.; Cotarca, L.; Delogu, P. Oxidative decarboxylation of cyclohexane monocarboxylic acid as a degenerate branching chain reaction II. Mechanism. Bet. Bunsenges. Phys. Chem. 1994, 98, 1303-1307.
34. κ≤4).
35. The following criteria must be fulfilled when comparing reactions: (i) all the reactants should be the same; (ii) the type of the reaction (e.g. in case of free radical processes initiation, propagation, termination) should be identical; and (iii) the molecularity of the reaction on the product side should be identical. The justification of these requirements is discussed in ref 36.
36. Vidóczy, T.; Hajdu, I.P.; Nemes, I.; Gál, D. A Possible Construction of a Complex Chemical Reaction Network IV. Compilation of the Possible Mechanism by Combinatorial Method and its Reduction by Thermochemical Kinetic Treatment. Oxid. Commun. 1983, 4, 203221.
37. Németh, A.; Héberger, K. Generation and Reduction of the Reaction Mechanism Representing the Initial Attack upon Methane in Combustion, Oxid. Commun. 1996, 19, 467-475.
38. Nemes, I.; Vidóczy, T.; Gál, D. A Possible Construction of a Complex Chemical Reaction Network III. The Systematization of the Elementary Processes. Theor. Chim. Acta 1977, 46, 243-250.
39. 43.
40. Stull, D.R.; Westrum, E.F., Jr.; Sinke, G.C. The Chemical Thermodynamics of Organic Compounds; John Wiley & Sons: New York, 1969.
41. Ritter, E.R.; Bozelli, J.W. THERM: Thermodynamic property estimation for gas-phase radicals and molecules. Int. J. Chem. Kinet. 1991, 23, 767-778.
42. Ritter, E.R. THERM: A computer code for estimating thermodynamic properties for species important to combustion and reaction modeling. J. Chem. Inf. Comput. Sci. 1991, 31, 400-408.
43. Müller, C.; Michael, V.; Scacchi, G.; Côme, G.M. THERGAS, a computer program for the evaluation of thermochemical data of molecules and free radicals in the gas phase. J. Chim. Phys. 1995, 92, 1154-1178.
44. In case a species is defined as "reactant only", it cannot occur on the right-hand side of a reaction. Similarly, species defined as "product only" cannot be taken into consideration on the left-hand side of a reaction.
45. This is the only filter where reactions are compared to each other (all other filtering is based on the reaction in question alone). Should later filtering result in omission of a reaction, which served as the reference reaction in a subgroup (because being the most exothermic/least endothermic within that subgroup), would render omission of reactions based on their reaction enthalpy from that given subgroup invalid. To avoid such ambiguities, filtering based on reaction enthalpy should be performed as the last filtering procedure.