Language-oriented rule-based reaction network generation and analysis: Description of RING

Abstract Applications of RING in the generation and analysis of complex thermochemical reaction networks are presented. Automated generation and topological network analysis features in RING allow for: (a) constructing reaction networks exhaustively in a rule-based manner, (b) identifying dominant pathways in networks using estimates of kinetic parameters, (c) hypothesis and testing of mechanisms by comparing pathway results from RING with experimental data, and (d) predicting atom-efficient synthetic routes to valuable chemicals from known chemistries and commonly available chemicals. Case studies involving three chemical systems are used to demonstrate these features in RING: (a) acid-catalyzed propane aromatization, (b) glycerol and acetone dehydration on acid catalysts, and (c) C 4 –C 9 mono-alcohols synthesis from C 2 and C 3 oxygenates on acid, base, and metal catalyzed chemistries. Through these case studies, we demonstrate that RING can be used to postulate mechanisms and predict likely products for a given system, thereby guiding experimentation and computational analysis.

[1]  Stephen B. Jaffe,et al.  Building useful models of complex reaction systems in petroleum refining , 1996 .

[2]  Venkat Venkatasubramanian,et al.  A domain-specific compiler theory based framework for automated reaction network generation , 2008, Comput. Chem. Eng..

[3]  Eric Van Wyk,et al.  Context-aware scanning for parsing extensible languages , 2007, GPCE '07.

[4]  Venkat Venkatasubramanian,et al.  An Intelligent System for Reaction Kinetic Modeling and Catalyst Design , 2004 .

[5]  L. Broadbelt,et al.  Detailed Kinetic Modeling of Silicon Nanoparticle Formation Chemistry via Automated Mechanism Generation , 2004 .

[6]  S. Schuster,et al.  ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE , 1994 .

[7]  David Eppstein,et al.  Finding the k Shortest Paths , 1999, SIAM J. Comput..

[8]  F. P. Di Maio,et al.  KING, a KInetic Network Generator , 1992 .

[9]  G. Huber,et al.  Production of Liquid Alkanes by Aqueous-Phase Processing of Biomass-Derived Carbohydrates , 2005, Science.

[10]  Venkat Venkatasubramanian,et al.  Catalyst design: knowledge extraction from high-throughput experimentation , 2003 .

[11]  Botond Bertók,et al.  Generation of light hydrocarbons through Fischer-Tropsch synthesis: Identification of potentially dominant catalytic pathways via the graph-theoretic method and energetic analysis , 2009, Comput. Chem. Eng..

[12]  Gerhard Ertl,et al.  Adsorption of hydrogen on palladium single crystal surfaces , 1974 .

[13]  Michel Waroquier,et al.  Carbon-centered radical addition and beta-scission reactions: modeling of activation energies and pre-exponential factors. , 2008, Chemphyschem : a European journal of chemical physics and physical chemistry.

[14]  V. Hatzimanikatis,et al.  Thermodynamics-based metabolic flux analysis. , 2007, Biophysical journal.

[15]  S. Narayanan,et al.  Thermal Cracking of Ethane and Ethane-Propane Mixtures , 1976 .

[16]  Jim Pfaendtner,et al.  Lexicography of kinetic modeling of complex reaction networks , 2005 .

[17]  Adam M. Feist,et al.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[18]  B. Palsson,et al.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.

[19]  Kevin Van Geem,et al.  Automatic reaction network generation using RMG for steam cracking of n‐hexane , 2006 .

[20]  Kenneth B. Bischoff,et al.  Lumping strategy. 1. Introductory techniques and applications of cluster analysis , 1987 .

[21]  R. Gómez-Bombarelli,et al.  Computational calculation of equilibrium constants: addition to carbonyl compounds. , 2009, The journal of physical chemistry. A.

[22]  Charles T. Campbell,et al.  Future Directions and Industrial Perspectives Micro- and macro-kinetics: Their relationship in heterogeneous catalysis , 1994 .

[23]  Edward S. Blurock,et al.  Reaction: System for Modeling Chemical Reactions , 1995, J. Chem. Inf. Comput. Sci..

[24]  Pierre-Alexandre Glaude,et al.  Computer Based Generation of Reaction Mechanisms for Gas-phase Oxidation , 2000, Comput. Chem..

[25]  Herschel Rabitz,et al.  A general analysis of exact lumping in chemical kinetics , 1989 .

[26]  Eric Van Wyk,et al.  Building Extensible Specifications and Implementations of Promela with AbleP , 2011, SPIN.

[27]  L. Broadbelt,et al.  Mechanistic Modeling of Lubricant Degradation. 2. The Autoxidation of Decane and Octane , 2008 .

[28]  T. Ho Kinetic Modeling of Large‐Scale Reaction Systems , 2008 .

[29]  K. Kobe,et al.  Chemical engineering kinetics , 1956 .

[30]  Joshua W. Allen,et al.  Automatic Reaction Mechanism Generation with Group Additive Kinetics , 2012 .

[31]  R. Sumathi,et al.  A priori rate constants for kinetic modeling , 2002 .

[32]  Julian R. Ullmann,et al.  An Algorithm for Subgraph Isomorphism , 1976, J. ACM.

[33]  Raymond S H Yang,et al.  Biochemical reaction network modeling: predicting metabolism of organic chemical mixtures. , 2005, Environmental science & technology.

[34]  Michel Waroquier,et al.  Ab initio group contribution method for activation energies of hydrogen abstraction reactions. , 2006, Chemphyschem : a European journal of chemical physics and physical chemistry.

[35]  Peter B. Ayscough,et al.  An expert system for hydrocarbon pyrolysis reactions , 1988 .

[36]  James Dugundji,et al.  An algebraic model of constitutional chemistry as a basis for chemical computer programs , 1973 .

[37]  G. Marin,et al.  Genesys: kinetic model construction using chemo-informatics , 2012 .

[38]  Hans-Heinrich Carstensen,et al.  Rate constant rules for the automated generation of gas-phase reaction mechanisms. , 2009, The journal of physical chemistry. A.

[39]  A. Corma,et al.  Chemical routes for the transformation of biomass into chemicals. , 2007, Chemical reviews.

[40]  G. N. Richards,et al.  Mechanism of formation of 5-(hydroxymethyl)-2-furaldehyde from D-fructose an sucrose. , 1990, Carbohydrate research.

[41]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. , 1997, Biotechnology and bioengineering.

[42]  Linda J. Broadbelt,et al.  Computer Generated Pyrolysis Modeling: On-the-Fly Generation of Species, Reactions, and Rates , 1994 .

[43]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[44]  Vassily Hatzimanikatis,et al.  Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways. , 2005, Journal of the American Chemical Society.

[45]  W. Patrick Walters,et al.  ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology , 1996, J. Chem. Inf. Comput. Sci..

[46]  René Fournet,et al.  Comprehensive mechanism for the gas-phase oxidation of propene , 2001 .

[47]  Michael L. Mavrovouniotis,et al.  Construction of complex reaction systems—II. Molecule manipulation and reaction application algorithms , 1997 .

[48]  J. Happel,et al.  Studies of the structure of chemical mechanisms , 1992 .

[49]  Lydia E. Kavraki,et al.  Finding metabolic pathways using atom tracking , 2010, Bioinform..

[50]  V. Kazansky,et al.  Quantum-chemical study of hydride transfer in catalytic transformation of paraffins on zeolites , 1997 .

[51]  J. Dumesic,et al.  2-Methylhexane Cracking on Y Zeolites: Catalytic Cycles and Reaction Selectivity , 1997 .

[52]  Francisco J. Planes,et al.  Path finding approaches and metabolic pathways , 2009, Discret. Appl. Math..

[53]  M. V. Frash,et al.  A quantum-chemical study of hydride transfer in catalytic transformations of paraffins on zeolites. Pathways through adsorbed nonclassical carbonium ions , 1997 .

[54]  D. Mohan,et al.  Pyrolysis of Wood/Biomass for Bio-oil: A Critical Review , 2006 .

[55]  Vassilios Sotiropoulos,et al.  SynBioSS: the synthetic biology modeling suite , 2008, Bioinform..

[56]  Simona Bohanec,et al.  Symmetry of chemical structures: A novel method of graph automorphism group determination , 1993, J. Chem. Inf. Comput. Sci..

[57]  Glenn J. Sunley,et al.  Site requirements and elementary steps in dimethyl ether carbonylation catalyzed by acidic zeolites , 2007 .

[58]  Linda J. Broadbelt,et al.  Computer generated reaction modelling: Decomposition and encoding algorithms for determining species uniqueness , 1996 .

[59]  W. T. Wipke,et al.  Stereochemically unique naming algorithm , 1974 .

[60]  Linda J. Broadbelt,et al.  Computational discovery of biochemical routes to specialty chemicals , 2004 .

[61]  Johann Gasteiger,et al.  Hash codes for the identification and classification of molecular structure elements , 1994, J. Comput. Chem..

[62]  I. Grossmann,et al.  Recursive MILP model for finding all the alternate optima in LP models for metabolic networks , 2000 .

[63]  Botond Bertók,et al.  A Graph-theoretic Method to Identify Candidate Mechanisms for Deriving the Rate Law of a Catalytic Reaction , 2002, Comput. Chem..

[64]  J. S. Buchanan,et al.  Mechanistic considerations in acid-catalyzed cracking of olefins , 1996 .

[65]  Venkat Venkatasubramanian,et al.  Microkinetic modeling of propane aromatization over HZSM-5 , 2005 .

[66]  V. Hatzimanikatis,et al.  Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3‐hydroxypropanoate , 2010, Biotechnology and bioengineering.

[68]  Vassily Hatzimanikatis,et al.  Computational framework for predictive biodegradation , 2009, Biotechnology and bioengineering.

[69]  W. S. Hlavacek,et al.  Investigation of Early Events in FcεRI-Mediated Signaling Using a Detailed Mathematical Model1 , 2003, The Journal of Immunology.

[70]  William H. Green,et al.  Capturing pressure‐dependence in automated mechanism generation: Reactions through cycloalkyl intermediates , 2003 .

[71]  Eric Van Wyk,et al.  Modular Well-Definedness Analysis for Attribute Grammars , 2012, SLE.

[72]  B. Palsson,et al.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.

[73]  Jason A. Papin,et al.  Comparison of network-based pathway analysis methods. , 2004, Trends in biotechnology.

[74]  Masanori Arita In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. , 2003, Genome research.

[75]  S. Wodak,et al.  Inferring meaningful pathways in weighted metabolic networks. , 2006, Journal of molecular biology.

[76]  Eric Van Wyk,et al.  Verifiable composition of deterministic grammars , 2009, PLDI '09.

[77]  Michael L. Mavrovouniotis,et al.  Construction of complex reaction systems—III. An example: alkylation of olefins , 1997 .

[78]  P. C. Milner,et al.  The Possible Mechanisms of Complex Reactions Involving Consecutive Steps , 1964 .

[79]  Manos Mavrikakis,et al.  Molecular-level descriptions of surface chemistry in kinetic models using density functional theory , 2004 .

[80]  S. Panke,et al.  Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data , 2006, Molecular systems biology.

[81]  Michael L. Mavrovouniotis,et al.  Construction of complex reaction systems—I. Reaction description language , 1997 .

[82]  Prodromos Daoutidis,et al.  Automated Generation and Optimal Selection of Biofuel-Gasoline Blends and Their Synthesis Routes , 2013 .

[83]  C. Muller,et al.  A Topological Method for Determining the External Symmetry Number of Molecules , 1991, Comput. Chem..

[84]  Morton E. Munk,et al.  Stereoisomer generation in computer-enhanced structure elucidation , 1993, J. Chem. Inf. Comput. Sci..

[85]  Jin Yang,et al.  'On-the-fly' or 'generate-first' modeling? , 2005, Nature Biotechnology.

[86]  A. Bhan,et al.  Catalytic consequences of hydroxyl group location on the rate and mechanism of parallel dehydration reactions of ethanol over acidic zeolites , 2010 .

[87]  M. Mavrovouniotis Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 2. Formalization and analysis of the synthesis algorithm , 1992 .

[88]  William H. Green,et al.  Predictive Kinetics: A New Approach for the 21st Century , 2010 .

[89]  J. Brønsted Acid and Basic Catalysis. , 1928 .

[90]  D. Vlachos,et al.  Adsorption of Acid, Ester, and Ether Functional Groups on Pt: Fast Prediction of Thermochemical Properties of Adsorbed Oxygenates via DFT-Based Group Additivity Methods , 2012 .

[91]  Alfred V. Aho,et al.  Compilers: Principles, Techniques, and Tools , 1986, Addison-Wesley series in computer science / World student series edition.

[92]  J. Dumesic,et al.  Kinetics of heterogeneous catalytic reactions: Analysis of reaction schemes , 2001 .

[93]  William H. Green,et al.  Rate-Based Construction of Kinetic Models for Complex Systems , 1997 .

[94]  Carol S. Woodward,et al.  Enabling New Flexibility in the SUNDIALS Suite of Nonlinear and Differential/Algebraic Equation Solvers , 2020, ACM Trans. Math. Softw..

[95]  S. Krishnan,et al.  Hash Functions for Rapid Storage and Retrieval of Chemical Structures , 1978, J. Chem. Inf. Comput. Sci..

[96]  G. Stephanopoulos,et al.  Synthesis of Reaction Mechanisms Consisting of Reversible and Irreversible Steps. 1. A Synthesis Approach in the Context of Simple Examples , 1992 .

[97]  Steffen Klamt,et al.  Two approaches for metabolic pathway analysis? , 2003, Trends in biotechnology.

[98]  Gilbert F. Froment,et al.  Computer generation of reaction networks and calculation of product distributions in the hydroisomerization and hydrocracking of paraffins on Pt-containing bifunctional catalysts , 1985 .

[99]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[100]  R. J. Quann,et al.  Structure-oriented lumping: describing the chemistry of complex hydrocarbon mixtures , 1992 .

[101]  A. Corma,et al.  Biomass to chemicals : Catalytic conversion of glycerol/water mixtures into acrolein, reaction network , 2008 .

[102]  Li Genyuan,et al.  A lumping analysis in mono- or/and bimolecular reaction systems , 1984 .

[103]  Gordon M. Crippen,et al.  Prediction of Physicochemical Parameters by Atomic Contributions , 1999, J. Chem. Inf. Comput. Sci..

[104]  Ilie Fishtik,et al.  Reaction Route Graphs. I. Theory and Algorithm , 2004 .

[105]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[106]  Yogesh V. Joshi,et al.  DFT-based reaction pathway analysis of hexadiene cyclization via carbenium ion intermediates: Mechanistic study of light alkane aromatization catalysis , 2004 .

[107]  Thanh N. Truong,et al.  Application of Chemical Graph Theory for Automated Mechanism Generation , 2003, J. Chem. Inf. Comput. Sci..

[108]  Eric Van Wyk,et al.  Silver: An extensible attribute grammar system , 2008, Sci. Comput. Program..

[109]  Ture R. Munter,et al.  Scaling properties of adsorption energies for hydrogen-containing molecules on transition-metal surfaces. , 2007, Physical review letters.

[110]  Tiziano Faravelli,et al.  Lumping procedures in detailed kinetic modeling of gasification, pyrolysis, partial oxidation and combustion of hydrocarbon mixtures , 2001 .

[111]  Arie van Deursen,et al.  Domain-specific languages: an annotated bibliography , 2000, SIGP.

[112]  Francisco J. Planes,et al.  A critical examination of stoichiometric and path-finding approaches to metabolic pathways , 2008, Briefings Bioinform..

[113]  N. Gnep,et al.  Kinetic modeling of propane aromatization reaction over HZSM-5 and GaHZSM-5 , 1995 .

[114]  Masanori Arita The metabolic world of Escherichia coli is not small. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[115]  Rainer Herges,et al.  Computer-assisted solution of chemical problems : the historical development and the present state of the art of a new discipline of chemistry , 1993 .

[116]  Linda J. Broadbelt,et al.  Termination of Computer-Generated Reaction Mechanisms: Species Rank-Based Convergence Criterion , 1995 .

[117]  Michel Waroquier,et al.  Ab initio thermochemistry and kinetics for carbon-centered radical addition and beta-scission reactions. , 2007, The journal of physical chemistry. A.

[118]  Jin Yang,et al.  Graph Theory for Rule-Based Modeling of Biochemical Networks , 2006, Trans. Comp. Sys. Biology.

[119]  Prodromos Daoutidis,et al.  Rule-Based Generation of Thermochemical Routes to Biomass Conversion , 2010 .

[120]  Linda J. Broadbelt,et al.  Computer generated reaction networks: on-the-fly calculation of species properties using computational quantum chemistry , 1994 .

[121]  Paul J. Dauenhauer,et al.  Chemical engineering: Hybrid routes to biofuels , 2007, Nature.

[122]  Michel Waroquier,et al.  Hydrogen radical additions to unsaturated hydrocarbons and the reverse beta-scission reactions: modeling of activation energies and pre-exponential factors. , 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.

[123]  Yogesh V. Joshi,et al.  Embedded cluster (QM/MM) investigation of C6 diene cyclization in HZSM-5 , 2005 .

[124]  R. Gorte,et al.  Characterization of acylating intermediates formed on H-ZSM-5 , 2004 .

[125]  Eric Van Wyk,et al.  Attribute Grammar-Based Language Extensions for Java , 2007, ECOOP.

[126]  Jean-Loup Faulon,et al.  Stochastic Generator of Chemical Structure. 3. Reaction Network Generation , 2000, J. Chem. Inf. Comput. Sci..