Unraveling reaction mechanisms by means of Quantum Chemical Topology Analysis

International Journal of Quantum Chemistry

Volumn 114, Issue 19, 2014, Pages 1239-1252

  Andrés, Juan ^a   González Navarrete, Patricio ^a   Safont, Vicent Sixte ^a  

^a UNIVERSITAT JAUME I   (Spain)

Author keywords

Bonding Evolution Theory; Chemical Structure and Reactivity; Quantum Chemical Topology Analysis

Indexed keywords

ATOMS; CHEMICAL BONDS; CHEMICAL REACTIVITY; ELECTRONIC STRUCTURE; ISOMERIZATION; ORGANIC COMPOUNDS; REACTION KINETICS;

ATOMIC REARRANGEMENTS; ELECTRON LOCALIZATION FUNCTION; EVOLUTION THEORY; GEOMETRICAL CHANGES; ISOMERIZATION REACTION; QUANTUM CHEMICAL TOPOLOGY; REACTION COORDINATES; REACTION MECHANISM;

QUANTUM CHEMISTRY;

EID: 84906316024     PISSN: 00207608     EISSN: 1097461X     Source Type: Journal    
DOI: 10.1002/qua.24665     Document Type: Review

References (115)

1. J. K. Gilbert, C. J. Boulter, R. Elmer, In Developing Models in Science Education;, J. K. Gilbert, C. J. Boulter, Eds.; Kluwer Academic Publisher: Dordrecht, 2000; p 3.
2. N. M. Gericke, M. Hagberg, Sci. Educ. 2007, 16, 849.
3. A. Bergqvist, M. Drechsler, O. De Jong, S.-N. C. Rundgren, Chem. Educ. Res. Pract. 2013, 14, 589.
4. H. Jacobsen, J. Comput. Chem. 2008, 30, 1093.
5. H. Jacobsen, Dalton Trans. 2010, 39, 5426.
6. J. F. Gonthier, S. N. Steinmann, M. D. Wodrich, C. Corminboeuf, Chem. Soc. Rev. 2012, 41, 4671.
7. S. Álvarez, R. Hoffmann, C. Mealli, Chem. Eur. J. 2009, 15, 8358.
8. P. Ball, Nature 2011, 469, 26.
9. G. Frenking, A. Krapp, J. Comput. Chem. 2007, 28, 15.
10. S. Shaik, H. S. Rzepa, R. Hoffmann, Angew. Chem. Int. Ed. Engl. 2013, 52, 3020.
11. G. Frenking, M. Hermann, Angew. Chem. Int. Ed. Engl. 2013, 52, 5922.
12. R. G. Parr, P. W. Ayers, R. F. Nalewajski, J. Phys. Chem. A 2005, 109, 3957.
13. H. Jacobsen, Phys. Chem. Chem. Phys. 2013, 15, 5057.
14. G. B. Bacskay, S. Nordholm, J. Phys. Chem. A 2013, 117, 7946.
15. C. Esterhuysen, G. Frenking, Theor. Chem. Acc. 2005, 113, 294.
16. V. Tognetti, L. Joubert, C. Adamo, J. Chem. Phys. 2010, 132, 211101.
17. R. B. Grossman, The Art of Writing Reasonable Organic Reaction Mechanisms; Springer-Verlag: New York, 2003.
18. J. A. Berson, In Rearrangements in Ground and Excited States;, P. de Mayo, Ed.; Academic Press: New York, 1980; p 311.
19. T. H. Lowry, K. S. Richardson, Mechanism and Theory in Organic Chemistry; Harper & Row: New York, 1987.
20. J. J. Gajewski, Hydrocarbon Thermal Isomerizations; Elsevier: Amsterdam, 2004.
21. E. V. Anslyn, D. A. Dougherty, Modern Physical Organic Chemistry; University Science Books: Sausalito, CA, 2006.
22. M. B. Smith, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure; Wiley: Hoboken, 2013.
23. K. P. C. Vollhardt, N. E. Schore, Organic Chemistry: Structure and Function; W. H. Freeman: New York, 2007.
24. R. G. Wilkins, Kinetics and Mechanism of Reactions of Transition Metal Complexes; Wiley-VCH Verlag: Weinheim, Germany, 2003.
25. R. B. Jordan, Reaction Mechanisms of Inorganic and Organometallic Systems; Oxford University Press: Oxford, 2007.
26. C. K. Mathews, K. E. van Holde, K. G. Ahern, Biochemistry; Prentice-Hall: Upper Saddle River, NJ, 1999.
27. D. L. Nelson, M. M. Cox, Lehninger Principles of Biochemistry; W. H. Freeman and Company: New York, 2008.
28. D. Himmel, I. Krossing, A. Schnepf, Angew. Chem. Int. Ed. Engl. 2014, 53, 370.
29. S. Alvarez, Angew.Chem. Int. Ed. Engl. 2012, 51, 590.
30. M. Born, K. Huang, Dynamical Theory of Crystal Lattices; Oxford University Press: Oxford, 1998.
31. M. Born, J. R. Oppenheimer, Ann. Phys. 1927, 84, 457.
32. J. C. Slater, Proc. Natl. Acad. Sci. 1927, 13, 423.
33. D. Wales, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses; Cambridge University Press: Cambridge, 2003.
34. C. A. Coulson, The Spirit of Applied Mathematics; Clarendon Press, 1953.
35. G. N. Lewis, J. Am. Chem. Soc. 1916, 38, 762.
36. S. Shaik, J. Comput. Chem. 2006, 28, 51.
37. C. Aslangul, R. Constanciél, R. Daudel, P. Kottis, In Advances in Quantum Chemistry;, P. O. Lowdin, Ed.; Academic Press: New York, 1972; p 94.
38. A. J. Cohen, P. Mori-Sánchez, W. Yang, Science 2008, 321, 792.
39. W. Kohn, L. J. Sham, Phys. Rev. 1965, 140, A1133.
40. R. G. Parr, W. Yang, Density Functional Theory of Atoms and Molecules; Oxford University Press: New York, 1989.
41. P. C. Hohenberg, W. Kohn, Phys. Rev. 1964, 136, B864.
42. R. F. W. Bader, G. A. Jones, J. Chem. Phys. 1963, 38, 2791.
43. P. O. Lowdin, Adv. Chem. Phys. 1959, 2, 207.
44. T. S. Koritsanszky, P. Coppens, Chem. Rev. 2001, 101, 1583.
45. P. Coppens, Phys. Scr. 2013, 87, 048104.
46. R. F. W. Bader, Found. Chem. 2011, 13, 11.
47. P. A. M. Dirac, The Principles of Quantum Mechanics; Oxford University Press: Oxford, 1981.
48. R. F. W. Bader, Atoms in Molecules: A Quantum Theory; Oxford University Press: Oxford, 1990.
49. P. L. Popelier, Atoms in Molecules: An Introduction; Pearson Education: Harlow, 2000.
50. C. F. Matta, J. B. Russel, A. Becke, The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design; Wiley-VCH: Weinheim, 2007.
51. R. F. W. Bader, Chem. Rev. 1991, 91, 893.
52. R. F. W. Bader, Theor. Chem. Acc. 2001, 105, 276.
53. P. L. Popelier, Coord. Chem. Rev. 2000, 197, 169.
54. F. Cortés-Guzmán, R. F. W. Bader, Coord. Chem. Rev. 2005, 249, 633.
55. G. Merino, A. Vela, T. Heine, Chem. Rev. 2005, 105, 3812.
56. R. F. W. Bader, J. Phys. Chem. A 1998, 102, 7314.
57. R. Bianchi, G. Gervasio, D. Marabello, Inorg. Chem. 2000, 39, 2360.
58. C. F. Matta, In Hydrogen Bonding-New Insights;, S. J. Grabowski, Ed.; Springer: Dordrecht, 2006; p 337.
59. R. Abraham, C. D. Shaw, Dynamics: The Geometry of Behavior; Addison Wesley: Redwood City, 1992.
60. R. Abraham, J. E. Marsden, Foundations of Mechanics; Addison Wesley: Redwood City, 1994.
61. Special Issue: Experimental Electron Density as Key to Understanding Chemical Interactions, J. Inorg. Gen. Chem. 2013, 639 1893.
62. A. D. Becke, K. E. Edgecombe, J. Chem. Phys. 1990, 92, 5397.
63. B. Silvi, A. Savin, Nature 1994, 371, 683.
64. A. Savin, B. Silvi, F. Colonna, Can. J. Chem. 1996, 74, 1088.
65. R. Nesper, Angew. Chem. Int. Ed. Engl. 1991, 30, 789.
66. A. Savin, R. Nesper, S. Wengert, T. F. Fässler, Angew. Chem. Int. Ed. Engl. 1997, 36, 1808.
67. D. B. Chesnut, J. Phys. Chem. A 2000, 104, 11644.
68. A. Kumar, S. R. Gadre, N. Mohan, C. H. Suresh, J. Phys. Chem. A 2014, 118, 526.
69. P. L. A. Popelier, Structure and Bonding: Intermolecular Forces and Clusters I;, D. J. Wales, Ed.; Springer: Heidelberg, 2005; pp 1.
70. P. L. A. Popelier, P. J. Smith, Specialist Periodical Reports Chemical Modelling: Applications and Theory;, A. Hinchliffe, Ed.; The Royal Socielty of Chemistry: Cambridge, 2002; p 391.
71. P. L. A. Popelier, F. M. Aicken, S. E. O'Brien, Specialist Periodical Reports Chemical Modelling: Applications and Theory;, A. Hinchliffe, Ed.; The Royal Society of Chemistry: Cambridge, 2000; p 143.
72. C. Gatti, The Quantum Theory of Atoms in Molecules: from Solid State to DNA and Drug Design;, R. J. Boyd, C. F. Matta, Eds.; Wiley-VCH: Weinheim, 2007; p 165.
73. A. M. Simas, V. H. Smith, Jr., A. J. Thakkar, Int. J. Quantum Chem. 1984, 26, 385.
74. R. F. W. Bader, G. L. Heard, J. Chem. Phys. 1999, 111, 8789.
75. Y. Tal, R. F. W. Bader, J. Erkku, Phys. Rev. A 1980, 21, 1.
76. T. A. Keith, R. F. W. Bader, Y. Aray, Int. J. Quantum Chem. 1996, 57, 183.
77. R. F. W. Bader, P. J. MacDougall, C. D. H. Lau, J. Am. Chem. Soc. 1984, 106, 1594.
78. R. F. W. Bader, R. J. Gillespie, P. J. MacDougall, J. Am. Chem. Soc. 1988, 110, 7329.
79. P. Balanarayan, R. Kavathekar, S. R. Gadre, J. Phys. Chem. A 2007, 111, 2733.
80. P. G. Mezey, Theor. Chim. Acta 1981, 58, 309.
81. P. G. Mezey, Potential Energy Hypersurfaces; Elsevier: Amsterdam, 1987.
82. R. F. W. Bader, Phys. Rev. B 1994, 49, 13348.
83. R. Thom, Nature 1977, 270, 658.
84. R. F. W. Bader, Y. Tal, S. G. Anderson, T. T. Nguyen-Dang, Isr. J. Chem. 1980, 19, 8.
85. R. F. W. Bader, T. T. Nguyen-Dang, Y. Tal, Rep. Prog. Phys. 1981, 44, 893.
86. R. Thom, Structural Stability and Morphogenesis; W. A. Benjamin Inc.: Redding, 1976.
87. T. Poston, I. Stewart, Catastrophe Theory and its Applications; Dover Publications: Pitman, 1978.
88. X. Krokidis, S. Noury, B. Silvi, J. Phys. Chem. A 1997, 101, 7277.
89. A. Savin, O. Jepsen, J. Flad, O. K. Andersen, H. Preuss, H. G. v. Schnering, Angew. Chem. Int. Ed. Engl. 1992, 31, 187.
90. X. Krokidis, R. Vuilleumier, D. Borgis, B. Silvi, Mol. Phys. 1999, 96, 265.
91. B. Silvi, J. Mol. Struct. 2002, 614, 3.
92. S. Berski, J. Andrés, B. Silvi, L. R. Domingo, J. Phys. Chem. A 2006, 110, 13939.
93. S. Noury, X. Krokidis, F. Fuster, B. Silvi, Comput. Chem. 1999, 23, 597.
94. K. Fukui, J. Phys. Chem. 1970, 74, 4161.
95. K. Fukui, Acc. Chem. Res. 1981, 14, 363.
96. Y. Zeng, L. Meng, X. Li, S. Zheng, J. Phys. Chem. A 2007, 111, 9093.
97. X. Li, H. Fan, L. Meng, Y. Zeng, S. Zheng, J. Phys. Chem. A 2007, 111, 2343.
98. Y. Zeng, S. Zheng, L. Meng, J. Phys. Chem. A 2004, 108, 10527.
99. Y. Zeng, S. Zheng, L. Meng, Inorg. Chem. 2004, 43, 5311.
100. N. O. Malcom, P. L. A. Popelier, J. Phys. Chem. A 2001, 105, 7638.
101. V. Polo, J. Andrés, R. Castillo, S. Berski, B. Silvi, Chem. Eur. J. 2004, 10, 5165.
102. P. González-Navarrete, J. Andrés, S. Berski, J. Phys. Chem. Lett. 2012, 3, 2500.
103. P. González-Navarrete, L. R. Domingo, J. Andrés, S. Berski, B. Silvi, J. Comput. Chem. 2012, 33, 2400.
104. M. E. Alikhani, M. d. C. Michelini, N. Russo, B. Silvi, J. Phys. Chem. A 2008, 112, 12966.
105. A. S. Nizovtsev, S. G. Kozlova, J. Phys. Chem. A 2013, 117, 481.
106. A. S. Nizovtsev, J. Comput. Chem. A 2013, 34, 1917.
107. C. H. Suresh, N. Koga, S. R. Gadre, J. Org. Chem. 2001, 66, 6883.
108. S. R. Barua, W. D. Allen, E. Kraka, P. Jerabek, R. Sure, G. Frenking, Chem. Eur. J. 2013, 19, 15941.
109. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision B.01; Gaussian, Inc.: Wallingford, CT, 2009.
110. O. A. McNamara, A. R. Maguire, Tetrahedron 2011, 67, 9.
111. R. Beniazza, V. Desvergnes, E. Girard, B. Kauffmann, M. Berlande, Y. Landais, Chem. Eur. J. 2012, 18, 11976.
112. E. Ciganek, J. Am. Chem. Soc. 1965, 87, 652.
113. F. Wang, V. N. Richards, S. P. Shields, W. E. Buhro, Chem. Mater. 2014, 26, 5.
114. C. W. Shoppee, Biogr. Mem. Fellows R. Soc. 1972, 18, 349.
115. D. H. R. Barton, Bull. Hist. Chem. 1996, 19, 43.