AFIRサンプル

Citation of the program and related papers

Citation of the program and related papers

 

Documents and presentations showing results obtained by GRRM17 should cite the program as follows:

  • S. Maeda, Y. Harabuchi, Y. Sumiya, M. Takagi, K. Suzuki, M. Hatanaka, Y. Osada, T. Taketsugu, K. Morokuma, K. Ohno, GRRM17, see http://iqce.jp/GRRM/index_e.shtml (accessed date DAY MONTH, YEAR).
  •  
  • S. Maeda, K. Ohno, K. Morokuma, "Systematic Exploration of the Mechanism of Chemical Reactions: The Global Reaction Route Mapping (GRRM) Strategy by the ADDF and AFIR Methods", Phys. Chem. Chem. Phys., 2013, 15, 3683–3701.

 

Documents and presentations showing results obtained by ADDF should cite the following paper:

 

Documents and presentations showing results obtained by the AFIR method should cite the following paper:

  • S. Maeda, Y. Harabuchi, M. Takagi, K. Saita, K. Suzuki, T. Ichino, Y. Sumiya, K. Sugiyama, Y. Ono, "Implementation and Performance of the Artificial Force Induced Reaction Method in the GRRM17 Program", J. Comput. Chem., 2018, 39, 233–251.

 

Authors of papers showing results obtained by GRRM17 are encouraged to cite original papers from the following list for options used:

MIN or SADDLE:
  1. A. Banerjee, N. Adams, J. Simons, R. Shepard, "Search for Stationary Points on Surfaces", J. Phys. Chem., 1985, 89, 52–57.
  2. P. Culot, G. Dive, V. H. Nguyen, J. M. Ghuysen, "A Quasi-Newton Algorithm for First-order Saddle-point Location", Theor. Chim. Acta, 1992, 82, 189–205.
IRC:
  1. M. Page, J. W. McIver, Jr., "On Evaluating the Reaction Path Hamiltonian", J. Chem. Phys., 1988, 88, 922–935.
  2. S. Maeda, Y. Harabuchi, Y. Ono, T. Taketsugu, K. Morokuma, "Intrinsic Reaction Coordinate: Calculation, Bifurcation, and Automated Search", Int. J. Quantum. Chem., 2015, 115, 258–269.
LUP:
  1. C. Choi, R. Elber, "Reaction Path Study of Helix Formation in Tetrapeptides: Effect of Side Chains", J. Chem. Phys., 1991, 94, 751–760.
  2. P. Y. Ayala, H. B. Schlegel, "A Combined Method for Determining Reaction Paths, Minima, and Transition State Geometries", J. Chem. Phys., 1997, 107, 375–384.
OptX with MIN, Saddle, or IRC:
  1. S. Maeda, K. Ohno, K. Morokuma, "Updated Branching Plane for Finding Conical Intersections without Coupling Derivative Vectors", J. Chem. Theory Comput., 2010, 6, 1538–1545.
  2. M. J. Bearpark, M. A. Robb, H. B. Schlegel, "A Direct Method for the Location of the Lowest Energy Point on a Potential Surface Crossing", Chem. Phys. Lett. 1994, 223, 269–274.
External atoms:
  1. S. Maeda, K. Ohno, K. Morokuma, "An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods", J. Chem. Theory Comput., 2009, 5, 2734–2743.
  2. T. Vreven, K. Morokuma, O. Farkas, H. B. Schlegel, M. J. Frisch, "Geometry Optimization with QM/MM, ONIOM, and Other Combined Methods. I. Microiterations and Constraints", J. Comput. Chem., 2003, 24, 760–769.
ADDF:
  1. K. Ohno, S. Maeda, "A Scaled Hypersphere Search Method for the Topography of Reaction Pathways on the Potential Energy Surface", Chem. Phys. Lett., 2004, 384, 277–282.
  2. S. Maeda, K. Ohno, "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", J. Phys. Chem. A, 2005, 109, 5742–5753.
  3. K. Ohno, S. Maeda, "Global Reaction Route Mapping on Potential Energy Surfaces of Formaldehyde, Formic Acid, and their Metal Substituted Analogues", J. Phys. Chem. A, 2006, 110, 8933–8941.
2PSHS:
  1. S. Maeda, K. Ohno, "A New Approach for Finding a Transition State Connecting a Reactant and a Product without Initial Guess: Applications of the Scaled Hypersphere Search Method to Isomerization Reactions of HCN, (H2O)2, and Alanine Dipeptide", Chem. Phys. Lett., 2005, 404, 95–99.
SCW:
  1. S. Maeda, K. Ohno, "Conversion Pathways between a Fullerene and a Ring among C20 Clusters by a Sphere Contracting Walk Method: Remarkable Difference in Local Potential Energy Landscapes around the Fullerene and the Ring", J. Chem. Phys., 2006, 124, 174306 (7 pages).
LADD:
  1. S. Maeda, K. Ohno, "Structures of Water Octamers (H2O)8: Exploration on Ab Initio Potential Energy Surfaces by the Scaled Hypersphere Search Method", J. Phys. Chem. A, 2007, 111, 4527–4534.
Frozen Atom with ADDF:
  1. S. Maeda, K. Ohno, "Lowest Transition State for the Chirality-Determining Step in Ru{(R)-BINAP}-Catalyzed Asymmetric Hydrogenation of Methyl-3-Oxobutanoate", J. Am. Chem. Soc., 2008, 130, 17228–17229.
External Atom with ADDF:
  1. S. Maeda, K. Ohno, K. Morokuma, "An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods", J. Chem. Theory Comput., 2009, 5, 2734–2743.
ModelF with ADDF:
  1. S. Maeda, K. Ohno, K. Morokuma, "Automated Global Mapping of Minimum Energy Points on Seams of Crossing by the Anharmonic Downward Distortion Following Method: A Case Study on H2CO", J. Phys. Chem. A, 2009, 113, 1704–1710.
MC-AFIR:
  1. S. Maeda, K. Morokuma, "A Systematic Method for Locating Transition Structures of A + B → X Type Reactions", J. Chem. Phys., 2010, 132, 241102 (4 pages).
  2. S. Maeda, K. Morokuma, "Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms", J. Chem. Theory Comput., 2011, 7, 2335–2345.
SC-AFIR:
  1. S. Maeda, T. Taketsugu, K. Morokuma, "Exploring Transition State Structures for Intramolecular Pathways by the Artificial Force Induced Reaction Method", J. Comput. Chem., 2014, 35, 166–173.
  2. S. Maeda, Y. Harabuchi, M. Takagi, T. Taketsugu, K. Morokuma, "Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces", Chem. Rec., 2016, 16, 2232–2248.
DS-AFIR:
  1. Same as the reference paper for AFIR: S. Maeda, K. Ohno, K. Morokuma, "Systematic Exploration of the Mechanism of Chemical Reactions: The Global Reaction Route Mapping (GRRM) Strategy by the ADDF and AFIR Methods", Phys. Chem. Chem. Phys., 2013, 15, 3683–3701.
Frozen Atom with AFIR:
  1. S. Maeda, K. Sugiyama, Y. Sumiya, M. Takagi, K. Saita, "Global Reaction Route Mapping for Surface Adsorbed Molecules: A Case Study for H2O on Cu(111) Surface", Chem. Lett., 2018, 47, in press.
External Atom with AFIR:
  1. S. Maeda, E. Abe, M. Hatanaka, T. Taketsugu, K. Morokuma, "Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration", J. Chem. Theory Comput., 2012, 8, 5058–5063.
ModelF with AFIR:
  1. S. Maeda, Y. Harabuchi, T. Taketsugu, K. Morokuma, "Systematic Exploration of Minimum Energy Conical Intersection Structures near the Franck-Condon Region", J. Phys. Chem. A, 2014, 118, 12050–12058.
OptX with AFIR:
  1. Y. Harabuchi, T. Taketsugu, S. Maeda, "Combined Gradient Projection/Single Component Artificial Force Induced Reaction (GP/SC-AFIR) Method for an Efficient Search of Minimum Energy Conical Intersection (MECI) Geometries", Chem. Phys. Lett., 2017, 674, 141–145.
ShiftE with OptX:
  1. M. Hatanaka, K. Morokuma, "Exploring the Reaction Coordinates for f-f Emission and Quenching of Lanthanide Complexes - Thermosensitivity of Terbium(III) Luminescence", J. Chem. Theory. Comput.2014, 10, 4184–4188.

 

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Updated At:June 30, 2018, 3:17 p.m.

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