tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics

A new software, called tsscds2018, has been developed to discover reaction mechanisms and solve the kinetics in a fully automated fashion. The program employs algorithms based on Graph Theory to find transition state (TS) geometries from accelerated semiempirical dynamics simulations carried out with MOPAC2016. Then, the TSs are connected to the corresponding minima and the reaction network is obtained. Kinetic data like populations vs time or the abundancies of each product can also be obtained with our program thanks to a Kinetic Monte Carlo routine. Highly accurate ab initio potential energy diagrams and kinetics can also be obtained using an interface with Gaussian09. The source code is available on the following site: http://forge.cesga.es/wiki/g/tsscds/HomePage © 2018 Wiley Periodicals, Inc.

[1]  Q. Peng,et al.  Catalytic Control in Cyclizations: From Computational Mechanistic Understanding to Selectivity Prediction. , 2016, Accounts of chemical research.

[2]  D. Truhlar,et al.  Multipath variational transition state theory: rate constant of the 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical. , 2012, The journal of physical chemistry. A.

[3]  Michael Hirsch,et al.  Determination of energy minima and saddle points using multireference configuration interaction methods in combination with reduced gradient following: The S0 surface of H2CO and the T1 and T2 surfaces of acetylene , 2002, J. Comput. Chem..

[4]  K. Tokuhashi,et al.  Relative reactivity and regioselectivity of halogen-substituted ethenes and propene toward addition of an OH radical or O (3P) atom: An ab initio study , 2006 .

[5]  R. Friesner,et al.  Automated Transition State Search and Its Application to Diverse Types of Organic Reactions. , 2017, Journal of chemical theory and computation.

[6]  Jon Baker,et al.  Isomerization of stilbene using enforced geometry optimization , 2011, J. Comput. Chem..

[7]  Satoshi Maeda,et al.  Global mapping of equilibrium and transition structures on potential energy surfaces by the scaled hypersphere search method: applications to ab initio surfaces of formaldehyde and propyne molecules. , 2005, The journal of physical chemistry. A.

[8]  J. Harvey,et al.  Computational kinetics of cobalt-catalyzed alkene hydroformylation. , 2014, Angewandte Chemie.

[9]  Jaroslav Koča,et al.  VADER: New Software for Exploring Interconversions on Potential Energy Surfaces , 1999, J. Chem. Inf. Comput. Sci..

[10]  Markus Reiher,et al.  Heuristics-Guided Exploration of Reaction Mechanisms. , 2015, Journal of chemical theory and computation.

[11]  C. J. Tsai,et al.  Use of an eigenmode method to locate the stationary points on the potential energy surfaces of selected argon and water clusters , 1993 .

[12]  Satoshi Maeda,et al.  Global reaction route mapping on potential energy surfaces of formaldehyde, formic acid, and their metal-substituted analogues. , 2006, The journal of physical chemistry. A.

[13]  William H. Green,et al.  Mechanism Generation with Integrated Pressure Dependence: A New Model for Methane Pyrolysis , 2003 .

[14]  Paul N. Mortenson,et al.  Energy landscapes: from clusters to biomolecules , 2007 .

[15]  Paul M. Zimmerman,et al.  Automated discovery of chemically reasonable elementary reaction steps , 2013, J. Comput. Chem..

[16]  D. Truhlar,et al.  Variational transition state theory: theoretical framework and recent developments. , 2017, Chemical Society reviews.

[17]  Robert T. McGibbon,et al.  Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways. , 2016, Journal of chemical theory and computation.

[18]  Fabio Pietrucci,et al.  Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale. , 2011, Physical review letters.

[19]  S. Vázquez,et al.  HCN elimination from vinyl cyanide: product energy partitioning, the role of hydrogen-deuterium exchange reactions and a new pathway. , 2015, Physical chemistry chemical physics : PCCP.

[20]  H. Grubmüller,et al.  Predicting unimolecular chemical reactions: Chemical flooding , 2002 .

[21]  Paul M. Zimmerman,et al.  Single‐ended transition state finding with the growing string method , 2015, J. Comput. Chem..

[22]  Zhi-Pan Liu,et al.  Reaction sampling and reactivity prediction using the stochastic surface walking method. , 2015, Physical chemistry chemical physics : PCCP.

[23]  Stefan Goedecker,et al.  Minima hopping guided path search: an efficient method for finding complex chemical reaction pathways. , 2014, The Journal of chemical physics.

[24]  Karl K. Irikura,et al.  Predicting Unexpected Chemical Reactions by Isopotential Searching , 2000 .

[25]  William H. Green,et al.  Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms , 2016, Comput. Phys. Commun..

[26]  Satoshi Maeda,et al.  Communications: A systematic method for locating transition structures of A+B-->X type reactions. , 2010, The Journal of chemical physics.

[27]  Shuhua Li,et al.  Automatic Reaction Pathway Search via Combined Molecular Dynamics and Coordinate Driving Method. , 2017, The journal of physical chemistry. A.

[28]  Sean C. Smith.  Unimolecular Reaction Dynamics , 2002 .

[29]  Y. Abashkin,et al.  Transition state structures and reaction profiles from constrained optimization procedure. Implementation in the framework of density functional theory , 1994 .

[30]  D. Truhlar,et al.  Multi-structural variational transition state theory. Kinetics of the 1,4-hydrogen shift isomerization of the pentyl radical with torsional anharmonicity , 2011 .

[31]  W. Hase,et al.  Monte carlo sampling of a microcanonical ensemble of classical harmonic oscillators , 1980 .

[32]  Jesús Ángel Varela Carrete,et al.  An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis , 2017, Chemical science.

[33]  H. Dai,et al.  Is Photolytic Production a Viable Source of HCN and HNC in Astrophysical Environments? A Laboratory-based Feasibility Study of Methyl Cyanoformate , 2017 .

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

[35]  Scott Habershon,et al.  Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis. , 2015, The Journal of chemical physics.

[36]  Tetsuya Taketsugu,et al.  Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method , 2014, J. Comput. Chem..

[37]  Tetsuya Taketsugu,et al.  Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces. , 2016, Chemical record.

[38]  R. McGibbon,et al.  Discovering chemistry with an ab initio nanoreactor , 2014, Nature chemistry.

[39]  J. R. Álvarez-Idaboy,et al.  MECHANISM OF THE OH-PROPENE-O2 REACTION : AN AB INITIO STUDY , 1999 .

[40]  Satoshi Maeda,et al.  Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. , 2013, Physical chemistry chemical physics : PCCP.

[41]  A. Fernández-Ramos,et al.  Accounting for conformational flexibility and torsional anharmonicity in the H + CH3CH2OH hydrogen abstraction reactions: a multi-path variational transition state theory study. , 2014, The Journal of chemical physics.

[42]  R. West,et al.  Automated Transition State Theory Calculations for High-Throughput Kinetics. , 2017, The journal of physical chemistry. A.

[43]  Gilles H. Peslherbe,et al.  Monte Carlo Sampling for Classical Trajectory Simulations , 2007 .

[44]  J. Doye,et al.  Surveying a potential energy surface by eigenvector-following , 1997 .

[45]  S. Rice,et al.  ADVANCES IN CHEMICAL PHYSICS , 2002 .

[46]  Paul M Zimmerman,et al.  Finding reaction mechanisms, intuitive or otherwise. , 2017, Organic & biomolecular chemistry.

[47]  Christodoulos A. Floudas,et al.  Locating all transition states and studying the reaction pathways of potential energy surfaces , 1999 .

[48]  S. Vázquez,et al.  Photodissociation of acryloyl chloride at 193 nm: interpretation of the product energy distributions, and new elimination pathways. , 2016, Physical chemistry chemical physics : PCCP.

[49]  James A. Miller,et al.  The reaction between propene and hydroxyl. , 2009, Physical chemistry chemical physics : PCCP.

[50]  Satoshi Maeda,et al.  A scaled hypersphere search method for the topography of reaction pathways on the potential energy surface , 2004 .

[51]  R. West,et al.  Transition state geometry prediction using molecular group contributions. , 2015, Physical chemistry chemical physics : PCCP.

[52]  Frank Jensen,et al.  Gradient extremal bifurcation and turning points: An application to the H2CO potential energy surface , 1996 .

[53]  Jun-qiang Sun,et al.  Gradient extremals and steepest descent lines on potential energy surfaces , 1993 .

[54]  H. Schwarz.  Chemistry with methane: concepts rather than recipes. , 2011, Angewandte Chemie.

[55]  J. Salpin,et al.  On the gas phase fragmentation of protonated uracil: a statistical perspective. , 2016, Physical chemistry chemical physics : PCCP.

[56]  Paul M. Zimmerman,et al.  Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method , 2017, J. Comput. Chem..

[57]  P. R. Westmoreland,et al.  Kinetics of enol formation from reaction of OH with propene. , 2009, The journal of physical chemistry. A.

[58]  Satoshi Maeda,et al.  Automated exploration of reaction channels , 2008 .

[59]  Scott Habershon,et al.  Automated Prediction of Catalytic Mechanism and Rate Law Using Graph-Based Reaction Path Sampling. , 2016, Journal of chemical theory and computation.

[60]  A. Fernández-Ramos,et al.  Influence of Multiple Conformations and Paths on Rate Constants and Product Branching Ratios. Thermal Decomposition of 1-Propanol Radicals. , 2018, The journal of physical chemistry. A.

[61]  K. Fukui.  The path of chemical reactions - the IRC approach , 1981 .

[62]  D. Wales,et al.  Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape. , 2015, The Journal of chemical physics.

[63]  Paul Zimmerman,et al.  Reliable Transition State Searches Integrated with the Growing String Method. , 2013, Journal of chemical theory and computation.

[64]  Cooper J. Galvin,et al.  Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry. , 2014, Journal of chemical theory and computation.

[65]  Benjamin A. Ellingson,et al.  Variational Transition State Theory with Multidimensional Tunneling , 2007 .

[66]  Franziska Schoenebeck,et al.  Computation and Experiment: A Powerful Combination to Understand and Predict Reactivities. , 2016, Accounts of chemical research.

[67]  B. Viskolcz,et al.  Allylic H-Abstraction Mechanism:  The Potential Energy Surface of the Reaction of Propene with OH Radical. , 2006, Journal of chemical theory and computation.

[68]  Paul M. Zimmerman,et al.  Growing string method with interpolation and optimization in internal coordinates: method and examples. , 2013, The Journal of chemical physics.

[69]  D. Heidrich,et al.  Searching for saddle points of potential energy surfaces by following a reduced gradient , 1998 .

[70]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[71]  T. Sperger,et al.  Computational Studies of Synthetically Relevant Homogeneous Organometallic Catalysis Involving Ni, Pd, Ir, and Rh: An Overview of Commonly Employed DFT Methods and Mechanistic Insights. , 2015, Chemical reviews.

[72]  Emilio Martínez-Núñez,et al.  An automated transition state search using classical trajectories initialized at multiple minima. , 2015, Physical chemistry chemical physics : PCCP.

[73]  Ze-Rong Li,et al.  Kinetics and mechanism for formation of enols in reaction of hydroxide radical with propene. , 2009, The journal of physical chemistry. A.

[74]  David J. Wales,et al.  Exploring potential energy surfaces with transition state calculations , 1990 .

[75]  K. Morokuma,et al.  Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms. , 2011, Journal of chemical theory and computation.

[76]  Paul M. Zimmerman,et al.  Navigating molecular space for reaction mechanisms: an efficient, automated procedure , 2015 .

[77]  William H Green,et al.  Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods. , 2015, Journal of chemical theory and computation.

[78]  J. Baker.  An algorithm for the location of transition states , 1986 .

[79]  Emilio Martínez-Núñez,et al.  An automated method to find transition states using chemical dynamics simulations , 2015, J. Comput. Chem..