Efficient prediction of reaction paths through molecular graph and reaction network analysis† †Electronic supplementary information (ESI) available: Detailed information on reaction networks and pathways for two example reactions, Cartesian coordinates of molecules in the reaction networks obtained
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Woo Youn Kim | Jin Woo Kim | Zeehyo Kim | Yeonjoon Kim | W. Kim | Yeonjoon Kim | Jin Woo Kim | Zeehyo Kim
[1] Alexandru T. Balaban,et al. Applications of graph theory in chemistry , 1985, J. Chem. Inf. Comput. Sci..
[2] Charles O Rock,et al. The Claisen condensation in biology. , 2002, Natural product reports.
[3] T. Frauenheim,et al. DFTB+, a sparse matrix-based implementation of the DFTB method. , 2007, The journal of physical chemistry. A.
[4] Woo Youn Kim,et al. Universal Structure Conversion Method for Organic Molecules: From Atomic Connectivity to Three‐Dimensional Geometry , 2015 .
[5] Pierre Baldi,et al. No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms , 2009, J. Chem. Inf. Model..
[6] Zhi-Pan Liu,et al. Constrained Broyden Dimer Method with Bias Potential for Exploring Potential Energy Surface of Multistep Reaction Process. , 2012, Journal of chemical theory and computation.
[7] Chris Morley,et al. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit , 2008, Chemistry Central journal.
[8] W. T. Wipke,et al. Computer-Assisted Organic Synthesis , 1977 .
[9] Woo Youn Kim,et al. Computational searching for new stable graphyne structures and their electronic properties , 2016 .
[10] Markus Reiher,et al. Context-Driven Exploration of Complex Chemical Reaction Networks. , 2017, Journal of chemical theory and computation.
[11] Richard F. Heck,et al. The Reaction of Cobalt Hydrotetracarbonyl with Olefins , 1961 .
[12] Paul Ha-Yeon Cheong,et al. Computational prediction of small-molecule catalysts , 2008, Nature.
[13] Bartosz A Grzybowski,et al. Chemical network algorithms for the risk assessment and management of chemical threats. , 2012, Angewandte Chemie.
[14] Danail Bonchev,et al. Chemical Reaction Networks: A Graph-Theoretical Approach , 1996 .
[15] S. Niu,et al. Theoretical studies on reactions of transition-metal complexes. , 2000, Chemical reviews.
[16] Pierre Baldi,et al. Learning to Predict Chemical Reactions , 2011, J. Chem. Inf. Model..
[17] Cooper J. Galvin,et al. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry. , 2014, Journal of chemical theory and computation.
[18] J. Gasteiger,et al. The Principle of Minimum Chemical Distance and the Principle of Minimum Structure Change , 1982 .
[19] Gábor Náray-Szabó,et al. Multicoordinate driven method for approximating enzymatic reaction paths: automatic definition of the reaction coordinate using a subset of chemical coordinates. , 2006, The journal of physical chemistry. A.
[20] 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.
[21] Igor I. Baskin,et al. SYMBEQ Program and Its Application in Computer-Assisted Reaction Design , 1994, J. Chem. Inf. Comput. Sci..
[22] Mojtaba Biniaz,et al. A systematic study of the effects of relative configuration, protecting group, and enolate type on the diastereoselectivities of aldol reactions of a chiral ethyl ketone with 2-methylpropanal. , 2014, The Journal of organic chemistry.
[23] S. Woodley,et al. Crystal structure prediction from first principles. , 2008, Nature materials.
[24] Timm Lankau,et al. A constrained reduced-dimensionality search algorithm to follow chemical reactions on potential energy surfaces. , 2013, The Journal of chemical physics.
[25] Paul M. Zimmerman,et al. Automated discovery of chemically reasonable elementary reaction steps , 2013, J. Comput. Chem..
[26] Markus Reiher,et al. Heuristics-Guided Exploration of Reaction Mechanisms. , 2015, Journal of chemical theory and computation.
[27] C. Levinthal. Are there pathways for protein folding , 1968 .
[28] 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.
[29] Emilio Martínez-Núñez,et al. An automated method to find transition states using chemical dynamics simulations , 2015, J. Comput. Chem..
[30] Jesús Ángel Varela Carrete,et al. An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis , 2017, Chemical science.
[31] Hiroko Satoh,et al. Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H3CNO3 , 2017, J. Comput. Chem..
[32] Thomas Frauenheim,et al. Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method: Sc, Ti, Fe, Co, and Ni. , 2007, Journal of chemical theory and computation.
[33] Paul Ha-Yeon Cheong,et al. Quantum mechanical investigations of organocatalysis: mechanisms, reactivities, and selectivities. , 2011, Chemical reviews.
[34] R. McGibbon,et al. Discovering chemistry with an ab initio nanoreactor , 2014, Nature chemistry.
[35] Chris Morley,et al. Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.
[36] Woo Youn Kim,et al. Efficient Basin-Hopping Sampling of Reaction Intermediates through Molecular Fragmentation and Graph Theory. , 2014, Journal of chemical theory and computation.
[37] B. Grzybowski,et al. Parallel optimization of synthetic pathways within the network of organic chemistry. , 2012, Angewandte Chemie.
[38] William L. Jorgensen,et al. Computer-assisted synthetic analysis. Synthetic strategies based on appendages and the use of reconnective transforms , 1976 .
[39] M. Frisch,et al. Using redundant internal coordinates to optimize equilibrium geometries and transition states , 1996, J. Comput. Chem..
[40] Matthew H Todd,et al. Computer-aided organic synthesis. , 2005, Chemical Society reviews.
[41] Sándor Suhai,et al. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .
[42] J. Y. Yen. Finding the K Shortest Loopless Paths in a Network , 1971 .
[43] Travis E. Oliphant,et al. Python for Scientific Computing , 2007, Computing in Science & Engineering.
[44] J. Stewart. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.
[45] T. Laue,et al. Named Organic Reactions: Laue/Named Organic Reactions , 2005 .
[46] V. Barone,et al. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .
[47] P. Baldi,et al. Synthesis Explorer : A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction , 2008 .
[48] 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.
[49] Edsger W. Dijkstra,et al. A note on two problems in connexion with graphs , 1959, Numerische Mathematik.
[50] S. Goedecker. Minima hopping: an efficient search method for the global minimum of the potential energy surface of complex molecular systems. , 2004, The Journal of chemical physics.
[51] Serge S. Tratch,et al. Symbolic equations and their applications to reaction design , 1991 .
[52] J. Gasteiger,et al. The Principle of Minimum Chemical Distance (PMCD) , 1980 .
[53] R. García-Domenech,et al. Some new trends in chemical graph theory. , 2008, Chemical reviews.
[54] Sidney M. Hecht,et al. Synthesis and evaluation of verticipyrone analogues as mitochondrial complex I inhibitors. , 2010, Bioorganic & medicinal chemistry.
[55] D. Wales. Energy landscapes and properties of biomolecules , 2005, Physical biology.
[56] H. Schlegel,et al. Optimization of equilibrium geometries and transition structures , 1982 .
[57] William H. Green,et al. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms , 2016, Comput. Phys. Commun..
[58] Guido Rossum,et al. Python Reference Manual , 2000 .
[59] H. Scheraga,et al. Global optimization of clusters, crystals, and biomolecules. , 1999, Science.
[60] Markus Reiher,et al. Uncertainty quantification for quantum chemical models of complex reaction networks. , 2016, Faraday discussions.
[61] 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.
[62] M. Perkins,et al. Total synthesis and structural elucidation of ent-micropyrone and (+)-ascosalipyrone. , 2012, Organic & biomolecular chemistry.
[63] H. Bernhard Schlegel,et al. Estimating the hessian for gradient-type geometry optimizations , 1984 .
[64] Marwin H. S. Segler,et al. Modelling Chemical Reasoning to Predict Reactions , 2016, Chemistry.
[65] Donald G Truhlar,et al. Density functionals with broad applicability in chemistry. , 2008, Accounts of chemical research.
[66] 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 .
[67] David A. Pensak,et al. LHASA—Logic and Heuristics Applied to Synthetic Analysis , 1977 .
[68] Paul M Zimmerman,et al. Highly Active Nickel Catalysts for C-H Functionalization Identified through Analysis of Off-Cycle Intermediates. , 2015, Journal of the American Chemical Society.
[69] B. Grzybowski,et al. The 'wired' universe of organic chemistry. , 2009, Nature chemistry.
[70] Alán Aspuru-Guzik,et al. Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle , 2015, Scientific Reports.
[71] Zhi-Pan Liu,et al. Stochastic Surface Walking Method for Structure Prediction and Pathway Searching. , 2013, Journal of chemical theory and computation.
[72] Christodoulos A. Floudas,et al. Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization , 2012, J. Chem. Inf. Model..
[73] Satoshi Maeda,et al. Toward Predicting Full Catalytic Cycle Using Automatic Reaction Path Search Method: A Case Study on HCo(CO)3-Catalyzed Hydroformylation. , 2012, Journal of chemical theory and computation.
[74] Paul Zimmerman,et al. Reliable Transition State Searches Integrated with the Growing String Method. , 2013, Journal of chemical theory and computation.
[75] David J Wales,et al. Potential energy and free energy landscapes. , 2006, The journal of physical chemistry. B.
[76] Satoshi Maeda,et al. Computational Catalysis Using the Arti fi cial Force Induced Reaction Method Published as part of the Accounts of Chemical Research special issue “ Computational Catalysis for Organic Synthesis ” , 2016 .
[77] Gerta Rücker,et al. Organic Synthesis - Art or Science? , 2004, J. Chem. Inf. Model..
[78] D. Truhlar,et al. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .
[79] J. Harvey,et al. Computational kinetics of cobalt-catalyzed alkene hydroformylation. , 2014, Angewandte Chemie.
[80] Rainer Herges. Reaction planning: prediction of new organic reactions , 1990, J. Chem. Inf. Comput. Sci..
[81] 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.
[82] Pierre Baldi,et al. ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning , 2012, J. Chem. Inf. Model..
[83] Paul M. Zimmerman,et al. Navigating molecular space for reaction mechanisms: an efficient, automated procedure , 2015 .
[84] George S. Hammond,et al. A Correlation of Reaction Rates , 1955 .
[85] Katrin Baumgartner,et al. Named Organic Reactions , 2016 .
[86] G. Pólya,et al. Combinatorial Enumeration Of Groups, Graphs, And Chemical Compounds , 1988 .
[87] Henning Hopf,et al. Heuristic thinking makes a chemist smart. , 2010, Chemical Society reviews.